/******************************COPYRIGHT NOTICE*******************************/ /* (c) Centro de Regulacio Genomica */ /* and */ /* Cedric Notredame */ /* 12 Aug 2014 - 22:07. */ /*All rights reserved. */ /*This file is part of T-COFFEE. */ /* */ /* T-COFFEE 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. */ /* */ /* T-COFFEE 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 Foobar; if not, write to the Free Software */ /* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA */ /*............................................... */ /* If you need some more information */ /* cedric.notredame@europe.com */ /*............................................... */ /******************************COPYRIGHT NOTICE*******************************/ #ifndef MATRICES_H #define MATRICES_H char *amino_acid_order = "ABCDEFGHIKLMNPQRSTVWXYZ"; //Jones Taylor Thornton, tm matrix, //H JOND940101 //D The 250 PAM transmembrane protein exchange matrix (Jones et al., 1994) //R LIT:2006072 PMID:8112466 //A Jones, D.T., Taylor, W.R. and Thornton, J.M. //T A mutation data matrix for transmembrane proteins //J FEBS Lett. 339, 269-275 (1994) int jtttm250mt[]={ 2, 0, 0, 0, 0, 6, 0, 0, -3, 12, 0, 0, -3, 8, 13, -2, 0, 1, -6, -6, 5, 1, 0, -1, 3, 3, -4, 6, -3, 0, -1, 3, 2, -3, -3, 11, 0, 0, -1, -3, -4, -1, -2, -4, 2, -2, 0, -3, 3, 1, -5, -1, 4, -4, 12, -2, 0, -1, -5, -5, 1, -4, -4, 1, -4, 3, -1, 0, -1, -3, -3, 0, -3, -3, 1, -1, 1, 3, -1, 0, -1, 6, 1, -4, -2, 3, -3, 5, -4, -2, 11, 0, 0, -4, -2, -3, -4, -2, -4, -3, -4, -1, -3, -2, 11, -2, 0, -3, 2, 7, -4, -1, 7, -4, 6, -2, -2, 3, 0, 11, -1, 0, -1, 1, 2, -4, 0, 5, -3, 9, -3, 0, 2, -3, 6, 7, 2, 0, 1, 0, 0, -1, 1, -2, -1, -1, -2, -2, 2, -1, -1, -1, 3, 1, 0, 0, 0, -1, -2, 0, -2, 0, -2, -1, 0, 1, -1, -2, -1, 2, 3, 0, 0, 0, -3, -2, -1, -1, -4, 2, -4, 0, 1, -3, -3, -4, -2, -1, 0, 2, -4, 0, 1, -4, -3, -3, -2, -1, -3, 3, -2, -2, -3, -6, 0, 5, -3, -4, -2, 12, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -3, 0, 3, -2, -5, 2, -5, 6, -4, 1, -3, -3, -1, -5, 0, -1, 0, -3, -4, -2, 0, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; int blosum30mt[]={ 4, 0, 5, -3, -2, 17, 0, 5, -3, 9, 0, 0, 1, 1, 6, -2, -3, -3, -5, -4, 10, 0, 0, -4, -1, -2, -3, 8, -2, -2, -5, -2, 0, -3, -3, 14, 0, -2, -2, -4, -3, 0, -1, -2, 6, 0, 0, -3, 0, 2, -1, -1, -2, -2, 4, -1, -1, 0, -1, -1, 2, -2, -1, 2, -2, 4, 1, -2, -2, -3, -1, -2, -2, 2, 1, 2, 2, 6, 0, 4, -1, 1, -1, -1, 0, -1, 0, 0, -2, 0, 8, -1, -2, -3, -1, 1, -4, -1, 1, -3, 1, -3, -4, -3, 11, 1, -1, -2, -1, 2, -3, -2, 0, -2, 0, -2, -1, -1, 0, 8, -1, -2, -2, -1, -1, -1, -2, -1, -3, 1, -2, 0, -2, -1, 3, 8, 1, 0, -2, 0, 0, -1, 0, -1, -1, 0, -2, -2, 0, -1, -1, -1, 4, 1, 0, -2, -1, -2, -2, -2, -2, 0, -1, 0, 0, 1, 0, 0, -3, 2, 5, 1, -2, -2, -2, -3, 1, -3, -3, 4, -2, 1, 0, -2, -4, -3, -1, -1, 1, 5, -5, -5, -2, -4, -1, 1, 1, -5, -3, -2, -2, -3, -7, -3, -1, 0, -3, -5, -3, 20, 0, -1, -2, -1, -1, -1, -1, -1, 0, 0, 0, 0, 0, -1, 0, -1, 0, 0, 0, -2, -1, -4, -3, -6, -1, -2, 3, -3, 0, -1, -1, 3, -1, -4, -2, -1, 0, -2, -1, 1, 5, -1, 9, 0, 0, 0, 0, 5, -4, -2, 0, -3, 1, -1, -1, -1, 0, 4, 0, -1, -1, -3, -1, 0, -2, 4}; int blosum40mt[]={ 5, -1, 5, -2, -2, 16, -1, 6, -2, 9, -1, 1, -2, 2, 7, -3, -3, -2, -4, -3, 9, 1, -1, -3, -2, -3, -3, 8, -2, 0, -4, 0, 0, -2, -2, 13, -1, -3, -4, -4, -4, 1, -4, -3, 6, -1, 0, -3, 0, 1, -3, -2, -1, -3, 6, -2, -3, -2, -3, -2, 2, -4, -2, 2, -2, 6, -1, -3, -3, -3, -2, 0, -2, 1, 1, -1, 3, 7, -1, 4, -2, 2, -1, -3, 0, 1, -2, 0, -3, -2, 8, -2, -2, -5, -2, 0, -4, -1, -2, -2, -1, -4, -2, -2, 11, 0, 0, -4, -1, 2, -4, -2, 0, -3, 1, -2, -1, 1, -2, 8, -2, -1, -3, -1, -1, -2, -3, 0, -3, 3, -2, -1, 0, -3, 2, 9, 1, 0, -1, 0, 0, -2, 0, -1, -2, 0, -3, -2, 1, -1, 1, -1, 5, 0, 0, -1, -1, -1, -1, -2, -2, -1, 0, -1, -1, 0, 0, -1, -2, 2, 6, 0, -3, -2, -3, -3, 0, -4, -4, 4, -2, 2, 1, -3, -3, -3, -2, -1, 1, 5, -3, -4, -6, -5, -2, 1, -2, -5, -3, -2, -1, -2, -4, -4, -1, -2, -5, -4, -3, 19, 0, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, 0, -1, -2, -1, -1, 0, 0, -1, -2, -1, -2, -3, -4, -3, -2, 4, -3, 2, 0, -1, 0, 1, -2, -3, -1, -1, -2, -1, -1, 3, -1, 9, -1, 2, -3, 1, 5, -4, -2, 0, -4, 1, -2, -2, 0, -1, 4, 0, 0, -1, -3, -2, -1, -2, 5}; int blosum45mt[]={ 5, -1, 4, -1, -2, 12, -2, 5, -3, 7, -1, 1, -3, 2, 6, -2, -3, -2, -4, -3, 8, 0, -1, -3, -1, -2, -3, 7, -2, 0, -3, 0, 0, -2, -2, 10, -1, -3, -3, -4, -3, 0, -4, -3, 5, -1, 0, -3, 0, 1, -3, -2, -1, -3, 5, -1, -3, -2, -3, -2, 1, -3, -2, 2, -3, 5, -1, -2, -2, -3, -2, 0, -2, 0, 2, -1, 2, 6, -1, 4, -2, 2, 0, -2, 0, 1, -2, 0, -3, -2, 6, -1, -2, -4, -1, 0, -3, -2, -2, -2, -1, -3, -2, -2, 9, -1, 0, -3, 0, 2, -4, -2, 1, -2, 1, -2, 0, 0, -1, 6, -2, -1, -3, -1, 0, -2, -2, 0, -3, 3, -2, -1, 0, -2, 1, 7, 1, 0, -1, 0, 0, -2, 0, -1, -2, -1, -3, -2, 1, -1, 0, -1, 4, 0, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, 0, -1, -1, -1, 2, 5, 0, -3, -1, -3, -3, 0, -3, -3, 3, -2, 1, 1, -3, -3, -3, -2, -1, 0, 5, -2, -4, -5, -4, -3, 1, -2, -3, -2, -2, -2, -2, -4, -3, -2, -2, -4, -3, -3, 15, 0, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 0, 0, -1, -2, -1, -2, -2, -3, -2, -2, 3, -3, 2, 0, -1, 0, 0, -2, -3, -1, -1, -2, -1, -1, 3, -1, 8, -1, 2, -3, 1, 4, -3, -2, 0, -3, 1, -2, -1, 0, -1, 4, 0, 0, -1, -3, -2, -1, -2, 4}; int blosum50mt[] = { 5, -2, 5, -1, -3, 13, -2, 5, -4, 8, -1, 1, -3, 2, 6, -3, -4, -2, -5, -3, 8, 0, -1, -3, -1, -3, -4, 8, -2, 0, -3, -1, 0, -1, -2, 10, -1, -4, -2, -4, -4, 0, -4, -4, 5, -1, 0, -3, -1, 1, -4, -2, 0, -3, 6, -2, -4, -2, -4, -3, 1, -4, -3, 2, -3, 5, -1, -3, -2, -4, -2, 0, -3, -1, 2, -2, 3, 7, -1, 4, -2, 2, 0, -4, 0, 1, -3, 0, -4, -2, 7, -1, -2, -4, -1, -1, -4, -2, -2, -3, -1, -4, -3, -2, 10, -1, 0, -3, 0, 2, -4, -2, 1, -3, 2, -2, 0, 0, -1, 7, -2, -1, -4, -2, 0, -3, -3, 0, -4, 3, -3, -2, -1, -3, 1, 7, 1, 0, -1, 0, -1, -3, 0, -1, -3, 0, -3, -2, 1, -1, 0, -1, 5, 0, 0, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, 0, -1, -1, -1, 2, 5, 0, -4, -1, -4, -3, -1, -4, -4, 4, -3, 1, 1, -3, -3, -3, -3, -2, 0, 5, -3, -5, -5, -5, -3, 1, -3, -3, -3, -3, -2, -1, -4, -4, -1, -3, -4, -3, -3, 15, -1, -1, -2, -1, -1, -2, -2, -1, -1, -1, -1, -1, -1, -2, -1, -1, -1, 0, -1, -3, -1, -2, -3, -3, -3, -2, 4, -3, 2, -1, -2, -1, 0, -2, -3, -1, -1, -2, -2, -1, 2, -1, 8, -1, 2, -3, 1, 5, -4, -2, 0, -3, 1, -3, -1, 0, -1, 4, 0, 0, -1, -3, -2, -1, -2, 5}; int blosum55mt[]={ 5, -2, 5, 0, -4, 13, -2, 5, -4, 8, -1, 1, -4, 2, 7, -3, -5, -3, -5, -4, 9, 0, -1, -3, -2, -3, -4, 8, -2, 0, -4, -1, -1, -1, -2, 11, -2, -4, -2, -4, -4, 0, -5, -4, 6, -1, 0, -4, -1, 1, -4, -2, 0, -4, 6, -2, -4, -2, -5, -4, 1, -5, -3, 2, -3, 6, -1, -3, -2, -4, -3, 0, -3, -2, 2, -2, 3, 8, -2, 4, -3, 2, 0, -4, 0, 1, -4, 0, -4, -3, 8, -1, -2, -3, -2, -1, -5, -3, -3, -3, -1, -4, -3, -2, 10, -1, 0, -4, 0, 2, -4, -2, 1, -4, 2, -3, 0, 0, -1, 7, -2, -1, -4, -2, 0, -3, -3, 0, -4, 3, -3, -2, -1, -3, 1, 8, 2, 0, -1, 0, 0, -3, 0, -1, -3, 0, -3, -2, 1, -1, 0, -1, 5, 0, -1, -1, -1, -1, -3, -2, -2, -1, -1, -2, -1, 0, -1, -1, -1, 2, 6, 0, -4, -1, -4, -3, -1, -4, -4, 4, -3, 1, 1, -4, -3, -3, -3, -2, 0, 5, -4, -5, -4, -5, -3, 2, -3, -3, -3, -4, -3, -2, -5, -5, -2, -3, -4, -3, -4, 15, -1, -1, -2, -2, -1, -2, -2, -1, -1, -1, -1, -1, -1, -2, -1, -1, -1, -1, -1, -3, -1, -2, -3, -3, -3, -2, 4, -4, 2, -1, -2, -1, -1, -2, -4, -1, -2, -2, -2, -2, 3, -1, 9, -1, 2, -4, 1, 5, -4, -3, 0, -4, 1, -3, -2, 0, -1, 4, 0, 0, -1, -3, -3, -1, -2, 5}; int blosum62mt[]={ 4, -2, 4, 0, -3, 9, -2, 4, -3, 6, -1, 1, -4, 2, 5, -2, -3, -2, -3, -3, 6, 0, -1, -3, -1, -2, -3, 6, -2, 0, -3, -1, 0, -1, -2, 8, -1, -3, -1, -3, -3, 0, -4, -3, 4, -1, 0, -3, -1, 1, -3, -2, -1, -3, 5, -1, -4, -1, -4, -3, 0, -4, -3, 2, -2, 4, -1, -3, -1, -3, -2, 0, -3, -2, 1, -1, 2, 5, -2, 3, -3, 1, 0, -3, 0, 1, -3, 0, -3, -2, 6, -1, -2, -3, -1, -1, -4, -2, -2, -3, -1, -3, -2, -2, 7, -1, 0, -3, 0, 2, -3, -2, 0, -3, 1, -2, 0, 0, -1, 5, -1, -1, -3, -2, 0, -3, -2, 0, -3, 2, -2, -1, 0, -2, 1, 5, 1, 0, -1, 0, 0, -2, 0, -1, -2, 0, -2, -1, 1, -1, 0, -1, 4, 0, -1, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, 0, -1, -1, -1, 1, 5, 0, -3, -1, -3, -2, -1, -3, -3, 3, -2, 1, 1, -3, -2, -2, -3, -2, 0, 4, -3, -4, -2, -4, -3, 1, -2, -2, -3, -3, -2, -1, -4, -4, -2, -3, -3, -2, -3, 11, 0, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, -1, 0, 0, -1, -2, -1, -2, -3, -2, -3, -2, 3, -3, 2, -1, -2, -1, -1, -2, -3, -1, -2, -2, -2, -1, 2, -1, 7, -1, 1, -3, 1, 4, -3, -2, 0, -3, 1, -3, -1, 0, -1, 3, 0, 0, -1, -2, -3, -1, -2, 4}; int blosum62mt3[]={ 0, -2, 0, 0, -3, 0, -2, 4, -3, 0, -1, 1, -4, 2, 0, -2, -3, -2, -3, -3, 0, 0, -1, -3, -1, -2, -3, 0, -2, 0, -3, -1, 0, -1, -2, 0, -1, -3, -1, -3, -3, 0, -4, -3, 0, -1, 0, -3, -1, 1, -3, -2, -1, -3, 0, -1, -4, -1, -4, -3, 0, -4, -3, 2, -2, 0, -1, -3, -1, -3, -2, 0, -3, -2, 1, -1, 2, 0, -2, 3, -3, 1, 0, -3, 0, 1, -3, 0, -3, -2, 0, -1, -2, -3, -1, -1, -4, -2, -2, -3, -1, -3, -2, -2, 0, -1, 0, -3, 0, 2, -3, -2, 0, -3, 1, -2, 0, 0, -1, 0, -1, -1, -3, -2, 0, -3, -2, 0, -3, 2, -2, -1, 0, -2, 1, 0, 1, 0, -1, 0, 0, -2, 0, -1, -2, 0, -2, -1, 1, -1, 0, -1, 0, 0, -1, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, 0, -1, -1, -1, 1, 0, 0, -3, -1, -3, -2, -1, -3, -3, 3, -2, 1, 1, -3, -2, -2, -3, -2, 0, 0, -3, -4, -2, -4, -3, 1, -2, -2, -3, -3, -2, -1, -4, -4, -2, -3, -3, -2, -3, 0, 0, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, -1, 0, 0, -1, -2, 0, -2, -3, -2, -3, -2, 3, -3, 2, -1, -2, -1, -1, -2, -3, -1, -2, -2, -2, -1, 2, -1, 0, -1, 1, -3, 1, 4, -3, -2, 0, -3, 1, -3, -1, 0, -1, 3, 0, 0, -1, -2, -3, -1, -2, 0}; int blosum62mt2[]={ 0, -2, 4, 0, -3, 0, -2, 4, -3, 2, -1, 1, -4, 2, 2, -2, -3, -2, -3, -3, 3, 0, -1, -3, -1, -2, -3, 0, -2, 0, -3, -1, 0, -1, -2, 2, -1, -3, -1, -3, -3, 0, -4, -3, 2, -1, 0, -3, -1, 1, -3, -2, -1, -3, 2, -1, -4, -1, -4, -3, 0, -4, -3, 2, -2, 1, -1, -3, -1, -3, -2, 0, -3, -2, 1, -1, 2, 0, -2, 3, -3, 1, 0, -3, 0, 1, -3, 0, -3, -2, 0, -1, -2, -3, -1, -1, -4, -2, -2, -3, -1, -3, -2, -2, 0, -1, 0, -3, 0, 2, -3, -2, 0, -3, 1, -2, 0, 0, -1, 2, -1, -1, -3, -2, 0, -3, -2, 0, -3, 2, -2, -1, 0, -2, 1, 0, 1, 0, -1, 0, 0, -2, 0, -1, -2, 0, -2, -1, 1, -1, 0, -1, 1, 0, -1, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, 0, -1, -1, -1, 1, 1, 0, -3, -1, -3, -2, -1, -3, -3, 3, -2, 1, 1, -3, -2, -2, -3, -2, 0, 1, -3, -4, -2, -4, -3, 1, -2, -2, -3, -3, -2, -1, -4, -4, -2, -3, -3, -2, -3, 1, 0, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, -1, 0, 0, -1, -2, -1, -2, -3, -2, -3, -2, 3, -3, 2, -1, -2, -1, -1, -2, -3, -1, -2, -2, -2, -1, 2, -1, 3, -1, 1, -3, 1, 4, -3, -2, 0, -3, 1, -3, -1, 0, -1, 3, 0, 0, -1, -2, -3, -1, -2, 4}; int blosum80mt[]={ 7, -3, 6, -1, -6, 13, -3, 6, -7, 10, -2, 1, -7, 2, 8, -4, -6, -4, -6, -6, 10, 0, -2, -6, -3, -4, -6, 9, -3, -1, -7, -2, 0, -2, -4, 12, -3, -6, -2, -7, -6, -1, -7, -6, 7, -1, -1, -6, -2, 1, -5, -3, -1, -5, 8, -3, -7, -3, -7, -6, 0, -7, -5, 2, -4, 6, -2, -5, -3, -6, -4, 0, -5, -4, 2, -3, 3, 9, -3, 5, -5, 2, -1, -6, -1, 1, -6, 0, -6, -4, 9, -1, -4, -6, -3, -2, -6, -5, -4, -5, -2, -5, -4, -4, 12, -2, -1, -5, -1, 3, -5, -4, 1, -5, 2, -4, -1, 0, -3, 9, -3, -2, -6, -3, -1, -5, -4, 0, -5, 3, -4, -3, -1, -3, 1, 9, 2, 0, -2, -1, -1, -4, -1, -2, -4, -1, -4, -3, 1, -2, -1, -2, 7, 0, -1, -2, -2, -2, -4, -3, -3, -2, -1, -3, -1, 0, -3, -1, -2, 2, 8, -1, -6, -2, -6, -4, -2, -6, -5, 4, -4, 1, 1, -5, -4, -4, -4, -3, 0, 7, -5, -8, -5, -8, -6, 0, -6, -4, -5, -6, -4, -3, -7, -7, -4, -5, -6, -5, -5, 16, -1, -3, -4, -3, -2, -3, -3, -2, -2, -2, -2, -2, -2, -3, -2, -2, -1, -1, -2, -5, -2, -4, -5, -5, -6, -5, 4, -6, 3, -3, -4, -2, -3, -4, -6, -3, -4, -3, -3, -3, 3, -3, 11, -2, 0, -7, 1, 6, -6, -4, 0, -6, 1, -5, -3, -1, -2, 5, 0, -1, -2, -4, -5, -1, -4, 6}; int pam120mt[]={ 3, 0, 4, -3, -6, 9, 0, 4, -7, 5, 0, 3, -7, 3, 5, -4, -5, -6, -7, -7, 8, 1, 0, -4, 0, -1, -5, 5, -3, 1, -4, 0, -1, -3, -4, 7, -1, -3, -3, -3, -3, 0, -4, -4, 6, -2, 0, -7, -1, -1, -7, -3, -2, -3, 5, -3, -4, -7, -5, -4, 0, -5, -3, 1, -4, 5, -2, -4, -6, -4, -3, -1, -4, -4, 1, 0, 3, 8, -1, 3, -5, 2, 1, -4, 0, 2, -2, 1, -4, -3, 4, 1, -2, -4, -3, -2, -5, -2, -1, -3, -2, -3, -3, -2, 6, -1, 0, -7, 1, 2, -6, -3, 3, -3, 0, -2, -1, 0, 0, 6, -3, -2, -4, -3, -3, -5, -4, 1, -2, 2, -4, -1, -1, -1, 1, 6, 1, 0, 0, 0, -1, -3, 1, -2, -2, -1, -4, -2, 1, 1, -2, -1, 3, 1, 0, -3, -1, -2, -4, -1, -3, 0, -1, -3, -1, 0, -1, -2, -2, 2, 4, 0, -3, -3, -3, -3, -3, -2, -3, 3, -4, 1, 1, -3, -2, -3, -3, -2, 0, 5, -7, -6, -8, -8, -8, -1, -8, -3, -6, -5, -3, -6, -4, -7, -6, 1, -2, -6, -8, 12, -1, -1, -4, -2, -1, -3, -2, -2, -1, -2, -2, -2, -1, -2, -1, -2, -1, -1, -1, -5, -2, -4, -3, -1, -5, -5, 4, -6, -1, -2, -5, -2, -4, -2, -6, -5, -5, -3, -3, -3, -2, -3, 8, -1, 2, -7, 3, 4, -6, -2, 1, -3, -1, -3, -2, 0, -1, 4, -1, -1, -2, -3, -7, -1, -5, 4}; int pam160mt[]={ 2, 0, 3, -2, -4, 9, 0, 3, -5, 4, 0, 2, -5, 3, 4, -3, -4, -5, -6, -5, 7, 1, 0, -3, 0, 0, -4, 4, -2, 1, -3, 0, 0, -2, -3, 6, -1, -2, -2, -3, -2, 0, -3, -3, 5, -2, 0, -5, 0, -1, -5, -2, -1, -2, 4, -2, -4, -6, -4, -3, 1, -4, -2, 2, -3, 5, -1, -3, -5, -3, -2, 0, -3, -3, 2, 0, 3, 7, 0, 2, -4, 2, 1, -3, 0, 2, -2, 1, -3, -2, 3, 1, -1, -3, -2, -1, -4, -1, -1, -2, -2, -3, -2, -1, 5, -1, 1, -5, 1, 2, -5, -2, 2, -2, 0, -2, -1, 0, 0, 5, -2, -1, -3, -2, -2, -4, -3, 1, -2, 3, -3, -1, -1, -1, 1, 6, 1, 0, 0, 0, 0, -3, 1, -1, -2, -1, -3, -2, 1, 1, -1, -1, 2, 1, 0, -2, -1, -1, -3, -1, -2, 0, 0, -2, -1, 0, 0, -1, -1, 1, 3, 0, -2, -2, -3, -2, -2, -2, -2, 3, -3, 1, 1, -2, -2, -2, -3, -1, 0, 4, -5, -5, -7, -6, -7, -1, -7, -3, -5, -4, -2, -4, -4, -5, -5, 1, -2, -5, -6, 12, 0, -1, -3, -1, -1, -3, -1, -1, -1, -1, -2, -1, 0, -1, -1, -1, 0, 0, -1, -4, -1, -3, -3, 0, -4, -4, 5, -5, 0, -2, -4, -2, -3, -2, -5, -4, -4, -3, -3, -3, -1, -3, 8, 0, 2, -5, 2, 3, -5, -1, 1, -2, 0, -3, -2, 1, -1, 3, 0, -1, -1, -2, -6, -1, -4, 3}; int pam250mt[]={ 2, 0, 3, -2, -4, 12, 0, 3, -5, 4, 0, 3, -5, 3, 4, -3, -4, -4, -6, -5, 9, 1, 0, -3, 1, 0, -5, 5, -1, 1, -3, 1, 1, -2, -2, 6, -1, -2, -2, -2, -2, 1, -3, -2, 5, -1, 1, -5, 0, 0, -5, -2, 0, -2, 5, -2, -3, -6, -4, -3, 2, -4, -2, 2, -3, 6, -1, -2, -5, -3, -2, 0, -3, -2, 2, 0, 4, 6, 0, 2, -4, 2, 1, -3, 0, 2, -2, 1, -3, -2, 2, 1, -1, -3, -1, -1, -5, 0, 0, -2, -1, -3, -2, 0, 6, 0, 1, -5, 2, 2, -5, -1, 3, -2, 1, -2, -1, 1, 0, 4, -2, -1, -4, -1, -1, -4, -3, 2, -2, 3, -3, 0, 0, 0, 1, 6, 1, 0, 0, 0, 0, -3, 1, -1, -1, 0, -3, -2, 1, 1, -1, 0, 2, 1, 0, -2, 0, 0, -3, 0, -1, 0, 0, -2, -1, 0, 0, -1, -1, 1, 3, 0, -2, -2, -2, -2, -1, -1, -2, 4, -2, 2, 2, -2, -1, -2, -2, -1, 0, 4, -6, -5, -8, -7, -7, 0, -7, -3, -5, -3, -2, -4, -4, -6, -5, 2, -2, -5, -6, 17, 0, -1, -3, -1, -1, -2, -1, -1, -1, -1, -1, -1, 0, -1, -1, -1, 0, 0, -1, -4, -1, -3, -3, 0, -4, -4, 7, -5, 0, -1, -4, -1, -2, -2, -5, -4, -4, -3, -3, -2, 0, -2, 10, 0, 2, -5, 3, 3, -5, 0, 2, -2, 0, -3, -2, 1, 0, 3, 0, 0, -1, -2, -6, -1, -4, 3}; int pam350mt[]={ 2, 1, 3, -2, -5, 18, 1, 3, -6, 4, 1, 3, -6, 4, 4, -4, -5, -5, -6, -6, 13, 2, 1, -4, 1, 1, -6, 5, -1, 1, -4, 1, 1, -2, -2, 7, 0, -2, -3, -2, -2, 2, -2, -2, 5, -1, 1, -6, 1, 0, -6, -1, 1, -2, 5, -2, -4, -7, -4, -4, 3, -4, -2, 4, -3, 8, -1, -2, -6, -3, -2, 1, -3, -2, 3, 0, 5, 6, 0, 2, -4, 2, 2, -4, 1, 2, -2, 1, -3, -2, 2, 1, 0, -3, 0, 0, -5, 0, 0, -2, -1, -3, -2, 0, 6, 0, 2, -6, 2, 3, -5, -1, 3, -2, 1, -2, -1, 1, 1, 4, -1, 0, -4, -1, 0, -5, -2, 2, -2, 4, -3, 0, 1, 0, 2, 7, 1, 1, 0, 1, 0, -4, 1, -1, -1, 0, -3, -2, 1, 1, 0, 0, 1, 1, 0, -2, 0, 0, -3, 1, -1, 0, 0, -2, -1, 1, 1, 0, -1, 1, 2, 0, -2, -2, -2, -2, -1, -1, -2, 4, -2, 3, 2, -2, -1, -2, -3, -1, 0, 5, -7, -6,-10, -8, -8, 1, -8, -3, -6, -4, -2, -5, -5, -7, -5, 4, -3, -6, -7, 27, 0, 0, -3, -1, 0, -2, -1, 0, 0, -1, -1, 0, 0, 0, 0, -1, 0, 0, 0, -5, -1, -4, -4, 1, -5, -5, 11, -6, 0, 0, -5, 0, -2, -3, -6, -5, -5, -3, -3, -2, 1, -2, 14, 0, 2, -6, 3, 3, -6, 0, 2, -2, 1, -3, -2, 2, 0, 3, 1, 0, 0, -2, -7, 0, -5, 3}; int md_40mt[]={ 9, 0, 0, -7, 0, 16, -6, 0,-13, 11, -5, 0,-15, 3, 11, -11, 0, -5,-15,-16, 13, -3, 0, -7, -4, -4,-15, 10, -9, 0, -6, -4, -8, -7,-10, 14, -6, 0,-11,-12,-12, -5,-13,-11, 11, -8, 0,-12, -8, -3,-16, -9, -6,-11, 11, -9, 0,-10,-14,-13, -1,-14, -7, -1,-12, 9, -6, 0, -9,-12,-11, -7,-12, -9, 1, -7, 1, 14, -6, 0, -8, 1, -5,-12, -5, 0, -8, -1,-12, -9, 12, -2, 0,-11,-11,-11,-11, -9, -4,-11,-10, -5,-10, -9, 12, -7, 0,-12, -6, 0,-14, -9, 2,-12, -1, -6, -8, -5, -3, 12, -7, 0, -5,-10, -8,-15, -4, 0,-10, 3, -9, -8, -6, -6, 0, 11, 0, 0, -2, -6, -8, -6, -2, -6, -8, -7, -7, -8, 1, -1, -7, -5, 9, 1, 0, -7, -8, -8,-11, -7, -7, -2, -5, -9, -2, -2, -4, -7, -6, 1, 10, -1, 0, -7, -9, -8, -6, -8,-12, 4,-12, -2, 0,-10, -9,-11,-11, -7, -4, 10, -14, 0, -4,-15,-15, -7, -7,-13,-13,-13, -8,-11,-14,-14,-11, -4, -9,-12,-10, 18, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -13, 0, -2, -8,-14, 2,-13, 2, -9,-13, -9,-11, -6,-13, -9,-10, -7,-10,-11, -6, 0, 14, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; int md_120mt[]={ 6, 0, 0, -3, 0, 14, -2, 0, -7, 8, -2, 0, -8, 5, 8, -6, 0, -2, -9,-10, 11, 0, 0, -3, 0, -1, -9, 8, -4, 0, -2, -1, -3, -2, -4, 11, -1, 0, -5, -7, -7, -1, -6, -6, 7, -4, 0, -6, -2, 0, -9, -4, -1, -6, 8, -4, 0, -5, -8, -8, 2, -8, -4, 2, -6, 7, -2, 0, -5, -7, -6, -2, -6, -5, 3, -4, 3, 10, -1, 0, -3, 3, -1, -6, -1, 2, -4, 1, -6, -5, 8, 0, 0, -5, -5, -5, -5, -4, -1, -5, -4, -2, -5, -3, 9, -3, 0, -6, -1, 2, -7, -4, 4, -6, 2, -3, -4, -1, 0, 9, -3, 0, -2, -4, -3, -8, -1, 2, -6, 4, -5, -4, -2, -2, 2, 8, 2, 0, 0, -2, -3, -3, 0, -2, -3, -3, -3, -3, 2, 1, -3, -2, 5, 2, 0, -3, -3, -4, -6, -2, -3, 0, -2, -4, 0, 1, 0, -3, -3, 2, 6, 1, 0, -3, -5, -5, -2, -4, -6, 5, -6, 1, 2, -5, -4, -6, -6, -3, 0, 7, -8, 0, 0, -9, -9, -3, -3, -6, -7, -6, -4, -6, -8, -8, -6, -1, -5, -7, -6, 17, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -7, 0, 2, -4, -7, 5, -8, 4, -5, -7, -4, -6, -2, -7, -4, -5, -3, -6, -6, -2, 0, 12, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; int md_250mt[]={ 2, 0, 0, -1, 0, 11, -1, 0, -3, 5, -1, 0, -4, 4, 5, -3, 0, 0, -5, -5, 8, 1, 0, -1, 1, 1, -5, 5, -2, 0, 0, 0, 0, 0, -2, 6, 0, 0, -2, -3, -3, 0, -3, -3, 4, -1, 0, -3, 0, 1, -5, -1, 1, -3, 5, -1, 0, -2, -4, -4, 2, -4, -2, 2, -3, 5, 0, 0, -2, -3, -3, 0, -3, -2, 3, -2, 3, 6, 0, 0, -1, 2, 1, -3, 0, 1, -2, 1, -3, -2, 3, 1, 0, -2, -2, -2, -2, -1, 0, -2, -1, 0, -2, -1, 6, -1, 0, -3, 0, 2, -4, -1, 3, -3, 2, -2, -2, 0, 0, 5, -1, 0, -1, -1, 0, -4, 0, 2, -3, 4, -3, -2, 0, -1, 2, 5, 1, 0, 1, 0, -1, -2, 1, -1, -1, -1, -2, -1, 1, 1, -1, -1, 2, 2, 0, -1, -1, -1, -2, 0, -1, 1, -1, -1, 0, 1, 1, -1, -1, 1, 2, 1, 0, -2, -3, -2, 0, -2, -3, 4, -3, 2, 2, -2, -1, -3, -3, -1, 0, 4, -4, 0, 1, -5, -5, -1, -1, -3, -4, -3, -2, -3, -4, -4, -3, 0, -3, -4, -3, 15, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -3, 0, 2, -2, -4, 5, -4, 4, -2, -3, -1, -3, -1, -3, -2, -2, -1, -3, -3, 0, 0, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; int md_350mt[]={ 1, 0, 0, 0, 0, 9, 0, 0, -2, 3, 0, 0, -2, 3, 3, -2, 0, 1, -3, -4, 6, 1, 0, 0, 1, 1, -3, 4, -1, 0, 0, 0, 0, 0, -1, 3, 0, 0, -1, -2, -2, 1, -2, -2, 3, -1, 0, -1, 0, 1, -3, 0, 1, -2, 3, -1, 0, -1, -3, -3, 2, -2, -1, 2, -2, 3, 0, 0, -1, -2, -2, 1, -2, -1, 2, -2, 2, 3, 0, 0, -1, 1, 1, -2, 0, 1, -1, 1, -2, -1, 2, 1, 0, -1, -1, -1, -2, -1, 0, -1, -1, 0, -1, 0, 4, -1, 0, -2, 1, 1, -2, 0, 2, -2, 2, -1, -1, 0, 0, 3, -1, 0, 0, 0, 0, -3, 0, 1, -2, 3, -2, -1, 0, 0, 2, 3, 1, 0, 0, 0, 0, -1, 1, 0, -1, 0, -1, -1, 1, 1, 0, 0, 1, 1, 0, 0, 0, -1, -1, 0, -1, 0, 0, -1, 0, 0, 1, -1, 0, 1, 1, 0, 0, -1, -2, -2, 0, -1, -2, 2, -2, 1, 2, -1, -1, -2, -2, 0, 0, 2, -3, 0, 1, -4, -3, 0, -1, -2, -3, -2, -1, -2, -3, -3, -2, 0, -2, -3, -2, 14, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -2, 0, 2, -2, -2, 5, -3, 3, -1, -2, 0, -1, -1, -2, -1, -1, -1, -2, -2, 0, 0, 7, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; int idmat[]={ 10, 0, 10, 0, 0, 10, 0, 0, 0, 10, 0, 0, 0, 0, 10, 0, 0, 0, 0, 0, 10, 0, 0, 0, 0, 0, 0, 10, 0, 0, 0, 0, 0, 0, 0, 10, 0, 0, 0, 0, 0, 0, 0, 0, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,10}; int dna_idmat[]={ 10, -1, 10, -1, -1, 10, -1, -1, -1, 10, -1, -1, -1, -1, 10, -1, -1, -1, -1, -1, 10, -1, -1, -1, -1, -1, -1, 10, -1, -1, -1, -1, -1, -1, -1, 10, -1, -1, -1, -1, -1, -1, -1, -1, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,10}; int est_idmat[]={ 10, -10, 10, -10, -10, 10, -10, -10, -10, 10, -10, -10, -10, -10, 10, -10, -10, -10, -10, -10, 10, -10, -10, -10, -10, -10, -10, 10, -10, -10, -10, -10, -10, -10, -10, 10, -10, -10, -10, -10, -10, -10, -10, -10, 10, -10, -10, -10, -10, -10, -10, -10, -10, -10, 10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, 10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, 10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, 10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, 10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, 10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, 10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, 10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, 10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10,10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10,10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10,10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10,10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10,10}; /*These are the three structure specific matrices descibed by Luthy, R., McLachlan, A.D. and Eisenberg, D. in Proteins 10, 229-239 (1991), taken from http://www.genome.ad.jp/dbget/dbget2.html ID: coil :LUTR910107 ID: alpha:LUTR910108 ID: beta :LUTR910109 */ int coil_mat []={ 11, 0, 0, 3, 0, 108, 2, 0, -5, 27, 2, 0, 7, -9, 15, -15, 0, 3, -11, -4, 83, 1, 0, 4, -15, -4, 2, 41, 5, 0, 4, 108, -6, -13, -3, 55, 27, 0, -11, 3, -2, -14, 0, -1, 49, -9, 0, 3, 4, -21, -2, -3, -4, -7, 38, -5, 0, 14, 7, -5, 2, 2, -6, -3, 1, 48, -9, 0, 3, 4, -6, -16, -23, -9, -7, -1, 7, 52, 28, 0, 1, 2, 27, 7, -5, -9, -9, 108, -15, 3, 10, 108, 0, 8, 14, 41, 0, -2, -4, -10, -3, 1, -15, 4, 58, 10, 0, 3, -9, 3, -4, 3, 3, 8, 6, -15, 15, 5, -6, 14, 1, 0, 10, 3, 1, 108, 5, 27, -5, -9, -9, -15, 2, 3, 2, 28, 3, 0, -15, 3, -3, -8, -12, -5, -6, -9, -19, -14, 4, 4, -2, 7, 19, 7, 0, 6, 3, 0, -7, 55, -18, -8, -7, 6, -20, -11, 2, -5, 4, 3, 31, -11, 0, -6, -15, -23, -6, -4, -3, 19, -15, -6, -22, 3, -11, -4, 14, -1, -7, 37, 4, 0, 15, 3, 2, -8, -1, -12, -22, -2, 5, -19, 14, 4, -21, 4, 0, -9, -1, 129, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, -4, 8, -3, -30, -6, 49, -10, -7, -12, -18, 3, 3, -6, -11, 3, 2, 2, -5, 0, 59, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }; int alpha_mat []={ 23, 0, 0, 5, 0, 51, 1, 0, 4, 28, 0, 0, 5, 1, 23, -4, 0, 5, 1, 3, 88, 3, 0, 5, -4, 2, 4, 37, 7, 0, 6, 51, 3, 5, -6, 52, 28, 0, 1, 1, 6, -21, 2, -6, 38, 1, 0, 0, 5, 4, -2, 3, -7, -10, 34, 4, 0, 11, 5, 4, 3, 5, -6, -19, -6, 45, 1, 0, 4, 6, 3, -23, -5, -12, -14, -4, 9, 40, 19, 0, 3, 0, 28, 5, 4, 1, 1, 51, -4, 1, 13, 51, 0, 10, 11, 37, 1, 1, -6, -8, -5, 2, -22, 5, 59, 13, 0, 1, 1, 0, 2, 4, 5, 10, 7, -5, 23, 7, 3, 11, -1, 0, 13, 5, 3, 51, 7, 28, 4, 1, 1, -4, 1, 1, 0, 19, 1, 0, -5, 0, -6, 2, -1, -10, -14, -9, -6, -22, 6, 3, 6, 5, 17, 5, 0, 7, 4, 2, 3, 52, -8, -18, 3, 4, -24, 1, 4, 4, 5, 2, 14, 1, 0, 3, -5, -5, 5, -7, -19, 7, -6, -2, -28, 4, 7, 3, 11, 2, -38, 40, 5, 0, 23, 5, 5, 5, -6, -9, -19, -2, 3, -4, 11, 5, 4, 6, 2, -43, -8, 162, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 6, 0, 2, 10, 3, -2, -6, 38, -14, -7, -1, -19, 0, 5, 3, 1, 4, -29, -6, -19, 0, 97, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }; int beta_mat []={ 23, 0, 0, 4, 0, 97, 1, 0, -5, 49, -1, 0, 9, -5, 31, -16, 0, 8, -11, 6, 57, 2, 0, 7, -16, 12, 8, 54, 13, 0, 9, 97, 2, -30, -4, 55, 49, 0, -11, 0, 0, -22, 2, -7, 28, -19, 0, 0, 7, -18, 2, 17, -12, -10, 34, -5, 0, 31, 9, 1, 7, 13, -9, -7, -3, 34, -5, 0, 2, 9, 4, -9, -12, -17, -13, 1, 14, 25, 40, 0, 2, -1, 49, 9, -5, -19, -5, 97, -16, 0, 15, 97, 0, 17, 31, 54, 5, 5, -13, -34, -2, 8, -11, 7, 78, 15, 0, 0, -19, 0, 12, 2, 8, 17, 11, -21, 31, 13, 2, 31, -2, 0, 15, 4, 2, 97, 13, 49, -5, -5, -19, -16, 1, 0, -1, 40, 0, 0, -21, 0, -4, -6, -5, -13, -12, -5, -23, -9, 9, 7, 0, 9, 26, 9, 0, 11, 2, 2, 2, 55, -11, -14, -28, 12, -21, -11, 1, 1, 7, 4, 21, -11, 0, 2, -21, -12, -2, -12, -7, 13, 2, -1, -13, 2, -10, 6, 31, 2, -22, 23, 7, 0, 31, 8, 13, -7, -7, -15, -15, -3, 10, -31, 31, 6, -18, 9, 6, -17, -5, 133, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 0, 12, 17, 17, -12, -9, 28, -13, -3, 0, -12, 0, 8, 4, -11, 2, -5, -5, -5, 0, 47, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }; /*EXPERIMENTAL MATRICES: Blosum Series*/ /*Blosum Series rescaled on blosum62mt, Lambda Blosum30mt=17 Lambda Blosum62mt=10 Lambda Blosum80mt=4.5 */ int rblosum30mt []={ 52, 33, 56, 18, 23, 113, 33, 56, 18, 75, 33, 33, 37, 37, 61, 23, 18, 18, 9, 14, 80, 33, 33, 14, 28, 23, 18, 71, 23, 23, 9, 23, 33, 18, 18, 99, 33, 23, 23, 14, 18, 33, 28, 23, 61, 33, 33, 18, 33, 42, 28, 28, 23, 23, 52, 28, 28, 33, 28, 28, 42, 23, 28, 42, 23, 52, 37, 23, 23, 18, 28, 23, 23, 42, 37, 42, 42, 61, 33, 52, 28, 37, 28, 28, 33, 28, 33, 33, 23, 33, 71, 28, 23, 18, 28, 37, 14, 28, 37, 18, 37, 18, 14, 18, 85, 37, 28, 23, 28, 42, 18, 23, 33, 23, 33, 23, 28, 28, 33, 71, 28, 23, 23, 28, 28, 28, 23, 28, 18, 37, 23, 33, 23, 28, 47, 71, 37, 33, 23, 33, 33, 28, 33, 28, 28, 33, 23, 23, 33, 28, 28, 28, 52, 37, 33, 23, 28, 23, 23, 23, 23, 33, 28, 33, 33, 37, 33, 33, 18, 42, 56, 37, 23, 23, 23, 18, 37, 18, 18, 52, 23, 37, 33, 23, 14, 18, 28, 28, 37, 56, 9, 9, 23, 14, 28, 37, 37, 9, 18, 23, 23, 18, 0, 18, 28, 33, 18, 9, 18, 128, 0, -1, -2, -1, -1, -1, -1, -1, 0, 0, 0, 0, 0, -1, 0, -1, 0, 0, 0, -2, -1, -4, -3, -6, -1, -2, 3, -3, 0, -1, -1, 3, -1, -4, -2, -1, 0, -2, -1, 1, 5, -1, 9, 0, 0, 0, 0, 5, -4, -2, 0, -3, 1, -1, -1, -1, 0, 4, 0, -1, -1, -3, -1, 0, -2, 4, }; int rblosum62mt[]={ 80, 20, 80, 40, 10, 130, 20, 80, 10, 100, 30, 50, 0, 60, 90, 20, 10, 20, 10, 10, 100, 40, 30, 10, 30, 20, 10, 100, 20, 40, 10, 30, 40, 30, 20, 120, 30, 10, 30, 10, 10, 40, 0, 10, 80, 30, 40, 10, 30, 50, 10, 20, 30, 10, 90, 30, 0, 30, 0, 10, 40, 0, 10, 60, 20, 80, 30, 10, 30, 10, 20, 40, 10, 20, 50, 30, 60, 90, 20, 70, 10, 50, 40, 10, 40, 50, 10, 40, 10, 20, 100, 30, 20, 10, 30, 30, 0, 20, 20, 10, 30, 10, 20, 20, 110, 30, 40, 10, 40, 60, 10, 20, 40, 10, 50, 20, 40, 40, 30, 90, 30, 30, 10, 20, 40, 10, 20, 40, 10, 60, 20, 30, 40, 20, 50, 90, 50, 40, 30, 40, 40, 20, 40, 30, 20, 40, 20, 30, 50, 30, 40, 30, 80, 40, 30, 30, 30, 30, 20, 20, 20, 30, 30, 30, 30, 40, 30, 30, 30, 50, 90, 40, 10, 30, 10, 20, 30, 10, 10, 70, 20, 50, 50, 10, 20, 20, 10, 20, 40, 80, 10, 0, 20, 0, 10, 50, 20, 20, 10, 10, 20, 30, 0, 0, 20, 10, 10, 20, 10, 150, 0, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, -1, 0, 0, -1, -2, -1, -2, -3, -2, -3, -2, 3, -3, 2, -1, -2, -1, -1, -2, -3, -1, -2, -2, -2, -1, 2, -1, 7, -1, 1, -3, 1, 4, -3, -2, 0, -3, 1, -3, -1, 0, -1, 3, 0, 0, -1, -2, -3, -1, -2, 4, }; int rblosum80mt[]={ 77, 25, 72, 36, 10, 108, 25, 72, 5, 93, 31, 46, 5, 51, 82, 20, 10, 20, 10, 10, 93, 41, 31, 10, 25, 20, 10, 87, 25, 36, 5, 31, 41, 31, 20, 103, 25, 10, 31, 5, 10, 36, 5, 10, 77, 36, 36, 10, 31, 46, 15, 25, 36, 15, 82, 25, 5, 25, 5, 10, 41, 5, 15, 51, 20, 72, 31, 15, 25, 10, 20, 41, 15, 20, 51, 25, 56, 87, 25, 67, 15, 51, 36, 10, 36, 46, 10, 41, 10, 20, 87, 36, 20, 10, 25, 31, 10, 15, 20, 15, 31, 15, 20, 20, 103, 31, 36, 15, 36, 56, 15, 20, 46, 15, 51, 20, 36, 41, 25, 87, 25, 31, 10, 25, 36, 15, 20, 41, 15, 56, 20, 25, 36, 25, 46, 87, 51, 41, 31, 36, 36, 20, 36, 31, 20, 36, 20, 25, 46, 31, 36, 31, 77, 41, 36, 31, 31, 31, 20, 25, 25, 31, 36, 25, 36, 41, 25, 36, 31, 51, 82, 36, 10, 31, 10, 20, 31, 10, 15, 62, 20, 46, 46, 15, 20, 20, 20, 25, 41, 77, 15, 0, 15, 0, 10, 41, 10, 20, 15, 10, 20, 25, 5, 5, 20, 15, 10, 15, 15, 124, -1, -3, -4, -3, -2, -3, -3, -2, -2, -2, -2, -2, -2, -3, -2, -2, -1, -1, -2, -5, -2, -4, -5, -5, -6, -5, 4, -6, 3, -3, -4, -2, -3, -4, -6, -3, -4, -3, -3, -3, 3, -3, 11, -2, 0, -7, 1, 6, -6, -4, 0, -6, 1, -5, -3, -1, -2, 5, 0, -1, -2, -4, -5, -1, -4, 6, }; int rpam120mt[]={ 52, 38, 57, 24, 9, 81, 38, 57, 4, 62, 38, 52, 4, 52, 62, 19, 14, 9, 4, 4, 77, 43, 38, 19, 38, 33, 14, 62, 24, 43, 19, 38, 33, 24, 19, 72, 33, 24, 24, 24, 24, 38, 19, 19, 67, 28, 38, 4, 33, 33, 4, 24, 28, 24, 62, 24, 19, 4, 14, 19, 38, 14, 24, 43, 19, 62, 28, 19, 9, 19, 24, 33, 19, 19, 43, 38, 52, 77, 33, 52, 14, 48, 43, 19, 38, 48, 28, 43, 19, 24, 57, 43, 28, 19, 24, 28, 14, 28, 33, 24, 28, 24, 24, 28, 67, 33, 38, 4, 43, 48, 9, 24, 52, 24, 38, 28, 33, 38, 38, 67, 24, 28, 19, 24, 24, 14, 19, 43, 28, 48, 19, 33, 33, 33, 43, 67, 43, 38, 38, 38, 33, 24, 43, 28, 28, 33, 19, 28, 43, 43, 28, 33, 52, 43, 38, 24, 33, 28, 19, 33, 24, 38, 33, 24, 33, 38, 33, 28, 28, 48, 57, 38, 24, 24, 24, 24, 24, 28, 24, 52, 19, 43, 43, 24, 28, 24, 24, 28, 38, 62, 4, 9, 0, 0, 0, 33, 0, 24, 9, 14, 24, 9, 19, 4, 9, 43, 28, 9, 0, 96, -1, -1, -4, -2, -1, -3, -2, -2, -1, -2, -2, -2, -1, -2, -1, -2, -1, -1, -1, -5, -2, -4, -3, -1, -5, -5, 4, -6, -1, -2, -5, -2, -4, -2, -6, -5, -5, -3, -3, -3, -2, -3, 8, -1, 2, -7, 3, 4, -6, -2, 1, -3, -1, -3, -2, 0, -1, 4, -1, -1, -2, -3, -7, -1, -5, 4, }; int rpam160mt[]={ 47, 36, 52, 26, 15, 83, 36, 52, 10, 57, 36, 47, 10, 52, 57, 20, 15, 10, 5, 10, 73, 41, 36, 20, 36, 36, 15, 57, 26, 41, 20, 36, 36, 26, 20, 68, 31, 26, 26, 20, 26, 36, 20, 20, 62, 26, 36, 10, 36, 31, 10, 26, 31, 26, 57, 26, 15, 5, 15, 20, 41, 15, 26, 47, 20, 62, 31, 20, 10, 20, 26, 36, 20, 20, 47, 36, 52, 73, 36, 47, 15, 47, 41, 20, 36, 47, 26, 41, 20, 26, 52, 41, 31, 20, 26, 31, 15, 31, 31, 26, 26, 20, 26, 31, 62, 31, 41, 10, 41, 47, 10, 26, 47, 26, 36, 26, 31, 36, 36, 62, 26, 31, 20, 26, 26, 15, 20, 41, 26, 52, 20, 31, 31, 31, 41, 68, 41, 36, 36, 36, 36, 20, 41, 31, 26, 31, 20, 26, 41, 41, 31, 31, 47, 41, 36, 26, 31, 31, 20, 31, 26, 36, 36, 26, 31, 36, 36, 31, 31, 41, 52, 36, 26, 26, 20, 26, 26, 26, 26, 52, 20, 41, 41, 26, 26, 26, 20, 31, 36, 57, 10, 10, 0, 5, 0, 31, 0, 20, 10, 15, 26, 15, 15, 10, 10, 41, 26, 10, 5, 99, 0, -1, -3, -1, -1, -3, -1, -1, -1, -1, -2, -1, 0, -1, -1, -1, 0, 0, -1, -4, -1, -3, -3, 0, -4, -4, 5, -5, 0, -2, -4, -2, -3, -2, -5, -4, -4, -3, -3, -3, -1, -3, 8, 0, 2, -5, 2, 3, -5, -1, 1, -2, 0, -3, -2, 1, -1, 3, 0, -1, -1, -2, -6, -1, -4, 3, }; int rpam250mt[]={ 42, 34, 47, 25, 17, 85, 34, 47, 12, 51, 34, 47, 12, 47, 51, 21, 17, 17, 8, 12, 72, 38, 34, 21, 38, 34, 12, 55, 30, 38, 21, 38, 38, 25, 25, 60, 30, 25, 25, 25, 25, 38, 21, 25, 55, 30, 38, 12, 34, 34, 12, 25, 34, 25, 55, 25, 21, 8, 17, 21, 42, 17, 25, 42, 21, 60, 30, 25, 12, 21, 25, 34, 21, 25, 42, 34, 51, 60, 34, 42, 17, 42, 38, 21, 34, 42, 25, 38, 21, 25, 42, 38, 30, 21, 30, 30, 12, 34, 34, 25, 30, 21, 25, 34, 60, 34, 38, 12, 42, 42, 12, 30, 47, 25, 38, 25, 30, 38, 34, 51, 25, 30, 17, 30, 30, 17, 21, 42, 25, 47, 21, 34, 34, 34, 38, 60, 38, 34, 34, 34, 34, 21, 38, 30, 30, 34, 21, 25, 38, 38, 30, 34, 42, 38, 34, 25, 34, 34, 21, 34, 30, 34, 34, 25, 30, 34, 34, 30, 30, 38, 47, 34, 25, 25, 25, 25, 30, 30, 25, 51, 25, 42, 42, 25, 30, 25, 25, 30, 34, 51, 8, 12, 0, 4, 4, 34, 4, 21, 12, 21, 25, 17, 17, 8, 12, 42, 25, 12, 8, 107, 0, -1, -3, -1, -1, -2, -1, -1, -1, -1, -1, -1, 0, -1, -1, -1, 0, 0, -1, -4, -1, -3, -3, 0, -4, -4, 7, -5, 0, -1, -4, -1, -2, -2, -5, -4, -4, -3, -3, -2, 0, -2, 10, 0, 2, -5, 3, 3, -5, 0, 2, -2, 0, -3, -2, 1, 0, 3, 0, 0, -1, -2, -6, -1, -4, 3, }; int rpam350mt[]={ 39, 36, 43, 26, 16, 92, 36, 43, 13, 46, 36, 43, 13, 46, 46, 19, 16, 16, 13, 13, 76, 39, 36, 19, 36, 36, 13, 49, 29, 36, 19, 36, 36, 26, 26, 56, 33, 26, 23, 26, 26, 39, 26, 26, 49, 29, 36, 13, 36, 33, 13, 29, 36, 26, 49, 26, 19, 9, 19, 19, 43, 19, 26, 46, 23, 59, 29, 26, 13, 23, 26, 36, 23, 26, 43, 33, 49, 53, 33, 39, 19, 39, 39, 19, 36, 39, 26, 36, 23, 26, 39, 36, 33, 23, 33, 33, 16, 33, 33, 26, 29, 23, 26, 33, 53, 33, 39, 13, 39, 43, 16, 29, 43, 26, 36, 26, 29, 36, 36, 46, 29, 33, 19, 29, 33, 16, 26, 39, 26, 46, 23, 33, 36, 33, 39, 56, 36, 36, 33, 36, 33, 19, 36, 29, 29, 33, 23, 26, 36, 36, 33, 33, 36, 36, 33, 26, 33, 33, 23, 36, 29, 33, 33, 26, 29, 36, 36, 33, 29, 36, 39, 33, 26, 26, 26, 26, 29, 29, 26, 46, 26, 43, 39, 26, 29, 26, 23, 29, 33, 49, 9, 13, 0, 6, 6, 36, 6, 23, 13, 19, 26, 16, 16, 9, 16, 46, 23, 13, 9, 122, 0, 0, -3, -1, 0, -2, -1, 0, 0, -1, -1, 0, 0, 0, 0, -1, 0, 0, 0, -5, -1, -4, -4, 1, -5, -5, 11, -6, 0, 0, -5, 0, -2, -3, -6, -5, -5, -3, -3, -2, 1, -2, 14, 0, 2, -6, 3, 3, -6, 0, 2, -2, 1, -3, -2, 2, 0, 3, 1, 0, 0, -2, -7, 0, -5, 3, }; int ralpha_mat []={ 42, 27, 27, 31, 27, 60, 28, 27, 30, 46, 27, 27, 31, 28, 42, 25, 27, 31, 28, 29, 84, 29, 27, 31, 25, 29, 30, 51, 32, 27, 31, 60, 29, 31, 23, 61, 46, 27, 28, 28, 31, 14, 29, 23, 52, 28, 27, 27, 31, 30, 26, 29, 23, 21, 49, 30, 27, 35, 31, 30, 29, 31, 23, 15, 23, 57, 28, 27, 30, 31, 29, 12, 24, 20, 18, 25, 33, 53, 40, 27, 29, 27, 46, 31, 30, 28, 28, 60, 25, 28, 36, 60, 27, 34, 35, 51, 28, 28, 23, 22, 24, 29, 13, 31, 66, 36, 27, 28, 28, 27, 29, 30, 31, 34, 32, 24, 42, 32, 29, 35, 27, 27, 36, 31, 29, 60, 32, 46, 30, 28, 28, 25, 28, 28, 27, 40, 28, 27, 24, 27, 23, 29, 27, 21, 18, 22, 23, 13, 31, 29, 31, 31, 38, 31, 27, 32, 30, 29, 29, 61, 22, 16, 29, 30, 12, 28, 30, 30, 31, 29, 36, 28, 27, 29, 24, 24, 31, 23, 15, 32, 23, 26, 9, 30, 32, 29, 35, 29, 3, 53, 31, 27, 42, 31, 31, 31, 23, 22, 15, 26, 29, 25, 35, 31, 30, 31, 29, 0, 22, 132, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 6, 0, 2, 10, 3, -2, -6, 38, -14, -7, -1, -19, 0, 5, 3, 1, 4, -29, -6, -19, 0, 97, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, }; int rbeta_mat[]={ 44, 26, 26, 29, 26, 102, 27, 26, 22, 64, 25, 26, 33, 22, 50, 14, 26, 32, 17, 31, 70, 28, 26, 31, 14, 35, 32, 68, 36, 26, 33, 102, 28, 3, 23, 69, 64, 26, 17, 26, 26, 9, 28, 21, 48, 11, 26, 26, 31, 12, 28, 39, 17, 18, 52, 22, 26, 50, 33, 27, 31, 36, 19, 21, 24, 52, 22, 26, 28, 33, 29, 19, 17, 13, 16, 27, 37, 45, 57, 26, 28, 25, 64, 33, 22, 11, 22, 102, 14, 26, 38, 102, 26, 39, 50, 68, 30, 30, 16, 0, 24, 32, 17, 31, 87, 38, 26, 26, 11, 26, 35, 28, 32, 39, 35, 10, 50, 36, 28, 50, 24, 26, 38, 29, 28, 102, 36, 64, 22, 22, 11, 14, 27, 26, 25, 57, 26, 26, 10, 26, 23, 21, 22, 16, 17, 22, 8, 19, 33, 31, 26, 33, 46, 33, 26, 35, 28, 28, 28, 69, 17, 15, 4, 35, 10, 17, 27, 27, 31, 29, 42, 17, 26, 28, 10, 17, 24, 17, 21, 36, 28, 25, 16, 28, 18, 31, 50, 28, 9, 44, 31, 26, 50, 32, 36, 21, 21, 14, 14, 24, 34, 2, 50, 31, 12, 33, 31, 13, 22, 130, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 0, 12, 17, 17, -12, -9, 28, -13, -3, 0, -12, 0, 8, 4, -11, 2, -5, -5, -5, 0, 47, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, }; int rcoil_mat[]={ 36, 27, 27, 29, 27, 124, 28, 27, 22, 51, 28, 27, 33, 18, 40, 13, 27, 29, 17, 23, 101, 27, 27, 30, 13, 23, 28, 64, 31, 27, 30, 124, 21, 15, 24, 76, 51, 27, 17, 29, 25, 14, 27, 26, 71, 18, 27, 29, 30, 8, 25, 24, 23, 20, 61, 22, 27, 39, 33, 22, 28, 28, 21, 24, 27, 70, 18, 27, 29, 30, 21, 12, 6, 18, 20, 26, 33, 73, 52, 27, 27, 28, 51, 33, 22, 18, 18, 124, 13, 29, 36, 124, 27, 34, 39, 64, 27, 25, 23, 18, 24, 27, 13, 30, 79, 36, 27, 29, 18, 29, 23, 29, 29, 34, 32, 13, 40, 31, 21, 39, 27, 27, 36, 29, 27, 124, 31, 51, 22, 18, 18, 13, 28, 29, 28, 52, 29, 27, 13, 29, 24, 19, 16, 22, 21, 18, 9, 14, 30, 30, 25, 33, 44, 33, 27, 32, 29, 27, 20, 76, 10, 19, 20, 32, 9, 17, 28, 22, 30, 29, 55, 17, 27, 21, 13, 6, 21, 23, 24, 44, 13, 21, 7, 29, 17, 23, 39, 26, 20, 60, 30, 27, 40, 29, 28, 19, 26, 16, 7, 25, 31, 9, 39, 30, 8, 30, 27, 18, 26, 143, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, -4, 8, -3, -30, -6, 49, -10, -7, -12, -18, 3, 3, -6, -11, 3, 2, 2, -5, 0, 59, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, }; int tmpam250mt[]={ 2, 0, 0, 2, 0, 6, -1, 0, 0, 12, 0, 0, 6, -1, 13, -3, 0, 1, -3, 3, 5, 1, 0, 3, -3, 1, 7, 6, 6, 0, 2, 6, 0, -1, -3, 11, 12, 0, -3, -2, -2, -5, 5, 0, 2, -1, 0, 0, 3, -1, 0, 3, -3, -3, 12, 0, 0, 11, 6, 3, 5, 3, -3, -2, -2, 3, -1, 0, 2, 2, -1, -2, -1, -3, -4, -1, 9, 3, 7, 0, 1, 0, 12, 6, 0, -1, -1, 6, -3, -2, 11, 6, 0, 8, 11, 6, 0, 2, -4, -1, -2, 3, -4, 3, 11, 11, 0, -2, -1, 0, 1, 2, 1, 8, 7, -3, 13, 6, 0, 11, -1, 0, 11, 2, 1, 6, 6, 12, 0, -1, -1, -3, -1, -2, 0, 7, -2, 0, -3, 0, -3, -3, -3, -4, -2, -3, -3, -4, 2, 2, -2, 6, 3, 6, 0, 7, 2, 5, -2, 11, -2, -5, -1, 6, -6, -3, -1, 3, 3, 1, 3, -3, 0, 0, -3, -1, 0, -3, -2, 1, -3, 4, -6, 2, 1, 3, 11, 0, -3, 2, 3, 0, 13, 1, 3, -2, 0, -4, -4, -2, 1, 1, 11, 2, -1, 2, -1, -4, -1, 12, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 1, 8, 3, -4, -3, 2, -4, -3, -1, -4, 0, 0, -1, -3, 1, 5, 0, -3, 0, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, }; int rtmpam250mt[]={ 32, 24, 24, 32, 24, 49, 20, 24, 24, 73, 24, 24, 49, 20, 77, 12, 24, 28, 12, 36, 45, 28, 24, 36, 12, 28, 53, 49, 49, 24, 32, 49, 24, 20, 12, 69, 73, 24, 12, 16, 16, 4, 45, 24, 32, 20, 24, 24, 36, 20, 24, 36, 12, 12, 73, 24, 24, 69, 49, 36, 45, 36, 12, 16, 16, 36, 20, 24, 32, 32, 20, 16, 20, 12, 8, 20, 61, 36, 53, 24, 28, 24, 73, 49, 24, 20, 20, 49, 12, 16, 69, 49, 24, 57, 69, 49, 24, 32, 8, 20, 16, 36, 8, 36, 69, 69, 24, 16, 20, 24, 28, 32, 28, 57, 53, 12, 77, 49, 24, 69, 20, 24, 69, 32, 28, 49, 49, 73, 24, 20, 20, 12, 20, 16, 24, 53, 16, 24, 12, 24, 12, 12, 12, 8, 16, 12, 12, 8, 32, 32, 16, 49, 36, 49, 24, 53, 32, 45, 16, 69, 16, 4, 20, 49, 0, 12, 20, 36, 36, 28, 36, 12, 24, 24, 12, 20, 24, 12, 16, 28, 12, 40, 0, 32, 28, 36, 69, 24, 12, 32, 36, 24, 77, 28, 36, 16, 24, 8, 8, 16, 28, 28, 69, 32, 20, 32, 20, 8, 20, 73, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 1, 8, 3, -4, -3, 2, -4, -3, -1, -4, 0, 0, -1, -3, 1, 5, 0, -3, 0, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, }; int promoter_tf1[]={ 0, 0, 0, 0, 0, 0, 0, 0, 0, 5, 0, 0, 0, 4, 6, 0, 0, 0, 5, 7, 5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 5, 5, 5, 0, 5, 0, 0, 0, -7, -3, -3, 0, -6, 6, 0, 0, 0, -7, -6, -2, 0, -7, 3, 5, 0, 0, 0, -4, -2, -2, 0, -4, 5, 5, 7, 0, 0, 0, -3, -2, -1, 0, -5, 6, 6, 7, 6, 0, 0, 0, -7, -3, 0, 0, -5, -7, -5, -2, -3, 5, 0, 0, 0, -5, -5, -2, 0, -5, -4, -7, -3, -3, 7, 4, 0, 0, 0, -5, -6, -4, 0, -9, -7, -6, -7, -6, 4, 2, 3, 0, 0, 0, -5, -3, -2, 0, -5, -5, -6, -4, -4, 4, 5, 3, 4, 0, 0, 0, -6, -3, -2, 0, -3, -6, -4, -4, -2, -7, -5, -8, -2, 6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -5, -5, -2, 0, -4, -3, -5, -2, -1, -4, -6, -6, -2, 4, 0, 6, 0, 0, 0, -4, -3, -3, 0, -2, -4, -3, -3, 0, -2, -4, -7, 0, 6, 0, 6, 6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, -4, -5, -2, 0, -4, -4, -5, -4, -4, -6, -7, -9, -6, 5, 0, 4, 5, 0, 5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, }; int blosumR[]={ 0, 0, 0, 0, 0, 0, 0, 0, 0, 6, 0, 0, 0, 1, 6, 0, 0, 0, 2, 2, 5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 1, 0, 6, 0, 0, 0, 1, -1, -1, 0, -2, 6, 0, 0, 0, -3, 1, -2, 0, -3, 1, 6, 0, 0, 0, -2, -1, 2, 0, -2, 2, 1, 6, 0, 0, 0, -1, -1, -1, 0, 1, 2, 2, 2, 6, 0, 0, 0, 1, -1, 0, 0, -2, 1, -2, -1, -1, 6, 0, 0, 0, -2, 2, -1, 0, -2, -2, 1, -2, -1, 2, 6, 0, 0, 0, -3, -3, 2, 0, -4, -3, -3, 0, -3, 1, 0, 4, 0, 0, 0, -2, -1, -2, 0, 2, -2, -2, -2, 2, 1, 2, 0, 6, 0, 0, 0, 1, -1, -1, 0, -1, 1, -2, -2, -1, 1, -2, -3, -1, 6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -2, 2, -2, 0, -2, -1, 2, -2, 0, -2, 1, -3, -1, 1, 0, 6, 0, 0, 0, -2, -2, 2, 0, -2, -2, -2, 2, -1, -1, -2, 0, -1, 2, 0, 1, 5, 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, -2, -2, 0, 2, -2, -2, -2, 2, -2, -3, -4, 1, 2, 0, 2, 1, 0, 6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,}; //matrix in alphabetic format double strikeP_mat[][26] ={ {-0.744055875823878, 0, -0.302714763884203, -8.18065408358324, -9.43250108594488, 4.0024319077819, 0, -3.44290454108591, 3.85786863942911, 0, -7.48891663653909, 2.85310469061013, 1.44275947475201, -6.88728722453311, 0, -4.60033702306021, -5.07604456146783, -4.07450237434039, -6.01162469424305, -3.79684159474661, 0, 3.68503771993837, 3.77629309202085, 0, 2.30547732746785, 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, 0, 0 }, {0.563429964483508, 0, 23.216631475072, -2.46542154563067, -6.72154030935699, 8.8817354132774, 0, 3.20305900859143, 6.45432849214352, 0, -2.50078977078133, 6.00125028548607, 6.25869831131468, 0.378437968143603, 0, 2.11768974544946, -1.70881749866372, 1.18009003408374, 0.334810553015332, 0.225137748719709, 0, 7.82014196956194, 9.577338158519, 0, 7.06811548677035, 0 }, {-8.35163406201817, 0, -2.18731267859346, -0.218002408932713, -8.83887440995716, -0.686016175955611, 0, 2.17660681512101, -3.79113118180437, 0, 1.24650083684101, -4.94895524022016, -4.55988908963644, -1.43633017659302, 0, -5.01220415079131, 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