amap-align/align/0000755000120200001440000000000010754706703013355 5ustar sarielusersamap-align/align/MultiSequence.h0000644000120200001440000005106510635655116016317 0ustar sarielusers//////////////////////////////////////////////////////////////// // MultiSequence.h // // Utilities for reading/writing multiple sequence data. ///////////////////////////////////////////////////////////////// #ifndef MULTISEQUENCE_H #define MULTISEQUENCE_H #include #include #include #include #include #include #include #include "SafeVector.h" #include "Sequence.h" #include "FileBuffer.h" ///////////////////////////////////////////////////////////////// // MultiSequence // // Class for multiple sequence alignment input/output. ///////////////////////////////////////////////////////////////// class MultiSequence { SafeVector *sequences; public: ///////////////////////////////////////////////////////////////// // MultiSequence::MultiSequence() // // Default constructor. ///////////////////////////////////////////////////////////////// MultiSequence () : sequences (NULL) {} ///////////////////////////////////////////////////////////////// // MultiSequence::MultiSequence() // // Constructor. Load MFA from a FileBuffer object. ///////////////////////////////////////////////////////////////// MultiSequence (FileBuffer &infile) : sequences (NULL) { LoadMFA (infile); } ///////////////////////////////////////////////////////////////// // MultiSequence::MultiSequence() // // Constructor. Load MFA from a filename. ///////////////////////////////////////////////////////////////// MultiSequence (const string &filename) : sequences (NULL){ LoadMFA (filename); } ///////////////////////////////////////////////////////////////// // MultiSequence::~MultiSequence() // // Destructor. Gets rid of sequence objects contained in the // multiple alignment. ///////////////////////////////////////////////////////////////// ~MultiSequence(){ // if sequences allocated if (sequences){ // free all sequences for (SafeVector::iterator iter = sequences->begin(); iter != sequences->end(); ++iter){ assert (*iter); delete *iter; *iter = NULL; } // free sequence vector delete sequences; sequences = NULL; } } ///////////////////////////////////////////////////////////////// // MultiSequence::LoadMFA() // // Load MFA from a filename. ///////////////////////////////////////////////////////////////// void LoadMFA (const string &filename, bool stripGaps = false){ // try opening file FileBuffer infile (filename.c_str()); if (infile.fail()){ cerr << "ERROR: Could not open file '" << filename << "' for reading." << endl; exit (1); } // if successful, then load using other LoadMFA() routine LoadMFA (infile, stripGaps); infile.close(); } ///////////////////////////////////////////////////////////////// // MultiSequence::LoadMFA() // // Load MSF from a FileBuffer object. ///////////////////////////////////////////////////////////////// void ParseMSF (FileBuffer &infile, string header, bool stripGaps = false){ SafeVector *> seqData; SafeVector seqNames; SafeVector seqLengths; istringstream in; bool valid = true; bool missingHeader = false; bool clustalW = false; // read until data starts while (!infile.eof() && header.find ("..", 0) == string::npos){ if (header.find ("CLUSTAL", 0) == 0 || header.find ("AMAP", 0) == 0){ clustalW = true; break; } infile.GetLine (header); if (header.find ("//", 0) != string::npos){ missingHeader = true; break; } } // read until end-of-file while (valid){ infile.GetLine (header); if (infile.eof()) break; string word; in.clear(); in.str(header); // check if there's anything on this line if (in >> word){ // clustalw name parsing if (clustalW){ if (!isspace(header[0]) && find (seqNames.begin(), seqNames.end(), word) == seqNames.end()){ seqNames.push_back (word); seqData.push_back (new SafeVector()); seqLengths.push_back (0); seqData[(int) seqData.size() - 1]->push_back ('@'); } } // look for new sequence label if (word == string ("Name:")){ if (in >> word){ seqNames.push_back (word); seqData.push_back (new SafeVector()); seqLengths.push_back (0); seqData[(int) seqData.size() - 1]->push_back ('@'); } else valid = false; } // check if this is sequence data else if (find (seqNames.begin(), seqNames.end(), word) != seqNames.end()){ int index = find (seqNames.begin(), seqNames.end(), word) - seqNames.begin(); // read all remaining characters on the line char ch; while (in >> ch){ if (isspace (ch)) continue; if (ch >= 'a' && ch <= 'z') ch = ch - 'a' + 'A'; if (ch == '.') ch = '-'; if (stripGaps && ch == '-') continue; if (!((ch >= 'A' && ch <= 'Z') || ch == '*' || ch == '-')){ cerr << "ERROR: Unknown character encountered: " << ch << endl; exit (1); } // everything's ok so far, so just store this character. seqData[index]->push_back (ch); seqLengths[index]++; } } else if (missingHeader){ seqNames.push_back (word); seqData.push_back (new SafeVector()); seqLengths.push_back (0); seqData[(int) seqData.size() - 1]->push_back ('@'); int index = (int) seqNames.size() - 1; // read all remaining characters on the line char ch; while (in >> ch){ if (isspace (ch)) continue; if (ch >= 'a' && ch <= 'z') ch = ch - 'a' + 'A'; if (ch == '.') ch = '-'; if (stripGaps && ch == '-') continue; if (!((ch >= 'A' && ch <= 'Z') || ch == '*' || ch == '-')){ cerr << "ERROR: Unknown character encountered: " << ch << endl; exit (1); } // everything's ok so far, so just store this character. seqData[index]->push_back (ch); seqLengths[index]++; } } } } // check for errors if (seqNames.size() == 0){ cerr << "ERROR: No sequences read!" << endl; exit (1); } assert (!sequences); sequences = new SafeVector; for (int i = 0; i < (int) seqNames.size(); i++){ if (seqLengths[i] == 0){ cerr << "ERROR: Sequence of zero length!" << endl; exit (1); } Sequence *seq = new Sequence (seqData[i], seqNames[i], seqLengths[i], i, i); sequences->push_back (seq); } } ///////////////////////////////////////////////////////////////// // MultiSequence::LoadMFA() // // Load MFA from a FileBuffer object. ///////////////////////////////////////////////////////////////// void LoadMFA (FileBuffer &infile, bool stripGaps = false){ // check to make sure that file reading is ok if (infile.fail()){ cerr << "ERROR: Error reading file." << endl; exit (1); } // read all sequences while (true){ // get the sequence label as being the current # of sequences // NOTE: sequence labels here are zero-based int index = (!sequences) ? 0 : sequences->size(); // read the sequence Sequence *seq = new Sequence (infile, stripGaps); if (seq->Fail()){ // check if alternative file format (i.e. not MFA) if (index == 0){ string header = seq->GetHeader(); if (header.length() > 0 && header[0] != '>'){ // try MSF format ParseMSF (infile, header); break; } } delete seq; break; } seq->SetLabel (index); // add the sequence to the list of current sequences if (!sequences) sequences = new SafeVector; sequences->push_back (seq); } // make sure at least one sequence was read if (!sequences){ cerr << "ERROR: No sequences read." << endl; exit (1); } } ///////////////////////////////////////////////////////////////// // MultiSequence::AddSequence() // // Add another sequence to an existing sequence list ///////////////////////////////////////////////////////////////// void AddSequence (Sequence *sequence){ assert (sequence); assert (!sequence->Fail()); // add sequence if (!sequences) sequences = new SafeVector; sequences->push_back (sequence); } ///////////////////////////////////////////////////////////////// // MultiSequence::RemoveSequence() // // Remove a sequence from the MultiSequence ///////////////////////////////////////////////////////////////// void RemoveSequence (int index){ assert (sequences); assert (index >= 0 && index < (int) sequences->size()); delete (*sequences)[index]; sequences->erase (sequences->begin() + index); } ///////////////////////////////////////////////////////////////// // MultiSequence::WriteMFA() // // Write MFA to the outfile. Allows the user to specify the // number of columns for the output. Also, useIndices determines // whether or not the actual sequence comments will be printed // out or whether the artificially assigned sequence labels will // be used instead. ///////////////////////////////////////////////////////////////// void WriteMFA (ostream &outfile, int numColumns = 60, bool useIndices = false){ if (!sequences) return; // loop through all sequences and write them out for (SafeVector::iterator iter = sequences->begin(); iter != sequences->end(); ++iter){ (*iter)->WriteMFA (outfile, numColumns, useIndices); } } ///////////////////////////////////////////////////////////////// // MultiSequence::GetAnnotationChar() // // Return CLUSTALW annotation for column. ///////////////////////////////////////////////////////////////// char GetAnnotationChar (SafeVector &column){ SafeVector counts (256, 0); int allChars = (int) column.size(); for (int i = 0; i < allChars; i++){ counts[(unsigned char) toupper(column[i])]++; } allChars -= counts[(unsigned char) '-']; if (allChars == 1) return ' '; for (int i = 0; i < 256; i++) if ((char) i != '-' && counts[i] == allChars) return '*'; if (counts[(unsigned char) 'S'] + counts[(unsigned char) 'T'] + counts[(unsigned char) 'A'] == allChars) return ':'; if (counts[(unsigned char) 'N'] + counts[(unsigned char) 'E'] + counts[(unsigned char) 'Q'] + counts[(unsigned char) 'K'] == allChars) return ':'; if (counts[(unsigned char) 'N'] + counts[(unsigned char) 'H'] + counts[(unsigned char) 'Q'] + counts[(unsigned char) 'K'] == allChars) return ':'; if (counts[(unsigned char) 'N'] + counts[(unsigned char) 'D'] + counts[(unsigned char) 'E'] + counts[(unsigned char) 'Q'] == allChars) return ':'; if (counts[(unsigned char) 'Q'] + counts[(unsigned char) 'H'] + counts[(unsigned char) 'R'] + counts[(unsigned char) 'K'] == allChars) return ':'; if (counts[(unsigned char) 'M'] + counts[(unsigned char) 'I'] + counts[(unsigned char) 'L'] + counts[(unsigned char) 'V'] == allChars) return ':'; if (counts[(unsigned char) 'M'] + counts[(unsigned char) 'I'] + counts[(unsigned char) 'L'] + counts[(unsigned char) 'F'] == allChars) return ':'; if (counts[(unsigned char) 'H'] + counts[(unsigned char) 'Y'] == allChars) return ':'; if (counts[(unsigned char) 'F'] + counts[(unsigned char) 'Y'] + counts[(unsigned char) 'W'] == allChars) return ':'; if (counts[(unsigned char) 'C'] + counts[(unsigned char) 'S'] + counts[(unsigned char) 'A'] == allChars) return '.'; if (counts[(unsigned char) 'A'] + counts[(unsigned char) 'T'] + counts[(unsigned char) 'V'] == allChars) return '.'; if (counts[(unsigned char) 'S'] + counts[(unsigned char) 'A'] + counts[(unsigned char) 'G'] == allChars) return '.'; if (counts[(unsigned char) 'S'] + counts[(unsigned char) 'T'] + counts[(unsigned char) 'N'] + counts[(unsigned char) 'K'] == allChars) return '.'; if (counts[(unsigned char) 'S'] + counts[(unsigned char) 'T'] + counts[(unsigned char) 'P'] + counts[(unsigned char) 'A'] == allChars) return '.'; if (counts[(unsigned char) 'S'] + counts[(unsigned char) 'G'] + counts[(unsigned char) 'N'] + counts[(unsigned char) 'D'] == allChars) return '.'; if (counts[(unsigned char) 'S'] + counts[(unsigned char) 'N'] + counts[(unsigned char) 'D'] + counts[(unsigned char) 'E'] + counts[(unsigned char) 'Q'] + counts[(unsigned char) 'K'] == allChars) return '.'; if (counts[(unsigned char) 'N'] + counts[(unsigned char) 'D'] + counts[(unsigned char) 'E'] + counts[(unsigned char) 'Q'] + counts[(unsigned char) 'H'] + counts[(unsigned char) 'K'] == allChars) return '.'; if (counts[(unsigned char) 'N'] + counts[(unsigned char) 'E'] + counts[(unsigned char) 'H'] + counts[(unsigned char) 'Q'] + counts[(unsigned char) 'R'] + counts[(unsigned char) 'K'] == allChars) return '.'; if (counts[(unsigned char) 'F'] + counts[(unsigned char) 'V'] + counts[(unsigned char) 'L'] + counts[(unsigned char) 'I'] + counts[(unsigned char) 'M'] == allChars) return '.'; if (counts[(unsigned char) 'H'] + counts[(unsigned char) 'F'] + counts[(unsigned char) 'Y'] == allChars) return '.'; return ' '; } ///////////////////////////////////////////////////////////////// // MultiSequence::WriteALN() // // Write ALN to the outfile. Allows the user to specify the // number of columns for the output. ///////////////////////////////////////////////////////////////// void WriteALN (ostream &outfile, int numColumns = 60){ if (!sequences) return; outfile << "AMAP version " << VERSION << " multiple sequence alignment" << endl; int longestComment = 0; SafeVector::iterator> ptrs (GetNumSequences()); SafeVector lengths (GetNumSequences()); for (int i = 0; i < GetNumSequences(); i++){ ptrs[i] = GetSequence (i)->GetDataPtr(); lengths[i] = GetSequence (i)->GetLength(); longestComment = max (longestComment, (int) GetSequence(i)->GetName().length()); } longestComment += 4; int writtenChars = 0; bool allDone = false; while (!allDone){ outfile << endl; allDone = true; // loop through all sequences and write them out for (int i = 0; i < GetNumSequences(); i++){ if (writtenChars < lengths[i]){ outfile << GetSequence(i)->GetName(); for (int j = 0; j < longestComment - (int) GetSequence(i)->GetName().length(); j++) outfile << ' '; for (int j = 0; j < numColumns; j++){ if (writtenChars + j < lengths[i]) outfile << ptrs[i][writtenChars + j + 1]; else break; } outfile << endl; if (writtenChars + numColumns < lengths[i]) allDone = false; } } // write annotation line for (int j = 0; j < longestComment; j++) outfile << ' '; for (int j = 0; j < numColumns; j++){ SafeVector column; for (int i = 0; i < GetNumSequences(); i++) if (writtenChars + j < lengths[i]) column.push_back (ptrs[i][writtenChars + j + 1]); if (column.size() > 0) outfile << GetAnnotationChar (column); } outfile << endl; writtenChars += numColumns; } } ///////////////////////////////////////////////////////////////// // MultiSequence::GetSequence() // // Retrieve a sequence from the MultiSequence object. ///////////////////////////////////////////////////////////////// Sequence* GetSequence (int i){ assert (sequences); assert (0 <= i && i < (int) sequences->size()); return (*sequences)[i]; } ///////////////////////////////////////////////////////////////// // MultiSequence::GetSequence() // // Retrieve a sequence from the MultiSequence object // (const version). ///////////////////////////////////////////////////////////////// const Sequence* GetSequence (int i) const { assert (sequences); assert (0 <= i && i < (int) sequences->size()); return (*sequences)[i]; } ///////////////////////////////////////////////////////////////// // MultiSequence::GetNumSequences() // // Returns the number of sequences in the MultiSequence. ///////////////////////////////////////////////////////////////// int GetNumSequences () const { if (!sequences) return 0; return (int) sequences->size(); } ///////////////////////////////////////////////////////////////// // MultiSequence::SortByHeader() // // Organizes the sequences according to their sequence headers // in ascending order. ///////////////////////////////////////////////////////////////// void SortByHeader () { assert (sequences); // a quick and easy O(n^2) sort for (int i = 0; i < (int) sequences->size()-1; i++){ for (int j = i+1; j < (int) sequences->size(); j++){ if ((*sequences)[i]->GetHeader() > (*sequences)[j]->GetHeader()) swap ((*sequences)[i], (*sequences)[j]); } } } ///////////////////////////////////////////////////////////////// // MultiSequence::SortByLabel() // // Organizes the sequences according to their sequence labels // in ascending order. ///////////////////////////////////////////////////////////////// void SortByLabel () { assert (sequences); // a quick and easy O(n^2) sort for (int i = 0; i < (int) sequences->size()-1; i++){ for (int j = i+1; j < (int) sequences->size(); j++){ if ((*sequences)[i]->GetSortLabel() > (*sequences)[j]->GetSortLabel()) swap ((*sequences)[i], (*sequences)[j]); } } } ///////////////////////////////////////////////////////////////// // MultiSequence::SaveOrdering() // // Relabels sequences so as to preserve the current ordering. ///////////////////////////////////////////////////////////////// void SaveOrdering () { assert (sequences); for (int i = 0; i < (int) sequences->size(); i++) (*sequences)[i]->SetSortLabel (i); } ///////////////////////////////////////////////////////////////// // MultiSequence::Project() // // Given a set of indices, extract all sequences from the current // MultiSequence object whose index is included in the set. // Then, project the multiple alignments down to the desired // subset, and return the projection as a new MultiSequence // object. ///////////////////////////////////////////////////////////////// MultiSequence *Project (const set &indices){ SafeVector::iterator> oldPtrs (indices.size()); SafeVector *> newPtrs (indices.size()); assert (indices.size() != 0); // grab old data int i = 0; for (set::const_iterator iter = indices.begin(); iter != indices.end(); ++iter){ oldPtrs[i++] = GetSequence (*iter)->GetDataPtr(); } // compute new length int oldLength = GetSequence (*indices.begin())->GetLength(); int newLength = 0; for (i = 1; i <= oldLength; i++){ // check to see if there is a gap in every sequence of the set bool found = false; for (int j = 0; !found && j < (int) indices.size(); j++) found = (oldPtrs[j][i] != '-'); // if not, then this column counts towards the sequence length if (found) newLength++; } // build new alignments for (i = 0; i < (int) indices.size(); i++){ newPtrs[i] = new SafeVector(); assert (newPtrs[i]); newPtrs[i]->push_back ('@'); } // add all needed columns for (i = 1; i <= oldLength; i++){ // make sure column is not gapped in all sequences in the set bool found = false; for (int j = 0; !found && j < (int) indices.size(); j++) found = (oldPtrs[j][i] != '-'); // if not, then add it if (found){ for (int j = 0; j < (int) indices.size(); j++) newPtrs[j]->push_back (oldPtrs[j][i]); } } // wrap sequences in MultiSequence object MultiSequence *ret = new MultiSequence(); i = 0; for (set::const_iterator iter = indices.begin(); iter != indices.end(); ++iter){ ret->AddSequence (new Sequence (newPtrs[i++], GetSequence (*iter)->GetHeader(), newLength, GetSequence (*iter)->GetSortLabel(), GetSequence (*iter)->GetLabel())); } return ret; } }; #endif amap-align/align/dna.params0000644000120200001440000000022710637064234015321 0ustar sarielusers0.4 0.3 0.3 0.01993141696 0.01993141696 0.7943345308 0.7943345308 ACGT 0.175 0.025 0.175 0.025 0.025 0.175 0.025 0.025 0.025 0.175 0.25 0.25 0.25 0.25 amap-align/align/SparseMatrix.h0000644000120200001440000002330110635655116016146 0ustar sarielusers///////////////////////////////////////////////////////////////// // SparseMatrix.h // // Sparse matrix computations ///////////////////////////////////////////////////////////////// #ifndef SPARSEMATRIX_H #define SPARSEMATRIX_H #include using namespace std; const float POSTERIOR_CUTOFF = 0.01; // minimum posterior probability // value that is maintained in the // sparse matrix representation typedef pair PIF; // Sparse matrix entry type // first --> column // second --> value ///////////////////////////////////////////////////////////////// // SparseMatrix // // Class for sparse matrix computations ///////////////////////////////////////////////////////////////// class SparseMatrix { int seq1Length, seq2Length; // dimensions of matrix VI rowSize; // rowSize[i] = # of cells in row i SafeVector data; // data values SafeVector::iterator> rowPtrs; // pointers to the beginning of each row VF gapPosteriors; // gap posteriors (sum of pairs) for first and second sequences int gapPostBase; // offset to begining of gapPosteriors ///////////////////////////////////////////////////////////////// // SparseMatrix::SparseMatrix() // // Private constructor. ///////////////////////////////////////////////////////////////// SparseMatrix (){} public: ///////////////////////////////////////////////////////////////// // SparseMatrix::SparseMatrix() // // Constructor. Builds a sparse matrix from a posterior matrix. // Note that the expected format for the posterior matrix is as // a (seq1Length+1) x (seq2Length+1) matrix where the 0th row // and 0th column are ignored (they should contain all zeroes). ///////////////////////////////////////////////////////////////// SparseMatrix (int seq1Length, int seq2Length, const VF &posterior) : seq1Length (seq1Length), seq2Length (seq2Length), gapPostBase ((seq1Length + 1) * (seq2Length + 1)) { int numCells = 0; assert (seq1Length > 0); assert (seq2Length > 0); // calculate memory required; count the number of cells in the // posterior matrix above the threshold VF::const_iterator postPtr = posterior.begin(); for (int i = 0; i <= seq1Length; i++){ for (int j = 0; j <= seq2Length; j++){ if (*(postPtr++) >= POSTERIOR_CUTOFF){ assert (i != 0 && j != 0); numCells++; } } } // allocate memory data.resize(numCells); rowSize.resize (seq1Length + 1); rowSize[0] = -1; rowPtrs.resize (seq1Length + 1); rowPtrs[0] = data.end(); gapPosteriors.resize(seq1Length + seq2Length + 2); // build sparse matrix for (int i = 0; i < seq2Length + 1; i++) gapPosteriors[seq1Length + i + 1] = 1; postPtr = posterior.begin() + seq2Length + 1; // note that we're skipping the first row here SafeVector::iterator dataPtr = data.begin(); for (int i = 1; i <= seq1Length; i++){ gapPosteriors[i] = 1; postPtr++; // and skipping the first column of each row rowPtrs[i] = dataPtr; for (int j = 1; j <= seq2Length; j++){ if (*postPtr >= POSTERIOR_CUTOFF){ dataPtr->first = j; dataPtr->second = *postPtr; gapPosteriors[i] -= *postPtr; gapPosteriors[seq1Length + j + 1] -= *postPtr; dataPtr++; if (gapPosteriors[i] < 1e-4) gapPosteriors[i] = 1e-4; if (gapPosteriors[seq1Length + j + 1] < 1e-4) gapPosteriors[seq1Length + j + 1] = 1e-4; } postPtr++; } rowSize[i] = dataPtr - rowPtrs[i]; } // for (int i = 0; i < seq1Length + seq2Length + 2; i++) // gapPosteriors[i] = *(postPtr++); } ///////////////////////////////////////////////////////////////// // SparseMatrix::GetRowPtr() // // Returns the pointer to a particular row in the sparse matrix. ///////////////////////////////////////////////////////////////// SafeVector::iterator GetRowPtr (int row) const { assert (row >= 1 && row <= seq1Length); return rowPtrs[row]; } ///////////////////////////////////////////////////////////////// // SparseMatrix::GetValue() // // Returns value at a particular row, column. ///////////////////////////////////////////////////////////////// float GetValue (int row, int col){ assert (row >= 1 && row <= seq1Length); assert (col >= 1 && col <= seq2Length); for (int i = 0; i < rowSize[row]; i++){ if (rowPtrs[row][i].first == col) return rowPtrs[row][i].second; } return 0; } ///////////////////////////////////////////////////////////////// // SparseMatrix::GetRowSize() // // Returns the number of entries in a particular row. ///////////////////////////////////////////////////////////////// int GetRowSize (int row) const { assert (row >= 1 && row <= seq1Length); return rowSize[row]; } ///////////////////////////////////////////////////////////////// // SparseMatrix::GetSeq1Length() // // Returns the first dimension of the matrix. ///////////////////////////////////////////////////////////////// int GetSeq1Length () const { return seq1Length; } ///////////////////////////////////////////////////////////////// // SparseMatrix::GetSeq2Length() // // Returns the second dimension of the matrix. ///////////////////////////////////////////////////////////////// int GetSeq2Length () const { return seq2Length; } ///////////////////////////////////////////////////////////////// // SparseMatrix::GetRowPtr // // Returns the pointer to a particular row in the sparse matrix. ///////////////////////////////////////////////////////////////// int GetNumCells () const { return data.size(); } ///////////////////////////////////////////////////////////////// // SparseMatrix::Print() // // Prints out a sparse matrix. ///////////////////////////////////////////////////////////////// void Print (ostream &outfile) const { outfile << "Match posteriors:" << endl; for (int i = 1; i <= seq1Length; i++){ outfile << " " << i << ":"; for (int j = 0; j < rowSize[i]; j++){ outfile << " (" << rowPtrs[i][j].first << "," << rowPtrs[i][j].second << ")"; } outfile << endl; } outfile << "Gap posteriors 0: "; for (int i = 1; i <= seq1Length; i++){ outfile << " (" << i << "," << gapPosteriors[i] << ")"; } outfile << endl << "Gap posteriors 1: "; for (int i = 1; i <= seq2Length; i++){ outfile << " (" << i << "," << gapPosteriors[i + seq1Length + 1] << ")"; } outfile << endl; } ///////////////////////////////////////////////////////////////// // SparseMatrix::ComputeTranspose() // // Returns a new sparse matrix containing the transpose of the // current matrix. ///////////////////////////////////////////////////////////////// SparseMatrix *ComputeTranspose () const { // create a new sparse matrix SparseMatrix *ret = new SparseMatrix(); int numCells = data.size(); ret->seq1Length = seq2Length; ret->seq2Length = seq1Length; // allocate memory ret->data.resize (numCells); ret->rowSize.resize (seq2Length + 1); ret->rowSize[0] = -1; ret->rowPtrs.resize (seq2Length + 1); ret->rowPtrs[0] = ret->data.end(); ret->gapPosteriors.resize(seq1Length + seq2Length + 2); // compute row sizes for (int i = 1; i <= seq2Length; i++) ret->rowSize[i] = 0; for (int i = 0; i < numCells; i++) ret->rowSize[data[i].first]++; // compute row ptrs for (int i = 1; i <= seq2Length; i++){ ret->rowPtrs[i] = (i == 1) ? ret->data.begin() : ret->rowPtrs[i-1] + ret->rowSize[i-1]; } // now fill in data SafeVector::iterator> currPtrs = ret->rowPtrs; for (int i = 1; i <= seq1Length; i++){ SafeVector::iterator row = rowPtrs[i]; for (int j = 0; j < rowSize[i]; j++){ currPtrs[row[j].first]->first = i; currPtrs[row[j].first]->second = row[j].second; currPtrs[row[j].first]++; } } for (int i = 0; i <= seq1Length; i++) { ret->gapPosteriors[i + seq2Length + 1] = gapPosteriors[i]; } for (int i = 0; i <= seq2Length; i++) { ret->gapPosteriors[i] = gapPosteriors[i + seq1Length + 1]; } return ret; } ///////////////////////////////////////////////////////////////// // SparseMatrix::GetPosterior() // // Return the posterior representation of the sparse matrix. ///////////////////////////////////////////////////////////////// VF *GetPosterior () const { // create a new posterior matrix VF *posteriorPtr = new VF((seq1Length+1) * (seq2Length+1) + seq1Length + seq2Length + 2,0); assert (posteriorPtr); VF &posterior = *posteriorPtr; // build the posterior matrix for (int i = 0; i < (seq1Length+1) * (seq2Length+1); i++) posterior[i] = 0; for (int i = 1; i <= seq1Length; i++){ VF::iterator postPtr = posterior.begin() + i * (seq2Length+1); for (int j = 0; j < rowSize[i]; j++){ postPtr[rowPtrs[i][j].first] = rowPtrs[i][j].second; } } for (int i = 0; i < seq1Length + seq2Length + 2; i++) posterior[gapPostBase + i] = gapPosteriors[i]; return posteriorPtr; } float GetGapPosterior(int seqNum, int position) const { assert(seqNum == 0 && position <= seq1Length || seqNum == 1 && position <= seq2Length); return gapPosteriors[position + seqNum * (seq1Length + 1)]; } }; #endif amap-align/align/FileBuffer.h0000644000120200001440000000506610635655116015545 0ustar sarielusers///////////////////////////////////////////////////////////////// // FileBuffer.h // // Buffered file reading. ///////////////////////////////////////////////////////////////// #ifndef FILEBUFFER_H #define FILEBUFFER_H #include #include #include using namespace std; const int BufferSize = 1000; ///////////////////////////////////////////////////////////////// // FileBuffer // // Class for buffering file reading. ///////////////////////////////////////////////////////////////// class FileBuffer { ifstream file; char buffer[BufferSize]; int currPos; int size; bool isEOF; bool isValid; bool canUnget; public: // Some common routines FileBuffer (const char *filename) : file (filename), currPos (0), size (0), isEOF (false), isValid (!file.fail()), canUnget (false){} ~FileBuffer (){ close(); } bool fail () const { return !isValid; } bool eof () const { return (!isValid || isEOF); } void close(){ file.close(); isValid = false; } ///////////////////////////////////////////////////////////////// // FileBuffer::Get() // // Retrieve a character from the file buffer. Returns true if // and only if a character is read. ///////////////////////////////////////////////////////////////// bool Get (char &ch){ // check to make sure that there's more stuff in the file if (!isValid || isEOF) return false; // if the buffer is empty, it's time to reload it if (currPos == size){ file.read (buffer, BufferSize); size = file.gcount(); isEOF = (size == 0); currPos = 0; if (isEOF) return false; } // store the read character ch = buffer[currPos++]; canUnget = true; return true; } ///////////////////////////////////////////////////////////////// // FileBuffer::UnGet() // // Unretrieve the most recently read character from the file // buffer. Note that this allows only a one-level undo. ///////////////////////////////////////////////////////////////// void UnGet (){ assert (canUnget); assert (isValid); assert (currPos > 0); currPos--; assert (currPos < size); isEOF = false; canUnget = false; } ///////////////////////////////////////////////////////////////// // FileBuffer::GetLine() // // Retrieve characters of text until a newline character is // encountered. Terminates properly on end-of-file condition. ///////////////////////////////////////////////////////////////// void GetLine (string &s){ char ch; s = ""; while (Get (ch) && ch != '\n') s += ch; } }; #endif amap-align/align/README0000644000120200001440000000542110650432527014232 0ustar sarielusers AMAP 2.01 ~~~~~~~~~ A fast and accurate multiple sequence alignment program ------------------------------------------------------------------------ AMAP is a novel algorithm for producing multiple sequence alignments. It utilizes posterior decoding, and a novel sequence-annealing alignment, instead of the traditional progressive alignment method. It is the only alignment program that allows to control the sensitivity / specificity tradeoff. In its default configuration, AMAP is tuned to maximize the expected Alignment Metric Accuracy (AMA) score - a new alignment accuracy measure, based on a metric for the multiple-alignment space, which integrates sensitivity and specificity into a single balanced measure. AMA is defined as the fraction of correctly aligned residues (either to another residue or to a gap) out of the total number of residues in all the sequences. For more details on AMAP and AMA, see Schwartz, Ariel S., Myers, Eugene W., and Pachter, Lior. Alignment Metric Accuracy (Submitted for publication). and for more details on sequence-annealing, see Schwartz, Ariel S. and Pachter, Lior. Multiple Alignment by Sequence Annealing. in the Proceedings of the European Conference on Computation Biology (ECCB), Eilat, Israel, September 2006. The current version of AMAP uses the PROBCONS 1.09 code base for some of the input/output procedures, and for the calculation of posterior probabilities (see PROBCONS.README). Future releases might implement the algorithm using a new independent code base. ----------------------------------------------------------------- AMAP has been made freely available as PUBLIC DOMAIN software and hence is not subject to copyright in the United States. This system and/or any portion of the source code may be used, modified, or redistributed without restrictions. AMAP is distributed WITHOUT WARRANTY, express or implied. The authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for loss due to reliance on the program. ----------------------------------------------------------------- Version History AMAP.1.0, 8/15/2005 (Ariel Schwartz) -- initial release AMAP.1.1, 2/20/2006 (Ariel Schwartz) -- Fixed a bug with the calculation of gap posterior probabilities of multiple-sequence-alignments (no effect on pairwise alignments). AMAP.2.0 4/16/2006 (Ariel Schwartz) -- Implemented the sequence-annealing alignment methods as an improved alternative to progressive alignment. AMAP.2.01 6/8/2006 (Ariel Schwartz) -- Corrected DNA alignment parameters file. Improved debug output. AMAP.2.1 7/21/2007 (Ariel Schwartz) -- Includes new output for the AMAP Display Java based GUIamap-align/align/Defaults.h0000644000120200001440000001305610651502112015262 0ustar sarielusers///////////////////////////////////////////////////////////////// // Defaults.h // // Default constants for use in AMAP. The emission // probabilities were computed using the program used to build // the BLOSUM62 matrix from the BLOCKS 5.0 dataset. Transition // parameters were obtained via unsupervised EM training on the // BALIBASE 2.0 benchmark alignment database. ///////////////////////////////////////////////////////////////// #ifndef DEFAULTS_H #define DEFAULTS_H #include using namespace std; /* float initDistrib1Default[] = { 0.3202854395, 0.3398572505, 0.3398572505 }; float gapOpen1Default[] = { 0.1375414133, 0.1375414133 }; float gapExtend1Default[] = { 0.7832147479, 0.7832147479 }; */ float gapFactorDefault = 1; //float initDistrib1Default[] = { 0.6080327034f, 0.1959836632f, 0.1959836632f }; float initDistrib1Default[] = { 0.400000006f, 0.3000000119f, 0.3000000119f }; float gapOpen1Default[] = { 0.01993141696f, 0.01993141696f }; float gapExtend1Default[] = { 0.7943345308f, 0.7943345308f }; float initDistrib2Default[] = { 0.6814756989f, 8.615339902e-05f, 8.615339902e-05f, 0.1591759622f, 0.1591759622 }; float gapOpen2Default[] = { 0.0119511066f, 0.0119511066f, 0.008008334786f, 0.008008334786 }; float gapExtend2Default[] = { 0.3965826333f, 0.3965826333f, 0.8988758326f, 0.8988758326 }; string alphabetDefault = "ARNDCQEGHILKMFPSTWYV"; float emitSingleDefault[20] = { 0.07831005f, 0.05246024f, 0.04433257f, 0.05130349f, 0.02189704f, 0.03585766f, 0.05615771f, 0.07783433f, 0.02601093f, 0.06511648f, 0.09716489f, 0.05877077f, 0.02438117f, 0.04463228f, 0.03940142f, 0.05849916f, 0.05115306f, 0.01203523f, 0.03124726f, 0.07343426f }; float emitPairsDefault[20][20] = { {0.02373072f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f}, {0.00244502f, 0.01775118f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f}, {0.00210228f, 0.00207782f, 0.01281864f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f}, {0.00223549f, 0.00161657f, 0.00353540f, 0.01911178f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f}, {0.00145515f, 0.00044701f, 0.00042479f, 0.00036798f, 0.01013470f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f}, {0.00219102f, 0.00253532f, 0.00158223f, 0.00176784f, 0.00032102f, 0.00756604f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f}, {0.00332218f, 0.00268865f, 0.00224738f, 0.00496800f, 0.00037956f, 0.00345128f, 0.01676565f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f}, {0.00597898f, 0.00194865f, 0.00288882f, 0.00235249f, 0.00071206f, 0.00142432f, 0.00214860f, 0.04062876f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f}, {0.00114353f, 0.00132105f, 0.00141205f, 0.00097077f, 0.00026421f, 0.00113901f, 0.00131767f, 0.00103704f, 0.00867996f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f}, {0.00318853f, 0.00138145f, 0.00104273f, 0.00105355f, 0.00094040f, 0.00100883f, 0.00124207f, 0.00142520f, 0.00059716f, 0.01778263f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f}, {0.00449576f, 0.00246811f, 0.00160275f, 0.00161966f, 0.00138494f, 0.00180553f, 0.00222063f, 0.00212853f, 0.00111754f, 0.01071834f, 0.03583921f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f}, {0.00331693f, 0.00595650f, 0.00257310f, 0.00252518f, 0.00046951f, 0.00312308f, 0.00428420f, 0.00259311f, 0.00121376f, 0.00157852f, 0.00259626f, 0.01612228f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f}, {0.00148878f, 0.00076734f, 0.00063401f, 0.00047808f, 0.00037421f, 0.00075546f, 0.00076105f, 0.00066504f, 0.00042237f, 0.00224097f, 0.00461939f, 0.00096120f, 0.00409522f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f}, {0.00165004f, 0.00090768f, 0.00084658f, 0.00069041f, 0.00052274f, 0.00059248f, 0.00078814f, 0.00115204f, 0.00072545f, 0.00279948f, 0.00533369f, 0.00087222f, 0.00116111f, 0.01661038f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f}, {0.00230618f, 0.00106268f, 0.00100282f, 0.00125381f, 0.00034766f, 0.00090111f, 0.00151550f, 0.00155601f, 0.00049078f, 0.00103767f, 0.00157310f, 0.00154836f, 0.00046718f, 0.00060701f, 0.01846071f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f}, {0.00631752f, 0.00224540f, 0.00301397f, 0.00285226f, 0.00094867f, 0.00191155f, 0.00293898f, 0.00381962f, 0.00116422f, 0.00173565f, 0.00250962f, 0.00312633f, 0.00087787f, 0.00119036f, 0.00180037f, 0.01346609f, 0.0f, 0.0f, 0.0f, 0.0f}, {0.00389995f, 0.00186053f, 0.00220144f, 0.00180488f, 0.00073798f, 0.00154526f, 0.00216760f, 0.00214841f, 0.00077747f, 0.00248968f, 0.00302273f, 0.00250862f, 0.00093371f, 0.00107595f, 0.00147982f, 0.00487295f, 0.01299436f, 0.0f, 0.0f, 0.0f}, {0.00039119f, 0.00029139f, 0.00021006f, 0.00016015f, 0.00010666f, 0.00020592f, 0.00023815f, 0.00038786f, 0.00019097f, 0.00039549f, 0.00076736f, 0.00028448f, 0.00016253f, 0.00085751f, 0.00015674f, 0.00026525f, 0.00024961f, 0.00563625f, 0.0f, 0.0f}, {0.00131840f, 0.00099430f, 0.00074960f, 0.00066005f, 0.00036626f, 0.00070192f, 0.00092548f, 0.00089301f, 0.00131038f, 0.00127857f, 0.00219713f, 0.00100817f, 0.00054105f, 0.00368739f, 0.00047608f, 0.00102648f, 0.00094759f, 0.00069226f, 0.00999315f, 0.0f}, {0.00533241f, 0.00169359f, 0.00136609f, 0.00127915f, 0.00119152f, 0.00132844f, 0.00178697f, 0.00194579f, 0.00071553f, 0.01117956f, 0.00914460f, 0.00210897f, 0.00197461f, 0.00256159f, 0.00135781f, 0.00241601f, 0.00343452f, 0.00038538f, 0.00148001f, 0.02075171f} }; #endif amap-align/align/SafeVector.h0000644000120200001440000000273310635655116015573 0ustar sarielusers///////////////////////////////////////////////////////////////// // SafeVector.h // // STL vector with array bounds checking. To enable bounds // checking, #define ENABLE_CHECKS. ///////////////////////////////////////////////////////////////// #ifndef SAFEVECTOR_H #define SAFEVECTOR_H #include #include ///////////////////////////////////////////////////////////////// // SafeVector // // Class derived from the STL std::vector for bounds checking. ///////////////////////////////////////////////////////////////// template class SafeVector : public std::vector{ public: // miscellaneous constructors SafeVector () {} SafeVector (size_t size) : std::vector(size) {} SafeVector (size_t size, const TYPE &value) : std::vector(size, value) {} SafeVector (const SafeVector &source) : std::vector(source) {} #ifdef ENABLE_CHECKS // [] array bounds checking TYPE &operator[](int index){ assert (index >= 0 && index < (int) size()); return std::vector::operator[] ((size_t) index); } // [] const array bounds checking const TYPE &operator[] (int index) const { assert (index >= 0 && index < (int) size()); return std::vector::operator[] ((size_t) index) ; } #endif }; // some commonly used vector types typedef SafeVector VI; typedef SafeVector VVI; typedef SafeVector VVVI; typedef SafeVector VF; typedef SafeVector VVF; typedef SafeVector VVVF; #endif amap-align/align/Sequence.h0000644000120200001440000003067310635655116015306 0ustar sarielusers///////////////////////////////////////////////////////////////// // Sequence.h // // Class for reading/manipulating single sequence character data. ///////////////////////////////////////////////////////////////// #ifndef SEQUENCE_H #define SEQUENCE_H #include #include #include #include #include #include "SafeVector.h" #include "FileBuffer.h" ///////////////////////////////////////////////////////////////// // Sequence // // Class for storing sequence information. ///////////////////////////////////////////////////////////////// class Sequence { bool isValid; // a boolean indicating whether the sequence data is valid or not string header; // string containing the comment line of the FASTA file SafeVector *data; // pointer to character data int length; // length of the sequence int sequenceLabel; // integer sequence label, typically to indicate the ordering of sequences // in a Multi-FASTA file int inputLabel; // position of sequence in original input ///////////////////////////////////////////////////////////////// // Sequence::Sequence() // // Default constructor. Does nothing. ///////////////////////////////////////////////////////////////// Sequence () : isValid (false), header (""), data (NULL), length (0), sequenceLabel (0), inputLabel (0) {} public: ///////////////////////////////////////////////////////////////// // Sequence::Sequence() // // Constructor. Reads the sequence from a FileBuffer. ///////////////////////////////////////////////////////////////// Sequence (FileBuffer &infile, bool stripGaps = false) : isValid (false), header ("~"), data (NULL), length(0), sequenceLabel (0), inputLabel (0) { // read until the first non-blank line while (!infile.eof()){ infile.GetLine (header); if (header.length() != 0) break; } // check to make sure that it is a correct header line if (header[0] == '>'){ // if so, remove the leading ">" header = header.substr (1); // remove any leading or trailing white space in the header comment while (header.length() > 0 && isspace (header[0])) header = header.substr (1); while (header.length() > 0 && isspace (header[header.length() - 1])) header = header.substr(0, header.length() - 1); // get ready to read the data[] array; note that data[0] is always '@' char ch; data = new SafeVector; assert (data); data->push_back ('@'); // get a character from the file while (infile.Get(ch)){ // if we've reached a new comment line, put the character back and stop if (ch == '>'){ infile.UnGet(); break; } // skip whitespace if (isspace (ch)) continue; // substitute gap character if (ch == '.') ch = '-'; if (stripGaps && ch == '-') continue; // check for known characters if (!((ch >= 'A' && ch <= 'Z') || (ch >= 'a' && ch <= 'z') || ch == '*' || ch == '-')){ cerr << "ERROR: Unknown character encountered: " << ch << endl; exit (1); } // everything's ok so far, so just store this character. data->push_back(ch); ++length; } // sequence must contain data in order to be valid isValid = length > 0; if (!isValid){ delete data; data = NULL; } } } ///////////////////////////////////////////////////////////////// // Sequence::Sequence() // // Constructor. Builds a sequence from existing data. Note // that the data must use one-based indexing where data[0] should // be set to '@'. ///////////////////////////////////////////////////////////////// Sequence (SafeVector *data, string header, int length, int sequenceLabel, int inputLabel) : isValid (data != NULL), header(header), data(data), length (length), sequenceLabel (sequenceLabel), inputLabel (inputLabel) { assert (data); assert ((*data)[0] == '@'); } ///////////////////////////////////////////////////////////////// // Sequence::Sequence() // // Destructor. Release allocated memory. ///////////////////////////////////////////////////////////////// ~Sequence (){ if (data){ assert (isValid); delete data; data = NULL; isValid = false; } } ///////////////////////////////////////////////////////////////// // Sequence::GetHeader() // // Return the string comment associated with this sequence. ///////////////////////////////////////////////////////////////// string GetHeader () const { return header; } ///////////////////////////////////////////////////////////////// // Sequence::GetName() // // Return the first word of the string comment associated with this sequence. ///////////////////////////////////////////////////////////////// string GetName () const { char name[1024]; sscanf (header.c_str(), "%s", name); return string(name); } ///////////////////////////////////////////////////////////////// // Sequence::GetDataPtr() // // Return the iterator to data associated with this sequence. ///////////////////////////////////////////////////////////////// SafeVector::iterator GetDataPtr(){ assert (isValid); assert (data); return data->begin(); } ///////////////////////////////////////////////////////////////// // Sequence::GetPosition() // // Return the character at position i. Recall that the character // data is stored with one-based indexing. ///////////////////////////////////////////////////////////////// char GetPosition (int i) const { assert (isValid); assert (data); assert (i >= 1 && i <= length); return (*data)[i]; } ///////////////////////////////////////////////////////////////// // Sequence::SetLabel() // // Sets the sequence label to i. ///////////////////////////////////////////////////////////////// void SetLabel (int i){ assert (isValid); sequenceLabel = i; inputLabel = i; } ///////////////////////////////////////////////////////////////// // Sequence::SetSortLabel() // // Sets the sequence sorting label to i. ///////////////////////////////////////////////////////////////// void SetSortLabel (int i){ assert (isValid); sequenceLabel = i; } ///////////////////////////////////////////////////////////////// // Sequence::GetLabel() // // Retrieves the input label. ///////////////////////////////////////////////////////////////// int GetLabel () const { assert (isValid); return inputLabel; } ///////////////////////////////////////////////////////////////// // Sequence::GetSortLabel() // // Retrieves the sorting label. ///////////////////////////////////////////////////////////////// int GetSortLabel () const { assert (isValid); return sequenceLabel; } ///////////////////////////////////////////////////////////////// // Sequence::Fail() // // Checks to see if the sequence successfully loaded. ///////////////////////////////////////////////////////////////// bool Fail () const { return !isValid; } ///////////////////////////////////////////////////////////////// // Sequence::Length() // // Returns the length of the sequence. ///////////////////////////////////////////////////////////////// int GetLength () const { assert (isValid); assert (data); return length; } ///////////////////////////////////////////////////////////////// // Sequence::WriteMFA() // // Writes the sequence to outfile in MFA format. Uses numColumns // columns per line. If useIndex is set to false, then the // header is printed as normal, but if useIndex is true, then // ">S###" is printed where ### represents the sequence label. ///////////////////////////////////////////////////////////////// void WriteMFA (ostream &outfile, int numColumns, bool useIndex = false) const { assert (isValid); assert (data); assert (!outfile.fail()); // print out heading if (useIndex) outfile << ">S" << GetLabel() << endl; else outfile << ">" << header << endl; // print out character data int ct = 1; for (; ct <= length; ct++){ outfile << (*data)[ct]; if (ct % numColumns == 0) outfile << endl; } if ((ct-1) % numColumns != 0) outfile << endl; } ///////////////////////////////////////////////////////////////// // Sequence::Clone() // // Returns a new deep copy of the seqeuence. ///////////////////////////////////////////////////////////////// Sequence *Clone () const { Sequence *ret = new Sequence(); assert (ret); ret->isValid = isValid; ret->header = header; ret->data = new SafeVector; assert (ret->data); *(ret->data) = *data; ret->length = length; ret->sequenceLabel = sequenceLabel; ret->inputLabel = inputLabel; return ret; } ///////////////////////////////////////////////////////////////// // Sequence::GetRange() // // Returns a new sequence object consisting of a range of // characters from the current seuquence. ///////////////////////////////////////////////////////////////// Sequence *GetRange (int start, int end) const { Sequence *ret = new Sequence(); assert (ret); assert (start >= 1 && start <= length); assert (end >= 1 && end <= length); assert (start <= end); ret->isValid = isValid; ret->header = header; ret->data = new SafeVector; assert (ret->data); ret->data->push_back ('@'); for (int i = start; i <= end; i++) ret->data->push_back ((*data)[i]); ret->length = end - start + 1; ret->sequenceLabel = sequenceLabel; ret->inputLabel = inputLabel; return ret; } ///////////////////////////////////////////////////////////////// // Sequence::AddGaps() // // Given an SafeVector containing the skeleton for an // alignment and the identity of the current character, this // routine will create a new sequence with all necesssary gaps added. // For instance, // alignment = "XXXBBYYYBBYYXX" // id = 'X' // will perform the transformation // "ATGCAGTCA" --> "ATGCC---GT--CA" // (XXXBBYYYBBYYXX) ///////////////////////////////////////////////////////////////// Sequence *AddGaps (SafeVector *alignment, char id){ Sequence *ret = new Sequence(); assert (ret); ret->isValid = isValid; ret->header = header; ret->data = new SafeVector; assert (ret->data); ret->length = (int) alignment->size(); ret->sequenceLabel = sequenceLabel; ret->inputLabel = inputLabel; ret->data->push_back ('@'); SafeVector::iterator dataIter = data->begin() + 1; for (SafeVector::iterator iter = alignment->begin(); iter != alignment->end(); ++iter){ if (*iter == 'B' || *iter == id){ ret->data->push_back (*dataIter); ++dataIter; } else ret->data->push_back ('-'); } return ret; } ///////////////////////////////////////////////////////////////// // Sequence::GetString() // // Returns the sequence as a string with gaps removed. ///////////////////////////////////////////////////////////////// string GetString (){ string s = ""; for (int i = 1; i <= length; i++){ if ((*data)[i] != '-') s += (*data)[i]; } return s; } ///////////////////////////////////////////////////////////////// // Sequence::GetMapping() // // Returns a SafeVector containing the indices of every // character in the sequence. For instance, if the data is // "ATGCC---GT--CA", the method returns {1,2,3,4,5,9,10,13,14}. ///////////////////////////////////////////////////////////////// SafeVector *GetMapping () const { SafeVector *ret = new SafeVector(1, 0); for (int i = 1; i <= length; i++){ if ((*data)[i] != '-') ret->push_back (i); } return ret; } ///////////////////////////////////////////////////////////////// // Sequence::Highlight() // // Changes all positions with score >= cutoff to upper case and // all positions with score < cutoff to lower case. ///////////////////////////////////////////////////////////////// void Highlight (const SafeVector &scores, const float cutoff){ for (int i = 1; i <= length; i++){ if (scores[i-1] >= cutoff) (*data)[i] = toupper ((*data)[i]); else (*data)[i] = tolower ((*data)[i]); } } }; #endif amap-align/align/EvolutionaryTree.h0000644000120200001440000001364410635655116017055 0ustar sarielusers///////////////////////////////////////////////////////////////// // EvolutionaryTree.h // // Utilities for reading/writing multiple sequence data. ///////////////////////////////////////////////////////////////// #ifndef EVOLUTIONARYTREE_H #define EVOLUTIONARYTREE_H #include #include #include #include "SafeVector.h" #include "MultiSequence.h" #include "Sequence.h" using namespace std; ///////////////////////////////////////////////////////////////// // TreeNode // // The fundamental unit for representing an alignment tree. The // guide tree is represented as a binary tree. ///////////////////////////////////////////////////////////////// class TreeNode { int sequenceLabel; // sequence label TreeNode *left, *right, *parent; // pointers to left, right children ///////////////////////////////////////////////////////////////// // TreeNode::PrintNode() // // Internal routine used to print out the sequence comments // associated with the evolutionary tree, using a hierarchical // parenthesized format. ///////////////////////////////////////////////////////////////// void PrintNode (ostream &outfile, const MultiSequence *sequences) const { // if this is a leaf node, print out the associated sequence comment if (sequenceLabel >= 0) outfile << sequences->GetSequence (sequenceLabel)->GetHeader(); // otherwise, it must have two children; print out their subtrees recursively else { assert (left); assert (right); outfile << "("; left->PrintNode (outfile, sequences); outfile << " "; right->PrintNode (outfile, sequences); outfile << ")"; } } public: ///////////////////////////////////////////////////////////////// // TreeNode::TreeNode() // // Constructor for a tree node. Note that sequenceLabel = -1 // implies that the current node is not a leaf in the tree. ///////////////////////////////////////////////////////////////// TreeNode (int sequenceLabel) : sequenceLabel (sequenceLabel), left (NULL), right (NULL), parent (NULL) { assert (sequenceLabel >= -1); } ///////////////////////////////////////////////////////////////// // TreeNode::~TreeNode() // // Destructor for a tree node. Recursively deletes all children. ///////////////////////////////////////////////////////////////// ~TreeNode (){ if (left){ delete left; left = NULL; } if (right){ delete right; right = NULL; } parent = NULL; } // getters int GetSequenceLabel () const { return sequenceLabel; } TreeNode *GetLeftChild () const { return left; } TreeNode *GetRightChild () const { return right; } TreeNode *GetParent () const { return parent; } // setters void SetSequenceLabel (int sequenceLabel){ this->sequenceLabel = sequenceLabel; assert (sequenceLabel >= -1); } void SetLeftChild (TreeNode *left){ this->left = left; } void SetRightChild (TreeNode *right){ this->right = right; } void SetParent (TreeNode *parent){ this->parent = parent; } ///////////////////////////////////////////////////////////////// // TreeNode::ComputeTree() // // Routine used to compute an evolutionary tree based on the // given distance matrix. We assume the distance matrix has the // form, distMatrix[i][j] = expected accuracy of aligning i with j. ///////////////////////////////////////////////////////////////// static TreeNode *ComputeTree (const VVF &distMatrix){ int numSeqs = distMatrix.size(); // number of sequences in distance matrix VVF distances (numSeqs, VF (numSeqs)); // a copy of the distance matrix SafeVector nodes (numSeqs, NULL); // list of nodes for each sequence SafeVector valid (numSeqs, 1); // valid[i] tells whether or not the ith // nodes in the distances and nodes array // are valid // initialization: make a copy of the distance matrix for (int i = 0; i < numSeqs; i++) for (int j = 0; j < numSeqs; j++) distances[i][j] = distMatrix[i][j]; // initialization: create all the leaf nodes for (int i = 0; i < numSeqs; i++){ nodes[i] = new TreeNode (i); assert (nodes[i]); } // repeat until only a single node left for (int numNodesLeft = numSeqs; numNodesLeft > 1; numNodesLeft--){ float bestProb = -1; pair bestPair; // find the closest pair for (int i = 0; i < numSeqs; i++) if (valid[i]){ for (int j = i+1; j < numSeqs; j++) if (valid[j]){ if (distances[i][j] > bestProb){ bestProb = distances[i][j]; bestPair = make_pair(i, j); } } } // merge the closest pair TreeNode *newParent = new TreeNode (-1); newParent->SetLeftChild (nodes[bestPair.first]); newParent->SetRightChild (nodes[bestPair.second]); nodes[bestPair.first]->SetParent (newParent); nodes[bestPair.second]->SetParent (newParent); nodes[bestPair.first] = newParent; nodes[bestPair.second] = NULL; // now update the distance matrix for (int i = 0; i < numSeqs; i++) if (valid[i]){ distances[bestPair.first][i] = distances[i][bestPair.first] = (distances[i][bestPair.first] + distances[i][bestPair.second]) * bestProb / 2; } // finally, mark the second node entry as no longer valid valid[bestPair.second] = 0; } assert (nodes[0]); return nodes[0]; } ///////////////////////////////////////////////////////////////// // TreeNode::Print() // // Print out the subtree associated with this node in a // parenthesized representation. ///////////////////////////////////////////////////////////////// void Print (ostream &outfile, const MultiSequence *sequences) const { outfile << "Alignment tree: "; PrintNode (outfile, sequences); outfile << endl; } }; #endif amap-align/align/ScoreType.h0000644000120200001440000002534310635655116015451 0ustar sarielusers///////////////////////////////////////////////////////////////// // ScoreType.h // // Routines for doing math operations in PROBCONS. ///////////////////////////////////////////////////////////////// #ifndef SCORETYPE_H #define SCORETYPE_H #include #include #include typedef float ScoreType; const float LOG_ZERO = -2e20; const float LOG_ONE = 0.0; ///////////////////////////////////////////////////////////////// // LOG() // // Compute the logarithm of x. ///////////////////////////////////////////////////////////////// inline ScoreType LOG (ScoreType x){ return log (x); } ///////////////////////////////////////////////////////////////// // EXP() // // Computes exp(x). ///////////////////////////////////////////////////////////////// inline ScoreType EXP (ScoreType x){ //return exp(x); if (x > -2){ if (x > -0.5){ if (x > 0) return exp(x); return (((0.03254409303190190000*x + 0.16280432765779600000)*x + 0.49929760485974900000)*x + 0.99995149601363700000)*x + 0.99999925508501600000; } if (x > -1) return (((0.01973899026052090000*x + 0.13822379685007000000)*x + 0.48056651562365000000)*x + 0.99326940370383500000)*x + 0.99906756856399500000; return (((0.00940528203591384000*x + 0.09414963667859410000)*x + 0.40825793595877300000)*x + 0.93933625499130400000)*x + 0.98369508190545300000; } if (x > -8){ if (x > -4) return (((0.00217245711583303000*x + 0.03484829428350620000)*x + 0.22118199801337800000)*x + 0.67049462206469500000)*x + 0.83556950223398500000; return (((0.00012398771025456900*x + 0.00349155785951272000)*x + 0.03727721426017900000)*x + 0.17974997741536900000)*x + 0.33249299994217400000; } if (x > -16) return (((0.00000051741713416603*x + 0.00002721456879608080)*x + 0.00053418601865636800)*x + 0.00464101989351936000)*x + 0.01507447981459420000; return 0; } /* ///////////////////////////////////////////////////////////////// // LOOKUP() // // Computes log (exp (x) + 1), for 0 <= x <= 7.5. ///////////////////////////////////////////////////////////////// inline ScoreType LOOKUP (ScoreType x){ //return log (exp(x) + 1); if (x < 2){ if (x < 0.5){ if (x < 0) return log (exp(x) + 1); return (((-0.00486373205785640000*x - 0.00020245408813934800)*x + 0.12504222666029800000)*x + 0.49999685320563000000)*x + 0.69314723138948900000; } if (x < 1) return (((-0.00278634205460548000*x - 0.00458097251248546000)*x + 0.12865849880472500000)*x + 0.49862228499205200000)*x + 0.69334810088688000000; return (((0.00059633755154209200*x - 0.01918996666063320000)*x + 0.15288232492093800000)*x + 0.48039958825756900000)*x + 0.69857578503189200000; } if (x < 8){ if (x < 4) return (((0.00135958539181047000*x - 0.02329807659316430000)*x + 0.15885799609532100000)*x + 0.48167498563270800000)*x + 0.69276185058669200000; return (((0.00011992394456683500*x - 0.00338464503306568000)*x + 0.03622746366545470000)*x + 0.82481250248383700000)*x + 0.32507892994863100000; } if (x < 16) return (((0.00000051726300753785*x - 0.00002720671238876090)*x + 0.00053403733818413500)*x + 0.99536021775747900000)*x + 0.01507065715532010000; return x; } ///////////////////////////////////////////////////////////////// // LOOKUP_SLOW() // // Computes log (exp (x) + 1). ///////////////////////////////////////////////////////////////// inline ScoreType LOOKUP_SLOW (ScoreType x){ return log (exp (x) + 1); } ///////////////////////////////////////////////////////////////// // MAX() // // Compute max of three numbers ///////////////////////////////////////////////////////////////// inline ScoreType MAX (ScoreType x, ScoreType y, ScoreType z){ if (x >= y){ if (x >= z) return x; return z; } if (y >= z) return y; return z; } ///////////////////////////////////////////////////////////////// // LOG_PLUS_EQUALS() // // Add two log probabilities and store in the first argument ///////////////////////////////////////////////////////////////// inline void LOG_PLUS_EQUALS (ScoreType &x, ScoreType y){ if (x < y) x = (x <= LOG_ZERO) ? y : LOOKUP(y-x) + x; else x = (y <= LOG_ZERO) ? x : LOOKUP(x-y) + y; } ///////////////////////////////////////////////////////////////// // LOG_PLUS_EQUALS_SLOW() // // Add two log probabilities and store in the first argument ///////////////////////////////////////////////////////////////// inline void LOG_PLUS_EQUALS_SLOW (ScoreType &x, ScoreType y){ if (x < y) x = (x <= LOG_ZERO) ? y : LOOKUP_SLOW(y-x) + x; else x = (y <= LOG_ZERO) ? x : LOOKUP_SLOW(x-y) + y; } ///////////////////////////////////////////////////////////////// // LOG_ADD() // // Add two log probabilities ///////////////////////////////////////////////////////////////// inline ScoreType LOG_ADD (ScoreType x, ScoreType y){ if (x < y) return (x <= LOG_ZERO) ? y : LOOKUP(y-x) + x; return (y <= LOG_ZERO) ? x : LOOKUP(x-y) + y; } */ /* ///////////////////////////////////////////////////////////////// // LOG() // // Compute the logarithm of x. ///////////////////////////////////////////////////////////////// inline float LOG (float x){ return log (x); } ///////////////////////////////////////////////////////////////// // EXP() // // Computes exp(x), fr -4.6 <= x <= 0. ///////////////////////////////////////////////////////////////// inline float EXP (float x){ assert (x <= 0.00f); if (x < EXP_UNDERFLOW_THRESHOLD) return 0.0f; return (((0.006349841068584 * x + 0.080775412572352) * x + 0.397982026296272) * x + 0.95279335963787f) * x + 0.995176455837312f; //return (((0.00681169825657f * x + 0.08386267698832f) * x + 0.40413983195844f) * x + 0.95656674979767f) * x + 0.99556744049130f; } */ const float EXP_UNDERFLOW_THRESHOLD = -4.6; const float LOG_UNDERFLOW_THRESHOLD = 7.5; ///////////////////////////////////////////////////////////////// // LOOKUP() // // Computes log (exp (x) + 1), for 0 <= x <= 7.5. ///////////////////////////////////////////////////////////////// inline float LOOKUP (float x){ assert (x >= 0.00f); assert (x <= LOG_UNDERFLOW_THRESHOLD); //return ((-0.00653779113685f * x + 0.09537236626558f) * x + 0.55317574459331f) * x + 0.68672959851568f; if (x <= 1.00f) return ((-0.009350833524763f * x + 0.130659527668286f) * x + 0.498799810682272f) * x + 0.693203116424741f; if (x <= 2.50f) return ((-0.014532321752540f * x + 0.139942324101744f) * x + 0.495635523139337f) * x + 0.692140569840976f; if (x <= 4.50f) return ((-0.004605031767994f * x + 0.063427417320019f) * x + 0.695956496475118f) * x + 0.514272634594009f; assert (x <= LOG_UNDERFLOW_THRESHOLD); return ((-0.000458661602210f * x + 0.009695946122598f) * x + 0.930734667215156f) * x + 0.168037164329057f; //return (((0.00089738532761f * x - 0.01859488697982f) * x + 0.14415772028626f) * x + 0.49515490689159f) * x + 0.69311928966454f; } ///////////////////////////////////////////////////////////////// // LOOKUP_SLOW() // // Computes log (exp (x) + 1). ///////////////////////////////////////////////////////////////// inline float LOOKUP_SLOW (float x){ return log (exp (x) + 1); } ///////////////////////////////////////////////////////////////// // MAX() // // Compute max of three numbers ///////////////////////////////////////////////////////////////// inline float MAX (float x, float y, float z){ if (x >= y){ if (x >= z) return x; return z; } if (y >= z) return y; return z; } ///////////////////////////////////////////////////////////////// // LOG_PLUS_EQUALS() // // Add two log probabilities and store in the first argument ///////////////////////////////////////////////////////////////// inline void LOG_PLUS_EQUALS (float &x, float y){ if (x < y) x = (x == LOG_ZERO || y - x >= LOG_UNDERFLOW_THRESHOLD) ? y : LOOKUP(y-x) + x; else x = (y == LOG_ZERO || x - y >= LOG_UNDERFLOW_THRESHOLD) ? x : LOOKUP(x-y) + y; } ///////////////////////////////////////////////////////////////// // LOG_PLUS_EQUALS_SLOW() // // Add two log probabilities and store in the first argument ///////////////////////////////////////////////////////////////// inline void LOG_PLUS_EQUALS_SLOW (float &x, float y){ if (x < y) x = (x == LOG_ZERO) ? y : LOOKUP_SLOW(y-x) + x; else x = (y == LOG_ZERO) ? x : LOOKUP_SLOW(x-y) + y; } ///////////////////////////////////////////////////////////////// // LOG_ADD() // // Add two log probabilities ///////////////////////////////////////////////////////////////// inline float LOG_ADD (float x, float y){ if (x < y) return (x == LOG_ZERO || y - x >= LOG_UNDERFLOW_THRESHOLD) ? y : LOOKUP(y-x) + x; return (y == LOG_ZERO || x - y >= LOG_UNDERFLOW_THRESHOLD) ? x : LOOKUP(x-y) + y; } ///////////////////////////////////////////////////////////////// // LOG_ADD() // // Add three log probabilities ///////////////////////////////////////////////////////////////// inline float LOG_ADD (float x1, float x2, float x3){ return LOG_ADD (x1, LOG_ADD (x2, x3)); } ///////////////////////////////////////////////////////////////// // LOG_ADD() // // Add four log probabilities ///////////////////////////////////////////////////////////////// inline float LOG_ADD (float x1, float x2, float x3, float x4){ return LOG_ADD (x1, LOG_ADD (x2, LOG_ADD (x3, x4))); } ///////////////////////////////////////////////////////////////// // LOG_ADD() // // Add five log probabilities ///////////////////////////////////////////////////////////////// inline float LOG_ADD (float x1, float x2, float x3, float x4, float x5){ return LOG_ADD (x1, LOG_ADD (x2, LOG_ADD (x3, LOG_ADD (x4, x5)))); } ///////////////////////////////////////////////////////////////// // LOG_ADD() // // Add siz log probabilities ///////////////////////////////////////////////////////////////// inline float LOG_ADD (float x1, float x2, float x3, float x4, float x5, float x6){ return LOG_ADD (x1, LOG_ADD (x2, LOG_ADD (x3, LOG_ADD (x4, LOG_ADD (x5, x6))))); } ///////////////////////////////////////////////////////////////// // LOG_ADD() // // Add seven log probabilities ///////////////////////////////////////////////////////////////// inline float LOG_ADD (float x1, float x2, float x3, float x4, float x5, float x6, float x7){ return LOG_ADD (x1, LOG_ADD (x2, LOG_ADD (x3, LOG_ADD (x4, LOG_ADD (x5, LOG_ADD (x6, x7)))))); } ///////////////////////////////////////////////////////////////// // ChooseBestOfThree() // // Store the largest of three values x1, x2, and x3 in *x. Also // if xi is the largest value, then store bi in *b. ///////////////////////////////////////////////////////////////// inline void ChooseBestOfThree (float x1, float x2, float x3, char b1, char b2, char b3, float *x, char *b){ if (x1 >= x2){ if (x1 >= x3){ *x = x1; *b = b1; return; } *x = x3; *b = b3; return; } if (x2 >= x3){ *x = x2; *b = b2; return; } *x = x3; *b = b3; } #endif amap-align/align/Amap.cc0000644000120200001440000016266310651502112014540 0ustar sarielusers///////////////////////////////////////////////////////////////// // Amap.cc // // Main routines for AMAP program. ///////////////////////////////////////////////////////////////// #include "SafeVector.h" #include "MultiSequence.h" #include "MultiSequenceDag.h" #include "Defaults.h" #include "ScoreType.h" #include "ProbabilisticModel.h" #include "EvolutionaryTree.h" #include "SparseMatrix.h" #include #include #include #include #include #include #include #include #include #include #include string parametersInputFilename = ""; string parametersOutputFilename = "no training"; string annotationFilename = ""; bool enableTraining = false; bool enableVerbose = false; bool enableAllPairs = false; bool enableAnnotation = false; bool enableViterbi = false; bool enableClustalWOutput = false; bool enableTrainEmissions = false; bool enableAlignOrder = false; bool enableDagAlignment = true; bool enableEdgeReordering = true; bool useTgf = true; bool onlyPrintPosteriors = false; bool outputForGUI = false; int numConsistencyReps = 0; int numPreTrainingReps = 0; int numIterativeRefinementReps = 0; int guiStepSize = 1; float guiStartWeight = std::numeric_limits::max(); float cutoff = 0; float gapOpenPenalty = 0; float gapContinuePenalty = 0; VF initDistrib (NumMatrixTypes); VF gapOpen (2*NumInsertStates); VF gapExtend (2*NumInsertStates); VVF emitPairs (256, VF (256, 1e-10)); VF emitSingle (256, 1e-5); string alphabet = alphabetDefault; float gapFactor = gapFactorDefault; float edgeWeightThreshold = 0; const int MIN_PRETRAINING_REPS = 0; const int MAX_PRETRAINING_REPS = 20; const int MIN_CONSISTENCY_REPS = 0; const int MAX_CONSISTENCY_REPS = 5; const int MIN_ITERATIVE_REFINEMENT_REPS = 0; const int MAX_ITERATIVE_REFINEMENT_REPS = 1000; ///////////////////////////////////////////////////////////////// // Function prototypes ///////////////////////////////////////////////////////////////// void PrintHeading(); void PrintParameters (const char *message, const VF &initDistrib, const VF &gapOpen, const VF &gapExtend, const VVF &emitPairs, const VF &emitSingle, const char *filename); MultiSequence *DoAlign (MultiSequence *sequence, const ProbabilisticModel &model, VF &initDistrib, VF &gapOpen, VF &gapExtend, VVF &emitPairs, VF &emitSingle); SafeVector ParseParams (int argc, char **argv); void ReadParameters (); MultiSequence *ComputeFinalAlignment (const TreeNode *tree, MultiSequence *sequences, const SafeVector > &sparseMatrices, const ProbabilisticModel &model); MultiSequence *AlignAlignments (MultiSequence *align1, MultiSequence *align2, const SafeVector > &sparseMatrices, const ProbabilisticModel &model); SafeVector > DoRelaxation (MultiSequence *sequences, SafeVector > &sparseMatrices); void Relax (SparseMatrix *matXZ, SparseMatrix *matZY, VF &posterior); set GetSubtree (const TreeNode *tree); void TreeBasedBiPartitioning (const SafeVector > &sparseMatrices, const ProbabilisticModel &model, MultiSequence* &alignment, const TreeNode *tree); void DoIterativeRefinement (const SafeVector > &sparseMatrices, const ProbabilisticModel &model, MultiSequence* &alignment); void WriteAnnotation (MultiSequence *alignment, const SafeVector > &sparseMatrices); int ComputeScore (const SafeVector > &active, const SafeVector > &sparseMatrices); ///////////////////////////////////////////////////////////////// // main() // // Calls all initialization routines and runs the AMAP // aligner. ///////////////////////////////////////////////////////////////// int main (int argc, char **argv){ // print AMAP heading PrintHeading(); // parse program parameters SafeVector sequenceNames = ParseParams (argc, argv); ReadParameters(); PrintParameters ("Using parameter set:", initDistrib, gapOpen, gapExtend, emitPairs, emitSingle, NULL); // now, we'll process all the files given as input. If we are given // several filenames as input, then we'll load all of those sequences // simultaneously, as long as we're not training. On the other hand, // if we are training, then we'll treat each file as a separate // training instance // if we are training if (enableTraining){ // build new model for aligning ProbabilisticModel model (initDistrib, gapOpen, gapExtend, emitPairs, emitSingle); // prepare to average parameters for (int i = 0; i < (int) initDistrib.size(); i++) initDistrib[i] = 0; for (int i = 0; i < (int) gapOpen.size(); i++) gapOpen[i] = 0; for (int i = 0; i < (int) gapExtend.size(); i++) gapExtend[i] = 0; if (enableTrainEmissions){ for (int i = 0; i < (int) emitPairs.size(); i++) for (int j = 0; j < (int) emitPairs[i].size(); j++) emitPairs[i][j] = 0; for (int i = 0; i < (int) emitSingle.size(); i++) emitSingle[i] = 0; } // align each file individually for (int i = 0; i < (int) sequenceNames.size(); i++){ VF thisInitDistrib (NumMatrixTypes); VF thisGapOpen (2*NumInsertStates); VF thisGapExtend (2*NumInsertStates); VVF thisEmitPairs (256, VF (256, 1e-10)); VF thisEmitSingle (256, 1e-5); // load sequence file MultiSequence *sequences = new MultiSequence(); assert (sequences); cerr << "Loading sequence file: " << sequenceNames[i] << endl; sequences->LoadMFA (sequenceNames[i], true); // align sequences MultiSequence *tmpMsa = DoAlign (sequences, model, thisInitDistrib, thisGapOpen, thisGapExtend, thisEmitPairs, thisEmitSingle); delete tmpMsa; // add in contribution of the derived parameters for (int i = 0; i < (int) initDistrib.size(); i++) initDistrib[i] += thisInitDistrib[i]; for (int i = 0; i < (int) gapOpen.size(); i++) gapOpen[i] += thisGapOpen[i]; for (int i = 0; i < (int) gapExtend.size(); i++) gapExtend[i] += thisGapExtend[i]; if (enableTrainEmissions){ for (int i = 0; i < (int) emitPairs.size(); i++) for (int j = 0; j < (int) emitPairs[i].size(); j++) emitPairs[i][j] += thisEmitPairs[i][j]; for (int i = 0; i < (int) emitSingle.size(); i++) emitSingle[i] += thisEmitSingle[i]; } delete sequences; } // compute new parameters and print them out for (int i = 0; i < (int) initDistrib.size(); i++) initDistrib[i] /= (int) sequenceNames.size(); for (int i = 0; i < (int) gapOpen.size(); i++) gapOpen[i] /= (int) sequenceNames.size(); for (int i = 0; i < (int) gapExtend.size(); i++) gapExtend[i] /= (int) sequenceNames.size(); if (enableTrainEmissions){ for (int i = 0; i < (int) emitPairs.size(); i++) for (int j = 0; j < (int) emitPairs[i].size(); j++) emitPairs[i][j] /= (int) sequenceNames.size(); for (int i = 0; i < (int) emitSingle.size(); i++) emitSingle[i] /= sequenceNames.size(); } PrintParameters ("Trained parameter set:", initDistrib, gapOpen, gapExtend, emitPairs, emitSingle, parametersOutputFilename.c_str()); } // if we are not training, we must simply want to align some sequences else { bool allStartWithM = true; // load all files together MultiSequence *sequences = new MultiSequence(); assert (sequences); for (int i = 0; i < (int) sequenceNames.size(); i++){ cerr << "Loading sequence file: " << sequenceNames[i] << endl; sequences->LoadMFA (sequenceNames[i], true); } for (int i = 0; i < sequences->GetNumSequences(); i++){ char firstChar = *(++(sequences->GetSequence(i)->GetDataPtr())); allStartWithM = firstChar == 'M' ? allStartWithM : false; } if (allStartWithM) { for (int i = 0; i < sequences->GetNumSequences(); i++){ int seqLength = sequences->GetSequence(0)->GetLength(); Sequence* newSeq = sequences->GetSequence(0)->GetRange(2,seqLength); sequences->RemoveSequence(0); sequences->AddSequence(newSeq); } } // do all "pre-training" repetitions first for (int ct = 0; ct < numPreTrainingReps; ct++){ enableTraining = true; // build new model for aligning ProbabilisticModel model (initDistrib, gapOpen, gapExtend, emitPairs, emitSingle); // do initial alignments DoAlign (sequences, model, initDistrib, gapOpen, gapExtend, emitPairs, emitSingle); // print new parameters PrintParameters ("Recomputed parameter set:", initDistrib, gapOpen, gapExtend, emitPairs, emitSingle, NULL); enableTraining = false; } // now, we can perform the alignments and write them out MultiSequence *alignment = DoAlign (sequences, ProbabilisticModel (initDistrib, gapOpen, gapExtend, emitPairs, emitSingle), initDistrib, gapOpen, gapExtend, emitPairs, emitSingle); if (allStartWithM) { for (int i = 0; i < alignment->GetNumSequences(); i++){ SafeVector* newData = new SafeVector; Sequence* currSeq = alignment->GetSequence(0); SafeVector::iterator dataItr = currSeq->GetDataPtr(); newData->push_back(*dataItr++); newData->push_back('M'); for (int j = 0; j < currSeq->GetLength(); j++) { newData->push_back(*dataItr++); } Sequence *newSeq = new Sequence(newData, currSeq->GetHeader(), currSeq->GetLength() + 1, currSeq->GetSortLabel(), currSeq->GetLabel()); alignment->AddSequence(newSeq); alignment->RemoveSequence(0); } } if (onlyPrintPosteriors) return 0; if (!enableAllPairs && !outputForGUI){ if (enableClustalWOutput) alignment->WriteALN (cout); else alignment->WriteMFA (cout); } delete alignment; delete sequences; } } ///////////////////////////////////////////////////////////////// // PrintHeading() // // Prints heading for AMAP program. ///////////////////////////////////////////////////////////////// void PrintHeading (){ cerr << endl << "AMAP version " << VERSION << " - align multiple protein sequences and print to standard output" << endl << "PROBCONS Written by Chuong Do" << endl << "AMAP algorithm implemented by Ariel Schwartz" << endl << endl; } ///////////////////////////////////////////////////////////////// // PrintParameters() // // Prints AMAP parameters to STDERR. If a filename is // specified, then the parameters are also written to the file. ///////////////////////////////////////////////////////////////// void PrintParameters (const char *message, const VF &initDistrib, const VF &gapOpen, const VF &gapExtend, const VVF &emitPairs, const VF &emitSingle, const char *filename){ // print parameters to the screen cerr << message << endl << " initDistrib[] = { "; for (int i = 0; i < NumMatrixTypes; i++) cerr << setprecision (10) << initDistrib[i] << " "; cerr << "}" << endl << " gapOpen[] = { "; for (int i = 0; i < NumInsertStates*2; i++) cerr << setprecision (10) << gapOpen[i] << " "; cerr << "}" << endl << " gapExtend[] = { "; for (int i = 0; i < NumInsertStates*2; i++) cerr << setprecision (10) << gapExtend[i] << " "; cerr << "}" << endl << endl; /* for (int i = 0; i < 5; i++){ for (int j = 0; j <= i; j++){ cerr << emitPairs[(unsigned char) alphabet[i]][(unsigned char) alphabet[j]] << " "; } cerr << endl; }*/ // if a file name is specified if (filename){ // attempt to open the file for writing FILE *file = fopen (filename, "w"); if (!file){ cerr << "ERROR: Unable to write parameter file: " << filename << endl; exit (1); } // if successful, then write the parameters to the file for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); fprintf (file, "%s\n", alphabet.c_str()); for (int i = 0; i < (int) alphabet.size(); i++){ for (int j = 0; j <= i; j++) fprintf (file, "%.10f ", emitPairs[(unsigned char) alphabet[i]][(unsigned char) alphabet[j]]); fprintf (file, "\n"); } for (int i = 0; i < (int) alphabet.size(); i++) fprintf (file, "%.10f ", emitSingle[(unsigned char) alphabet[i]]); fprintf (file, "\n"); fclose (file); } } ///////////////////////////////////////////////////////////////// // DoAlign() // // First computes all pairwise posterior probability matrices. // Then, computes new parameters if training, or a final // alignment, otherwise. ///////////////////////////////////////////////////////////////// MultiSequence *DoAlign (MultiSequence *sequences, const ProbabilisticModel &model, VF &initDistrib, VF &gapOpen, VF &gapExtend, VVF &emitPairs, VF &emitSingle){ assert (sequences); const int numSeqs = sequences->GetNumSequences(); VVF distances (numSeqs, VF (numSeqs, 0)); SafeVector > sparseMatrices (numSeqs, SafeVector(numSeqs, NULL)); SafeVector > originalSparseMatrices (numSeqs, SafeVector(numSeqs, NULL)); if (enableTraining){ // prepare to average parameters for (int i = 0; i < (int) initDistrib.size(); i++) initDistrib[i] = 0; for (int i = 0; i < (int) gapOpen.size(); i++) gapOpen[i] = 0; for (int i = 0; i < (int) gapExtend.size(); i++) gapExtend[i] = 0; if (enableTrainEmissions){ for (int i = 0; i < (int) emitPairs.size(); i++) for (int j = 0; j < (int) emitPairs[i].size(); j++) emitPairs[i][j] = 0; for (int i = 0; i < (int) emitSingle.size(); i++) emitSingle[i] = 0; } } // skip posterior calculations if we just want to do Viterbi alignments if (!enableViterbi){ cerr << "Computing posterior matrices" << endl; // do all pairwise alignments for posterior probability matrices for (int a = 0; a < numSeqs-1; a++){ for (int b = a+1; b < numSeqs; b++){ Sequence *seq1 = sequences->GetSequence (a); Sequence *seq2 = sequences->GetSequence (b); // verbose output if (enableVerbose) cerr << "Computing posterior matrix: (" << a+1 << ") " << seq1->GetHeader() << " vs. " << "(" << b+1 << ") " << seq2->GetHeader() << " -- "; // compute forward and backward probabilities VF *forward = model.ComputeForwardMatrix (seq1, seq2); assert (forward); VF *backward = model.ComputeBackwardMatrix (seq1, seq2); assert (backward); // if we are training, then we'll simply want to compute the // expected counts for each region within the matrix separately; // otherwise, we'll need to put all of the regions together and // assemble a posterior probability match matrix // so, if we're training if (enableTraining){ // compute new parameters VF thisInitDistrib (NumMatrixTypes); VF thisGapOpen (2*NumInsertStates); VF thisGapExtend (2*NumInsertStates); VVF thisEmitPairs (256, VF (256, 1e-10)); VF thisEmitSingle (256, 1e-5); model.ComputeNewParameters (seq1, seq2, *forward, *backward, thisInitDistrib, thisGapOpen, thisGapExtend, thisEmitPairs, thisEmitSingle, enableTrainEmissions); // add in contribution of the derived parameters for (int i = 0; i < (int) initDistrib.size(); i++) initDistrib[i] += thisInitDistrib[i]; for (int i = 0; i < (int) gapOpen.size(); i++) gapOpen[i] += thisGapOpen[i]; for (int i = 0; i < (int) gapExtend.size(); i++) gapExtend[i] += thisGapExtend[i]; if (enableTrainEmissions){ for (int i = 0; i < (int) emitPairs.size(); i++) for (int j = 0; j < (int) emitPairs[i].size(); j++) emitPairs[i][j] += thisEmitPairs[i][j]; for (int i = 0; i < (int) emitSingle.size(); i++) emitSingle[i] += thisEmitSingle[i]; } // let us know that we're done. if (enableVerbose) cerr << "done." << endl; } else { // compute posterior probability matrix VF *posterior = model.ComputePosteriorMatrix (seq1, seq2, *forward, *backward); assert (posterior); // compute sparse representations originalSparseMatrices[a][b] = new SparseMatrix (seq1->GetLength(), seq2->GetLength(), *posterior); originalSparseMatrices[b][a] = originalSparseMatrices[a][b]->ComputeTranspose(); if (!enableAllPairs){ if (!enableDagAlignment) { // perform the pairwise sequence alignment pair *, float> alignment = model.ComputeAlignment (seq1->GetLength(), seq2->GetLength(), *posterior); // compute "expected accuracy" distance for evolutionary tree computation float distance = alignment.second / min (seq1->GetLength(), seq2->GetLength()); //float distance = (gapFactor == 0) ? alignment.second / min (seq1->GetLength(), seq2->GetLength()): // alignment.second / (seq1->GetLength() + seq2->GetLength()) * gapFactor; distances[a][b] = distances[b][a] = distance; if (enableVerbose) { cerr << setprecision (10) << distance << endl; // if (distance == 1) // cerr << setprecision(10) << (*posterior)[4 * (seq1->GetLength() + 1) + 4] << endl; // originalSparseMatrices[a][b]->Print(cerr); } delete alignment.first; } } else { // let us know that we're done. if (enableVerbose) cerr << "done." << endl; } delete posterior; } delete forward; delete backward; } } } // now average out parameters derived if (enableTraining){ // compute new parameters for (int i = 0; i < (int) initDistrib.size(); i++) initDistrib[i] /= numSeqs * (numSeqs - 1) / 2; for (int i = 0; i < (int) gapOpen.size(); i++) gapOpen[i] /= numSeqs * (numSeqs - 1) / 2; for (int i = 0; i < (int) gapExtend.size(); i++) gapExtend[i] /= numSeqs * (numSeqs - 1) / 2; if (enableTrainEmissions){ for (int i = 0; i < (int) emitPairs.size(); i++) for (int j = 0; j < (int) emitPairs[i].size(); j++) emitPairs[i][j] /= numSeqs * (numSeqs - 1) / 2; for (int i = 0; i < (int) emitSingle.size(); i++) emitSingle[i] /= numSeqs * (numSeqs - 1) / 2; } } // see if we still want to do some alignments else { if (!enableViterbi){ sparseMatrices = originalSparseMatrices; // perform the consistency transformation the desired number of times for (int r = 0; r < numConsistencyReps; r++){ SafeVector > newSparseMatrices = DoRelaxation (sequences, sparseMatrices); // now replace the old posterior matrices for (int i = 0; i < numSeqs; i++){ for (int j = 0; j < numSeqs; j++){ // don't delete the original sparse matrices if (r > 0) delete sparseMatrices[i][j]; sparseMatrices[i][j] = newSparseMatrices[i][j]; } } } } MultiSequence *finalAlignment = NULL; if (onlyPrintPosteriors) { for (int i = 0; i < numSeqs; i++){ string seq1name = sequences->GetSequence(i)->GetHeader(); for (int j = i + 1; j < numSeqs; j++){ cout << "Sparse Matrix: " << i << "," << j << endl; cout << "Sequence names: " << seq1name << ", " << sequences->GetSequence(j)->GetHeader() << endl; sparseMatrices[i][j]->Print(cout); } } } else if (enableAllPairs){ for (int a = 0; a < numSeqs-1; a++){ for (int b = a+1; b < numSeqs; b++){ Sequence *seq1 = sequences->GetSequence (a); Sequence *seq2 = sequences->GetSequence (b); if (enableVerbose) cerr << "Performing pairwise alignment: (" << a+1 << ") " << seq1->GetHeader() << " vs. " << "(" << b+1 << ") " << seq2->GetHeader() << " -- "; // perform the pairwise sequence alignment pair *, float> alignment; if (enableViterbi) alignment = model.ComputeViterbiAlignment (seq1, seq2); else { // build posterior matrix VF *posterior = sparseMatrices[a][b]->GetPosterior(); assert (posterior); int length = (seq1->GetLength() + 1) * (seq2->GetLength() + 1); for (int i = 0; i < length; i++) (*posterior)[i] -= cutoff; alignment = model.ComputeAlignment (seq1->GetLength(), seq2->GetLength(), *posterior, gapFactor); delete posterior; } // write pairwise alignments string name = seq1->GetHeader() + "-" + seq2->GetHeader() + (enableClustalWOutput ? ".aln" : ".fasta"); ofstream outfile (name.c_str()); MultiSequence *result = new MultiSequence(); result->AddSequence (seq1->AddGaps(alignment.first, 'X')); result->AddSequence (seq2->AddGaps(alignment.first, 'Y')); if (enableClustalWOutput) result->WriteALN (outfile); else result->WriteMFA (outfile); outfile.close(); delete alignment.first; } } } // now if we still need to do a final multiple alignment else { if (enableVerbose) cerr << endl; if (!enableDagAlignment) { // compute the evolutionary tree TreeNode *tree = TreeNode::ComputeTree (distances); tree->Print (cerr, sequences); cerr << endl; // make the final alignment finalAlignment = ComputeFinalAlignment (tree, sequences, sparseMatrices, model); delete tree; } else { cerr << "Building DAG" << endl; MultiSequenceDag mds(sequences,false,outputForGUI,guiStartWeight,guiStepSize); cerr << "Starting the sequence annealing process" << endl; finalAlignment = mds.AlignDag(sparseMatrices, gapFactor, enableVerbose, enableEdgeReordering, useTgf, edgeWeightThreshold); } // build annotation if (enableAnnotation){ WriteAnnotation (finalAlignment, originalSparseMatrices); } } if (!enableViterbi){ // delete sparse matrices for (int a = 0; a < numSeqs-1; a++){ for (int b = a+1; b < numSeqs; b++){ delete originalSparseMatrices[a][b]; delete originalSparseMatrices[b][a]; if (numConsistencyReps > 0){ delete sparseMatrices[a][b]; delete sparseMatrices[b][a]; } } } } return finalAlignment; } return NULL; } ///////////////////////////////////////////////////////////////// // GetInteger() // // Attempts to parse an integer from the character string given. // Returns true only if no parsing error occurs. ///////////////////////////////////////////////////////////////// bool GetInteger (char *data, int *val){ char *endPtr; long int retVal; assert (val); errno = 0; retVal = strtol (data, &endPtr, 0); if (retVal == 0 && (errno != 0 || data == endPtr)) return false; if (errno != 0 && (retVal == LONG_MAX || retVal == LONG_MIN)) return false; if (retVal < (long) INT_MIN || retVal > (long) INT_MAX) return false; *val = (int) retVal; return true; } ///////////////////////////////////////////////////////////////// // GetFloat() // // Attempts to parse a float from the character string given. // Returns true only if no parsing error occurs. ///////////////////////////////////////////////////////////////// bool GetFloat (char *data, float *val){ char *endPtr; double retVal; assert (val); errno = 0; retVal = strtod (data, &endPtr); if (retVal == 0 && (errno != 0 || data == endPtr)) return false; if (errno != 0 && (retVal >= 1000000.0 || retVal <= -1000000.0)) return false; *val = (float) retVal; return true; } ///////////////////////////////////////////////////////////////// // ParseParams() // // Parse all command-line options. ///////////////////////////////////////////////////////////////// SafeVector ParseParams (int argc, char **argv){ if (argc < 2){ cerr << "AMAP comes with ABSOLUTELY NO WARRANTY. This is free software, and" << endl << "you are welcome to redistribute it under certain conditions. See the" << endl << "files README and README.PROBCONS for details." << endl << endl << "Usage:" << endl << " amap [OPTION]... [MFAFILE]..." << endl << endl << "Description:" << endl << " Align sequences in MFAFILE(s) and print result to standard output" << endl << endl << " -clustalw" << endl << " use CLUSTALW output format instead of MFA" << endl << endl << " -c, --consistency REPS" << endl << " use " << MIN_CONSISTENCY_REPS << " <= REPS <= " << MAX_CONSISTENCY_REPS << " (default: " << numConsistencyReps << ") passes of consistency transformation" << endl << endl << " -ir, --iterative-refinement REPS" << endl << " use " << MIN_ITERATIVE_REFINEMENT_REPS << " <= REPS <= " << MAX_ITERATIVE_REFINEMENT_REPS << " (default: " << numIterativeRefinementReps << ") passes of iterative-refinement" << endl << endl << " -pre, --pre-training REPS" << endl << " use " << MIN_PRETRAINING_REPS << " <= REPS <= " << MAX_PRETRAINING_REPS << " (default: " << numPreTrainingReps << ") rounds of pretraining" << endl << endl << " -pairs" << endl << " generate all-pairs pairwise alignments" << endl << endl << " -viterbi" << endl << " use Viterbi algorithm to generate all pairs (automatically enables -pairs)" << endl << endl << " -v, --verbose" << endl << " report progress while aligning (default: " << (enableVerbose ? "on" : "off") << ")" << endl << endl << " -annot FILENAME" << endl << " write annotation for multiple alignment to FILENAME" << endl << endl << " -t, --train FILENAME" << endl << " compute EM transition probabilities, store in FILENAME (default: " << parametersOutputFilename << ")" << endl << endl << " -e, --emissions" << endl << " also reestimate emission probabilities (default: " << (enableTrainEmissions ? "on" : "off") << ")" << endl << endl << " -p, --paramfile FILENAME" << endl << " read parameters from FILENAME (default: " << parametersInputFilename << ")" << endl << endl << " -a, --alignment-order" << endl << " print sequences in alignment order rather than input order (default: " << (enableAlignOrder ? "on" : "off") << ")" << endl << endl << " -g, --gap-factor GF" << endl << " use GF as the gap-factor parameter, set to 0 for best sensitivity, higher values for better specificity (default: " << gapFactor << ")" << endl << endl << " -w, --edge-weight-threshold W" << endl << " stop the sequence annealing process when best edge has lower weight than W," << endl << " set to 0 for best sensitivity, higher values for better specificity (default: " << edgeWeightThreshold << ")" << endl << endl << " -prog, --progressive" << endl << " use progresive alignment instead of sequence annealing alignment (default: " << (!enableDagAlignment ? "on" : "off") << ")" << endl << endl << " -noreorder, --no-edge-reordering" << endl << " disable reordring of edges during sequence annealing alignment (default: " << (!enableEdgeReordering ? "on" : "off") << ")" << endl << endl << " -maxstep, --use-max-stepsize" << endl << " use maximum improvement step size instead of tGf edge ranking (default: " << (!useTgf ? "on" : "off") << ")" << endl << endl << " -print, --print-posteriors" << endl << " only print the posterior probability matrices (default: " << (onlyPrintPosteriors ? "on" : "off") << ")" << endl << endl << " -gui [START] [STEP]" << endl << " print output for the AMAP Display Java based GUI (default: " << (outputForGUI ? "on" : "off") << ") " << endl << " starting at weight START (default: infinity) with step size STEP (default: " << guiStepSize << ")" << endl << endl; exit (1); } SafeVector sequenceNames; int tempInt; float tempFloat; for (int i = 1; i < argc; i++){ if (argv[i][0] == '-'){ // training if (!strcmp (argv[i], "-t") || !strcmp (argv[i], "--train")){ enableTraining = true; if (i < argc - 1) parametersOutputFilename = string (argv[++i]); else { cerr << "ERROR: Filename expected for option " << argv[i] << endl; exit (1); } } // emission training else if (!strcmp (argv[i], "-e") || !strcmp (argv[i], "--emissions")){ enableTrainEmissions = true; } // parameter file else if (!strcmp (argv[i], "-p") || !strcmp (argv[i], "--paramfile")){ if (i < argc - 1) parametersInputFilename = string (argv[++i]); else { cerr << "ERROR: Filename expected for option " << argv[i] << endl; exit (1); } } // number of consistency transformations else if (!strcmp (argv[i], "-c") || !strcmp (argv[i], "--consistency")){ if (i < argc - 1){ if (!GetInteger (argv[++i], &tempInt)){ cerr << "ERROR: Invalid integer following option " << argv[i-1] << ": " << argv[i] << endl; exit (1); } else { if (tempInt < MIN_CONSISTENCY_REPS || tempInt > MAX_CONSISTENCY_REPS){ cerr << "ERROR: For option " << argv[i-1] << ", integer must be between " << MIN_CONSISTENCY_REPS << " and " << MAX_CONSISTENCY_REPS << "." << endl; exit (1); } else numConsistencyReps = tempInt; } } else { cerr << "ERROR: Integer expected for option " << argv[i] << endl; exit (1); } } // number of randomized partitioning iterative refinement passes else if (!strcmp (argv[i], "-ir") || !strcmp (argv[i], "--iterative-refinement")){ if (i < argc - 1){ if (!GetInteger (argv[++i], &tempInt)){ cerr << "ERROR: Invalid integer following option " << argv[i-1] << ": " << argv[i] << endl; exit (1); } else { if (tempInt < MIN_ITERATIVE_REFINEMENT_REPS || tempInt > MAX_ITERATIVE_REFINEMENT_REPS){ cerr << "ERROR: For option " << argv[i-1] << ", integer must be between " << MIN_ITERATIVE_REFINEMENT_REPS << " and " << MAX_ITERATIVE_REFINEMENT_REPS << "." << endl; exit (1); } else numIterativeRefinementReps = tempInt; } } else { cerr << "ERROR: Integer expected for option " << argv[i] << endl; exit (1); } } // number of EM pre-training rounds else if (!strcmp (argv[i], "-pre") || !strcmp (argv[i], "--pre-training")){ if (i < argc - 1){ if (!GetInteger (argv[++i], &tempInt)){ cerr << "ERROR: Invalid integer following option " << argv[i-1] << ": " << argv[i] << endl; exit (1); } else { if (tempInt < MIN_PRETRAINING_REPS || tempInt > MAX_PRETRAINING_REPS){ cerr << "ERROR: For option " << argv[i-1] << ", integer must be between " << MIN_PRETRAINING_REPS << " and " << MAX_PRETRAINING_REPS << "." << endl; exit (1); } else numPreTrainingReps = tempInt; } } else { cerr << "ERROR: Integer expected for option " << argv[i] << endl; exit (1); } } // gap open penalty else if (!strcmp (argv[i], "-go") || !strcmp (argv[i], "--gap-open")){ if (i < argc - 1){ if (!GetFloat (argv[++i], &tempFloat)){ cerr << "ERROR: Invalid floating-point value following option " << argv[i-1] << ": " << argv[i] << endl; exit (1); } else { if (tempFloat > 0){ cerr << "ERROR: For option " << argv[i-1] << ", floating-point value must not be positive." << endl; exit (1); } else gapOpenPenalty = tempFloat; } } else { cerr << "ERROR: Floating-point value expected for option " << argv[i] << endl; exit (1); } } // gap extension penalty else if (!strcmp (argv[i], "-ge") || !strcmp (argv[i], "--gap-extension")){ if (i < argc - 1){ if (!GetFloat (argv[++i], &tempFloat)){ cerr << "ERROR: Invalid floating-point value following option " << argv[i-1] << ": " << argv[i] << endl; exit (1); } else { if (tempFloat > 0){ cerr << "ERROR: For option " << argv[i-1] << ", floating-point value must not be positive." << endl; exit (1); } else gapContinuePenalty = tempFloat; } } else { cerr << "ERROR: Floating-point value expected for option " << argv[i] << endl; exit (1); } } // all-pairs pairwise alignments else if (!strcmp (argv[i], "-pairs")){ enableAllPairs = true; } // all-pairs pairwise Viterbi alignments else if (!strcmp (argv[i], "-viterbi")){ enableAllPairs = true; enableViterbi = true; } // annotation files else if (!strcmp (argv[i], "-annot")){ enableAnnotation = true; if (i < argc - 1) annotationFilename = argv[++i]; else { cerr << "ERROR: FILENAME expected for option " << argv[i] << endl; exit (1); } } // clustalw output format else if (!strcmp (argv[i], "-clustalw")){ enableClustalWOutput = true; } // cutoff else if (!strcmp (argv[i], "-co") || !strcmp (argv[i], "--cutoff")){ if (i < argc - 1){ if (!GetFloat (argv[++i], &tempFloat)){ cerr << "ERROR: Invalid floating-point value following option " << argv[i-1] << ": " << argv[i] << endl; exit (1); } else { if (tempFloat < 0 || tempFloat > 1){ cerr << "ERROR: For option " << argv[i-1] << ", floating-point value must be between 0 and 1." << endl; exit (1); } else cutoff = tempFloat; } } else { cerr << "ERROR: Floating-point value expected for option " << argv[i] << endl; exit (1); } } // verbose reporting else if (!strcmp (argv[i], "-v") || !strcmp (argv[i], "--verbose")){ enableVerbose = true; } // output for AMAP Display else if (!strcmp (argv[i], "-gui")) { outputForGUI = true; if (i < argc - 1){ if (GetFloat (argv[i + 1], &tempFloat)){ if (tempFloat < 0){ cerr << "ERROR: For option " << argv[i-1] << ", floating-point value must be non-negative." << endl; exit (1); } else { guiStartWeight = tempFloat; i++; if (i < argc - 1){ if (GetInteger (argv[i + 1], &tempInt)){ if (tempInt < 1){ cerr << "ERROR: For option " << argv[i-1] << ", integer must be positive." << endl; exit (1); } else { guiStepSize = tempInt; i++; } } } } } } } // alignment order else if (!strcmp (argv[i], "-a") || !strcmp (argv[i], "--alignment-order")){ enableAlignOrder = true; } // progressive else if (!strcmp (argv[i], "-prog") || !strcmp (argv[i], "--progressive")){ enableDagAlignment = false; } // edge reordering else if (!strcmp (argv[i], "-noreorder") || !strcmp (argv[i], "--no-edge-reordering")){ enableEdgeReordering = false; } // edge ranking method else if (!strcmp (argv[i], "-maxstep") || !strcmp (argv[i], "--use-max-stepsize")){ useTgf = false; } // print posteriors else if (!strcmp (argv[i], "-print") || !strcmp (argv[i], "--print-posteriors")){ onlyPrintPosteriors = true; } // gap factor else if (!strcmp (argv[i], "-g") || !strcmp (argv[i], "--gap-factor")){ if (i < argc - 1){ if (!GetFloat (argv[++i], &tempFloat)){ cerr << "ERROR: Invalid floating-point value following option " << argv[i-1] << ": " << argv[i] << endl; exit (1); } else { if (tempFloat < 0){ cerr << "ERROR: For option " << argv[i-1] << ", floating-point value must not be negative." << endl; exit (1); } else gapFactor = tempFloat; } } else { cerr << "ERROR: Floating-point value expected for option " << argv[i] << endl; exit (1); } } // edge weight threshold else if (!strcmp (argv[i], "-w") || !strcmp (argv[i], "--edge-weight-threshold")){ if (i < argc - 1){ if (!GetFloat (argv[++i], &tempFloat)){ cerr << "ERROR: Invalid floating-point value following option " << argv[i-1] << ": " << argv[i] << endl; exit (1); } else { if (tempFloat < 0){ cerr << "ERROR: For option " << argv[i-1] << ", floating-point value must not be negative." << endl; exit (1); } else edgeWeightThreshold = tempFloat; } } else { cerr << "ERROR: Floating-point value expected for option " << argv[i] << endl; exit (1); } } // bad arguments else { cerr << "ERROR: Unrecognized option: " << argv[i] << endl; exit (1); } } else { sequenceNames.push_back (string (argv[i])); } } if (enableTrainEmissions && !enableTraining){ cerr << "ERROR: Training emissions (-e) requires training (-t)" << endl; exit (1); } return sequenceNames; } ///////////////////////////////////////////////////////////////// // ReadParameters() // // Read initial distribution, transition, and emission // parameters from a file. ///////////////////////////////////////////////////////////////// void ReadParameters (){ ifstream data; emitPairs = VVF (256, VF (256, 1e-10)); emitSingle = VF (256, 1e-5); // read initial state distribution and transition parameters if (NumInsertStates == 1){ for (int i = 0; i < NumMatrixTypes; i++) initDistrib[i] = initDistrib1Default[i]; for (int i = 0; i < 2*NumInsertStates; i++) gapOpen[i] = gapOpen1Default[i]; for (int i = 0; i < 2*NumInsertStates; i++) gapExtend[i] = gapExtend1Default[i]; } else if (NumInsertStates == 2){ for (int i = 0; i < NumMatrixTypes; i++) initDistrib[i] = initDistrib2Default[i]; for (int i = 0; i < 2*NumInsertStates; i++) gapOpen[i] = gapOpen2Default[i]; for (int i = 0; i < 2*NumInsertStates; i++) gapExtend[i] = gapExtend2Default[i]; } else { cerr << "ERROR: No default initial distribution/parameter settings exist" << endl << " for " << NumInsertStates << " pairs of insert states. Use --paramfile." << endl; exit (1); } alphabet = alphabetDefault; for (int i = 0; i < (int) alphabet.length(); i++){ emitSingle[(unsigned char) tolower(alphabet[i])] = emitSingleDefault[i]; emitSingle[(unsigned char) toupper(alphabet[i])] = emitSingleDefault[i]; for (int j = 0; j <= i; j++){ emitPairs[(unsigned char) tolower(alphabet[i])][(unsigned char) tolower(alphabet[j])] = emitPairsDefault[i][j]; emitPairs[(unsigned char) tolower(alphabet[i])][(unsigned char) toupper(alphabet[j])] = emitPairsDefault[i][j]; emitPairs[(unsigned char) toupper(alphabet[i])][(unsigned char) tolower(alphabet[j])] = emitPairsDefault[i][j]; emitPairs[(unsigned char) toupper(alphabet[i])][(unsigned char) toupper(alphabet[j])] = emitPairsDefault[i][j]; emitPairs[(unsigned char) tolower(alphabet[j])][(unsigned char) tolower(alphabet[i])] = emitPairsDefault[i][j]; emitPairs[(unsigned char) tolower(alphabet[j])][(unsigned char) toupper(alphabet[i])] = emitPairsDefault[i][j]; emitPairs[(unsigned char) toupper(alphabet[j])][(unsigned char) tolower(alphabet[i])] = emitPairsDefault[i][j]; emitPairs[(unsigned char) toupper(alphabet[j])][(unsigned char) toupper(alphabet[i])] = emitPairsDefault[i][j]; } } if (parametersInputFilename != string ("")){ data.open (parametersInputFilename.c_str()); if (data.fail()){ cerr << "ERROR: Unable to read parameter file: " << parametersInputFilename << endl; exit (1); } string line[3]; for (int i = 0; i < 3; i++){ if (!getline (data, line[i])){ cerr << "ERROR: Unable to read transition parameters from parameter file: " << parametersInputFilename << endl; exit (1); } } istringstream data2; data2.clear(); data2.str (line[0]); for (int i = 0; i < NumMatrixTypes; i++) data2 >> initDistrib[i]; data2.clear(); data2.str (line[1]); for (int i = 0; i < 2*NumInsertStates; i++) data2 >> gapOpen[i]; data2.clear(); data2.str (line[2]); for (int i = 0; i < 2*NumInsertStates; i++) data2 >> gapExtend[i]; if (!getline (data, line[0])){ return; cerr << "ERROR: Unable to read alphabet from scoring matrix file: " << parametersInputFilename << endl; exit (1); } // read alphabet as concatenation of all characters on alphabet line alphabet = ""; string token; data2.clear(); data2.str (line[0]); while (data2 >> token) alphabet += token; for (int i = 0; i < (int) alphabet.size(); i++){ for (int j = 0; j <= i; j++){ float val; data >> val; emitPairs[(unsigned char) tolower(alphabet[i])][(unsigned char) tolower(alphabet[j])] = val; emitPairs[(unsigned char) tolower(alphabet[i])][(unsigned char) toupper(alphabet[j])] = val; emitPairs[(unsigned char) toupper(alphabet[i])][(unsigned char) tolower(alphabet[j])] = val; emitPairs[(unsigned char) toupper(alphabet[i])][(unsigned char) toupper(alphabet[j])] = val; emitPairs[(unsigned char) tolower(alphabet[j])][(unsigned char) tolower(alphabet[i])] = val; emitPairs[(unsigned char) tolower(alphabet[j])][(unsigned char) toupper(alphabet[i])] = val; emitPairs[(unsigned char) toupper(alphabet[j])][(unsigned char) tolower(alphabet[i])] = val; emitPairs[(unsigned char) toupper(alphabet[j])][(unsigned char) toupper(alphabet[i])] = val; } } for (int i = 0; i < (int) alphabet.size(); i++){ float val; data >> val; emitSingle[(unsigned char) tolower(alphabet[i])] = val; emitSingle[(unsigned char) toupper(alphabet[i])] = val; } data.close(); } } ///////////////////////////////////////////////////////////////// // ProcessTree() // // Process the tree recursively. Returns the aligned sequences // corresponding to a node or leaf of the tree. ///////////////////////////////////////////////////////////////// MultiSequence *ProcessTree (const TreeNode *tree, MultiSequence *sequences, const SafeVector > &sparseMatrices, const ProbabilisticModel &model){ MultiSequence *result; // check if this is a node of the alignment tree if (tree->GetSequenceLabel() == -1){ MultiSequence *alignLeft = ProcessTree (tree->GetLeftChild(), sequences, sparseMatrices, model); MultiSequence *alignRight = ProcessTree (tree->GetRightChild(), sequences, sparseMatrices, model); assert (alignLeft); assert (alignRight); result = AlignAlignments (alignLeft, alignRight, sparseMatrices, model); assert (result); delete alignLeft; delete alignRight; } // otherwise, this is a leaf of the alignment tree else { result = new MultiSequence(); assert (result); result->AddSequence (sequences->GetSequence(tree->GetSequenceLabel())->Clone()); } return result; } ///////////////////////////////////////////////////////////////// // ComputeFinalAlignment() // // Compute the final alignment by calling ProcessTree(), then // performing iterative refinement as needed. ///////////////////////////////////////////////////////////////// MultiSequence *ComputeFinalAlignment (const TreeNode *tree, MultiSequence *sequences, const SafeVector > &sparseMatrices, const ProbabilisticModel &model){ MultiSequence *alignment = ProcessTree (tree, sequences, sparseMatrices, model); if (enableAlignOrder){ alignment->SaveOrdering(); enableAlignOrder = false; } // tree-based refinement // TreeBasedBiPartitioning (sparseMatrices, model, alignment, tree); // iterative refinement for (int i = 0; i < numIterativeRefinementReps; i++) DoIterativeRefinement (sparseMatrices, model, alignment); cerr << endl; // return final alignment return alignment; } ///////////////////////////////////////////////////////////////// // AlignAlignments() // // Returns the alignment of two MultiSequence objects. ///////////////////////////////////////////////////////////////// MultiSequence *AlignAlignments (MultiSequence *align1, MultiSequence *align2, const SafeVector > &sparseMatrices, const ProbabilisticModel &model){ // print some info about the alignment if (enableVerbose){ for (int i = 0; i < align1->GetNumSequences(); i++) cerr << ((i==0) ? "[" : ",") << align1->GetSequence(i)->GetLabel(); cerr << "] vs. "; for (int i = 0; i < align2->GetNumSequences(); i++) cerr << ((i==0) ? "[" : ",") << align2->GetSequence(i)->GetLabel(); cerr << "]: "; } VF *posterior = model.BuildPosterior (align1, align2, sparseMatrices, cutoff, gapFactor); pair *, float> alignment; // choose the alignment routine depending on the "cosmetic" gap penalties used if (gapOpenPenalty == 0 && gapContinuePenalty == 0) alignment = model.ComputeAlignment (align1->GetSequence(0)->GetLength(), align2->GetSequence(0)->GetLength(), *posterior, gapFactor); else alignment = model.ComputeAlignmentWithGapPenalties (align1, align2, *posterior, align1->GetNumSequences(), align2->GetNumSequences(), gapOpenPenalty, gapContinuePenalty); // if (enableVerbose) // cerr << "finished computing alignment\n"; delete posterior; if (enableVerbose){ // compute total length of sequences int totLength = 0; for (int i = 0; i < align1->GetNumSequences(); i++) for (int j = 0; j < align2->GetNumSequences(); j++) totLength += min (align1->GetSequence(i)->GetLength(), align2->GetSequence(j)->GetLength()); // give an "accuracy" measure for the alignment cerr << alignment.second / totLength << endl; } // now build final alignment MultiSequence *result = new MultiSequence(); for (int i = 0; i < align1->GetNumSequences(); i++) result->AddSequence (align1->GetSequence(i)->AddGaps(alignment.first, 'X')); for (int i = 0; i < align2->GetNumSequences(); i++) result->AddSequence (align2->GetSequence(i)->AddGaps(alignment.first, 'Y')); if (!enableAlignOrder) result->SortByLabel(); // free temporary alignment delete alignment.first; return result; } ///////////////////////////////////////////////////////////////// // DoRelaxation() // // Performs one round of the consistency transformation. The // formula used is: // 1 // P'(x[i]-y[j]) = --- sum sum P(x[i]-z[k]) P(z[k]-y[j]) // |S| z in S k // // where S = {x, y, all other sequences...} // ///////////////////////////////////////////////////////////////// SafeVector > DoRelaxation (MultiSequence *sequences, SafeVector > &sparseMatrices){ const int numSeqs = sequences->GetNumSequences(); SafeVector > newSparseMatrices (numSeqs, SafeVector(numSeqs, NULL)); // for every pair of sequences for (int i = 0; i < numSeqs; i++){ for (int j = i+1; j < numSeqs; j++){ Sequence *seq1 = sequences->GetSequence (i); Sequence *seq2 = sequences->GetSequence (j); if (enableVerbose) cerr << "Relaxing (" << i+1 << ") " << seq1->GetHeader() << " vs. " << "(" << j+1 << ") " << seq2->GetHeader() << ": "; // get the original posterior matrix VF *posteriorPtr = sparseMatrices[i][j]->GetPosterior(); assert (posteriorPtr); VF &posterior = *posteriorPtr; const int seq1Length = seq1->GetLength(); const int seq2Length = seq2->GetLength(); VF *oldSumsPtr = new VF(seq1Length + seq2Length + 2,0); VF &oldSums = *oldSumsPtr; VF *newSumsPtr = new VF(seq1Length + seq2Length + 2,0); VF &newSums = *newSumsPtr; for (int k = 0, kl = 0; k <= seq1Length; k++) { for (int l = 0; l <= seq2Length; l++) { oldSums[k] += posterior[kl]; oldSums[seq1Length + 1 + l] += posterior[kl++]; } } // contribution from the summation where z = x and z = y for (int k = 0; k < (seq1Length+1) * (seq2Length+1); k++) posterior[k] += posterior[k]; if (enableVerbose) cerr << sparseMatrices[i][j]->GetNumCells() << " --> "; // contribution from all other sequences for (int k = 0; k < numSeqs; k++) if (k != i && k != j){ Relax (sparseMatrices[i][k], sparseMatrices[k][j], posterior); } // now renormalization for (int k = 0; k < (seq1Length+1) * (seq2Length+1); k++) posterior[k] /= numSeqs; for (int k = 0, kl = 0; k <= seq1Length; k++) { for (int l = 0; l <= seq2Length; l++) { newSums[k] += posterior[kl]; newSums[seq1Length + 1 + l] += posterior[kl++]; } } int gapPostBase = (seq1Length+1) * (seq2Length+1); for (int k = 0; k < seq1Length + seq2Length + 2; k++) { if (oldSums[k] < POSTERIOR_CUTOFF) { if (newSums[k] > 1) cerr << "negative new gap posterior!\n"; else { if (enableVerbose) cerr << setprecision(5) << posterior[gapPostBase + k] << "->" << setprecision(5) << 1 - newSums[k] << ", "; posterior[gapPostBase + k] = 1 - newSums[k]; } } else { posterior[gapPostBase + k] *= newSums[k] / oldSums[k]; if (enableVerbose && newSums[k] > oldSums[k]) cerr << setprecision(5) << newSums[k] / oldSums[k] << ", "; } } if (enableVerbose) cerr << endl; // save the new posterior matrix newSparseMatrices[i][j] = new SparseMatrix (seq1->GetLength(), seq2->GetLength(), posterior); newSparseMatrices[j][i] = newSparseMatrices[i][j]->ComputeTranspose(); if (enableVerbose) cerr << newSparseMatrices[i][j]->GetNumCells() << " -- "; delete posteriorPtr; delete oldSumsPtr; delete newSumsPtr; if (enableVerbose) cerr << "done." << endl; } } return newSparseMatrices; } ///////////////////////////////////////////////////////////////// // Relax() // // Computes the consistency transformation for a single sequence // z, and adds the transformed matrix to "posterior". ///////////////////////////////////////////////////////////////// void Relax (SparseMatrix *matXZ, SparseMatrix *matZY, VF &posterior){ assert (matXZ); assert (matZY); int lengthX = matXZ->GetSeq1Length(); int lengthY = matZY->GetSeq2Length(); assert (matXZ->GetSeq2Length() == matZY->GetSeq1Length()); // for every x[i] for (int i = 1; i <= lengthX; i++){ SafeVector::iterator XZptr = matXZ->GetRowPtr(i); SafeVector::iterator XZend = XZptr + matXZ->GetRowSize(i); VF::iterator base = posterior.begin() + i * (lengthY + 1); // iterate through all x[i]-z[k] while (XZptr != XZend){ SafeVector::iterator ZYptr = matZY->GetRowPtr(XZptr->first); SafeVector::iterator ZYend = ZYptr + matZY->GetRowSize(XZptr->first); const float XZval = XZptr->second; // iterate through all z[k]-y[j] while (ZYptr != ZYend){ base[ZYptr->first] += XZval * ZYptr->second; ZYptr++; } XZptr++; } } } ///////////////////////////////////////////////////////////////// // GetSubtree // // Returns set containing all leaf labels of the current subtree. ///////////////////////////////////////////////////////////////// set GetSubtree (const TreeNode *tree){ set s; if (tree->GetSequenceLabel() == -1){ s = GetSubtree (tree->GetLeftChild()); set t = GetSubtree (tree->GetRightChild()); for (set::iterator iter = t.begin(); iter != t.end(); ++iter) s.insert (*iter); } else { s.insert (tree->GetSequenceLabel()); } return s; } ///////////////////////////////////////////////////////////////// // TreeBasedBiPartitioning // // Uses the iterative refinement scheme from MUSCLE. ///////////////////////////////////////////////////////////////// void TreeBasedBiPartitioning (const SafeVector > &sparseMatrices, const ProbabilisticModel &model, MultiSequence* &alignment, const TreeNode *tree){ // check if this is a node of the alignment tree if (tree->GetSequenceLabel() == -1){ TreeBasedBiPartitioning (sparseMatrices, model, alignment, tree->GetLeftChild()); TreeBasedBiPartitioning (sparseMatrices, model, alignment, tree->GetRightChild()); set leftSubtree = GetSubtree (tree->GetLeftChild()); set rightSubtree = GetSubtree (tree->GetRightChild()); set leftSubtreeComplement, rightSubtreeComplement; // calculate complement of each subtree for (int i = 0; i < alignment->GetNumSequences(); i++){ if (leftSubtree.find(i) == leftSubtree.end()) leftSubtreeComplement.insert (i); if (rightSubtree.find(i) == rightSubtree.end()) rightSubtreeComplement.insert (i); } // perform realignments for edge to left child if (!leftSubtree.empty() && !leftSubtreeComplement.empty()){ MultiSequence *groupOneSeqs = alignment->Project (leftSubtree); assert (groupOneSeqs); MultiSequence *groupTwoSeqs = alignment->Project (leftSubtreeComplement); assert (groupTwoSeqs); delete alignment; alignment = AlignAlignments (groupOneSeqs, groupTwoSeqs, sparseMatrices, model); } // perform realignments for edge to right child if (!rightSubtree.empty() && !rightSubtreeComplement.empty()){ MultiSequence *groupOneSeqs = alignment->Project (rightSubtree); assert (groupOneSeqs); MultiSequence *groupTwoSeqs = alignment->Project (rightSubtreeComplement); assert (groupTwoSeqs); delete alignment; alignment = AlignAlignments (groupOneSeqs, groupTwoSeqs, sparseMatrices, model); } } } ///////////////////////////////////////////////////////////////// // DoIterativeRefinement() // // Performs a single round of randomized partionining iterative // refinement. ///////////////////////////////////////////////////////////////// void DoIterativeRefinement (const SafeVector > &sparseMatrices, const ProbabilisticModel &model, MultiSequence* &alignment){ set groupOne, groupTwo; // create two separate groups for (int i = 0; i < alignment->GetNumSequences(); i++){ if (rand() % 2) groupOne.insert (i); else groupTwo.insert (i); } if (groupOne.empty() || groupTwo.empty()) return; // project into the two groups MultiSequence *groupOneSeqs = alignment->Project (groupOne); assert (groupOneSeqs); MultiSequence *groupTwoSeqs = alignment->Project (groupTwo); assert (groupTwoSeqs); delete alignment; // realign alignment = AlignAlignments (groupOneSeqs, groupTwoSeqs, sparseMatrices, model); } ///////////////////////////////////////////////////////////////// // WriteAnnotation() // // Computes annotation for multiple alignment and write values // to a file. ///////////////////////////////////////////////////////////////// void WriteAnnotation (MultiSequence *alignment, const SafeVector > &sparseMatrices){ ofstream outfile (annotationFilename.c_str()); if (outfile.fail()){ cerr << "ERROR: Unable to write annotation file." << endl; exit (1); } const int alignLength = alignment->GetSequence(0)->GetLength(); const int numSeqs = alignment->GetNumSequences(); SafeVector position (numSeqs, 0); SafeVector::iterator> seqs (numSeqs); for (int i = 0; i < numSeqs; i++) seqs[i] = alignment->GetSequence(i)->GetDataPtr(); SafeVector > active; active.reserve (numSeqs); // for every column for (int i = 1; i <= alignLength; i++){ // find all aligned residues in this particular column active.clear(); for (int j = 0; j < numSeqs; j++){ if (seqs[j][i] != '-'){ active.push_back (make_pair(j, ++position[j])); } } outfile << setw(4) << ComputeScore (active, sparseMatrices) << endl; } outfile.close(); } ///////////////////////////////////////////////////////////////// // ComputeScore() // // Computes the annotation score for a particular column. ///////////////////////////////////////////////////////////////// int ComputeScore (const SafeVector > &active, const SafeVector > &sparseMatrices){ if (active.size() <= 1) return 0; // ALTERNATIVE #1: Compute the average alignment score. float val = 0; for (int i = 0; i < (int) active.size(); i++){ for (int j = i+1; j < (int) active.size(); j++){ val += sparseMatrices[active[i].first][active[j].first]->GetValue(active[i].second, active[j].second); } } return (int) (200 * val / ((int) active.size() * ((int) active.size() - 1))); } amap-align/align/ProbabilisticModel.h0000644000120200001440000012314410651502112017262 0ustar sarielusers///////////////////////////////////////////////////////////////// // ProbabilisticModel.h // // Routines for (1) posterior probability computations // (2) chained anchoring // (3) maximum weight trace alignment ///////////////////////////////////////////////////////////////// #ifndef PROBABILISTICMODEL_H #define PROBABILISTICMODEL_H #include #include #include #include "SafeVector.h" #include "ScoreType.h" #include "SparseMatrix.h" #include "MultiSequence.h" using namespace std; const int NumMatchStates = 1; // note that in this version the number // of match states is fixed at 1...will // change in future versions const int NumMatrixTypes = NumMatchStates + NumInsertStates * 2; ///////////////////////////////////////////////////////////////// // ProbabilisticModel // // Class for storing the parameters of a probabilistic model and // performing different computations based on those parameters. // In particular, this class handles the computation of // posterior probabilities that may be used in alignment. ///////////////////////////////////////////////////////////////// class ProbabilisticModel { float initialDistribution[NumMatrixTypes]; // holds the initial probabilities for each state float transProb[NumMatrixTypes][NumMatrixTypes]; // holds all state-to-state transition probabilities float matchProb[256][256]; // emission probabilities for match states float insProb[256][NumMatrixTypes]; // emission probabilities for insert states public: ///////////////////////////////////////////////////////////////// // ProbabilisticModel::ProbabilisticModel() // // Constructor. Builds a new probabilistic model using the // given parameters. ///////////////////////////////////////////////////////////////// ProbabilisticModel (const VF &initDistribMat, const VF &gapOpen, const VF &gapExtend, const VVF &emitPairs, const VF &emitSingle){ // build transition matrix VVF transMat (NumMatrixTypes, VF (NumMatrixTypes, 0.0f)); transMat[0][0] = 1; for (int i = 0; i < NumInsertStates; i++){ transMat[0][2*i+1] = gapOpen[2*i]; transMat[0][2*i+2] = gapOpen[2*i+1]; transMat[0][0] -= (gapOpen[2*i] + gapOpen[2*i+1]); assert (transMat[0][0] > 0); transMat[2*i+1][2*i+1] = gapExtend[2*i]; transMat[2*i+2][2*i+2] = gapExtend[2*i+1]; transMat[2*i+1][2*i+2] = 0; transMat[2*i+2][2*i+1] = 0; transMat[2*i+1][0] = 1 - gapExtend[2*i]; transMat[2*i+2][0] = 1 - gapExtend[2*i+1]; } // create initial and transition probability matrices for (int i = 0; i < NumMatrixTypes; i++){ initialDistribution[i] = LOG (initDistribMat[i]); for (int j = 0; j < NumMatrixTypes; j++) transProb[i][j] = LOG (transMat[i][j]); } // create insertion and match probability matrices for (int i = 0; i < 256; i++){ for (int j = 0; j < NumMatrixTypes; j++) insProb[i][j] = LOG (emitSingle[i]); for (int j = 0; j < 256; j++) matchProb[i][j] = LOG (emitPairs[i][j]); } } ///////////////////////////////////////////////////////////////// // ProbabilisticModel::ComputeForwardMatrix() // // Computes a set of forward probability matrices for aligning // seq1 and seq2. // // For efficiency reasons, a single-dimensional floating-point // array is used here, with the following indexing scheme: // // forward[i + NumMatrixTypes * (j * (seq2Length+1) + k)] // refers to the probability of aligning through j characters // of the first sequence, k characters of the second sequence, // and ending in state i. ///////////////////////////////////////////////////////////////// VF *ComputeForwardMatrix (Sequence *seq1, Sequence *seq2) const { assert (seq1); assert (seq2); const int seq1Length = seq1->GetLength(); const int seq2Length = seq2->GetLength(); // retrieve the points to the beginning of each sequence SafeVector::iterator iter1 = seq1->GetDataPtr(); SafeVector::iterator iter2 = seq2->GetDataPtr(); // create matrix VF *forwardPtr = new VF (NumMatrixTypes * (seq1Length+1) * (seq2Length+1), LOG_ZERO); assert (forwardPtr); VF &forward = *forwardPtr; // initialization condition forward[0 + NumMatrixTypes * (1 * (seq2Length+1) + 1)] = initialDistribution[0] + matchProb[(unsigned char) iter1[1]][(unsigned char) iter2[1]]; for (int k = 0; k < NumInsertStates; k++){ forward[2*k+1 + NumMatrixTypes * (1 * (seq2Length+1) + 0)] = initialDistribution[2*k+1] + insProb[(unsigned char) iter1[1]][k]; forward[2*k+2 + NumMatrixTypes * (0 * (seq2Length+1) + 1)] = initialDistribution[2*k+2] + insProb[(unsigned char) iter2[1]][k]; } // remember offset for each index combination int ij = 0; int i1j = -seq2Length - 1; int ij1 = -1; int i1j1 = -seq2Length - 2; ij *= NumMatrixTypes; i1j *= NumMatrixTypes; ij1 *= NumMatrixTypes; i1j1 *= NumMatrixTypes; // compute forward scores for (int i = 0; i <= seq1Length; i++){ unsigned char c1 = (i == 0) ? '~' : (unsigned char) iter1[i]; for (int j = 0; j <= seq2Length; j++){ unsigned char c2 = (j == 0) ? '~' : (unsigned char) iter2[j]; if (i > 1 || j > 1){ if (i > 0 && j > 0){ forward[0 + ij] = forward[0 + i1j1] + transProb[0][0]; for (int k = 1; k < NumMatrixTypes; k++) LOG_PLUS_EQUALS (forward[0 + ij], forward[k + i1j1] + transProb[k][0]); forward[0 + ij] += matchProb[c1][c2]; } if (i > 0){ for (int k = 0; k < NumInsertStates; k++) forward[2*k+1 + ij] = insProb[c1][k] + LOG_ADD (forward[0 + i1j] + transProb[0][2*k+1], forward[2*k+1 + i1j] + transProb[2*k+1][2*k+1]); } if (j > 0){ for (int k = 0; k < NumInsertStates; k++) forward[2*k+2 + ij] = insProb[c2][k] + LOG_ADD (forward[0 + ij1] + transProb[0][2*k+2], forward[2*k+2 + ij1] + transProb[2*k+2][2*k+2]); } } ij += NumMatrixTypes; i1j += NumMatrixTypes; ij1 += NumMatrixTypes; i1j1 += NumMatrixTypes; } } return forwardPtr; } ///////////////////////////////////////////////////////////////// // ProbabilisticModel::ComputeBackwardMatrix() // // Computes a set of backward probability matrices for aligning // seq1 and seq2. // // For efficiency reasons, a single-dimensional floating-point // array is used here, with the following indexing scheme: // // backward[i + NumMatrixTypes * (j * (seq2Length+1) + k)] // refers to the probability of starting in state i and // aligning from character j+1 to the end of the first // sequence and from character k+1 to the end of the second // sequence. ///////////////////////////////////////////////////////////////// VF *ComputeBackwardMatrix (Sequence *seq1, Sequence *seq2) const { assert (seq1); assert (seq2); const int seq1Length = seq1->GetLength(); const int seq2Length = seq2->GetLength(); SafeVector::iterator iter1 = seq1->GetDataPtr(); SafeVector::iterator iter2 = seq2->GetDataPtr(); // create matrix VF *backwardPtr = new VF (NumMatrixTypes * (seq1Length+1) * (seq2Length+1), LOG_ZERO); assert (backwardPtr); VF &backward = *backwardPtr; // initialization condition for (int k = 0; k < NumMatrixTypes; k++) backward[NumMatrixTypes * ((seq1Length+1) * (seq2Length+1) - 1) + k] = initialDistribution[k]; // remember offset for each index combination int ij = (seq1Length+1) * (seq2Length+1) - 1; int i1j = ij + seq2Length + 1; int ij1 = ij + 1; int i1j1 = ij + seq2Length + 2; ij *= NumMatrixTypes; i1j *= NumMatrixTypes; ij1 *= NumMatrixTypes; i1j1 *= NumMatrixTypes; // compute backward scores for (int i = seq1Length; i >= 0; i--){ unsigned char c1 = (i == seq1Length) ? '~' : (unsigned char) iter1[i+1]; for (int j = seq2Length; j >= 0; j--){ unsigned char c2 = (j == seq2Length) ? '~' : (unsigned char) iter2[j+1]; if (i < seq1Length && j < seq2Length){ const float ProbXY = backward[0 + i1j1] + matchProb[c1][c2]; for (int k = 0; k < NumMatrixTypes; k++) LOG_PLUS_EQUALS (backward[k + ij], ProbXY + transProb[k][0]); } if (i < seq1Length){ for (int k = 0; k < NumInsertStates; k++){ LOG_PLUS_EQUALS (backward[0 + ij], backward[2*k+1 + i1j] + insProb[c1][k] + transProb[0][2*k+1]); LOG_PLUS_EQUALS (backward[2*k+1 + ij], backward[2*k+1 + i1j] + insProb[c1][k] + transProb[2*k+1][2*k+1]); } } if (j < seq2Length){ for (int k = 0; k < NumInsertStates; k++){ LOG_PLUS_EQUALS (backward[0 + ij], backward[2*k+2 + ij1] + insProb[c2][k] + transProb[0][2*k+2]); LOG_PLUS_EQUALS (backward[2*k+2 + ij], backward[2*k+2 + ij1] + insProb[c2][k] + transProb[2*k+2][2*k+2]); } } ij -= NumMatrixTypes; i1j -= NumMatrixTypes; ij1 -= NumMatrixTypes; i1j1 -= NumMatrixTypes; } } return backwardPtr; } ///////////////////////////////////////////////////////////////// // ProbabilisticModel::ComputeTotalProbability() // // Computes the total probability of an alignment given // the forward and backward matrices. ///////////////////////////////////////////////////////////////// float ComputeTotalProbability (int seq1Length, int seq2Length, const VF &forward, const VF &backward) const { // compute total probability float totalForwardProb = LOG_ZERO; float totalBackwardProb = LOG_ZERO; for (int k = 0; k < NumMatrixTypes; k++){ LOG_PLUS_EQUALS (totalForwardProb, forward[k + NumMatrixTypes * ((seq1Length+1) * (seq2Length+1) - 1)] + backward[k + NumMatrixTypes * ((seq1Length+1) * (seq2Length+1) - 1)]); } totalBackwardProb = forward[0 + NumMatrixTypes * (1 * (seq2Length+1) + 1)] + backward[0 + NumMatrixTypes * (1 * (seq2Length+1) + 1)]; for (int k = 0; k < NumInsertStates; k++){ LOG_PLUS_EQUALS (totalBackwardProb, forward[2*k+1 + NumMatrixTypes * (1 * (seq2Length+1) + 0)] + backward[2*k+1 + NumMatrixTypes * (1 * (seq2Length+1) + 0)]); LOG_PLUS_EQUALS (totalBackwardProb, forward[2*k+2 + NumMatrixTypes * (0 * (seq2Length+1) + 1)] + backward[2*k+2 + NumMatrixTypes * (0 * (seq2Length+1) + 1)]); } // cerr << totalForwardProb << " " << totalBackwardProb << endl; return (totalForwardProb + totalBackwardProb) / 2; } ///////////////////////////////////////////////////////////////// // ProbabilisticModel::ComputePosteriorMatrix() // // Computes the posterior probability matrix based on // the forward and backward matrices. ///////////////////////////////////////////////////////////////// VF *ComputePosteriorMatrix (Sequence *seq1, Sequence *seq2, const VF &forward, const VF &backward) const { assert (seq1); assert (seq2); const int seq1Length = seq1->GetLength(); const int seq2Length = seq2->GetLength(); float totalProb = ComputeTotalProbability (seq1Length, seq2Length, forward, backward); // compute posterior matrices int seq1GapPostBase = (seq1Length + 1) * (seq2Length + 1); int seq2GapPostBase = seq1GapPostBase + seq1Length + 1; VF *posteriorPtr = new VF((seq1Length+2) * (seq2Length+2) - 1); assert (posteriorPtr); VF &posterior = *posteriorPtr; int ij = 0; VF::iterator ptr = posterior.begin(); for (int i = 0; i < seq1Length + seq2Length + 2; i++) posterior[seq1GapPostBase + i] = 1; for (int i = 0; i <= seq1Length; i++){ for (int j = 0; j <= seq2Length; j++){ *ptr = EXP (min (LOG_ONE, forward[ij] + backward[ij] - totalProb)); ij += NumMatrixTypes; posterior[seq1GapPostBase + i] -= *ptr; posterior[seq2GapPostBase + j] -= *ptr; ptr++; } } for (int i = 0; i < seq1Length + seq2Length + 2; i++) if (posterior[seq1GapPostBase + i] < 0) posterior[seq1GapPostBase + i] = 0.0001; posterior[0] = 0; return posteriorPtr; } /* ///////////////////////////////////////////////////////////////// // ProbabilisticModel::ComputeExpectedCounts() // // Computes the expected counts for the various transitions. ///////////////////////////////////////////////////////////////// VVF *ComputeExpectedCounts () const { assert (seq1); assert (seq2); const int seq1Length = seq1->GetLength(); const int seq2Length = seq2->GetLength(); SafeVector::iterator iter1 = seq1->GetDataPtr(); SafeVector::iterator iter2 = seq2->GetDataPtr(); // compute total probability float totalProb = ComputeTotalProbability (seq1Length, seq2Length, forward, backward); // initialize expected counts VVF *countsPtr = new VVF(NumMatrixTypes + 1, VF(NumMatrixTypes, LOG_ZERO)); assert (countsPtr); VVF &counts = *countsPtr; // remember offset for each index combination int ij = 0; int i1j = -seq2Length - 1; int ij1 = -1; int i1j1 = -seq2Length - 2; ij *= NumMatrixTypes; i1j *= NumMatrixTypes; ij1 *= NumMatrixTypes; i1j1 *= NumMatrixTypes; // compute expected counts for (int i = 0; i <= seq1Length; i++){ unsigned char c1 = (i == 0) ? '~' : (unsigned char) iter1[i]; for (int j = 0; j <= seq2Length; j++){ unsigned char c2 = (j == 0) ? '~' : (unsigned char) iter2[j]; if (i > 0 && j > 0){ for (int k = 0; k < NumMatrixTypes; k++) LOG_PLUS_EQUALS (counts[k][0], forward[k + i1j1] + transProb[k][0] + matchProb[c1][c2] + backward[0 + ij]); } if (i > 0){ for (int k = 0; k < NumInsertStates; k++){ LOG_PLUS_EQUALS (counts[0][2*k+1], forward[0 + i1j] + transProb[0][2*k+1] + insProb[c1][k] + backward[2*k+1 + ij]); LOG_PLUS_EQUALS (counts[2*k+1][2*k+1], forward[2*k+1 + i1j] + transProb[2*k+1][2*k+1] + insProb[c1][k] + backward[2*k+1 + ij]); } } if (j > 0){ for (int k = 0; k < NumInsertStates; k++){ LOG_PLUS_EQUALS (counts[0][2*k+2], forward[0 + ij1] + transProb[0][2*k+2] + insProb[c2][k] + backward[2*k+2 + ij]); LOG_PLUS_EQUALS (counts[2*k+2][2*k+2], forward[2*k+2 + ij1] + transProb[2*k+2][2*k+2] + insProb[c2][k] + backward[2*k+2 + ij]); } } ij += NumMatrixTypes; i1j += NumMatrixTypes; ij1 += NumMatrixTypes; i1j1 += NumMatrixTypes; } } // scale all expected counts appropriately for (int i = 0; i < NumMatrixTypes; i++) for (int j = 0; j < NumMatrixTypes; j++) counts[i][j] -= totalProb; } */ ///////////////////////////////////////////////////////////////// // ProbabilisticModel::ComputeNewParameters() // // Computes a new parameter set based on the expected counts // given. ///////////////////////////////////////////////////////////////// void ComputeNewParameters (Sequence *seq1, Sequence *seq2, const VF &forward, const VF &backward, VF &initDistribMat, VF &gapOpen, VF &gapExtend, VVF &emitPairs, VF &emitSingle, bool enableTrainEmissions) const { assert (seq1); assert (seq2); const int seq1Length = seq1->GetLength(); const int seq2Length = seq2->GetLength(); SafeVector::iterator iter1 = seq1->GetDataPtr(); SafeVector::iterator iter2 = seq2->GetDataPtr(); // compute total probability float totalProb = ComputeTotalProbability (seq1Length, seq2Length, forward, backward); // initialize expected counts VVF transCounts (NumMatrixTypes, VF (NumMatrixTypes, LOG_ZERO)); VF initCounts (NumMatrixTypes, LOG_ZERO); VVF pairCounts (256, VF (256, LOG_ZERO)); VF singleCounts (256, LOG_ZERO); // remember offset for each index combination int ij = 0; int i1j = -seq2Length - 1; int ij1 = -1; int i1j1 = -seq2Length - 2; ij *= NumMatrixTypes; i1j *= NumMatrixTypes; ij1 *= NumMatrixTypes; i1j1 *= NumMatrixTypes; // compute initial distribution posteriors initCounts[0] = LOG_ADD (forward[0 + NumMatrixTypes * (1 * (seq2Length+1) + 1)] + backward[0 + NumMatrixTypes * (1 * (seq2Length+1) + 1)], forward[0 + NumMatrixTypes * ((seq1Length+1) * (seq2Length+1) - 1)] + backward[0 + NumMatrixTypes * ((seq1Length+1) * (seq2Length+1) - 1)]); for (int k = 0; k < NumInsertStates; k++){ initCounts[2*k+1] = LOG_ADD (forward[2*k+1 + NumMatrixTypes * (1 * (seq2Length+1) + 0)] + backward[2*k+1 + NumMatrixTypes * (1 * (seq2Length+1) + 0)], forward[2*k+1 + NumMatrixTypes * ((seq1Length+1) * (seq2Length+1) - 1)] + backward[2*k+1 + NumMatrixTypes * ((seq1Length+1) * (seq2Length+1) - 1)]); initCounts[2*k+2] = LOG_ADD (forward[2*k+2 + NumMatrixTypes * (0 * (seq2Length+1) + 1)] + backward[2*k+2 + NumMatrixTypes * (0 * (seq2Length+1) + 1)], forward[2*k+2 + NumMatrixTypes * ((seq1Length+1) * (seq2Length+1) - 1)] + backward[2*k+2 + NumMatrixTypes * ((seq1Length+1) * (seq2Length+1) - 1)]); } // compute expected counts for (int i = 0; i <= seq1Length; i++){ unsigned char c1 = (i == 0) ? '~' : (unsigned char) toupper(iter1[i]); for (int j = 0; j <= seq2Length; j++){ unsigned char c2 = (j == 0) ? '~' : (unsigned char) toupper(iter2[j]); if (i > 0 && j > 0){ if (enableTrainEmissions && i == 1 && j == 1){ LOG_PLUS_EQUALS (pairCounts[c1][c2], initialDistribution[0] + matchProb[c1][c2] + backward[0 + ij]); LOG_PLUS_EQUALS (pairCounts[c2][c1], initialDistribution[0] + matchProb[c2][c1] + backward[0 + ij]); } for (int k = 0; k < NumMatrixTypes; k++){ LOG_PLUS_EQUALS (transCounts[k][0], forward[k + i1j1] + transProb[k][0] + matchProb[c1][c2] + backward[0 + ij]); if (enableTrainEmissions && i != 1 || j != 1){ LOG_PLUS_EQUALS (pairCounts[c1][c2], forward[k + i1j1] + transProb[k][0] + matchProb[c1][c2] + backward[0 + ij]); LOG_PLUS_EQUALS (pairCounts[c2][c1], forward[k + i1j1] + transProb[k][0] + matchProb[c2][c1] + backward[0 + ij]); } } } if (i > 0){ for (int k = 0; k < NumInsertStates; k++){ LOG_PLUS_EQUALS (transCounts[0][2*k+1], forward[0 + i1j] + transProb[0][2*k+1] + insProb[c1][k] + backward[2*k+1 + ij]); LOG_PLUS_EQUALS (transCounts[2*k+1][2*k+1], forward[2*k+1 + i1j] + transProb[2*k+1][2*k+1] + insProb[c1][k] + backward[2*k+1 + ij]); if (enableTrainEmissions){ if (i == 1 && j == 0){ LOG_PLUS_EQUALS (singleCounts[c1], initialDistribution[2*k+1] + insProb[c1][k] + backward[2*k+1 + ij]); } else { LOG_PLUS_EQUALS (singleCounts[c1], forward[0 + i1j] + transProb[0][2*k+1] + insProb[c1][k] + backward[2*k+1 + ij]); LOG_PLUS_EQUALS (singleCounts[c1], forward[2*k+1 + i1j] + transProb[2*k+1][2*k+1] + insProb[c1][k] + backward[2*k+1 + ij]); } } } } if (j > 0){ for (int k = 0; k < NumInsertStates; k++){ LOG_PLUS_EQUALS (transCounts[0][2*k+2], forward[0 + ij1] + transProb[0][2*k+2] + insProb[c2][k] + backward[2*k+2 + ij]); LOG_PLUS_EQUALS (transCounts[2*k+2][2*k+2], forward[2*k+2 + ij1] + transProb[2*k+2][2*k+2] + insProb[c2][k] + backward[2*k+2 + ij]); if (enableTrainEmissions){ if (i == 0 && j == 1){ LOG_PLUS_EQUALS (singleCounts[c2], initialDistribution[2*k+2] + insProb[c2][k] + backward[2*k+2 + ij]); } else { LOG_PLUS_EQUALS (singleCounts[c2], forward[0 + ij1] + transProb[0][2*k+2] + insProb[c2][k] + backward[2*k+2 + ij]); LOG_PLUS_EQUALS (singleCounts[c2], forward[2*k+2 + ij1] + transProb[2*k+2][2*k+2] + insProb[c2][k] + backward[2*k+2 + ij]); } } } } ij += NumMatrixTypes; i1j += NumMatrixTypes; ij1 += NumMatrixTypes; i1j1 += NumMatrixTypes; } } // scale all expected counts appropriately for (int i = 0; i < NumMatrixTypes; i++){ initCounts[i] -= totalProb; for (int j = 0; j < NumMatrixTypes; j++) transCounts[i][j] -= totalProb; } if (enableTrainEmissions){ for (int i = 0; i < 256; i++){ for (int j = 0; j < 256; j++) pairCounts[i][j] -= totalProb; singleCounts[i] -= totalProb; } } // compute new initial distribution float totalInitDistribCounts = 0; for (int i = 0; i < NumMatrixTypes; i++) totalInitDistribCounts += exp (initCounts[i]); // should be 2 initDistribMat[0] = min (1.0f, max (0.0f, (float) exp (initCounts[0]) / totalInitDistribCounts)); for (int k = 0; k < NumInsertStates; k++){ float val = (exp (initCounts[2*k+1]) + exp (initCounts[2*k+2])) / 2; initDistribMat[2*k+1] = initDistribMat[2*k+2] = min (1.0f, max (0.0f, val / totalInitDistribCounts)); } // compute total counts for match state float inMatchStateCounts = 0; for (int i = 0; i < NumMatrixTypes; i++) inMatchStateCounts += exp (transCounts[0][i]); for (int i = 0; i < NumInsertStates; i++){ // compute total counts for gap state float inGapStateCounts = exp (transCounts[2*i+1][0]) + exp (transCounts[2*i+1][2*i+1]) + exp (transCounts[2*i+2][0]) + exp (transCounts[2*i+2][2*i+2]); gapOpen[2*i] = gapOpen[2*i+1] = (exp (transCounts[0][2*i+1]) + exp (transCounts[0][2*i+2])) / (2 * inMatchStateCounts); gapExtend[2*i] = gapExtend[2*i+1] = (exp (transCounts[2*i+1][2*i+1]) + exp (transCounts[2*i+2][2*i+2])) / inGapStateCounts; } if (enableTrainEmissions){ float totalPairCounts = 0; float totalSingleCounts = 0; for (int i = 0; i < 256; i++){ for (int j = 0; j <= i; j++) totalPairCounts += exp (pairCounts[j][i]); totalSingleCounts += exp (singleCounts[i]); } for (int i = 0; i < 256; i++) if (!islower ((char) i)){ int li = (int)((unsigned char) tolower ((char) i)); for (int j = 0; j <= i; j++) if (!islower ((char) j)){ int lj = (int)((unsigned char) tolower ((char) j)); emitPairs[i][j] = emitPairs[i][lj] = emitPairs[li][j] = emitPairs[li][lj] = emitPairs[j][i] = emitPairs[j][li] = emitPairs[lj][i] = emitPairs[lj][li] = exp(pairCounts[j][i]) / totalPairCounts; } emitSingle[i] = emitSingle[li] = exp(singleCounts[i]) / totalSingleCounts; } } } ///////////////////////////////////////////////////////////////// // ProbabilisticModel::ComputeAlignment() // // Computes an alignment based on the given posterior matrix. // This is done by finding the maximum summing path (or // maximum weight trace) through the posterior matrix. The // final alignment is returned as a pair consisting of: // (1) a string (e.g., XXXBBXXXBBBBBBYYYYBBB) where X's and // denote insertions in one of the two sequences and // B's denote that both sequences are present (i.e. // matches). // (2) a float indicating the sum achieved ///////////////////////////////////////////////////////////////// /* pair *, float> ComputeAlignment (int seq1Length, int seq2Length, */ /* const VF &posterior) const { */ /* return ComputeAlignment(seq1Length, seq2Length, posterior, 0); */ /* } */ pair *, float> ComputeAlignment (int seq1Length, int seq2Length, const VF &posterior, float gapFactor = 0) const { float *twoRows = new float[(seq2Length+1)*2]; assert (twoRows); float *oldRow = twoRows; float *newRow = twoRows + seq2Length + 1; char *tracebackMatrix = new char[(seq1Length+1)*(seq2Length+1)]; assert (tracebackMatrix); char *tracebackPtr = tracebackMatrix; VF::const_iterator posteriorPtr = posterior.begin() + seq2Length + 1; // initialization int seq1GapPostBase = (seq1Length+1) * (seq2Length+1); int seq2GapPostBase = seq1GapPostBase + (seq1Length+1); for (int j = 0; j <= seq2Length; j++){ oldRow[j] = 0; *(tracebackPtr++) = 'L'; } // fill in matrix for (int i = 1; i <= seq1Length; i++){ // initialize left column newRow[0] = 0; posteriorPtr++; *(tracebackPtr++) = 'U'; // fill in rest of row for (int j = 1; j <= seq2Length; j++){ ChooseBestOfThree (*(posteriorPtr++) + oldRow[j-1], newRow[j-1] + posterior[seq2GapPostBase + j] * gapFactor / 2, oldRow[j] + posterior[seq1GapPostBase + i] * gapFactor / 2, 'D', 'L', 'U', &newRow[j], tracebackPtr++); } // swap rows float *temp = oldRow; oldRow = newRow; newRow = temp; } // store best score float total = oldRow[seq2Length]; delete [] twoRows; // compute traceback SafeVector *alignment = new SafeVector; assert (alignment); int y_count = 0; int r = seq1Length, c = seq2Length; while (r != 0 || c != 0){ char ch = tracebackMatrix[r*(seq2Length+1) + c]; switch (ch){ // case 'L': c--; alignment->push_back ('Y'); break; case 'L': c--; y_count++; break; case 'U': r--; alignment->push_back ('X'); break; case 'D': c--; r--; alignment->insert(alignment->end(), y_count, 'Y'); alignment->push_back ('B'); y_count = 0; break; default: assert (false); } } alignment->insert(alignment->end(), y_count, 'Y'); delete [] tracebackMatrix; reverse (alignment->begin(), alignment->end()); return make_pair(alignment, total); } ///////////////////////////////////////////////////////////////// // ProbabilisticModel::ComputeAlignmentWithGapPenalties() // // Similar to ComputeAlignment() except with gap penalties. ///////////////////////////////////////////////////////////////// pair *, float> ComputeAlignmentWithGapPenalties (MultiSequence *align1, MultiSequence *align2, const VF &posterior, int numSeqs1, int numSeqs2, float gapOpenPenalty, float gapContinuePenalty) const { int seq1Length = align1->GetSequence(0)->GetLength(); int seq2Length = align2->GetSequence(0)->GetLength(); SafeVector::iterator > dataPtrs1 (align1->GetNumSequences()); SafeVector::iterator > dataPtrs2 (align2->GetNumSequences()); // grab character data for (int i = 0; i < align1->GetNumSequences(); i++) dataPtrs1[i] = align1->GetSequence(i)->GetDataPtr(); for (int i = 0; i < align2->GetNumSequences(); i++) dataPtrs2[i] = align2->GetSequence(i)->GetDataPtr(); // the number of active sequences at any given column is defined to be the // number of non-gap characters in that column; the number of gap opens at // any given column is defined to be the number of gap characters in that // column where the previous character in the respective sequence was not // a gap SafeVector numActive1 (seq1Length+1), numGapOpens1 (seq1Length+1); SafeVector numActive2 (seq2Length+1), numGapOpens2 (seq2Length+1); // compute number of active sequences and gap opens for each group for (int i = 0; i < align1->GetNumSequences(); i++){ SafeVector::iterator dataPtr = align1->GetSequence(i)->GetDataPtr(); numActive1[0] = numGapOpens1[0] = 0; for (int j = 1; j <= seq1Length; j++){ if (dataPtr[j] != '-'){ numActive1[j]++; numGapOpens1[j] += (j != 1 && dataPtr[j-1] != '-'); } } } for (int i = 0; i < align2->GetNumSequences(); i++){ SafeVector::iterator dataPtr = align2->GetSequence(i)->GetDataPtr(); numActive2[0] = numGapOpens2[0] = 0; for (int j = 1; j <= seq2Length; j++){ if (dataPtr[j] != '-'){ numActive2[j]++; numGapOpens2[j] += (j != 1 && dataPtr[j-1] != '-'); } } } VVF openingPenalty1 (numSeqs1+1, VF (numSeqs2+1)); VF continuingPenalty1 (numSeqs1+1); VVF openingPenalty2 (numSeqs1+1, VF (numSeqs2+1)); VF continuingPenalty2 (numSeqs2+1); // precompute penalties for (int i = 0; i <= numSeqs1; i++) for (int j = 0; j <= numSeqs2; j++) openingPenalty1[i][j] = i * (gapOpenPenalty * j + gapContinuePenalty * (numSeqs2 - j)); for (int i = 0; i <= numSeqs1; i++) continuingPenalty1[i] = i * gapContinuePenalty * numSeqs2; for (int i = 0; i <= numSeqs2; i++) for (int j = 0; j <= numSeqs1; j++) openingPenalty2[i][j] = i * (gapOpenPenalty * j + gapContinuePenalty * (numSeqs1 - j)); for (int i = 0; i <= numSeqs2; i++) continuingPenalty2[i] = i * gapContinuePenalty * numSeqs1; float *twoRows = new float[6*(seq2Length+1)]; assert (twoRows); float *oldRowMatch = twoRows; float *newRowMatch = twoRows + (seq2Length+1); float *oldRowInsertX = twoRows + 2*(seq2Length+1); float *newRowInsertX = twoRows + 3*(seq2Length+1); float *oldRowInsertY = twoRows + 4*(seq2Length+1); float *newRowInsertY = twoRows + 5*(seq2Length+1); char *tracebackMatrix = new char[3*(seq1Length+1)*(seq2Length+1)]; assert (tracebackMatrix); char *tracebackPtr = tracebackMatrix; VF::const_iterator posteriorPtr = posterior.begin() + seq2Length + 1; // initialization for (int i = 0; i <= seq2Length; i++){ oldRowMatch[i] = oldRowInsertX[i] = (i == 0) ? 0 : LOG_ZERO; oldRowInsertY[i] = (i == 0) ? 0 : oldRowInsertY[i-1] + continuingPenalty2[numActive2[i]]; *(tracebackPtr) = *(tracebackPtr+1) = *(tracebackPtr+2) = 'Y'; tracebackPtr += 3; } // fill in matrix for (int i = 1; i <= seq1Length; i++){ // initialize left column newRowMatch[0] = newRowInsertY[0] = LOG_ZERO; newRowInsertX[0] = oldRowInsertX[0] + continuingPenalty1[numActive1[i]]; posteriorPtr++; *(tracebackPtr) = *(tracebackPtr+1) = *(tracebackPtr+2) = 'X'; tracebackPtr += 3; // fill in rest of row for (int j = 1; j <= seq2Length; j++){ // going to MATCH state ChooseBestOfThree (oldRowMatch[j-1], oldRowInsertX[j-1], oldRowInsertY[j-1], 'M', 'X', 'Y', &newRowMatch[j], tracebackPtr++); newRowMatch[j] += *(posteriorPtr++); // going to INSERT X state ChooseBestOfThree (oldRowMatch[j] + openingPenalty1[numActive1[i]][numGapOpens2[j]], oldRowInsertX[j] + continuingPenalty1[numActive1[i]], oldRowInsertY[j] + openingPenalty1[numActive1[i]][numGapOpens2[j]], 'M', 'X', 'Y', &newRowInsertX[j], tracebackPtr++); // going to INSERT Y state ChooseBestOfThree (newRowMatch[j-1] + openingPenalty2[numActive2[j]][numGapOpens1[i]], newRowInsertX[j-1] + openingPenalty2[numActive2[j]][numGapOpens1[i]], newRowInsertY[j-1] + continuingPenalty2[numActive2[j]], 'M', 'X', 'Y', &newRowInsertY[j], tracebackPtr++); } // swap rows float *temp; temp = oldRowMatch; oldRowMatch = newRowMatch; newRowMatch = temp; temp = oldRowInsertX; oldRowInsertX = newRowInsertX; newRowInsertX = temp; temp = oldRowInsertY; oldRowInsertY = newRowInsertY; newRowInsertY = temp; } // store best score float total; char matrix; ChooseBestOfThree (oldRowMatch[seq2Length], oldRowInsertX[seq2Length], oldRowInsertY[seq2Length], 'M', 'X', 'Y', &total, &matrix); delete [] twoRows; // compute traceback SafeVector *alignment = new SafeVector; assert (alignment); int r = seq1Length, c = seq2Length; while (r != 0 || c != 0){ int offset = (matrix == 'M') ? 0 : (matrix == 'X') ? 1 : 2; char ch = tracebackMatrix[(r*(seq2Length+1) + c) * 3 + offset]; switch (matrix){ case 'Y': c--; alignment->push_back ('Y'); break; case 'X': r--; alignment->push_back ('X'); break; case 'M': c--; r--; alignment->push_back ('B'); break; default: assert (false); } matrix = ch; } delete [] tracebackMatrix; reverse (alignment->begin(), alignment->end()); return make_pair(alignment, 1.0f); } ///////////////////////////////////////////////////////////////// // ProbabilisticModel::ComputeViterbiAlignment() // // Computes the highest probability pairwise alignment using the // probabilistic model. The final alignment is returned as a // pair consisting of: // (1) a string (e.g., XXXBBXXXBBBBBBYYYYBBB) where X's and // denote insertions in one of the two sequences and // B's denote that both sequences are present (i.e. // matches). // (2) a float containing the log probability of the best // alignment (not used) ///////////////////////////////////////////////////////////////// pair *, float> ComputeViterbiAlignment (Sequence *seq1, Sequence *seq2) const { assert (seq1); assert (seq2); const int seq1Length = seq1->GetLength(); const int seq2Length = seq2->GetLength(); // retrieve the points to the beginning of each sequence SafeVector::iterator iter1 = seq1->GetDataPtr(); SafeVector::iterator iter2 = seq2->GetDataPtr(); // create viterbi matrix VF *viterbiPtr = new VF (NumMatrixTypes * (seq1Length+1) * (seq2Length+1), LOG_ZERO); assert (viterbiPtr); VF &viterbi = *viterbiPtr; // create traceback matrix VI *tracebackPtr = new VI (NumMatrixTypes * (seq1Length+1) * (seq2Length+1), -1); assert (tracebackPtr); VI &traceback = *tracebackPtr; // initialization condition for (int k = 0; k < NumMatrixTypes; k++) viterbi[k] = initialDistribution[k]; // remember offset for each index combination int ij = 0; int i1j = -seq2Length - 1; int ij1 = -1; int i1j1 = -seq2Length - 2; ij *= NumMatrixTypes; i1j *= NumMatrixTypes; ij1 *= NumMatrixTypes; i1j1 *= NumMatrixTypes; // compute viterbi scores for (int i = 0; i <= seq1Length; i++){ unsigned char c1 = (i == 0) ? '~' : (unsigned char) iter1[i]; for (int j = 0; j <= seq2Length; j++){ unsigned char c2 = (j == 0) ? '~' : (unsigned char) iter2[j]; if (i > 0 && j > 0){ for (int k = 0; k < NumMatrixTypes; k++){ float newVal = viterbi[k + i1j1] + transProb[k][0] + matchProb[c1][c2]; if (viterbi[0 + ij] < newVal){ viterbi[0 + ij] = newVal; traceback[0 + ij] = k; } } } if (i > 0){ for (int k = 0; k < NumInsertStates; k++){ float valFromMatch = insProb[c1][k] + viterbi[0 + i1j] + transProb[0][2*k+1]; float valFromIns = insProb[c1][k] + viterbi[2*k+1 + i1j] + transProb[2*k+1][2*k+1]; if (valFromMatch >= valFromIns){ viterbi[2*k+1 + ij] = valFromMatch; traceback[2*k+1 + ij] = 0; } else { viterbi[2*k+1 + ij] = valFromIns; traceback[2*k+1 + ij] = 2*k+1; } } } if (j > 0){ for (int k = 0; k < NumInsertStates; k++){ float valFromMatch = insProb[c2][k] + viterbi[0 + ij1] + transProb[0][2*k+2]; float valFromIns = insProb[c2][k] + viterbi[2*k+2 + ij1] + transProb[2*k+2][2*k+2]; if (valFromMatch >= valFromIns){ viterbi[2*k+2 + ij] = valFromMatch; traceback[2*k+2 + ij] = 0; } else { viterbi[2*k+2 + ij] = valFromIns; traceback[2*k+2 + ij] = 2*k+2; } } } ij += NumMatrixTypes; i1j += NumMatrixTypes; ij1 += NumMatrixTypes; i1j1 += NumMatrixTypes; } } // figure out best terminating cell float bestProb = LOG_ZERO; int state = -1; for (int k = 0; k < NumMatrixTypes; k++){ float thisProb = viterbi[k + NumMatrixTypes * ((seq1Length+1)*(seq2Length+1) - 1)] + initialDistribution[k]; if (bestProb < thisProb){ bestProb = thisProb; state = k; } } assert (state != -1); delete viterbiPtr; // compute traceback SafeVector *alignment = new SafeVector; assert (alignment); int r = seq1Length, c = seq2Length; while (r != 0 || c != 0){ int newState = traceback[state + NumMatrixTypes * (r * (seq2Length+1) + c)]; if (state == 0){ c--; r--; alignment->push_back ('B'); } else if (state % 2 == 1){ r--; alignment->push_back ('X'); } else { c--; alignment->push_back ('Y'); } state = newState; } delete tracebackPtr; reverse (alignment->begin(), alignment->end()); return make_pair(alignment, bestProb); } ///////////////////////////////////////////////////////////////// // ProbabilisticModel::BuildPosterior() // // Builds a posterior probability matrix needed to align a pair // of alignments. Mathematically, the returned matrix M is // defined as follows: // M[i,j] = sum sum f(s,t,i,j) // s in align1 t in align2 // where // [ P(s[i'] <--> t[j']) // [ if s[i'] is a letter in the ith column of align1 and // [ t[j'] it a letter in the jth column of align2 // f(s,t,i,j) = [ // [ 0 otherwise // ///////////////////////////////////////////////////////////////// VF *BuildPosterior (MultiSequence *align1, MultiSequence *align2, const SafeVector > &sparseMatrices, float cutoff = 0.0f, float gapFactor = 0) const { const int seq1Length = align1->GetSequence(0)->GetLength(); const int seq2Length = align2->GetSequence(0)->GetLength(); VF *posteriorPtr = new VF((seq1Length+1) * (seq2Length+1) + seq1Length + seq2Length + 2, 0); assert (posteriorPtr); VF &posterior = *posteriorPtr; // VF::iterator postPtr = posterior.begin(); int gapPostBase = (seq1Length+1) * (seq2Length+1); // for each s in align1 for (int i = 0; i < align1->GetNumSequences(); i++){ Sequence *s = align1->GetSequence(i); int first = s->GetLabel(); // SafeVector *mapping1 = s->GetMapping(); SafeVector::iterator iter1 = s->GetDataPtr(); // for each t in align2 for (int j = 0; j < align2->GetNumSequences(); j++){ Sequence *t = align2->GetSequence(j); int second = t->GetLabel(); // SafeVector *mapping2 = t->GetMapping(); SafeVector::iterator iter2 = t->GetDataPtr(); // get the associated sparse matrix SparseMatrix *matrix = sparseMatrices[first][second]; if (cutoff == 0.0f){ int ii = 0; for (int align1Pos = 1; align1Pos <= seq1Length; align1Pos++){ if (iter1[align1Pos] != '-') { // a non gap character in s ii++; SafeVector::iterator row = matrix->GetRowPtr(ii); int rowSize = matrix->GetRowSize(ii); int base = align1Pos * (seq2Length+1); int jj = 0; int rowPos = 0; for (int align2Pos = 1; align2Pos <= seq2Length; align2Pos++){ // add in all relevant values if (iter2[align2Pos] != '-') { // a non gap character in t jj++; while (row[rowPos].first < jj && rowPos < rowSize) rowPos++; if (jj == row[rowPos].first) posterior[base + align2Pos] += row[rowPos++].second; } else { // a gap character in t posterior[base + align2Pos] += matrix->GetGapPosterior(0,ii) * gapFactor / 2; } } posterior[gapPostBase + align1Pos] += matrix->GetGapPosterior(0,ii); } else { // a gap character in s int base = align1Pos * (seq2Length+1); int jj = 0; for (int align2Pos = 1; align2Pos <= seq2Length; align2Pos++){ // add in all relevant values if (iter2[align2Pos] != '-') { // a non gap character in t jj++; posterior[base + align2Pos] += matrix->GetGapPosterior(1,jj) * gapFactor / 2; } else { // a gap character in t } } } } for (int align2Pos = 1, jj = 0; align2Pos <= seq2Length; align2Pos++){ if (iter2[align2Pos] != '-') { // a non gap character in t jj++; posterior[gapPostBase + seq1Length + 1 + align2Pos] += matrix->GetGapPosterior(1,jj); } } } else { cerr << "In >0 cutoff\n"; /* for (int ii = 1; ii <= matrix->GetSeq1Length(); ii++){ */ /* SafeVector::iterator row = matrix->GetRowPtr(ii); */ /* int base = (*mapping1)[ii] * (seq2Length+1); */ /* int rowSize = matrix->GetRowSize(ii); */ /* for (int jj = 0; jj < rowSize; jj++) */ /* // add in all relevant values */ /* posterior[base + (*mapping2)[row[jj].first]] += row[jj].second; */ /* // subtract cutoff */ /* for (int jj = 1; jj <= matrix->GetSeq2Length(); jj++) */ /* posterior[base + (*mapping2)[jj]] -= cutoff; */ /* } */ } // delete mapping2; } // delete mapping1; } return posteriorPtr; } }; #endif amap-align/align/params.text0000644000120200001440000000603210635655116015546 0ustar sarielusers0.4 0.3 0.3 0.01993141696 0.01993141696 0.7943345308 0.7943345308 ARNDCQEGHILKMFPSTWYV 0.0237307195 0.0024450200 0.0177511796 0.0021022800 0.0020778200 0.0128186401 0.0022354899 0.0016165701 0.0035353999 0.0191117804 0.0014551500 0.0004470100 0.0004247900 0.0003679800 0.0101346998 0.0021910199 0.0025353199 0.0015822300 0.0017678400 0.0003210200 0.0075660399 0.0033221799 0.0026886500 0.0022473801 0.0049680001 0.0003795600 0.0034512801 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Choose C++ compiler. ################################################################################ CXX = g++ ################################################################################ # 2) Set C++ flags. # a) DEBUG mode -- no optimizations, enable SafeVector checking, no inlining # b) PROFILE mode -- for gprof # c) RELEASE mode ################################################################################ OTHERFLAGS = -DNumInsertStates=1 -DVERSION='"AMAP.2.2"' # debug mode #CXXFLAGS = -g -W -Wall -pedantic -DENABLE_CHECKS -fno-inline $(OTHERFLAGS) #CXXFLAGS = -g -W -Wall -pedantic -fno-inline $(OTHERFLAGS) # profile mode #CXXFLAGS = -pg -W -Wall -pedantic $(OTHERFLAGS) # release mode #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops ################################################################################ # 3) Dependencies ################################################################################ TARGETS = amap .PHONY : all all : $(TARGETS) amap : MultiSequenceDag.h MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Amap.cc $(CXX) $(CXXFLAGS) -lm -o amap Amap.cc .PHONY : clean clean: rm -f $(TARGETS) amap-align/align/PROBCONS.README0000644000120200001440000000751010635655116015463 0ustar sarielusers PROBCONS ~~~~~~~~ Probabilistic consistency-based multiple sequence alignment ----------------------------------------------------------------- PROBCONS is a novel tool for generating multiple alignments of protein sequences. Using a combination of probabilistic modeling and consistency-based alignment techniques, PROBCONS has achieved the highest accuracy of all alignment methods to date. PROBCONS was developed by Chuong B. Do in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University. For more information on the algorithms, please see Do, C.B., Brudno, M., and Batzoglou, S. (2004) PROBCONS: Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences. 12th International Conference on Intelligent Systems for Molecular Biology. In press. and Do, C.B., Brudno, M., and Batzoglou, S. (2004) PROBCONS: Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences. The 19th National Conference on Artificial Intelligence (AAAI-04). In press. ----------------------------------------------------------------- PROBCONS has been made freely available as PUBLIC DOMAIN software and hence is not subject to copyright in the United States. This system and/or any portion of the source code may be used, modified, or redistributed without restrictions. PROBCONS is distributed WITHOUT WARRANTY, express or implied. The authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for loss due to reliance on the program. ----------------------------------------------------------------- Version History 1.0, 3/23/2004 (Chuong Do) -- initial release 1.01, 3/25/2004 (Chuong Do) -- fixed error in training procedure -- retrained default parameters for 1 and 2 pairs of insert states 1.02, 4/17/2004 (Chuong Do) -- replaced LOG_ADD and EXP routines -- added support for reading MSF format files -- added two extra utilities for scoring PROBCONS alignments (for benchmarking purposes) -- added the "compare" program for scoring alignments according to a reference alignment with respect to sum-of-pairs and column scores -- added the "fixref" program for adjusting PREFAB alignments to contain all letters of the input sequences; basically the main program for PROBCONS "hacked" to get the job done 1.03, 5/3/2004 (Chuong Do) -- added option to do all-pairs pairwise alignments instead of constructing a full multiple alignment -- added support for reading DIALIGN style files -- enabled support for using BAliBASE annotations for scoring BAliBASE alignments -- several minor bug fixes thanks to Bob Edgar -- added "project" program to project multiple alignment to pairwise alignments 1.04, 5/9/2004 (Chuong Do) -- switched over to default of one-insert state pair -- retrained default parameters -- added annotation scores -- small changes to model topology to make end gaps symmetrical -- added makegnuplot utility to plot annotation scores 1.05, 5/26/2004 (Chuong Do) -- added cutoff filtering for posterior scores -- made small corrections to recurrences for computing alignments -- added CLUSTALW output support 1.06, 7/13/2004 (Chuong Do) -- ProbCons is now PUBLIC DOMAIN software. 1.07, 8/30/2004 (Chuong Do) -- Fixed CLUSTALW output for sequence names (thanks to John Calley for pointing this out) 1.08, 8/31/2004 (Chuong Do) -- Added option for alignment order output (-a). 1.09, 9/1/2004 (Chuong Do) -- PROBCONS now allows input files with existing gaps -- these are automatically stripped before alignment. amap-align/align/MultiSequenceDag.h0000644000120200001440000010227710651502112016716 0ustar sarielusers/*****************************************************************/ // MultiSequenceDag.h // // Classes for representing a multiple sequence alignment as a DAG, // and aligning using sequence-annealing. /*****************************************************************/ #ifndef MULTISEQUENCEDAG_H #define MULTISEQUENCEDAG_H #include #include #include #include #include "MultiSequence.h" #include "SparseMatrix.h" using namespace std; typedef map MII; typedef pair PII; const float INVALID_EDGE = -1e10; /*****************************************************************/ // Column // // A class for storing alignment column information. /*****************************************************************/ class Column { int index; // the position of the column in the alignment bool visited; // indicates if the column has been visited by the dfs MII seqPositions; // map of (seq_id,pos) pairs in the column Column *mergedInto; // the Column this column has merged into char consensus; // the consensus character for this column public: /*****************************************************************/ // Column::Column() // // Constructor. Creates a new empty column. /*****************************************************************/ Column (int pos) : index (pos), visited (false), mergedInto (this), consensus (0) { } /*****************************************************************/ // Column::operator<() // // Compares two columns based on their current position. /*****************************************************************/ bool operator< (Column const &c2) { return index < c2.index; } /*****************************************************************/ // Column::operator==() // // Compares two columns based on their current position. /*****************************************************************/ bool operator== (Column const &c2) { return index == c2.index; } /*****************************************************************/ // Column::Marked() // // Checks if the column has been marked as visited. /*****************************************************************/ bool Marked () { return visited; } /*****************************************************************/ // Column::Mark() // // Marks the column as visited. /*****************************************************************/ void Mark () { visited = true; } /*****************************************************************/ // Column::Unmark() // // Unmarks the column as visited. /*****************************************************************/ void Unmark () { visited = false; } /*****************************************************************/ // Column::GetIndex() // // Returns the current position of the column in the alignment. /*****************************************************************/ int GetIndex () { return index; } /*****************************************************************/ // Column::SetIndex() // // Sets the current position of the column in the alignment. /*****************************************************************/ void SetIndex (int idx) { index = idx; } /*****************************************************************/ // Column::GetMergedInto() // // Gets a pointer to the column this column has been merged into. /*****************************************************************/ Column* GetMergedInto () { return mergedInto; } /*****************************************************************/ // Column::SetMergedInto() // // Sets a pointer to the column this column has been merged into. /*****************************************************************/ void SetMergedInto (Column *newcol) { mergedInto = newcol; } /*****************************************************************/ // Column::GetSeqPositions() // // Returns the sequence positions in this column. /*****************************************************************/ const MII & GetSeqPositions () const { return seqPositions; } /*****************************************************************/ // Column::AddSeqPositions() // // Adds a sequence positions to this column. /*****************************************************************/ void AddSeqPosition (const PII &seqPos) { seqPositions.insert(seqPos); } void UpdateConsensus(MultiSequence* sequences, int numSequences); /*****************************************************************/ // Column::GetConsensus() // // Returns the current character consensus /*****************************************************************/ char GetConsensus () { return consensus; } /*****************************************************************/ // Column::operator<<() // // Output operator of the column. /*****************************************************************/ friend ostream& operator<<(ostream& os,const Column& col) { os << "Column index: " << col.index << endl; os << "Visited: " << col.visited << endl; os << "Sequence positions: "; MII seqs = col.seqPositions; os << '['; for (MII::iterator iter = seqs.begin(); iter != seqs.end(); iter++) os << '(' << iter->first << ',' << iter->second << ')'; os << ']' << endl; return os; } }; /*****************************************************************/ // Edge // // A class for storing information of // a candidate edge (match of column-pairs), // and for calculating the edge weight. /*****************************************************************/ class Edge { public: Column* sourceColumn; Column* targetColumn; float weight; /*****************************************************************/ // Edge::Edge() // // Constructor. Creates a new edge with pointers // to two columns and the edge weight. /*****************************************************************/ Edge (Column* c1, Column* c2, float initWeight) : sourceColumn(c1), targetColumn(c2), weight(initWeight) {}; /*****************************************************************/ // Edge::calcTgfWeight() // // Updates weights based on tgf, // and returns the expected accuracy improvement of the edge. /*****************************************************************/ float calcTgfWeight (const SafeVector > &sparseMatrices, bool enableVerbose) { float sumPmatch = 0; float sumPgap = 0; while (sourceColumn->GetMergedInto() != sourceColumn) // Find current source column sourceColumn = sourceColumn->GetMergedInto(); while (targetColumn->GetMergedInto() != targetColumn) // Find current target column targetColumn = targetColumn->GetMergedInto(); const MII &c1pos = sourceColumn->GetSeqPositions(); const MII &c2pos = targetColumn->GetSeqPositions(); for (MII::const_iterator c1posIter = c1pos.begin(); c1posIter != c1pos.end(); c1posIter++) { int i = c1posIter->first; int ii = c1posIter->second; for (MII::const_iterator c2posIter = c2pos.begin(); c2posIter != c2pos.end(); c2posIter++) { int j = c2posIter->first; if (i == j) // Cannot match two columns with the same sequence return INVALID_EDGE; int jj = c2posIter->second; SparseMatrix *ijMatrix = sparseMatrices[i][j]; sumPmatch += ijMatrix->GetValue(ii,jj); sumPgap += ijMatrix->GetGapPosterior(0,ii); sumPgap += ijMatrix->GetGapPosterior(1,jj); } } if (enableVerbose) { cerr << "previous weight= " << weight; cerr << " sumPmatch= " << sumPmatch << " sumPgap= " << sumPgap << endl; } weight = 2 * sumPmatch / sumPgap; if (enableVerbose) { cerr << "new weight= " << weight << endl; } return 2 * sumPmatch - sumPgap; } /*****************************************************************/ // Edge::calcMaxStepWeight() // // Updates weights based on maxstep, // and returns the expected accuracy improvement of the edge. /*****************************************************************/ float calcMaxStepWeight (const SafeVector > &sparseMatrices, bool enableVerbose, float gapFactor) { float sumPmatch = 0; float sumPgap = 0; while (sourceColumn->GetMergedInto() != sourceColumn) // Find current source column sourceColumn = sourceColumn->GetMergedInto(); while (targetColumn->GetMergedInto() != targetColumn) // Find current target column targetColumn = targetColumn->GetMergedInto(); const MII &c1pos = sourceColumn->GetSeqPositions(); const MII &c2pos = targetColumn->GetSeqPositions(); for (MII::const_iterator c1posIter = c1pos.begin(); c1posIter != c1pos.end(); c1posIter++) { int i = c1posIter->first; int ii = c1posIter->second; for (MII::const_iterator c2posIter = c2pos.begin(); c2posIter != c2pos.end(); c2posIter++) { int j = c2posIter->first; if (i == j) // Cannot match two columns with the same sequence return INVALID_EDGE; int jj = c2posIter->second; SparseMatrix *ijMatrix = sparseMatrices[i][j]; sumPmatch += ijMatrix->GetValue(ii,jj); sumPgap += ijMatrix->GetGapPosterior(0,ii); sumPgap += ijMatrix->GetGapPosterior(1,jj); } } if (enableVerbose) { cerr << "previous weight= " << weight; cerr << " sumPmatch= " << sumPmatch << " sumPgap= " << sumPgap << endl; } weight = (2 * sumPmatch - gapFactor * sumPgap) / (c1pos.size() * c2pos.size()); if (enableVerbose) { cerr << "new weight= " << weight << endl; } return 2 * sumPmatch - sumPgap; } /*****************************************************************/ // Edge::operator<() // // Compares two edges based on their weights. /*****************************************************************/ bool operator< (Edge const e2) { return weight < e2.weight; } /*****************************************************************/ // Edge::ostream&() // // Output operator for edges. /*****************************************************************/ friend ostream& operator<<(ostream& os,const Edge& edge) { os << "sourceColumn: " << endl << *edge.sourceColumn; os << "targetColumn: " << endl << *edge.targetColumn; os << "weight: " << edge.weight << endl; return os; } }; /*****************************************************************/ // greater_index // // An empty class. Used only for defining a binary comparison // operator for column pointers. /*****************************************************************/ class greater_index : binary_function { public: bool operator()(Column* x, Column* y) { return *y < *x; } }; /*****************************************************************/ // smaller_index // // An empty class. Used only for defining a binary comparison // operator for column pointers. /*****************************************************************/ class smaller_index : binary_function { public: bool operator()(Column* x, Column* y) { return *x < *y; } }; /*****************************************************************/ // smaller_weight // // An empty class. Used only for defining a binary comparison // operator for edge pointers. /*****************************************************************/ class smaller_weight : binary_function { public: bool operator()(Edge* x, Edge* y) { return x->weight < y->weight; } }; typedef map < pair , Column* > MPIIC; /*****************************************************************/ // MultiSequenceDag // // A class for storing a multiple alignment as a DAG, // and for producing an alignment using sequence-annealing. /*****************************************************************/ class MultiSequenceDag { list columns; // the current columns of the alignment list oldColumns; // old columns that have been merged with current columns MultiSequence *sequences; // the sequences to be aligned int numSequences; // num of sequences int alignLength; // num of columns in the alignment MPIIC seqPos2colIndex; // mapping from sequence positions to columns float expectedAccuracy; // the expected accuracy of the alignment bool outputForGUI; // true if the output is for the AMAP GUI float guiStartWeight; // the edge weight at which output for GUI starts int guiStepSize; // the step size for the GUI output public: static const char pepGroup[26]; // peptide groups for GUI coloring (from TEXshade) static const bool pepSim[26][26]; // peptide similarities for GUI coloring (from TEXshade) private: /*****************************************************************/ // MultiSequenceDag::init() // // Initializes the DAG data structures. /*****************************************************************/ void init (bool aligned) { if (aligned) { // initialize DAG to input alignment for (int seqNum = 0; seqNum < numSequences; seqNum++) { if (alignLength < sequences->GetSequence(seqNum)->GetLength()) alignLength = sequences->GetSequence(seqNum)->GetLength(); } for (int col = 1; col <= alignLength; col++) { columns.push_back(new Column(col)); } for (int seqNum = 0; seqNum < numSequences; seqNum++) { Sequence *seq = sequences->GetSequence(seqNum); list::iterator colIter = columns.begin(); for (int col = 1, seqPos = 1; col <= seq->GetLength(); col++, colIter++) { if (seq->GetPosition(col) == '-') continue; PII newSeqPos(seqNum,seqPos++); (*colIter)->AddSeqPosition(newSeqPos); seqPos2colIndex[newSeqPos] = *colIter; } } } else { // initialize DAG to the null alignment alignLength = 0; expectedAccuracy = 0; for (int seqNum = 0; seqNum < numSequences; seqNum++) { Sequence *seq = sequences->GetSequence(seqNum); for (int col = 1, seqPos = 1; col <= seq->GetLength(); col++) { if (seq->GetPosition(col) == '-') continue; columns.push_back(new Column(++alignLength)); PII newSeqPos(seqNum,seqPos++); (*(--columns.end()))->AddSeqPosition(newSeqPos); seqPos2colIndex[newSeqPos] = *(--columns.end()); } } } } /*****************************************************************/ // MultiSequenceDag::DfsF() // // Implementation of the dfs-f() procedure of the Pearce and Kelly // online topological ordering algorithm. /*****************************************************************/ bool DfsF (Column* node, Column* upperBound,vector &rForward) { node->Mark(); rForward.push_back(node); push_heap(rForward.begin(),rForward.end(),greater_index()); for (MII::const_iterator posIter = node->GetSeqPositions().begin(); posIter != node->GetSeqPositions().end(); posIter++) { PII u = PII(posIter->first,posIter->second + 1); if (seqPos2colIndex.find(u) == seqPos2colIndex.end()){ // reached end of the current sequence continue; } Column* w = seqPos2colIndex[u]; if (*w == *upperBound){ return true; // found a cycle } if (!w->Marked() && *w < *upperBound && DfsF(w, upperBound, rForward)) return true; // found a cycle } return false; // no cycles found } /*****************************************************************/ // MultiSequenceDag::DfsB() // // Implementation of the dfs-b() procedure of the Pearce and Kelly // online topological ordering algorithm. /*****************************************************************/ void DfsB (Column* node, Column* lowerBound,vector &rBackward) { node->Mark(); rBackward.push_back(node); push_heap(rBackward.begin(),rBackward.end(),greater_index()); for (MII::const_iterator posIter = node->GetSeqPositions().begin(); posIter != node->GetSeqPositions().end(); posIter++) { PII u = PII(posIter->first,posIter->second - 1); if (seqPos2colIndex.find(u) == seqPos2colIndex.end()) // reached end of the current sequence continue; Column* w = seqPos2colIndex[u]; if (!w->Marked() && *lowerBound < *w) DfsB(w, lowerBound, rBackward); } } /*****************************************************************/ // MultiSequenceDag::Reorder() // // Implementation of the reorder() procedure of the Pearce and Kelly // online topological ordering algorithm. /*****************************************************************/ void Reorder(vector &rForward, vector &rBackward) { list indexes; for (vector::iterator rbIter = rBackward.begin(); rbIter != rBackward.end(); rbIter++) { indexes.push_back((*rbIter)->GetIndex()); } for (vector::iterator rfIter = rForward.begin(); rfIter != rForward.end(); rfIter++) { indexes.push_back((*rfIter)->GetIndex()); } indexes.sort(); list::iterator idxIter = indexes.begin(); for (unsigned i = 0; i < rBackward.size(); i++) { // if (outputForGUI) // cout << rBackward[0]->GetIndex() << ' '; rBackward[0]->SetIndex(*(idxIter++)); pop_heap(rBackward.begin(),rBackward.end() - i,greater_index()); } for (unsigned i = 0; i < rForward.size(); i++) { // if (outputForGUI) // cout << rForward[0]->GetIndex() << ' '; rForward[0]->SetIndex(*(idxIter++)); pop_heap(rForward.begin(),rForward.end() - i,greater_index()); } columns.sort(smaller_index()); // brute-foce. Can be done more efficiently using splice() in the previous steps. } /*****************************************************************/ // MultiSequenceDag::Unmark() // // Unmarks all columns in the list. /*****************************************************************/ void Unmark(vector &rColist) { for (vector::iterator rcIter = rColist.begin(); rcIter != rColist.end(); rcIter++) (*rcIter)->Unmark(); } /*****************************************************************/ // MultiSequenceDag::Merge() // // Merges the source and target columns of the edge // into the source column. /*****************************************************************/ void Merge (Edge *newEdge) { Column* col1 = newEdge->sourceColumn; Column* col2 = newEdge->targetColumn; MII map1 = col1->GetSeqPositions(); MII map2 = col2->GetSeqPositions(); for (MII::iterator iter = map2.begin(); iter != map2.end(); iter++) { col1->AddSeqPosition(PII(iter->first,iter->second)); seqPos2colIndex[PII(iter->first,iter->second)] = col1; } col2->SetMergedInto(col1); if (outputForGUI) col1->UpdateConsensus(sequences, numSequences); } public: /*****************************************************************/ // MultiSequenceDag::MultiSequenceDag() // // Constructor. // Initialized alignment DAG. // Uses input alignment if aligned is true. /*****************************************************************/ MultiSequenceDag (MultiSequence *msa, bool aligned, bool forGUI, float start, int step) : sequences (msa), numSequences(msa->GetNumSequences()), outputForGUI(forGUI), guiStartWeight(start), guiStepSize(step) { init(aligned); } /*****************************************************************/ // MultiSequenceDag::~MultiSequenceDag() // // Destructor. /*****************************************************************/ ~MultiSequenceDag() { for (list::iterator colIter = columns.begin(); colIter != columns.end(); colIter++) { (*colIter)->SetMergedInto(NULL); } for (list::iterator colIter = columns.begin(); colIter != columns.end(); colIter++) { Column* colPtr = *colIter; *colIter = NULL; delete colPtr; } columns.clear(); for (list::iterator colIter = oldColumns.begin(); colIter != oldColumns.end(); colIter++) { (*colIter)->SetMergedInto(NULL); } for (list::iterator colIter = oldColumns.begin(); colIter != oldColumns.end(); colIter++) { Column* colPtr = *colIter; *colIter = NULL; delete colPtr; } oldColumns.clear(); } /*****************************************************************/ // MultiSequenceDag::AddEdge() // // Adds a new edge to the alignment DAG. // Implementation of the add_edge() procedure of the Pearce and Kelly // online topological ordering algorithm. /*****************************************************************/ int AddEdge (Edge *newEdge) { Column* col1 = newEdge->sourceColumn; Column* col2 = newEdge->targetColumn; while (col1->GetMergedInto() != col1) // get current source column col1 = col1->GetMergedInto(); while (col2->GetMergedInto() != col2) // get current target column col2 = col2->GetMergedInto(); MII colSeqPos1 = col1->GetSeqPositions(); MII colSeqPos2 = col2->GetSeqPositions(); for (MII::iterator pos1Iter = colSeqPos1.begin(); pos1Iter != colSeqPos1.end(); pos1Iter++) { for (MII::iterator pos2Iter = colSeqPos2.begin(); pos2Iter != colSeqPos2.end(); pos2Iter++){ if (pos1Iter->first == pos2Iter->first) return 1; // both columns contain positions from the same sequence } } vector rForward, rBackward; Column *lBound, *uBound; if (*col1 < *col2) { lBound = col1; uBound = col2; } else { lBound = col2; uBound = col1; } if (DfsF(lBound,uBound,rForward)){ // new edge introduces a cycle in the DAG for (vector::iterator rfIter = rForward.begin(); rfIter != rForward.end(); rfIter++) (*rfIter)->Unmark(); return 2; } DfsB(uBound,lBound,rBackward); Unmark(rForward); Unmark(rBackward); if (rForward.size() == 1) { col1 = uBound; col2 = lBound; } else if (rBackward.size() == 1) { col1 = lBound; col2 = uBound; } else { // if (outputForGUI) // cout << "Reorder "; Reorder(rForward, rBackward); // if (outputForGUI) // cout << endl; } newEdge->sourceColumn = col1; newEdge->targetColumn = col2; // if (outputForGUI) // cout << "Merge " << col2->GetIndex() << ' ' << col1->GetIndex() << endl; Merge(newEdge); oldColumns.push_back(col2); // keep pointers to old columns for later memory deallocation columns.remove(col2); return 0; } /*****************************************************************/ // MultiSequenceDag::GetColumns() // // Returns the list of current columns in the the alignment DAG. /*****************************************************************/ list *GetColumns() { return &columns; } /*****************************************************************/ // MultiSequenceDag::operator<<() // // Output operator. /*****************************************************************/ friend ostream& operator<<(ostream& os,const MultiSequenceDag& msaDag) { for (list::const_iterator iter = msaDag.columns.begin(); iter != msaDag.columns.end(); iter++) os << **iter; os << "seqPos2colIndex: \n"; for (MPIIC::const_iterator iter = msaDag.seqPos2colIndex.begin(); iter != msaDag.seqPos2colIndex.end(); iter++) os << '(' << iter->first.first << ',' << iter->first.second << ',' << iter->second->GetIndex() << ')' << endl; return os; } /*****************************************************************/ // MultiSequenceDag::GetMultiSequence() // // Converts the alignment DAG to a standard MSA. /*****************************************************************/ MultiSequence *GetMultiSequence () { SafeVector::iterator> oldPtrs(numSequences); SafeVector *> newPtrs(numSequences); // grab old data for (int i = 0; i < numSequences; i++){ oldPtrs[i] = sequences->GetSequence(i)->GetDataPtr(); } int newLength = columns.size(); // build new alignments for (int i = 0; i < numSequences; i++){ newPtrs[i] = new SafeVector(); assert (newPtrs[i]); newPtrs[i]->push_back ('@'); } // add all needed columns for (list::iterator colIter = columns.begin(); colIter != columns.end(); colIter++) { MII colPos = (*colIter)->GetSeqPositions(); for (int j = 0; j < numSequences; j++) { if (colPos.find(j) != colPos.end()) newPtrs[j]->push_back(oldPtrs[j][colPos[j]]); else newPtrs[j]->push_back('-'); } } // wrap sequences in MultiSequence object MultiSequence *ret = new MultiSequence(); for (int i = 0; i < numSequences; i++){ ret->AddSequence (new Sequence(newPtrs[i], sequences->GetSequence(i)->GetName(), newLength, sequences->GetSequence(i)->GetSortLabel(), sequences->GetSequence(i)->GetLabel())); } return ret; } /*****************************************************************/ // MultiSequenceDag::GetSequences() // // Returns the current sequences including gaps and color codes /*****************************************************************/ string GetSequences() { string s = ""; string colors = ""; SafeVector::iterator> oldPtrs(numSequences); // grab old data for (int i = 0; i < numSequences; i++){ oldPtrs[i] = sequences->GetSequence(i)->GetDataPtr(); } // add all needed columns for (int j = 0; j < numSequences; j++) { s += '>' + sequences->GetSequence(j)->GetName() + ' '; colors += '@' + sequences->GetSequence(j)->GetName() + ' '; for (list::iterator colIter = columns.begin(); colIter != columns.end(); colIter++) { MII colPos = (*colIter)->GetSeqPositions(); if (colPos.find(j) != colPos.end()) { s += oldPtrs[j][colPos[j]]; char consensus = (*colIter)->GetConsensus(); if (consensus) { if (oldPtrs[j][colPos[j]] == consensus) colors += '1'; else if (oldPtrs[j][colPos[j]] == -consensus) colors += '2'; else if (pepGroup[(int) oldPtrs[j][colPos[j]] - 'A'] == consensus || consensus >= 'A' && pepSim[(int) consensus - 'A'][(int) oldPtrs[j][colPos[j]] - 'A']) colors += '3'; else colors += '0'; } else colors += '0'; } else { s += '-'; colors += '0'; } } s += '\n'; colors += '\n'; } return s + colors; } /*****************************************************************/ // MultiSequenceDag::AlignDag() // // Produces an alignment using the sequence-annealing method. // Input parameters include the posterior probabilities matrices, // the gap-factor used in the objective function, // parameter for dynamic/static weights, // tgf/maxweight weight function, and threshold for edge weight. /*****************************************************************/ MultiSequence* AlignDag(const SafeVector > &sparseMatrices, float gapFactor, bool enableVerbose, bool enableEdgeReordering, bool useTgf, float edgeWeightThreshold){ priority_queue, smaller_weight> edges; Edge *edge; int guiFrame = 0; cerr << "Creating candidate edge list" << endl; if (outputForGUI && guiStartWeight == std::numeric_limits::max()) { cout << "Weight " << std::numeric_limits::max() << endl << this->GetSequences() << endl; } for (int i = 0; i < numSequences; i++) { int seq1Length = sequences->GetSequence(i)->GetLength(); for (int j = i + 1; j < numSequences; j++) { SparseMatrix* ijMatrix = sparseMatrices[i][j]; for (int ii = 1; ii <= seq1Length; ii++) { float pGapii = ijMatrix->GetGapPosterior(0,ii); for (SafeVector::iterator rowPtr = ijMatrix->GetRowPtr(ii), rowEnd = rowPtr + ijMatrix->GetRowSize(ii); rowPtr != rowEnd; rowPtr++) { int jj = rowPtr->first; float pMatch = 2 * rowPtr->second; if (!pMatch) continue; float pGapjj = ijMatrix->GetGapPosterior(1,jj); float weight = useTgf ? 2 * pMatch / (pGapii + pGapjj) : 2* pMatch - gapFactor * (pGapii + pGapjj); if (weight < edgeWeightThreshold || (useTgf && weight < gapFactor)) continue; edge = new Edge(seqPos2colIndex[PII(i,ii)], seqPos2colIndex[PII(j,jj)], weight); edges.push(edge); } } } } cerr << "Adding edges to the DAG" << endl; while (!edges.empty()) { Edge *edge = edges.top(); edges.pop(); float delta = 0; if (enableEdgeReordering) { // recalculate edge weight if using dynamic edge weights delta = useTgf ? (edge->calcTgfWeight)(sparseMatrices,enableVerbose) : (edge->calcMaxStepWeight)(sparseMatrices,enableVerbose,gapFactor); if (delta == INVALID_EDGE) { // edge is no longer valid delete edge; continue; } if (edge->weight < edges.top()->weight) { edges.push(edge); if (enableVerbose) cerr << "wrong order" << endl << *edge << endl; continue; } if (edge->weight < edgeWeightThreshold || (useTgf && edge->weight < gapFactor)) { // done. Delete remaining edges while (!edges.empty()) { edge = edges.top(); edges.pop(); delete edge; } break; } } if (enableVerbose) cerr << "Adding edge" << endl << *edge; int result = AddEdge(edge); if (enableVerbose) { if (result) cerr << "Failed to add edge with error code: " << result << endl; else cerr << "Edge added successfully" << endl; } if (!result) { expectedAccuracy += delta; if (outputForGUI && guiStartWeight >= edge->weight && !(guiFrame = ++guiFrame % guiStepSize)) { cout << "Weight " << edge->weight << endl << this->GetSequences() << endl; } if (enableVerbose) { cerr << "Alignment at edge-weight " << edge->weight << endl << "with incermental expected accuracy improvement of " << delta << endl << "and total improvement of " << expectedAccuracy << endl; MultiSequence* msa = this->GetMultiSequence(); msa->WriteALN(cerr); delete msa; cerr << endl; } } delete edge; } return GetMultiSequence(); } }; // A B C D E F G H I J K L M N O P Q R S T U V W X Y Z const char MultiSequenceDag::pepGroup[26] = {5,0,0,4,4,1,5,3,2,0,3,2,2,7,0,0,7,3,6,6,0,2,1,0,1,0}; const bool MultiSequenceDag::pepSim[26][26] = {{1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0}, // A {0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, // B {0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, // C {0,0,0,1,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0}, // D {0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0}, // E {0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0}, // F {1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, // G {0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0}, // H {0,0,0,0,0,0,0,0,1,0,0,1,1,0,0,0,0,0,0,0,0,1,0,0,0,0}, // I {0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, // J {0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0}, // K {0,0,0,0,0,0,0,0,1,0,0,1,1,0,0,0,0,0,0,0,0,1,0,0,0,0}, // L {0,0,0,0,0,0,0,0,1,0,0,1,1,0,0,0,0,0,0,0,0,1,0,0,0,0}, // M {0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0}, // N {0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0}, // O {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0}, // P {0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0}, // Q {0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0}, // R {1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0}, // S {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0}, // T {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0}, // U {0,0,0,0,0,0,0,0,1,0,0,1,1,0,0,0,0,0,0,0,0,1,0,0,0,0}, // V {0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0}, // W {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0}, // X {0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0}, // Y {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1}};// Z /*****************************************************************/ // Column::UpdateConsensus() // // Updates the consensus character /*****************************************************************/ void Column::UpdateConsensus(MultiSequence* sequences, int numSequences) { unsigned int pepCount[26] = {0}; unsigned int pepGroupCount[10] = {0}; unsigned int threshold = seqPositions.size() / 2; char groupConsensus = 0; if (!threshold) { consensus = 0; return; } for (MII::iterator posIter = seqPositions.begin(); posIter != seqPositions.end(); posIter++) { int currChar = sequences->GetSequence(posIter->first)->GetDataPtr()[posIter->second] - 'A'; if (++pepCount[currChar] > threshold) { consensus = (char) currChar + 'A'; if ((int) pepCount[currChar] == numSequences) consensus = -consensus; } if (++pepGroupCount[(int) MultiSequenceDag::pepGroup[currChar]] > threshold) { groupConsensus = MultiSequenceDag::pepGroup[currChar]; } } if (!consensus) consensus = groupConsensus; } #endif amap-align/display/0000755000120200001440000000000010754706702013727 5ustar sarielusersamap-align/display/lib/0000755000120200001440000000000010754706701014474 5ustar sarielusersamap-align/display/src/0000755000120200001440000000000010754706701014515 5ustar sarielusersamap-align/display/src/amap/0000755000120200001440000000000010754706702015434 5ustar sarielusersamap-align/display/src/amap/Alignment.java0000644000120200001440000000417310647172542020222 0ustar sarielusers //============================================================================ // // file: Alignment.java // // Copyright (c) 2007, Michael E. Smoot // // This program is free software; you can redistribute it and/or modify it // under the terms of the GNU General Public License as published by the // Free Software Foundation; either version 2 of the License, or (at your // option) any later version. // // This program is distributed in the hope that it will be useful, but // WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY // or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License // for more details. // // You should have received a copy of the GNU General Public License along // with this program; if not, write to the Free Software Foundation, Inc., // 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA // //============================================================================ package amap; import java.util.*; public class Alignment { Map seqs; Map colors; List keys; double nWeight; public Alignment(List keys, Map seqs, Map colors, double nWeight) { this.keys = keys; this.seqs = seqs; this.colors = colors; this.nWeight = nWeight; } public List getOrderedKeys() { return keys; } public Map getSequences() { return seqs; } public Map getColors() { return colors; } public double getWeight() { return nWeight; } public String toString() { StringBuffer sb = new StringBuffer(); sb.append("Weight = "); sb.append((new Double(nWeight)).toString()); sb.append("\n"); for ( String key : seqs.keySet() ) { sb.append(key); sb.append("\t"); sb.append(seqs.get(key)); sb.append("\n"); } sb.append("\n"); sb.append("\n"); return sb.toString(); } public String toMultiFasta() { StringBuffer sb = new StringBuffer(); for ( String key : keys ) { sb.append(">"); sb.append(key); sb.append("\n"); sb.append(seqs.get(key)); sb.append("\n"); } return sb.toString(); } } amap-align/display/src/amap/SaveAsFastaAction.java0000644000120200001440000000463310647002340021570 0ustar sarielusers //============================================================================ // // file: SaveAsFastaAction.java // // Copyright (c) 2007, Michael E. Smoot // // This program is free software; you can redistribute it and/or modify it // under the terms of the GNU General Public License as published by the // Free Software Foundation; either version 2 of the License, or (at your // option) any later version. // // This program is distributed in the hope that it will be useful, but // WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY // or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License // for more details. // // You should have received a copy of the GNU General Public License along // with this program; if not, write to the Free Software Foundation, Inc., // 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA // //============================================================================ package amap; import java.util.*; import java.beans.*; import java.io.*; import javax.swing.*; import java.awt.event.ActionEvent; import java.awt.Component; public class SaveAsFastaAction extends AbstractAction implements PropertyChangeListener { Alignment a; Component parent; JFileChooser fc; SaveAsFastaAction(Component parent ) { super("Save as Mulitple FASTA"); this.parent = parent; fc = new JFileChooser(); PropertyChangeHandler.getPropertyChangeSupport() .addPropertyChangeListener(PropertyChangeIDs.CHANGE_ALIGNMENT.toString(), this); a = null; } public void actionPerformed(ActionEvent e) { System.out.println("saving as multiple fasta"); if ( a != null ) { try { int returnVal = fc.showSaveDialog(parent); if (returnVal == JFileChooser.APPROVE_OPTION) { File file = fc.getSelectedFile(); FileWriter fw = new FileWriter(file); String mfa = a.toMultiFasta(); fw.write(mfa,0,mfa.length()); fw.close(); } } catch (Exception ioe) { JOptionPane.showMessageDialog(parent, "Failed to Save Multiple FASTA file:\n\n" + ioe.getMessage(), "ERROR Saving File!", JOptionPane.ERROR_MESSAGE); ioe.printStackTrace(); } } else System.err.println("no alignment found"); } public void propertyChange(PropertyChangeEvent e) { a = (Alignment)e.getNewValue(); } } amap-align/display/src/amap/AmapReader.java0000644000120200001440000000607110647207433020302 0ustar sarielusers //============================================================================ // // file: AmapReader.java // // Copyright (c) 2007, Michael E. Smoot // // This program is free software; you can redistribute it and/or modify it // under the terms of the GNU General Public License as published by the // Free Software Foundation; either version 2 of the License, or (at your // option) any later version. // // This program is distributed in the hope that it will be useful, but // WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY // or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License // for more details. // // You should have received a copy of the GNU General Public License along // with this program; if not, write to the Free Software Foundation, Inc., // 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA // //============================================================================ package amap; import java.util.regex.Pattern; import java.util.regex.Matcher; import java.util.*; import java.io.*; public class AmapReader { private Map nameSeqMap; private Map nameColorMap; List alignments; List keys; InputStream is; boolean firstTime; double pWeight; public AmapReader(InputStream is) { this.is = is; alignments = new ArrayList(); keys = new ArrayList(); reset(); read(); } public List getAlignments() { return alignments; } private void read() { Pattern pw = Pattern.compile("^Weight\\s+([+-]?(?=\\d|\\.\\d)\\d*(\\.\\d*)?([Ee]([+-]?\\d+))?)$"); Matcher pwm = pw.matcher(""); Pattern s = Pattern.compile("^>(\\S+)\\s+(\\S+)$"); Matcher sm = s.matcher(""); Pattern c = Pattern.compile("^@(\\S+)\\s+(\\S+)$"); Matcher cm = c.matcher(""); firstTime = true; try { BufferedReader br = new BufferedReader(new InputStreamReader(is)); String line = null; while ( (line = br.readLine()) != null ) { pwm.reset(line); if ( pwm.matches() ) { saveAlignment(); pWeight = new Double( pwm.group(1) ).doubleValue(); continue; } sm.reset(line); if ( sm.matches() ) { String key = sm.group(1); String val = sm.group(2); if ( nameSeqMap.containsKey( key ) ) val = nameSeqMap.get(key) + val; nameSeqMap.put(key,val); if ( firstTime ) keys.add(key); continue; } cm.reset(line); if ( cm.matches() ) { String key = cm.group(1); String val = cm.group(2); if ( nameColorMap.containsKey( key ) ) val = nameColorMap.get(key) + val; nameColorMap.put(key,val); continue; } } saveAlignment(); } catch (IOException ioe) { ioe.printStackTrace(); } } private void saveAlignment() { if ( pWeight > 0 ) { Alignment a = new Alignment( keys, nameSeqMap, nameColorMap, pWeight ); alignments.add(a); reset(); } } private void reset() { nameSeqMap = new HashMap(); nameColorMap = new HashMap(); pWeight = -1; firstTime = false; } } amap-align/display/src/amap/AlignmentPanel.java0000644000120200001440000001272010647002340021163 0ustar sarielusers //============================================================================ // // file: AlignmentPanel.java // // Copyright (c) 2007, Michael E. Smoot // // This program is free software; you can redistribute it and/or modify it // under the terms of the GNU General Public License as published by the // Free Software Foundation; either version 2 of the License, or (at your // option) any later version. // // This program is distributed in the hope that it will be useful, but // WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY // or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License // for more details. // // You should have received a copy of the GNU General Public License along // with this program; if not, write to the Free Software Foundation, Inc., // 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA // //============================================================================ package amap; import javax.swing.*; import java.util.*; import java.awt.event.*; import java.awt.Dimension; import java.awt.Color; import java.awt.Font; import java.awt.FontMetrics; import java.awt.Graphics; import java.awt.Graphics2D; import java.awt.RenderingHints; import java.awt.Shape; import java.awt.geom.Point2D; import java.awt.font.GlyphVector; import java.awt.font.FontRenderContext; public class AlignmentPanel extends JPanel implements ComponentListener { List aligns; List orderedKeys; int index; int xOff; int yOff; int numCharsAcross; int nameWidth; int glyphWidth; int len; int groupOff; Font defaultFont; int height; int width; int os; Map backColMap; Map textColMap; public AlignmentPanel(List aligns, int initWidth) { super(); this.aligns = aligns; this.width = initWidth; Map seqs = aligns.get(0).getSequences(); orderedKeys = aligns.get(0).getOrderedKeys(); defaultFont = new Font("Courier",Font.BOLD,12); index = 0; // Aaaaargh if ( System.getProperty("os.name").matches(".*[Mm][Aa][Cc].*") ) os = -1; else os = 1; backColMap = new HashMap(); backColMap.put("0",new Color(255,255,255)); backColMap.put("1",new Color(0,128,255)); // CMYK 1, 0.5, 0, 0 backColMap.put("2",new Color(64,25,255)); // CMYK 0.75, 0.9, 0, 0 backColMap.put("3",new Color(255,0,255)); // CMYK 0, 1, 0, 0 textColMap = new HashMap(); textColMap.put("0",Color.black); textColMap.put("1",Color.white); textColMap.put("2",new Color(255,230,41)); // CMYK 0, 0.1, 0.84, 0 textColMap.put("3",Color.black); sizeScreen( new Dimension(initWidth,0) ); } private void sizeScreen(Dimension d) { width = (int)(d.getWidth()); glyphWidth = 10; // find the width of the sequence name FontMetrics fm = getFontMetrics(defaultFont); nameWidth = 0; for ( String key : orderedKeys ) nameWidth = Math.max(nameWidth,fm.stringWidth(key)); // give the seq name some breathing room nameWidth += glyphWidth; // set margins xOff = 20; yOff = 20; // size of one multiple alignment row groupOff = yOff * (orderedKeys.size() + 1); // figure out how many multiple alignment rows there will be int seqAllowedWidth = width - xOff - nameWidth - xOff - xOff; numCharsAcross = seqAllowedWidth/glyphWidth; len = aligns.get(0).getSequences().get(orderedKeys.get(0)).length(); height = ((len/numCharsAcross)+1) * groupOff; height = Math.max(height, (int)d.getHeight()); setPreferredSize( new Dimension(width,height) ); } public void setIndex(int i) { if ( i >= 0 && i < aligns.size() ) index = i; else System.out.println("invalid index: " + i); } public void paint(Graphics g) { Graphics2D g2 = (Graphics2D)g; g2.setBackground(Color.white); g2.setPaint(Color.white); g2.fillRect(0,0,width,height); g2.setPaint(Color.black); g2.setFont( defaultFont ); g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); g2.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON); FontRenderContext frc = g2.getFontRenderContext(); Map seqs = aligns.get(index).getSequences(); Map cols = aligns.get(index).getColors(); int i = 0; for ( String name : orderedKeys ) { i++; String seq = seqs.get(name); String colString = cols.get(name); if ( seq == null ) continue; GlyphVector gv = defaultFont.createGlyphVector(frc,seq); for ( int j = 0; j < gv.getNumGlyphs(); j++ ) { int xLoc = xOff+nameWidth+((j%numCharsAcross)*glyphWidth); int yLoc = ((j/numCharsAcross)*groupOff)+(yOff*i); // set glyph position Point2D pos = gv.getGlyphPosition(j); pos.setLocation(xLoc, yLoc); gv.setGlyphPosition(j,pos); // draw the background rect String colCode = colString.substring(j,j+1); g2.setPaint(backColMap.get( colCode )); g2.fillRect(xLoc-1,yLoc-yOff+6,glyphWidth,yOff); // draw the sequence name if ( j%numCharsAcross == 0 ) { g2.setPaint(Color.black); g2.drawString(name,xOff,yLoc ); } // draw the glyph Shape glyph = gv.getGlyphOutline(j); g2.setPaint(textColMap.get( colCode )); g2.fill(glyph); } } } public void componentResized(ComponentEvent e) { sizeScreen( e.getComponent().getSize() ); } public void componentShown(ComponentEvent e) {}; public void componentHidden(ComponentEvent e) {}; public void componentMoved(ComponentEvent e) {}; } amap-align/display/src/amap/AmapPanel.java0000644000120200001440000002207410650406673020141 0ustar sarielusers //============================================================================ // // file: AmapPanel.java // // Copyright (c) 2007, Michael E. Smoot // // This program is free software; you can redistribute it and/or modify it // under the terms of the GNU General Public License as published by the // Free Software Foundation; either version 2 of the License, or (at your // option) any later version. // // This program is distributed in the hope that it will be useful, but // WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY // or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License // for more details. // // You should have received a copy of the GNU General Public License along // with this program; if not, write to the Free Software Foundation, Inc., // 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA // //============================================================================ package amap; import java.awt.*; import java.awt.event.*; import javax.swing.*; import javax.swing.event.*; import javax.swing.text.NumberFormatter; import java.beans.*; import java.text.DecimalFormat; import java.util.Map; import java.util.HashMap; public class AmapPanel extends JPanel implements ChangeListener, PropertyChangeListener, ActionListener { AlignmentPanel alignPanel; JFormattedTextField indexField; JFormattedTextField weightField; JSlider alignSlider; java.util.List aligns; JButton nextButton; JButton prevButton; JButton startStopButton; int maxSliderVal; Map ok2update; Timer timer; boolean frozen = true; int delay = 200; public AmapPanel(java.util.List aligns) { this.aligns = aligns; maxSliderVal = aligns.size()-1; ok2update = new HashMap(); setLayout(new BoxLayout(this, BoxLayout.Y_AXIS)); // set up animation timer timer = new Timer(delay,this); timer.setCoalesce(true); //Create the label. JLabel sliderLabel = new JLabel("Alignment: ", JLabel.CENTER); sliderLabel.setAlignmentX(Component.CENTER_ALIGNMENT); //Create the alignment number field java.text.NumberFormat intFormat = java.text.NumberFormat.getIntegerInstance(); NumberFormatter intFormatter = new NumberFormatter(intFormat); intFormatter.setMinimum(new Integer(0)); intFormatter.setMaximum(new Integer(maxSliderVal)); indexField = new JFormattedTextField(intFormatter); indexField.setColumns(5); //get some space indexField.addPropertyChangeListener( this ); handleEnterKeyStroke( indexField ); ok2update.put(indexField,false); JLabel weightLabel = new JLabel("Weight: ", JLabel.CENTER); //Create the alignment weight field java.text.NumberFormat numFormat = java.text.NumberFormat.getNumberInstance(); NumberFormatter numFormatter = new NumberFormatter(numFormat); numFormatter.setMinimum(new Float(0f)); numFormatter.setMaximum(new Float(Float.MAX_VALUE)); weightField = new JFormattedTextField(numFormatter); weightField.setColumns(10); //get some space weightField.addPropertyChangeListener( this ); handleEnterKeyStroke( weightField ); ok2update.put(weightField,false); // create next button nextButton = new JButton("Next"); nextButton.addActionListener(this); startStopButton = new JButton("Start Animation"); startStopButton.addActionListener(this); // create prev button prevButton = new JButton("Prev"); prevButton.addActionListener(this); //Create the slider. alignSlider = new JSlider(JSlider.HORIZONTAL, 0, maxSliderVal, 0); alignSlider.addChangeListener(this); //Turn on labels at major tick marks. alignSlider.setMajorTickSpacing(calcTickSpacing(maxSliderVal)); alignSlider.setPaintTicks(true); alignSlider.setPaintLabels(true); //Create the label that displays the animation. alignPanel = new AlignmentPanel(aligns,450); alignPanel.setBorder(BorderFactory.createCompoundBorder( BorderFactory.createLoweredBevelBorder(), BorderFactory.createEmptyBorder(10,10,10,10))); updatePicture(0); //display first frame // set up scrolling JScrollPane alignScroll = new JScrollPane(alignPanel); alignScroll.setPreferredSize(new Dimension(500,700)); alignScroll.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER); alignScroll.addComponentListener(alignPanel); //Create a subpanel for the label and text field. JPanel labelAndTextField = new JPanel(); //use FlowLayout labelAndTextField.add(prevButton); labelAndTextField.add(startStopButton); labelAndTextField.add(nextButton); labelAndTextField.add(sliderLabel); labelAndTextField.add(indexField); labelAndTextField.add(weightLabel); labelAndTextField.add(weightField); //Put everything together. add(alignScroll); add(alignSlider); add(labelAndTextField); setBorder(BorderFactory.createEmptyBorder(10,10,10,10)); update(maxSliderVal); } public void stateChanged(ChangeEvent e) { JSlider source = (JSlider)e.getSource(); if ( source == alignSlider ) update((int)alignSlider.getValue()); } private void update(int index) { updatePicture(index); alignSlider.setValue(index); indexField.setText(Integer.toString(index)); weightField.setText(Double.toString(aligns.get(index).getWeight())); PropertyChangeHandler.firePropertyChange(PropertyChangeIDs.CHANGE_ALIGNMENT.toString(), null, aligns.get(index)); } public void propertyChange(PropertyChangeEvent e) { if (!"value".equals(e.getPropertyName())) return; //new Exception().printStackTrace(); //System.out.println("pc weightfield: " + ok2update.get(weightField)); //System.out.println("pc indexfield: " + ok2update.get(indexField)); //System.out.print("prop change: " + e.getNewValue() + " " ); if ( e.getSource() == indexField && ok2update.get(indexField) ) { // System.out.println("index" ); Number value = (Number)e.getNewValue(); if (value != null) { update(value.intValue()); ok2update.put(indexField,false); // System.out.println("index alignSilder val: " + alignSlider.getValue()); } } else if ( e.getSource() == weightField && ok2update.get(weightField) ) { //System.out.println("weight" ); Float weight = (Float)e.getNewValue(); int index = getIndexFromWeight( weight.floatValue() ); if (index >= 0 && index <= maxSliderVal) { update(index); ok2update.put(weightField,false); //System.out.println("weight alignSilder val: " + alignSlider.getValue()); } } } public void actionPerformed(ActionEvent e) { int curr = (int)alignSlider.getValue(); //System.out.println("curr val: " + curr); if ( e.getSource() == nextButton || e.getSource() == timer ) { if ( curr == maxSliderVal ) update(0); else update(curr+1); } else if ( e.getSource() == prevButton ) { if ( curr == 0 ) update(maxSliderVal); else update(curr-1); } else if ( e.getSource() == startStopButton ) { if ( frozen ) { timer.start(); frozen = false; startStopButton.setText("Stop Animation"); } else { timer.stop(); frozen = true; startStopButton.setText("Start Animation"); } } } protected void updatePicture(int frameNum) { alignPanel.setIndex(frameNum); repaint(); } protected int calcTickSpacing(int val) { return ((val/10) - (val%10)); } private int getIndexFromWeight(float w) { return bSearch(0,aligns.size()-1,w); } private int bSearch(int low, int high, float weight) { //System.out.println(low + " " + high + " " + weight); if ( high < low ) return -1; if ( weight <= aligns.get(high).getWeight() ) return high; if ( weight >= aligns.get(low).getWeight() ) return low; if ( low == high - 1 ) return low; int mid = (high + low) / 2; if ( weight < aligns.get(mid).getWeight() ) return bSearch(mid,high,weight); else if ( weight > aligns.get(mid).getWeight() ) return bSearch(low,mid,weight); else return mid; } //React when the user presses Enter. private void handleEnterKeyStroke( final JFormattedTextField field ) { field.getInputMap().put(KeyStroke.getKeyStroke( KeyEvent.VK_ENTER, 0), "check"); field.getActionMap().put("check", new AbstractAction() { public void actionPerformed(ActionEvent e) { //The text is invalid. if (!field.isEditValid()) { Toolkit.getDefaultToolkit().beep(); field.selectAll(); //The text is valid, so use it. } else try { //System.out.println("commitEdit"); ok2update.put(field,true); //System.out.println("weightfield: " + ok2update.get(weightField)); //System.out.println("indexfield: " + ok2update.get(indexField)); field.commitEdit(); } catch (java.text.ParseException exc) { } } }); } } amap-align/display/src/amap/AmapDisplay.java0000644000120200001440000000405610647002340020474 0ustar sarielusers //============================================================================ // // file: AmapDisplay.java // // Copyright (c) 2007, Michael E. Smoot // // This program is free software; you can redistribute it and/or modify it // under the terms of the GNU General Public License as published by the // Free Software Foundation; either version 2 of the License, or (at your // option) any later version. // // This program is distributed in the hope that it will be useful, but // WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY // or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License // for more details. // // You should have received a copy of the GNU General Public License along // with this program; if not, write to the Free Software Foundation, Inc., // 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA // //============================================================================ package amap; import java.io.*; import java.util.*; import javax.swing.*; import java.awt.Dimension; public class AmapDisplay { public static void main(String[] args) { if ( args.length != 1 ) { System.out.println("USAGE: java -jar amapDisplay.jar "); System.exit(1); } try { FileInputStream fis = new FileInputStream(args[0]); AmapReader ar = new AmapReader(fis); List aligns = ar.getAlignments(); final JFrame frame = new JFrame("AMAP Display"); frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); JMenuBar menuBar = new JMenuBar(); JMenu fileMenu = new JMenu("File"); menuBar.add(fileMenu); JMenuItem saveAsFasta = new JMenuItem( new SaveAsFastaAction(frame) ); fileMenu.add(saveAsFasta); frame.setJMenuBar(menuBar); AmapPanel panel = new AmapPanel(aligns); panel.setPreferredSize( new Dimension(700,700) ); //Display the window. frame.setContentPane(panel); frame.pack(); frame.setVisible(true); } catch (Exception ioe) { ioe.printStackTrace(); } } } amap-align/display/src/amap/PropertyChangeHandler.java0000644000120200001440000000323410647002340022515 0ustar sarielusers //============================================================================ // // file: PropertyChangeHandler.java // // Copyright (c) 2007, Michael E. Smoot // // This program is free software; you can redistribute it and/or modify it // under the terms of the GNU General Public License as published by the // Free Software Foundation; either version 2 of the License, or (at your // option) any later version. // // This program is distributed in the hope that it will be useful, but // WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY // or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License // for more details. // // You should have received a copy of the GNU General Public License along // with this program; if not, write to the Free Software Foundation, Inc., // 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA // //============================================================================ package amap; import java.util.*; import java.beans.*; public class PropertyChangeHandler { private static PropertyChangeSupport pcs; private static Object o; static { o = new Object(); pcs = new PropertyChangeSupport( o ); } public static PropertyChangeSupport getPropertyChangeSupport() { return pcs; } public static void firePropertyChange(String id, Object oldValue, Object newValue) { try { PropertyChangeIDs.valueOf(id); } catch (IllegalArgumentException ex) { System.err.println("Illegal PropertyChangeEvent ID: " + id + " ignoring!"); return; } PropertyChangeEvent e = new PropertyChangeEvent(pcs, id, oldValue, newValue); pcs.firePropertyChange(e); } } amap-align/display/src/amap/PropertyChangeIDs.java0000644000120200001440000000203410647002340021614 0ustar sarielusers //============================================================================ // // file: PropertyChangeIDs.java // // Copyright (c) 2007, Michael E. Smoot // // This program is free software; you can redistribute it and/or modify it // under the terms of the GNU General Public License as published by the // Free Software Foundation; either version 2 of the License, or (at your // option) any later version. // // This program is distributed in the hope that it will be useful, but // WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY // or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License // for more details. // // You should have received a copy of the GNU General Public License along // with this program; if not, write to the Free Software Foundation, Inc., // 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA // //============================================================================ package amap; public enum PropertyChangeIDs { CHANGE_ALIGNMENT, } amap-align/display/build.xml0000644000120200001440000002113210635655116015547 0ustar sarielusers amap-align/display/AmapDisplay.jar0000755000120200001440000004125310650431733016633 0ustar sarielusersPK I}õ6 META-INF/þÊPK H}õ6‘t؉”²META-INF/MANIFEST.MFMޱ Â0E÷@þá :$D‡ ÝÚº8ÁUž1Ú@ûòâPÄ7—;œs¹ÜÉ?'uq‘ýL5lµ‘¢¡?Ò´ƒƒÌ²ÜÝE‡ÉÝU»”~¥ÍÕìÔÍT°>¿zoãÌ '71Éê=zR݈Ì5à„A79žÃˆKÞ+B0 5¬ÞÓï“¶‡L5§èéù‘BŠ/PK 5Aó6amap/PK u>ó6logs/PK ¦žñ6áu˜i`í amap/Alignment.classVÛNW]cÆ6ƒ!NJ¡- !„â–\ å’MŠ1'èu0ƒ0¶c«F}¨Ô—¼÷­?>6• ÈTå­Rû9•zYçŒízƦªâ\öÙ{½ö^gÄoýü €q‚èÃB½¸#†E1| †»*îÑŽ?>ó’ŠDA,‹!éÇJîcµkHuàŠa]ņÄɦˆIv` 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>1ckl_A -------------------------------------------------------------------------------------------------------------------------------------------------------------------CEEPPTFEAMELIGKPKPYYEIG---------------------------------------------------ERVDYKCKKGYFYIPPLATHTICDRNHTWLPVSDDACYRETCPYIRDPLNGQAVPANGTYEFGYQMHFICNEGY-------------------------YLIGEEILYCELKGSVAIWSGKPPICEKV-------------------------------------------------------------------------------------------------------------------------------- >1nwv_A 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-------------------------------------------------------------AISCGSPPPILNGRISYYSTPIAVGTVIRYSCSGTFRLIGEKSLLCITKDKVDGTWDKPAPKCEYFNKYSSCPEP--------------------------------------------------IVPGGYKIRGSTPYRHGDSVTFACKTNFSMNGNKSVWCQANNMWGPTRLPT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CVS------------------------- >1ckl_A -------------------------------------------------------------------------------------------------------------------------------------------------------------------CEEPPTFEAMELIGKPKPYYEIG---------------------------------------------------ERVDYKCKKGYFYIPPLATHTICDRNHTWLPVSDDACYRETCPYIRDPLNGQAVPANGTYEFGYQMHFICNEGY-------------------------YLIGEEILYCELKGSVAIWSGKPPICEKV------------------------------------------------------------------------------------------------------------------------------- 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-------------------------------------------------------------AISCGSPPPILNGRISYYSTPIAVGTVIRYSCSGTFRLIGEKSLLCITKDKVDGTWDKPAPKCEYFNKYSSCPEP--------------------------------------------------IVPGGYKIRGSTPYRHGDSVTFACKTNFSMNGNKSVWCQANNMWGPTRLPT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CVS------------------------- >1ckl_A -------------------------------------------------------------------------------------------------------------------------------------------------------------------CEEPPTFEAMELIGKPKPYYEIG---------------------------------------------------ERVDYKCKKGYFYIPPLATHTICDRNHTWLPVSDDACYRETCPYIRDPLNGQAVPANGTYEFGYQMHFICNEGY------------------------YLIGEEILYCELKGSVAIWSGKPPICEKV------------------------------------------------------------------------------------------------------------------------------- >1nwv_A ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FRSCEVPTRLNSASLKQPYITQN-----------------------------YFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFG---------------------STSSFCLISGSSVQWSDPLPECREH @1vvc_ 00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001010000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000011000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001010000000000000000001100000000000000000000000000 @1ghq_B 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VKCQSPPSISNGRHNGYEDFYTDGSVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVKC------------------------------------------------------------------------PHPTISNGYLSSGFKRSYSYNDNVDFKCKY--------------------------------------------------------------------------------------------------------------------------------------------------GYK----------------------------------------------------------------------------------------------------------------------------------LSGSSSSTCSPGNTWKPEL-------------------PKCVR----- >1ghq_B -------------------------------------------------------------AISCGSPPPILNGRISYYSTPIAVGTVIRYSCSGTFRLIGEKSLLCITKDKVDGTWDKPAPKCEYFNKYSSCPEP--------------------------------------------------IVPGGYKIRGSTPYRHGDSVTFACKTNFSMNGNKSVWCQANNMWGPTRLPT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CVS----- >1ckl_A -------------------------------------------------------------------------------------------------------------------------------------------------------------------CEEPPTFEAMELIGKPKPYYEIG---------------------------------------------------ERVDYKCKKGYFYIPPLATHTICDRNHTWLPVSDDACYRETCPYIRDPLNGQAVPANGTYEFGYQMHFICNEGY------------------------YLIGEEILYCELKGSVAIWSGKPPICEKV------------------------------------------------------------------------------------------------------------------------------ >1nwv_A ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FRSCEVPTRLNSASLKQPYITQN-----------------------------YFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFG----------------STSSFCLISGSSVQWSDPLP----ECREH @1vvc_ 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-------------------------------------------------------------AISCGSPPPILNGRISYYSTPIAVGTVIRYSCSGTFRLIGEKSLLCITKDKVDGTWDKPAPKCEYFNKYSSCPEP--------------------------------------------------IVPGGYKIRGSTPYRHGDSVTFACKTNFSMNGNKSVWCQANNMWGPTRLPT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CVS----- >1ckl_A -------------------------------------------------------------------------------------------------------------------------------------------------------------------CEEPPTFEAMELIGKPKPYYEIG---------------------------------------------------ERVDYKCKKGYFYIPPLATHTICDRNHTWLPVSDDACYRETCPYIRDPLNGQAVPANGTYEFGYQMHFICNEGY-----------------------YLIGEEILYCELKGSVAIWSGKPPICEKV------------------------------------------------------------------------------------------------------------------------------ >1nwv_A 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VKCQSPPSISNGRHNGYEDFYTDGSVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVKC------------------------------------------------------------------------PHPTISNGYLSSGFKRSYSYNDNVDFKCKY--------------------------------------------------------------------------------------------------------------------------------------------------GY---------------------------------------------------------------------------------------------------------------------------------KLSGSSSSTCSPGNTWKPE------------------LPKCVR----- >1ghq_B -------------------------------------------------------------AISCGSPPPILNGRISYYSTPIAVGTVIRYSCSGTFRLIGEKSLLCITKDKVDGTWDKPAPKCEYFNKYSSCPEP--------------------------------------------------IVPGGYKIRGSTPYRHGDSVTFACKTNFSMNGNKSVWCQANNMWGPTRLPT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CVS----- >1ckl_A -------------------------------------------------------------------------------------------------------------------------------------------------------------------CEEPPTFEAMELIGKPKPYYEIG---------------------------------------------------ERVDYKCKKGYFYIPPLATHTICDRNHTWLPVSDDACYRETCPYIRDPLNGQAVPANGTYEFGYQMHFICNEGY-----------------------YLIGEEILYCELKGSVAIWSGKPPICEKV----------------------------------------------------------------------------------------------------------------------------- >1nwv_A -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FRSCEVPTRLNSASLKQPYITQN-----------------------------YFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFG---------------STSSFCLISGSSVQWSDPLP----ECREH @1vvc_ 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Weight 495.897 >1vvc_ VKCQSPPSISNGRHNGYEDFYTDGSVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVKC------------------------------------------------------------------------PHPTISNGYLSSGFKRSYSYNDNVDFKCKY--------------------------------------------------------------------------------------------------------------------------------------------------GY---------------------------------------------------------------------------------------------------------------------------------KLSGSSSSTCSPGNTWKPE-----------------LPKCVR----- >1ghq_B -------------------------------------------------------------AISCGSPPPILNGRISYYSTPIAVGTVIRYSCSGTFRLIGEKSLLCITKDKVDGTWDKPAPKCEYFNKYSSCPEP--------------------------------------------------IVPGGYKIRGSTPYRHGDSVTFACKTNFSMNGNKSVWCQANNMWGPTRLPT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CVS----- >1ckl_A -------------------------------------------------------------------------------------------------------------------------------------------------------------------CEEPPTFEAMELIGKPKPYYEIG---------------------------------------------------ERVDYKCKKGYFYIPPLATHTICDRNHTWLPVSDDACYRETCPYIRDPLNGQAVPANGTYEFGYQMHFICNEGY-----------------------YLIGEEILYCELKGSVAIWSGKPPICEKV---------------------------------------------------------------------------------------------------------------------------- >1nwv_A 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VKCQSPPSISNGRHNGYEDFYTD------------------------GSVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVKC-----------------------------------------------PHPTISNGYLSSGFKRSYSYNDNVDFKCKY--------------------------------------------------------------------------------------------------------------------------------------------------GY---------------------------------------------------------------------------------------------------------------------------------KLSGSSSSTCSPGNTWKPE-----------------LPKCVR----- >1ghq_B -----------------------AISCGSPPPILNGRISYYSTPIAVG-------------------------------------TVIRYSCSGTFRLIGEKSLLCITKDKVDGTWDKPAPKCEYFNKYSSCPEP--------------------------------------------------IVPGGYKIRGSTPYRHGDSVTFACKTNFSMNGNKSVWCQANNMWGPTRLPT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CVS----- >1ckl_A ------------------------------------------------------------------------------------------------------------------------------------------------------------------CEEPPTFEAMELIGKPKPYYEIG---------------------------------------------------ERVDYKCKKGYFYIPPLATHTICDRNHTWLPVSDDACYRETCPYIRDPLNGQAVPANGTYEFGYQMHFICNEGY-----------------------YLIGEEILYCELKGSVAIWSGKPPICEKV---------------------------------------------------------------------------------------------------------------------------- >1nwv_A ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FRSCEVPTRLNSASLKQPYITQN-----------------------------YFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGS--------------TSSFCLISGSSVQWSDPLP----ECREH @1vvc_ 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VK---CQSPPSISNGRHNGYEDFYTD-------------------GSVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVKC-----------------------------------------------PHPTISNGYLSSGFKRSYSYNDNVDFKCKY--------------------------------------------------------------------------------------------------------------------------------------------------GY---------------------------------------------------------------------------------------------------------------------------------KLSGSSSSTCSPGNTWKPE-----------------LPKCVR----- >1ghq_B --AISCG-------------------SPPPILNGRISYYSTPIAVG-------------------------------------TVIRYSCSGTFRLIGEKSLLCITKDKVDGTWDKPAPKCEYFNKYSSCPEP--------------------------------------------------IVPGGYKIRGSTPYRHGDSVTFACKTNFSMNGNKSVWCQANNMWGPTRLPT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CVS----- >1ckl_A ----------------------------------------------------------------------------------------------------------------------------------------------------------------CEEPPTFEAMELIGKPKPYYEIG---------------------------------------------------ERVDYKCKKGYFYIPPLATHTICDRNHTWLPVSDDACYRETCPYIRDPLNGQAVPANGTYEFGYQMHFICNEGY-----------------------YLIGEEILYCELKGSVAIWSGKPPICEKV---------------------------------------------------------------------------------------------------------------------------- >1nwv_A --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FRSCEVPTRLNSASLKQPYITQN-----------------------------YFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGS--------------TSSFCLISGSSVQWSDPLP----ECREH @1vvc_ 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--------------------------------------------------------------------------------------------------------------------------------------------------------------CEEPPTFEAMELIGKPKPYYEIG---------------------------------------------------ERVDYKCKKGYFYIPPLATHTICDRNHTWLPVSDDACYRETCPYIRDPLNGQAVPANGTYEFGYQMHFICNEGY-----------------------YLIGEEILYCELKGSVAIWSGKPPICEKV---------------------------------------------------------------------------------------------------------------------------- >1nwv_A ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FRSCEVPTRLNSASLKQPYITQN-----------------------------YFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGS--------------TSSFCLISGSSVQWSDPLP----ECREH @1vvc_ 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>1vvc_ VK---CQSPPSISNGRHNGYEDFYTD------------------GSVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVKC---------------------------------------------PHPTISNGYLSSGFKRSYSYNDNVDFKCKY--------------------------------------------------------------------------------------------------------------------------------------------------GY---------------------------------------------------------------------------------------------------------------------------------KLSGSSSSTCSPGNTWKPE-----------------LPKCVR----- >1ghq_B --AISCGS------------------PPPILNGRISYYSTPIAVGTV-----------------------------------IRYSCSGTFRLIGEKSLLCITKDKVDGTWDKPAPKCEYFNKYSSCPEP--------------------------------------------------IVPGGYKIRGSTPYRHGDSVTFACKTNFSMNGNKSVWCQANNMWGPTRLPT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CVS----- >1ckl_A -------------------------------------------------------------------------------------------------------------------------------------------------------------CEEPPTFEAMELIGKPKPYYEIG---------------------------------------------------ERVDYKCKKGYFYIPPLATHTICDRNHTWLPVSDDACYRETCPYIRDPLNGQAVPANGTYEFGYQMHFICNEGY-----------------------YLIGEEILYCELKGSVAIWSGKPPICEKV---------------------------------------------------------------------------------------------------------------------------- >1nwv_A -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FRSCEVPTRLNSASLKQPYITQN-----------------------------YFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGS--------------TSSFCLISGSSVQWSDPLP----ECREH @1vvc_ 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>1vvc_ VK---CQSPPSISNGRHNGYEDFYTD-----------------GSVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVKC---------------------------------------------PHPTISNGYLSSGFKRSYSYNDNVDFKCKY--------------------------------------------------------------------------------------------------------------------------------------------------GY---------------------------------------------------------------------------------------------------------------------------------KLSGSSSSTCSPGNTWKPE-----------------LPKCVR----- >1ghq_B --AISCGSP-----------------PPILNGRISYYSTPIAVGTV-----------------------------------IRYSCSGTFRLIGEKSLLCITKDKVDGTWDKPAPKCEYFNKYSSCPEP--------------------------------------------------IVPGGYKIRGSTPYRHGDSVTFACKTNFSMNGNKSVWCQANNMWGPTRLPT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CVS----- >1ckl_A ------------------------------------------------------------------------------------------------------------------------------------------------------------CEEPPTFEAMELIGKPKPYYEIG---------------------------------------------------ERVDYKCKKGYFYIPPLATHTICDRNHTWLPVSDDACYRETCPYIRDPLNGQAVPANGTYEFGYQMHFICNEGY-----------------------YLIGEEILYCELKGSVAIWSGKPPICEKV---------------------------------------------------------------------------------------------------------------------------- >1nwv_A ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FRSCEVPTRLNSASLKQPYITQN-----------------------------YFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGS--------------TSSFCLISGSSVQWSDPLP----ECREH @1vvc_ 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>1vvc_ VK---CQSPPSISNGRHNGYEDFYTD----------------GSVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVKC---------------------------------------------PHPTISNGYLSSGFKRSYSYNDNVDFKCKY--------------------------------------------------------------------------------------------------------------------------------------------------GY---------------------------------------------------------------------------------------------------------------------------------KLSGSSSSTCSPGNTWKPE-----------------LPKCVR----- >1ghq_B --AISCGSPP----------------PILNGRISYYSTPIAVGTV-----------------------------------IRYSCSGTFRLIGEKSLLCITKDKVDGTWDKPAPKCEYFNKYSSCPEP--------------------------------------------------IVPGGYKIRGSTPYRHGDSVTFACKTNFSMNGNKSVWCQANNMWGPTRLPT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CVS----- >1ckl_A -----------------------------------------------------------------------------------------------------------------------------------------------------------CEEPPTFEAMELIGKPKPYYEIG---------------------------------------------------ERVDYKCKKGYFYIPPLATHTICDRNHTWLPVSDDACYRETCPYIRDPLNGQAVPANGTYEFGYQMHFICNEGY-----------------------YLIGEEILYCELKGSVAIWSGKPPICEKV---------------------------------------------------------------------------------------------------------------------------- >1nwv_A ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FRSCEVPTRLNSASLKQPYITQN-----------------------------YFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGS--------------TSSFCLISGSSVQWSDPLP----ECREH @1vvc_ 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>1vvc_ VK---CQSPPSISNGRHNGYEDFYTD----------------GSVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVKC--------------------------------------------PHPTISNGYLSSGFKRSYSYNDNVDFKCKY--------------------------------------------------------------------------------------------------------------------------------------------------GY---------------------------------------------------------------------------------------------------------------------------------KLSGSSSSTCSPGNTWKPE-----------------LPKCVR----- >1ghq_B --AISCGSPP----------------PILNGRISYYSTPIAVGTVI----------------------------------RYSCSGTFRLIGEKSLLCITKDKVDGTWDKPAPKCEYFNKYSSCPEP--------------------------------------------------IVPGGYKIRGSTPYRHGDSVTFACKTNFSMNGNKSVWCQANNMWGPTRLPT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CVS----- >1ckl_A ----------------------------------------------------------------------------------------------------------------------------------------------------------CEEPPTFEAMELIGKPKPYYEIG---------------------------------------------------ERVDYKCKKGYFYIPPLATHTICDRNHTWLPVSDDACYRETCPYIRDPLNGQAVPANGTYEFGYQMHFICNEGY-----------------------YLIGEEILYCELKGSVAIWSGKPPICEKV---------------------------------------------------------------------------------------------------------------------------- >1nwv_A --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FRSCEVPTRLNSASLKQPYITQN-----------------------------YFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGS--------------TSSFCLISGSSVQWSDPLP----ECREH @1vvc_ 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VK---CQSPPSISNGRHNGYEDFYTD----------GSVVTYSCNSGYSL------IG-NSGVLCSGGEWSDPPTCQIVKC-------------------------------PHPTISNGYLSSGFKRSYSYNDNVDFKCKY-----------------------------------------------------------------------------------------------------------------------------------GY---------------------------------------------------------------------------------------------------------------------------------KLSGSSSSTCSPGNTW------KPE-----------------LPKCVR----- >1ghq_B --AISCGSPPPILNGR----------ISYYSTPIAVGTVIRYSC------SGTFRLI-GE---------------------KSLLCITKDKVDGTWDKPAPKCEYFNKYSSCPEP--------------------------------------------------IVPGGYKIRGSTPYRHGDSVTFACKTNFSMNGNKSV-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WCQANNMWGPTRLP----------------------TCVS----- >1ckl_A 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---------------------------------------------------------------------------------------------------------------------------------------------CEEPPTFEAMELIGKPKPYYEIG------------------------------------ERVDYKCKKGYFYIPPLATHTICDRNHTWLPVSDDACYRETCPYIRDPLNGQAVPANGTYEFGYQMHFICNEGY-------------------------------YLIGEEILYCELKGSVAIWSGKPPICEKV-------------------------------------------------------------------------------------------------------------------------- >1nwv_A ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FRSCEVPTRLNSASLKQPYITQNYFPVGTVV-----------------------------EYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGS--------------------TSSFCLISGSSVQWSDPLP----ECREH @1vvc_ 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--------------------------------------------------------------------------------------------------------------------------------------------CEEPPTFEAMELIGKPKPYYEIG------------------------------------ERVDYKCKKGYFYIPPLATHTICDRNHTWLPVSDDACYRETCPYIRDPLNGQAVPANGTYEFGYQMHFICNEGY-------------------------------YLIGEEILYCELKGSVAIWSGKPPICEKV-------------------------------------------------------------------------------------------------------------------------- >1nwv_A ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FRSCEVPTRLNSASLKQPYITQNYFPVGTVV-----------------------------EYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGS--------------------TSSFCLISGSSVQWSDPLP----ECREH @1vvc_ 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-------------------------------------------------------------------------------------------------------------------------------------------CEEPPTFEAMELIGKPKPYYEIG------------------------------------ERVDYKCKKGYFYIPPLATHTICDRNHTWLPVSDDACYRETCPYIRDPLNGQAVPANGTYEFGYQMHFICNEGY-------------------------------YLIGEEILYCELKGSVAIWSGKPPICEKV-------------------------------------------------------------------------------------------------------------------------- >1nwv_A --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FRSCEVPTRLNSASLKQPYITQNYFPVGTVV-----------------------------EYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGS--------------------TSSFCLISGSSVQWSDPLP----ECREH @1vvc_ 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------------------------------------------------------------------------------------------------------------------------------------------CEEPPTFEAMELIGKPKPYYEIG------------------------------------ERVDYKCKKGYFYIPPLATHTICDRNHTWLPVSDDACYRETCPYIRDPLNGQAVPANGTYEFGYQMHFICNEGY-------------------------------YLIGEEILYCELKGSVAIWSGKPPICEKV-------------------------------------------------------------------------------------------------------------------------- >1nwv_A -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FRSCEVPTRLNSASLKQPYITQNYFPVGTVV-----------------------------EYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGS--------------------TSSFCLISGSSVQWSDPLP----ECREH @1vvc_ 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-----------------------------------------------------------------------------------------------------------------------------------------CEEPPTFEAMELIGKPKPYYEIG------------------------------------ERVDYKCKKGYFYIPPLATHTICDRNHTWLPVSDDACYRETCPYIRDPLNGQAVPANGTYEFGYQMHFICNEGY-------------------------------YLIGEEILYCELKGSVAIWSGKPPICEKV-------------------------------------------------------------------------------------------------------------------------- >1nwv_A ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FRSCEVPTRLNSASLKQPYITQNYFPVGTVV-----------------------------EYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGS--------------------TSSFCLISGSSVQWSDPLP----ECREH @1vvc_ 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395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 454 455 456 457 458 459 468 469 470 473 474 475 476 478 479 480 481 482 483 484 485 486 487 488 489 490 491 493 498 499 370 371 372 373 Merge 490 491 Weight 289.302 >1vvc_ VK---CQSPPSISNGRHNGYEDFYTD----------GSVVTYSCNSG---YSLIGNSGVLCSGGEWSDPPTCQIVKC----------------------------PHPTISNGYLSSGFKRSYSYNDNVDFKCKY---------------------------------------------------------------------------------------------------------------------------------GY-----------------------------------------------------------------------------------------------------------------------------KLSGSSSSTCSPGNTWKPE-----------------------LP---KCVR----- >1ghq_B 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VK---CQSPPSISNGRHNGYEDFYTD----------GSVVTYSCNSG---YSLIGNSGVLCSGGEWSDPPTCQIVKC---------------------------PHPTISNGYLSSGFKRSYSYNDN-----------------------------------------VDFKCKY------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GY---------KLSGS------SSSTCSPGNTWKPE---------------------LP--KCVR--- >1ghq_B --AISCGSPPPILNGR----------ISYYSTPIAVGTVIRYSC---SGTFRLIGEKSLL-----------------CITKDKVDGTWDKPAPKCEYFNKYSSCPEPI------------------------------------------VPGGYKIRGSTPYRHGDSVTFACKTNFSMNGN---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KSVWCQANNMW----GPTRLP------------------TCVS--- >1ckl_A 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VK---CQSPPSISNGRHNGYEDFYTD----------GSVVTYSCNSG---YSLIGNSGVLCSGGEWSDPPTCQIVKC---------------------------PHPTISNGYLSSGFKRSYSYNDN-----------------------------------------VDFKCKY------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GY--------KLSGS------SSSTCSPGNTWKPE---------------------LP--KCVR--- >1ghq_B --AISCGSPPPILNGR----------ISYYSTPIAVGTVIRYSC---SGTFRLIGEKSLL-----------------CITKDKVDGTWDKPAPKCEYFNKYSSCPEPI------------------------------------------VPGGYKIRGSTPYRHGDSVTFACKTNFSMNGN--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KSVWCQANNMW----GPTRLP------------------TCVS--- >1ckl_A 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275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 311 312 313 314 315 316 317 319 322 323 324 325 326 327 328 329 330 331 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 218 219 220 221 222 223 224 Merge 405 404 Weight 182.791 >1vvc_ VK---CQSPPSISNGRHNGYEDFYTD----------GSVVTYSCNSG---YSLIGNSGVLCSGGEWSDPPTCQIVKC---------------------------PHPTISNGYLSSGFKRSYSYNDN-----------------------------------------VDFKCKY-----------------------------------------------------------------------------------------------------------------------------------------------------------------------G------Y-------KLSGS------SSSTCSPGNTWKPE---------------------LP--KCVR--- 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VK---CQSPPSISNGRHNGYEDFYTD----------GSVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVKC---------------------------PHPTISNGYLSSGFKRSYSYND---------------------------------------NVDFKCK------------------------------------------------------------------------------------------------------------------------------------------YGYKLS-----GS------SSSTCSPGNTWKPE---------------------LP--KCVR--- >1ghq_B --AISCGSPPPILNGR----------ISYYSTPIAVGTVIRYSCSGTFRLIGEKSLL-----------------CITKDKVDGTWDKPAPKCEYFNKYSSCPEPIV----------------------------------------PGGYKIRGSTPYRHGDSVTFACK------------------------------------------------------------------------------------------------------------------------------------------TNFSMN-----GN------KSVWCQANNMW----GPTRLP------------------TCVS--- >1ckl_A 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VK---CQSPPSISNGRHNGYEDFYTD----------GSVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVKC---------------------------PHPTISNGYLSSGFKRSYSYND---------------------------------------NVDFKCK-----------------------------------------------------------------------------------------------------------------------------------------YGYKLS-----GS------SSSTCSPGNTWKPE---------------------LP--KCVR--- >1ghq_B --AISCGSPPPILNGR----------ISYYSTPIAVGTVIRYSCSGTFRLIGEKSLL-----------------CITKDKVDGTWDKPAPKCEYFNKYSSCPEPIV----------------------------------------PGGYKIRGSTPYRHGDSVTFACK-----------------------------------------------------------------------------------------------------------------------------------------TNFSMN-----GN------KSVWCQANNMW----GPTRLP------------------TCVS--- >1ckl_A 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VK---CQSPPSISNGRHNGYEDFYTD----------GSVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVKC---------------------------PHPTISNGYLSSGFKRSYSYND---------------------------------------NVDFKCK----------------------------------------------------------------------------------------------------------------------------------------YGYKLS-----GS------SSSTCSPGNTWKPE---------------------LP--KCVR--- >1ghq_B --AISCGSPPPILNGR----------ISYYSTPIAVGTVIRYSCSGTFRLIGEKSLL-----------------CITKDKVDGTWDKPAPKCEYFNKYSSCPEPIV----------------------------------------PGGYKIRGSTPYRHGDSVTFACK----------------------------------------------------------------------------------------------------------------------------------------TNFSMN-----GN------KSVWCQANNMW----GPTRLP------------------TCVS--- >1ckl_A 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VK---CQSPPSISNGRHNGYEDFYTD----------GSVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVKC---------------------------PHPTISNGYLSSGFKRSYSYND---------------------------------------NVDFKCK---------------------------------------------------------------------------------------------------------------------------------------YGYKLS-----GS------SSSTCSPGNTWKPE---------------------LP--KCVR--- >1ghq_B --AISCGSPPPILNGR----------ISYYSTPIAVGTVIRYSCSGTFRLIGEKSLL-----------------CITKDKVDGTWDKPAPKCEYFNKYSSCPEPIV----------------------------------------PGGYKIRGSTPYRHGDSVTFACK---------------------------------------------------------------------------------------------------------------------------------------TNFSMN-----GN------KSVWCQANNMW----GPTRLP------------------TCVS--- >1ckl_A 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VK---CQSPPSISNGRHNGYEDFYTD----------GSVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVKC---------------------------PHPTISNGYLSSGFKRSYSYND---------------------------------------NVDFKCK--------------------------------------------------------------------------------------------------------------------------------------YGYKLS-----GS------SSSTCSPGNTWKPE---------------------LP--KCVR--- >1ghq_B --AISCGSPPPILNGR----------ISYYSTPIAVGTVIRYSCSGTFRLIGEKSLL-----------------CITKDKVDGTWDKPAPKCEYFNKYSSCPEPIV----------------------------------------PGGYKIRGSTPYRHGDSVTFACK--------------------------------------------------------------------------------------------------------------------------------------TNFSMN-----GN------KSVWCQANNMW----GPTRLP------------------TCVS--- >1ckl_A 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VK---CQSPPSISNGRHNGYEDFYTD----------GSVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVKC---------------------------PHPTISNGYLSSGFKRSYSYND---------------------------------------NVDFKCK-------------------------------------------------------------------------------------------------------------------------------------YGYKLS-----GS------SSSTCSPGNTWKPE---------------------LP--KCVR--- >1ghq_B --AISCGSPPPILNGR----------ISYYSTPIAVGTVIRYSCSGTFRLIGEKSLL-----------------CITKDKVDGTWDKPAPKCEYFNKYSSCPEPIV----------------------------------------PGGYKIRGSTPYRHGDSVTFACK-------------------------------------------------------------------------------------------------------------------------------------TNFSMN-----GN------KSVWCQANNMW----GPTRLP------------------TCVS--- >1ckl_A 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000000000000000000000000000000000000000000000000000000000000000000000000000310113202000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000003011000101003001001001000000000000010303110000000000000000000000000000000000000100302021011110210003100000000000000030000000110001100011010000000 Merge 44 26 Weight 41.922 >1vvc_ -VKCQSPPSISNGRHNGYEDFY-TDGS--------------------------------------------------VVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYSYN------------DNVD------------------------------------------------------------------------------------FKCKYGYKLSGS------SSSTCSPGNTWKPE------------------LP--KCVR--- >1ghq_B AISCGSPPPILNGRISYYSTP-IAVGT--------------------------------------------------VIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGG-------------YKIRGSTPYRHGDSVT------------------------------------------------------------------------------------FACKTNFSMNGN------KSVWCQANNMW----GPTRLP---------------TCVS--- >1ckl_A ---------------------------CEEPPTFEAMELIGKPKPYYE--------------------------IGERVDYKC--------------------------------------------------------------------------------------------KKGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDPLNGQAVPANGTYEF------------------GYQMHFICNEGYYLIGEEILYCE--------------L------KGSVAIWSGKP-PIC----EKV >1nwv_A ------------------------------------------------FRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYEC--------------------------------------------------------------------------------------------RPGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP-------------------NPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGSTSSFCL--------------I------SGSSVQWSDP-LPEC----REH @1vvc_ 03010111010111000100000001300000000000000000000000000000000000000000000000000110212000301110003110000000000000000000000000000000000000000110103001000000000000000000000000010100000000000000000000000000000000000000000000000000000000000000000000000000000000000002020011110210000000100100010100000000000000000000011000110000 @1ghq_B 03010111010111000100000001300000000000000000000000000000000000000000000000000130212000301110003110000000000000000000000000000000000000000110103001000000000000000000000000010100000000000000000000000000000000000000000000000000000000000000000000000000000000000002020003030200000000100100010100000000000000000000000000110000 @1ckl_A 00000000000000000000000000000000000000000000000000000000000000000000000000310013202000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000003011000101003001001001000000000000010303110000000000000000000000000000000000000100302021011010200003100000000000000030000000110001100001010000000 @1nwv_A 00000000000000000000000000000000000000000000000000000000000000000000000000310113202000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000003011000101003001001001000000000000010303110000000000000000000000000000000000000100302021011110210003100000000000000030000000110001100011010000000 Merge 27 45 Weight 41.733 >1vvc_ -VKCQSPPSISNGRHNGYEDFYTDGS--------------------------------------------------VVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYSYN------------DNVD------------------------------------------------------------------------------------FKCKYGYKLSGS------SSSTCSPGNTWKPE------------------LP--KCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIAVGT--------------------------------------------------VIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGG-------------YKIRGSTPYRHGDSVT------------------------------------------------------------------------------------FACKTNFSMNGN------KSVWCQANNMW----GPTRLP---------------TCVS--- >1ckl_A --------------------------CEEPPTFEAMELIGKPKPYYE--------------------------IGERVDYKC--------------------------------------------------------------------------------------------KKGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDPLNGQAVPANGTYEF------------------GYQMHFICNEGYYLIGEEILYCE--------------L------KGSVAIWSGKP-PIC----EKV >1nwv_A -----------------------------------------------FRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYEC--------------------------------------------------------------------------------------------RPGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP-------------------NPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGSTSSFCL--------------I------SGSSVQWSDP-LPEC----REH @1vvc_ 0301011101011100010000001300000000000000000000000000000000000000000000000000110212000301110003110000000000000000000000000000000000000000110103001000000000000000000000000010100000000000000000000000000000000000000000000000000000000000000000000000000000000000002020011110210000000100100010100000000000000000000011000110000 @1ghq_B 0301011101011100010000001300000000000000000000000000000000000000000000000000130212000301110003110000000000000000000000000000000000000000110103001000000000000000000000000010100000000000000000000000000000000000000000000000000000000000000000000000000000000000002020003030200000000100100010100000000000000000000000000110000 @1ckl_A 0000000000000000000000000000000000000000000000000000000000000000000000000310013202000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000003011000101003001001001000000000000010303110000000000000000000000000000000000000100302021011010200003100000000000000030000000110001100001010000000 @1nwv_A 0000000000000000000000000000000000000000000000000000000000000000000000000310113202000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000003011000101003001001001000000000000010303110000000000000000000000000000000000000100302021011110210003100000000000000030000000110001100011010000000 Merge 482 487 Weight 40.5234 >1vvc_ -VKCQSPPSISNGRHNGYEDFYTDGS--------------------------------------------------VVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYSYN------------DNVD------------------------------------------------------------------------------------FKCKYGYKLSGS------SSSTCSPGNTWKPE-----------------LP--KCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIAVGT--------------------------------------------------VIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGG-------------YKIRGSTPYRHGDSVT------------------------------------------------------------------------------------FACKTNFSMNGN------KSVWCQANNMW----GPTRLP--------------TCVS--- >1ckl_A --------------------------CEEPPTFEAMELIGKPKPYYE--------------------------IGERVDYKC--------------------------------------------------------------------------------------------KKGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDPLNGQAVPANGTYEF------------------GYQMHFICNEGYYLIGEEILYCE--------------L------KGSVAIWSGKPPIC----EKV >1nwv_A -----------------------------------------------FRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYEC--------------------------------------------------------------------------------------------RPGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP-------------------NPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGSTSSFCL--------------I------SGSSVQWSDPLPEC----REH @1vvc_ 030101110101110001000000130000000000000000000000000000000000000000000000000011021200030111000311000000000000000000000000000000000000000011010300100000000000000000000000001010000000000000000000000000000000000000000000000000000000000000000000000000000000000000202001111021000000010010001010000000000000000000011000110000 @1ghq_B 030101110101110001000000130000000000000000000000000000000000000000000000000013021200030111000311000000000000000000000000000000000000000011010300100000000000000000000000001010000000000000000000000000000000000000000000000000000000000000000000000000000000000000202000303020000000010010001010000000000000000000000000110000 @1ckl_A 000000000000000000000000000000000000000000000000000000000000000000000000031001320200000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000301100010100300100100100000000000001030311000000000000000000000000000000000000010030202101101020000310000000000000003000000011000110001010000000 @1nwv_A 000000000000000000000000000000000000000000000000000000000000000000000000031011320200000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000301100010100300100100100000000000001030311000000000000000000000000000000000000010030202101111021000310000000000000003000000011000110011010000000 Reorder 376 377 378 379 380 381 382 383 353 354 355 356 357 358 359 360 361 362 363 364 Merge 360 361 Weight 39.1536 >1vvc_ -VKCQSPPSISNGRHNGYEDFYTDGS--------------------------------------------------VVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYSYN------------DNVD-----------------------------------------------------------------------------------FKCKYGYKLSGS------SSSTCSPGNTWKPE-----------------LP--KCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIAVGT--------------------------------------------------VIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGG-------------YKIRGSTPYRHGDSVT-----------------------------------------------------------------------------------FACKTNFSMNGN------KSVWCQANNMW----GPTRLP--------------TCVS--- >1ckl_A --------------------------CEEPPTFEAMELIGKPKPYYE--------------------------IGERVDYKC--------------------------------------------------------------------------------------------KKGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDPLN-------GQAVPANGTYEF----------GYQMHFICNEGYYLIGEEILYCE--------------L------KGSVAIWSGKPPIC----EKV >1nwv_A -----------------------------------------------FRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYEC--------------------------------------------------------------------------------------------RPGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP-------NPGEIRNG-----------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL--------------I------SGSSVQWSDPLPEC----REH @1vvc_ 03010111010111000100000013000000000000000000000000000000000000000000000000001102120003011100031100000000000000000000000000000000000000001101030010000000000000000000000000101000000000000000000000000000000000000000000000000000000000000000000000000000000000000202001111021000000010010001010000000000000000000011000110000 @1ghq_B 03010111010111000100000013000000000000000000000000000000000000000000000000001302120003011100031100000000000000000000000000000000000000001101030010000000000000000000000000101000000000000000000000000000000000000000000000000000000000000000000000000000000000000202000303020000000010010001010000000000000000000000000110000 @1ckl_A 00000000000000000000000000000000000000000000000000000000000000000000000003100132020000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000030110001010030010010010000000000000103031100000000000000100000000000000000000010030202101101020000310000000000000003000000011000110001010000000 @1nwv_A 00000000000000000000000000000000000000000000000000000000000000000000000003101132020000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000030110001010030010010010000000000000103031100000000000000100000000000000000000010030202101111021000310000000000000003000000011000110011010000000 Reorder 82 83 84 85 52 53 54 55 56 57 62 63 64 66 68 70 72 74 75 76 77 78 79 80 81 Merge 55 56 Weight 39.1252 >1vvc_ -VKCQSPPSISNGRHNGYEDFYTDGS-------------------------------------------------VVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYSYN------------DNVD-----------------------------------------------------------------------------------FKCKYGYKLSGS------SSSTCSPGNTWKPE-----------------LP--KCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIAVGT-------------------------------------------------VIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGG-------------YKIRGSTPYRHGDSVT-----------------------------------------------------------------------------------FACKTNFSMNGN------KSVWCQANNMW----GPTRLP--------------TCVS--- >1ckl_A -----------------------------CEEPPTFEAMELIGKPKPYYE----------------------IGERVDYKC--------------------------------------------------------------------------------------------KKGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDPLN-------GQAVPANGTYEF----------GYQMHFICNEGYYLIGEEILYCE--------------L------KGSVAIWSGKPPIC----EKV >1nwv_A --------------------------FRSC--------------------EVPTRLNSASLKQPYITQNYFPVGTVVEYEC--------------------------------------------------------------------------------------------RPGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP-------NPGEIRNG-----------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL--------------I------SGSSVQWSDPLPEC----REH @1vvc_ 0301011101011100010000001300000000000000000000000000000000000000000000000001102120003011100031100000000000000000000000000000000000000001101030010000000000000000000000000101000000000000000000000000000000000000000000000000000000000000000000000000000000000000202001111021000000010010001010000000000000000000011000110000 @1ghq_B 0301011101011100010000001300000000000000000000000000000000000000000000000001302120003011100031100000000000000000000000000000000000000001101030010000000000000000000000000101000000000000000000000000000000000000000000000000000000000000000000000000000000000000202000303020000000010010001010000000000000000000000000110000 @1ckl_A 0000000000000000000000000000010000000000000000000000000000000000000000003100132020000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000030110001010030010010010000000000000103031100000000000000100000000000000000000010030202101101020000310000000000000003000000011000110001010000000 @1nwv_A 0000000000000000000000000000010000000000000000000000000000000000000000003101132020000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000030110001010030010010010000000000000103031100000000000000100000000000000000000010030202101111021000310000000000000003000000011000110011010000000 Merge 243 220 Weight 38.5744 >1vvc_ -VKCQSPPSISNGRHNGYEDFYTDGS-------------------------------------------------VVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYSYN-----------DNVD-----------------------------------------------------------------------------------FKCKYGYKLSGS------SSSTCSPGNTWKPE-----------------LP--KCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIAVGT-------------------------------------------------VIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGY------------KIRGSTPYRHGDSVT-----------------------------------------------------------------------------------FACKTNFSMNGN------KSVWCQANNMW----GPTRLP--------------TCVS--- >1ckl_A -----------------------------CEEPPTFEAMELIGKPKPYYE----------------------IGERVDYKC-------------------------------------------------------------------------------------------KKGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDPLN-------GQAVPANGTYEF----------GYQMHFICNEGYYLIGEEILYCE--------------L------KGSVAIWSGKPPIC----EKV >1nwv_A --------------------------FRSC--------------------EVPTRLNSASLKQPYITQNYFPVGTVVEYEC-------------------------------------------------------------------------------------------RPGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP-------NPGEIRNG-----------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL--------------I------SGSSVQWSDPLPEC----REH @1vvc_ 030101110101110001000000130000000000000000000000000000000000000000000000000110212000301110003110000000000000000000000000000000000000000110103001100000000000000000000000101000000000000000000000000000000000000000000000000000000000000000000000000000000000000202001111021000000010010001010000000000000000000011000110000 @1ghq_B 030101110101110001000000130000000000000000000000000000000000000000000000000130212000301110003110000000000000000000000000000000000000000110103001100000000000000000000000101000000000000000000000000000000000000000000000000000000000000000000000000000000000000202000303020000000010010001010000000000000000000000000110000 @1ckl_A 000000000000000000000000000001000000000000000000000000000000000000000000310013202000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000030110001010030010010010000000000000103031100000000000000100000000000000000000010030202101101020000310000000000000003000000011000110001010000000 @1nwv_A 000000000000000000000000000001000000000000000000000000000000000000000000310113202000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000030110001010030010010010000000000000103031100000000000000100000000000000000000010030202101111021000310000000000000003000000011000110011010000000 Merge 444 438 Weight 36.3599 >1vvc_ -VKCQSPPSISNGRHNGYEDFYTDGS-------------------------------------------------VVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYSYN-----------DNVD-----------------------------------------------------------------------------------FKCKYGYKLSGSS-----SSTCSPGNTWKPE-----------------LP--KCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIAVGT-------------------------------------------------VIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGY------------KIRGSTPYRHGDSVT-----------------------------------------------------------------------------------FACKTNFSMNGNK-----SVWCQANNMW----GPTRLP--------------TCVS--- >1ckl_A -----------------------------CEEPPTFEAMELIGKPKPYYE----------------------IGERVDYKC-------------------------------------------------------------------------------------------KKGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDPLN-------GQAVPANGTYEF----------GYQMHFICNEGYYLIGEEILYCE-------------L------KGSVAIWSGKPPIC----EKV >1nwv_A --------------------------FRSC--------------------EVPTRLNSASLKQPYITQNYFPVGTVVEYEC-------------------------------------------------------------------------------------------RPGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP-------NPGEIRNG-----------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL-------------I------SGSSVQWSDPLPEC----REH @1vvc_ 03010111010111000100000013000000000000000000000000000000000000000000000000011021200030111000311000000000000000000000000000000000000000011010300110000000000000000000000010100000000000000000000000000000000000000000000000000000000000000000000000000000000000020200111102100000010010001010000000000000000000011000110000 @1ghq_B 03010111010111000100000013000000000000000000000000000000000000000000000000013021200030111000311000000000000000000000000000000000000000011010300110000000000000000000000010100000000000000000000000000000000000000000000000000000000000000000000000000000000000020200030302000000010010001010000000000000000000000000110000 @1ckl_A 00000000000000000000000000000100000000000000000000000000000000000000000031001320200000000000000000000000000000000000000000000000000000000000000000000000000000000000000000003011000101003001001001000000000000010303110000000000000010000000000000000000001003020210110102000031000000000000003000000011000110001010000000 @1nwv_A 00000000000000000000000000000100000000000000000000000000000000000000000031011320200000000000000000000000000000000000000000000000000000000000000000000000000000000000000000003011000101003001001001000000000000010303110000000000000010000000000000000000001003020210111102100031000000000000003000000011000110011010000000 Merge 352 359 Weight 36.1508 >1vvc_ -VKCQSPPSISNGRHNGYEDFYTDGS-------------------------------------------------VVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYSYN-----------DNVD----------------------------------------------------------------------------------FKCKYGYKLSGSS-----SSTCSPGNTWKPE-----------------LP--KCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIAVGT-------------------------------------------------VIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGY------------KIRGSTPYRHGDSVT----------------------------------------------------------------------------------FACKTNFSMNGNK-----SVWCQANNMW----GPTRLP--------------TCVS--- >1ckl_A -----------------------------CEEPPTFEAMELIGKPKPYYE----------------------IGERVDYKC-------------------------------------------------------------------------------------------KKGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDPL------NGQAVPANGTYEF----------GYQMHFICNEGYYLIGEEILYCE-------------L------KGSVAIWSGKPPIC----EKV >1nwv_A --------------------------FRSC--------------------EVPTRLNSASLKQPYITQNYFPVGTVVEYEC-------------------------------------------------------------------------------------------RPGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP------NPGEIRNG-----------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL-------------I------SGSSVQWSDPLPEC----REH @1vvc_ 0301011101011100010000001300000000000000000000000000000000000000000000000001102120003011100031100000000000000000000000000000000000000001101030011000000000000000000000001010000000000000000000000000000000000000000000000000000000000000000000000000000000000020200111102100000010010001010000000000000000000011000110000 @1ghq_B 0301011101011100010000001300000000000000000000000000000000000000000000000001302120003011100031100000000000000000000000000000000000000001101030011000000000000000000000001010000000000000000000000000000000000000000000000000000000000000000000000000000000000020200030302000000010010001010000000000000000000000000110000 @1ckl_A 0000000000000000000000000000010000000000000000000000000000000000000000003100132020000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000301100010100300100100100000000000001030311000000000000110000000000000000000001003020210110102000031000000000000003000000011000110001010000000 @1nwv_A 0000000000000000000000000000010000000000000000000000000000000000000000003101132020000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000301100010100300100100100000000000001030311000000000000110000000000000000000001003020210111102100031000000000000003000000011000110011010000000 Merge 458 481 Weight 34.2327 >1vvc_ -VKCQSPPSISNGRHNGYEDFYTDGS-------------------------------------------------VVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYSYN-----------DNVD----------------------------------------------------------------------------------FKCKYGYKLSGSS-----SSTCSPGNTWKP----------------ELP--KCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIAVGT-------------------------------------------------VIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGY------------KIRGSTPYRHGDSVT----------------------------------------------------------------------------------FACKTNFSMNGNK-----SVWCQANNMW---GPTRLP--------------TCVS--- >1ckl_A -----------------------------CEEPPTFEAMELIGKPKPYYE----------------------IGERVDYKC-------------------------------------------------------------------------------------------KKGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDPL------NGQAVPANGTYEF----------GYQMHFICNEGYYLIGEEILYCE------------L------KGSVAIWSGKPPIC----EKV >1nwv_A --------------------------FRSC--------------------EVPTRLNSASLKQPYITQNYFPVGTVVEYEC-------------------------------------------------------------------------------------------RPGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP------NPGEIRNG-----------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL------------I------SGSSVQWSDPLPEC----REH @1vvc_ 030101110101110001000000130000000000000000000000000000000000000000000000000110212000301110003110000000000000000000000000000000000000000110103001100000000000000000000000101000000000000000000000000000000000000000000000000000000000000000000000000000000000002020011110210000001001000101000000000000000000011000110000 @1ghq_B 030101110101110001000000130000000000000000000000000000000000000000000000000130212000301110003110000000000000000000000000000000000000000110103001100000000000000000000000101000000000000000000000000000000000000000000000000000000000000000000000000000000000002020003030200000001001000101000000000000000000000000110000 @1ckl_A 000000000000000000000000000001000000000000000000000000000000000000000000310013202000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000030110001010030010010010000000000000103031100000000000011000000000000000000000100302021011010200003100000000000003000000011000110001010000000 @1nwv_A 000000000000000000000000000001000000000000000000000000000000000000000000310113202000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000030110001010030010010010000000000000103031100000000000011000000000000000000000100302021011110210003100000000000003000000011000110011010000000 Merge 383 393 Weight 33.9905 >1vvc_ -VKCQSPPSISNGRHNGYEDFYTDGS-------------------------------------------------VVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYSYN-----------DNVD---------------------------------------------------------------------------------FKCKYGYKLSGSS-----SSTCSPGNTWKP----------------ELP--KCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIAVGT-------------------------------------------------VIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGY------------KIRGSTPYRHGDSVT---------------------------------------------------------------------------------FACKTNFSMNGNK-----SVWCQANNMW---GPTRLP--------------TCVS--- >1ckl_A -----------------------------CEEPPTFEAMELIGKPKPYYE----------------------IGERVDYKC-------------------------------------------------------------------------------------------KKGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDPL------NGQAVPANGTYE---------FGYQMHFICNEGYYLIGEEILYCE------------L------KGSVAIWSGKPPIC----EKV >1nwv_A --------------------------FRSC--------------------EVPTRLNSASLKQPYITQNYFPVGTVVEYEC-------------------------------------------------------------------------------------------RPGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP------NPGEIRNG----------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL------------I------SGSSVQWSDPLPEC----REH @1vvc_ 03010111010111000100000013000000000000000000000000000000000000000000000000011021200030111000311000000000000000000000000000000000000000011010300110000000000000000000000010100000000000000000000000000000000000000000000000000000000000000000000000000000000002020011110210000001001000101000000000000000000011000110000 @1ghq_B 03010111010111000100000013000000000000000000000000000000000000000000000000013021200030111000311000000000000000000000000000000000000000011010300110000000000000000000000010100000000000000000000000000000000000000000000000000000000000000000000000000000000002020003030200000001001000101000000000000000000000000110000 @1ckl_A 00000000000000000000000000000100000000000000000000000000000000000000000031001320200000000000000000000000000000000000000000000000000000000000000000000000000000000000000000003011000101003001001001000000000000010303110000000000001100000000000000000001100302021011010200003100000000000003000000011000110001010000000 @1nwv_A 00000000000000000000000000000100000000000000000000000000000000000000000031011320200000000000000000000000000000000000000000000000000000000000000000000000000000000000000000003011000101003001001001000000000000010303110000000000001100000000000000000001100302021011110210003100000000000003000000011000110011010000000 Merge 50 123 Weight 33.9547 >1vvc_ -VKCQSPPSISNGRHNGYEDFYTDG------------------------------------------------SVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYSYN-----------DNVD---------------------------------------------------------------------------------FKCKYGYKLSGSS-----SSTCSPGNTWKP----------------ELP--KCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIAVG------------------------------------------------TVIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGY------------KIRGSTPYRHGDSVT---------------------------------------------------------------------------------FACKTNFSMNGNK-----SVWCQANNMW---GPTRLP--------------TCVS--- >1ckl_A ----------------------------CEEPPTFEAMELIGKPKPYYE----------------------IGERVDYKC-------------------------------------------------------------------------------------------KKGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDPL------NGQAVPANGTYE---------FGYQMHFICNEGYYLIGEEILYCE------------L------KGSVAIWSGKPPIC----EKV >1nwv_A -------------------------FRSC--------------------EVPTRLNSASLKQPYITQNYFPVGTVVEYEC-------------------------------------------------------------------------------------------RPGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP------NPGEIRNG----------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL------------I------SGSSVQWSDPLPEC----REH @1vvc_ 0301011101011100010000001000000000000000000000000000000000000000000000000311021200030111000311000000000000000000000000000000000000000011010300110000000000000000000000010100000000000000000000000000000000000000000000000000000000000000000000000000000000002020011110210000001001000101000000000000000000011000110000 @1ghq_B 0301011101011100010000001000000000000000000000000000000000000000000000000313021200030111000311000000000000000000000000000000000000000011010300110000000000000000000000010100000000000000000000000000000000000000000000000000000000000000000000000000000000002020003030200000001001000101000000000000000000000000110000 @1ckl_A 0000000000000000000000000000100000000000000000000000000000000000000000031001320200000000000000000000000000000000000000000000000000000000000000000000000000000000000000000003011000101003001001001000000000000010303110000000000001100000000000000000001100302021011010200003100000000000003000000011000110001010000000 @1nwv_A 0000000000000000000000000000100000000000000000000000000000000000000000031311320200000000000000000000000000000000000000000000000000000000000000000000000000000000000000000003011000101003001001001000000000000010303110000000000001100000000000000000001100302021011110210003100000000000003000000011000110011010000000 Merge 86 57 Weight 33.5364 >1vvc_ -VKCQSPPSISNGRHNGYEDFYTDG-----------------------------------------------SVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYSYN-----------DNVD---------------------------------------------------------------------------------FKCKYGYKLSGSS-----SSTCSPGNTWKP----------------ELP--KCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIAVG-----------------------------------------------TVIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGY------------KIRGSTPYRHGDSVT---------------------------------------------------------------------------------FACKTNFSMNGNK-----SVWCQANNMW---GPTRLP--------------TCVS--- >1ckl_A ----------------------------CEEPPTFEAMELIGKPKPYYE---------------------IGERVDYKC-------------------------------------------------------------------------------------------KKGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDPL------NGQAVPANGTYE---------FGYQMHFICNEGYYLIGEEILYCE------------L------KGSVAIWSGKPPIC----EKV >1nwv_A -------------------------FRSCE-------------------VPTRLNSASLKQPYITQNYFPVGTVVEYEC-------------------------------------------------------------------------------------------RPGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP------NPGEIRNG----------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL------------I------SGSSVQWSDPLPEC----REH @1vvc_ 030101110101110001000000100000000000000000000000000000000000000000000000311021200030111000311000000000000000000000000000000000000000011010300110000000000000000000000010100000000000000000000000000000000000000000000000000000000000000000000000000000000002020011110210000001001000101000000000000000000011000110000 @1ghq_B 030101110101110001000000100000000000000000000000000000000000000000000000313021200030111000311000000000000000000000000000000000000000011010300110000000000000000000000010100000000000000000000000000000000000000000000000000000000000000000000000000000000002020003030200000001001000101000000000000000000000000110000 @1ckl_A 000000000000000000000000000011000000000000000000000000000000000000000031001320200000000000000000000000000000000000000000000000000000000000000000000000000000000000000000003011000101003001001001000000000000010303110000000000001100000000000000000001100302021011010200003100000000000003000000011000110001010000000 @1nwv_A 000000000000000000000000000011000000000000000000000000000000000000000031311320200000000000000000000000000000000000000000000000000000000000000000000000000000000000000000003011000101003001001001000000000000010303110000000000001100000000000000000001100302021011110210003100000000000003000000011000110011010000000 Reorder 52 53 54 56 57 62 63 10 11 12 13 14 16 18 19 20 21 22 23 24 25 26 45 46 47 49 Merge 18 19 Weight 31.481 >1vvc_ -VKCQS------PPSISNGRHNGYEDFYTDG----------------------------------------SVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYSYN-----------DNVD---------------------------------------------------------------------------------FKCKYGYKLSGSS-----SSTCSPGNTWKP----------------ELP--KCVR--- >1ghq_B AISCGS------PPPILNGRISYYSTPIAVG----------------------------------------TVIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGY------------KIRGSTPYRHGDSVT---------------------------------------------------------------------------------FACKTNFSMNGNK-----SVWCQANNMW---GPTRLP--------------TCVS--- >1ckl_A ---------CEEP------------------PTFEAMELIGKPKPYYE---------------------IGERVDYKC-------------------------------------------------------------------------------------------KKGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDPL------NGQAVPANGTYE---------FGYQMHFICNEGYYLIGEEILYCE------------L------KGSVAIWSGKPPIC----EKV >1nwv_A ------FRSCE-------------------------------------VPTRLNSASLKQPYITQNYFPVGTVVEYEC-------------------------------------------------------------------------------------------RPGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP------NPGEIRNG----------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL------------I------SGSSVQWSDPLPEC----REH @1vvc_ 03010100000011010111000100000010000000000000000000000000000000000000000311021200030111000311000000000000000000000000000000000000000011010300110000000000000000000000010100000000000000000000000000000000000000000000000000000000000000000000000000000000002020011110210000001001000101000000000000000000011000110000 @1ghq_B 03010100000011010111000100000010000000000000000000000000000000000000000313021200030111000311000000000000000000000000000000000000000011010300110000000000000000000000010100000000000000000000000000000000000000000000000000000000000000000000000000000000002020003030200000001001000101000000000000000000000000110000 @1ckl_A 00000000011010000000000000000000000000000000000000000000000000000000031001320200000000000000000000000000000000000000000000000000000000000000000000000000000000000000000003011000101003001001001000000000000010303110000000000001100000000000000000001100302021011010200003100000000000003000000011000110001010000000 @1nwv_A 00000000011000000000000000000000000000000000000000000000000000000000031311320200000000000000000000000000000000000000000000000000000000000000000000000000000000000000000003011000101003001001001000000000000010303110000000000001100000000000000000001100302021011110210003100000000000003000000011000110011010000000 Merge 242 257 Weight 31.1674 >1vvc_ -VKCQS------PPSISNGRHNGYEDFYTDG----------------------------------------SVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYSY----------NDNVD---------------------------------------------------------------------------------FKCKYGYKLSGSS-----SSTCSPGNTWKP----------------ELP--KCVR--- >1ghq_B AISCGS------PPPILNGRISYYSTPIAVG----------------------------------------TVIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGY-----------KIRGSTPYRHGDSVT---------------------------------------------------------------------------------FACKTNFSMNGNK-----SVWCQANNMW---GPTRLP--------------TCVS--- >1ckl_A ---------CEEP------------------PTFEAMELIGKPKPYYE---------------------IGERVDYKC------------------------------------------------------------------------------------------KKGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDPL------NGQAVPANGTYE---------FGYQMHFICNEGYYLIGEEILYCE------------L------KGSVAIWSGKPPIC----EKV >1nwv_A ------FRSCE-------------------------------------VPTRLNSASLKQPYITQNYFPVGTVVEYEC------------------------------------------------------------------------------------------RPGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP------NPGEIRNG----------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL------------I------SGSSVQWSDPLPEC----REH @1vvc_ 0301010000001101011100010000001000000000000000000000000000000000000000031102120003011100031100000000000000000000000000000000000000001101030011000000000000000000000010100000000000000000000000000000000000000000000000000000000000000000000000000000000002020011110210000001001000101000000000000000000011000110000 @1ghq_B 0301010000001101011100010000001000000000000000000000000000000000000000031302120003011100031100000000000000000000000000000000000000001101030011000000000000000000000010100000000000000000000000000000000000000000000000000000000000000000000000000000000002020003030200000001001000101000000000000000000000000110000 @1ckl_A 0000000001101000000000000000000000000000000000000000000000000000000003100132020000000000000000000000000000000000000000000000000000000000000000000000000000000000000000003011000101003001001001000000000000010303110000000000001100000000000000000001100302021011010200003100000000000003000000011000110001010000000 @1nwv_A 0000000001100000000000000000000000000000000000000000000000000000000003131132020000000000000000000000000000000000000000000000000000000000000000000000000000000000000000003011000101003001001001000000000000010303110000000000001100000000000000000001100302021011110210003100000000000003000000011000110011010000000 Merge 9 16 Weight 30.697 >1vvc_ -VKCQ-----SPPSISNGRHNGYEDFYTDG----------------------------------------SVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYSY----------NDNVD---------------------------------------------------------------------------------FKCKYGYKLSGSS-----SSTCSPGNTWKP----------------ELP--KCVR--- >1ghq_B AISCG-----SPPPILNGRISYYSTPIAVG----------------------------------------TVIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGY-----------KIRGSTPYRHGDSVT---------------------------------------------------------------------------------FACKTNFSMNGNK-----SVWCQANNMW---GPTRLP--------------TCVS--- >1ckl_A --------CEEP------------------PTFEAMELIGKPKPYYE---------------------IGERVDYKC------------------------------------------------------------------------------------------KKGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDPL------NGQAVPANGTYE---------FGYQMHFICNEGYYLIGEEILYCE------------L------KGSVAIWSGKPPIC----EKV >1nwv_A -----FRSCE-------------------------------------VPTRLNSASLKQPYITQNYFPVGTVVEYEC------------------------------------------------------------------------------------------RPGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP------NPGEIRNG----------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL------------I------SGSSVQWSDPLPEC----REH @1vvc_ 030100000011101011100010000001000000000000000000000000000000000000000031102120003011100031100000000000000000000000000000000000000001101030011000000000000000000000010100000000000000000000000000000000000000000000000000000000000000000000000000000000002020011110210000001001000101000000000000000000011000110000 @1ghq_B 030100000011101011100010000001000000000000000000000000000000000000000031302120003011100031100000000000000000000000000000000000000001101030011000000000000000000000010100000000000000000000000000000000000000000000000000000000000000000000000000000000002020003030200000001001000101000000000000000000000000110000 @1ckl_A 000000001101000000000000000000000000000000000000000000000000000000003100132020000000000000000000000000000000000000000000000000000000000000000000000000000000000000000003011000101003001001001000000000000010303110000000000001100000000000000000001100302021011010200003100000000000003000000011000110001010000000 @1nwv_A 000000001100000000000000000000000000000000000000000000000000000000003131132020000000000000000000000000000000000000000000000000000000000000000000000000000000000000000003011000101003001001001000000000000010303110000000000001100000000000000000001100302021011110210003100000000000003000000011000110011010000000 Merge 445 439 Weight 29.039 >1vvc_ -VKCQ-----SPPSISNGRHNGYEDFYTDG----------------------------------------SVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYSY----------NDNVD---------------------------------------------------------------------------------FKCKYGYKLSGSSS----STCSPGNTWKP----------------ELP--KCVR--- >1ghq_B AISCG-----SPPPILNGRISYYSTPIAVG----------------------------------------TVIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGY-----------KIRGSTPYRHGDSVT---------------------------------------------------------------------------------FACKTNFSMNGNKS----VWCQANNMW---GPTRLP--------------TCVS--- >1ckl_A --------CEEP------------------PTFEAMELIGKPKPYYE---------------------IGERVDYKC------------------------------------------------------------------------------------------KKGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDPL------NGQAVPANGTYE---------FGYQMHFICNEGYYLIGEEILYCE-----------L------KGSVAIWSGKPPIC----EKV >1nwv_A -----FRSCE-------------------------------------VPTRLNSASLKQPYITQNYFPVGTVVEYEC------------------------------------------------------------------------------------------RPGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP------NPGEIRNG----------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL-----------I------SGSSVQWSDPLPEC----REH @1vvc_ 03010000001110101110001000000100000000000000000000000000000000000000003110212000301110003110000000000000000000000000000000000000000110103001100000000000000000000001010000000000000000000000000000000000000000000000000000000000000000000000000000000000202001111021010000001000101000000000000000000011000110000 @1ghq_B 03010000001110101110001000000100000000000000000000000000000000000000003130212000301110003110000000000000000000000000000000000000000110103001100000000000000000000001010000000000000000000000000000000000000000000000000000000000000000000000000000000000202000303020010000001000101000000000000000000000000110000 @1ckl_A 00000000110100000000000000000000000000000000000000000000000000000000310013202000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000301100010100300100100100000000000001030311000000000000110000000000000000000110030202101101020000310000000000003000000011000110001010000000 @1nwv_A 00000000110000000000000000000000000000000000000000000000000000000000313113202000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000301100010100300100100100000000000001030311000000000000110000000000000000000110030202101111021010310000000000003000000011000110011010000000 Merge 85 120 Weight 28.6983 >1vvc_ -VKCQ-----SPPSISNGRHNGYEDFYTDG---------------------------------------SVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYSY----------NDNVD---------------------------------------------------------------------------------FKCKYGYKLSGSSS----STCSPGNTWKP----------------ELP--KCVR--- >1ghq_B AISCG-----SPPPILNGRISYYSTPIAVG---------------------------------------TVIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGY-----------KIRGSTPYRHGDSVT---------------------------------------------------------------------------------FACKTNFSMNGNKS----VWCQANNMW---GPTRLP--------------TCVS--- >1ckl_A --------CEEP------------------PTFEAMELIGKPKPYY--------------------EIGERVDYKC------------------------------------------------------------------------------------------KKGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDPL------NGQAVPANGTYE---------FGYQMHFICNEGYYLIGEEILYCE-----------L------KGSVAIWSGKPPIC----EKV >1nwv_A -----FRSCE------------------------------------VPTRLNSASLKQPYITQNYFPVGTVVEYEC------------------------------------------------------------------------------------------RPGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP------NPGEIRNG----------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL-----------I------SGSSVQWSDPLPEC----REH @1vvc_ 0301000000111010111000100000010000000000000000000000000000000000000003110212000301110003110000000000000000000000000000000000000000110103001100000000000000000000001010000000000000000000000000000000000000000000000000000000000000000000000000000000000202001111021010000001000101000000000000000000011000110000 @1ghq_B 0301000000111010111000100000010000000000000000000000000000000000000003130212000301110003110000000000000000000000000000000000000000110103001100000000000000000000001010000000000000000000000000000000000000000000000000000000000000000000000000000000000202000303020010000001000101000000000000000000000000110000 @1ckl_A 0000000011010000000000000000000000000000000000000000000000000000000310013202000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000301100010100300100100100000000000001030311000000000000110000000000000000000110030202101101020000310000000000003000000011000110001010000000 @1nwv_A 0000000011000000000000000000000000000000000000000000000000000000000313113202000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000301100010100300100100100000000000001030311000000000000110000000000000000000110030202101111021010310000000000003000000011000110011010000000 Merge 457 462 Weight 28.647 >1vvc_ -VKCQ-----SPPSISNGRHNGYEDFYTDG---------------------------------------SVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYSY----------NDNVD---------------------------------------------------------------------------------FKCKYGYKLSGSSS----STCSPGNTWK--P-------------ELP--KCVR--- >1ghq_B AISCG-----SPPPILNGRISYYSTPIAVG---------------------------------------TVIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGY-----------KIRGSTPYRHGDSVT---------------------------------------------------------------------------------FACKTNFSMNGNKS----VWCQANNMW--GPTRLP--------------TCVS--- >1ckl_A --------CEEP------------------PTFEAMELIGKPKPYY--------------------EIGERVDYKC------------------------------------------------------------------------------------------KKGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDPL------NGQAVPANGTYE---------FGYQMHFICNEGYYLIGEEILYCE----------L------KGSVAIWSGKPPIC----EKV >1nwv_A -----FRSCE------------------------------------VPTRLNSASLKQPYITQNYFPVGTVVEYEC------------------------------------------------------------------------------------------RPGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP------NPGEIRNG----------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL----------I------SGSSVQWSDPLPEC----REH @1vvc_ 030100000011101011100010000001000000000000000000000000000000000000000311021200030111000311000000000000000000000000000000000000000011010300110000000000000000000000101000000000000000000000000000000000000000000000000000000000000000000000000000000000020200111102101000000100010100010000000000000011000110000 @1ghq_B 030100000011101011100010000001000000000000000000000000000000000000000313021200030111000311000000000000000000000000000000000000000011010300110000000000000000000000101000000000000000000000000000000000000000000000000000000000000000000000000000000000020200030302001000000100010100010000000000000000000110000 @1ckl_A 000000001101000000000000000000000000000000000000000000000000000000031001320200000000000000000000000000000000000000000000000000000000000000000000000000000000000000000030110001010030010010010000000000000103031100000000000011000000000000000000011003020210110102000031000000000003000000011000110001010000000 @1nwv_A 000000001100000000000000000000000000000000000000000000000000000000031311320200000000000000000000000000000000000000000000000000000000000000000000000000000000000000000030110001010030010010010000000000000103031100000000000011000000000000000000011003020210111102101031000000000003000000011000110011010000000 Merge 351 358 Weight 27.9839 >1vvc_ -VKCQ-----SPPSISNGRHNGYEDFYTDG---------------------------------------SVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYSY----------NDNVD--------------------------------------------------------------------------------FKCKYGYKLSGSSS----STCSPGNTWK--P-------------ELP--KCVR--- >1ghq_B AISCG-----SPPPILNGRISYYSTPIAVG---------------------------------------TVIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGY-----------KIRGSTPYRHGDSVT--------------------------------------------------------------------------------FACKTNFSMNGNKS----VWCQANNMW--GPTRLP--------------TCVS--- >1ckl_A --------CEEP------------------PTFEAMELIGKPKPYY--------------------EIGERVDYKC------------------------------------------------------------------------------------------KKGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDP-----LNGQAVPANGTYE---------FGYQMHFICNEGYYLIGEEILYCE----------L------KGSVAIWSGKPPIC----EKV >1nwv_A -----FRSCE------------------------------------VPTRLNSASLKQPYITQNYFPVGTVVEYEC------------------------------------------------------------------------------------------RPGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP-----NPGEIRNG----------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL----------I------SGSSVQWSDPLPEC----REH @1vvc_ 03010000001110101110001000000100000000000000000000000000000000000000031102120003011100031100000000000000000000000000000000000000001101030011000000000000000000000010100000000000000000000000000000000000000000000000000000000000000000000000000000000020200111102101000000100010100010000000000000011000110000 @1ghq_B 03010000001110101110001000000100000000000000000000000000000000000000031302120003011100031100000000000000000000000000000000000000001101030011000000000000000000000010100000000000000000000000000000000000000000000000000000000000000000000000000000000020200030302001000000100010100010000000000000000000110000 @1ckl_A 00000000110100000000000000000000000000000000000000000000000000000003100132020000000000000000000000000000000000000000000000000000000000000000000000000000000000000000003011000101003001001001000000000000010303110000000000011000000000000000000011003020210110102000031000000000003000000011000110001010000000 @1nwv_A 00000000110000000000000000000000000000000000000000000000000000000003131132020000000000000000000000000000000000000000000000000000000000000000000000000000000000000000003011000101003001001001000000000000010303110000000000011000000000000000000011003020210111102101031000000000003000000011000110011010000000 Reorder 265 266 267 268 270 272 273 274 275 277 279 291 292 296 301 302 303 304 305 306 308 312 313 314 315 316 317 319 329 331 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 353 354 355 356 357 358 359 361 362 363 364 376 377 378 379 380 381 253 254 255 257 258 259 260 261 Merge 362 363 Weight 26.7259 >1vvc_ -VKCQ-----SPPSISNGRHNGYEDFYTDG---------------------------------------SVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYSY-------------------------------------------------------------------------NDNVD----------------FKCKYGYKLSGSSS----STCSPGNTWK--P-------------ELP--KCVR--- >1ghq_B AISCG-----SPPPILNGRISYYSTPIAVG---------------------------------------TVIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGY-----------KIRGSTP---------------------------------------------------------------YRHGDSVT----------------FACKTNFSMNGNKS----VWCQANNMW--GPTRLP--------------TCVS--- >1ckl_A --------CEEP------------------PTFEAMELIGKPKPYY--------------------EIGERVDYKC----------------------------------------------------------------------------------KKGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDP-----LNGQAVPANGTY-------E---------FGYQMHFICNEGYYLIGEEILYCE----------L------KGSVAIWSGKPPIC----EKV >1nwv_A -----FRSCE------------------------------------VPTRLNSASLKQPYITQNYFPVGTVVEYEC----------------------------------------------------------------------------------RPGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP-----NPGEIRNG-----------------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL----------I------SGSSVQWSDPLPEC----REH @1vvc_ 0301000000111010111000100000010000000000000000000000000000000000000003110212000301110003110000000000000000000000000000000000000000110103001100000000000000000000000000000000000000000000000000000000000000000000000000000000000001010000000000000000020200111102101000000100010100010000000000000011000110000 @1ghq_B 0301000000111010111000100000010000000000000000000000000000000000000003130212000301110003110000000000000000000000000000000000000000110103001100000000000000000000000000000000000000000000000000000000000000000000000000000000010001010000000000000000020200030302001000000100010100010000000000000000000110000 @1ckl_A 0000000011010000000000000000000000000000000000000000000000000000000310013202000000000000000000000000000000000000000000000000000000000000000000000000000000000030110001010030010010010000000000000103031100000000000110000000010000000000000000011003020210110102000031000000000003000000011000110001010000000 @1nwv_A 0000000011000000000000000000000000000000000000000000000000000000000313113202000000000000000000000000000000000000000000000000000000000000000000000000000000000030110001010030010010010000000000000103031100000000000110000000000000000000000000011003020210111102101031000000000003000000011000110011010000000 Merge 342 337 Weight 26.2192 >1vvc_ -VKCQ-----SPPSISNGRHNGYEDFYTDG---------------------------------------SVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYSY------------------------------------------------------------------------NDNVD----------------FKCKYGYKLSGSSS----STCSPGNTWK--P-------------ELP--KCVR--- >1ghq_B AISCG-----SPPPILNGRISYYSTPIAVG---------------------------------------TVIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGY-----------KIRGSTP--------------------------------------------------------------YRHGDSVT----------------FACKTNFSMNGNKS----VWCQANNMW--GPTRLP--------------TCVS--- >1ckl_A --------CEEP------------------PTFEAMELIGKPKPYY--------------------EIGERVDYKC----------------------------------------------------------------------------------KKGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDP----LNGQAVPANGTY-------E---------FGYQMHFICNEGYYLIGEEILYCE----------L------KGSVAIWSGKPPIC----EKV >1nwv_A -----FRSCE------------------------------------VPTRLNSASLKQPYITQNYFPVGTVVEYEC----------------------------------------------------------------------------------RPGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCPN----PGEIRNG-----------------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL----------I------SGSSVQWSDPLPEC----REH @1vvc_ 030100000011101011100010000001000000000000000000000000000000000000000311021200030111000311000000000000000000000000000000000000000011010300110000000000000000000000000000000000000000000000000000000000000000000000000000000000001010000000000000000020200111102101000000100010100010000000000000011000110000 @1ghq_B 030100000011101011100010000001000000000000000000000000000000000000000313021200030111000311000000000000000000000000000000000000000011010300110000000000000000000000000000000000000000000000000000000000000000000000000000000010001010000000000000000020200030302001000000100010100010000000000000000000110000 @1ckl_A 000000001101000000000000000000000000000000000000000000000000000000031001320200000000000000000000000000000000000000000000000000000000000000000000000000000000003011000101003001001001000000000000010303110000000000110000000010000000000000000011003020210110102000031000000000003000000011000110001010000000 @1nwv_A 000000001100000000000000000000000000000000000000000000000000000000031311320200000000000000000000000000000000000000000000000000000000000000000000000000000000003011000101003001001001000000000000010303110000000000110000000000000000000000000011003020210111102101031000000000003000000011000110011010000000 Merge 63 122 Weight 25.9849 >1vvc_ -VKCQ-----SPPSISNGRHNGYEDFYTD--------------------------------------GSVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYSY------------------------------------------------------------------------NDNVD----------------FKCKYGYKLSGSSS----STCSPGNTWK--P-------------ELP--KCVR--- >1ghq_B AISCG-----SPPPILNGRISYYSTPIAV--------------------------------------GTVIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGY-----------KIRGSTP--------------------------------------------------------------YRHGDSVT----------------FACKTNFSMNGNKS----VWCQANNMW--GPTRLP--------------TCVS--- >1ckl_A --------CEEP-----------------PTFEAMELIGKPKPYY--------------------EIGERVDYKC----------------------------------------------------------------------------------KKGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDP----LNGQAVPANGTY-------E---------FGYQMHFICNEGYYLIGEEILYCE----------L------KGSVAIWSGKPPIC----EKV >1nwv_A -----FRSCE-----------------------------------VPTRLNSASLKQPYITQNYFPVGTVVEYEC----------------------------------------------------------------------------------RPGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCPN----PGEIRNG-----------------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL----------I------SGSSVQWSDPLPEC----REH @1vvc_ 03010000001110101110001000000000000000000000000000000000000000000002311021200030111000311000000000000000000000000000000000000000011010300110000000000000000000000000000000000000000000000000000000000000000000000000000000000001010000000000000000020200111102101000000100010100010000000000000011000110000 @1ghq_B 03010000001110101110001000000000000000000000000000000000000000000002313021200030111000311000000000000000000000000000000000000000011010300110000000000000000000000000000000000000000000000000000000000000000000000000000000010001010000000000000000020200030302001000000100010100010000000000000000000110000 @1ckl_A 00000000110100000000000000000000000000000000000000000000000000000032001320200000000000000000000000000000000000000000000000000000000000000000000000000000000003011000101003001001001000000000000010303110000000000110000000010000000000000000011003020210110102000031000000000003000000011000110001010000000 @1nwv_A 00000000110000000000000000000000000000000000000000000000000000000032311320200000000000000000000000000000000000000000000000000000000000000000000000000000000003011000101003001001001000000000000010303110000000000110000000000000000000000000011003020210111102101031000000000003000000011000110011010000000 Merge 456 461 Weight 25.0208 >1vvc_ -VKCQ-----SPPSISNGRHNGYEDFYTD--------------------------------------GSVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYSY------------------------------------------------------------------------NDNVD----------------FKCKYGYKLSGSSS----STCSPGNTW-KP-------------ELP--KCVR--- >1ghq_B AISCG-----SPPPILNGRISYYSTPIAV--------------------------------------GTVIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGY-----------KIRGSTP--------------------------------------------------------------YRHGDSVT----------------FACKTNFSMNGNKS----VWCQANNMW-GPTRLP--------------TCVS--- >1ckl_A --------CEEP-----------------PTFEAMELIGKPKPYY--------------------EIGERVDYKC----------------------------------------------------------------------------------KKGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDP----LNGQAVPANGTY-------E---------FGYQMHFICNEGYYLIGEEILYCE---------L------KGSVAIWSGKPPIC----EKV >1nwv_A -----FRSCE-----------------------------------VPTRLNSASLKQPYITQNYFPVGTVVEYEC----------------------------------------------------------------------------------RPGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCPN----PGEIRNG-----------------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL---------I------SGSSVQWSDPLPEC----REH @1vvc_ 0301000000111010111000100000000000000000000000000000000000000000000231102120003011100031100000000000000000000000000000000000000001101030011000000000000000000000000000000000000000000000000000000000000000000000000000000000000101000000000000000002020011110210100000010001010010000000000000011000110000 @1ghq_B 0301000000111010111000100000000000000000000000000000000000000000000231302120003011100031100000000000000000000000000000000000000001101030011000000000000000000000000000000000000000000000000000000000000000000000000000000001000101000000000000000002020003030200100000010001010010000000000000000000110000 @1ckl_A 0000000011010000000000000000000000000000000000000000000000000000003200132020000000000000000000000000000000000000000000000000000000000000000000000000000000000301100010100300100100100000000000001030311000000000011000000001000000000000000001100302021011010200003100000000003000000011000110001010000000 @1nwv_A 0000000011000000000000000000000000000000000000000000000000000000003231132020000000000000000000000000000000000000000000000000000000000000000000000000000000000301100010100300100100100000000000001030311000000000011000000000000000000000000001100302021011110210103100000000003000000011000110011010000000 Merge 64 20 Weight 24.3623 >1vvc_ -VKCQ-----SPPSISNGRHNGYEDFYTD-------------------------------------GSVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYSY------------------------------------------------------------------------NDNVD----------------FKCKYGYKLSGSSS----STCSPGNTW-KP-------------ELP--KCVR--- >1ghq_B AISCG-----SPPPILNGRISYYSTPIAV-------------------------------------GTVIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGY-----------KIRGSTP--------------------------------------------------------------YRHGDSVT----------------FACKTNFSMNGNKS----VWCQANNMW-GPTRLP--------------TCVS--- >1ckl_A --------CEEPP----------------TFEAMELIGKPKPYY--------------------EIGERVDYKC----------------------------------------------------------------------------------KKGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDP----LNGQAVPANGTY-------E---------FGYQMHFICNEGYYLIGEEILYCE---------L------KGSVAIWSGKPPIC----EKV >1nwv_A -----FRSCE----------------------------------VPTRLNSASLKQPYITQNYFPVGTVVEYEC----------------------------------------------------------------------------------RPGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCPN----PGEIRNG-----------------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL---------I------SGSSVQWSDPLPEC----REH @1vvc_ 030100000011101011100010000000000000000000000000000000000000000000231102120003011100031100000000000000000000000000000000000000001101030011000000000000000000000000000000000000000000000000000000000000000000000000000000000000101000000000000000002020011110210100000010001010010000000000000011000110000 @1ghq_B 030100000011101011100010000000000000000000000000000000000000000000231302120003011100031100000000000000000000000000000000000000001101030011000000000000000000000000000000000000000000000000000000000000000000000000000000001000101000000000000000002020003030200100000010001010010000000000000000000110000 @1ckl_A 000000001101100000000000000000000000000000000000000000000000000003200132020000000000000000000000000000000000000000000000000000000000000000000000000000000000301100010100300100100100000000000001030311000000000011000000001000000000000000001100302021011010200003100000000003000000011000110001010000000 @1nwv_A 000000001100000000000000000000000000000000000000000000000000000003231132020000000000000000000000000000000000000000000000000000000000000000000000000000000000301100010100300100100100000000000001030311000000000011000000000000000000000000001100302021011110210103100000000003000000011000110011010000000 Merge 491 495 Weight 23.6584 >1vvc_ -VKCQ-----SPPSISNGRHNGYEDFYTD-------------------------------------GSVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYSY------------------------------------------------------------------------NDNVD----------------FKCKYGYKLSGSSS----STCSPGNTW-KP-------------ELP-KCVR--- >1ghq_B AISCG-----SPPPILNGRISYYSTPIAV-------------------------------------GTVIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGY-----------KIRGSTP--------------------------------------------------------------YRHGDSVT----------------FACKTNFSMNGNKS----VWCQANNMW-GPTRLP-------------TCVS--- >1ckl_A --------CEEPP----------------TFEAMELIGKPKPYY--------------------EIGERVDYKC----------------------------------------------------------------------------------KKGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDP----LNGQAVPANGTY-------E---------FGYQMHFICNEGYYLIGEEILYCE---------L------KGSVAIWSGKPPI-C--EKV >1nwv_A -----FRSCE----------------------------------VPTRLNSASLKQPYITQNYFPVGTVVEYEC----------------------------------------------------------------------------------RPGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCPN----PGEIRNG-----------------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL---------I------SGSSVQWSDPLPE-C--REH @1vvc_ 03010000001110101110001000000000000000000000000000000000000000000023110212000301110003110000000000000000000000000000000000000000110103001100000000000000000000000000000000000000000000000000000000000000000000000000000000000010100000000000000000202001111021010000001000101001000000000000001100210000 @1ghq_B 03010000001110101110001000000000000000000000000000000000000000000023130212000301110003110000000000000000000000000000000000000000110103001100000000000000000000000000000000000000000000000000000000000000000000000000000000100010100000000000000000202000303020010000001000101001000000000000000000210000 @1ckl_A 00000000110110000000000000000000000000000000000000000000000000000320013202000000000000000000000000000000000000000000000000000000000000000000000000000000000030110001010030010010010000000000000103031100000000001100000000100000000000000000110030202101101020000310000000000300000001100011000100200000 @1nwv_A 00000000110000000000000000000000000000000000000000000000000000000323113202000000000000000000000000000000000000000000000000000000000000000000000000000000000030110001010030010010010000000000000103031100000000001100000000000000000000000000110030202101111021010310000000000300000001100011001100200000 Merge 446 440 Weight 23.3972 >1vvc_ -VKCQ-----SPPSISNGRHNGYEDFYTD-------------------------------------GSVVTYSCNSGYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYSY------------------------------------------------------------------------NDNVD----------------FKCKYGYKLSGSSSS---TCSPGNTW-KP-------------ELP-KCVR--- >1ghq_B AISCG-----SPPPILNGRISYYSTPIAV-------------------------------------GTVIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGY-----------KIRGSTP--------------------------------------------------------------YRHGDSVT----------------FACKTNFSMNGNKSV---WCQANNMW-GPTRLP-------------TCVS--- >1ckl_A --------CEEPP----------------TFEAMELIGKPKPYY--------------------EIGERVDYKC----------------------------------------------------------------------------------KKGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDP----LNGQAVPANGTY-------E---------FGYQMHFICNEGYYLIGEEILYCE--------L------KGSVAIWSGKPPI-C--EKV >1nwv_A -----FRSCE----------------------------------VPTRLNSASLKQPYITQNYFPVGTVVEYEC----------------------------------------------------------------------------------RPGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCPN----PGEIRNG-----------------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL--------I------SGSSVQWSDPLPE-C--REH @1vvc_ 0301000000111010111000100000000000000000000000000000000000000000002311021200030111000311000000000000000000000000000000000000000011010300110000000000000000000000000000000000000000000000000000000000000000000000000000000000001010000000000000000020200111102101000001000101001000000000000001100210000 @1ghq_B 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---FRSC-E---------------------------------VPTRLNSASLKQPYITQNYFPVGTVVEYECR--------------------------------------------------------------------------------PGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCPNPG-EIRNG---------------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 030000200111010111000100000000000000000000000000000000000000000023110212000301110003110000000000000000000000000000000000000000110103001100000000000000000000000000000000000000000000000000000000000000000000000000000001010000000000000002020011110210100200001010010000000000000120210000 @1ghq_B 030000200111010111000100000000000000000000000000000000000000000023130212000301110003110000000000000000000000000000000000000000110103001100000000000000000000000000000000000000000000000000000000000000000000000000010001010000000000000002020003030200103200001010010000000000000020210000 @1ckl_A 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AIS--CG-SPPPILNGRISYYSTPIAV------------------------------------GTVIRYSCSGTFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGY----------KIRGSTP----------------------------------------------------------YRHGDSV--------------TFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A -----C-EEPP----------------TFEAMELIGKPKPY-------------------YEIGERVDYKCK--------------------------------------------------------------------------------KGYFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRD-PLNGQAVPANGTYE--------------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A F--RSC-E---------------------------------VPTRLNSASLKQPYITQNYFPVGTVVEYECR--------------------------------------------------------------------------------PGYRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCPNPG-EIRNG---------------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 03000200111010111000100000000000000000000000000000000000000000023110212000301110003110000000000000000000000000000000000000000110103001100000000000000000000000000000000000000000000000000000000000000000000000000000001010000000000000002020011110210100200001010010000000000000120210000 @1ghq_B 03000200111010111000100000000000000000000000000000000000000000023130212000301110003110000000000000000000000000000000000000000110103001100000000000000000000000000000000000000000000000000000000000000000000000000010001010000000000000002020003030200103200001010010000000000000020210000 @1ckl_A 00000201011000000000000000000000000000000000000000000000000030320013202000000000000000000000000000000000000000000000000000000000000000000000000000000000011000101003001001001000000000000010303110000000110000000010000000000000001100302021011010200003200000003000000110001100020200000 @1nwv_A 00000201000000000000000000000000000000000000000000000000000030323113202000000000000000000000000000000000000000000000000000000000000000000000000000000000011000101003001001001000000000000010303110000000110000000000000000000000001100302021011110210103200000003000000110001100120200000 Reorder 254 255 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 167 168 169 170 171 172 174 175 176 177 178 179 180 181 182 183 184 185 186 187 189 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 218 219 220 221 222 223 224 235 236 237 238 239 240 245 247 248 249 250 251 252 Merge 137 138 Weight 15.8184 >1vvc_ -VK--CQ-SPPSISNGRHNGYEDFYTD------------------------------------GSVVTYSCNS-GYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYS-----------------------------------------------------------------YNDNV--------------DFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AIS--CG-SPPPILNGRISYYSTPIAV------------------------------------GTVIRYSCSG-TFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGY----------KIRGSTP--------------------------------------------------------YRHGDSV--------------TFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A -----C-EEPP----------------TFEAMELIGKPKPY-------------------YEIGERVDYKCK-KG------------------------------------------------------------------------------YFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRD-PLNGQAVPANGTYE--------------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A F--RSC-E---------------------------------VPTRLNSASLKQPYITQNYFPVGTVVEYECR-PG------------------------------------------------------------------------------YRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCPNPG-EIRNG---------------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 0300020011101011100010000000000000000000000000000000000000000002311021200013011100031100000000000000000000000000000000000000001101030011000000000000000000000000000000000000000000000000000000000000000000000000000001010000000000000002020011110210100200001010010000000000000120210000 @1ghq_B 0300020011101011100010000000000000000000000000000000000000000002313021200003011100031100000000000000000000000000000000000000001101030011000000000000000000000000000000000000000000000000000000000000000000000000010001010000000000000002020003030200103200001010010000000000000020210000 @1ckl_A 0000020101100000000000000000000000000000000000000000000000003032001320200010000000000000000000000000000000000000000000000000000000000000000000000000000001000101003001001001000000000000010303110000000110000000010000000000000001100302021011010200003200000003000000110001100020200000 @1nwv_A 0000020100000000000000000000000000000000000000000000000000003032311320200010000000000000000000000000000000000000000000000000000000000000000000000000000001000101003001001001000000000000010303110000000110000000000000000000000001100302021011110210103200000003000000110001100120200000 Merge 13 14 Weight 15.5026 >1vvc_ -VK--CQSPPSISNGRHNGYEDFYTD------------------------------------GSVVTYSCNS-GYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYS-----------------------------------------------------------------YNDNV--------------DFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AIS--CGSPPPILNGRISYYSTPIAV------------------------------------GTVIRYSCSG-TFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGY----------KIRGSTP--------------------------------------------------------YRHGDSV--------------TFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A -----CEEPP----------------TFEAMELIGKPKPY-------------------YEIGERVDYKCK-KG------------------------------------------------------------------------------YFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRD-PLNGQAVPANGTYE--------------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A F--RSCE---------------------------------VPTRLNSASLKQPYITQNYFPVGTVVEYECR-PG------------------------------------------------------------------------------YRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCPNPG-EIRNG---------------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 030002311101011100010000000000000000000000000000000000000000002311021200013011100031100000000000000000000000000000000000000001101030011000000000000000000000000000000000000000000000000000000000000000000000000000001010000000000000002020011110210100200001010010000000000000120210000 @1ghq_B 030002011101011100010000000000000000000000000000000000000000002313021200003011100031100000000000000000000000000000000000000001101030011000000000000000000000000000000000000000000000000000000000000000000000000010001010000000000000002020003030200103200001010010000000000000020210000 @1ckl_A 000002101100000000000000000000000000000000000000000000000003032001320200010000000000000000000000000000000000000000000000000000000000000000000000000000001000101003001001001000000000000010303110000000110000000010000000000000001100302021011010200003200000003000000110001100020200000 @1nwv_A 000002100000000000000000000000000000000000000000000000000003032311320200010000000000000000000000000000000000000000000000000000000000000000000000000000001000101003001001001000000000000010303110000000110000000000000000000000001100302021011110210103200000003000000110001100120200000 Merge 380 397 Weight 15.3117 >1vvc_ -VK--CQSPPSISNGRHNGYEDFYTD------------------------------------GSVVTYSCNS-GYSLIGNSGVLCSGGEWSDPPTCQIVK-------------------------CPHPTISNGYLSSGFKRSYS-----------------------------------------------------------------YNDN-------------VDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AIS--CGSPPPILNGRISYYSTPIAV------------------------------------GTVIRYSCSG-TFRLIGEKSLLC---------------ITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGY----------KIRGSTP--------------------------------------------------------YRHGDS-------------VTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A -----CEEPP----------------TFEAMELIGKPKPY-------------------YEIGERVDYKCK-KG------------------------------------------------------------------------------YFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRD-PLNGQAVPANGTYE-------------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A F--RSCE---------------------------------VPTRLNSASLKQPYITQNYFPVGTVVEYECR-PG------------------------------------------------------------------------------YRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCPNPG-EIRNG--------------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 03000231110101110001000000000000000000000000000000000000000000231102120001301110003110000000000000000000000000000000000000000110103001100000000000000000000000000000000000000000000000000000000000000000000000000000100000000000000302020011110210100200001010010000000000000120210000 @1ghq_B 03000201110101110001000000000000000000000000000000000000000000231302120000301110003110000000000000000000000000000000000000000110103001100000000000000000000000000000000000000000000000000000000000000000000000001000100000000000000302020003030200103200001010010000000000000020210000 @1ckl_A 00000210110000000000000000000000000000000000000000000000000303200132020001000000000000000000000000000000000000000000000000000000000000000000000000000000100010100300100100100000000000001030311000000011000000001000000000000001100302021011010200003200000003000000110001100020200000 @1nwv_A 00000210000000000000000000000000000000000000000000000000000303231132020001000000000000000000000000000000000000000000000000000000000000000000000000000000100010100300100100100000000000001030311000000011000000000000000000000001100302021011110210103200000003000000110001100120200000 Reorder 176 177 178 179 180 181 182 183 184 185 154 155 156 167 168 169 170 171 172 174 175 Merge 174 175 Weight 14.9939 >1vvc_ -VK--CQSPPSISNGRHNGYEDFYTD------------------------------------GSVVTYSCNS-GYSLIGNSGVLCSGGE---------WSDPPTCQIVK---------------CPHPTISNGYLSSGFKRSYS-----------------------------------------------------------------YNDN-------------VDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AIS--CGSPPPILNGRISYYSTPIAV------------------------------------GTVIRYSCSG-TFRLIGEKSLLC----ITKDKVDGTW----------DKPAPKCEYFNKYSSCPEPIVPGGY----------KIRGSTP--------------------------------------------------------YRHGDS-------------VTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A -----CEEPP----------------TFEAMELIGKPKPY-------------------YEIGERVDYKCK-KG-----------------------------------------------------------------------------YFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRD-PLNGQAVPANGTYE-------------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A F--RSCE---------------------------------VPTRLNSASLKQPYITQNYFPVGTVVEYECR-PG-----------------------------------------------------------------------------YRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCPNPG-EIRNG--------------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 0300023111010111000100000000000000000000000000000000000000000023110212000130111000311000000000000010000000000000000000000000110103001100000000000000000000000000000000000000000000000000000000000000000000000000000100000000000000302020011110210100200001010010000000000000120210000 @1ghq_B 0300020111010111000100000000000000000000000000000000000000000023130212000030111000311000000000000010000000000000000000000000110103001100000000000000000000000000000000000000000000000000000000000000000000000001000100000000000000302020003030200103200001010010000000000000020210000 @1ckl_A 0000021011000000000000000000000000000000000000000000000000030320013202000100000000000000000000000000000000000000000000000000000000000000000000000000000100010100300100100100000000000001030311000000011000000001000000000000001100302021011010200003200000003000000110001100020200000 @1nwv_A 0000021000000000000000000000000000000000000000000000000000030323113202000100000000000000000000000000000000000000000000000000000000000000000000000000000100010100300100100100000000000001030311000000011000000000000000000000001100302021011110210103200000003000000110001100120200000 Merge 134 136 Weight 14.6416 >1vvc_ -VK--CQSPPSISNGRHNGYEDFYTD------------------------------------GSVVTYSCNSGYSLIGNSGVLCSGGE---------WSDPPTCQIVK---------------CPHPTISNGYLSSGFKRSYS-----------------------------------------------------------------YNDN-------------VDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AIS--CGSPPPILNGRISYYSTPIAV------------------------------------GTVIRYSCSGTFRLIGEKSLLC----ITKDKVDGTW----------DKPAPKCEYFNKYSSCPEPIVPGGY----------KIRGSTP--------------------------------------------------------YRHGDS-------------VTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A -----CEEPP----------------TFEAMELIGKPKPY-------------------YEIGERVDYKCKKG-----------------------------------------------------------------------------YFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRD-PLNGQAVPANGTYE-------------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A F--RSCE---------------------------------VPTRLNSASLKQPYITQNYFPVGTVVEYECRPG-----------------------------------------------------------------------------YRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCPNPG-EIRNG--------------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 030002311101011100010000000000000000000000000000000000000000002311021200130111000311000000000000010000000000000000000000000110103001100000000000000000000000000000000000000000000000000000000000000000000000000000100000000000000302020011110210100200001010010000000000000120210000 @1ghq_B 030002011101011100010000000000000000000000000000000000000000002313021200030111000311000000000000010000000000000000000000000110103001100000000000000000000000000000000000000000000000000000000000000000000000001000100000000000000302020003030200103200001010010000000000000020210000 @1ckl_A 000002101100000000000000000000000000000000000000000000000003032001320200100000000000000000000000000000000000000000000000000000000000000000000000000000100010100300100100100000000000001030311000000011000000001000000000000001100302021011010200003200000003000000110001100020200000 @1nwv_A 000002100000000000000000000000000000000000000000000000000003032311320200100000000000000000000000000000000000000000000000000000000000000000000000000000100010100300100100100000000000001030311000000011000000000000000000000001100302021011110210103200000003000000110001100120200000 Merge 340 345 Weight 13.6717 >1vvc_ -VK--CQSPPSISNGRHNGYEDFYTD------------------------------------GSVVTYSCNSGYSLIGNSGVLCSGGE---------WSDPPTCQIVK---------------CPHPTISNGYLSSGFKRSYS----------------------------------------------------------------YNDN-------------VDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AIS--CGSPPPILNGRISYYSTPIAV------------------------------------GTVIRYSCSGTFRLIGEKSLLC----ITKDKVDGTW----------DKPAPKCEYFNKYSSCPEPIVPGGY----------KIRGSTP-------------------------------------------------------YRHGDS-------------VTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A -----CEEPP----------------TFEAMELIGKPKPY-------------------YEIGERVDYKCKKG-----------------------------------------------------------------------------YFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDPLNGQAVPANGTYE-------------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A F--RSCE---------------------------------VPTRLNSASLKQPYITQNYFPVGTVVEYECRPG-----------------------------------------------------------------------------YRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCPNPGEIRNG--------------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 03000231110101110001000000000000000000000000000000000000000000231102120013011100031100000000000001000000000000000000000000011010300110000000000000000000000000000000000000000000000000000000000000000000000000000100000000000000302020011110210100200001010010000000000000120210000 @1ghq_B 03000201110101110001000000000000000000000000000000000000000000231302120003011100031100000000000001000000000000000000000000011010300110000000000000000000000000000000000000000000000000000000000000000000000001000100000000000000302020003030200103200001010010000000000000020210000 @1ckl_A 00000210110000000000000000000000000000000000000000000000000303200132020010000000000000000000000000000000000000000000000000000000000000000000000000000010001010030010010010000000000000103031100030011000000001000000000000001100302021011010200003200000003000000110001100020200000 @1nwv_A 00000210000000000000000000000000000000000000000000000000000303231132020010000000000000000000000000000000000000000000000000000000000000000000000000000010001010030010010010000000000000103031100030011000000000000000000000001100302021011110210103200000003000000110001100120200000 Merge 94 16 Weight 12.739 >1vvc_ -VK--CQSPPSISNGRHNGYEDFYTD-----------------------------------GSVVTYSCNSGYSLIGNSGVLCSGGE---------WSDPPTCQIVK---------------CPHPTISNGYLSSGFKRSYS----------------------------------------------------------------YNDN-------------VDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AIS--CGSPPPILNGRISYYSTPIAV-----------------------------------GTVIRYSCSGTFRLIGEKSLLC----ITKDKVDGTW----------DKPAPKCEYFNKYSSCPEPIVPGGY----------KIRGSTP-------------------------------------------------------YRHGDS-------------VTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A -----CEEPP----------------TFEAMELIGKPKPY------------------YEIGERVDYKCKKG-----------------------------------------------------------------------------YFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDPLNGQAVPANGTYE-------------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A F--RSCEV--------------------------------PTRLNSASLKQPYITQNYFPVGTVVEYECRPG-----------------------------------------------------------------------------YRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCPNPGEIRNG--------------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 0300023111010111000100000000000000000000000000000000000000000231102120013011100031100000000000001000000000000000000000000011010300110000000000000000000000000000000000000000000000000000000000000000000000000000100000000000000302020011110210100200001010010000000000000120210000 @1ghq_B 0300020111010111000100000000000000000000000000000000000000000231302120003011100031100000000000001000000000000000000000000011010300110000000000000000000000000000000000000000000000000000000000000000000000001000100000000000000302020003030200103200001010010000000000000020210000 @1ckl_A 0000021011000000000000000000000000000000000000000000000000303200132020010000000000000000000000000000000000000000000000000000000000000000000000000000010001010030010010010000000000000103031100030011000000001000000000000001100302021011010200003200000003000000110001100020200000 @1nwv_A 0000021000000000000000000000000000000000000000000000000000303231132020010000000000000000000000000000000000000000000000000000000000000000000000000000010001010030010010010000000000000103031100030011000000000000000000000001100302021011110210103200000003000000110001100120200000 Merge 95 19 Weight 12.1521 >1vvc_ -VK--CQSPPSISNGRHNGYEDFYTD----------------------------------GSVVTYSCNSGYSLIGNSGVLCSGGE---------WSDPPTCQIVK---------------CPHPTISNGYLSSGFKRSYS----------------------------------------------------------------YNDN-------------VDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AIS--CGSPPPILNGRISYYSTPIAV----------------------------------GTVIRYSCSGTFRLIGEKSLLC----ITKDKVDGTW----------DKPAPKCEYFNKYSSCPEPIVPGGY----------KIRGSTP-------------------------------------------------------YRHGDS-------------VTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A -----CEEPP----------------TFEAMELIGKPKPY-----------------YEIGERVDYKCKKG-----------------------------------------------------------------------------YFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDPLNGQAVPANGTYE-------------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A F--RSCEVP-------------------------------TRLNSASLKQPYITQNYFPVGTVVEYECRPG-----------------------------------------------------------------------------YRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCPNPGEIRNG--------------QIDVPGGILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 030002312101011100010000000000000000000000000000000000000000231102120013011100031100000000000001000000000000000000000000011010300110000000000000000000000000000000000000000000000000000000000000000000000000000100000000000000302020011110210100200001010010000000000000120210000 @1ghq_B 030002012101011100010000000000000000000000000000000000000000231302120003011100031100000000000001000000000000000000000000011010300110000000000000000000000000000000000000000000000000000000000000000000000001000100000000000000302020003030200103200001010010000000000000020210000 @1ckl_A 000002102100000000000000000000000000000000000000000000000303200132020010000000000000000000000000000000000000000000000000000000000000000000000000000010001010030010010010000000000000103031100030011000000001000000000000001100302021011010200003200000003000000110001100020200000 @1nwv_A 000002102000000000000000000000000000000000000000000000000303231132020010000000000000000000000000000000000000000000000000000000000000000000000000000010001010030010010010000000000000103031100030011000000000000000000000001100302021011110210103200000003000000110001100120200000 Merge 384 353 Weight 12.1099 >1vvc_ -VK--CQSPPSISNGRHNGYEDFYTD----------------------------------GSVVTYSCNSGYSLIGNSGVLCSGGE---------WSDPPTCQIVK---------------CPHPTISNGYLSSGFKRSYS----------------------------------------------------------------YNDN------------VDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AIS--CGSPPPILNGRISYYSTPIAV----------------------------------GTVIRYSCSGTFRLIGEKSLLC----ITKDKVDGTW----------DKPAPKCEYFNKYSSCPEPIVPGGY----------KIRGSTP-------------------------------------------------------YRHGDS------------VTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A -----CEEPP----------------TFEAMELIGKPKPY-----------------YEIGERVDYKCKKG-----------------------------------------------------------------------------YFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDPLNGQAVPANGTYE------------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A F--RSCEVP-------------------------------TRLNSASLKQPYITQNYFPVGTVVEYECRPG-----------------------------------------------------------------------------YRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCPNPGEIRNGQ-------------IDVPGGILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 03000231210101110001000000000000000000000000000000000000000023110212001301110003110000000000000100000000000000000000000001101030011000000000000000000000000000000000000000000000000000000000000000000000000000010000000000000302020011110210100200001010010000000000000120210000 @1ghq_B 03000201210101110001000000000000000000000000000000000000000023130212000301110003110000000000000100000000000000000000000001101030011000000000000000000000000000000000000000000000000000000000000000000000000100010000000000000302020003030200103200001010010000000000000020210000 @1ckl_A 00000210210000000000000000000000000000000000000000000000030320013202001000000000000000000000000000000000000000000000000000000000000000000000000000001000101003001001001000000000000010303110003001110000000100000000000001100302021011010200003200000003000000110001100020200000 @1nwv_A 00000210200000000000000000000000000000000000000000000000030323113202001000000000000000000000000000000000000000000000000000000000000000000000000000001000101003001001001000000000000010303110003001110000000000000000000001100302021011110210103200000003000000110001100120200000 Reorder 385 386 387 388 389 359 361 363 364 376 377 378 379 Merge 376 377 Weight 11.8073 >1vvc_ -VK--CQSPPSISNGRHNGYEDFYTD----------------------------------GSVVTYSCNSGYSLIGNSGVLCSGGE---------WSDPPTCQIVK---------------CPHPTISNGYLSSGFKRSYS--------------------------------------------------------------------YNDN-------VDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AIS--CGSPPPILNGRISYYSTPIAV----------------------------------GTVIRYSCSGTFRLIGEKSLLC----ITKDKVDGTW----------DKPAPKCEYFNKYSSCPEPIVPGGY----------KIRGSTP-----------------------------------------------------------YRHGDS-------VTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A -----CEEPP----------------TFEAMELIGKPKPY-----------------YEIGERVDYKCKKG-----------------------------------------------------------------------------YFYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDPLNGQAVPAN----GTYE-------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A F--RSCEVP-------------------------------TRLNSASLKQPYITQNYFPVGTVVEYECRPG-----------------------------------------------------------------------------YRREPSLSPKLTCLQNLKW-------STAVEFCKKKSCPNPGEIRNGQ-----IDVPG-------GILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 0300023121010111000100000000000000000000000000000000000000002311021200130111000311000000000000010000000000000000000000000110103001100000000000000000000000000000000000000000000000000000000000000000000000000000000100000000302020011110210100200001010010000000000000120210000 @1ghq_B 0300020121010111000100000000000000000000000000000000000000002313021200030111000311000000000000010000000000000000000000000110103001100000000000000000000000000000000000000000000000000000000000000000000000000001000100000000302020003030200103200001010010000000000000020210000 @1ckl_A 0000021021000000000000000000000000000000000000000000000003032001320200100000000000000000000000000000000000000000000000000000000000000000000000000000100010100300100100100000000000001030311000300111000000000101000000001100302021011010200003200000003000000110001100020200000 @1nwv_A 0000021020000000000000000000000000000000000000000000000003032311320200100000000000000000000000000000000000000000000000000000000000000000000000000000100010100300100100100000000000001030311000300111000000000100000000001100302021011110210103200000003000000110001100120200000 Merge 257 139 Weight 11.7122 >1vvc_ -VK--CQSPPSISNGRHNGYEDFYTD----------------------------------GSVVTYSCNSGYSLIGNSGVLCSGGE---------WSDPPTCQIVK---------------CPHPTISNGYLSSGFKRSYS-------------------------------------------------------------------YNDN-------VDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AIS--CGSPPPILNGRISYYSTPIAV----------------------------------GTVIRYSCSGTFRLIGEKSLLC----ITKDKVDGTW----------DKPAPKCEYFNKYSSCPEPIVPGGY----------KIRGSTP----------------------------------------------------------YRHGDS-------VTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A -----CEEPP----------------TFEAMELIGKPKPY-----------------YEIGERVDYKCKKGY----------------------------------------------------------------------------FYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDPLNGQAVPAN----GTYE-------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A F--RSCEVP-------------------------------TRLNSASLKQPYITQNYFPVGTVVEYECRPGY----------------------------------------------------------------------------RREPSLSPKLTCLQNLKW-------STAVEFCKKKSCPNPGEIRNGQ-----IDVPG-------GILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 030002312101011100010000000000000000000000000000000000000000231102120011011100031100000000000001000000000000000000000000011010300110000000000000000000000000000000000000000000000000000000000000000000000000000000100000000302020011110210100200001010010000000000000120210000 @1ghq_B 030002012101011100010000000000000000000000000000000000000000231302120003011100031100000000000001000000000000000000000000011010300110000000000000000000000000000000000000000000000000000000000000000000000000001000100000000302020003030200103200001010010000000000000020210000 @1ckl_A 000002102100000000000000000000000000000000000000000000000303200132020011000000000000000000000000000000000000000000000000000000000000000000000000000000010100300100100100000000000001030311000300111000000000101000000001100302021011010200003200000003000000110001100020200000 @1nwv_A 000002102000000000000000000000000000000000000000000000000303231132020011000000000000000000000000000000000000000000000000000000000000000000000000000000010100300100100100000000000001030311000300111000000000100000000001100302021011110210103200000003000000110001100120200000 Merge 8 4 Weight 10.8282 >1vvc_ -VK-CQSPPSISNGRHNGYEDFYTD----------------------------------GSVVTYSCNSGYSLIGNSGVLCSGGE---------WSDPPTCQIVK---------------CPHPTISNGYLSSGFKRSYS-------------------------------------------------------------------YNDN-------VDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AIS-CGSPPPILNGRISYYSTPIAV----------------------------------GTVIRYSCSGTFRLIGEKSLLC----ITKDKVDGTW----------DKPAPKCEYFNKYSSCPEPIVPGGY----------KIRGSTP----------------------------------------------------------YRHGDS-------VTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A ----CEEPP----------------TFEAMELIGKPKPY-----------------YEIGERVDYKCKKGY----------------------------------------------------------------------------FYIPPLATHTICDRNHTWLPVSDDA------CYRETCPYIRDPLNGQAVPAN----GTYE-------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A FR-SCEVP-------------------------------TRLNSASLKQPYITQNYFPVGTVVEYECRPGY----------------------------------------------------------------------------RREPSLSPKLTCLQNLKW-------STAVEFCKKKSCPNPGEIRNGQ-----IDVPG-------GILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 03002312101011100010000000000000000000000000000000000000000231102120011011100031100000000000001000000000000000000000000011010300110000000000000000000000000000000000000000000000000000000000000000000000000000000100000000302020011110210100200001010010000000000000120210000 @1ghq_B 03002012101011100010000000000000000000000000000000000000000231302120003011100031100000000000001000000000000000000000000011010300110000000000000000000000000000000000000000000000000000000000000000000000000001000100000000302020003030200103200001010010000000000000020210000 @1ckl_A 00002102100000000000000000000000000000000000000000000000303200132020011000000000000000000000000000000000000000000000000000000000000000000000000000000010100300100100100000000000001030311000300111000000000101000000001100302021011010200003200000003000000110001100020200000 @1nwv_A 00002102000000000000000000000000000000000000000000000000303231132020011000000000000000000000000000000000000000000000000000000000000000000000000000000010100300100100100000000000001030311000300111000000000100000000001100302021011110210103200000003000000110001100120200000 Reorder 258 259 260 261 265 266 267 268 270 272 273 274 275 277 279 291 292 296 301 302 303 304 305 306 308 312 313 314 315 316 317 319 329 331 333 334 335 209 210 211 212 213 218 219 220 221 222 223 224 235 236 237 238 239 240 245 247 248 249 250 251 252 254 255 Merge 272 273 Weight 10.5171 >1vvc_ -VK-CQSPPSISNGRHNGYEDFYTD----------------------------------GSVVTYSCNSGYSLIGNSGVLCSGGE---------WSDPPTCQIVK---------------------------------------------------CPHPTISNGYLSSGFKRSYS------------------------------YNDN-------VDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AIS-CGSPPPILNGRISYYSTPIAV----------------------------------GTVIRYSCSGTFRLIGEKSLLC----ITKDKVDGTW----------DKPAPKCEYFNKYSS------------------------------------CPEPIVPGGY----------KIRGSTP---------------------YRHGDS-------VTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A ----CEEPP----------------TFEAMELIGKPKPY-----------------YEIGERVDYKCKKGY-------------------------------------------------FYIPPLATHTICDRNHTWLPVSDDA------CYRETC--------------------------PYIRDPLNGQAVPAN----GTYE-------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A FR-SCEVP-------------------------------TRLNSASLKQPYITQNYFPVGTVVEYECRPGY-------------------------------------------------RREPSLSPKLTCLQNLKW-------STAVEFCKKKSC--------------------------PNPGEIRNGQ-----IDVPG-------GILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 0300231210101110001000000000000000000000000000000000000000023110212001101110003110000000000000100000000000000000000000000000000000000000000000000000000000002101030011000000000000000000000000000000000000000000100000000302020011110210100200001010010000000000000120210000 @1ghq_B 0300201210101110001000000000000000000000000000000000000000023130212000301110003110000000000000100000000000000000000000000000000000000000000000000000000000002101030011000000000000000000000000000000000000001000100000000302020003030200103200001010010000000000000020210000 @1ckl_A 0000210210000000000000000000000000000000000000000000000030320013202001100000000000000000000000000000000000000000000000000001010030010010010000000000000103032000000000000000000000000001000300111000000000101000000001100302021011010200003200000003000000110001100020200000 @1nwv_A 0000210200000000000000000000000000000000000000000000000030323113202001100000000000000000000000000000000000000000000000000001010030010010010000000000000103032000000000000000000000000001000300111000000000100000000001100302021011110210103200000003000000110001100120200000 Merge 336 274 Weight 9.7481 >1vvc_ -VK-CQSPPSISNGRHNGYEDFYTD----------------------------------GSVVTYSCNSGYSLIGNSGVLCSGGE---------WSDPPTCQIVK---------------------------------------------------CPHPTISNGYLSSGFKRSYS-----------------------------YNDN-------VDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AIS-CGSPPPILNGRISYYSTPIAV----------------------------------GTVIRYSCSGTFRLIGEKSLLC----ITKDKVDGTW----------DKPAPKCEYFNKYSS------------------------------------CPEPIVPGGY----------KIRGSTP--------------------YRHGDS-------VTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A ----CEEPP----------------TFEAMELIGKPKPY-----------------YEIGERVDYKCKKGY-------------------------------------------------FYIPPLATHTICDRNHTWLPVSDDA------CYRETCP-------------------------YIRDPLNGQAVPAN----GTYE-------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A FR-SCEVP-------------------------------TRLNSASLKQPYITQNYFPVGTVVEYECRPGY-------------------------------------------------RREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP-------------------------NPGEIRNGQ-----IDVPG-------GILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 030023121010111000100000000000000000000000000000000000000002311021200110111000311000000000000010000000000000000000000000000000000000000000000000000000000000220103001100000000000000000000000000000000000000000100000000302020011110210100200001010010000000000000120210000 @1ghq_B 030020121010111000100000000000000000000000000000000000000002313021200030111000311000000000000010000000000000000000000000000000000000000000000000000000000000220103001100000000000000000000000000000000000001000100000000302020003030200103200001010010000000000000020210000 @1ckl_A 000021021000000000000000000000000000000000000000000000003032001320200110000000000000000000000000000000000000000000000000000101003001001001000000000000010303220000000000000000000000000000300111000000000101000000001100302021011010200003200000003000000110001100020200000 @1nwv_A 000021020000000000000000000000000000000000000000000000003032311320200110000000000000000000000000000000000000000000000000000101003001001001000000000000010303220000000000000000000000000000300111000000000100000000001100302021011110210103200000003000000110001100120200000 Reorder 186 187 177 178 179 180 181 182 183 184 185 Merge 178 179 Weight 9.6926 >1vvc_ -VK-CQSPPSISNGRHNGYEDFYTD----------------------------------GSVVTYSCNSGYSLIGNSGVLCSGGE---------WS-DPPTCQIVK-------------------------------------------------CPHPTISNGYLSSGFKRSYS-----------------------------YNDN-------VDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AIS-CGSPPPILNGRISYYSTPIAV----------------------------------GTVIRYSCSGTFRLIGEKSLLC----ITKDKVDGTW-DK--------PAPKCEYFNKYSS------------------------------------CPEPIVPGGY----------KIRGSTP--------------------YRHGDS-------VTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A ----CEEPP----------------TFEAMELIGKPKPY-----------------YEIGERVDYKCKKGY------------------------------------------------FYIPPLATHTICDRNHTWLPVSDDA------CYRETCP-------------------------YIRDPLNGQAVPAN----GTYE-------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A FR-SCEVP-------------------------------TRLNSASLKQPYITQNYFPVGTVVEYECRPGY------------------------------------------------RREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP-------------------------NPGEIRNGQ-----IDVPG-------GILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 03002312101011100010000000000000000000000000000000000000000231102120011011100031100000000000001000000000000000000000000000000000000000000000000000000000000220103001100000000000000000000000000000000000000000100000000302020011110210100200001010010000000000000120210000 @1ghq_B 03002012101011100010000000000000000000000000000000000000000231302120003011100031100000000000001000000000000000000000000000000000000000000000000000000000000220103001100000000000000000000000000000000000001000100000000302020003030200103200001010010000000000000020210000 @1ckl_A 00002102100000000000000000000000000000000000000000000000303200132020011000000000000000000000000000000000000000000000000000101003001001001000000000000010303220000000000000000000000000000300111000000000101000000001100302021011010200003200000003000000110001100020200000 @1nwv_A 00002102000000000000000000000000000000000000000000000000303231132020011000000000000000000000000000000000000000000000000000101003001001001000000000000010303220000000000000000000000000000300111000000000100000000001100302021011110210103200000003000000110001100120200000 Merge 317 303 Weight 9.47093 >1vvc_ -VK-CQSPPSISNGRHNGYEDFYTD----------------------------------GSVVTYSCNSGYSLIGNSGVLCSGGE---------WS-DPPTCQIVK-------------------------------------------------CPHPTISNGYLSSGFKRSYS----------------------------YNDN-------VDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AIS-CGSPPPILNGRISYYSTPIAV----------------------------------GTVIRYSCSGTFRLIGEKSLLC----ITKDKVDGTW-DK--------PAPKCEYFNKYSS------------------------------------CPEPIVPGGYK---------IRGSTP--------------------YRHGDS-------VTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A ----CEEPP----------------TFEAMELIGKPKPY-----------------YEIGERVDYKCKKGY------------------------------------------------FYIPPLATHTICDRNHTWLPVSDDA------CYRETCP------------------------YIRDPLNGQAVPAN----GTYE-------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A FR-SCEVP-------------------------------TRLNSASLKQPYITQNYFPVGTVVEYECRPGY------------------------------------------------RREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP------------------------NPGEIRNGQ-----IDVPG-------GILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 0300231210101110001000000000000000000000000000000000000000023110212001101110003110000000000000100000000000000000000000000000000000000000000000000000000000022010300110000000000000000000000000000000000000000100000000302020011110210100200001010010000000000000120210000 @1ghq_B 0300201210101110001000000000000000000000000000000000000000023130212000301110003110000000000000100000000000000000000000000000000000000000000000000000000000022010300110000000000000000000000000000000000001000100000000302020003030200103200001010010000000000000020210000 @1ckl_A 0000210210000000000000000000000000000000000000000000000030320013202001100000000000000000000000000000000000000000000000000010100300100100100000000000001030322000000000000000000000000000300111000000000101000000001100302021011010200003200000003000000110001100020200000 @1nwv_A 0000210200000000000000000000000000000000000000000000000030323113202001100000000000000000000000000000000000000000000000000010100300100100100000000000001030322000000000000000000000000000300111000000000100000000001100302021011110210103200000003000000110001100120200000 Reorder 96 97 66 68 70 72 74 75 76 77 78 79 80 81 82 83 Merge 68 70 Weight 9.08399 >1vvc_ -VK-CQSPPSISNGRHNGYEDFYTD---------------------------------GSVVTYSCNSGYSLIGNSGVLCSGGE---------WS-DPPTCQIVK-------------------------------------------------CPHPTISNGYLSSGFKRSYS----------------------------YNDN-------VDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AIS-CGSPPPILNGRISYYSTPIAV---------------------------------GTVIRYSCSGTFRLIGEKSLLC----ITKDKVDGTW-DK--------PAPKCEYFNKYSS------------------------------------CPEPIVPGGYK---------IRGSTP--------------------YRHGDS-------VTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A ----CEEPP-----------------TFEAMELIGKPKPY---------------YEIGERVDYKCKKGY------------------------------------------------FYIPPLATHTICDRNHTWLPVSDDA------CYRETCP------------------------YIRDPLNGQAVPAN----GTYE-------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A FR-SCEVP-----------------TR-------------LNSASLKQPYITQNYFPVGTVVEYECRPGY------------------------------------------------RREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP------------------------NPGEIRNGQ-----IDVPG-------GILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 030023121010111000100000000000000000000000000000000000000023110212001101110003110000000000000100000000000000000000000000000000000000000000000000000000000022010300110000000000000000000000000000000000000000100000000302020011110210100200001010010000000000000120210000 @1ghq_B 030020121010111000100000000000000000000000000000000000000023130212000301110003110000000000000100000000000000000000000000000000000000000000000000000000000022010300110000000000000000000000000000000000001000100000000302020003030200103200001010010000000000000020210000 @1ckl_A 000021021000000000000000000000000000000000000000000000030320013202001100000000000000000000000000000000000000000000000000010100300100100100000000000001030322000000000000000000000000000300111000000000101000000001100302021011010200003200000003000000110001100020200000 @1nwv_A 000021020000000000000000000000000000000000000000000000030323113202001100000000000000000000000000000000000000000000000000010100300100100100000000000001030322000000000000000000000000000300111000000000100000000001100302021011110210103200000003000000110001100120200000 Merge 176 177 Weight 9.02913 >1vvc_ -VK-CQSPPSISNGRHNGYEDFYTD---------------------------------GSVVTYSCNSGYSLIGNSGVLCSGGE---------WSDPPTCQIVK-------------------------------------------------CPHPTISNGYLSSGFKRSYS----------------------------YNDN-------VDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AIS-CGSPPPILNGRISYYSTPIAV---------------------------------GTVIRYSCSGTFRLIGEKSLLC----ITKDKVDGTWDK--------PAPKCEYFNKYSS------------------------------------CPEPIVPGGYK---------IRGSTP--------------------YRHGDS-------VTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A ----CEEPP-----------------TFEAMELIGKPKPY---------------YEIGERVDYKCKKGY-----------------------------------------------FYIPPLATHTICDRNHTWLPVSDDA------CYRETCP------------------------YIRDPLNGQAVPAN----GTYE-------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A FR-SCEVP-----------------TR-------------LNSASLKQPYITQNYFPVGTVVEYECRPGY-----------------------------------------------RREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP------------------------NPGEIRNGQ-----IDVPG-------GILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 03002312101011100010000000000000000000000000000000000000002311021200110111000311000000000000010000000000000000000000000000000000000000000000000000000000022010300110000000000000000000000000000000000000000100000000302020011110210100200001010010000000000000120210000 @1ghq_B 03002012101011100010000000000000000000000000000000000000002313021200030111000311000000000000010000000000000000000000000000000000000000000000000000000000022010300110000000000000000000000000000000000001000100000000302020003030200103200001010010000000000000020210000 @1ckl_A 00002102100000000000000000000000000000000000000000000003032001320200110000000000000000000000000000000000000000000000000010100300100100100000000000001030322000000000000000000000000000300111000000000101000000001100302021011010200003200000003000000110001100020200000 @1nwv_A 00002102000000000000000000000000000000000000000000000003032311320200110000000000000000000000000000000000000000000000000010100300100100100000000000001030322000000000000000000000000000300111000000000100000000001100302021011110210103200000003000000110001100120200000 Merge 5 10 Weight 8.99089 >1vvc_ -VKCQSPPSISNGRHNGYEDFYTD---------------------------------GSVVTYSCNSGYSLIGNSGVLCSGGE---------WSDPPTCQIVK-------------------------------------------------CPHPTISNGYLSSGFKRSYS----------------------------YNDN-------VDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIAV---------------------------------GTVIRYSCSGTFRLIGEKSLLC----ITKDKVDGTWDK--------PAPKCEYFNKYSS------------------------------------CPEPIVPGGYK---------IRGSTP--------------------YRHGDS-------VTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A ---CEEPP-----------------TFEAMELIGKPKPY---------------YEIGERVDYKCKKGY-----------------------------------------------FYIPPLATHTICDRNHTWLPVSDDA------CYRETCP------------------------YIRDPLNGQAVPAN----GTYE-------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A FRSCEVP-----------------TR-------------LNSASLKQPYITQNYFPVGTVVEYECRPGY-----------------------------------------------RREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP------------------------NPGEIRNGQ-----IDVPG-------GILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 0302312101011100010000000000000000000000000000000000000002311021200110111000311000000000000010000000000000000000000000000000000000000000000000000000000022010300110000000000000000000000000000000000000000100000000302020011110210100200001010010000000000000120210000 @1ghq_B 0312012101011100010000000000000000000000000000000000000002313021200030111000311000000000000010000000000000000000000000000000000000000000000000000000000022010300110000000000000000000000000000000000001000100000000302020003030200103200001010010000000000000020210000 @1ckl_A 0002102100000000000000000000000000000000000000000000003032001320200110000000000000000000000000000000000000000000000000010100300100100100000000000001030322000000000000000000000000000300111000000000101000000001100302021011010200003200000003000000110001100020200000 @1nwv_A 0012102000000000000000000000000000000000000000000000003032311320200110000000000000000000000000000000000000000000000000010100300100100100000000000001030322000000000000000000000000000300111000000000100000000001100302021011110210103200000003000000110001100120200000 Merge 389 396 Weight 8.82968 >1vvc_ -VKCQSPPSISNGRHNGYEDFYTD---------------------------------GSVVTYSCNSGYSLIGNSGVLCSGGE---------WSDPPTCQIVK-------------------------------------------------CPHPTISNGYLSSGFKRSYS----------------------------YND------NVDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIAV---------------------------------GTVIRYSCSGTFRLIGEKSLLC----ITKDKVDGTWDK--------PAPKCEYFNKYSS------------------------------------CPEPIVPGGYK---------IRGSTP--------------------YRHGD------SVTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A ---CEEPP-----------------TFEAMELIGKPKPY---------------YEIGERVDYKCKKGY-----------------------------------------------FYIPPLATHTICDRNHTWLPVSDDA------CYRETCP------------------------YIRDPLNGQAVPAN----GTYE------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A FRSCEVP-----------------TR-------------LNSASLKQPYITQNYFPVGTVVEYECRPGY-----------------------------------------------RREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP------------------------NPGEIRNGQ-----IDVPG------GILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 030231210101110001000000000000000000000000000000000000000231102120011011100031100000000000001000000000000000000000000000000000000000000000000000000000002201030011000000000000000000000000000000000000000010000000302020011110210100200001010010000000000000120210000 @1ghq_B 031201210101110001000000000000000000000000000000000000000231302120003011100031100000000000001000000000000000000000000000000000000000000000000000000000002201030011000000000000000000000000000000000000100010000000302020003030200103200001010010000000000000020210000 @1ckl_A 000210210000000000000000000000000000000000000000000000303200132020011000000000000000000000000000000000000000000000000001010030010010010000000000000103032200000000000000000000000000030011100000000010100000001100302021011010200003200000003000000110001100020200000 @1nwv_A 001210200000000000000000000000000000000000000000000000303231132020011000000000000000000000000000000000000000000000000001010030010010010000000000000103032200000000000000000000000000030011100000000010000000001100302021011110210103200000003000000110001100120200000 Merge 62 121 Weight 8.28681 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT--------------------------------DGSVVTYSCNSGYSLIGNSGVLCSGGE---------WSDPPTCQIVK-------------------------------------------------CPHPTISNGYLSSGFKRSYS----------------------------YND------NVDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA--------------------------------VGTVIRYSCSGTFRLIGEKSLLC----ITKDKVDGTWDK--------PAPKCEYFNKYSS------------------------------------CPEPIVPGGYK---------IRGSTP--------------------YRHGD------SVTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A ---CEEPP----------------TFEAMELIGKPKPY---------------YEIGERVDYKCKKGY-----------------------------------------------FYIPPLATHTICDRNHTWLPVSDDA------CYRETCP------------------------YIRDPLNGQAVPAN----GTYE------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A FRSCEVP----------------TR-------------LNSASLKQPYITQNYFPVGTVVEYECRPGY-----------------------------------------------RREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP------------------------NPGEIRNGQ-----IDVPG------GILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 03023121010111000100000000000000000000000000000000000000231102120011011100031100000000000001000000000000000000000000000000000000000000000000000000000002201030011000000000000000000000000000000000000000010000000302020011110210100200001010010000000000000120210000 @1ghq_B 03120121010111000100000000000000000000000000000000000003231302120003011100031100000000000001000000000000000000000000000000000000000000000000000000000002201030011000000000000000000000000000000000000100010000000302020003030200103200001010010000000000000020210000 @1ckl_A 00021021000000000000000000000000000000000000000000000303200132020011000000000000000000000000000000000000000000000000001010030010010010000000000000103032200000000000000000000000000030011100000000010100000001100302021011010200003200000003000000110001100020200000 @1nwv_A 00121020000000000000000000000000000000000000000000000303231132020011000000000000000000000000000000000000000000000000001010030010010010000000000000103032200000000000000000000000000030011100000000010000000001100302021011110210103200000003000000110001100120200000 Merge 189 180 Weight 8.25373 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT--------------------------------DGSVVTYSCNSGYSLIGNSGVLCSGGE---------WSDPPTCQIVK------------------------------------------------CPHPTISNGYLSSGFKRSYS----------------------------YND------NVDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA--------------------------------VGTVIRYSCSGTFRLIGEKSLLC----ITKDKVDGTWDKP-------APKCEYFNKYSS------------------------------------CPEPIVPGGYK---------IRGSTP--------------------YRHGD------SVTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A ---CEEPP----------------TFEAMELIGKPKPY---------------YEIGERVDYKCKKGY----------------------------------------------FYIPPLATHTICDRNHTWLPVSDDA------CYRETCP------------------------YIRDPLNGQAVPAN----GTYE------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A FRSCEVP----------------TR-------------LNSASLKQPYITQNYFPVGTVVEYECRPGY----------------------------------------------RREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP------------------------NPGEIRNGQ-----IDVPG------GILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 0302312101011100010000000000000000000000000000000000000023110212001101110003110000000000000100100000000000000000000000000000000000000000000000000000002201030011000000000000000000000000000000000000000010000000302020011110210100200001010010000000000000120210000 @1ghq_B 0312012101011100010000000000000000000000000000000000000323130212000301110003110000000000000100100000000000000000000000000000000000000000000000000000002201030011000000000000000000000000000000000000100010000000302020003030200103200001010010000000000000020210000 @1ckl_A 0002102100000000000000000000000000000000000000000000030320013202001100000000000000000000000000000000000000000000000001010030010010010000000000000103032200000000000000000000000000030011100000000010100000001100302021011010200003200000003000000110001100020200000 @1nwv_A 0012102000000000000000000000000000000000000000000000030323113202001100000000000000000000000000000000000000000000000001010030010010010000000000000103032200000000000000000000000000030011100000000010000000001100302021011110210103200000003000000110001100120200000 Reorder 197 198 199 200 183 184 185 186 187 Merge 186 187 Weight 8.06415 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT--------------------------------DGSVVTYSCNSGYSLIGNSGVLCSGGE---------WSDPPT---CQIVK--------------------------------------------CPHPTISNGYLSSGFKRSYS----------------------------YND------NVDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA--------------------------------VGTVIRYSCSGTFRLIGEKSLLC----ITKDKVDGTWDKP--APKC----EYFNKYSS------------------------------------CPEPIVPGGYK---------IRGSTP--------------------YRHGD------SVTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A ---CEEPP----------------TFEAMELIGKPKPY---------------YEIGERVDYKCKKGY---------------------------------------------FYIPPLATHTICDRNHTWLPVSDDA------CYRETCP------------------------YIRDPLNGQAVPAN----GTYE------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A FRSCEVP----------------TR-------------LNSASLKQPYITQNYFPVGTVVEYECRPGY---------------------------------------------RREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP------------------------NPGEIRNGQ-----IDVPG------GILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 030231210101110001000000000000000000000000000000000000002311021200110111000311000000000000010010000010000000000000000000000000000000000000000000000002201030011000000000000000000000000000000000000000010000000302020011110210100200001010010000000000000120210000 @1ghq_B 031201210101110001000000000000000000000000000000000000032313021200030111000311000000000000010010000010000000000000000000000000000000000000000000000002201030011000000000000000000000000000000000000100010000000302020003030200103200001010010000000000000020210000 @1ckl_A 000210210000000000000000000000000000000000000000000003032001320200110000000000000000000000000000000000000000000000001010030010010010000000000000103032200000000000000000000000000030011100000000010100000001100302021011010200003200000003000000110001100020200000 @1nwv_A 001210200000000000000000000000000000000000000000000003032311320200110000000000000000000000000000000000000000000000001010030010010010000000000000103032200000000000000000000000000030011100000000010000000001100302021011110210103200000003000000110001100120200000 Merge 319 304 Weight 8.01868 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT--------------------------------DGSVVTYSCNSGYSLIGNSGVLCSGGE---------WSDPPT---CQIVK--------------------------------------------CPHPTISNGYLSSGFKRSYS---------------------------YND------NVDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA--------------------------------VGTVIRYSCSGTFRLIGEKSLLC----ITKDKVDGTWDKP--APKC----EYFNKYSS------------------------------------CPEPIVPGGYKI--------RGSTP--------------------YRHGD------SVTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A ---CEEPP----------------TFEAMELIGKPKPY---------------YEIGERVDYKCKKGY---------------------------------------------FYIPPLATHTICDRNHTWLPVSDDA------CYRETCP-----------------------YIRDPLNGQAVPAN----GTYE------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A FRSCEVP----------------TR-------------LNSASLKQPYITQNYFPVGTVVEYECRPGY---------------------------------------------RREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP-----------------------NPGEIRNGQ-----IDVPG------GILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 03023121010111000100000000000000000000000000000000000000231102120011011100031100000000000001001000001000000000000000000000000000000000000000000000000220103001100000000000000000000000000000000000000010000000302020011110210100200001010010000000000000120210000 @1ghq_B 03120121010111000100000000000000000000000000000000000003231302120003011100031100000000000001001000001000000000000000000000000000000000000000000000000220103001100000000000000000000000000000000000100010000000302020003030200103200001010010000000000000020210000 @1ckl_A 00021021000000000000000000000000000000000000000000000303200132020011000000000000000000000000000000000000000000000000101003001001001000000000000010303220000000000000000000000000030011100000000010100000001100302021011010200003200000003000000110001100020200000 @1nwv_A 00121020000000000000000000000000000000000000000000000303231132020011000000000000000000000000000000000000000000000000101003001001001000000000000010303220000000000000000000000000030011100000000010000000001100302021011110210103200000003000000110001100120200000 Reorder 329 331 333 334 335 337 338 339 345 346 347 348 349 353 354 355 356 357 358 359 361 363 364 377 378 379 315 316 Merge 377 378 Weight 7.98917 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT--------------------------------DGSVVTYSCNSGYSLIGNSGVLCSGGE---------WSDPPT---CQIVK--------------------------------------------CPHPTISNGYLSSGFKRS-------------------------YS-YND------NVDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA--------------------------------VGTVIRYSCSGTFRLIGEKSLLC----ITKDKVDGTWDKP--APKC----EYFNKYSS------------------------------------CPEPIVPGGYKI------RGSTP--------------------Y-RHGD------SVTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A ---CEEPP----------------TFEAMELIGKPKPY---------------YEIGERVDYKCKKGY---------------------------------------------FYIPPLATHTICDRNHTWLPVSDDA------CYRETCP---------------------YIRDPLNGQAVPAN----GTY-E------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A FRSCEVP----------------TR-------------LNSASLKQPYITQNYFPVGTVVEYECRPGY---------------------------------------------RREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP---------------------NPGEIRNGQ-----IDVPG-------GILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 0302312101011100010000000000000000000000000000000000000023110212001101110003110000000000000100100000100000000000000000000000000000000000000000000000022010300110000000000000000000000000000000001000010000000302020011110210100200001010010000000000000120210000 @1ghq_B 0312012101011100010000000000000000000000000000000000000323130212000301110003110000000000000100100000100000000000000000000000000000000000000000000000022010300110000000000000000000000000000000001000010000000302020003030200103200001010010000000000000020210000 @1ckl_A 0002102100000000000000000000000000000000000000000000030320013202001100000000000000000000000000000000000000000000000010100300100100100000000000001030322000000000000000000000000300111000000000101000000001100302021011010200003200000003000000110001100020200000 @1nwv_A 0012102000000000000000000000000000000000000000000000030323113202001100000000000000000000000000000000000000000000000010100300100100100000000000001030322000000000000000000000000300111000000000100000000001100302021011110210103200000003000000110001100120200000 Merge 200 270 Weight 7.73088 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT--------------------------------DGSVVTYSCNSGYSLIGNSGVLCSGGE---------WSDPPT---CQIV-------------------------------------------KCPHPTISNGYLSSGFKRS-------------------------YS-YND------NVDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA--------------------------------VGTVIRYSCSGTFRLIGEKSLLC----ITKDKVDGTWDKP--APKC---EYFNKYSS------------------------------------CPEPIVPGGYKI------RGSTP--------------------Y-RHGD------SVTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A ---CEEPP----------------TFEAMELIGKPKPY---------------YEIGERVDYKCKKGY--------------------------------------------FYIPPLATHTICDRNHTWLPVSDDA------CYRETCP---------------------YIRDPLNGQAVPAN----GTY-E------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A FRSCEVP----------------TR-------------LNSASLKQPYITQNYFPVGTVVEYECRPGY--------------------------------------------RREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP---------------------NPGEIRNGQ-----IDVPG-------GILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 030231210101110001000000000000000000000000000000000000002311021200110111000311000000000000010010000010000000000000000000000000000000000000000000000022010300110000000000000000000000000000000001000010000000302020011110210100200001010010000000000000120210000 @1ghq_B 031201210101110001000000000000000000000000000000000000032313021200030111000311000000000000010010000010000000000000000000000000000000000000000000000022010300110000000000000000000000000000000001000010000000302020003030200103200001010010000000000000020210000 @1ckl_A 000210210000000000000000000000000000000000000000000003032001320200110000000000000000000000000000000000000000000000010100300100100100000000000001030322000000000000000000000000300111000000000101000000001100302021011010200003200000003000000110001100020200000 @1nwv_A 001210200000000000000000000000000000000000000000000003032311320200110000000000000000000000000000000000000000000000010100300100100100000000000001030322000000000000000000000000300111000000000100000000001100302021011110210103200000003000000110001100120200000 Merge 98 72 Weight 7.56552 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT-------------------------------DGSVVTYSCNSGYSLIGNSGVLCSGGE---------WSDPPT---CQIV-------------------------------------------KCPHPTISNGYLSSGFKRS-------------------------YS-YND------NVDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA-------------------------------VGTVIRYSCSGTFRLIGEKSLLC----ITKDKVDGTWDKP--APKC---EYFNKYSS------------------------------------CPEPIVPGGYKI------RGSTP--------------------Y-RHGD------SVTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A ---CEEPP----------------TFEAMELIGKPKPY--------------YEIGERVDYKCKKGY--------------------------------------------FYIPPLATHTICDRNHTWLPVSDDA------CYRETCP---------------------YIRDPLNGQAVPAN----GTY-E------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A FRSCEVP----------------TRL------------NSASLKQPYITQNYFPVGTVVEYECRPGY--------------------------------------------RREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP---------------------NPGEIRNGQ-----IDVPG-------GILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 03023121010111000100000000000000000000000000000000000002311021200110111000311000000000000010010000010000000000000000000000000000000000000000000000022010300110000000000000000000000000000000001000010000000302020011110210100200001010010000000000000120210000 @1ghq_B 03120121010111000100000000000000000000000000000000000032313021200030111000311000000000000010010000010000000000000000000000000000000000000000000000022010300110000000000000000000000000000000001000010000000302020003030200103200001010010000000000000020210000 @1ckl_A 00021021000000000000000000000000000000000000000000003032001320200110000000000000000000000000000000000000000000000010100300100100100000000000001030322000000000000000000000000300111000000000101000000001100302021011010200003200000003000000110001100020200000 @1nwv_A 00121020000000000000000000000000000000000000000000003032311320200110000000000000000000000000000000000000000000000010100300100100100000000000001030322000000000000000000000000300111000000000100000000001100302021011110210103200000003000000110001100120200000 Merge 379 385 Weight 7.53134 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT-------------------------------DGSVVTYSCNSGYSLIGNSGVLCSGGE---------WSDPPT---CQIV-------------------------------------------KCPHPTISNGYLSSGFKRS-------------------------YSYND------NVDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA-------------------------------VGTVIRYSCSGTFRLIGEKSLLC----ITKDKVDGTWDKP--APKC---EYFNKYSS------------------------------------CPEPIVPGGYKI------RGSTP--------------------YRHGD------SVTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A ---CEEPP----------------TFEAMELIGKPKPY--------------YEIGERVDYKCKKGY--------------------------------------------FYIPPLATHTICDRNHTWLPVSDDA------CYRETCP---------------------YIRDPLNGQAVPAN----GTYE------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A FRSCEVP----------------TRL------------NSASLKQPYITQNYFPVGTVVEYECRPGY--------------------------------------------RREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP---------------------NPGEIRNGQ-----IDVPG------GILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 0302312101011100010000000000000000000000000000000000000231102120011011100031100000000000001001000001000000000000000000000000000000000000000000000002201030011000000000000000000000000000000000100010000000302020011110210100200001010010000000000000120210000 @1ghq_B 0312012101011100010000000000000000000000000000000000003231302120003011100031100000000000001001000001000000000000000000000000000000000000000000000002201030011000000000000000000000000000000000100010000000302020003030200103200001010010000000000000020210000 @1ckl_A 0002102100000000000000000000000000000000000000000000303200132020011000000000000000000000000000000000000000000000001010030010010010000000000000103032200000000000000000000000030011100000000010100000001100302021011010200003200000003000000110001100020200000 @1nwv_A 0012102000000000000000000000000000000000000000000000303231132020011000000000000000000000000000000000000000000000001010030010010010000000000000103032200000000000000000000000030011100000000010000000001100302021011110210103200000003000000110001100120200000 Merge 97 118 Weight 7.44965 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT------------------------------DGSVVTYSCNSGYSLIGNSGVLCSGGE---------WSDPPT---CQIV-------------------------------------------KCPHPTISNGYLSSGFKRS-------------------------YSYND------NVDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA------------------------------VGTVIRYSCSGTFRLIGEKSLLC----ITKDKVDGTWDKP--APKC---EYFNKYSS------------------------------------CPEPIVPGGYKI------RGSTP--------------------YRHGD------SVTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A ---CEEPP----------------TFEAMELIGKPKP-------------YYEIGERVDYKCKKGY--------------------------------------------FYIPPLATHTICDRNHTWLPVSDDA------CYRETCP---------------------YIRDPLNGQAVPAN----GTYE------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A FRSCEVP----------------TRL-----------NSASLKQPYITQNYFPVGTVVEYECRPGY--------------------------------------------RREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP---------------------NPGEIRNGQ-----IDVPG------GILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 030231210101110001000000000000000000000000000000000000231102120011011100031100000000000001001000001000000000000000000000000000000000000000000000002201030011000000000000000000000000000000000100010000000302020011110210100200001010010000000000000120210000 @1ghq_B 031201210101110001000000000000000000000000000000000003231302120003011100031100000000000001001000001000000000000000000000000000000000000000000000002201030011000000000000000000000000000000000100010000000302020003030200103200001010010000000000000020210000 @1ckl_A 000210210000000000000000000000000000000000000000001303200132020011000000000000000000000000000000000000000000000001010030010010010000000000000103032200000000000000000000000030011100000000010100000001100302021011010200003200000003000000110001100020200000 @1nwv_A 001210200000000000000000000000000000000000000000001303231132020011000000000000000000000000000000000000000000000001010030010010010000000000000103032200000000000000000000000030011100000000010000000001100302021011110210103200000003000000110001100120200000 Merge 153 172 Weight 7.30005 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT------------------------------DGSVVTYSCNSGYSLIGNSGVLCSGG--------EWSDPPT---CQIV-------------------------------------------KCPHPTISNGYLSSGFKRS-------------------------YSYND------NVDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA------------------------------VGTVIRYSCSGTFRLIGEKSLLC---ITKDKVDGTWDKP--APKC---EYFNKYSS------------------------------------CPEPIVPGGYKI------RGSTP--------------------YRHGD------SVTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A ---CEEPP----------------TFEAMELIGKPKP-------------YYEIGERVDYKCKKGY-------------------------------------------FYIPPLATHTICDRNHTWLPVSDDA------CYRETCP---------------------YIRDPLNGQAVPAN----GTYE------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A FRSCEVP----------------TRL-----------NSASLKQPYITQNYFPVGTVVEYECRPGY-------------------------------------------RREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP---------------------NPGEIRNGQ-----IDVPG------GILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 03023121010111000100000000000000000000000000000000000023110212001101110003110000000000001001000001000000000000000000000000000000000000000000000002201030011000000000000000000000000000000000100010000000302020011110210100200001010010000000000000120210000 @1ghq_B 03120121010111000100000000000000000000000000000000000323130212000301110003110000000000001001000001000000000000000000000000000000000000000000000002201030011000000000000000000000000000000000100010000000302020003030200103200001010010000000000000020210000 @1ckl_A 00021021000000000000000000000000000000000000000000130320013202001100000000000000000000000000000000000000000000001010030010010010000000000000103032200000000000000000000000030011100000000010100000001100302021011010200003200000003000000110001100020200000 @1nwv_A 00121020000000000000000000000000000000000000000000130323113202001100000000000000000000000000000000000000000000001010030010010010000000000000103032200000000000000000000000030011100000000010000000001100302021011110210103200000003000000110001100120200000 Reorder 183 184 181 182 Merge 182 183 Weight 7.25182 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT------------------------------DGSVVTYSCNSGYSLIGNSGVLCSGG--------EWSDP-PT-CQIV-------------------------------------------KCPHPTISNGYLSSGFKRS-------------------------YSYND------NVDFKCKYGYKLSGSSSSTC-SPGNTW-KP------------ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA------------------------------VGTVIRYSCSGTFRLIGEKSLLC---ITKDKVDGTWDKPAP-KC---EYFNKYSS------------------------------------CPEPIVPGGYKI------RGSTP--------------------YRHGD------SVTFACKTNFSMNGNKSVWC-QANNMW-GPTRL-----------PTCVS--- >1ckl_A ---CEEPP----------------TFEAMELIGKPKP-------------YYEIGERVDYKCKKGY------------------------------------------FYIPPLATHTICDRNHTWLPVSDDA------CYRETCP---------------------YIRDPLNGQAVPAN----GTYE------FGYQMHFICNEGYYLIGEEILYCE------L-----KGSVAIWSGKPPIC--EKV >1nwv_A FRSCEVP----------------TRL-----------NSASLKQPYITQNYFPVGTVVEYECRPGY------------------------------------------RREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP---------------------NPGEIRNGQ-----IDVPG------GILFGATISFSCNTGYKLFGSTSSFCL------I-----SGSSVQWSDPLPEC--REH @1vvc_ 0302312101011100010000000000000000000000000000000000002311021200110111000311000000000000100101001000000000000000000000000000000000000000000000002201030011000000000000000000000000000000000100010000000302020011110210100200001010010000000000000120210000 @1ghq_B 0312012101011100010000000000000000000000000000000000032313021200030111000311000000000000100101001000000000000000000000000000000000000000000000002201030011000000000000000000000000000000000100010000000302020003030200103200001010010000000000000020210000 @1ckl_A 0002102100000000000000000000000000000000000000000013032001320200110000000000000000000000000000000000000000000001010030010010010000000000000103032200000000000000000000000030011100000000010100000001100302021011010200003200000003000000110001100020200000 @1nwv_A 0012102000000000000000000000000000000000000000000013032311320200110000000000000000000000000000000000000000000001010030010010010000000000000103032200000000000000000000000030011100000000010000000001100302021011110210103200000003000000110001100120200000 Merge 465 487 Weight 7.05697 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT------------------------------DGSVVTYSCNSGYSLIGNSGVLCSGG--------EWSDP-PT-CQIV-------------------------------------------KCPHPTISNGYLSSGFKRS-------------------------YSYND------NVDFKCKYGYKLSGSSSSTC-SPGNTW-KP-----------ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA------------------------------VGTVIRYSCSGTFRLIGEKSLLC---ITKDKVDGTWDKPAP-KC---EYFNKYSS------------------------------------CPEPIVPGGYKI------RGSTP--------------------YRHGD------SVTFACKTNFSMNGNKSVWC-QANNMW-GPTR----------LPTCVS--- >1ckl_A ---CEEPP----------------TFEAMELIGKPKP-------------YYEIGERVDYKCKKGY------------------------------------------FYIPPLATHTICDRNHTWLPVSDDA------CYRETCP---------------------YIRDPLNGQAVPAN----GTYE------FGYQMHFICNEGYYLIGEEILYCE------L----KGSVAIWSGKPPIC--EKV >1nwv_A FRSCEVP----------------TRL-----------NSASLKQPYITQNYFPVGTVVEYECRPGY------------------------------------------RREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP---------------------NPGEIRNGQ-----IDVPG------GILFGATISFSCNTGYKLFGSTSSFCL------I----SGSSVQWSDPLPEC--REH @1vvc_ 030231210101110001000000000000000000000000000000000000231102120011011100031100000000000010010100100000000000000000000000000000000000000000000000220103001100000000000000000000000000000000010001000000030202001111021010020000101001000000000000120210000 @1ghq_B 031201210101110001000000000000000000000000000000000003231302120003011100031100000000000010010100100000000000000000000000000000000000000000000000220103001100000000000000000000000000000000010001000000030202000303020010320000101001000000000000120210000 @1ckl_A 000210210000000000000000000000000000000000000000001303200132020011000000000000000000000000000000000000000000000101003001001001000000000000010303220000000000000000000000003001110000000001010000000110030202101101020000320000000300000110001100020200000 @1nwv_A 001210200000000000000000000000000000000000000000001303231132020011000000000000000000000000000000000000000000000101003001001001000000000000010303220000000000000000000000003001110000000001000000000110030202101111021010320000000300000110001100120200000 Merge 184 185 Weight 7.01329 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT------------------------------DGSVVTYSCNSGYSLIGNSGVLCSGG--------EWSDP-PTCQIV-------------------------------------------KCPHPTISNGYLSSGFKRS-------------------------YSYND------NVDFKCKYGYKLSGSSSSTC-SPGNTW-KP-----------ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA------------------------------VGTVIRYSCSGTFRLIGEKSLLC---ITKDKVDGTWDKPAPKC---EYFNKYSS------------------------------------CPEPIVPGGYKI------RGSTP--------------------YRHGD------SVTFACKTNFSMNGNKSVWC-QANNMW-GPTR----------LPTCVS--- >1ckl_A ---CEEPP----------------TFEAMELIGKPKP-------------YYEIGERVDYKCKKGY-----------------------------------------FYIPPLATHTICDRNHTWLPVSDDA------CYRETCP---------------------YIRDPLNGQAVPAN----GTYE------FGYQMHFICNEGYYLIGEEILYCE------L----KGSVAIWSGKPPIC--EKV >1nwv_A FRSCEVP----------------TRL-----------NSASLKQPYITQNYFPVGTVVEYECRPGY-----------------------------------------RREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP---------------------NPGEIRNGQ-----IDVPG------GILFGATISFSCNTGYKLFGSTSSFCL------I----SGSSVQWSDPLPEC--REH @1vvc_ 03023121010111000100000000000000000000000000000000000023110212001101110003110000000000001001010100000000000000000000000000000000000000000000000220103001100000000000000000000000000000000010001000000030202001111021010020000101001000000000000120210000 @1ghq_B 03120121010111000100000000000000000000000000000000000323130212000301110003110000000000001001010100000000000000000000000000000000000000000000000220103001100000000000000000000000000000000010001000000030202000303020010320000101001000000000000120210000 @1ckl_A 00021021000000000000000000000000000000000000000000130320013202001100000000000000000000000000000000000000000000101003001001001000000000000010303220000000000000000000000003001110000000001010000000110030202101101020000320000000300000110001100020200000 @1nwv_A 00121020000000000000000000000000000000000000000000130323113202001100000000000000000000000000000000000000000000101003001001001000000000000010303220000000000000000000000003001110000000001000000000110030202101111021010320000000300000110001100120200000 Merge 390 364 Weight 6.95422 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT------------------------------DGSVVTYSCNSGYSLIGNSGVLCSGG--------EWSDP-PTCQIV-------------------------------------------KCPHPTISNGYLSSGFKRS-------------------------YSYND-----NVDFKCKYGYKLSGSSSSTC-SPGNTW-KP-----------ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA------------------------------VGTVIRYSCSGTFRLIGEKSLLC---ITKDKVDGTWDKPAPKC---EYFNKYSS------------------------------------CPEPIVPGGYKI------RGSTP--------------------YRHGD-----SVTFACKTNFSMNGNKSVWC-QANNMW-GPTR----------LPTCVS--- >1ckl_A ---CEEPP----------------TFEAMELIGKPKP-------------YYEIGERVDYKCKKGY-----------------------------------------FYIPPLATHTICDRNHTWLPVSDDA------CYRETCP---------------------YIRDPLNGQAVPAN----GTYE-----FGYQMHFICNEGYYLIGEEILYCE------L----KGSVAIWSGKPPIC--EKV >1nwv_A FRSCEVP----------------TRL-----------NSASLKQPYITQNYFPVGTVVEYECRPGY-----------------------------------------RREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP---------------------NPGEIRNGQ-----IDVPGG-----ILFGATISFSCNTGYKLFGSTSSFCL------I----SGSSVQWSDPLPEC--REH @1vvc_ 0302312101011100010000000000000000000000000000000000002311021200110111000311000000000000100101010000000000000000000000000000000000000000000000022010300110000000000000000000000000000000001000100000030202001111021010020000101001000000000000120210000 @1ghq_B 0312012101011100010000000000000000000000000000000000032313021200030111000311000000000000100101010000000000000000000000000000000000000000000000022010300110000000000000000000000000000000001000100000030202000303020010320000101001000000000000120210000 @1ckl_A 0002102100000000000000000000000000000000000000000013032001320200110000000000000000000000000000000000000000000010100300100100100000000000001030322000000000000000000000000300111000000000101000000110030202101101020000320000000300000110001100020200000 @1nwv_A 0012102000000000000000000000000000000000000000000013032311320200110000000000000000000000000000000000000000000010100300100100100000000000001030322000000000000000000000000300111000000000100000000110030202101111021010320000000300000110001100120200000 Merge 315 305 Weight 6.81727 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT------------------------------DGSVVTYSCNSGYSLIGNSGVLCSGG--------EWSDP-PTCQIV-------------------------------------------KCPHPTISNGYLSSGFKRS------------------------YSYND-----NVDFKCKYGYKLSGSSSSTC-SPGNTW-KP-----------ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA------------------------------VGTVIRYSCSGTFRLIGEKSLLC---ITKDKVDGTWDKPAPKC---EYFNKYSS------------------------------------CPEPIVPGGYKIR-----GSTP--------------------YRHGD-----SVTFACKTNFSMNGNKSVWC-QANNMW-GPTR----------LPTCVS--- >1ckl_A ---CEEPP----------------TFEAMELIGKPKP-------------YYEIGERVDYKCKKGY-----------------------------------------FYIPPLATHTICDRNHTWLPVSDDA------CYRETCP--------------------YIRDPLNGQAVPAN----GTYE-----FGYQMHFICNEGYYLIGEEILYCE------L----KGSVAIWSGKPPIC--EKV >1nwv_A FRSCEVP----------------TRL-----------NSASLKQPYITQNYFPVGTVVEYECRPGY-----------------------------------------RREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP--------------------NPGEIRNGQ-----IDVPGG-----ILFGATISFSCNTGYKLFGSTSSFCL------I----SGSSVQWSDPLPEC--REH @1vvc_ 030231210101110001000000000000000000000000000000000000231102120011011100031100000000000010010101000000000000000000000000000000000000000000000002201030011000000000000000000000000000000001000100000030202001111021010020000101001000000000000120210000 @1ghq_B 031201210101110001000000000000000000000000000000000003231302120003011100031100000000000010010101000000000000000000000000000000000000000000000002201030011000000000000000000000000000000001000100000030202000303020010320000101001000000000000120210000 @1ckl_A 000210210000000000000000000000000000000000000000001303200132020011000000000000000000000000000000000000000000001010030010010010000000000000103032200000000000000000000000300111000000000101000000110030202101101020000320000000300000110001100020200000 @1nwv_A 001210200000000000000000000000000000000000000000001303231132020011000000000000000000000000000000000000000000001010030010010010000000000000103032200000000000000000000000300111000000000100000000110030202101111021010320000000300000110001100120200000 Merge 152 171 Weight 6.63222 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT------------------------------DGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTCQIV-------------------------------------------KCPHPTISNGYLSSGFKRS------------------------YSYND-----NVDFKCKYGYKLSGSSSSTC-SPGNTW-KP-----------ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA------------------------------VGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKC---EYFNKYSS------------------------------------CPEPIVPGGYKIR-----GSTP--------------------YRHGD-----SVTFACKTNFSMNGNKSVWC-QANNMW-GPTR----------LPTCVS--- >1ckl_A ---CEEPP----------------TFEAMELIGKPKP-------------YYEIGERVDYKCKKGY----------------------------------------FYIPPLATHTICDRNHTWLPVSDDA------CYRETCP--------------------YIRDPLNGQAVPAN----GTYE-----FGYQMHFICNEGYYLIGEEILYCE------L----KGSVAIWSGKPPIC--EKV >1nwv_A FRSCEVP----------------TRL-----------NSASLKQPYITQNYFPVGTVVEYECRPGY----------------------------------------RREPSLSPKLTCLQNLKW-------STAVEFCKKKSCP--------------------NPGEIRNGQ-----IDVPGG-----ILFGATISFSCNTGYKLFGSTSSFCL------I----SGSSVQWSDPLPEC--REH @1vvc_ 03023121010111000100000000000000000000000000000000000023110212001101110003110000000001010010101000000000000000000000000000000000000000000000002201030011000000000000000000000000000000001000100000030202001111021010020000101001000000000000120210000 @1ghq_B 03120121010111000100000000000000000000000000000000000323130212000301110003110000000001010010101000000000000000000000000000000000000000000000002201030011000000000000000000000000000000001000100000030202000303020010320000101001000000000000120210000 @1ckl_A 00021021000000000000000000000000000000000000000000130320013202001100000000000000000000000000000000000000000001010030010010010000000000000103032200000000000000000000000300111000000000101000000110030202101101020000320000000300000110001100020200000 @1nwv_A 00121020000000000000000000000000000000000000000000130323113202001100000000000000000000000000000000000000000001010030010010010000000000000103032200000000000000000000000300111000000000100000000110030202101111021010320000000300000110001100120200000 Merge 252 261 Weight 6.14757 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT------------------------------DGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTCQIV------------------------------------------KCPHPTISNGYLSSGFKRS------------------------YSYND-----NVDFKCKYGYKLSGSSSSTC-SPGNTW-KP-----------ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA------------------------------VGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKC---EYFNKYSS-----------------------------------CPEPIVPGGYKIR-----GSTP--------------------YRHGD-----SVTFACKTNFSMNGNKSVWC-QANNMW-GPTR----------LPTCVS--- >1ckl_A ---CEEPP----------------TFEAMELIGKPKP-------------YYEIGERVDYKCKKGY----------------------------------------FYIPPLATHTICDRNHTWLPVSDD-----ACYRETCP--------------------YIRDPLNGQAVPAN----GTYE-----FGYQMHFICNEGYYLIGEEILYCE------L----KGSVAIWSGKPPIC--EKV >1nwv_A FRSCEVP----------------TRL-----------NSASLKQPYITQNYFPVGTVVEYECRPGY----------------------------------------RREPSLSPKLTCLQNLKW------STAVEFCKKKSCP--------------------NPGEIRNGQ-----IDVPGG-----ILFGATISFSCNTGYKLFGSTSSFCL------I----SGSSVQWSDPLPEC--REH @1vvc_ 0302312101011100010000000000000000000000000000000000002311021200110111000311000000000101001010100000000000000000000000000000000000000000000002201030011000000000000000000000000000000001000100000030202001111021010020000101001000000000000120210000 @1ghq_B 0312012101011100010000000000000000000000000000000000032313021200030111000311000000000101001010100000000000000000000000000000000000000000000002201030011000000000000000000000000000000001000100000030202000303020010320000101001000000000000120210000 @1ckl_A 0002102100000000000000000000000000000000000000000013032001320200110000000000000000000000000000000000000000000101003001001001000000000000103032200000000000000000000000300111000000000101000000110030202101101020000320000000300000110001100020200000 @1nwv_A 0012102000000000000000000000000000000000000000000013032311320200110000000000000000000000000000000000000000000101003001001001000000000000103032200000000000000000000000300111000000000100000000110030202101111021010320000000300000110001100120200000 Merge 388 395 Weight 6.10206 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT------------------------------DGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTCQIV------------------------------------------KCPHPTISNGYLSSGFKRS------------------------YSYN----DNVDFKCKYGYKLSGSSSSTC-SPGNTW-KP-----------ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA------------------------------VGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKC---EYFNKYSS-----------------------------------CPEPIVPGGYKIR-----GSTP--------------------YRHG----DSVTFACKTNFSMNGNKSVWC-QANNMW-GPTR----------LPTCVS--- >1ckl_A ---CEEPP----------------TFEAMELIGKPKP-------------YYEIGERVDYKCKKGY----------------------------------------FYIPPLATHTICDRNHTWLPVSDD-----ACYRETCP--------------------YIRDPLNGQAVPAN----GTYE----FGYQMHFICNEGYYLIGEEILYCE------L----KGSVAIWSGKPPIC--EKV >1nwv_A FRSCEVP----------------TRL-----------NSASLKQPYITQNYFPVGTVVEYECRPGY----------------------------------------RREPSLSPKLTCLQNLKW------STAVEFCKKKSCP--------------------NPGEIRNGQ-----IDVPGG----ILFGATISFSCNTGYKLFGSTSSFCL------I----SGSSVQWSDPLPEC--REH @1vvc_ 030231210101110001000000000000000000000000000000000000231102120011011100031100000000010100101010000000000000000000000000000000000000000000000220103001100000000000000000000000000000000100000000030202001111021010020000101001000000000000120210000 @1ghq_B 031201210101110001000000000000000000000000000000000003231302120003011100031100000000010100101010000000000000000000000000000000000000000000000220103001100000000000000000000000000000000100000000030202000303020010320000101001000000000000120210000 @1ckl_A 000210210000000000000000000000000000000000000000001303200132020011000000000000000000000000000000000000000000010100300100100100000000000010303220000000000000000000000030011100000000010100000110030202101101020000320000000300000110001100020200000 @1nwv_A 001210200000000000000000000000000000000000000000001303231132020011000000000000000000000000000000000000000000010100300100100100000000000010303220000000000000000000000030011100000000010000000110030202101111021010320000000300000110001100120200000 Merge 99 74 Weight 5.98845 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT-----------------------------DGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTCQIV------------------------------------------KCPHPTISNGYLSSGFKRS------------------------YSYN----DNVDFKCKYGYKLSGSSSSTC-SPGNTW-KP-----------ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA-----------------------------VGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKC---EYFNKYSS-----------------------------------CPEPIVPGGYKIR-----GSTP--------------------YRHG----DSVTFACKTNFSMNGNKSVWC-QANNMW-GPTR----------LPTCVS--- >1ckl_A ---CEEPP----------------TFEAMELIGKPKP------------YYEIGERVDYKCKKGY----------------------------------------FYIPPLATHTICDRNHTWLPVSDD-----ACYRETCP--------------------YIRDPLNGQAVPAN----GTYE----FGYQMHFICNEGYYLIGEEILYCE------L----KGSVAIWSGKPPIC--EKV >1nwv_A FRSCEVP----------------TRLN----------SASLKQPYITQNYFPVGTVVEYECRPGY----------------------------------------RREPSLSPKLTCLQNLKW------STAVEFCKKKSCP--------------------NPGEIRNGQ-----IDVPGG----ILFGATISFSCNTGYKLFGSTSSFCL------I----SGSSVQWSDPLPEC--REH @1vvc_ 03023121010111000100000000000000000000000000000000000231102120011011100031100000000010100101010000000000000000000000000000000000000000000000220103001100000000000000000000000000000000100000000030202001111021010020000101001000000000000120210000 @1ghq_B 03120121010111000100000000000000000000000000000000003231302120003011100031100000000010100101010000000000000000000000000000000000000000000000220103001100000000000000000000000000000000100000000030202000303020010320000101001000000000000120210000 @1ckl_A 00021021000000000000000000000000000000000000000001303200132020011000000000000000000000000000000000000000000010100300100100100000000000010303220000000000000000000000030011100000000010100000110030202101101020000320000000300000110001100020200000 @1nwv_A 00121020000000000000000000000000000000000000000001303231132020011000000000000000000000000000000000000000000010100300100100100000000000010303220000000000000000000000030011100000000010000000110030202101111021010320000000300000110001100120200000 Merge 316 306 Weight 5.69175 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT-----------------------------DGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTCQIV------------------------------------------KCPHPTISNGYLSSGFKRS-----------------------YSYN----DNVDFKCKYGYKLSGSSSSTC-SPGNTW-KP-----------ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA-----------------------------VGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKC---EYFNKYSS-----------------------------------CPEPIVPGGYKIRG----STP--------------------YRHG----DSVTFACKTNFSMNGNKSVWC-QANNMW-GPTR----------LPTCVS--- >1ckl_A ---CEEPP----------------TFEAMELIGKPKP------------YYEIGERVDYKCKKGY----------------------------------------FYIPPLATHTICDRNHTWLPVSDD-----ACYRETCP-------------------YIRDPLNGQAVPAN----GTYE----FGYQMHFICNEGYYLIGEEILYCE------L----KGSVAIWSGKPPIC--EKV >1nwv_A FRSCEVP----------------TRLN----------SASLKQPYITQNYFPVGTVVEYECRPGY----------------------------------------RREPSLSPKLTCLQNLKW------STAVEFCKKKSCP-------------------NPGEIRNGQ-----IDVPGG----ILFGATISFSCNTGYKLFGSTSSFCL------I----SGSSVQWSDPLPEC--REH @1vvc_ 0302312101011100010000000000000000000000000000000000023110212001101110003110000000001010010101000000000000000000000000000000000000000000000022010300110001000000000000000000000000000100000000030202001111021010020000101001000000000000120210000 @1ghq_B 0312012101011100010000000000000000000000000000000000323130212000301110003110000000001010010101000000000000000000000000000000000000000000000022010300110001000000000000000000000000000100000000030202000303020010320000101001000000000000120210000 @1ckl_A 0002102100000000000000000000000000000000000000000130320013202001100000000000000000000000000000000000000000001010030010010010000000000001030322000000000000000000000030011100000000010100000110030202101101020000320000000300000110001100020200000 @1nwv_A 0012102000000000000000000000000000000000000000000130323113202001100000000000000000000000000000000000000000001010030010010010000000000001030322000000000000000000000030011100000000010000000110030202101111021010320000000300000110001100120200000 Merge 66 20 Weight 5.53104 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT----------------------------DGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTCQIV------------------------------------------KCPHPTISNGYLSSGFKRS-----------------------YSYN----DNVDFKCKYGYKLSGSSSSTC-SPGNTW-KP-----------ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA----------------------------VGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKC---EYFNKYSS-----------------------------------CPEPIVPGGYKIRG----STP--------------------YRHG----DSVTFACKTNFSMNGNKSVWC-QANNMW-GPTR----------LPTCVS--- >1ckl_A ---CEEPP---------------TFEAMELIGKPKP------------YYEIGERVDYKCKKGY----------------------------------------FYIPPLATHTICDRNHTWLPVSDD-----ACYRETCP-------------------YIRDPLNGQAVPAN----GTYE----FGYQMHFICNEGYYLIGEEILYCE------L----KGSVAIWSGKPPIC--EKV >1nwv_A FRSCEVPT---------------RLN----------SASLKQPYITQNYFPVGTVVEYECRPGY----------------------------------------RREPSLSPKLTCLQNLKW------STAVEFCKKKSCP-------------------NPGEIRNGQ-----IDVPGG----ILFGATISFSCNTGYKLFGSTSSFCL------I----SGSSVQWSDPLPEC--REH @1vvc_ 030231210101110001000000000000000000000000000000000023110212001101110003110000000001010010101000000000000000000000000000000000000000000000022010300110001000000000000000000000000000100000000030202001111021010020000101001000000000000120210000 @1ghq_B 031201210101110001000000000000000000000000000000000323130212000301110003110000000001010010101000000000000000000000000000000000000000000000022010300110001000000000000000000000000000100000000030202000303020010320000101001000000000000120210000 @1ckl_A 000210210000000000000000000000000000000000000000130320013202001100000000000000000000000000000000000000000001010030010010010000000000001030322000000000000000000000030011100000000010100000110030202101101020000320000000300000110001100020200000 @1nwv_A 001210200000000000000000000000000000000000000000130323113202001100000000000000000000000000000000000000000001010030010010010000000000001030322000000000000000000000030011100000000010000000110030202101111021010320000000300000110001100120200000 Reorder 334 335 337 338 339 345 346 347 348 349 353 354 355 356 329 331 333 Merge 353 354 Weight 5.47833 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT----------------------------DGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTCQIV------------------------------------------KCPHPTISNGYLSSGFKRS----------------------YSYN----DNVDFKCKYGYKLSGSSSSTC-SPGNTW-KP-----------ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA----------------------------VGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKC---EYFNKYSS-----------------------------------CPEPIVPGGYKIRG-----------------STP------YRHG----DSVTFACKTNFSMNGNKSVWC-QANNMW-GPTR----------LPTCVS--- >1ckl_A ---CEEPP---------------TFEAMELIGKPKP------------YYEIGERVDYKCKKGY----------------------------------------FYIPPLATHTICDRNHTWLPVSDD-----ACYRETCP----------------YIRDPLNGQAVPAN------GTYE----FGYQMHFICNEGYYLIGEEILYCE------L----KGSVAIWSGKPPIC--EKV >1nwv_A FRSCEVPT---------------RLN----------SASLKQPYITQNYFPVGTVVEYECRPGY----------------------------------------RREPSLSPKLTCLQNLKW------STAVEFCKKKSCP----------------NPGEIRNGQ-------IDVPGG----ILFGATISFSCNTGYKLFGSTSSFCL------I----SGSSVQWSDPLPEC--REH @1vvc_ 03023121010111000100000000000000000000000000000000002311021200110111000311000000000101001010100000000000000000000000000000000000000000000002201030011000100000000000000000000000000100000000030202001111021010020000101001000000000000120210000 @1ghq_B 03120121010111000100000000000000000000000000000000032313021200030111000311000000000101001010100000000000000000000000000000000000000000000002201030011000100000000000000000000000000100000000030202000303020010320000101001000000000000120210000 @1ckl_A 00021021000000000000000000000000000000000000000013032001320200110000000000000000000000000000000000000000000101003001001001000000000000103032200000000000000000003001110000000000010100000110030202101101020000320000000300000110001100020200000 @1nwv_A 00121020000000000000000000000000000000000000000013032311320200110000000000000000000000000000000000000000000101003001001001000000000000103032200000000000000000003001110000000000010000000110030202101111021010320000000300000110001100120200000 Merge 387 394 Weight 5.44693 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT----------------------------DGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTCQIV------------------------------------------KCPHPTISNGYLSSGFKRS----------------------YSY---NDNVDFKCKYGYKLSGSSSSTC-SPGNTW-KP-----------ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA----------------------------VGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKC---EYFNKYSS-----------------------------------CPEPIVPGGYKIRG-----------------STP------YRH---GDSVTFACKTNFSMNGNKSVWC-QANNMW-GPTR----------LPTCVS--- >1ckl_A ---CEEPP---------------TFEAMELIGKPKP------------YYEIGERVDYKCKKGY----------------------------------------FYIPPLATHTICDRNHTWLPVSDD-----ACYRETCP----------------YIRDPLNGQAVPAN------GTYE---FGYQMHFICNEGYYLIGEEILYCE------L----KGSVAIWSGKPPIC--EKV >1nwv_A FRSCEVPT---------------RLN----------SASLKQPYITQNYFPVGTVVEYECRPGY----------------------------------------RREPSLSPKLTCLQNLKW------STAVEFCKKKSCP----------------NPGEIRNGQ-------IDVPGG---ILFGATISFSCNTGYKLFGSTSSFCL------I----SGSSVQWSDPLPEC--REH @1vvc_ 0302312101011100010000000000000000000000000000000000231102120011011100031100000000010100101010000000000000000000000000000000000000000000000220103001100010000000000000000000000000010000000030202001111021010020000101001000000000000120210000 @1ghq_B 0312012101011100010000000000000000000000000000000003231302120003011100031100000000010100101010000000000000000000000000000000000000000000000220103001100010000000000000000000000000010000010030202000303020010320000101001000000000000120210000 @1ckl_A 0002102100000000000000000000000000000000000000001303200132020011000000000000000000000000000000000000000000010100300100100100000000000010303220000000000000000000300111000000000001010000110030202101101020000320000000300000110001100020200000 @1nwv_A 0012102000000000000000000000000000000000000000001303231132020011000000000000000000000000000000000000000000010100300100100100000000000010303220000000000000000000300111000000000001000000110030202101111021010320000000300000110001100120200000 Merge 199 268 Weight 5.40422 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT----------------------------DGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTCQI-----------------------------------------VKCPHPTISNGYLSSGFKRS----------------------YSY---NDNVDFKCKYGYKLSGSSSSTC-SPGNTW-KP-----------ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA----------------------------VGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKC--EYFNKYSS-----------------------------------CPEPIVPGGYKIRG-----------------STP------YRH---GDSVTFACKTNFSMNGNKSVWC-QANNMW-GPTR----------LPTCVS--- >1ckl_A ---CEEPP---------------TFEAMELIGKPKP------------YYEIGERVDYKCKKGY---------------------------------------FYIPPLATHTICDRNHTWLPVSDD-----ACYRETCP----------------YIRDPLNGQAVPAN------GTYE---FGYQMHFICNEGYYLIGEEILYCE------L----KGSVAIWSGKPPIC--EKV >1nwv_A FRSCEVPT---------------RLN----------SASLKQPYITQNYFPVGTVVEYECRPGY---------------------------------------RREPSLSPKLTCLQNLKW------STAVEFCKKKSCP----------------NPGEIRNGQ-------IDVPGG---ILFGATISFSCNTGYKLFGSTSSFCL------I----SGSSVQWSDPLPEC--REH @1vvc_ 030231210101110001000000000000000000000000000000000023110212001101110003110000000001010010101000000000000000000000000000000000000000000000220103001100010000000000000000000000000010000000030202001111021010020000101001000000000000120210000 @1ghq_B 031201210101110001000000000000000000000000000000000323130212000301110003110000000001010010101000000000000000000000000000000000000000000000220103001100010000000000000000000000000010000010030202000303020010320000101001000000000000120210000 @1ckl_A 000210210000000000000000000000000000000000000000130320013202001100000000000000000000000000000000000000000010100300100100100000000000010303220000000000000000000300111000000000001010000110030202101101020000320000000300000110001100020200000 @1nwv_A 001210200000000000000000000000000000000000000000130323113202001100000000000000000000000000000000000000000010100300100100100000000000010303220000000000000000000300111000000000001000000110030202101111021010320000000300000110001100120200000 Reorder 459 468 469 470 473 474 475 476 455 461 462 463 464 Merge 469 470 Weight 5.21759 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT----------------------------DGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTCQI-----------------------------------------VKCPHPTISNGYLSSGFKRS----------------------YSY---NDNVDFKCKYGYKLSGSSSSTC-SPGNT-------WKP----ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA----------------------------VGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKC--EYFNKYSS-----------------------------------CPEPIVPGGYKIRG-----------------STP------YRH---GDSVTFACKTNFSMNGNKSVWC-QANNM-------WGPTR---LPTCVS--- >1ckl_A ---CEEPP---------------TFEAMELIGKPKP------------YYEIGERVDYKCKKGY---------------------------------------FYIPPLATHTICDRNHTWLPVSDD-----ACYRETCP----------------YIRDPLNGQAVPAN------GTYE---FGYQMHFICNEGYYLIGEEILYCE-----LKGSVAIW----SGKPPIC--EKV >1nwv_A FRSCEVPT---------------RLN----------SASLKQPYITQNYFPVGTVVEYECRPGY---------------------------------------RREPSLSPKLTCLQNLKW------STAVEFCKKKSCP----------------NPGEIRNGQ-------IDVPGG---ILFGATISFSCNTGYKLFGSTSSFCL-----ISGSSVQW----SDPLPEC--REH @1vvc_ 03023121010111000100000000000000000000000000000000002311021200110111000311000000000101001010100000000000000000000000000000000000000000000022010300110001000000000000000000000000001000000003020200111102101002000010000000020100000120210000 @1ghq_B 03120121010111000100000000000000000000000000000000032313021200030111000311000000000101001010100000000000000000000000000000000000000000000022010300110001000000000000000000000000001000001003020200030302001032000010000000020100000120210000 @1ckl_A 00021021000000000000000000000000000000000000000013032001320200110000000000000000000000000000000000000000001010030010010010000000000001030322000000000000000000030011100000000000101000011003020210110102000032000000301100020000100020200000 @1nwv_A 00121020000000000000000000000000000000000000000013032311320200110000000000000000000000000000000000000000001010030010010010000000000001030322000000000000000000030011100000000000100000011003020210111102101032000000301100020000100120200000 Merge 100 75 Weight 4.55073 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT---------------------------DGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTCQI-----------------------------------------VKCPHPTISNGYLSSGFKRS----------------------YSY---NDNVDFKCKYGYKLSGSSSSTC-SPGNT-------WKP----ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA---------------------------VGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKC--EYFNKYSS-----------------------------------CPEPIVPGGYKIRG-----------------STP------YRH---GDSVTFACKTNFSMNGNKSVWC-QANNM-------WGPTR---LPTCVS--- >1ckl_A ---CEEPP---------------TFEAMELIGKPKP-----------YYEIGERVDYKCKKGY---------------------------------------FYIPPLATHTICDRNHTWLPVSDD-----ACYRETCP----------------YIRDPLNGQAVPAN------GTYE---FGYQMHFICNEGYYLIGEEILYCE-----LKGSVAIW----SGKPPIC--EKV >1nwv_A FRSCEVPT---------------RLNS---------ASLKQPYITQNYFPVGTVVEYECRPGY---------------------------------------RREPSLSPKLTCLQNLKW------STAVEFCKKKSCP----------------NPGEIRNGQ-------IDVPGG---ILFGATISFSCNTGYKLFGSTSSFCL-----ISGSSVQW----SDPLPEC--REH @1vvc_ 0302312101011100010000000000000000000000000000000002311021200110111000311000000000101001010100000000000000000000000000000000000000000000022010300110001000000000000000000000000001000000003020200111102101002000010000000020100000120210000 @1ghq_B 0312012101011100010000000000000000000000000000000032313021200030111000311000000000101001010100000000000000000000000000000000000000000000022010300110001000000000000000000000000001000001003020200030302001032000010000000020100000120210000 @1ckl_A 0002102100000000000000000000000000000000000000013032001320200110000000000000000000000000000000000000000001010030010010010000000000001030322000000000000000000030011100000000000101000011003020210110102000032000000301100020000100020200000 @1nwv_A 0012102000000000000000000000000000000000000000013032311320200110000000000000000000000000000000000000000001010030010010010000000000001030322000000000000000000030011100000000000100000011003020210111102101032000000301100020000100120200000 Merge 198 267 Weight 4.31861 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT---------------------------DGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTCQ----------------------------------------IVKCPHPTISNGYLSSGFKRS----------------------YSY---NDNVDFKCKYGYKLSGSSSSTC-SPGNT-------WKP----ELPKCVR--- >1ghq_B AISCGSPPPILNGRISYYSTPIA---------------------------VGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKC-EYFNKYSS-----------------------------------CPEPIVPGGYKIRG-----------------STP------YRH---GDSVTFACKTNFSMNGNKSVWC-QANNM-------WGPTR---LPTCVS--- >1ckl_A ---CEEPP---------------TFEAMELIGKPKP-----------YYEIGERVDYKCKKGY--------------------------------------FYIPPLATHTICDRNHTWLPVSDD-----ACYRETCP----------------YIRDPLNGQAVPAN------GTYE---FGYQMHFICNEGYYLIGEEILYCE-----LKGSVAIW----SGKPPIC--EKV >1nwv_A FRSCEVPT---------------RLNS---------ASLKQPYITQNYFPVGTVVEYECRPGY--------------------------------------RREPSLSPKLTCLQNLKW------STAVEFCKKKSCP----------------NPGEIRNGQ-------IDVPGG---ILFGATISFSCNTGYKLFGSTSSFCL-----ISGSSVQW----SDPLPEC--REH @1vvc_ 030231210101110001000000000000000000000000000000000231102120011011100031100000000010100101010000000000000000000000000000000000000000000022010300110001000000000000000000000000001000000003020200111102101002000010000000020100000120210000 @1ghq_B 031201210101110001000000000000000000000000000000003231302120003011100031100000000010100101010000000000000000000000000000000000000000000022010300110001000000000000000000000000001000001003020200030302001032000010000000020100000120210000 @1ckl_A 000210210000000000000000000000000000000000000001303200132020011000000000000000000000000000000000000000001010030010010010000000000001030322000000000000000000030011100000000000101000011003020210110102000032000000301100020000100020200000 @1nwv_A 001210200000000000000000000000000000000000000001303231132020011000000000000000000000000000000000000000001010030010010010000000000001030322000000000000000000030011100000000000100000011003020210111102101032000000301100020000100120200000 Merge 500 496 Weight 4.24024 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT---------------------------DGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTCQ----------------------------------------IVKCPHPTISNGYLSSGFKRS----------------------YSY---NDNVDFKCKYGYKLSGSSSSTC-SPGNT-------WKP----ELPKCVR-- >1ghq_B AISCGSPPPILNGRISYYSTPIA---------------------------VGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKC-EYFNKYSS-----------------------------------CPEPIVPGGYKIRG-----------------STP------YRH---GDSVTFACKTNFSMNGNKSVWC-QANNM-------WGPTR---LPTCVS-- >1ckl_A ---CEEPP---------------TFEAMELIGKPKP-----------YYEIGERVDYKCKKGY--------------------------------------FYIPPLATHTICDRNHTWLPVSDD-----ACYRETCP----------------YIRDPLNGQAVPAN------GTYE---FGYQMHFICNEGYYLIGEEILYCE-----LKGSVAIW----SGKPPICE-KV >1nwv_A FRSCEVPT---------------RLNS---------ASLKQPYITQNYFPVGTVVEYECRPGY--------------------------------------RREPSLSPKLTCLQNLKW------STAVEFCKKKSCP----------------NPGEIRNGQ-------IDVPGG---ILFGATISFSCNTGYKLFGSTSSFCL-----ISGSSVQW----SDPLPECR-EH @1vvc_ 03023121010111000100000000000000000000000000000000023110212001101110003110000000001010010101000000000000000000000000000000000000000000002201030011000100000000000000000000000000100000000302020011110210100200001000000002010000012021000 @1ghq_B 03120121010111000100000000000000000000000000000000323130212000301110003110000000001010010101000000000000000000000000000000000000000000002201030011000100000000000000000000000000100000100302020003030200103200001000000002010000012021000 @1ckl_A 00021021000000000000000000000000000000000000000130320013202001100000000000000000000000000000000000000000101003001001001000000000000103032200000000000000000003001110000000000010100001100302021011010200003200000030110002000010002020000 @1nwv_A 00121020000000000000000000000000000000000000000130323113202001100000000000000000000000000000000000000000101003001001001000000000000103032200000000000000000003001110000000000010000001100302021011110210103200000030110002000010012020000 Merge 329 275 Weight 4.08275 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT---------------------------DGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTCQ----------------------------------------IVKCPHPTISNGYLSSGFKRS---------------------YSY---NDNVDFKCKYGYKLSGSSSSTC-SPGNT-------WKP----ELPKCVR-- >1ghq_B AISCGSPPPILNGRISYYSTPIA---------------------------VGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKC-EYFNKYSS-----------------------------------CPEPIVPGGYKIRG----------------STP------YRH---GDSVTFACKTNFSMNGNKSVWC-QANNM-------WGPTR---LPTCVS-- >1ckl_A ---CEEPP---------------TFEAMELIGKPKP-----------YYEIGERVDYKCKKGY--------------------------------------FYIPPLATHTICDRNHTWLPVSDD-----ACYRETCPY---------------IRDPLNGQAVPAN------GTYE---FGYQMHFICNEGYYLIGEEILYCE-----LKGSVAIW----SGKPPICE-KV >1nwv_A FRSCEVPT---------------RLNS---------ASLKQPYITQNYFPVGTVVEYECRPGY--------------------------------------RREPSLSPKLTCLQNLKW------STAVEFCKKKSCPN---------------PGEIRNGQ-------IDVPGG---ILFGATISFSCNTGYKLFGSTSSFCL-----ISGSSVQW----SDPLPECR-EH @1vvc_ 0302312101011100010000000000000000000000000000000002311021200110111000311000000000101001010100000000000000000000000000000000000000000000220103001100010000000000000000000000000100000000302020011110210100200001000000002010000012021000 @1ghq_B 0312012101011100010000000000000000000000000000000032313021200030111000311000000000101001010100000000000000000000000000000000000000000000220103001100010000000000000000000000000100000100302020003030200103200001000000002010000012021000 @1ckl_A 0002102100000000000000000000000000000000000000013032001320200110000000000000000000000000000000000000000010100300100100100000000000010303220000000000000000003001110000000000010100001100302021011010200003200000030110002000010002020000 @1nwv_A 0012102000000000000000000000000000000000000000013032311320200110000000000000000000000000000000000000000010100300100100100000000000010303220000000000000000003001110000000000010000001100302021011110210103200000030110002000010012020000 Merge 197 266 Weight 3.99307 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT---------------------------DGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC---------------------------------------QIVKCPHPTISNGYLSSGFKRS---------------------YSY---NDNVDFKCKYGYKLSGSSSSTC-SPGNT-------WKP----ELPKCVR-- >1ghq_B AISCGSPPPILNGRISYYSTPIA---------------------------VGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYSS-----------------------------------CPEPIVPGGYKIRG----------------STP------YRH---GDSVTFACKTNFSMNGNKSVWC-QANNM-------WGPTR---LPTCVS-- >1ckl_A ---CEEPP---------------TFEAMELIGKPKP-----------YYEIGERVDYKCKKGY-------------------------------------FYIPPLATHTICDRNHTWLPVSDD-----ACYRETCPY---------------IRDPLNGQAVPAN------GTYE---FGYQMHFICNEGYYLIGEEILYCE-----LKGSVAIW----SGKPPICE-KV >1nwv_A FRSCEVPT---------------RLNS---------ASLKQPYITQNYFPVGTVVEYECRPGY-------------------------------------RREPSLSPKLTCLQNLKW------STAVEFCKKKSCPN---------------PGEIRNGQ-------IDVPGG---ILFGATISFSCNTGYKLFGSTSSFCL-----ISGSSVQW----SDPLPECR-EH @1vvc_ 030231210101110001000000000000000000000000000000000231102120011011100031100000000010100101010000000000000000000000000000000000000000000220103001100010000000000000000000000000100000000302020011110210100200001000000002010000012021000 @1ghq_B 031201210101110001000000000000000000000000000000003231302120003011100031100000000010100101010000000000000000000000000000000000000000000220103001100010000000000000000000000000100000100302020003030200103200001000000002010000012021000 @1ckl_A 000210210000000000000000000000000000000000000001303200132020011000000000000000000000000000000000000000010100300100100100000000000010303220000000000000000003001110000000000010100001100302021011010200003200000030110002000010002020000 @1nwv_A 001210200000000000000000000000000000000000000001303231132020011000000000000000000000000000000000000000010100300100100100000000000010303220000000000000000003001110000000000010000001100302021011110210103200000030110002000010012020000 Merge 208 270 Weight 3.97743 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT---------------------------DGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC--------------------------------------QIVKCPHPTISNGYLSSGFKRS---------------------YSY---NDNVDFKCKYGYKLSGSSSSTC-SPGNT-------WKP----ELPKCVR-- >1ghq_B AISCGSPPPILNGRISYYSTPIA---------------------------VGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS----------------------------------SCPEPIVPGGYKIRG----------------STP------YRH---GDSVTFACKTNFSMNGNKSVWC-QANNM-------WGPTR---LPTCVS-- >1ckl_A ---CEEPP---------------TFEAMELIGKPKP-----------YYEIGERVDYKCKKGY------------------------------------FYIPPLATHTICDRNHTWLPVSDD-----ACYRETCPY---------------IRDPLNGQAVPAN------GTYE---FGYQMHFICNEGYYLIGEEILYCE-----LKGSVAIW----SGKPPICE-KV >1nwv_A FRSCEVPT---------------RLNS---------ASLKQPYITQNYFPVGTVVEYECRPGY------------------------------------RREPSLSPKLTCLQNLKW------STAVEFCKKKSCPN---------------PGEIRNGQ-------IDVPGG---ILFGATISFSCNTGYKLFGSTSSFCL-----ISGSSVQW----SDPLPECR-EH @1vvc_ 03023121010111000100000000000000000000000000000000023110212001101110003110000000001010010101000000000000000000000000000000000000000000220103001100010000000000000000000000000100000000302020011110210100200001000000002010000012021000 @1ghq_B 03120121010111000100000000000000000000000000000000323130212000301110003110000000001010010101000000000000000000000000000000000000000003220103001100010000000000000000000000000100000100302020003030200103200001000000002010000012021000 @1ckl_A 00021021000000000000000000000000000000000000000130320013202001100000000000000000000000000000000000000010100300100100100000000000010303220000000000000000003001110000000000010100001100302021011010200003200000030110002000010002020000 @1nwv_A 00121020000000000000000000000000000000000000000130323113202001100000000000000000000000000000000000000010100300100100100000000000010303220000000000000000003001110000000000010000001100302021011110210103200000030110002000010012020000 Merge 479 473 Weight 3.86592 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT---------------------------DGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC--------------------------------------QIVKCPHPTISNGYLSSGFKRS---------------------YSY---NDNVDFKCKYGYKLSGSSSSTC-SPGNT-------WKP---ELPKCVR-- >1ghq_B AISCGSPPPILNGRISYYSTPIA---------------------------VGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS----------------------------------SCPEPIVPGGYKIRG----------------STP------YRH---GDSVTFACKTNFSMNGNKSVWC-QANNM-------WGPTR--LPTCVS-- >1ckl_A ---CEEPP---------------TFEAMELIGKPKP-----------YYEIGERVDYKCKKGY------------------------------------FYIPPLATHTICDRNHTWLPVSDD-----ACYRETCPY---------------IRDPLNGQAVPAN------GTYE---FGYQMHFICNEGYYLIGEEILYCE-----LKGSVAIWS---GKPPICE-KV >1nwv_A FRSCEVPT---------------RLNS---------ASLKQPYITQNYFPVGTVVEYECRPGY------------------------------------RREPSLSPKLTCLQNLKW------STAVEFCKKKSCPN---------------PGEIRNGQ-------IDVPGG---ILFGATISFSCNTGYKLFGSTSSFCL-----ISGSSVQWS---DPLPECR-EH @1vvc_ 0302312101011100010000000000000000000000000000000002311021200110111000311000000000101001010100000000000000000000000000000000000000000022010300110001000000000000000000000000010000000030202001111021010020000100000000201000012021000 @1ghq_B 0312012101011100010000000000000000000000000000000032313021200030111000311000000000101001010100000000000000000000000000000000000000000322010300110001000000000000000000000000010000010030202000303020010320000100000000201000012021000 @1ckl_A 0002102100000000000000000000000000000000000000013032001320200110000000000000000000000000000000000000001010030010010010000000000001030322000000000000000000300111000000000001010000110030202101101020000320000003011000200000002020000 @1nwv_A 0012102000000000000000000000000000000000000000013032311320200110000000000000000000000000000000000000001010030010010010000000000001030322000000000000000000300111000000000001000000110030202101111021010320000003011000200000012020000 Merge 251 260 Weight 3.84904 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT---------------------------DGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC-------------------------------------QIVKCPHPTISNGYLSSGFKRS---------------------YSY---NDNVDFKCKYGYKLSGSSSSTC-SPGNT-------WKP---ELPKCVR-- >1ghq_B AISCGSPPPILNGRISYYSTPIA---------------------------VGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS---------------------------------SCPEPIVPGGYKIRG----------------STP------YRH---GDSVTFACKTNFSMNGNKSVWC-QANNM-------WGPTR--LPTCVS-- >1ckl_A ---CEEPP---------------TFEAMELIGKPKP-----------YYEIGERVDYKCKKGY------------------------------------FYIPPLATHTICDRNHTWLPVSD----DACYRETCPY---------------IRDPLNGQAVPAN------GTYE---FGYQMHFICNEGYYLIGEEILYCE-----LKGSVAIWS---GKPPICE-KV >1nwv_A FRSCEVPT---------------RLNS---------ASLKQPYITQNYFPVGTVVEYECRPGY------------------------------------RREPSLSPKLTCLQNLKW-----STAVEFCKKKSCPN---------------PGEIRNGQ-------IDVPGG---ILFGATISFSCNTGYKLFGSTSSFCL-----ISGSSVQWS---DPLPECR-EH @1vvc_ 030231210101110001000000000000000000000000000000000231102120011011100031100000000010100101010000000000000000000000000000000000000000022010300110001000000000000000000000000010000000030202001111021010020000100000000201000012021000 @1ghq_B 031201210101110001000000000000000000000000000000003231302120003011100031100000000010100101010000000000000000000000000000000000000000322010300110001000000000000000000000000010000010030202000303020010320000100000000201000012021000 @1ckl_A 000210210000000000000000000000000000000000000001303200132020011000000000000000000000000000000000000000101003001001001000000000301030322000000000000000000300111000000000001010000110030202101101020000320000003011000200000002020000 @1nwv_A 001210200000000000000000000000000000000000000001303231132020011000000000000000000000000000000000000000101003001001001000000000301030322000000000000000000300111000000000001000000110030202101111021010320000003011000200000012020000 Merge 101 76 Weight 3.70476 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT--------------------------DGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC-------------------------------------QIVKCPHPTISNGYLSSGFKRS---------------------YSY---NDNVDFKCKYGYKLSGSSSSTC-SPGNT-------WKP---ELPKCVR-- >1ghq_B AISCGSPPPILNGRISYYSTPIA--------------------------VGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS---------------------------------SCPEPIVPGGYKIRG----------------STP------YRH---GDSVTFACKTNFSMNGNKSVWC-QANNM-------WGPTR--LPTCVS-- >1ckl_A ---CEEPP---------------TFEAMELIGKPKP----------YYEIGERVDYKCKKGY------------------------------------FYIPPLATHTICDRNHTWLPVSD----DACYRETCPY---------------IRDPLNGQAVPAN------GTYE---FGYQMHFICNEGYYLIGEEILYCE-----LKGSVAIWS---GKPPICE-KV >1nwv_A FRSCEVPT---------------RLNSA--------SLKQPYITQNYFPVGTVVEYECRPGY------------------------------------RREPSLSPKLTCLQNLKW-----STAVEFCKKKSCPN---------------PGEIRNGQ-------IDVPGG---ILFGATISFSCNTGYKLFGSTSSFCL-----ISGSSVQWS---DPLPECR-EH @1vvc_ 03023121010111000100000000000000000000000000000000231102120011011100031100000000010100101010000000000000000000000000000000000000000022010300110001000000000000000000000000010000000030202001111021010020000100000000201000012021000 @1ghq_B 03120121010111000100000000000000000000000000000003231302120003011100031100000000010100101010000000000000000000000000000000000000000322010300110001000000000000000000000000010000010030202000303020010320000100000000201000012021000 @1ckl_A 00021021000000000000000000000000000000000000001303200132020011000000000000000000000000000000000000000101003001001001000000000301030322000000000000000000300111000000000001010000110030202101101020000320000003011000200000002020000 @1nwv_A 00121020000000000000000000000000000000000000001303231132020011000000000000000000000000000000000000000101003001001001000000000301030322000000000000000000300111000000000001000000110030202101111021010320000003011000200000012020000 Merge 70 21 Weight 3.66593 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT-------------------------DGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC-------------------------------------QIVKCPHPTISNGYLSSGFKRS---------------------YSY---NDNVDFKCKYGYKLSGSSSSTC-SPGNT-------WKP---ELPKCVR-- >1ghq_B AISCGSPPPILNGRISYYSTPIA-------------------------VGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS---------------------------------SCPEPIVPGGYKIRG----------------STP------YRH---GDSVTFACKTNFSMNGNKSVWC-QANNM-------WGPTR--LPTCVS-- >1ckl_A ---CEEPPT--------------FEAMELIGKPKP----------YYEIGERVDYKCKKGY------------------------------------FYIPPLATHTICDRNHTWLPVSD----DACYRETCPY---------------IRDPLNGQAVPAN------GTYE---FGYQMHFICNEGYYLIGEEILYCE-----LKGSVAIWS---GKPPICE-KV >1nwv_A FRSCEVPTR--------------LNSA--------SLKQPYITQNYFPVGTVVEYECRPGY------------------------------------RREPSLSPKLTCLQNLKW-----STAVEFCKKKSCPN---------------PGEIRNGQ-------IDVPGG---ILFGATISFSCNTGYKLFGSTSSFCL-----ISGSSVQWS---DPLPECR-EH @1vvc_ 0302312101011100010000000000000000000000000000000231102120011011100031100000000010100101010000000000000000000000000000000000000000022010300110001000000000000000000000000010000000030202001111021010020000100000000201000012021000 @1ghq_B 0312012101011100010000000000000000000000000000003231302120003011100031100000000010100101010000000000000000000000000000000000000000322010300110001000000000000000000000000010000010030202000303020010320000100000000201000012021000 @1ckl_A 0002102100000000000000000000000000000000000001303200132020011000000000000000000000000000000000000000101003001001001000000000301030322000000000000000000300111000000000001010000110030202101101020000320000003011000200000002020000 @1nwv_A 0012102000000000000000000000000000000000000001303231132020011000000000000000000000000000000000000000101003001001001000000000301030322000000000000000000300111000000000001000000110030202101111021010320000003011000200000012020000 Merge 209 140 Weight 3.65367 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT-------------------------DGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC------------------------------------QIVKCPHPTISNGYLSSGFKRS---------------------YSY---NDNVDFKCKYGYKLSGSSSSTC-SPGNT-------WKP---ELPKCVR-- >1ghq_B AISCGSPPPILNGRISYYSTPIA-------------------------VGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS--------------------------------SCPEPIVPGGYKIRG----------------STP------YRH---GDSVTFACKTNFSMNGNKSVWC-QANNM-------WGPTR--LPTCVS-- >1ckl_A ---CEEPPT--------------FEAMELIGKPKP----------YYEIGERVDYKCKKGYF-----------------------------------YIPPLATHTICDRNHTWLPVSD----DACYRETCPY---------------IRDPLNGQAVPAN------GTYE---FGYQMHFICNEGYYLIGEEILYCE-----LKGSVAIWS---GKPPICE-KV >1nwv_A FRSCEVPTR--------------LNSA--------SLKQPYITQNYFPVGTVVEYECRPGYR-----------------------------------REPSLSPKLTCLQNLKW-----STAVEFCKKKSCPN---------------PGEIRNGQ-------IDVPGG---ILFGATISFSCNTGYKLFGSTSSFCL-----ISGSSVQWS---DPLPECR-EH @1vvc_ 030231210101110001000000000000000000000000000000023110212001101110003110000000001010010101000000000000000000000000000000000000000022010300110001000000000000000000000000010000000030202001111021010020000100000000201000012021000 @1ghq_B 031201210101110001000000000000000000000000000000323130212000301110003110000000001010010101000000000000000000000000000000000000000322010300110001000000000000000000000000010000010030202000303020010320000100000000201000012021000 @1ckl_A 000210210000000000000000000000000000000000000130320013202001100000000000000000000000000000000000000101003001001001000000000301030322000000000000000000300111000000000001010000110030202101101020000320000003011000200000002020000 @1nwv_A 001210200000000000000000000000000000000000000130323113202001100000000000000000000000000000000000000101003001001001000000000301030322000000000000000000300111000000000001000000110030202101111021010320000003011000200000012020000 Merge 107 77 Weight 3.62165 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT------------------------DGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC------------------------------------QIVKCPHPTISNGYLSSGFKRS---------------------YSY---NDNVDFKCKYGYKLSGSSSSTC-SPGNT-------WKP---ELPKCVR-- >1ghq_B AISCGSPPPILNGRISYYSTPIA------------------------VGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS--------------------------------SCPEPIVPGGYKIRG----------------STP------YRH---GDSVTFACKTNFSMNGNKSVWC-QANNM-------WGPTR--LPTCVS-- >1ckl_A ---CEEPPT--------------FEAMELIGKPKP---------YYEIGERVDYKCKKGYF-----------------------------------YIPPLATHTICDRNHTWLPVSD----DACYRETCPY---------------IRDPLNGQAVPAN------GTYE---FGYQMHFICNEGYYLIGEEILYCE-----LKGSVAIWS---GKPPICE-KV >1nwv_A FRSCEVPTR--------------LNSAS-------LKQPYITQNYFPVGTVVEYECRPGYR-----------------------------------REPSLSPKLTCLQNLKW-----STAVEFCKKKSCPN---------------PGEIRNGQ-------IDVPGG---ILFGATISFSCNTGYKLFGSTSSFCL-----ISGSSVQWS---DPLPECR-EH @1vvc_ 03023121010111000100000000000000000000000000000023110212001101110003110000000001010010101000000000000000000000000000000000000000022010300110001000000000000000000000000010000000030202001111021010020000100000000201000012021000 @1ghq_B 03120121010111000100000000000000000000000000000323130212000301110003110000000001010010101000000000000000000000000000000000000000322010300110001000000000000000000000000010000010030202000303020010320000100000000201000012021000 @1ckl_A 00021021000000000000000000000000000000000000130320013202001100000000000000000000000000000000000000101003001001001000000000301030322000000000000000000300111000000000001010000110030202101101020000320000003011000200000002020000 @1nwv_A 00121020000000000000000000000000000000000000130323113202001100000000000000000000000000000000000000101003001001001000000000301030322000000000000000000300111000000000001000000110030202101111021010320000003011000200000012020000 Merge 480 474 Weight 3.5814 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT------------------------DGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC------------------------------------QIVKCPHPTISNGYLSSGFKRS---------------------YSY---NDNVDFKCKYGYKLSGSSSSTC-SPGNT-------WKP--ELPKCVR-- >1ghq_B AISCGSPPPILNGRISYYSTPIA------------------------VGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS--------------------------------SCPEPIVPGGYKIRG----------------STP------YRH---GDSVTFACKTNFSMNGNKSVWC-QANNM-------WGPTR-LPTCVS-- >1ckl_A ---CEEPPT--------------FEAMELIGKPKP---------YYEIGERVDYKCKKGYF-----------------------------------YIPPLATHTICDRNHTWLPVSD----DACYRETCPY---------------IRDPLNGQAVPAN------GTYE---FGYQMHFICNEGYYLIGEEILYCE-----LKGSVAIWSG--KPPICE-KV >1nwv_A FRSCEVPTR--------------LNSAS-------LKQPYITQNYFPVGTVVEYECRPGYR-----------------------------------REPSLSPKLTCLQNLKW-----STAVEFCKKKSCPN---------------PGEIRNGQ-------IDVPGG---ILFGATISFSCNTGYKLFGSTSSFCL-----ISGSSVQWSD--PLPECR-EH @1vvc_ 0302312101011100010000000000000000000000000000002311021200110111000311000000000101001010100000000000000000000000000000000000000002201030011000100000000000000000000000001000000003020200111102101002000010000000020100012021000 @1ghq_B 0312012101011100010000000000000000000000000000032313021200030111000311000000000101001010100000000000000000000000000000000000000032201030011000100000000000000000000000001000001003020200030302001032000010000000020100012021000 @1ckl_A 0002102100000000000000000000000000000000000013032001320200110000000000000000000000000000000000000010100300100100100000000030103032200000000000000000030011100000000000101000011003020210110102000032000000301100020000002020000 @1nwv_A 0012102000000000000000000000000000000000000013032311320200110000000000000000000000000000000000000010100300100100100000000030103032200000000000000000030011100000000000100000011003020210111102101032000000301100020000012020000 Merge 314 356 Weight 3.51555 >1vvc_ -VKCQSPPSISNGRHNGYEDFYT------------------------DGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC------------------------------------QIVKCPHPTISNGYLSSGFKR--------------S------YSY---NDNVDFKCKYGYKLSGSSSSTC-SPGNT-------WKP--ELPKCVR-- >1ghq_B AISCGSPPPILNGRISYYSTPIA------------------------VGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS--------------------------------SCPEPIVPGGYKIRG---------------STP------YRH---GDSVTFACKTNFSMNGNKSVWC-QANNM-------WGPTR-LPTCVS-- >1ckl_A ---CEEPPT--------------FEAMELIGKPKP---------YYEIGERVDYKCKKGYF-----------------------------------YIPPLATHTICDRNHTWLPVSD----DACYRETCPY--------------IRDPLNGQAVPAN------GTYE---FGYQMHFICNEGYYLIGEEILYCE-----LKGSVAIWSG--KPPICE-KV >1nwv_A FRSCEVPTR--------------LNSAS-------LKQPYITQNYFPVGTVVEYECRPGYR-----------------------------------REPSLSPKLTCLQNLKW-----STAVEFCKKKSCPN--------------PGEIRNGQ-------IDVPGG---ILFGATISFSCNTGYKLFGSTSSFCL-----ISGSSVQWSD--PLPECR-EH @1vvc_ 030231210101110001000000000000000000000000000000231102120011011100031100000000010100101010000000000000000000000000000000000000000220103001100010000000000000000000000001000000003020200111102101002000010000000020100012021000 @1ghq_B 031201210101110001000000000000000000000000000003231302120003011100031100000000010100101010000000000000000000000000000000000000003220103001100010000000000000000000000001000001003020200030302001032000010000000020100012021000 @1ckl_A 000210210000000000000000000000000000000000001303200132020011000000000000000000000000000000000000001010030010010010000000003010303220000000000000000030011100000000000101000011003020210110102000032000000301100020000002020000 @1nwv_A 001210200000000000000000000000000000000000001303231132020011000000000000000000000000000000000000001010030010010010000000003010303220000000000000000030011100000000000100000011003020210111102101032000000301100020000012020000 Merge 57 120 Weight 3.47493 >1vvc_ -VKCQSPPSISNGRHNGYEDFY-----------------------TDGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC------------------------------------QIVKCPHPTISNGYLSSGFKR--------------S------YSY---NDNVDFKCKYGYKLSGSSSSTC-SPGNT-------WKP--ELPKCVR-- >1ghq_B AISCGSPPPILNGRISYYSTPI-----------------------AVGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS--------------------------------SCPEPIVPGGYKIRG---------------STP------YRH---GDSVTFACKTNFSMNGNKSVWC-QANNM-------WGPTR-LPTCVS-- >1ckl_A ---CEEPPT-------------FEAMELIGKPKP---------YYEIGERVDYKCKKGYF-----------------------------------YIPPLATHTICDRNHTWLPVSD----DACYRETCPY--------------IRDPLNGQAVPAN------GTYE---FGYQMHFICNEGYYLIGEEILYCE-----LKGSVAIWSG--KPPICE-KV >1nwv_A FRSCEVPTR-------------LNSAS-------LKQPYITQNYFPVGTVVEYECRPGYR-----------------------------------REPSLSPKLTCLQNLKW-----STAVEFCKKKSCPN--------------PGEIRNGQ-------IDVPGG---ILFGATISFSCNTGYKLFGSTSSFCL-----ISGSSVQWSD--PLPECR-EH @1vvc_ 03023121010111000100000000000000000000000000000231102120011011100031100000000010100101010000000000000000000000000000000000000000220103001100010000000000000000000000001000000003020200111102101002000010000000020100012021000 @1ghq_B 03120121010111000100000000000000000000000000003231302120003011100031100000000010100101010000000000000000000000000000000000000003220103001100010000000000000000000000001000001003020200030302001032000010000000020100012021000 @1ckl_A 00021021000000000000000000000000000000000001303200132020011000000000000000000000000000000000000001010030010010010000000003010303220000000000000000030011100000000000101000011003020210110102000032000000301100020000002020000 @1nwv_A 00121020000000000000000000000000000000000001303231132020011000000000000000000000000000000000000001010030010010010000000003010303220000000000000000030011100000000000100000011003020210111102101032000000301100020000012020000 Merge 497 501 Weight 3.33246 >1vvc_ -VKCQSPPSISNGRHNGYEDFY-----------------------TDGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC------------------------------------QIVKCPHPTISNGYLSSGFKR--------------S------YSY---NDNVDFKCKYGYKLSGSSSSTC-SPGNT-------WKP--ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTPI-----------------------AVGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS--------------------------------SCPEPIVPGGYKIRG---------------STP------YRH---GDSVTFACKTNFSMNGNKSVWC-QANNM-------WGPTR-LPTCVS- >1ckl_A ---CEEPPT-------------FEAMELIGKPKP---------YYEIGERVDYKCKKGYF-----------------------------------YIPPLATHTICDRNHTWLPVSD----DACYRETCPY--------------IRDPLNGQAVPAN------GTYE---FGYQMHFICNEGYYLIGEEILYCE-----LKGSVAIWSG--KPPICEKV >1nwv_A FRSCEVPTR-------------LNSAS-------LKQPYITQNYFPVGTVVEYECRPGYR-----------------------------------REPSLSPKLTCLQNLKW-----STAVEFCKKKSCPN--------------PGEIRNGQ-------IDVPGG---ILFGATISFSCNTGYKLFGSTSSFCL-----ISGSSVQWSD--PLPECREH @1vvc_ 0302312101011100010000000000000000000000000000023110212001101110003110000000001010010101000000000000000000000000000000000000000022010300110001000000000000000000000000100000000302020011110210100200001000000002010001202100 @1ghq_B 0312012101011100010000000000000000000000000000323130212000301110003110000000001010010101000000000000000000000000000000000000000322010300110001000000000000000000000000100000100302020003030200103200001000000002010001202100 @1ckl_A 0002102100000000000000000000000000000000000130320013202001100000000000000000000000000000000000000101003001001001000000000301030322000000000000000003001110000000000010100001100302021011010200003200000030110002000000202000 @1nwv_A 0012102000000000000000000000000000000000000130323113202001100000000000000000000000000000000000000101003001001001000000000301030322000000000000000003001110000000000010000001100302021011110210103200000030110002000001202000 Reorder 357 358 359 349 354 355 356 Merge 355 356 Weight 3.28724 >1vvc_ -VKCQSPPSISNGRHNGYEDFY-----------------------TDGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC------------------------------------QIVKCPHPTISNGYLSSGFKR----------------S---YSY---NDNVDFKCKYGYKLSGSSSSTC-SPGNT-------WKP--ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTPI-----------------------AVGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS--------------------------------SCPEPIVPGGYKIRG-----------------STP---YRH---GDSVTFACKTNFSMNGNKSVWC-QANNM-------WGPTR-LPTCVS- >1ckl_A ---CEEPPT-------------FEAMELIGKPKP---------YYEIGERVDYKCKKGYF-----------------------------------YIPPLATHTICDRNHTWLPVSD----DACYRETCPY--------------IRDPLNGQAVP--AN---GTYE---FGYQMHFICNEGYYLIGEEILYCE-----LKGSVAIWSG--KPPICEKV >1nwv_A FRSCEVPTR-------------LNSAS-------LKQPYITQNYFPVGTVVEYECRPGYR-----------------------------------REPSLSPKLTCLQNLKW-----STAVEFCKKKSCPN--------------PGEIRNGQ---IDV---PGG---ILFGATISFSCNTGYKLFGSTSSFCL-----ISGSSVQWSD--PLPECREH @1vvc_ 030231210101110001000000000000000000000000000002311021200110111000311000000000101001010100000000000000000000000000000000000000002201030011000100000000000000000000000100000000302020011110210100200001000000002010001202100 @1ghq_B 031201210101110001000000000000000000000000000032313021200030111000311000000000101001010100000000000000000000000000000000000000032201030011000100000000000000000000000100000100302020003030200103200001000000002010001202100 @1ckl_A 000210210000000000000000000000000000000000013032001320200110000000000000000000000000000000000000010100300100100100000000030103032200000000000000000300111000000000010100001100302021011010200003200000030110002000000202000 @1nwv_A 001210200000000000000000000000000000000000013032311320200110000000000000000000000000000000000000010100300100100100000000030103032200000000000000000300111000000000010000001100302021011110210103200000030110002000001202000 Merge 386 393 Weight 3.26665 >1vvc_ -VKCQSPPSISNGRHNGYEDFY-----------------------TDGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC------------------------------------QIVKCPHPTISNGYLSSGFKR----------------S---YS--YNDNVDFKCKYGYKLSGSSSSTC-SPGNT-------WKP--ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTPI-----------------------AVGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS--------------------------------SCPEPIVPGGYKIRG-----------------STP---YR--HGDSVTFACKTNFSMNGNKSVWC-QANNM-------WGPTR-LPTCVS- >1ckl_A ---CEEPPT-------------FEAMELIGKPKP---------YYEIGERVDYKCKKGYF-----------------------------------YIPPLATHTICDRNHTWLPVSD----DACYRETCPY--------------IRDPLNGQAVP--AN---GTYE--FGYQMHFICNEGYYLIGEEILYCE-----LKGSVAIWSG--KPPICEKV >1nwv_A FRSCEVPTR-------------LNSAS-------LKQPYITQNYFPVGTVVEYECRPGYR-----------------------------------REPSLSPKLTCLQNLKW-----STAVEFCKKKSCPN--------------PGEIRNGQ---IDV---PGG--ILFGATISFSCNTGYKLFGSTSSFCL-----ISGSSVQWSD--PLPECREH @1vvc_ 03023121010111000100000000000000000000000000000231102120011011100031100000000010100101010000000000000000000000000000000000000000220103001100010000000000000000000000010003000302020011110210100200001000000002010001202100 @1ghq_B 03120121010111000100000000000000000000000000003231302120003011100031100000000010100101010000000000000000000000000000000000000003220103001100010000000000000000000000010000100302020003030200103200001000000002010001202100 @1ckl_A 00021021000000000000000000000000000000000001303200132020011000000000000000000000000000000000000001010030010010010000000003010303220000000000000000030011100000000001010001100302021011010200003200000030110002000000202000 @1nwv_A 00121020000000000000000000000000000000000001303231132020011000000000000000000000000000000000000001010030010010010000000003010303220000000000000000030011100000000001000001100302021011110210103200000030110002000001202000 Merge 108 78 Weight 3.11234 >1vvc_ -VKCQSPPSISNGRHNGYEDFY----------------------TDGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC------------------------------------QIVKCPHPTISNGYLSSGFKR----------------S---YS--YNDNVDFKCKYGYKLSGSSSSTC-SPGNT-------WKP--ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTPI----------------------AVGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS--------------------------------SCPEPIVPGGYKIRG-----------------STP---YR--HGDSVTFACKTNFSMNGNKSVWC-QANNM-------WGPTR-LPTCVS- >1ckl_A ---CEEPPT-------------FEAMELIGKPKP--------YYEIGERVDYKCKKGYF-----------------------------------YIPPLATHTICDRNHTWLPVSD----DACYRETCPY--------------IRDPLNGQAVP--AN---GTYE--FGYQMHFICNEGYYLIGEEILYCE-----LKGSVAIWSG--KPPICEKV >1nwv_A FRSCEVPTR-------------LNSASL------KQPYITQNYFPVGTVVEYECRPGYR-----------------------------------REPSLSPKLTCLQNLKW-----STAVEFCKKKSCPN--------------PGEIRNGQ---IDV---PGG--ILFGATISFSCNTGYKLFGSTSSFCL-----ISGSSVQWSD--PLPECREH @1vvc_ 0302312101011100010000000000000000000000000000231102120011011100031100000000010100101010000000000000000000000000000000000000000220103001100010000000000000000000000010003000302020011110210100200001000000002010001202100 @1ghq_B 0312012101011100010000000000000000000000000003231302120003011100031100000000010100101010000000000000000000000000000000000000003220103001100010000000000000000000000010000100302020003030200103200001000000002010001202100 @1ckl_A 0002102100000000000000000001000000000000001303200132020011000000000000000000000000000000000000001010030010010010000000003010303220000000000000000030011100000000001010001100302021011010200003200000030110002000000202000 @1nwv_A 0012102000000000000000000001000000000000001303231132020011000000000000000000000000000000000000001010030010010010000000003010303220000000000000000030011100000000001000001100302021011110210103200000030110002000001202000 Reorder 254 255 258 249 250 Merge 254 255 Weight 3.04596 >1vvc_ -VKCQSPPSISNGRHNGYEDFY----------------------TDGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC-----------------------------------QIVKCPHPTISNGYLSSGFKR----------------S---YS--YNDNVDFKCKYGYKLSGSSSSTC-SPGNT-------WKP--ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTPI----------------------AVGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS-------------------------------SCPEPIVPGGYKIRG-----------------STP---YR--HGDSVTFACKTNFSMNGNKSVWC-QANNM-------WGPTR-LPTCVS- >1ckl_A ---CEEPPT-------------FEAMELIGKPKP--------YYEIGERVDYKCKKGYF-----------------------------------YIPPLATHTICDRNHTWLPV--SD-DACYRETCPY--------------IRDPLNGQAVP--AN---GTYE--FGYQMHFICNEGYYLIGEEILYCE-----LKGSVAIWSG--KPPICEKV >1nwv_A FRSCEVPTR-------------LNSASL------KQPYITQNYFPVGTVVEYECRPGYR-----------------------------------REPSLSPKLTCLQNLKW---STA-VEFCKKKSCPN--------------PGEIRNGQ---IDV---PGG--ILFGATISFSCNTGYKLFGSTSSFCL-----ISGSSVQWSD--PLPECREH @1vvc_ 030231210101110001000000000000000000000000000023110212001101110003110000000001010010101000000000000000000000000000000000000000220103001100010000000000000000000000010003000302020011110210100200001000000002010001202100 @1ghq_B 031201210101110001000000000000000000000000000323130212000301110003110000000001010010101000000000000000000000000000000000000003220103001100010000000000000000000000010000100302020003030200103200001000000002010001202100 @1ckl_A 000210210000000000000000000100000000000000130320013202001100000000000000000000000000000000000000101003001001001000000003010303220000000000000000030011100000000001010001100302021011010200003200000030110002000000202000 @1nwv_A 001210200000000000000000000100000000000000130323113202001100000000000000000000000000000000000000101003001001001000000003010303220000000000000000030011100000000001000001100302021011110210103200000030110002000001202000 Merge 348 354 Weight 2.88778 >1vvc_ -VKCQSPPSISNGRHNGYEDFY----------------------TDGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC-----------------------------------QIVKCPHPTISNGYLSSGFKR---------------S---YS--YNDNVDFKCKYGYKLSGSSSSTC-SPGNT-------WKP--ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTPI----------------------AVGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS-------------------------------SCPEPIVPGGYKIRG----------------STP---YR--HGDSVTFACKTNFSMNGNKSVWC-QANNM-------WGPTR-LPTCVS- >1ckl_A ---CEEPPT-------------FEAMELIGKPKP--------YYEIGERVDYKCKKGYF-----------------------------------YIPPLATHTICDRNHTWLPV--SD-DACYRETCPY--------------IRDPLNGQAV-PAN---GTYE--FGYQMHFICNEGYYLIGEEILYCE-----LKGSVAIWSG--KPPICEKV >1nwv_A FRSCEVPTR-------------LNSASL------KQPYITQNYFPVGTVVEYECRPGYR-----------------------------------REPSLSPKLTCLQNLKW---STA-VEFCKKKSCPN--------------PGEIRNGQ--IDV---PGG--ILFGATISFSCNTGYKLFGSTSSFCL-----ISGSSVQWSD--PLPECREH @1vvc_ 03023121010111000100000000000000000000000000002311021200110111000311000000000101001010100000000000000000000000000000000000000022010300110001000000000000000000000010003000302020011110210100200001000000002010001202100 @1ghq_B 03120121010111000100000000000000000000000000032313021200030111000311000000000101001010100000000000000000000000000000000000000322010300110001000000000000000000000010000100302020003030200103200001000000002010001202100 @1ckl_A 00021021000000000000000000010000000000000013032001320200110000000000000000000000000000000000000010100300100100100000000301030322000000000000000003001110000000001010001100302021011010200003200000030110002000000202000 @1nwv_A 00121020000000000000000000010000000000000013032311320200110000000000000000000000000000000000000010100300100100100000000301030322000000000000000003001110000000001000001100302021011110210103200000030110002000001202000 Merge 443 449 Weight 2.77737 >1vvc_ -VKCQSPPSISNGRHNGYEDFY----------------------TDGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC-----------------------------------QIVKCPHPTISNGYLSSGFKR---------------S---YS--YNDNVDFKCKYGYKLSGSSSSTCSPGNT-------WKP--ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTPI----------------------AVGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS-------------------------------SCPEPIVPGGYKIRG----------------STP---YR--HGDSVTFACKTNFSMNGNKSVWCQANNM-------WGPTR-LPTCVS- >1ckl_A ---CEEPPT-------------FEAMELIGKPKP--------YYEIGERVDYKCKKGYF-----------------------------------YIPPLATHTICDRNHTWLPV--SD-DACYRETCPY--------------IRDPLNGQAV-PAN---GTYE--FGYQMHFICNEGYYLIGEEILYCE----LKGSVAIWSG--KPPICEKV >1nwv_A FRSCEVPTR-------------LNSASL------KQPYITQNYFPVGTVVEYECRPGYR-----------------------------------REPSLSPKLTCLQNLKW---STA-VEFCKKKSCPN--------------PGEIRNGQ--IDV---PGG--ILFGATISFSCNTGYKLFGSTSSFCL----ISGSSVQWSD--PLPECREH @1vvc_ 0302312101011100010000000000000000000000000000231102120011011100031100000000010100101010000000000000000000000000000000000000002201030011000100000000000000000000001000300030202001111021010020001000000002010001202100 @1ghq_B 0312012101011100010000000000000000000000000003231302120003011100031100000000010100101010000000000000000000000000000000000000032201030011000100000000000000000000001000010030202000303020010320001000000002010001202100 @1ckl_A 0002102100000000000000000001000000000000001303200132020011000000000000000000000000000000000000001010030010010010000000030103032200000000000000000300111000000000101000110030202101101020000320000030110002000000202000 @1nwv_A 0012102000000000000000000001000000000000001303231132020011000000000000000000000000000000000000001010030010010010000000030103032200000000000000000300111000000000100000110030202101111021010320000030110002000001202000 Merge 258 259 Weight 2.73571 >1vvc_ -VKCQSPPSISNGRHNGYEDFY----------------------TDGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC----------------------------------QIVKCPHPTISNGYLSSGFKR---------------S---YS--YNDNVDFKCKYGYKLSGSSSSTCSPGNT-------WKP--ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTPI----------------------AVGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS------------------------------SCPEPIVPGGYKIRG----------------STP---YR--HGDSVTFACKTNFSMNGNKSVWCQANNM-------WGPTR-LPTCVS- >1ckl_A ---CEEPPT-------------FEAMELIGKPKP--------YYEIGERVDYKCKKGYF-----------------------------------YIPPLATHTICDRNHTWLPV--SDDACYRETCPY--------------IRDPLNGQAV-PAN---GTYE--FGYQMHFICNEGYYLIGEEILYCE----LKGSVAIWSG--KPPICEKV >1nwv_A FRSCEVPTR-------------LNSASL------KQPYITQNYFPVGTVVEYECRPGYR-----------------------------------REPSLSPKLTCLQNLKW---STAVEFCKKKSCPN--------------PGEIRNGQ--IDV---PGG--ILFGATISFSCNTGYKLFGSTSSFCL----ISGSSVQWSD--PLPECREH @1vvc_ 030231210101110001000000000000000000000000000023110212001101110003110000000001010010101000000000000000000000000000000000000002201030011000100000000000000000000001000300030202001111021010020001000000002010001202100 @1ghq_B 031201210101110001000000000000000000000000000323130212000301110003110000000001010010101000000000000000000000000000000000000032201030011000100000000000000000000001000010030202000303020010320001000000002010001202100 @1ckl_A 000210210000000000000000000100000000000000130320013202001100000000000000000000000000000000000000101003001001001000000030103032200000000000000000300111000000000101000110030202101101020000320000030110002000000202000 @1nwv_A 001210200000000000000000000100000000000000130323113202001100000000000000000000000000000000000000101003001001001000000030103032200000000000000000300111000000000100000110030202101111021010320000030110002000001202000 Merge 331 277 Weight 2.63272 >1vvc_ -VKCQSPPSISNGRHNGYEDFY----------------------TDGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC----------------------------------QIVKCPHPTISNGYLSSGFKR--------------S---YS--YNDNVDFKCKYGYKLSGSSSSTCSPGNT-------WKP--ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTPI----------------------AVGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS------------------------------SCPEPIVPGGYKIRG---------------STP---YR--HGDSVTFACKTNFSMNGNKSVWCQANNM-------WGPTR-LPTCVS- >1ckl_A ---CEEPPT-------------FEAMELIGKPKP--------YYEIGERVDYKCKKGYF-----------------------------------YIPPLATHTICDRNHTWLPV--SDDACYRETCPYI-------------RDPLNGQAV-PAN---GTYE--FGYQMHFICNEGYYLIGEEILYCE----LKGSVAIWSG--KPPICEKV >1nwv_A FRSCEVPTR-------------LNSASL------KQPYITQNYFPVGTVVEYECRPGYR-----------------------------------REPSLSPKLTCLQNLKW---STAVEFCKKKSCPNP-------------GEIRNGQ--IDV---PGG--ILFGATISFSCNTGYKLFGSTSSFCL----ISGSSVQWSD--PLPECREH @1vvc_ 03023121010111000100000000000000000000000000002311021200110111000311000000000101001010100000000000000000000000000000000000000220103001100010000000000000000000001000300030202001111021010020001000000002010001202100 @1ghq_B 03120121010111000100000000000000000000000000032313021200030111000311000000000101001010100000000000000000000000000000000000003220103001100010000000000000000000001000010030202000303020010320001000000002010001202100 @1ckl_A 00021021000000000000000000010000000000000013032001320200110000000000000000000000000000000000000010100300100100100000003010303220000000000000000300111000000000101000110030202101101020000320000030110002000000202000 @1nwv_A 00121020000000000000000000010000000000000013032311320200110000000000000000000000000000000000000010100300100100100000003010303220100000000000000300111000000000100000110030202101111021010320000030110002000001202000 Merge 96 117 Weight 2.61277 >1vvc_ -VKCQSPPSISNGRHNGYEDFY---------------------TDGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC----------------------------------QIVKCPHPTISNGYLSSGFKR--------------S---YS--YNDNVDFKCKYGYKLSGSSSSTCSPGNT-------WKP--ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTPI---------------------AVGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS------------------------------SCPEPIVPGGYKIRG---------------STP---YR--HGDSVTFACKTNFSMNGNKSVWCQANNM-------WGPTR-LPTCVS- >1ckl_A ---CEEPPT-------------FEAMELIGKPK-------PYYEIGERVDYKCKKGYF-----------------------------------YIPPLATHTICDRNHTWLPV--SDDACYRETCPYI-------------RDPLNGQAV-PAN---GTYE--FGYQMHFICNEGYYLIGEEILYCE----LKGSVAIWSG--KPPICEKV >1nwv_A FRSCEVPTR-------------LNSASL-----KQPYITQNYFPVGTVVEYECRPGYR-----------------------------------REPSLSPKLTCLQNLKW---STAVEFCKKKSCPNP-------------GEIRNGQ--IDV---PGG--ILFGATISFSCNTGYKLFGSTSSFCL----ISGSSVQWSD--PLPECREH @1vvc_ 0302312101011100010000000000000000000000000002311021200110111000311000000000101001010100000000000000000000000000000000000000220103001100010000000000000000000001000300030202001111021010020001000000002010001202100 @1ghq_B 0312012101011100010000000000000000000000000032313021200030111000311000000000101001010100000000000000000000000000000000000003220103001100010000000000000000000001000010030202000303020010320001000000002010001202100 @1ckl_A 0002102100000000000000000001000000000000013032001320200110000000000000000000000000000000000000010100300100100100000003010303220000000000000000300111000000000101000110030202101101020000320000030110002000000202000 @1nwv_A 0012102000000000000000000001000000000000013032311320200110000000000000000000000000000000000000010100300100100100000003010303220100000000000000300111000000000100000110030202101111021010320000030110002000001202000 Reorder 249 250 247 248 Merge 248 249 Weight 2.49033 >1vvc_ -VKCQSPPSISNGRHNGYEDFY---------------------TDGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC---------------------------------QIVKCPHPTISNGYLSSGFKR--------------S---YS--YNDNVDFKCKYGYKLSGSSSSTCSPGNT-------WKP--ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTPI---------------------AVGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS-----------------------------SCPEPIVPGGYKIRG---------------STP---YR--HGDSVTFACKTNFSMNGNKSVWCQANNM-------WGPTR-LPTCVS- >1ckl_A ---CEEPPT-------------FEAMELIGKPK-------PYYEIGERVDYKCKKGYF-----------------------------------YIPPLATHTICDRNHTWL-PVSDDACYRETCPYI-------------RDPLNGQAV-PAN---GTYE--FGYQMHFICNEGYYLIGEEILYCE----LKGSVAIWSG--KPPICEKV >1nwv_A FRSCEVPTR-------------LNSASL-----KQPYITQNYFPVGTVVEYECRPGYR-----------------------------------REPSLSPKLTCLQNLKW-ST-AVEFCKKKSCPNP-------------GEIRNGQ--IDV---PGG--ILFGATISFSCNTGYKLFGSTSSFCL----ISGSSVQWSD--PLPECREH @1vvc_ 030231210101110001000000000000000000000000000231102120011011100031100000000010100101010000000000000000000000000000000000000220103001100010000000000000000000001000300030202001111021010020001000000002010001202100 @1ghq_B 031201210101110001000000000000000000000000003231302120003011100031100000000010100101010000000000000000000000000000000000003220103001100010000000000000000000001000010030202000303020010320001000000002010001202100 @1ckl_A 000210210000000000000000000100000000000001303200132020011000000000000000000000000000000000000001010030010010010000003010303220000000000000000300111000000000101000110030202101101020000320000030110002000000202000 @1nwv_A 001210200000000000000000000100000000000001303231132020011000000000000000000000000000000000000001010030010010010000003010303220100000000000000300111000000000100000110030202101111021010320000030110002000001202000 Merge 72 22 Weight 2.42145 >1vvc_ -VKCQSPPSISNGRHNGYEDFY--------------------TDGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC---------------------------------QIVKCPHPTISNGYLSSGFKR--------------S---YS--YNDNVDFKCKYGYKLSGSSSSTCSPGNT-------WKP--ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTPI--------------------AVGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS-----------------------------SCPEPIVPGGYKIRG---------------STP---YR--HGDSVTFACKTNFSMNGNKSVWCQANNM-------WGPTR-LPTCVS- >1ckl_A ---CEEPPTF------------EAMELIGKPK-------PYYEIGERVDYKCKKGYF-----------------------------------YIPPLATHTICDRNHTWL-PVSDDACYRETCPYI-------------RDPLNGQAV-PAN---GTYE--FGYQMHFICNEGYYLIGEEILYCE----LKGSVAIWSG--KPPICEKV >1nwv_A FRSCEVPTRL------------NSASL-----KQPYITQNYFPVGTVVEYECRPGYR-----------------------------------REPSLSPKLTCLQNLKW-ST-AVEFCKKKSCPNP-------------GEIRNGQ--IDV---PGG--ILFGATISFSCNTGYKLFGSTSSFCL----ISGSSVQWSD--PLPECREH @1vvc_ 03023121010111000100000000000000000000000000231102120011011100031100000000010100101010000000000000000000000000000000000000220103001100010000000000000000000001000300030202001111021010020001000000002010001202100 @1ghq_B 03120121010111000100000000000000000000000003231302120003011100031100000000010100101010000000000000000000000000000000000003220103001100010000000000000000000001000010030202000303020010320001000000002010001202100 @1ckl_A 00021021000000000000000000100000000000001303200132020011000000000000000000000000000000000000001010030010010010000003010303220000000000000000300111000000000101000110030202101101020000320000030110002000000202000 @1nwv_A 00121020030000000000000000100000000000001303231132020011000000000000000000000000000000000000001010030010010010000003010303220100000000000000300111000000000100000110030202101111021010320000030110002000001202000 Merge 245 247 Weight 2.22353 >1vvc_ -VKCQSPPSISNGRHNGYEDFY--------------------TDGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC--------------------------------QIVKCPHPTISNGYLSSGFKR--------------S---YS--YNDNVDFKCKYGYKLSGSSSSTCSPGNT-------WKP--ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTPI--------------------AVGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS----------------------------SCPEPIVPGGYKIRG---------------STP---YR--HGDSVTFACKTNFSMNGNKSVWCQANNM-------WGPTR-LPTCVS- >1ckl_A ---CEEPPTF------------EAMELIGKPK-------PYYEIGERVDYKCKKGYF-----------------------------------YIPPLATHTICDRNHTWLPVSDDACYRETCPYI-------------RDPLNGQAV-PAN---GTYE--FGYQMHFICNEGYYLIGEEILYCE----LKGSVAIWSG--KPPICEKV >1nwv_A FRSCEVPTRL------------NSASL-----KQPYITQNYFPVGTVVEYECRPGYR-----------------------------------REPSLSPKLTCLQNLKWST-AVEFCKKKSCPNP-------------GEIRNGQ--IDV---PGG--ILFGATISFSCNTGYKLFGSTSSFCL----ISGSSVQWSD--PLPECREH @1vvc_ 0302312101011100010000000000000000000000000023110212001101110003110000000001010010101000000000000000000000000000000000000220103001100010000000000000000000001000300030202001111021010020001000000002010001202100 @1ghq_B 0312012101011100010000000000000000000000000323130212000301110003110000000001010010101000000000000000000000000000000000003220103001100010000000000000000000001000010030202000303020010320001000000002010001202100 @1ckl_A 0002102100000000000000000010000000000000130320013202001100000000000000000000000000000000000000101003001001001000003010303220000000000000000300111000000000101000110030202101101020000320000030110002000000202000 @1nwv_A 0012102003000000000000000010000000000000130323113202001100000000000000000000000000000000000000101003001001001000003010303220100000000000000300111000000000100000110030202101111021010320000030110002000001202000 Merge 56 119 Weight 2.09621 >1vvc_ -VKCQSPPSISNGRHNGYEDF-------------------YTDGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC--------------------------------QIVKCPHPTISNGYLSSGFKR--------------S---YS--YNDNVDFKCKYGYKLSGSSSSTCSPGNT-------WKP--ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTP-------------------IAVGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS----------------------------SCPEPIVPGGYKIRG---------------STP---YR--HGDSVTFACKTNFSMNGNKSVWCQANNM-------WGPTR-LPTCVS- >1ckl_A ---CEEPPTF-----------EAMELIGKPK-------PYYEIGERVDYKCKKGYF-----------------------------------YIPPLATHTICDRNHTWLPVSDDACYRETCPYI-------------RDPLNGQAV-PAN---GTYE--FGYQMHFICNEGYYLIGEEILYCE----LKGSVAIWSG--KPPICEKV >1nwv_A FRSCEVPTRL-----------NSASL-----KQPYITQNYFPVGTVVEYECRPGYR-----------------------------------REPSLSPKLTCLQNLKWST-AVEFCKKKSCPNP-------------GEIRNGQ--IDV---PGG--ILFGATISFSCNTGYKLFGSTSSFCL----ISGSSVQWSD--PLPECREH @1vvc_ 030231210101110001000000000000000000000030023110212001101110003110000000001010010101000000000000000000000000000000000000220103001100010000000000000000000001000300030202001111021010020001000000002010001202100 @1ghq_B 031201210101110001000000000000000000000000323130212000301110003110000000001010010101000000000000000000000000000000000003220103001100010000000000000000000001000010030202000303020010320001000000002010001202100 @1ckl_A 000210210000000000000000010000000000000130320013202001100000000000000000000000000000000000000101003001001001000003010303220000000000000000300111000000000101000110030202101101020000320000030110002000000202000 @1nwv_A 001210200300000000000000010000000000000130323113202001100000000000000000000000000000000000000101003001001001000003010303220100000000000000300111000000000100000110030202101111021010320000030110002000001202000 Merge 476 481 Weight 2.03823 >1vvc_ -VKCQSPPSISNGRHNGYEDF-------------------YTDGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC--------------------------------QIVKCPHPTISNGYLSSGFKR--------------S---YS--YNDNVDFKCKYGYKLSGSSSSTCSPGNT-------WKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTP-------------------IAVGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS----------------------------SCPEPIVPGGYKIRG---------------STP---YR--HGDSVTFACKTNFSMNGNKSVWCQANNM-------WGPTRLPTCVS- >1ckl_A ---CEEPPTF-----------EAMELIGKPK-------PYYEIGERVDYKCKKGYF-----------------------------------YIPPLATHTICDRNHTWLPVSDDACYRETCPYI-------------RDPLNGQAV-PAN---GTYE--FGYQMHFICNEGYYLIGEEILYCE----LKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRL-----------NSASL-----KQPYITQNYFPVGTVVEYECRPGYR-----------------------------------REPSLSPKLTCLQNLKWST-AVEFCKKKSCPNP-------------GEIRNGQ--IDV---PGG--ILFGATISFSCNTGYKLFGSTSSFCL----ISGSSVQWSD-PLPECREH @1vvc_ 03023121010111000100000000000000000000003002311021200110111000311000000000101001010100000000000000000000000000000000000022010300110001000000000000000000000100030003020200111102101002000100000000201001202100 @1ghq_B 03120121010111000100000000000000000000000032313021200030111000311000000000101001010100000000000000000000000000000000000322010300110001000000000000000000000100001003020200030302001032000100000000201001202100 @1ckl_A 00021021000000000000000001000000000000013032001320200110000000000000000000000000000000000000010100300100100100000301030322000000000000000030011100000000010100011003020210110102000032000003011000200000202000 @1nwv_A 00121020030000000000000001000000000000013032311320200110000000000000000000000000000000000000010100300100100100000301030322010000000000000030011100000000010000011003020210111102101032000003011000200001202000 Merge 347 349 Weight 2.00746 >1vvc_ -VKCQSPPSISNGRHNGYEDF-------------------YTDGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC--------------------------------QIVKCPHPTISNGYLSSGFKR-------------S---YS--YNDNVDFKCKYGYKLSGSSSSTCSPGNT-------WKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTP-------------------IAVGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS----------------------------SCPEPIVPGGYKIRG--------------STP---YR--HGDSVTFACKTNFSMNGNKSVWCQANNM-------WGPTRLPTCVS- >1ckl_A ---CEEPPTF-----------EAMELIGKPK-------PYYEIGERVDYKCKKGYF-----------------------------------YIPPLATHTICDRNHTWLPVSDDACYRETCPYI-------------RDPLNGQAVPAN---GTYE--FGYQMHFICNEGYYLIGEEILYCE----LKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRL-----------NSASL-----KQPYITQNYFPVGTVVEYECRPGYR-----------------------------------REPSLSPKLTCLQNLKWST-AVEFCKKKSCPNP-------------GEIRNGQ-IDV---PGG--ILFGATISFSCNTGYKLFGSTSSFCL----ISGSSVQWSD-PLPECREH @1vvc_ 0302312101011100010000000000000000000000300231102120011011100031100000000010100101010000000000000000000000000000000000002201030011000100000000000000000000100030003020200111102101002000100000000201001202100 @1ghq_B 0312012101011100010000000000000000000000003231302120003011100031100000000010100101010000000000000000000000000000000000032201030011000100000000000000000000100001003020200030302001032000100000000201001202100 @1ckl_A 0002102100000000000000000100000000000001303200132020011000000000000000000000000000000000000001010030010010010000030103032200000000000000003001110300000010100011003020210110102000032000003011000200000202000 @1nwv_A 0012102003000000000000000100000000000001303231132020011000000000000000000000000000000000000001010030010010010000030103032201000000000000003001110300000010000011003020210111102101032000003011000200001202000 Merge 210 141 Weight 1.98335 >1vvc_ -VKCQSPPSISNGRHNGYEDF-------------------YTDGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC-------------------------------QIVKCPHPTISNGYLSSGFKR-------------S---YS--YNDNVDFKCKYGYKLSGSSSSTCSPGNT-------WKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTP-------------------IAVGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKYS---------------------------SCPEPIVPGGYKIRG--------------STP---YR--HGDSVTFACKTNFSMNGNKSVWCQANNM-------WGPTRLPTCVS- >1ckl_A ---CEEPPTF-----------EAMELIGKPK-------PYYEIGERVDYKCKKGYFY----------------------------------IPPLATHTICDRNHTWLPVSDDACYRETCPYI-------------RDPLNGQAVPAN---GTYE--FGYQMHFICNEGYYLIGEEILYCE----LKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRL-----------NSASL-----KQPYITQNYFPVGTVVEYECRPGYRR----------------------------------EPSLSPKLTCLQNLKWST-AVEFCKKKSCPNP-------------GEIRNGQ-IDV---PGG--ILFGATISFSCNTGYKLFGSTSSFCL----ISGSSVQWSD-PLPECREH @1vvc_ 030231210101110001000000000000000000000030023110212001101110003110000000001010010101000000000000000000000000000000000002201030011000100000000000000000000100030003020200111102101002000100000000201001202100 @1ghq_B 031201210101110001000000000000000000000000323130212000301110003110000000001010010101000000000000000000000000000000000032201030011000100000000000000000000100001003020200030302001032000100000000201001202100 @1ckl_A 000210210000000000000000010000000000000130320013202001100000000000000000000000000000000000001010030010010010000030103032200000000000000003001110300000010100011003020210110102000032000003011000200000202000 @1nwv_A 001210200300000000000000010000000000000130323113202001100000000000000000000000000000000000001010030010010010000030103032201000000000000003001110300000010000011003020210111102101032000003011000200001202000 Merge 207 268 Weight 1.93535 >1vvc_ -VKCQSPPSISNGRHNGYEDF-------------------YTDGSVVTYSCNSGYSLIGNSGVLCSG-------GEWSDP-PTC------------------------------QIVKCPHPTISNGYLSSGFKR-------------S---YS--YNDNVDFKCKYGYKLSGSSSSTCSPGNT-------WKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTP-------------------IAVGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGTWDKPAPKCEYFNKY--------------------------SSCPEPIVPGGYKIRG--------------STP---YR--HGDSVTFACKTNFSMNGNKSVWCQANNM-------WGPTRLPTCVS- >1ckl_A ---CEEPPTF-----------EAMELIGKPK-------PYYEIGERVDYKCKKGYFY---------------------------------IPPLATHTICDRNHTWLPVSDDACYRETCPYI-------------RDPLNGQAVPAN---GTYE--FGYQMHFICNEGYYLIGEEILYCE----LKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRL-----------NSASL-----KQPYITQNYFPVGTVVEYECRPGYRR---------------------------------EPSLSPKLTCLQNLKWST-AVEFCKKKSCPNP-------------GEIRNGQ-IDV---PGG--ILFGATISFSCNTGYKLFGSTSSFCL----ISGSSVQWSD-PLPECREH @1vvc_ 03023121010111000100000000000000000000003002311021200110111000311000000000101001010100000000000000000000000000000000002201030011000100000000000000000000100030003020200111102101002000100000000201001202100 @1ghq_B 03120121010111000100000000000000000000000032313021200030111000311000000000101001010100000000000000000000000000000000032201030011000100000000000000000000100001003020200030302001032000100000000201001202100 @1ckl_A 00021021000000000000000001000000000000013032001320200110000000000000000000000000000000000001010030010010010000030103032200000000000000003001110300000010100011003020210110102000032000003011000200000202000 @1nwv_A 00121020030000000000000001000000000000013032311320200110000000000000000000000000000000000001010030010010010000030103032201000000000000003001110300000010000011003020210111102101032000003011000200001202000 Reorder 211 212 213 218 219 220 221 222 223 224 235 236 237 238 239 240 175 177 179 180 181 183 185 187 201 202 203 204 205 206 Merge 212 213 Weight 1.8845 >1vvc_ -VKCQSPPSISNGRHNGYEDF-------------------YTDGSVVTYSCNSGYSLIGNSGVLCSG-------GE---------------WSDP-PTC--------------QIVKCPHPTISNGYLSSGFKR-------------S---YS--YNDNVDFKCKYGYKLSGSSSSTCSPGNT-------WKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTP-------------------IAVGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGT---------------WDKPAPKCEYFNKY----------SSCPEPIVPGGYKIRG--------------STP---YR--HGDSVTFACKTNFSMNGNKSVWCQANNM-------WGPTRLPTCVS- >1ckl_A ---CEEPPTF-----------EAMELIGKPK-------PYYEIGERVDYKCKKGYFY-------------------IPPLATHTICDRNHTW-------------LPVSDDACYRETCPYI-------------RDPLNGQAVPAN---GTYE--FGYQMHFICNEGYYLIGEEILYCE----LKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRL-----------NSASL-----KQPYITQNYFPVGTVVEYECRPGYRR-------------------EPSLSPKLTCLQNLKW-------------ST-AVEFCKKKSCPNP-------------GEIRNGQ-IDV---PGG--ILFGATISFSCNTGYKLFGSTSSFCL----ISGSSVQWSD-PLPECREH @1vvc_ 0302312101011100010000000000000000000000300231102120011011100031100000000010000000000000000200101010000000000000000002201030011000100000000000000000000100030003020200111102101002000100000000201001202100 @1ghq_B 0312012101011100010000000000000000000000003231302120003011100031100000000010000000000000000200101010000000000000000032201030011000100000000000000000000100001003020200030302001032000100000000201001202100 @1ckl_A 0002102100000000000000000100000000000001303200132020011000000000000000000000010100300100100200000000000000000030103032200000000000000003001110300000010100011003020210110102000032000003011000200000202000 @1nwv_A 0012102003000000000000000100000000000001303231132020011000000000000000000000010100300100100200000000000000000030103032201000000000000003001110300000010000011003020210111102101032000003011000200001202000 Reorder 247 249 250 255 259 260 261 265 224 235 236 237 238 239 240 Merge 247 249 Weight 1.78403 >1vvc_ -VKCQSPPSISNGRHNGYEDF-------------------YTDGSVVTYSCNSGYSLIGNSGVLCSG-------GE---------------WSDP-PT-------C------QIVKCPHPTISNGYLSSGFKR-------------S---YS--YNDNVDFKCKYGYKLSGSSSSTCSPGNT-------WKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTP-------------------IAVGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGT---------------WDKPAPK-------CEYFNKY--SSCPEPIVPGGYKIRG--------------STP---YR--HGDSVTFACKTNFSMNGNKSVWCQANNM-------WGPTRLPTCVS- >1ckl_A ---CEEPPTF-----------EAMELIGKPK-------PYYEIGERVDYKCKKGYFY-------------------IPPLATHTICDRNHTW------LPVSDDAC------YRETCPYI-------------RDPLNGQAVPAN---GTYE--FGYQMHFICNEGYYLIGEEILYCE----LKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRL-----------NSASL-----KQPYITQNYFPVGTVVEYECRPGYRR-------------------EPSLSPKLTCLQNLKW------ST-AVEFC------KKKSCPNP-------------GEIRNGQ-IDV---PGG--ILFGATISFSCNTGYKLFGSTSSFCL----ISGSSVQWSD-PLPECREH @1vvc_ 030231210101110001000000000000000000000030023110212001101110003110000000001000000000000000020010100000000200000000002201030011000100000000000000000000100030003020200111102101002000100000000201001202100 @1ghq_B 031201210101110001000000000000000000000000323130212000301110003110000000001000000000000000020010100000000200000000032201030011000100000000000000000000100001003020200030302001032000100000000201001202100 @1ckl_A 000210210000000000000000010000000000000130320013202001100000000000000000000001010030010010020000000000030200000003032200000000000000003001110300000010100011003020210110102000032000003011000200000202000 @1nwv_A 001210200300000000000000010000000000000130323113202001100000000000000000000001010030010010020000000000030200000003032201000000000000003001110300000010000011003020210111102101032000003011000200001202000 Merge 313 358 Weight 1.75216 >1vvc_ -VKCQSPPSISNGRHNGYEDF-------------------YTDGSVVTYSCNSGYSLIGNSGVLCSG-------GE---------------WSDP-PT-------C------QIVKCPHPTISNGYLSSGFK------------RS---YS--YNDNVDFKCKYGYKLSGSSSSTCSPGNT-------WKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTP-------------------IAVGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGT---------------WDKPAPK-------CEYFNKY--SSCPEPIVPGGYKIRG-------------STP---YR--HGDSVTFACKTNFSMNGNKSVWCQANNM-------WGPTRLPTCVS- >1ckl_A ---CEEPPTF-----------EAMELIGKPK-------PYYEIGERVDYKCKKGYFY-------------------IPPLATHTICDRNHTW------LPVSDDAC------YRETCPYI------------RDPLNGQAVPAN---GTYE--FGYQMHFICNEGYYLIGEEILYCE----LKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRL-----------NSASL-----KQPYITQNYFPVGTVVEYECRPGYRR-------------------EPSLSPKLTCLQNLKW------ST-AVEFC------KKKSCPNP------------GEIRNGQ-IDV---PGG--ILFGATISFSCNTGYKLFGSTSSFCL----ISGSSVQWSD-PLPECREH @1vvc_ 03023121010111000100000000000000000000003002311021200110111000311000000000100000000000000002001010000000020000000000220103001100010000000000000000000100030003020200111102101002000100000000201001202100 @1ghq_B 03120121010111000100000000000000000000000032313021200030111000311000000000100000000000000002001010000000020000000003220103001100010000000000000000000100001003020200030302001032000100000000201001202100 @1ckl_A 00021021000000000000000001000000000000013032001320200110000000000000000000000101003001001002000000000003020000000303220000000000000003001110300000010100011003020210110102000032000003011000200000202000 @1nwv_A 00121020030000000000000001000000000000013032311320200110000000000000000000000101003001001002000000000003020000000303220100000000000003001110300000010000011003020210111102101032000003011000200001202000 Merge 385 392 Weight 1.65623 >1vvc_ -VKCQSPPSISNGRHNGYEDF-------------------YTDGSVVTYSCNSGYSLIGNSGVLCSG-------GE---------------WSDP-PT-------C------QIVKCPHPTISNGYLSSGFK------------RS---Y-SYNDNVDFKCKYGYKLSGSSSSTCSPGNT-------WKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTP-------------------IAVGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGT---------------WDKPAPK-------CEYFNKY--SSCPEPIVPGGYKIRG-------------STP---Y-RHGDSVTFACKTNFSMNGNKSVWCQANNM-------WGPTRLPTCVS- >1ckl_A ---CEEPPTF-----------EAMELIGKPK-------PYYEIGERVDYKCKKGYFY-------------------IPPLATHTICDRNHTW------LPVSDDAC------YRETCPYI------------RDPLNGQAVPAN---GTY-EFGYQMHFICNEGYYLIGEEILYCE----LKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRL-----------NSASL-----KQPYITQNYFPVGTVVEYECRPGYRR-------------------EPSLSPKLTCLQNLKW------ST-AVEFC------KKKSCPNP------------GEIRNGQ-IDV---PGG-ILFGATISFSCNTGYKLFGSTSSFCL----ISGSSVQWSD-PLPECREH @1vvc_ 0302312101011100010000000000000000000000300231102120011011100031100000000010000000000000000200101000000002000000000022010300110001000000000000000000010030003020200111102101002000100000000201001202100 @1ghq_B 0312012101011100010000000000000000000000003231302120003011100031100000000010000000000000000200101000000002000000000322010300110001000000000000000000010001003020200030302001032000100000000201001202100 @1ckl_A 0002102100000000000000000100000000000001303200132020011000000000000000000000010100300100100200000000000302000000030322000000000000000300111030000001010011003020210110102000032000003011000200000202000 @1nwv_A 0012102003000000000000000100000000000001303231132020011000000000000000000000010100300100100200000000000302000000030322010000000000000300111030000001000011003020210111102101032000003011000200001202000 Merge 83 115 Weight 1.60915 >1vvc_ -VKCQSPPSISNGRHNGYEDF------------------YTDGSVVTYSCNSGYSLIGNSGVLCSG-------GE---------------WSDP-PT-------C------QIVKCPHPTISNGYLSSGFK------------RS---Y-SYNDNVDFKCKYGYKLSGSSSSTCSPGNT-------WKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTP------------------IAVGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGT---------------WDKPAPK-------CEYFNKY--SSCPEPIVPGGYKIRG-------------STP---Y-RHGDSVTFACKTNFSMNGNKSVWCQANNM-------WGPTRLPTCVS- >1ckl_A ---CEEPPTF-----------EAMELIGKP------KPYYEIGERVDYKCKKGYFY-------------------IPPLATHTICDRNHTW------LPVSDDAC------YRETCPYI------------RDPLNGQAVPAN---GTY-EFGYQMHFICNEGYYLIGEEILYCE----LKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRL-----------NSASL----KQPYITQNYFPVGTVVEYECRPGYRR-------------------EPSLSPKLTCLQNLKW------ST-AVEFC------KKKSCPNP------------GEIRNGQ-IDV---PGG-ILFGATISFSCNTGYKLFGSTSSFCL----ISGSSVQWSD-PLPECREH @1vvc_ 030231210101110001000000000000000000000300231102120011011100031100000000010000000000000000200101000000002000000000022010300110001000000000000000000010030003020200111102101002000100000000201001202100 @1ghq_B 031201210101110001000000000000000000000003231302120003011100031100000000010000000000000000200101000000002000000000322010300110001000000000000000000010001003020200030302001032000100000000201001202100 @1ckl_A 000210210000000000000000010000000000001303200132020011000000000000000000000010100300100100200000000000302000000030322000000000000000300111030000001010011003020210110102000032000003011000200000202000 @1nwv_A 001210200300000000000000010000000000001303231132020011000000000000000000000010100300100100200000000000302000000030322010000000000000300111030000001000011003020210111102101032000003011000200001202000 Merge 74 23 Weight 1.58065 >1vvc_ -VKCQSPPSISNGRHNGYEDF-----------------YTDGSVVTYSCNSGYSLIGNSGVLCSG-------GE---------------WSDP-PT-------C------QIVKCPHPTISNGYLSSGFK------------RS---Y-SYNDNVDFKCKYGYKLSGSSSSTCSPGNT-------WKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTP-----------------IAVGTVIRYSCSGTFRLIGEKSLLC--ITKDKVDGT---------------WDKPAPK-------CEYFNKY--SSCPEPIVPGGYKIRG-------------STP---Y-RHGDSVTFACKTNFSMNGNKSVWCQANNM-------WGPTRLPTCVS- >1ckl_A ---CEEPPTFE----------AMELIGKP------KPYYEIGERVDYKCKKGYFY-------------------IPPLATHTICDRNHTW------LPVSDDAC------YRETCPYI------------RDPLNGQAVPAN---GTY-EFGYQMHFICNEGYYLIGEEILYCE----LKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLN----------SASL----KQPYITQNYFPVGTVVEYECRPGYRR-------------------EPSLSPKLTCLQNLKW------ST-AVEFC------KKKSCPNP------------GEIRNGQ-IDV---PGG-ILFGATISFSCNTGYKLFGSTSSFCL----ISGSSVQWSD-PLPECREH @1vvc_ 03023121010111000100000000000000000000300231102120011011100031100000000010000000000000000200101000000002000000000022010300110001000000000000000000010030003020200111102101002000100000000201001202100 @1ghq_B 03120121010111000100000000000000000000003231302120003011100031100000000010000000000000000200101000000002000000000322010300110001000000000000000000010001003020200030302001032000100000000201001202100 @1ckl_A 00021021000000000000000010000000000001303200132020011000000000000000000000010100300100100200000000000302000000030322000000000000000300111030000001010011003020210110102000032000003011000200000202000 @1nwv_A 00121020030000000000000010000000000001303231132020011000000000000000000000010100300100100200000000000302000000030322010000000000000300111030000001000011003020210111102101032000003011000200001202000 Merge 154 150 Weight 1.56667 >1vvc_ -VKCQSPPSISNGRHNGYEDF-----------------YTDGSVVTYSCNSGYSLIGNSGVLCSG------GE---------------WSDP-PT-------C------QIVKCPHPTISNGYLSSGFK------------RS---Y-SYNDNVDFKCKYGYKLSGSSSSTCSPGNT-------WKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTP-----------------IAVGTVIRYSCSGTFRLIGEKSLLCI-TKDKVDGT---------------WDKPAPK-------CEYFNKY--SSCPEPIVPGGYKIRG-------------STP---Y-RHGDSVTFACKTNFSMNGNKSVWCQANNM-------WGPTRLPTCVS- >1ckl_A ---CEEPPTFE----------AMELIGKP------KPYYEIGERVDYKCKKGYFY------------------IPPLATHTICDRNHTW------LPVSDDAC------YRETCPYI------------RDPLNGQAVPAN---GTY-EFGYQMHFICNEGYYLIGEEILYCE----LKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLN----------SASL----KQPYITQNYFPVGTVVEYECRPGYRR------------------EPSLSPKLTCLQNLKW------ST-AVEFC------KKKSCPNP------------GEIRNGQ-IDV---PGG-ILFGATISFSCNTGYKLFGSTSSFCL----ISGSSVQWSD-PLPECREH @1vvc_ 0302312101011100010000000000000000000030023110212001101110003110000000010000000000000000200101000000002000000000022010300110001000000000000000000010030003020200111102101002000100000000201001202100 @1ghq_B 0312012101011100010000000000000000000000323130212000301110003110000000010000000000000000200101000000002000000000322010300110001000000000000000000010001003020200030302001032000100000000201001202100 @1ckl_A 0002102100000000000000001000000000000130320013202001100000000000000000000010100300100100200000000000302000000030322000000000000000300111030000001010011003020210110102000032000003011000200000202000 @1nwv_A 0012102003000000000000001000000000000130323113202001100000000000000000000010100300100100200000000000302000000030322010000000000000300111030000001000011003020210111102101032000003011000200001202000 Merge 151 170 Weight 1.5614 >1vvc_ -VKCQSPPSISNGRHNGYEDF-----------------YTDGSVVTYSCNSGYSLIGNSGVLCS-----GGE---------------WSDP-PT-------C------QIVKCPHPTISNGYLSSGFK------------RS---Y-SYNDNVDFKCKYGYKLSGSSSSTCSPGNT-------WKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTP-----------------IAVGTVIRYSCSGTFRLIGEKSLLCITKDKVDGT---------------WDKPAPK-------CEYFNKY--SSCPEPIVPGGYKIRG-------------STP---Y-RHGDSVTFACKTNFSMNGNKSVWCQANNM-------WGPTRLPTCVS- >1ckl_A ---CEEPPTFE----------AMELIGKP------KPYYEIGERVDYKCKKGYFY-----------------IPPLATHTICDRNHTW------LPVSDDAC------YRETCPYI------------RDPLNGQAVPAN---GTY-EFGYQMHFICNEGYYLIGEEILYCE----LKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLN----------SASL----KQPYITQNYFPVGTVVEYECRPGYRR-----------------EPSLSPKLTCLQNLKW------ST-AVEFC------KKKSCPNP------------GEIRNGQ-IDV---PGG-ILFGATISFSCNTGYKLFGSTSSFCL----ISGSSVQWSD-PLPECREH @1vvc_ 030231210101110001000000000000000000003002311021200110111000311000000010000000000000000200101000000002000000000022010300110001000000000000000000010030003020200111102101002000100000000201001202100 @1ghq_B 031201210101110001000000000000000000000032313021200030111000311000000010000000000000000200101000000002000000000322010300110001000000000000000000010001003020200030302001032000100000000201001202100 @1ckl_A 000210210000000000000000100000000000013032001320200110000000000000000000010100300100100200000000000302000000030322000000000000000300111030000001010011003020210110102000032000003011000200000202000 @1nwv_A 001210200300000000000000100000000000013032311320200110000000000000000000010100300100100200000000000302000000030322010000000000000300111030000001000011003020210111102101032000003011000200001202000 Merge 454 468 Weight 1.5371 >1vvc_ -VKCQSPPSISNGRHNGYEDF-----------------YTDGSVVTYSCNSGYSLIGNSGVLCS-----GGE---------------WSDP-PT-------C------QIVKCPHPTISNGYLSSGFK------------RS---Y-SYNDNVDFKCKYGYKLSGSSSSTCSPGN------TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYYSTP-----------------IAVGTVIRYSCSGTFRLIGEKSLLCITKDKVDGT---------------WDKPAPK-------CEYFNKY--SSCPEPIVPGGYKIRG-------------STP---Y-RHGDSVTFACKTNFSMNGNKSVWCQANN------MWGPTRLPTCVS- >1ckl_A ---CEEPPTFE----------AMELIGKP------KPYYEIGERVDYKCKKGYFY-----------------IPPLATHTICDRNHTW------LPVSDDAC------YRETCPYI------------RDPLNGQAVPAN---GTY-EFGYQMHFICNEGYYLIGEEILYCE---LKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLN----------SASL----KQPYITQNYFPVGTVVEYECRPGYRR-----------------EPSLSPKLTCLQNLKW------ST-AVEFC------KKKSCPNP------------GEIRNGQ-IDV---PGG-ILFGATISFSCNTGYKLFGSTSSFCL---ISGSSVQWSD-PLPECREH @1vvc_ 03023121010111000100000000000000000000300231102120011011100031100000001000000000000000020010100000000200000000002201030011000100000000000000000001003000302020011110210100200010000000201001202100 @1ghq_B 03120121010111000100000000000000000000003231302120003011100031100000001000000000000000020010100000000200000000032201030011000100000000000000000001000100302020003030200103200010000000201001202100 @1ckl_A 00021021000000000000000010000000000001303200132020011000000000000000000001010030010010020000000000030200000003032200000000000000030011103000000101001100302021011010200003200003011000200000202000 @1nwv_A 00121020030000000000000010000000000001303231132020011000000000000000000001010030010010020000000000030200000003032201000000000000030011103000000100001100302021011110210103200003011000200001202000 Reorder 75 76 77 78 79 80 47 49 52 53 54 Merge 75 76 Weight 1.49322 >1vvc_ -VKCQSPPSISNGRHN-----GYEDF-----------YTDGSVVTYSCNSGYSLIGNSGVLCS-----GGE---------------WSDP-PT-------C------QIVKCPHPTISNGYLSSGFK------------RS---Y-SYNDNVDFKCKYGYKLSGSSSSTCSPGN------TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRIS-----YYSTP-----------IAVGTVIRYSCSGTFRLIGEKSLLCITKDKVDGT---------------WDKPAPK-------CEYFNKY--SSCPEPIVPGGYKIRG-------------STP---Y-RHGDSVTFACKTNFSMNGNKSVWCQANN------MWGPTRLPTCVS- >1ckl_A ---CEEPPTFE-----AMELIG----KP------KPYYEIGERVDYKCKKGYFY-----------------IPPLATHTICDRNHTW------LPVSDDAC------YRETCPYI------------RDPLNGQAVPAN---GTY-EFGYQMHFICNEGYYLIGEEILYCE---LKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLN-----SASL--------KQPYITQNYFPVGTVVEYECRPGYRR-----------------EPSLSPKLTCLQNLKW------ST-AVEFC------KKKSCPNP------------GEIRNGQ-IDV---PGG-ILFGATISFSCNTGYKLFGSTSSFCL---ISGSSVQWSD-PLPECREH @1vvc_ 0302312101011100000001100000000000000300231102120011011100031100000001000000000000000020010100000000200000000002201030011000100000000000000000001003000302020011110210100200010000000201001202100 @1ghq_B 0312012101011100000000100000000000000003231302120003011100031100000001000000000000000020010100000000200000000032201030011000100000000000000000001000100302020003030200103200010000000201001202100 @1ckl_A 0002102100000000000101000000000000001303200132020011000000000000000000001010030010010020000000000030200000003032200000000000000030011103000000101001100302021011010200003200003011000200000202000 @1nwv_A 0012102003000000000100000000000000001303231132020011000000000000000000001010030010010020000000000030200000003032201000000000000030011103000000100001100302021011110210103200003011000200001202000 Merge 80 118 Weight 1.45044 >1vvc_ -VKCQSPPSISNGRHN-----GYED----------FYTDGSVVTYSCNSGYSLIGNSGVLCS-----GGE---------------WSDP-PT-------C------QIVKCPHPTISNGYLSSGFK------------RS---Y-SYNDNVDFKCKYGYKLSGSSSSTCSPGN------TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRIS-----YYST----------PIAVGTVIRYSCSGTFRLIGEKSLLCITKDKVDGT---------------WDKPAPK-------CEYFNKY--SSCPEPIVPGGYKIRG-------------STP---Y-RHGDSVTFACKTNFSMNGNKSVWCQANN------MWGPTRLPTCVS- >1ckl_A ---CEEPPTFE-----AMELIG---KP------KPYYEIGERVDYKCKKGYFY-----------------IPPLATHTICDRNHTW------LPVSDDAC------YRETCPYI------------RDPLNGQAVPAN---GTY-EFGYQMHFICNEGYYLIGEEILYCE---LKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLN-----SASL-------KQPYITQNYFPVGTVVEYECRPGYRR-----------------EPSLSPKLTCLQNLKW------ST-AVEFC------KKKSCPNP------------GEIRNGQ-IDV---PGG-ILFGATISFSCNTGYKLFGSTSSFCL---ISGSSVQWSD-PLPECREH @1vvc_ 030231210101110000000110000000000003300231102120011011100031100000001000000000000000020010100000000200000000002201030011000100000000000000000001003000302020011110210100200010000000201001202100 @1ghq_B 031201210101110000000010000000000000003231302120003011100031100000001000000000000000020010100000000200000000032201030011000100000000000000000001000100302020003030200103200010000000201001202100 @1ckl_A 000210210000000000010100000000000001303200132020011000000000000000000001010030010010020000000000030200000003032200000000000000030011103000000101001100302021011010200003200003011000200000202000 @1nwv_A 001210200300000000010000000000000001303231132020011000000000000000000001010030010010020000000000030200000003032201000000000000030011103000000100001100302021011110210103200003011000200001202000 Reorder 333 334 335 337 338 339 345 346 349 354 356 361 292 296 301 302 303 304 305 306 308 312 357 358 359 Merge 334 335 Weight 1.44131 >1vvc_ -VKCQSPPSISNGRHN-----GYED----------FYTDGSVVTYSCNSGYSLIGNSGVLCS-----GGE---------------WSDP-PT-------C------QIVKCPHPTI-----------SNGYLSSGFK-RS--Y-SYNDNVDFKCKYGYKLSGSSSSTCSPGN------TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRIS-----YYST----------PIAVGTVIRYSCSGTFRLIGEKSLLCITKDKVDGT---------------WDKPAPK-------CEYFNKY--SSCPEPIV-----------PGGYKIRG--STP--Y-RHGDSVTFACKTNFSMNGNKSVWCQANN------MWGPTRLPTCVS- >1ckl_A ---CEEPPTFE-----AMELIG---KP------KPYYEIGERVDYKCKKGYFY-----------------IPPLATHTICDRNHTW------LPVSDDAC------YRETCPYI--RDPLNGQAVPA----------N--GTY-EFGYQMHFICNEGYYLIGEEILYCE---LKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLN-----SASL-------KQPYITQNYFPVGTVVEYECRPGYRR-----------------EPSLSPKLTCLQNLKW------ST-AVEFC------KKKSCPNP--GEIRNGQ-IDVP------------GG-ILFGATISFSCNTGYKLFGSTSSFCL---ISGSSVQWSD-PLPECREH @1vvc_ 03023121010111000000011000000000000330023110212001101110003110000000100000000000000002001010000000020000000000220103000000000000011000100000001003000302020011110210100200010000000201001202100 @1ghq_B 03120121010111000000001000000000000000323130212000301110003110000000100000000000000002001010000000020000000003220103000000000001011000100000001000100302020003030200103200010000000201001202100 @1ckl_A 00021021000000000001010000000000000130320013202001100000000000000000000101003001001002000000000003020000000303220000030011103000000000000000101001100302021011010200003200003011000200000202000 @1nwv_A 00121020030000000001000000000000000130323113202001100000000000000000000101003001001002000000000003020000000303220100030011103001000000000000100001100302021011110210103200003011000200001202000 Merge 47 24 Weight 1.33865 >1vvc_ -VKCQSPPSISNGRHN----GYED----------FYTDGSVVTYSCNSGYSLIGNSGVLCS-----GGE---------------WSDP-PT-------C------QIVKCPHPTI-----------SNGYLSSGFK-RS--Y-SYNDNVDFKCKYGYKLSGSSSSTCSPGN------TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRIS----YYST----------PIAVGTVIRYSCSGTFRLIGEKSLLCITKDKVDGT---------------WDKPAPK-------CEYFNKY--SSCPEPIV-----------PGGYKIRG--STP--Y-RHGDSVTFACKTNFSMNGNKSVWCQANN------MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEA----MELIG---KP------KPYYEIGERVDYKCKKGYFY-----------------IPPLATHTICDRNHTW------LPVSDDAC------YRETCPYI--RDPLNGQAVPA----------N--GTY-EFGYQMHFICNEGYYLIGEEILYCE---LKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNS----ASL-------KQPYITQNYFPVGTVVEYECRPGYRR-----------------EPSLSPKLTCLQNLKW------ST-AVEFC------KKKSCPNP--GEIRNGQ-IDVP------------GG-ILFGATISFSCNTGYKLFGSTSSFCL---ISGSSVQWSD-PLPECREH @1vvc_ 0302312101011100000011000000000000330023110212001101110003110000000100000000000000002001010000000020000000000220103000000000000011000100000001003000302020011110210100200010000000201001202100 @1ghq_B 0312012101011100000001000000000000000323130212000301110003110000000100000000000000002001010000000020000000003220103000000000001011000100000001000100302020003030200103200010000000201001202100 @1ckl_A 0002102100000000001010000000000000130320013202001100000000000000000000101003001001002000000000003020000000303220000030011103000000000000000101001100302021011010200003200003011000200000202000 @1nwv_A 0012102003000000001000000000000000130323113202001100000000000000000000101003001001002000000000003020000000303220100030011103001000000000000100001100302021011110210103200003011000200001202000 Merge 361 364 Weight 1.30692 >1vvc_ -VKCQSPPSISNGRHN----GYED----------FYTDGSVVTYSCNSGYSLIGNSGVLCS-----GGE---------------WSDP-PT-------C------QIVKCPHPTI-----------SNGYLSSGFK-R-SY-SYNDNVDFKCKYGYKLSGSSSSTCSPGN------TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRIS----YYST----------PIAVGTVIRYSCSGTFRLIGEKSLLCITKDKVDGT---------------WDKPAPK-------CEYFNKY--SSCPEPIV-----------PGGYKIRG--ST-PY-RHGDSVTFACKTNFSMNGNKSVWCQANN------MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEA----MELIG---KP------KPYYEIGERVDYKCKKGYFY-----------------IPPLATHTICDRNHTW------LPVSDDAC------YRETCPYI--RDPLNGQAVPA----------N-GTY-EFGYQMHFICNEGYYLIGEEILYCE---LKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNS----ASL-------KQPYITQNYFPVGTVVEYECRPGYRR-----------------EPSLSPKLTCLQNLKW------ST-AVEFC------KKKSCPNP--GEIRNGQ-IDVP-----------GG-ILFGATISFSCNTGYKLFGSTSSFCL---ISGSSVQWSD-PLPECREH @1vvc_ 030231210101110000001100000000000033002311021200110111000311000000010000000000000000200101000000002000000000022010300000000000001100010000001003000302020011110210100200010000000201001202100 @1ghq_B 031201210101110000000100000000000000032313021200030111000311000000010000000000000000200101000000002000000000322010300000000000101100010000001000100302020003030200103200010000000201001202100 @1ckl_A 000210210000000000101000000000000013032001320200110000000000000000000010100300100100200000000000302000000030322000003001110300000000000000101001100302021011010200003200003011000200000202000 @1nwv_A 001210200300000000100000000000000013032311320200110000000000000000000010100300100100200000000000302000000030322010003001110300100000000000100001100302021011110210103200003011000200001202000 Merge 378 391 Weight 1.30631 >1vvc_ -VKCQSPPSISNGRHN----GYED----------FYTDGSVVTYSCNSGYSLIGNSGVLCS-----GGE---------------WSDP-PT-------C------QIVKCPHPTI-----------SNGYLSSGFK-R-SYSYNDNVDFKCKYGYKLSGSSSSTCSPGN------TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRIS----YYST----------PIAVGTVIRYSCSGTFRLIGEKSLLCITKDKVDGT---------------WDKPAPK-------CEYFNKY--SSCPEPIV-----------PGGYKIRG--ST-PYRHGDSVTFACKTNFSMNGNKSVWCQANN------MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEA----MELIG---KP------KPYYEIGERVDYKCKKGYFY-----------------IPPLATHTICDRNHTW------LPVSDDAC------YRETCPYI--RDPLNGQAVPA----------N-GTYEFGYQMHFICNEGYYLIGEEILYCE---LKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNS----ASL-------KQPYITQNYFPVGTVVEYECRPGYRR-----------------EPSLSPKLTCLQNLKW------ST-AVEFC------KKKSCPNP--GEIRNGQ-IDVP-----------GGILFGATISFSCNTGYKLFGSTSSFCL---ISGSSVQWSD-PLPECREH @1vvc_ 03023121010111000000110000000000003300231102120011011100031100000001000000000000000020010100000000200000000002201030000000000000110001000000103000302020011110210100200010000000201001202100 @1ghq_B 03120121010111000000010000000000000003231302120003011100031100000001000000000000000020010100000000200000000032201030000000000010110001000000100100302020003030200103200010000000201001202100 @1ckl_A 00021021000000000010100000000000001303200132020011000000000000000000001010030010010020000000000030200000003032200000300111030000000000000010101100302021011010200003200003011000200000202000 @1nwv_A 00121020030000000010000000000000001303231132020011000000000000000000001010030010010020000000000030200000003032201000300111030010000000000010001100302021011110210103200003011000200001202000 Merge 175 142 Weight 1.29885 >1vvc_ -VKCQSPPSISNGRHN----GYED----------FYTDGSVVTYSCNSGYSLIGNSGVLCS-----GGE--------------WSDP-PT-------C------QIVKCPHPTI-----------SNGYLSSGFK-R-SYSYNDNVDFKCKYGYKLSGSSSSTCSPGN------TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRIS----YYST----------PIAVGTVIRYSCSGTFRLIGEKSLLCITKDKVDGT--------------WDKPAPK-------CEYFNKY--SSCPEPIV-----------PGGYKIRG--ST-PYRHGDSVTFACKTNFSMNGNKSVWCQANN------MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEA----MELIG---KP------KPYYEIGERVDYKCKKGYFYI----------------PPLATHTICDRNHTW------LPVSDDAC------YRETCPYI--RDPLNGQAVPA----------N-GTYEFGYQMHFICNEGYYLIGEEILYCE---LKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNS----ASL-------KQPYITQNYFPVGTVVEYECRPGYRRE----------------PSLSPKLTCLQNLKW------ST-AVEFC------KKKSCPNP--GEIRNGQ-IDVP-----------GGILFGATISFSCNTGYKLFGSTSSFCL---ISGSSVQWSD-PLPECREH @1vvc_ 0302312101011100000011000000000000330023110212001101110003110000000100000000000000020010100000000200000000002201030000000000000110001000000103000302020011110210100200010000000201001202100 @1ghq_B 0312012101011100000001000000000000000323130212000301110003110000000100000000000000020010100000000200000000032201030000000000010110001000000100100302020003030200103200010000000201001202100 @1ckl_A 0002102100000000001010000000000000130320013202001100100000000000000001010030010010020000000000030200000003032200000300111030000000000000010101100302021011010200003200003011000200000202000 @1nwv_A 0012102003000000001000000000000000130323113202001100000000000000000001010030010010020000000000030200000003032201000300111030010000000000010001100302021011110210103200003011000200001202000 Merge 455 450 Weight 1.29154 >1vvc_ -VKCQSPPSISNGRHN----GYED----------FYTDGSVVTYSCNSGYSLIGNSGVLCS-----GGE--------------WSDP-PT-------C------QIVKCPHPTI-----------SNGYLSSGFK-R-SYSYNDNVDFKCKYGYKLSGSSSSTCSPGN-----TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRIS----YYST----------PIAVGTVIRYSCSGTFRLIGEKSLLCITKDKVDGT--------------WDKPAPK-------CEYFNKY--SSCPEPIV-----------PGGYKIRG--ST-PYRHGDSVTFACKTNFSMNGNKSVWCQANN-----MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEA----MELIG---KP------KPYYEIGERVDYKCKKGYFYI----------------PPLATHTICDRNHTW------LPVSDDAC------YRETCPYI--RDPLNGQAVPA----------N-GTYEFGYQMHFICNEGYYLIGEEILYCEL--KGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNS----ASL-------KQPYITQNYFPVGTVVEYECRPGYRRE----------------PSLSPKLTCLQNLKW------ST-AVEFC------KKKSCPNP--GEIRNGQ-IDVP-----------GGILFGATISFSCNTGYKLFGSTSSFCLI--SGSSVQWSD-PLPECREH @1vvc_ 030231210101110000001100000000000033002311021200110111000311000000010000000000000002001010000000020000000000220103000000000000011000100000010300030202001111021010020001000000201001202100 @1ghq_B 031201210101110000000100000000000000032313021200030111000311000000010000000000000002001010000000020000000003220103000000000001011000100000010010030202000303020010320001000000201001202100 @1ckl_A 000210210000000000101000000000000013032001320200110010000000000000000101003001001002000000000003020000000303220000030011103000000000000001010110030202101101020000320000011000200000202000 @1nwv_A 001210200300000000100000000000000013032311320200110000000000000000000101003001001002000000000003020000000303220100030011103001000000000001000110030202101111021010320000011000200001202000 Merge 172 211 Weight 1.28622 >1vvc_ -VKCQSPPSISNGRHN----GYED----------FYTDGSVVTYSCNSGYSLIGNSGVLCS-----GG-------------EWSDP-PT-------C------QIVKCPHPTI-----------SNGYLSSGFK-R-SYSYNDNVDFKCKYGYKLSGSSSSTCSPGN-----TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRIS----YYST----------PIAVGTVIRYSCSGTFRLIGEKSLLCITKDKVDG-------------TWDKPAPK-------CEYFNKY--SSCPEPIV-----------PGGYKIRG--ST-PYRHGDSVTFACKTNFSMNGNKSVWCQANN-----MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEA----MELIG---KP------KPYYEIGERVDYKCKKGYFYI---------------PPLATHTICDRNHTW------LPVSDDAC------YRETCPYI--RDPLNGQAVPA----------N-GTYEFGYQMHFICNEGYYLIGEEILYCEL--KGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNS----ASL-------KQPYITQNYFPVGTVVEYECRPGYRRE---------------PSLSPKLTCLQNLKW------ST-AVEFC------KKKSCPNP--GEIRNGQ-IDVP-----------GGILFGATISFSCNTGYKLFGSTSSFCLI--SGSSVQWSD-PLPECREH @1vvc_ 03023121010111000000110000000000003300231102120011011100031100000001000000000000002001010000000020000000000220103000000000000011000100000010300030202001111021010020001000000201001202100 @1ghq_B 03120121010111000000010000000000000003231302120003011100031100000001000000000000002001010000000020000000003220103000000000001011000100000010010030202000303020010320001000000201001202100 @1ckl_A 00021021000000000010100000000000001303200132020011001000000000000000101003001001002000000000003020000000303220000030011103000000000000001010110030202101101020000320000011000200000202000 @1nwv_A 00121020030000000010000000000000001303231132020011000000000000000000101003001001002000000000003020000000303220100030011103001000000000001000110030202101111021010320000011000200001202000 Merge 224 218 Weight 1.24835 >1vvc_ -VKCQSPPSISNGRHN----GYED----------FYTDGSVVTYSCNSGYSLIGNSGVLCS-----GG-------------EWSDP-PT------C------QIVKCPHPTI-----------SNGYLSSGFK-R-SYSYNDNVDFKCKYGYKLSGSSSSTCSPGN-----TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRIS----YYST----------PIAVGTVIRYSCSGTFRLIGEKSLLCITKDKVDG-------------TWDKPAPK------CEYFNKY--SSCPEPIV-----------PGGYKIRG--ST-PYRHGDSVTFACKTNFSMNGNKSVWCQANN-----MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEA----MELIG---KP------KPYYEIGERVDYKCKKGYFYI---------------PPLATHTICDRNHTWL-----PVSDDAC------YRETCPYI--RDPLNGQAVPA----------N-GTYEFGYQMHFICNEGYYLIGEEILYCEL--KGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNS----ASL-------KQPYITQNYFPVGTVVEYECRPGYRRE---------------PSLSPKLTCLQNLKWS-----T-AVEFC------KKKSCPNP--GEIRNGQ-IDVP-----------GGILFGATISFSCNTGYKLFGSTSSFCLI--SGSSVQWSD-PLPECREH @1vvc_ 0302312101011100000011000000000000330023110212001101110003110000000100000000000000200101000000020000000000220103000000000000011000100000010300030202001111021010020001000000201001202100 @1ghq_B 0312012101011100000001000000000000000323130212000301110003110000000100000000000000200101000000020000000003220103000000000001011000100000010010030202000303020010320001000000201001202100 @1ckl_A 0002102100000000001010000000000000130320013202001100100000000000000010100300100100200000000003020000000303220000030011103000000000000001010110030202101101020000320000011000200000202000 @1nwv_A 0012102003000000001000000000000000130323113202001100000000000000000010100300100100200000000003020000000303220100030011103001000000000001000110030202101111021010320000011000200001202000 Merge 46 54 Weight 1.2443 >1vvc_ -VKCQSPPSISNGRH---NGYED----------FYTDGSVVTYSCNSGYSLIGNSGVLCS-----GG-------------EWSDP-PT------C------QIVKCPHPTI-----------SNGYLSSGFK-R-SYSYNDNVDFKCKYGYKLSGSSSSTCSPGN-----TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRI---SYYST----------PIAVGTVIRYSCSGTFRLIGEKSLLCITKDKVDG-------------TWDKPAPK------CEYFNKY--SSCPEPIV-----------PGGYKIRG--ST-PYRHGDSVTFACKTNFSMNGNKSVWCQANN-----MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEA---MELIG---KP------KPYYEIGERVDYKCKKGYFYI---------------PPLATHTICDRNHTWL-----PVSDDAC------YRETCPYI--RDPLNGQAVPA----------N-GTYEFGYQMHFICNEGYYLIGEEILYCEL--KGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNS---ASL-------KQPYITQNYFPVGTVVEYECRPGYRRE---------------PSLSPKLTCLQNLKWS-----T-AVEFC------KKKSCPNP--GEIRNGQ-IDVP-----------GGILFGATISFSCNTGYKLFGSTSSFCLI--SGSSVQWSD-PLPECREH @1vvc_ 030231210101110000011000000000000330023110212001101110003110000000100000000000000200101000000020000000000220103000000000000011000100000010300030202001111021010020001000000201001202100 @1ghq_B 031201210101110000001000000000000000323130212000301110003110000000100000000000000200101000000020000000003220103000000000001011000100000010010030202000303020010320001000000201001202100 @1ckl_A 000210210000000001010000000000000130320013202001100100000000000000010100300100100200000000003020000000303220000030011103000000000000001010110030202101101020000320000011000200000202000 @1nwv_A 001210200300000001000000000000000130323113202001100000000000000000010100300100100200000000003020000000303220100030011103001000000000001000110030202101111021010320000011000200001202000 Reorder 177 179 180 181 183 185 187 201 202 149 150 155 156 167 168 169 170 171 Merge 171 177 Weight 1.23761 >1vvc_ -VKCQSPPSISNGRH---NGYED----------FYTDGSVVTYSCNSGYSLIGNSGVL--------CS-----GG----EWSDP-PT------C------QIVKCPHPTI-----------SNGYLSSGFK-R-SYSYNDNVDFKCKYGYKLSGSSSSTCSPGN-----TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRI---SYYST----------PIAVGTVIRYSCSGTFRLIGEKSLL--------CITKDKVDG----TWDKPAPK------CEYFNKY--SSCPEPIV-----------PGGYKIRG--ST-PYRHGDSVTFACKTNFSMNGNKSVWCQANN-----MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEA---MELIG---KP------KPYYEIGERVDYKCKKGYFYI------PPLATHTIC--------DRNHTWL-----PVSDDAC------YRETCPYI--RDPLNGQAVPA----------N-GTYEFGYQMHFICNEGYYLIGEEILYCEL--KGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNS---ASL-------KQPYITQNYFPVGTVVEYECRPGYRRE------PSLSPKLTC--------LQNLKWS-----T-AVEFC------KKKSCPNP--GEIRNGQ-IDVP-----------GGILFGATISFSCNTGYKLFGSTSSFCLI--SGSSVQWSD-PLPECREH @1vvc_ 03023121010111000001100000000000033002311021200110111000310000000020000000100000200101000000020000000000220103000000000000011000100000010300030202001111021010020001000000201001202100 @1ghq_B 03120121010111000000100000000000000032313021200030111000310000000020000000100000200101000000020000000003220103000000000001011000100000010010030202000303020010320001000000201001202100 @1ckl_A 00021021000000000101000000000000013032001320200110010000001010030020000000000100200000000003020000000303220000030011103000000000000001010110030202101101020000320000011000200000202000 @1nwv_A 00121020030000000100000000000000013032311320200110000000001010030020000000000100200000000003020000000303220100030011103001000000000001000110030202101111021010320000011000200001202000 Merge 265 267 Weight 1.20488 >1vvc_ -VKCQSPPSISNGRH---NGYED----------FYTDGSVVTYSCNSGYSLIGNSGVL--------CS-----GG----EWSDP-PT------C-----QIVKCPHPTI-----------SNGYLSSGFK-R-SYSYNDNVDFKCKYGYKLSGSSSSTCSPGN-----TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRI---SYYST----------PIAVGTVIRYSCSGTFRLIGEKSLL--------CITKDKVDG----TWDKPAPK------CEYFNK-YSSCPEPIV-----------PGGYKIRG--ST-PYRHGDSVTFACKTNFSMNGNKSVWCQANN-----MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEA---MELIG---KP------KPYYEIGERVDYKCKKGYFYI------PPLATHTIC--------DRNHTWL-----PVSDDAC-----YRETCPYI--RDPLNGQAVPA----------N-GTYEFGYQMHFICNEGYYLIGEEILYCEL--KGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNS---ASL-------KQPYITQNYFPVGTVVEYECRPGYRRE------PSLSPKLTC--------LQNLKWS-----T-AVEFC-----KKKSCPNP--GEIRNGQ-IDVP-----------GGILFGATISFSCNTGYKLFGSTSSFCLI--SGSSVQWSD-PLPECREH @1vvc_ 0302312101011100000110000000000003300231102120011011100031000000002000000010000020010100000002000000000220103000000000000011000100000010300030202001111021010020001000000201001202100 @1ghq_B 0312012101011100000010000000000000003231302120003011100031000000002000000010000020010100000002000000003220103000000000001011000100000010010030202000303020010320001000000201001202100 @1ckl_A 0002102100000000010100000000000001303200132020011001000000101003002000000000010020000000000302000000303220000030011103000000000000001010110030202101101020000320000011000200000202000 @1nwv_A 0012102003000000010000000000000001303231132020011000000000101003002000000000010020000000000302000000303220100030011103001000000000001000110030202101111021010320000011000200001202000 Merge 79 117 Weight 1.10724 >1vvc_ -VKCQSPPSISNGRH---NGYE---------DFYTDGSVVTYSCNSGYSLIGNSGVL--------CS-----GG----EWSDP-PT------C-----QIVKCPHPTI-----------SNGYLSSGFK-R-SYSYNDNVDFKCKYGYKLSGSSSSTCSPGN-----TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRI---SYYS---------TPIAVGTVIRYSCSGTFRLIGEKSLL--------CITKDKVDG----TWDKPAPK------CEYFNK-YSSCPEPIV-----------PGGYKIRG--ST-PYRHGDSVTFACKTNFSMNGNKSVWCQANN-----MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEA---MELIG--KP------KPYYEIGERVDYKCKKGYFYI------PPLATHTIC--------DRNHTWL-----PVSDDAC-----YRETCPYI--RDPLNGQAVPA----------N-GTYEFGYQMHFICNEGYYLIGEEILYCEL--KGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNS---ASL------KQPYITQNYFPVGTVVEYECRPGYRRE------PSLSPKLTC--------LQNLKWS-----T-AVEFC-----KKKSCPNP--GEIRNGQ-IDVP-----------GGILFGATISFSCNTGYKLFGSTSSFCLI--SGSSVQWSD-PLPECREH @1vvc_ 030231210101110000011000000000003300231102120011011100031000000002000000010000020010100000002000000000220103000000000000011000100000010300030202001111021010020001000000201001202100 @1ghq_B 031201210101110000001000000000000003231302120003011100031000000002000000010000020010100000002000000003220103000000000001011000100000010010030202000303020010320001000000201001202100 @1ckl_A 000210210000000001010000000000001303200132020011001000000101003002000000000010020000000000302000000303220000030011103000000000000001010110030202101101020000320000011000200000202000 @1nwv_A 001210200300000001000000000000001303231132020011000000000101003002000000000010020000000000302000000303220100030011103001000000000001000110030202101111021010320000011000200001202000 Merge 81 77 Weight 1.08446 >1vvc_ -VKCQSPPSISNGRH---NGYE--------DFYTDGSVVTYSCNSGYSLIGNSGVL--------CS-----GG----EWSDP-PT------C-----QIVKCPHPTI-----------SNGYLSSGFK-R-SYSYNDNVDFKCKYGYKLSGSSSSTCSPGN-----TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRI---SYYS--------TPIAVGTVIRYSCSGTFRLIGEKSLL--------CITKDKVDG----TWDKPAPK------CEYFNK-YSSCPEPIV-----------PGGYKIRG--ST-PYRHGDSVTFACKTNFSMNGNKSVWCQANN-----MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEA---MELIGK-P------KPYYEIGERVDYKCKKGYFYI------PPLATHTIC--------DRNHTWL-----PVSDDAC-----YRETCPYI--RDPLNGQAVPA----------N-GTYEFGYQMHFICNEGYYLIGEEILYCEL--KGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNS---ASL-----KQPYITQNYFPVGTVVEYECRPGYRRE------PSLSPKLTC--------LQNLKWS-----T-AVEFC-----KKKSCPNP--GEIRNGQ-IDVP-----------GGILFGATISFSCNTGYKLFGSTSSFCLI--SGSSVQWSD-PLPECREH @1vvc_ 03023121010111000001100000000003300231102120011011100031000000002000000010000020010100000002000000000220103000000000000011000100000010300030202001111021010020001000000201001202100 @1ghq_B 03120121010111000000100000000000003231302120003011100031000000002000000010000020010100000002000000003220103000000000001011000100000010010030202000303020010320001000000201001202100 @1ckl_A 00021021000000000101000000000001303200132020011001000000101003002000000000010020000000000302000000303220000030011103000000000000001010110030202101101020000320000011000200000202000 @1nwv_A 00121020030000000100000000000001303231132020011000000000101003002000000000010020000000000302000000303220100030011103001000000000001000110030202101111021010320000011000200001202000 Merge 49 25 Weight 1.07462 >1vvc_ -VKCQSPPSISNGRH--NGYE--------DFYTDGSVVTYSCNSGYSLIGNSGVL--------CS-----GG----EWSDP-PT------C-----QIVKCPHPTI-----------SNGYLSSGFK-R-SYSYNDNVDFKCKYGYKLSGSSSSTCSPGN-----TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRI--SYYS--------TPIAVGTVIRYSCSGTFRLIGEKSLL--------CITKDKVDG----TWDKPAPK------CEYFNK-YSSCPEPIV-----------PGGYKIRG--ST-PYRHGDSVTFACKTNFSMNGNKSVWCQANN-----MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEAM--ELIGK-P------KPYYEIGERVDYKCKKGYFYI------PPLATHTIC--------DRNHTWL-----PVSDDAC-----YRETCPYI--RDPLNGQAVPA----------N-GTYEFGYQMHFICNEGYYLIGEEILYCEL--KGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNSA--SL-----KQPYITQNYFPVGTVVEYECRPGYRRE------PSLSPKLTC--------LQNLKWS-----T-AVEFC-----KKKSCPNP--GEIRNGQ-IDVP-----------GGILFGATISFSCNTGYKLFGSTSSFCLI--SGSSVQWSD-PLPECREH @1vvc_ 0302312101011100001100000000003300231102120011011100031000000002000000010000020010100000002000000000220103000000000000011000100000010300030202001111021010020001000000201001202100 @1ghq_B 0312012101011100000100000000000003231302120003011100031000000002000000010000020010100000002000000003220103000000000001011000100000010010030202000303020010320001000000201001202100 @1ckl_A 0002102100000000101000000000001303200132020011001000000101003002000000000010020000000000302000000303220000030011103000000000000001010110030202101101020000320000011000200000202000 @1nwv_A 0012102003003000100000000000001303231132020011000000000101003002000000000010020000000000302000000303220100030011103001000000000001000110030202101111021010320000011000200001202000 Merge 148 170 Weight 1.06664 >1vvc_ -VKCQSPPSISNGRH--NGYE--------DFYTDGSVVTYSCNSGYSLIGNSGV-------LCS-----GG----EWSDP-PT------C-----QIVKCPHPTI-----------SNGYLSSGFK-R-SYSYNDNVDFKCKYGYKLSGSSSSTCSPGN-----TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRI--SYYS--------TPIAVGTVIRYSCSGTFRLIGEKSL-------LCITKDKVDG----TWDKPAPK------CEYFNK-YSSCPEPIV-----------PGGYKIRG--ST-PYRHGDSVTFACKTNFSMNGNKSVWCQANN-----MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEAM--ELIGK-P------KPYYEIGERVDYKCKKGYFYI-----PPLATHTIC--------DRNHTWL-----PVSDDAC-----YRETCPYI--RDPLNGQAVPA----------N-GTYEFGYQMHFICNEGYYLIGEEILYCEL--KGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNSA--SL-----KQPYITQNYFPVGTVVEYECRPGYRRE-----PSLSPKLTC--------LQNLKWS-----T-AVEFC-----KKKSCPNP--GEIRNGQ-IDVP-----------GGILFGATISFSCNTGYKLFGSTSSFCLI--SGSSVQWSD-PLPECREH @1vvc_ 030231210101110000110000000000330023110212001101110003000000032000000010000020010100000002000000000220103000000000000011000100000010300030202001111021010020001000000201001202100 @1ghq_B 031201210101110000010000000000000323130212000301110003000000032000000010000020010100000002000000003220103000000000001011000100000010010030202000303020010320001000000201001202100 @1ckl_A 000210210000000010100000000000130320013202001100100000101003032000000000010020000000000302000000303220000030011103000000000000001010110030202101101020000320000011000200000202000 @1nwv_A 001210200300300010000000000000130323113202001100000000101003002000000000010020000000000302000000303220100030011103001000000000001000110030202101111021010320000011000200001202000 Merge 357 358 Weight 1.06006 >1vvc_ -VKCQSPPSISNGRH--NGYE--------DFYTDGSVVTYSCNSGYSLIGNSGV-------LCS-----GG----EWSDP-PT------C-----QIVKCPHPTI-----------SNGYLSSGFKR-SYSYNDNVDFKCKYGYKLSGSSSSTCSPGN-----TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRI--SYYS--------TPIAVGTVIRYSCSGTFRLIGEKSL-------LCITKDKVDG----TWDKPAPK------CEYFNK-YSSCPEPIV-----------PGGYKIRG-ST-PYRHGDSVTFACKTNFSMNGNKSVWCQANN-----MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEAM--ELIGK-P------KPYYEIGERVDYKCKKGYFYI-----PPLATHTIC--------DRNHTWL-----PVSDDAC-----YRETCPYI--RDPLNGQAVPA---------N-GTYEFGYQMHFICNEGYYLIGEEILYCEL--KGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNSA--SL-----KQPYITQNYFPVGTVVEYECRPGYRRE-----PSLSPKLTC--------LQNLKWS-----T-AVEFC-----KKKSCPNP--GEIRNGQ-IDVP----------GGILFGATISFSCNTGYKLFGSTSSFCLI--SGSSVQWSD-PLPECREH @1vvc_ 03023121010111000011000000000033002311021200110111000300000003200000001000002001010000000200000000022010300000000000001100010000010300030202001111021010020001000000201001202100 @1ghq_B 03120121010111000001000000000000032313021200030111000300000003200000001000002001010000000200000000322010300000000000101100010000010010030202000303020010320001000000201001202100 @1ckl_A 00021021000000001010000000000013032001320200110010000010100303200000000001002000000000030200000030322000003001110300000000000001010110030202101101020000320000011000200000202000 @1nwv_A 00121020030030001000000000000013032311320200110000000010100300200000000001002000000000030200000030322010003001110300100000000001000110030202101111021010320000011000200001202000 Reorder 203 204 180 181 183 185 187 201 202 Merge 181 183 Weight 1.04572 >1vvc_ -VKCQSPPSISNGRH--NGYE--------DFYTDGSVVTYSCNSGYSLIGNSGV-------LCS------GG--EWSDP-PT------C-----QIVKCPHPTI-----------SNGYLSSGFKR-SYSYNDNVDFKCKYGYKLSGSSSSTCSPGN-----TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRI--SYYS--------TPIAVGTVIRYSCSGTFRLIGEKSL-------LCI-TKDKVDG--TWDKPAPK------CEYFNK-YSSCPEPIV-----------PGGYKIRG-ST-PYRHGDSVTFACKTNFSMNGNKSVWCQANN-----MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEAM--ELIGK-P------KPYYEIGERVDYKCKKGYFYI-----PPLATHTIC-DR------NHTWL-----PVSDDAC-----YRETCPYI--RDPLNGQAVPA---------N-GTYEFGYQMHFICNEGYYLIGEEILYCEL--KGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNSA--SL-----KQPYITQNYFPVGTVVEYECRPGYRRE-----PSLSPKLTC-LQ------NLKWS-----T-AVEFC-----KKKSCPNP--GEIRNGQ-IDVP----------GGILFGATISFSCNTGYKLFGSTSSFCLI--SGSSVQWSD-PLPECREH @1vvc_ 0302312101011100001100000000003300231102120011011100030000000320000000010002001010000000200000000022010300000000000001100010000010300030202001111021010020001000000201001202100 @1ghq_B 0312012101011100000100000000000003231302120003011100030000000320000000010002001010000000200000000322010300000000000101100010000010010030202000303020010320001000000201001202100 @1ckl_A 0002102100000000101000000000001303200132020011001000001010030320000000001002000000000030200000030322000003001110300000000000001010110030202101101020000320000011000200000202000 @1nwv_A 0012102003003000100000000000001303231132020011000000001010030020000000001002000000000030200000030322010003001110300100000000001000110030202101111021010320000011000200001202000 Merge 459 451 Weight 1.0356 >1vvc_ -VKCQSPPSISNGRH--NGYE--------DFYTDGSVVTYSCNSGYSLIGNSGV-------LCS------GG--EWSDP-PT------C-----QIVKCPHPTI-----------SNGYLSSGFKR-SYSYNDNVDFKCKYGYKLSGSSSSTCSPGN----TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRI--SYYS--------TPIAVGTVIRYSCSGTFRLIGEKSL-------LCI-TKDKVDG--TWDKPAPK------CEYFNK-YSSCPEPIV-----------PGGYKIRG-ST-PYRHGDSVTFACKTNFSMNGNKSVWCQANN----MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEAM--ELIGK-P------KPYYEIGERVDYKCKKGYFYI-----PPLATHTIC-DR------NHTWL-----PVSDDAC-----YRETCPYI--RDPLNGQAVPA---------N-GTYEFGYQMHFICNEGYYLIGEEILYCELK-GSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNSA--SL-----KQPYITQNYFPVGTVVEYECRPGYRRE-----PSLSPKLTC-LQ------NLKWS-----T-AVEFC-----KKKSCPNP--GEIRNGQ-IDVP----------GGILFGATISFSCNTGYKLFGSTSSFCLIS-GSSVQWSD-PLPECREH @1vvc_ 030231210101110000110000000000330023110212001101110003000000032000000001000200101000000020000000002201030000000000000110001000001030003020200111102101002000100000201001202100 @1ghq_B 031201210101110000010000000000000323130212000301110003000000032000000001000200101000000020000000032201030000000000010110001000001001003020200030302001032000100000201001202100 @1ckl_A 000210210000000010100000000000130320013202001100100000101003032000000000100200000000003020000003032200000300111030000000000000101011003020210110102000032000011000200000202000 @1nwv_A 001210200300300010000000000000130323113202001100000000101003002000000000100200000000003020000003032201000300111030010000000000100011003020210111102101032000011000200001202000 Merge 78 115 Weight 1.0098 >1vvc_ -VKCQSPPSISNGRH--NGY-------EDFYTDGSVVTYSCNSGYSLIGNSGV-------LCS------GG--EWSDP-PT------C-----QIVKCPHPTI-----------SNGYLSSGFKR-SYSYNDNVDFKCKYGYKLSGSSSSTCSPGN----TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRI--SYY-------STPIAVGTVIRYSCSGTFRLIGEKSL-------LCI-TKDKVDG--TWDKPAPK------CEYFNK-YSSCPEPIV-----------PGGYKIRG-ST-PYRHGDSVTFACKTNFSMNGNKSVWCQANN----MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEAM--ELIGKP------KPYYEIGERVDYKCKKGYFYI-----PPLATHTIC-DR------NHTWL-----PVSDDAC-----YRETCPYI--RDPLNGQAVPA---------N-GTYEFGYQMHFICNEGYYLIGEEILYCELK-GSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNSA--SL----KQPYITQNYFPVGTVVEYECRPGYRRE-----PSLSPKLTC-LQ------NLKWS-----T-AVEFC-----KKKSCPNP--GEIRNGQ-IDVP----------GGILFGATISFSCNTGYKLFGSTSSFCLIS-GSSVQWSD-PLPECREH @1vvc_ 03023121010111000011000000000330023110212001101110003000000032000000001000200101000000020000000002201030000000000000110001000001030003020200111102101002000100000201001202100 @1ghq_B 03120121010111000001000000000000323130212000301110003000000032000000001000200101000000020000000032201030000000000010110001000001001003020200030302001032000100000201001202100 @1ckl_A 00021021000000001010000000000130320013202001100100000101003032000000000100200000000003020000003032200000300111030000000000000101011003020210110102000032000011000200000202000 @1nwv_A 00121020030030001000000000000130323113202001100000000101003002000000000100200000000003020000003032201000300111030010000000000100011003020210111102101032000011000200001202000 Merge 52 26 Weight 0.97226 >1vvc_ -VKCQSPPSISNGRH-NGY-------EDFYTDGSVVTYSCNSGYSLIGNSGV-------LCS------GG--EWSDP-PT------C-----QIVKCPHPTI-----------SNGYLSSGFKR-SYSYNDNVDFKCKYGYKLSGSSSSTCSPGN----TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRI-SYY-------STPIAVGTVIRYSCSGTFRLIGEKSL-------LCI-TKDKVDG--TWDKPAPK------CEYFNK-YSSCPEPIV-----------PGGYKIRG-ST-PYRHGDSVTFACKTNFSMNGNKSVWCQANN----MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEAME-LIGKP------KPYYEIGERVDYKCKKGYFYI-----PPLATHTIC-DR------NHTWL-----PVSDDAC-----YRETCPYI--RDPLNGQAVPA---------N-GTYEFGYQMHFICNEGYYLIGEEILYCELK-GSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNSAS-L----KQPYITQNYFPVGTVVEYECRPGYRRE-----PSLSPKLTC-LQ------NLKWS-----T-AVEFC-----KKKSCPNP--GEIRNGQ-IDVP----------GGILFGATISFSCNTGYKLFGSTSSFCLIS-GSSVQWSD-PLPECREH @1vvc_ 0302312101011100011000000000330023110212001101110003000000032000000001000200101000000020000000002201030000000000000110001000001030003020200111102101002000100000201001202100 @1ghq_B 0312012101011100001000000000000323130212000301110003000000032000000001000200101000000020000000032201030000000000010110001000001001003020200030302001032000100000201001202100 @1ckl_A 0002102100000001010000000000130320013202001100100000101003032000000000100200000000003020000003032200000300111030000000000000101011003020210110102000032000011000200000202000 @1nwv_A 0012102003003001000000000000130323113202001100000000101003002000000000100200000000003020000003032201000300111030010000000000100011003020210111102101032000011000200001202000 Merge 179 180 Weight 0.959255 >1vvc_ -VKCQSPPSISNGRH-NGY-------EDFYTDGSVVTYSCNSGYSLIGNSGV-------LCS-----GG--EWSDP-PT------C-----QIVKCPHPTI-----------SNGYLSSGFKR-SYSYNDNVDFKCKYGYKLSGSSSSTCSPGN----TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRI-SYY-------STPIAVGTVIRYSCSGTFRLIGEKSL-------LCITKDKVDG--TWDKPAPK------CEYFNK-YSSCPEPIV-----------PGGYKIRG-ST-PYRHGDSVTFACKTNFSMNGNKSVWCQANN----MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEAME-LIGKP------KPYYEIGERVDYKCKKGYFYI-----PPLATHTICDR------NHTWL-----PVSDDAC-----YRETCPYI--RDPLNGQAVPA---------N-GTYEFGYQMHFICNEGYYLIGEEILYCELK-GSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNSAS-L----KQPYITQNYFPVGTVVEYECRPGYRRE-----PSLSPKLTCLQ------NLKWS-----T-AVEFC-----KKKSCPNP--GEIRNGQ-IDVP----------GGILFGATISFSCNTGYKLFGSTSSFCLIS-GSSVQWSD-PLPECREH @1vvc_ 030231210101110001100000000033002311021200110111000300000003200000001000200101000000020000000002201030000000000000110001000001030003020200111102101002000100000201001202100 @1ghq_B 031201210101110000100000000000032313021200030111000300000003200000001000200101000000020000000032201030000000000010110001000001001003020200030302001032000100000201001202100 @1ckl_A 000210210000000101000000000013032001320200110010000010100303200000000100200000000003020000003032200000300111030000000000000101011003020210110102000032000011000200000202000 @1nwv_A 001210200300300100000000000013032311320200110000000010100300200000000100200000000003020000003032201000300111030010000000000100011003020210111102101032000011000200001202000 Merge 149 143 Weight 0.94775 >1vvc_ -VKCQSPPSISNGRH-NGY-------EDFYTDGSVVTYSCNSGYSLIGNSGV------LCS-----GG--EWSDP-PT------C-----QIVKCPHPTI-----------SNGYLSSGFKR-SYSYNDNVDFKCKYGYKLSGSSSSTCSPGN----TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRI-SYY-------STPIAVGTVIRYSCSGTFRLIGEKSL------LCITKDKVDG--TWDKPAPK------CEYFNK-YSSCPEPIV-----------PGGYKIRG-ST-PYRHGDSVTFACKTNFSMNGNKSVWCQANN----MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEAME-LIGKP------KPYYEIGERVDYKCKKGYFYIP----PLATHTICDR------NHTWL-----PVSDDAC-----YRETCPYI--RDPLNGQAVPA---------N-GTYEFGYQMHFICNEGYYLIGEEILYCELK-GSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNSAS-L----KQPYITQNYFPVGTVVEYECRPGYRREP----SLSPKLTCLQ------NLKWS-----T-AVEFC-----KKKSCPNP--GEIRNGQ-IDVP----------GGILFGATISFSCNTGYKLFGSTSSFCLIS-GSSVQWSD-PLPECREH @1vvc_ 03023121010111000110000000003300231102120011011100030000003200000001000200101000000020000000002201030000000000000110001000001030003020200111102101002000100000201001202100 @1ghq_B 03120121010111000010000000000003231302120003011100030000003200000001000200101000000020000000032201030000000000010110001000001001003020200030302001032000100000201001202100 @1ckl_A 00021021000000010100000000001303200132020011001000000100303200000000100200000000003020000003032200000300111030000000000000101011003020210110102000032000011000200000202000 @1nwv_A 00121020030030010000000000001303231132020011000000000100300200000000100200000000003020000003032201000300111030010000000000100011003020210111102101032000011000200001202000 Merge 235 219 Weight 0.945469 >1vvc_ -VKCQSPPSISNGRH-NGY-------EDFYTDGSVVTYSCNSGYSLIGNSGV------LCS-----GG--EWSDP-PT-----C-----QIVKCPHPTI-----------SNGYLSSGFKR-SYSYNDNVDFKCKYGYKLSGSSSSTCSPGN----TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRI-SYY-------STPIAVGTVIRYSCSGTFRLIGEKSL------LCITKDKVDG--TWDKPAPK-----CEYFNK-YSSCPEPIV-----------PGGYKIRG-ST-PYRHGDSVTFACKTNFSMNGNKSVWCQANN----MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEAME-LIGKP------KPYYEIGERVDYKCKKGYFYIP----PLATHTICDR------NHTWLP----VSDDAC-----YRETCPYI--RDPLNGQAVPA---------N-GTYEFGYQMHFICNEGYYLIGEEILYCELK-GSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNSAS-L----KQPYITQNYFPVGTVVEYECRPGYRREP----SLSPKLTCLQ------NLKWST-----AVEFC-----KKKSCPNP--GEIRNGQ-IDVP----------GGILFGATISFSCNTGYKLFGSTSSFCLIS-GSSVQWSD-PLPECREH @1vvc_ 0302312101011100011000000000330023110212001101110003000000320000000100020010100000020000000002201030000000000000110001000001030003020200111102101002000100000201001202100 @1ghq_B 0312012101011100001000000000000323130212000301110003000000320000000100020010100000020000000032201030000000000010110001000001001003020200030302001032000100000201001202100 @1ckl_A 0002102100000001010000000000130320013202001100100000010030320000000010020000000003020000003032200000300111030000000000000101011003020210110102000032000011000200000202000 @1nwv_A 0012102003003001000000000000130323113202001100000000010030020000000010020000000003020000003032201000300111030010000000000100011003020210111102101032000011000200001202000 Merge 45 53 Weight 0.941278 >1vvc_ -VKCQSPPSISNGRHNGY-------EDFYTDGSVVTYSCNSGYSLIGNSGV------LCS-----GG--EWSDP-PT-----C-----QIVKCPHPTI-----------SNGYLSSGFKR-SYSYNDNVDFKCKYGYKLSGSSSSTCSPGN----TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYY-------STPIAVGTVIRYSCSGTFRLIGEKSL------LCITKDKVDG--TWDKPAPK-----CEYFNK-YSSCPEPIV-----------PGGYKIRG-ST-PYRHGDSVTFACKTNFSMNGNKSVWCQANN----MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEAMELIGKP------KPYYEIGERVDYKCKKGYFYIP----PLATHTICDR------NHTWLP----VSDDAC-----YRETCPYI--RDPLNGQAVPA---------N-GTYEFGYQMHFICNEGYYLIGEEILYCELK-GSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNSASL----KQPYITQNYFPVGTVVEYECRPGYRREP----SLSPKLTCLQ------NLKWST-----AVEFC-----KKKSCPNP--GEIRNGQ-IDVP----------GGILFGATISFSCNTGYKLFGSTSSFCLIS-GSSVQWSD-PLPECREH @1vvc_ 030231210101110011000000000330023110212001101110003000000320000000100020010100000020000000002201030000000000000110001000001030003020200111102101002000100000201001202100 @1ghq_B 031201210101113001000000000000323130212000301110003000000320000000100020010100000020000000032201030000000000010110001000001001003020200030302001032000100000201001202100 @1ckl_A 000210210000001010000000000130320013202001100100000010030320000000010020000000003020000003032200000300111030000000000000101011003020210110102000032000011000200000202000 @1nwv_A 001210200300301000000000000130323113202001100000000010030020000000010020000000003020000003032201000300111030010000000000100011003020210111102101032000011000200001202000 Merge 359 363 Weight 0.940758 >1vvc_ -VKCQSPPSISNGRHNGY-------EDFYTDGSVVTYSCNSGYSLIGNSGV------LCS-----GG--EWSDP-PT-----C-----QIVKCPHPTI-----------SNGYLSSGFKRSYSYNDNVDFKCKYGYKLSGSSSSTCSPGN----TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYY-------STPIAVGTVIRYSCSGTFRLIGEKSL------LCITKDKVDG--TWDKPAPK-----CEYFNK-YSSCPEPIV-----------PGGYKIRG-STPYRHGDSVTFACKTNFSMNGNKSVWCQANN----MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEAMELIGKP------KPYYEIGERVDYKCKKGYFYIP----PLATHTICDR------NHTWLP----VSDDAC-----YRETCPYI--RDPLNGQAVPA---------NGTYEFGYQMHFICNEGYYLIGEEILYCELK-GSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNSASL----KQPYITQNYFPVGTVVEYECRPGYRREP----SLSPKLTCLQ------NLKWST-----AVEFC-----KKKSCPNP--GEIRNGQ-IDVP---------GGILFGATISFSCNTGYKLFGSTSSFCLIS-GSSVQWSD-PLPECREH @1vvc_ 03023121010111001100000000033002311021200110111000300000032000000010002001010000002000000000220103000000000000011000100001030003020200111102101002000100000201001202100 @1ghq_B 03120121010111300100000000000032313021200030111000300000032000000010002001010000002000000003220103000000000001011000100001001003020200030302001032000100000201001202100 @1ckl_A 00021021000000101000000000013032001320200110010000001003032000000001002000000000302000000303220000030011103000000000000101011003020210110102000032000011000200000202000 @1nwv_A 00121020030030100000000000013032311320200110000000001003002000000001002000000000302000000303220100030011103001000000000100011003020210111102101032000011000200001202000 Merge 204 206 Weight 0.940086 >1vvc_ -VKCQSPPSISNGRHNGY-------EDFYTDGSVVTYSCNSGYSLIGNSGV------LCS-----G-GEWSDP-PT-----C-----QIVKCPHPTI-----------SNGYLSSGFKRSYSYNDNVDFKCKYGYKLSGSSSSTCSPGN----TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYY-------STPIAVGTVIRYSCSGTFRLIGEKSL------LCITKDKVD-GTWDKPAPK-----CEYFNK-YSSCPEPIV-----------PGGYKIRG-STPYRHGDSVTFACKTNFSMNGNKSVWCQANN----MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEAMELIGKP------KPYYEIGERVDYKCKKGYFYIP----PLATHTICDR-----NHTWLP----VSDDAC-----YRETCPYI--RDPLNGQAVPA---------NGTYEFGYQMHFICNEGYYLIGEEILYCELK-GSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNSASL----KQPYITQNYFPVGTVVEYECRPGYRREP----SLSPKLTCLQ-----NLKWST-----AVEFC-----KKKSCPNP--GEIRNGQ-IDVP---------GGILFGATISFSCNTGYKLFGSTSSFCLIS-GSSVQWSD-PLPECREH @1vvc_ 0302312101011100110000000003300231102120011011100030000003200000000002001010000002000000000220103000000000000011000100001030003020200111102101002000100000201001202100 @1ghq_B 0312012101011130010000000000003231302120003011100030000003200000000002001010000002000000003220103000000000001011000100001001003020200030302001032000100000201001202100 @1ckl_A 0002102100000010100000000001303200132020011001000000100303200000001002000000000302000000303220000030011103000000000000101011003020210110102000032000011000200000202000 @1nwv_A 0012102003003010000000000001303231132020011000000000100300200000001002000000000302000000303220100030011103001000000000100011003020210111102101032000011000200001202000 Merge 223 240 Weight 0.93276 >1vvc_ -VKCQSPPSISNGRHNGY-------EDFYTDGSVVTYSCNSGYSLIGNSGV------LCS-----G-GEWSDP-P----TC-----QIVKCPHPTI-----------SNGYLSSGFKRSYSYNDNVDFKCKYGYKLSGSSSSTCSPGN----TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYY-------STPIAVGTVIRYSCSGTFRLIGEKSL------LCITKDKVD-GTWDKPAP----KCEYFNK-YSSCPEPIV-----------PGGYKIRG-STPYRHGDSVTFACKTNFSMNGNKSVWCQANN----MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEAMELIGKP------KPYYEIGERVDYKCKKGYFYIP----PLATHTICDR-----NHTWLP---VSDDAC-----YRETCPYI--RDPLNGQAVPA---------NGTYEFGYQMHFICNEGYYLIGEEILYCELK-GSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNSASL----KQPYITQNYFPVGTVVEYECRPGYRREP----SLSPKLTCLQ-----NLKWST----AVEFC-----KKKSCPNP--GEIRNGQ-IDVP---------GGILFGATISFSCNTGYKLFGSTSSFCLIS-GSSVQWSD-PLPECREH @1vvc_ 030231210101110011000000000330023110212001101110003000000320000000000200101000002000000000220103000000000000011000100001030003020200111102101002000100000201001202100 @1ghq_B 031201210101113001000000000000323130212000301110003000000320000000000200101000002000000003220103000000000001011000100001001003020200030302001032000100000201001202100 @1ckl_A 000210210000001010000000000130320013202001100100000010030320000000100200000000302000000303220000030011103000000000000101011003020210110102000032000011000200000202000 @1nwv_A 001210200300301000000000000130323113202001100000000010030020000000100200000000302000000303220100030011103001000000000100011003020210111102101032000011000200001202000 Merge 452 461 Weight 0.888419 >1vvc_ -VKCQSPPSISNGRHNGY-------EDFYTDGSVVTYSCNSGYSLIGNSGV------LCS-----G-GEWSDP-P----TC-----QIVKCPHPTI-----------SNGYLSSGFKRSYSYNDNVDFKCKYGYKLSGSSSSTCSPGN---TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYY-------STPIAVGTVIRYSCSGTFRLIGEKSL------LCITKDKVD-GTWDKPAP----KCEYFNK-YSSCPEPIV-----------PGGYKIRG-STPYRHGDSVTFACKTNFSMNGNKSVWCQANN---MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEAMELIGKP------KPYYEIGERVDYKCKKGYFYIP----PLATHTICDR-----NHTWLP---VSDDAC-----YRETCPYI--RDPLNGQAVPA---------NGTYEFGYQMHFICNEGYYLIGEEILYCELKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNSASL----KQPYITQNYFPVGTVVEYECRPGYRREP----SLSPKLTCLQ-----NLKWST----AVEFC-----KKKSCPNP--GEIRNGQ-IDVP---------GGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSD-PLPECREH @1vvc_ 03023121010111001100000000033002311021200110111000300000032000000000020010100000200000000022010300000000000001100010000103000302020011110210100200000000201001202100 @1ghq_B 03120121010111300100000000000032313021200030111000300000032000000000020010100000200000000322010300000000000101100010000100100302020003030200103200000000201001202100 @1ckl_A 00021021000000101000000000013032001320200110010000001003032000000010020000000030200000030322000003001110300000000000010101100302021011010200003200011000200000202000 @1nwv_A 00121020030030100000000000013032311320200110000000001003002000000010020000000030200000030322010003001110300100000000010001100302021011110210103200011000200001202000 Merge 266 250 Weight 0.864333 >1vvc_ -VKCQSPPSISNGRHNGY-------EDFYTDGSVVTYSCNSGYSLIGNSGV------LCS-----G-GEWSDP-P----TCQ----IVKCPHPTI-----------SNGYLSSGFKRSYSYNDNVDFKCKYGYKLSGSSSSTCSPGN---TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYY-------STPIAVGTVIRYSCSGTFRLIGEKSL------LCITKDKVD-GTWDKPAP----KCEYFNKYSSCPEPIV-----------PGGYKIRG-STPYRHGDSVTFACKTNFSMNGNKSVWCQANN---MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEAMELIGKP------KPYYEIGERVDYKCKKGYFYIP----PLATHTICDR-----NHTWLP---VSDDACY----RETCPYI--RDPLNGQAVPA---------NGTYEFGYQMHFICNEGYYLIGEEILYCELKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNSASL----KQPYITQNYFPVGTVVEYECRPGYRREP----SLSPKLTCLQ-----NLKWST----AVEFCK----KKSCPNP--GEIRNGQ-IDVP---------GGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSD-PLPECREH @1vvc_ 0302312101011100110000000003300231102120011011100030000003200000000002001010000020000000022010300000000000001100010000103000302020011110210100200000000201001202100 @1ghq_B 0312012101011130010000000000003231302120003011100030000003200000000002001010000020000000322010300000000000101100010000100100302020003030200103200000000201001202100 @1ckl_A 0002102100000010100000000001303200132020011001000000100303200000001002000000003020000030322000003001110300000000000010101100302021011010200003200011000200000202000 @1nwv_A 0012102003003010000000000001303231132020011000000000100300200000001002000000003020000030322010003001110300100000000010001100302021011110210103200011000200001202000 Merge 147 169 Weight 0.84388 >1vvc_ -VKCQSPPSISNGRHNGY-------EDFYTDGSVVTYSCNSGYSLIGNSG-----VLCS-----G-GEWSDP-P----TCQ----IVKCPHPTI-----------SNGYLSSGFKRSYSYNDNVDFKCKYGYKLSGSSSSTCSPGN---TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYY-------STPIAVGTVIRYSCSGTFRLIGEKS-----LLCITKDKVD-GTWDKPAP----KCEYFNKYSSCPEPIV-----------PGGYKIRG-STPYRHGDSVTFACKTNFSMNGNKSVWCQANN---MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEAMELIGKP------KPYYEIGERVDYKCKKGYFYIP---PLATHTICDR-----NHTWLP---VSDDACY----RETCPYI--RDPLNGQAVPA---------NGTYEFGYQMHFICNEGYYLIGEEILYCELKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNSASL----KQPYITQNYFPVGTVVEYECRPGYRREP---SLSPKLTCLQ-----NLKWST----AVEFCK----KKSCPNP--GEIRNGQ-IDVP---------GGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSD-PLPECREH @1vvc_ 030231210101110011000000000330023110212001101110000000033200000000002001010000020000000022010300000000000001100010000103000302020011110210100200000000201001202100 @1ghq_B 031201210101113001000000000000323130212000301110000000033200000000002001010000020000000322010300000000000101100010000100100302020003030200103200000000201001202100 @1ckl_A 000210210000001010000000000130320013202001100100000100303200000001002000000003020000030322000003001110300000000000010101100302021011010200003200011000200000202000 @1nwv_A 001210200300301000000000000130323113202001100000000100330200000001002000000003020000030322010003001110300100000000010001100302021011110210103200011000200001202000 Merge 203 205 Weight 0.789542 >1vvc_ -VKCQSPPSISNGRHNGY-------EDFYTDGSVVTYSCNSGYSLIGNSG-----VLCS-----GGEWSDP-P----TCQ----IVKCPHPTI-----------SNGYLSSGFKRSYSYNDNVDFKCKYGYKLSGSSSSTCSPGN---TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYY-------STPIAVGTVIRYSCSGTFRLIGEKS-----LLCITKDKVDGTWDKPAP----KCEYFNKYSSCPEPIV-----------PGGYKIRG-STPYRHGDSVTFACKTNFSMNGNKSVWCQANN---MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEAMELIGKP------KPYYEIGERVDYKCKKGYFYIP---PLATHTICDR----NHTWLP---VSDDACY----RETCPYI--RDPLNGQAVPA---------NGTYEFGYQMHFICNEGYYLIGEEILYCELKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNSASL----KQPYITQNYFPVGTVVEYECRPGYRREP---SLSPKLTCLQ----NLKWST----AVEFCK----KKSCPNP--GEIRNGQ-IDVP---------GGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSD-PLPECREH @1vvc_ 03023121010111001100000000033002311021200110111000000003320000000002001010000020000000022010300000000000001100010000103000302020011110210100200000000201001202100 @1ghq_B 03120121010111300100000000000032313021200030111000000003320000003002001010000020000000322010300000000000101100010000100100302020003030200103200000000201001202100 @1ckl_A 00021021000000101000000000013032001320200110010000010030320000001002000000003020000030322000003001110300000000000010101100302021011010200003200011000200000202000 @1nwv_A 00121020030030100000000000013032311320200110000000010033020000001002000000003020000030322010003001110300100000000010001100302021011110210103200011000200001202000 Merge 150 144 Weight 0.77447 >1vvc_ -VKCQSPPSISNGRHNGY-------EDFYTDGSVVTYSCNSGYSLIGNSG----VLCS-----GGEWSDP-P----TCQ----IVKCPHPTI-----------SNGYLSSGFKRSYSYNDNVDFKCKYGYKLSGSSSSTCSPGN---TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYY-------STPIAVGTVIRYSCSGTFRLIGEKS----LLCITKDKVDGTWDKPAP----KCEYFNKYSSCPEPIV-----------PGGYKIRG-STPYRHGDSVTFACKTNFSMNGNKSVWCQANN---MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEAMELIGKP------KPYYEIGERVDYKCKKGYFYIPP--LATHTICDR----NHTWLP---VSDDACY----RETCPYI--RDPLNGQAVPA---------NGTYEFGYQMHFICNEGYYLIGEEILYCELKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNSASL----KQPYITQNYFPVGTVVEYECRPGYRREPS--LSPKLTCLQ----NLKWST----AVEFCK----KKSCPNP--GEIRNGQ-IDVP---------GGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSD-PLPECREH @1vvc_ 0302312101011100110000000003300231102120011011100000003320000000002001010000020000000022010300000000000001100010000103000302020011110210100200000000201001202100 @1ghq_B 0312012101011130010000000000003231302120003011100000003320000003002001010000020000000322010300000000000101100010000100100302020003030200103200000000201001202100 @1ckl_A 0002102100000010100000000001303200132020011001000010030320000001002000000003020000030322000003001110300000000000010101100302021011010200003200011000200000202000 @1nwv_A 0012102003003010000000000001303231132020011000000010033020000001002000000003020000030322010003001110300100000000010001100302021011110210103200011000200001202000 Merge 292 279 Weight 0.760604 >1vvc_ -VKCQSPPSISNGRHNGY-------EDFYTDGSVVTYSCNSGYSLIGNSG----VLCS-----GGEWSDP-P----TCQ----IVKCPHPTI----------SNGYLSSGFKRSYSYNDNVDFKCKYGYKLSGSSSSTCSPGN---TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYY-------STPIAVGTVIRYSCSGTFRLIGEKS----LLCITKDKVDGTWDKPAP----KCEYFNKYSSCPEPIV----------PGGYKIRG-STPYRHGDSVTFACKTNFSMNGNKSVWCQANN---MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEAMELIGKP------KPYYEIGERVDYKCKKGYFYIPP--LATHTICDR----NHTWLP---VSDDACY----RETCPYIR-DPLNGQAVPA---------NGTYEFGYQMHFICNEGYYLIGEEILYCELKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNSASL----KQPYITQNYFPVGTVVEYECRPGYRREPS--LSPKLTCLQ----NLKWST----AVEFCK----KKSCPNPG-EIRNGQ-IDVP---------GGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSD-PLPECREH @1vvc_ 030231210101110011000000000330023110212001101110000000332000000000200101000002000000002201030000000000001100010000103000302020011110210100200000000201001202100 @1ghq_B 031201210101113001000000000000323130212000301110000000332000000300200101000002000000032201030000000000101100010000100100302020003030200103200000000201001202100 @1ckl_A 000210210000001010000000000130320013202001100100001003032000000100200000000302000003032200003001110300000000000010101100302021011010200003200011000200000202000 @1nwv_A 001210200300301000000000000130323113202001100000001003302000000100200000000302000003032201003001110300100000000010001100302021011110210103200011000200001202000 Merge 222 239 Weight 0.716186 >1vvc_ -VKCQSPPSISNGRHNGY-------EDFYTDGSVVTYSCNSGYSLIGNSG----VLCS-----GGEWSDP----PTCQ----IVKCPHPTI----------SNGYLSSGFKRSYSYNDNVDFKCKYGYKLSGSSSSTCSPGN---TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYY-------STPIAVGTVIRYSCSGTFRLIGEKS----LLCITKDKVDGTWDKPA---PKCEYFNKYSSCPEPIV----------PGGYKIRG-STPYRHGDSVTFACKTNFSMNGNKSVWCQANN---MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEAMELIGKP------KPYYEIGERVDYKCKKGYFYIPP--LATHTICDR----NHTWLP--VSDDACY----RETCPYIR-DPLNGQAVPA---------NGTYEFGYQMHFICNEGYYLIGEEILYCELKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNSASL----KQPYITQNYFPVGTVVEYECRPGYRREPS--LSPKLTCLQ----NLKWST---AVEFCK----KKSCPNPG-EIRNGQ-IDVP---------GGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSD-PLPECREH @1vvc_ 03023121010111001100000000033002311021200110111000000033200000000020010000002000000002201030000000000001100010000103000302020011110210100200000000201001202100 @1ghq_B 03120121010111300100000000000032313021200030111000000033200000030020010000002000000032201030000000000101100010000100100302020003030200103200000000201001202100 @1ckl_A 00021021000000101000000000013032001320200110010000100303200000010020000000302000003032200003001110300000000000010101100302021011010200003200011000200000202000 @1nwv_A 00121020030030100000000000013032311320200110000000100330200000010020000000302000003032201003001110300100000000010001100302021011110210103200011000200001202000 Merge 109 54 Weight 0.70947 >1vvc_ -VKCQSPPSISNGRHNGY------EDFYTDGSVVTYSCNSGYSLIGNSG----VLCS-----GGEWSDP----PTCQ----IVKCPHPTI----------SNGYLSSGFKRSYSYNDNVDFKCKYGYKLSGSSSSTCSPGN---TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYY------STPIAVGTVIRYSCSGTFRLIGEKS----LLCITKDKVDGTWDKPA---PKCEYFNKYSSCPEPIV----------PGGYKIRG-STPYRHGDSVTFACKTNFSMNGNKSVWCQANN---MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEAMELIGKP-----KPYYEIGERVDYKCKKGYFYIPP--LATHTICDR----NHTWLP--VSDDACY----RETCPYIR-DPLNGQAVPA---------NGTYEFGYQMHFICNEGYYLIGEEILYCELKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNSASLK---QPYITQNYFPVGTVVEYECRPGYRREPS--LSPKLTCLQ----NLKWST---AVEFCK----KKSCPNPG-EIRNGQ-IDVP---------GGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSD-PLPECREH @1vvc_ 0302312101011100110000000033002311021200110111000000033200000000020010000002000000002201030000000000001100010000103000302020011110210100200000000201001202100 @1ghq_B 0312012101011130010000000000032313021200030111000000033200000030020010000002000000032201030000000000101100010000100100302020003030200103200000000201001202100 @1ckl_A 0002102100000010100000000013032001320200110010000100303200000010020000000302000003032200003001110300000000000010101100302021011010200003200011000200000202000 @1nwv_A 0012102003003010000000000013032311320200110000000100330200000010020000000302000003032201003001110300100000000010001100302021011110210103200011000200001202000 Merge 221 237 Weight 0.670727 >1vvc_ -VKCQSPPSISNGRHNGY------EDFYTDGSVVTYSCNSGYSLIGNSG----VLCS-----GGEWSDP---PTCQ----IVKCPHPTI----------SNGYLSSGFKRSYSYNDNVDFKCKYGYKLSGSSSSTCSPGN---TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYY------STPIAVGTVIRYSCSGTFRLIGEKS----LLCITKDKVDGTWDKP-A-PKCEYFNKYSSCPEPIV----------PGGYKIRG-STPYRHGDSVTFACKTNFSMNGNKSVWCQANN---MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEAMELIGKP-----KPYYEIGERVDYKCKKGYFYIPP--LATHTICDR----NHTWLP-VSDDACY----RETCPYIR-DPLNGQAVPA---------NGTYEFGYQMHFICNEGYYLIGEEILYCELKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNSASLK---QPYITQNYFPVGTVVEYECRPGYRREPS--LSPKLTCLQ----NLKWST--AVEFCK----KKSCPNPG-EIRNGQ-IDVP---------GGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSD-PLPECREH @1vvc_ 030231210101110011000000003300231102120011011100000003320000000002001000002000000002201030000000000001100010000103000302020011110210100200000000201001202100 @1ghq_B 031201210101113001000000000003231302120003011100000003320000003002001010002000000032201030000000000101100010000100100302020003030200103200000000201001202100 @1ckl_A 000210210000001010000000001303200132020011001000010030320000001002000030302000003032200003001110300000000000010101100302021011010200003200011000200000202000 @1nwv_A 001210200300301000000000001303231132020011000000010033020000001002000010302000003032201003001110300100000000010001100302021011110210103200011000200001202000 Merge 82 114 Weight 0.667586 >1vvc_ -VKCQSPPSISNGRHNGY-----EDFYTDGSVVTYSCNSGYSLIGNSG----VLCS-----GGEWSDP---PTCQ----IVKCPHPTI----------SNGYLSSGFKRSYSYNDNVDFKCKYGYKLSGSSSSTCSPGN---TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYY-----STPIAVGTVIRYSCSGTFRLIGEKS----LLCITKDKVDGTWDKP-A-PKCEYFNKYSSCPEPIV----------PGGYKIRG-STPYRHGDSVTFACKTNFSMNGNKSVWCQANN---MWGPTRLPTCVS- >1ckl_A 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0.626801 >1vvc_ -VKCQSPPSISNGRHNGY-----EDFYTDGSVVTYSCNSGYSLIGNSG----VLCS-----GGEWSDP--PTCQ----IVKCPHPTI----------SNGYLSSGFKRSYSYNDNVDFKCKYGYKLSGSSSSTCSPGN---TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYY-----STPIAVGTVIRYSCSGTFRLIGEKS----LLCITKDKVDGTWDKPA-PKCEYFNKYSSCPEPIV----------PGGYKIRG-STPYRHGDSVTFACKTNFSMNGNKSVWCQANN---MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEAMELIGK----PKPYYEIGERVDYKCKKGYFYIPP--LATHTICDR----NHTWLPVSDDACY----RETCPYIR-DPLNGQAVPA---------NGTYEFGYQMHFICNEGYYLIGEEILYCELKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNSASLK--QPYITQNYFPVGTVVEYECRPGYRREPS--LSPKLTCLQ----NLKWST-AVEFCK----KKSCPNPG-EIRNGQ-IDVP---------GGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSD-PLPECREH @1vvc_ 0302312101011100110000000330023110212001101110000000332000000000200100002000000002201030000000000001100010000103000302020011110210100200000000201001202100 @1ghq_B 0312012101011130010000000000323130212000301110000000332000000300200110002000000032201030000000000101100010000100100302020003030200103200000000201001202100 @1ckl_A 0002102100000010100000000130320013202001100100001003032000000100200030302000003032200003001110300000000000010101100302021011010200003200011000200000202000 @1nwv_A 0012102003003010000000000130323113202001100000001003302000000100200010302000003032201003001110300100000000010001100302021011110210103200011000200001202000 Merge 155 145 Weight 0.569217 >1vvc_ -VKCQSPPSISNGRHNGY-----EDFYTDGSVVTYSCNSGYSLIGNSG---VLCS-----GGEWSDP--PTCQ----IVKCPHPTI----------SNGYLSSGFKRSYSYNDNVDFKCKYGYKLSGSSSSTCSPGN---TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYY-----STPIAVGTVIRYSCSGTFRLIGEKS---LLCITKDKVDGTWDKPA-PKCEYFNKYSSCPEPIV----------PGGYKIRG-STPYRHGDSVTFACKTNFSMNGNKSVWCQANN---MWGPTRLPTCVS- >1ckl_A ---CEEPPTFEAMELIGK----PKPYYEIGERVDYKCKKGYFYIPPL-ATHTICDR----NHTWLPVSDDACY----RETCPYIR-DPLNGQAVPA---------NGTYEFGYQMHFICNEGYYLIGEEILYCELKGSVAIWSG-KPPICEKV >1nwv_A FRSCEVPTRLNSASLK--QPYITQNYFPVGTVVEYECRPGYRREPSL-SPKLTCLQ----NLKWST-AVEFCK----KKSCPNPG-EIRNGQ-IDVP---------GGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSD-PLPECREH @1vvc_ 030231210101110011000000033002311021200110111000000332000000000200100002000000002201030000000000001100010000103000302020011110210100200000000201001202100 @1ghq_B 031201210101113001000000000032313021200030111000000332000000300200110002000000032201030000000000101100010000100100302020003030200103200000000201001202100 @1ckl_A 000210210000001010000000013032001320200110010000003032000000100200030302000003032200003001110300000000000010101100302021011010200003200011000200000202000 @1nwv_A 001210200300301000000000013032311320200110000000003302000000100200010302000003032201003001110300100000000010001100302021011110210103200011000200001202000 Merge 146 156 Weight 0.531002 >1vvc_ -VKCQSPPSISNGRHNGY-----EDFYTDGSVVTYSCNSGYSLIGNSG--VLCS-----GGEWSDP--PTCQ----IVKCPHPTI----------SNGYLSSGFKRSYSYNDNVDFKCKYGYKLSGSSSSTCSPGN---TWKP-ELPKCVR- >1ghq_B AISCGSPPPILNGRISYY-----STPIAVGTVIRYSCSGTFRLIGEKS--LLCITKDKVDGTWDKPA-PKCEYFNKYSSCPEPIV----------PGGYKIRG-STPYRHGDSVTFACKTNFSMNGNKSVWCQANN---MWGPTRLPTCVS- 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0002102100000010100000000130320013202001100100000303200000010020003030200000303220003001110300000000000010101100302021011010200003200011000200000202000 @1nwv_A 0012102003003010000000000130323113202001100000000330200000010020001030200000303220103001110303100000000010001100302021011110210103200011000200001202000 amap-align/examples/BB12020.tfa0000755000120200001440000000104110650431733015435 0ustar sarielusers>1vvc_ VKCQSPPSISNGRHNGYEDFYTDGSVVTYSCNSGYSLIGNSGVLCSGGEW SDPPTCQIVKCPHPTISNGYLSSGFKRSYSYNDNVDFKCKYGYKLSGSSS STCSPGNTWKPELPKCVR >1ghq_B AISCGSPPPILNGRISYYSTPIAVGTVIRYSCSGTFRLIGEKSLLCITKD KVDGTWDKPAPKCEYFNKYSSCPEPIVPGGYKIRGSTPYRHGDSVTFACK TNFSMNGNKSVWCQANNMWGPTRLPTCVS >1ckl_A CEEPPTFEAMELIGKPKPYYEIGERVDYKCKKGYFYIPPLATHTICDRNH TWLPVSDDACYRETCPYIRDPLNGQAVPANGTYEFGYQMHFICNEGYYLI GEEILYCELKGSVAIWSGKPPICEKV >1nwv_A FRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLT CLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGY KLFGSTSSFCLISGSSVQWSDPLPECREH amap-align/license/0000755000120200001440000000000010754706700013702 5ustar sarielusersamap-align/license/License.txt0000644000120200001440000003501310635655116016031 0ustar sarielusersThe GNU General Public License (GPL) Version 2, June 1991 Copyright (C) 1989, 1991 Free Software Foundation, Inc. 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Library General Public License instead.) You can apply it to your programs, too. When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things. To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it. For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software. Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations. Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all. The precise terms and conditions for copying, distribution and modification follow. TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you". Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does. 1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program. You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. 2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions: a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.) These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it. Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License. 3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following: a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.) The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable. If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code. 4. You may not copy, modify, sublicense, or distribute the Program except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense or distribute the Program is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance. 5. You are not required to accept this License, since you have not signed it. However, nothing else grants you permission to modify or distribute the Program or its derivative works. These actions are prohibited by law if you do not accept this License. Therefore, by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying the Program or works based on it. 6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions. You may not impose any further restrictions on the recipients' exercise of the rights granted herein. You are not responsible for enforcing compliance by third parties to this License. 7. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not distribute the Program at all. For example, if a patent license would not permit royalty-free redistribution of the Program by all those who receive copies directly or indirectly through you, then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Program. If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances. It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice. This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License. 8. 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If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation. 10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. NO WARRANTY 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. END OF TERMS AND CONDITIONS amap-align/README0000644000120200001440000000203110650512722013126 0ustar sarielusers See http://baboon.math.berkeley.edu/amap/ for more information. INSTALL ======= To build the AMAP alignment code change to the 'align' directory and type: % make This distribution includes the compiled AmapDisplay.jar file. In case you want to build the AmapDisplay from the source code, you'll need ant (http://ant.apache.org) installed. Once ant is installed change to the 'display' directory, and type: % ant all USE === To run AMAP with the default options change to the 'align' directory and type: % amap If no file name is provided the list of options are printed. In order to use the AMAP Display run AMAP with the -gui option, and save the output to a file, then use the file as the input to AmapDisplay. For example, type: % align/amap -gui examples/BB12020.tfa > examples/BB12020.tfa.out % java -jar display/AmapDisplay.jar examples/BB12020.tfa.out LICENSE ======= The various bits of AMAP code are distributed under the GPL. Please see the license in the license directory for details.