Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d3iam6- CCCCHHHHHHHHHHHHHHHHCCCCCCEECC---CHHHHHCCC----CCC---------------------------------CCCCEEEECCCCC------------CCHHHHHHHHHCCCCCCCEEEEHHHHHCCCCCC---CCCCCCCHHH----CCCCCEEECCCCCCHHHHHHHHHHHHHHHCCCCCCC---------------------------------------------------------------------CCCCC--CCCCC----------- >P1;d4u9hs- -----------------CCCCCEEEEEECCCCCHHHHHHHCCCCCCHHHHHHCCCEEEECCCCCCCCHHHHHHHHHHHHCCCCCEEEEEECCEECHHHHCCCEECCEEHHHHHHHHHHHC---CEEEEECHHHHHCCHHHCCCCCCCEECHHHHHHHHCCCCEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHCCCCHHHCCCHHHHHCCCCCCCCCCHHHHCCCCCHHHCCCHHHCCCCHHHHCCCCCCCCHHHCCCCCCCCCCCHHHHCCCCCCC PSA >P1;d3iam6- a67799436646763794077174451114---603830850----889---------------------------------8210000003056------------a4154046515802a310000004102601849---5961143046----20300140876308174057045402400226254b---------------------------------------------------------------------89663--64338----------- >P1;d4u9hs- -----------------a9633000000031835104112403636264028720203003331b49ca7147317a10628510000000000145c0542334b42135002500250---720000001000006212884635040025007638080000002400150015006312747720812a43003400563024105137337563204349273176421046101001702000062327576040355401302012802250461684 Translating the sequences *****************HHHCC****EECC---*HHHHH*CC----***---------------------------------CC**EEEECC**C------------**HHHHHHHHH*C***C*EEEEHHHHH*CC***---CCCC**CHHH----*CCCCEEECCCCCCHHHHHHHHHHHHHHHCCCCCCC---------------------------------------------------------------------*CCCC--CCCCC----------- -----------------***CCEEEEEECC***HHHHHHHCC****HHH*********************************CCEEEEEECCEEC************EHHHHHHHHHHHC---CEEEEE*HHHHHCCHHH***CCCCEECHHH****HCCCCEEECCCCCCHHHHHHHHHHHHHH*CCCCCCC*********************************************************************HCCCC**CCCCC*********** 56770.tem _________________________________ -----------------HHHCCEEEEEECC---HHHHHHHCC----HHH---------------------------------CCEEEEEECCEEC------------EHHHHHHHHHHHC---CEEEEEHHHHHHCCHHH---CCCCEECHHH----HCCCCEEECCCCCCHHHHHHHHHHHHHHHCCCCCCC---------------------------------------------------------------------HCCCC--CCCCC----------- Structural block scores 0 16 - 3.0 P 6.4 75.0 17 19 H 3.0 P 3.7 8.5 20 21 C 5.0 H 4.0 3.0 22 27 E 3.7 M 3.7 0.0 28 29 C 5.0 H 2.5 1.5 30 32 - 3.0 P 75.0 4.0 33 39 H 4.4 M 4.0 2.0 40 41 C 5.0 H 2.5 2.0 42 45 - 3.0 P 75.0 4.5 46 48 H 3.0 P 8.3 4.0 49 81 - 3.0 P 75.0 4.2 82 83 C 5.0 H 5.0 3.0 84 89 E 4.3 M 0.2 0.0 90 91 C 5.0 H 1.5 0.0 92 93 E 3.0 P 2.5 0.0 95 106 - 3.0 P 75.0 4.8 108 118 H 4.6 H 3.9 2.1 120 122 - 3.0 P 5.2 75.0 124 128 E 4.6 H 0.0 0.4 129 134 H 4.3 M 2.2 0.2 135 136 C 5.0 H 0.5 0.0 137 139 H 3.0 P 7.0 3.0 140 142 - 3.0 P 75.0 6.0 143 146 C 5.0 H 5.2 4.5 147 148 E 3.0 P 2.5 2.0 150 152 H 5.0 H 3.3 2.3 153 156 - 3.0 P 75.0 3.2 158 161 C 5.0 H 0.8 4.0 162 164 E 5.0 H 1.7 0.0 165 170 C 5.0 H 5.3 1.0 171 185 H 4.9 H 2.9 2.8 186 192 C 5.0 H 4.6 4.4 193 261 - 3.0 P 75.0 2.9 263 266 C 5.0 H 6.0 2.5 267 268 - 3.0 P 75.0 1.5 269 273 C 5.0 H 4.8 2.6 274 284 - 3.0 P 75.0 3.5 >>>>>>