Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d5b5eb- ------------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH--CCCCHHHCCCCCCCCC-----CHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECC-CCCCCCEEECC-CCCCC-HHHHCC---------------CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHHHHCCHHHHHHHHHHHHHHHC-------------------------------------------------CCCHHHHHHCCCHHHHHHC--CHHHCCCCCCCCCCCCHHHCCCEEEEEEEEEEEECCCCEEEECCCCCCCCCCCCEEECCCCCEEEECCCCCCCCCCCHHHHCCEEEEECCCCCCCEECCHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCH--HHCCCCCC---CCCCCCCCCCCC >P1;d5b5ec- CCCCCCCCHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC----CCHHHCCCCCHHHHHHCCCCCCHHHCCC--------CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC--CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH-HHHH--CCCEEECCCCC--CCEEECCCCCCCCHHHHHHHHCCCCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHHHH--HHHHHHHHHHHHHC--CCCCCCCCCCCCCCCCEEECCCCCEEECCHHHHHCCCCCCCCHHHEECCEECHHHHHHCCCHHHHHHHHHHHCCCC-CCCC-------------CCCCCCC---------------------------------------------------------------------------------CCC----------CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHCHHHHCCCCC--- PSA >P1;d5b5eb- ------------e439536947148200324047247507613530620570075052832400000003031003102402200484200336ab2919560020105344652971574055256--6453a80348877142-----5014360563367059334301520107944000314-72018041551-92356-960956---------------623002006215405822740564375516886476642712115518613762872465064026101301100000024204733037106630762388-------------------------------------------------9283470057034100000--00000020056928730030101042020200040974305061030957916030207877420221b97aa28410553a03010103413355267363015105510200004134964a04761010001312542446077557525523620477--943a99a8---baab58ba38a5 >P1;d5b5ec- 896655616632a219733b3223a2001140463465087265304302601860649----4300317021005001304002770806--------63720553047437508836960752378043304872a--67017275272112350472387066137213-1017--8900000218c--90423508902645940451593569a45623131740211004323606522860553273516271475521-20102504712560763324161035000210010000020003--00620240062277--9390183818845251016088542000b9046334060200240129a103494047505740473053027120-6059-------------921066b---------------------------------------------------------------------------------a49----------9778000002411764666057445537833a3072245871896799736879698ac--- Translating the sequences ------------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC****CCHHHCCCCCHHHHHHCCCCCC***CCC********CC**HHHHHHHHHHHHHHHHHHHHHHHH--CCCCHHHCC**CCCCC-----*HHHHHHHHHHHHHHHHHHHHH*******CCCEEECC-CC**CCEEECC-CCCCC-HHHH**---------------CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCC*CHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHHHH**HHHHHHHHHHHHHH**-------------------------------------------------**CHHHHHHCCCHHHHHH*--*HHHCC*CCCC*************EEEEEEE*********************************************************************************CCE**********CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH*H--HHCCCCC*---****CCCCC*** ************CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC----CCHHHCCCCCHHHHHHCCCCCCHHHCCC--------CCHHHHHHHHHHHHHHHHHHHHHHHHHH**CCCC***CC--CCCCC*****HHHHHHHHHHHHHHHHHHHHHH-HHHH--CCCEEECC*CC--CCEEECC*CCCCC*HHHHHH***************CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHHHH--HHHHHHHHHHHHH*--*************************************************EECHHHHHHCCCHHHHHHH**HH**CC-CCCC-------------*******---------------------------------------------------------------------------------CC*----------CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH****CCCCCH***HHHHCCCCC--- 161077.tem _________________________________ ------------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC----CCHHHCCCCCHHHHHHCCCCCCHHHCCC--------CCHHHHHHHHHHHHHHHHHHHHHHHHHH--CCCCHHHCC--CCCCC-----HHHHHHHHHHHHHHHHHHHHHH-HHHH--CCCEEECC-CC--CCEEECC-CCCCC-HHHHHH---------------CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHHHH--HHHHHHHHHHHHHH---------------------------------------------------EECHHHHHHCCCHHHHHHH--HHHHCC-CCCC-------------EEEEEEE---------------------------------------------------------------------------------CCE----------CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHCCCCCH---HHHHCCCCC--- Structural block scores 0 11 - 3.0 P 75.0 5.2 12 14 C 5.0 H 7.2 4.5 15 22 H 5.0 H 5.5 5.1 23 25 C 5.0 H 4.7 5.2 26 54 H 5.0 H 3.3 3.3 55 58 C 5.0 H 3.8 4.8 59 62 - 3.0 P 2.2 75.0 63 64 C 5.0 H 0.0 3.5 65 67 H 5.0 H 0.0 1.0 68 72 C 5.0 H 1.4 2.2 73 78 H 5.0 H 1.0 1.0 79 84 C 5.0 H 1.3 1.5 85 87 H 3.0 P 5.3 4.7 88 90 C 5.0 H 0.7 4.7 91 98 - 3.0 P 5.8 75.0 99 100 C 5.0 H 7.0 4.5 101 126 H 4.8 H 3.6 4.5 127 128 - 3.0 P 75.0 4.0 129 132 C 5.0 H 4.5 2.5 133 135 H 3.0 P 6.2 6.3 136 137 C 5.0 H 3.5 6.2 138 139 - 3.0 P 8.0 75.0 140 144 C 5.0 H 4.2 4.2 145 149 - 3.0 P 75.0 4.6 150 171 H 4.9 H 3.5 3.4 173 176 H 3.0 P 0.8 2.2 177 178 - 3.0 P 8.0 75.0 179 181 C 5.0 H 2.7 5.7 182 184 E 5.0 H 1.0 0.0 185 186 C 5.0 H 2.5 1.0 188 189 C 5.0 H 4.5 10.2 190 191 - 3.0 P 0.5 75.0 192 193 C 5.0 H 4.0 4.5 194 196 E 5.0 H 3.3 3.0 197 198 C 5.0 H 3.0 2.5 200 204 C 5.0 H 5.0 4.2 206 211 H 4.3 M 5.8 3.8 212 226 - 3.0 P 75.0 4.8 227 228 C 5.0 H 4.0 5.5 229 252 H 5.0 H 3.2 3.0 253 256 C 5.0 H 4.2 3.8 257 262 H 5.0 H 6.5 4.3 263 265 C 5.0 H 4.0 2.7 268 292 H 5.0 H 3.9 3.0 293 298 C 5.0 H 1.0 0.5 299 302 H 5.0 H 0.2 0.2 303 305 C 5.0 H 0.0 0.0 306 310 H 5.0 H 2.4 1.0 311 312 - 3.0 P 5.0 75.0 313 326 H 4.9 H 3.4 2.7 327 377 - 3.0 P 72.4 6.6 378 379 E 3.0 P 5.5 0.5 381 386 H 5.0 H 3.2 4.7 387 389 C 5.0 H 3.3 3.3 390 396 H 4.7 H 0.7 3.6 397 398 - 3.0 P 75.0 4.0 399 402 H 3.5 M 0.0 2.5 403 404 C 5.0 H 0.0 1.0 406 409 C 5.0 H 2.8 5.0 410 422 - 3.0 P 2.6 75.0 423 429 E 3.0 P 1.4 5.1 430 510 - 3.0 P 3.5 75.0 511 512 C 5.0 H 0.0 7.2 514 523 - 3.0 P 4.2 75.0 524 530 C 5.0 H 2.7 4.4 531 560 H 4.9 H 3.7 4.0 561 562 - 3.0 P 75.0 4.5 563 564 H 3.0 P 6.5 7.5 565 569 C 5.0 H 8.4 6.2 571 573 - 3.0 P 75.0 6.3 574 577 H 3.0 P 11.0 7.5 578 582 C 5.0 H 7.6 9.2 583 585 - 3.0 P 7.8 75.0 >>>>>>