--- /dev/null
+
+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, 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,
+};
+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,};
+/******************************COPYRIGHT NOTICE*******************************/
+/*© Centro de Regulacio Genomica */
+/*and */
+/*Cedric Notredame */
+/*Fri Feb 18 08:27:45 CET 2011 - Revision 596. */
+/*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*******************************/
git://source.jalview.org / jabaws.git / blobdiff