Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2wmfa2 CEECCEEEEECCEEEEECCCCCCCCCEEEEEECCCCCCCEEEEEECCCCEEEEEECCCCEEEEEECCCCCCHHHHHCCCCCCHHHCCC---HHHHHHHHHHHHCCCCCCCCCCCEEEEEEEECCCCCCCC--EEEECCCCEE-EEEEEECCCCEEEEEEEECCEEEEEE-- >P1;d4d6ga2 CCCCCEEEEECCEEEEECCCCCCCCCEEEEEEEC-C--EEEEEEECCCCEEEEEEECCEEEEEEECCCCCCHHHHC--CCCCHHHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCEEEEEEEECCC-CCCEEEEEEECCCCCCCCEEEEEC-CCEEEEEEEECCEEEEEEEC PSA >P1;d2wmfa2 2867040615c600405052ab7a74150404063a10820404010405020504895040202044045863873b6627a83496---8258635824574556925088213030304616a9510--9071599217-3829066a633020303000303040-- >P1;d4d6ga2 376804073777313050529a69650602040c-a--030302010506030332b6003040303406486267--a096a84297289579955661564547681762a303040204809-75072481714aa11680618157-85103030300060302021 Translating the sequences CEECCEEEEECCEEEEECCCCCCCCCEEEEEE*C*C***EEEEEECCCCEEEEEE*CC*EEEEEECCCCCCHHHHH**CCCCHHH**C---HHHHHHHHHHHH*CCCCCCCCCCEEEEEEEECCC*CCC*--EEEECCCCEE-EEEEEEC*CCEEEEEEEECCEEEEEE-- C**CCEEEEECCEEEEECCCCCCCCCEEEEEEEC-C--EEEEEEECCCCEEEEEEECCEEEEEEECCCCCCHHHH*--CCCCHHHHHC*****HHHHHHHHHHHCCCCCCCCCCEEEEEEEECCC-CCCE**EEEECCCC****EEEEEC-CCEEEEEEEECCEEEEEE** 310597.tem _________________________________ CEECCEEEEECCEEEEECCCCCCCCCEEEEEEEC-C--EEEEEEECCCCEEEEEEECCEEEEEEECCCCCCHHHHH--CCCCHHHHHC---HHHHHHHHHHHHHCCCCCCCCCCEEEEEEEECCC-CCCE--EEEECCCCEE-EEEEEEC-CCEEEEEEEECCEEEEEE-- Structural block scores 1 2 E 3.0 P 7.0 6.5 3 4 C 5.0 H 3.5 4.0 5 9 E 5.0 H 3.2 4.2 10 11 C 5.0 H 9.2 7.0 12 16 E 5.0 H 1.8 2.4 17 25 C 5.0 H 6.4 5.8 26 32 E 4.7 H 2.0 1.7 36 37 - 3.0 P 0.5 75.0 38 44 E 4.7 H 2.6 1.1 45 48 C 5.0 H 1.2 1.5 49 55 E 4.7 H 2.3 2.4 56 57 C 5.0 H 8.5 8.8 58 64 E 4.7 H 1.9 1.4 65 70 C 5.0 H 2.8 2.8 71 75 H 4.6 H 6.4 5.8 76 77 - 3.0 P 7.2 75.0 78 81 C 5.0 H 5.2 6.4 82 86 H 4.2 M 6.9 6.7 88 90 - 3.0 P 75.0 6.3 91 103 H 4.5 M 5.2 5.6 104 113 C 5.0 H 5.0 5.5 114 121 E 5.0 H 1.8 1.6 122 124 C 5.0 H 4.3 5.7 126 128 C 5.0 H 5.0 4.0 130 131 - 3.0 P 75.0 3.0 132 135 E 5.0 H 4.2 4.2 136 139 C 5.0 H 6.2 6.5 140 141 E 3.0 P 4.0 3.5 143 148 E 4.7 H 4.7 3.5 151 152 C 5.0 H 4.5 6.5 153 160 E 5.0 H 1.4 1.2 161 162 C 5.0 H 0.0 0.0 163 168 E 5.0 H 1.7 1.8 169 170 - 3.0 P 75.0 1.5 >>>>>>