Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1fjgb- ---CCCCC--CCCCCCCCCCCCCCHHHHHHCCCCCC-CCCCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCHHHHHHHHHHHHHCCCCEECCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEECCCCCHHHCCEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHC >P1;d1vi6a- CCCCCCCHHHHHHHCCCCCCCCCCCCCHHHEEEECCCCCEEECHHHHHHHHHHHHHHHCCCCC---CEEEEECCHHHHHHHHHHHHHHCCEEEECCCCCCCCCC-CCCC--------------------------------------------CC-CCCCEEEECCCCCCHHHHHHHHHCCCCEEEEECCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC-HHHHCCCC- PSA >P1;d1fjgb- ---33648--36a1040209563366055006547c-85020227401621640061043106692300000218402700420051080000146017100461951174163057038228765376469a415705620670454030035098305000000064066008003739030000000103055032000000233300010002001001334b7a46915057207826 >P1;d1vi6a- a2810064950480302302672285057007654b662110214400330460073028249---50000032740230041006008044116704420045-583a--------------------------------------------42-370600000006407400600474a1300000002042a4061100010363300000010002100543a490836-16501088- Translating the sequences ---CCCC*--****CCCCCCCCCCHHHHHH****CC-CC***CHHHHHHHHHHHHHHHHHHHH***CEEEE*CCHHHHHHHHHHHHH*CC*EE*CCCCCCCCCC*HHHH********************************************CC*CCCCEEEECCCCCCHHHHHHHHHCCCCEEEEECCCCCHHHCCEEEECCCCCHHHHHHHHHHHHHHHH***CCCCCCC**HHHHHHH* ***CCCCH**HHHHCCCCCCCCCC***HHHEEEECC*CCEEECHHHHHHHHHHHHHHH*****---CEEEEECCHHHHHHHHHHHHHHCCEEEECCCCCCCCCC-****--------------------------------------------CC-CCCCEEEECCCCCCHHHHHHHHHCCCCEEEEECCCCC***CCEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC-HHHH****- 52313.tem _________________________________ ---CCCCH--HHHHCCCCCCCCCCHHHHHHEEEECC-CCEEECHHHHHHHHHHHHHHHHHHHH---CEEEEECCHHHHHHHHHHHHHHCCEEEECCCCCCCCCC-HHHH--------------------------------------------CC-CCCCEEEECCCCCCHHHHHHHHHCCCCEEEEECCCCCHHHCCEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC-HHHHHHHH- Structural block scores 0 2 - 3.0 P 75.0 6.8 3 6 C 5.0 H 4.0 1.8 8 9 - 3.0 P 75.0 7.0 10 13 H 3.0 P 5.1 3.0 14 23 C 5.0 H 3.2 2.7 24 29 H 4.0 M 3.7 4.2 30 33 E 3.0 P 3.8 4.5 34 35 C 5.0 H 9.8 7.8 37 38 C 5.0 H 6.5 4.0 39 41 E 3.0 P 0.7 0.7 43 62 H 4.5 M 2.7 3.0 63 65 - 3.0 P 5.7 75.0 67 71 E 4.6 H 0.0 0.0 72 73 C 5.0 H 1.5 2.5 74 87 H 4.9 H 2.4 1.9 88 89 C 5.0 H 4.0 4.0 90 93 E 4.0 M 0.2 2.5 94 103 C 5.0 H 2.9 3.2 105 108 H 3.0 P 4.0 6.6 109 152 - 3.0 P 4.1 75.0 153 154 C 5.0 H 2.5 3.0 156 159 C 5.0 H 4.0 4.0 160 163 E 5.0 H 0.0 0.0 164 169 C 5.0 H 1.7 1.7 170 178 H 5.0 H 3.3 3.1 179 182 C 5.0 H 3.8 4.6 183 187 E 5.0 H 0.0 0.0 188 192 C 5.0 H 0.8 1.2 193 195 H 3.0 P 3.3 5.5 196 197 C 5.0 H 1.5 3.0 198 201 E 5.0 H 0.5 0.5 202 206 C 5.0 H 1.0 2.0 207 225 H 4.7 H 1.1 1.2 226 232 C 5.0 H 7.0 5.8 234 241 H 3.8 M 3.9 3.6 >>>>>>