Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1jjcb6 CC---EECCCCCCEEEECCCCCCCEEEEEEEECCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEEEEHHHCCCEEEEEECCCCCEEECCCC-CEEECCC-------------CCEEEEEEECCEEEEEEECCCEECCCCCCCCCCCCEEEEEEECCHHHHHHHHHHCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCEEECCCEEECCCC >P1;d1ni5a3 CCCCCEEECCCCCCCEE-CCCCCCEEEEEE---------------------------------------CCCCCCCCCCC---CEEEECCCCC-EECCCCCCCCEEHHHHHHHHCCCHHHCCCCCEEEEC----CEEEEECCCEECHHHCCC--CCCCEEEEEECCC----------------------------------------------------------C PSA >P1;d1jjcb6 19---23849040605051690040000010180802703a503940684a18040002000220013460002000162025000003068615050446-5515043-------------500000025bb83210000102002703038a08200000020247105600521a19252052017507552034006300400361090500771243591a >P1;d1ni5a3 424845160a7287418-037a10303059---------------------------------------94903306971---9010105078-71405a6b8017175004339136842320000008----8300000c202047040a--8a9014041759a----------------------------------------------------------d Translating the sequences CC---EE*CCCCCEEEE*CCCCCCEEEEEE***************************************CCCEEEEEHHH***EEEEEECCCC*EEECCCC-CEEE***-------------CCEEEEEE****EEEEEECCCEEC***CCC**CCCEEEEEEECCH**********************************************************C CC***EEECCCCC**EE-CCCCCCEEEEEE---------------------------------------CCC********---*EEEE*CCCC-EE*CCCC*C*EEHHH*************CC*EEEE*----*EEEEECCCEECHHHCCC--CCC*EEEEEECC*----------------------------------------------------------C 56037.tem _________________________________ CC---EEECCCCCEEEE-CCCCCCEEEEEE---------------------------------------CCCEEEEEHHH---EEEEEECCCC-EEECCCC-CEEEHHH-------------CCEEEEEE----EEEEEECCCEECHHHCCC--CCCEEEEEEECCH----------------------------------------------------------C Structural block scores 0 1 C 5.0 H 5.0 3.0 2 4 - 3.0 P 75.0 5.3 5 7 E 4.3 M 4.3 4.0 8 12 C 5.0 H 3.4 5.5 13 16 E 4.0 M 2.8 5.0 18 23 C 5.0 H 3.3 3.6 24 29 E 5.0 H 0.2 3.3 30 68 - 3.0 P 3.0 75.0 69 71 C 5.0 H 2.0 7.3 72 76 E 3.0 P 0.4 2.4 77 79 H 3.0 P 3.0 5.7 80 82 - 3.0 P 2.3 75.0 83 88 E 4.3 M 0.5 1.8 89 92 C 5.0 H 5.0 5.0 94 96 E 4.3 M 3.3 4.0 97 100 C 5.0 H 3.5 5.4 103 105 E 4.3 M 3.7 2.7 106 108 H 3.0 P 2.3 4.3 109 121 - 3.0 P 75.0 3.5 122 123 C 5.0 H 2.5 1.0 124 129 E 4.3 M 0.3 1.3 130 133 - 3.0 P 9.0 75.0 134 139 E 4.7 H 1.0 1.8 140 142 C 5.0 H 0.3 4.8 143 144 E 5.0 H 1.0 1.0 146 148 H 3.0 P 3.0 3.7 149 151 C 5.0 H 2.0 4.8 152 153 - 3.0 P 9.2 75.0 154 156 C 5.0 H 3.3 9.2 157 163 E 4.7 H 0.3 2.4 164 165 C 5.0 H 1.0 7.0 167 224 - 3.0 P 3.1 75.0 >>>>>>