Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1hwla2 CCCCC---CCCCCHHHHHHHHHHC-CCCHHHHHHCCCCHHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCHHHHCCCCCCCCCCCCCCCEEEEEEEEECCEEEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEECCEEEEEEEECHHHHHHCCCC---CHHHHHHHHHHHHCHHHHHCCCCCEECCCHHHHHHHHHHHCCCCHHH-HHHHCC---------EEEEEEEECCCCCEEEEEEEECCCCCCCCCHHHH-CHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC- >P1;d4i6ya1 -CCCCCCCHHHCCHHHHHHHHHHHHCCC---------------HHHHHHHHCC------------CCCCHHHHHH-HCCCCCCCCCCCEEEECCCEECCEECCEEEECCCCCHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEEECHHHHCCCCCCHHHHHHHHHHHHHH-HHHCHHHHHHH---HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCEEEEECC--CCCEEEEEEEE-CCCCCCCCCCCCCHHHHHHHHHHCCC---------CHHHHHHHHHHHHHHHHHHHHHHHHHCC PSA >P1;d1hwla2 8564b---60a2546012420746-92435501950674230010014132873b7575179231592605401b62686030465363540040202b66050000276b9028405300700240a10507157412030504031710562061---70940173046403561577a3a563101063003000400107495-3a5014---------040507334877620301030540506066b306-166226106309022729a676321310020000000000003005403a- >P1;d4i6ya1 -250608718847894317400821907---------------9932331578------------a114593079-27ab0a649837140011011579010000127388038302500610161a00606049523030603011a2063b63608500550282276-04834a10660---062002002000300305565038603720468a52300040644c--85203040402-030317ad306422204001500809---------7214001000000000000502661084 Translating the sequences *CCCC---***CCHHHHHHHHHH*-CCC***************HHHHHHHHCC************CCCCHHHH****CCCCCCCCCCCEEEEEEEEECCEEEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEECCEEEEEEEECHHHHHHCCCC---*HHHHHHHHHH*H*HHHHH**********HHHHHHHHHHHCCCCHHH-HHHH**---------EEEEEEEEC**CCEEEEEEEE**CCCCCCCHHHH-CHHHHHHHHH*CCC*********HHHHHHHHHHHHHHHHHHHHHHHHHHC- -CCCC***HHHCCHHHHHHHHHHH*CCC---------------HHHHHHHHCC------------CCCCHHHHHH-HCCCCCCCCCCCEEEE***EECCEE**EEEECCCCCHHHHHHHHHHHHH*CCCCEEEE**CCEEEEEEEECHHHH**CCCC***HHHHHHHHHHH-HHH*HHHHHHH---HHHHHHHHHHHHHHCCCCHHH*HHHHHH***********EEEEE*C--CC*EEEEEEEE-CCCCCCC*****CHHHHHHHHHHCCC---------*HHHHHHHHHHHHHHHHHHHHHHHHHC* 56542.tem _________________________________ -CCCC---HHHCCHHHHHHHHHHH-CCC---------------HHHHHHHHCC------------CCCCHHHHHH-HCCCCCCCCCCCEEEEEEEEECCEEEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEECCEEEEEEEECHHHHHHCCCC---HHHHHHHHHHH-HHHHHHHHHHH---HHHHHHHHHHHHHHCCCCHHH-HHHHHH---------EEEEEEEEC--CCEEEEEEEEE-CCCCCCCHHHH-CHHHHHHHHHHCCC---------HHHHHHHHHHHHHHHHHHHHHHHHHHC- Structural block scores 1 4 C 5.0 H 6.6 3.2 5 7 - 3.0 P 75.0 5.0 8 10 H 3.0 P 5.5 5.7 11 12 C 5.0 H 3.5 5.5 13 23 H 4.8 H 3.3 4.2 25 27 C 5.0 H 5.0 5.3 28 42 - 3.0 P 3.3 75.0 43 50 H 5.0 H 1.5 4.4 51 52 C 5.0 H 7.5 7.5 53 64 - 3.0 P 5.1 75.0 65 68 C 5.0 H 5.5 4.1 69 74 H 4.3 M 3.6 5.5 77 87 C 5.0 H 4.3 7.0 88 96 E 4.3 M 2.0 1.0 97 98 C 5.0 H 6.8 6.0 99 106 E 4.5 M 2.1 1.4 107 111 C 5.0 H 7.1 5.6 112 125 H 4.9 H 2.5 2.5 126 129 C 5.0 H 2.9 2.9 130 135 E 4.3 M 4.2 4.2 136 137 C 5.0 H 2.5 3.5 138 145 E 5.0 H 1.8 1.9 147 152 H 4.3 M 3.3 3.8 153 156 C 5.0 H 2.2 6.6 157 159 - 3.0 P 75.0 4.3 160 170 H 4.8 H 3.7 3.4 172 182 H 3.9 M 5.3 3.9 183 185 - 3.0 P 4.7 75.0 186 199 H 4.6 H 1.3 1.1 200 203 C 5.0 H 2.0 2.0 204 206 H 5.0 H 6.0 5.3 208 213 H 4.3 M 3.9 4.5 214 222 - 3.0 P 75.0 4.5 223 230 E 4.2 M 2.8 2.2 232 233 - 3.0 P 7.5 75.0 234 235 C 5.0 H 6.5 6.5 236 244 E 4.6 H 1.6 1.7 246 252 C 5.0 H 3.3 3.5 253 256 H 3.0 P 5.1 5.6 259 268 H 4.8 H 3.2 1.4 269 271 C 5.0 H 3.7 5.7 272 280 - 3.0 P 5.8 75.0 281 306 H 4.9 H 0.9 1.3 >>>>>>