Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1fgha2 -----CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCC--------------CCCCCCCC-CEEEECCCEEEEEHHHHHHHHHHHHHHC---------CC--CCCC-CEEEECCCCCCCCCCH-----HHHHHHHHHHCHHHHHHHHHHHHHH-CCEEECCCCCCHHHHHHHHCCCCC---------CEEEECCCCHHHHHHHCCEEEECCHHHHHHHHCCCCEEEECCEEEEEEEECCCCCCCCHHHHHHHHHHHHCCC------------CCCCEEEEEECHHHHHCCHHHHHHHHHHHHHHCCCEEECCCC-HHHHHHHHHCCC------------HHHHHHHHHCHH--HCCCCC-----CCCCCEEEEEECCCC-CCEEECCCCCCCEEEHHHHHHHHHHH-------------------------------CCCCCEEEEEECCCCCCC-HHHHHHHHHHHHHHHHCCCCCC--CEEEECCCCHHHHHHHHHCCHHHHHHHCCEEECCCCCHHHHCCCCCC---CCCC----CCCEEEEECCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHCCCCCCCCCCC-EECCCCCEECCC--CCC---CCCCCCCCCCCCCCCEECCCCCCCCCC------------------ >P1;d1l5ja3 ------------------------------CCCCCCCCCCCHHHHHHHHCCC-----------------CCCCCCC--CEECCCCCEEEECCCCHHHHHHHHHHCCCC-----------CCCCCCEEECCCCCCCCCC---------------HHHHHHHHHHHHHHHCC-CCEECCCCCCCHHHHHHHH-CCCC---------CEEEECCCCCCCC---CCEECCCCHHHHHHHHHHCCCCEECCCEEEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEEC--CCCCCHHHHHHHHHHHHCCCCCEEEECCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEHHHCCCCEEECCCCCCCEEEHHHCCCC---------------------------------------CCCEEEECCCCC--CHHHHHHHHHHHHHCC---CCCC--CEEEECCCCHHHHHHHHHCCHHHHHHHHCCEECCCCCHHHCCCCCCCC-----------CCCEEEECCCCCCCCCCCC--CCEEEECCHHHHHHHHHHC------------------------CCCCHHHHHHHHHHHHCCHHHHCCCCCHHHCHHHHHHHH-------CCCCC- >P1;d2b3ya2 CCCCHHHEEECCCCCCCCEEE--CHHHHCCCCHHH----CCHHHHHHHHHHHHCCCCCCCCHHHHHHHHCHHHHCCCCCEEEECCCEEEEEHHHHHHHHHHHHHHHHHHHHCCCCHHHCCCCC-CEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHCCCCCEEEECCEEEECEEEECCHHHHHHHHHCCEEEECCHHHHHHHHCCCCEEEECCCEEEEEEECCCCCCCCHHHHHHHHHHHHHHH------------CCCCCEEEEECHHHCCCCHHHHHHHHHCHHHHCCCEEECCCC-HHHHHHHHHCCCC-----------HHHHHHHHHHHHHHCCCCCCCCHHHCCCCCEEEEEEHHHC-CCEEECCCCCCCEEEHHHHHHHHHHHHHCCCCCCCCCCCHHHCCCEEEEEECCEEEEEECCCEEEEEECCHHHHCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCHHHHHHHHHCCCHHHHHHCCCCCCCCCCHHHHCCCCCCCHHHHHHHHHHCCCCEEEECCCCCCCCCCCCCCC-EEEECCHHHHHHHHHHCCCCCCCCCCCCEEECCCEEECHHHHCCCHHHHHHHHHH----------HCCHHHHHHHHCCCCCCCHHHHHCCCCC PSA >P1;d1fgha2 -----53712006216633050350460043027319340000000000103415--------------80806136-2604040300000034037005404949---------48--4042-1000000120303505-----750263049527a307302300231-000003000000000000200000---------00000025000000000000001b1740130015630514004000030266177000100000300140548------------407900000227005200011000000000007020000101-610450041090------------660070056049--10312b-----c08125415040480-40100003401510305601830674-------------------------------911260300000010000-0110010000041027352606--05000000002031003427106303506051010011013240307---4086----635000000001056220060540000000000000000003050203745-150868851307--309---1410087804616a0144033972b4a------------------ >P1;d1l5ja3 ------------------------------8b3a96753100002000611a-----------------6a01125--251506000000003302602540684909-----------6050300000000001527---------------88258018401710381-5000043400000200000-0200---------1000001400000---0000002c063004001513031801500003058932810200000000011036483035879c27120592000024--138130220000001000060400003055600341050011002000229003380015006505911882812714b60612230506056073000002310120430551565---------------------------------------805000000100--0001000002005548---b805--040000000300261068281372078050410511110120412307-----------8601000000105572007--a050000000000000012------------------------5003194048107406863a5034101037287037509-------a0937- >P1;d2b3ya2 b22177013303895683300--1055183a2085----00000000000001204583066710420030560056a280102000000005402500640364177378997636800061-30000000003015127950374035301741593033012015206503000011000000000200300016a3401000000024000000000000000a2950040014600716003000030368164201000000000320372------------707920000015002305001000000001001030000000-6301710630016-----------8861810340054050106074793205016325120760-5300000130211021960273038002497863006147852a46450538a66240400100000000000000130000001004301619070440000000000400130055090062036000200010100131102602820350075390000000000304868007204-0000000000000000030104087420663a8b640317601044751451276----------306480066207604872960470a07b Translating the sequences -----*****CCCCCCCC******HHHH****HHH*CCCCCHHHHHHH*CCC*CC--------------CCCCCCCC-CEEEECCCEEEEEHHHHHHHHHHHHHHC---------**--CCCC-CEEEECCCCCCCCCC*-----HHHHHHHHHH*HHHHHHHHHHHHH*-CCEEECCCCCCHHHHHHHHCCCCC---------CEEEECCCCHHHHHHHCCEEEECCHHHHHHHHCCCCEEEECC*EEEEEEECCCCCCCCHHHHHHHHHHHH**C------------CCCC*EEEEECHHH**CCHHHHHHHHHHHHHHCCCEEECCCC-HHHHHHHHHCCC------------HHHHHHHHH*HH--HCCCCC-----CCCCCEEEEEE***C-CCEEECCCCCCCEEEHHHHHHHHHHH-------------------------------**CCCEEEEEECCCCC*C-HHHHHHHHHHHHHHHHCCCCCC--CEEEECCCCHHHHHHHHHCCHHHHHHHCC*EECCCCCHHHHCCCCCC---****----CCC*EEEECCCCCCCCCCCCCCC*EEEECCHHHHHHHHHHCCCCCCCCCCC-EE*CCC*EEC**--CCC---*********CC******CCC***C***------------------ ------------------------------CC****CCCCCHHHHHHHHCCC-----------------CCCCCCC--CEE**CCCEEEE****HHHHHHHHHH*C**-----------CCCC*CEEE*CCCCCCCCC---------------HHHHHHHHHHHHHHH*C-CCEE*CCCCCCHHHHHHHH-CCCC---------CEEEECCCC****---CCEE**CCHHHHHHHH**CC**EECCCEEEEEEECCCCCCCCHHHHHHHHHHHHHHC************CCCCCEEEEEC--*CCCCHHHHHHHHHHHH**CCCEEE*CCC*HHHHHHHHH***************HHHHHHHHHHHHHHH*CCCCCC***CCCCCEEEEEEHHHC*CCEEECCCCCCCEEEHHH****---------------------------------------C**EEEECCCCC--CHHHHHHHHHHHHH**---CCCC--CEEEECCCCHHHHHHHHHCCHHHHHHH*CCEECCCCCHHH*CCCCCCC-----------CCCEEEECCCCCCCCCCCC--C*EEEECCHHHHHHHHHHC------------------------*CCCHHHHHHHHHH**CC******CCCHHHCHHHH****-------*CCCC- **********CCCCCCCC***--*HHHH**CCHHH----CCHHHHHHHH****CC**************C****CCC*CEEEECCCEEEEEHHHHHHHHHHHHHH**************CCCC-CEEEECCCCCCCCCC******HHHHHHHHHHHHHHHHHHHHHHHHC*C*EEECCCCCCHHHHHHH*CCCC**********CEEEECC**HHHHHHHCCEEEECCHHHHHHHHCCCCEEEECCCEEEEEEECCCCCCCCHHHHHHHHHHHHHH*------------CCCCCEEEEECHHHCCCCHHHHHHHHH*HHHHCCCEEECCCC-HHHHHHHHHCCC*-----------HHHHHHHHHHHHHH*CCCCCCC***CCCCCEEEEEEHHHC-CCEEECCCCCCCEEEHHHHHHHHHHH*********************************CCCEEEEEECC****CCHHHHHHHHHHHHHHHHCCCCCC**CEEEECCCCHHHHHHHHHCC*HHHHHHCCC**CCCCCHHHHCCCCCCC**********CCCCEEEECCCCCCCCCCCCCCC-EEEECCHHHHHHHHHHCCCCCCCCCCC*EE*CCC*EEC****CCCHHHHHHHHHH----------*CCHHH*HHHH************CCCC* 53732.tem _________________________________ -----*****CCCCCCCC***--*HHHH**CCHHH*CCCCCHHHHHHHHCCC*CC--------------CCCCCCCC-CEEEECCCEEEEEHHHHHHHHHHHHHHC**-------**--CCCC-CEEEECCCCCCCCCC*-----HHHHHHHHHHHHHHHHHHHHHHHHC-CCEEECCCCCCHHHHHHHHCCCCC---------CEEEECCCCHHHHHHHCCEEEECCHHHHHHHHCCCCEEEECCCEEEEEEECCCCCCCCHHHHHHHHHHHHHHC------------CCCCCEEEEECHHHCCCCHHHHHHHHHHHHHHCCCEEECCCC-HHHHHHHHHCCC*-----------HHHHHHHHHHHHHHHCCCCCCC***CCCCCEEEEEEHHHC-CCEEECCCCCCCEEEHHHHHHHHHHH-------------------------------**CCCEEEEEECCCCC*CCHHHHHHHHHHHHHHHHCCCCCC--CEEEECCCCHHHHHHHHHCCHHHHHHHCCCEECCCCCHHHHCCCCCCC--****----CCCCEEEECCCCCCCCCCCCCCC*EEEECCHHHHHHHHHHCCCCCCCCCCC-EE*CCC*EEC**-*CCCHHHHHHHHHH**CC******CCCHHHCHHHH****-------*CCCC- Structural block scores 0 4 - 4.0 M 75.0 75.0 4.7 5 9 * 2.7 P 3.6 75.0 2.8 10 17 C 4.0 M 3.0 75.0 5.2 18 20 * 2.7 P 2.7 75.0 1.0 21 22 - 4.0 M 1.5 75.0 75.0 24 27 H 4.0 M 2.5 75.0 2.8 28 29 * 2.7 P 2.0 75.0 5.5 30 31 C 4.0 M 1.5 9.8 6.2 32 34 H 4.0 M 4.0 7.5 4.3 36 40 C 4.4 M 3.2 3.2 45.0 41 48 H 4.9 H 0.0 1.0 0.0 49 51 C 4.0 M 1.3 4.2 0.0 53 54 C 4.0 M 3.0 75.0 1.0 55 68 - 4.0 M 75.0 75.0 3.3 69 76 C 4.4 M 4.0 12.6 3.1 79 82 E 4.5 M 2.5 2.8 2.2 83 85 C 5.0 H 2.3 2.0 0.7 86 90 E 4.8 H 0.0 0.0 0.0 91 104 H 4.7 H 3.1 3.1 2.8 106 107 * 2.7 P 75.0 4.5 7.0 108 114 - 4.0 M 75.0 75.0 7.0 115 116 * 2.7 P 6.0 75.0 4.5 117 118 - 4.0 M 75.0 75.0 4.0 119 122 C 5.0 H 2.5 2.8 1.8 125 128 E 4.8 H 0.0 0.0 0.0 129 138 C 4.9 H 1.4 9.0 1.0 140 144 - 4.0 M 75.0 75.0 4.8 145 168 H 4.6 H 3.5 27.7 2.9 171 172 C 4.5 M 0.0 2.5 2.5 173 175 E 4.7 H 0.0 0.0 1.0 176 181 C 5.0 H 0.5 1.8 0.3 182 189 H 4.9 H 0.2 0.2 0.2 190 194 C 4.6 H 0.0 15.4 0.6 195 203 - 4.0 M 75.0 75.0 2.8 205 208 E 5.0 H 0.0 0.0 0.0 209 212 C 4.5 M 1.8 1.2 1.5 213 219 H 4.0 M 0.0 32.1 0.0 220 221 C 5.0 H 0.0 0.0 0.0 222 225 E 4.5 M 0.0 0.0 0.0 226 227 C 5.0 H 6.2 7.2 5.2 228 235 H 5.0 H 2.0 1.6 2.5 236 239 C 4.5 M 3.8 2.5 2.8 240 243 E 4.5 M 2.5 3.0 3.5 244 246 C 4.7 H 1.3 2.0 1.0 247 253 E 5.0 H 0.7 1.1 0.9 254 261 C 5.0 H 3.4 4.1 3.5 262 275 H 4.9 H 1.3 0.8 1.1 277 288 - 4.0 M 75.0 5.5 75.0 289 293 C 4.8 H 4.0 3.6 5.0 294 298 E 5.0 H 0.4 0.4 0.0 300 302 H 4.0 M 2.3 50.3 1.7 303 306 C 4.5 M 1.8 3.8 2.5 307 320 H 4.8 H 0.1 0.4 0.1 321 323 C 5.0 H 3.0 3.3 1.3 324 326 E 5.0 H 0.0 0.0 0.0 327 330 C 4.8 H 0.5 2.0 0.0 332 340 H 5.0 H 2.3 2.1 3.0 341 343 C 4.0 M 3.0 0.7 0.3 345 355 - 4.0 M 75.0 1.6 75.0 356 370 H 4.7 H 12.9 2.9 3.5 371 377 C 4.6 H 23.9 5.1 2.6 378 380 * 2.7 P 75.0 5.5 6.3 381 385 C 5.0 H 4.7 3.0 1.6 386 391 E 5.0 H 3.2 2.7 3.2 392 394 H 4.0 M 4.0 3.7 4.3 397 398 C 5.0 H 2.0 1.5 4.0 399 401 E 5.0 H 0.3 0.0 0.0 402 408 C 5.0 H 1.9 1.3 1.0 409 411 E 5.0 H 1.3 2.3 1.0 412 422 H 4.3 M 3.6 29.7 3.5 423 453 - 4.0 M 75.0 75.0 4.7 454 455 * 2.7 P 5.0 75.0 2.0 456 458 C 4.3 M 3.0 52.7 0.3 459 464 E 4.7 H 0.5 0.8 0.0 465 469 C 4.4 M 0.2 0.2 0.0 471 472 C 4.0 M 37.5 37.5 0.0 473 488 H 4.8 H 1.1 6.2 1.2 489 494 C 4.7 H 3.7 29.1 3.5 495 496 - 4.0 M 75.0 75.0 2.0 498 501 E 5.0 H 1.2 1.0 0.0 502 505 C 5.0 H 0.0 0.0 0.0 506 514 H 5.0 H 1.4 2.9 2.0 515 516 C 5.0 H 4.5 5.0 4.5 517 523 H 4.9 H 2.6 4.0 2.4 524 526 C 4.3 M 2.0 1.7 0.0 527 528 E 4.0 M 3.0 2.5 1.0 529 533 C 5.0 H 0.4 1.6 0.4 534 537 H 4.8 H 1.2 1.0 1.0 538 544 C 4.9 H 13.0 2.4 1.7 545 546 - 4.0 M 75.0 75.0 5.0 547 550 * 2.7 P 4.5 75.0 2.0 551 554 - 4.0 M 75.0 75.0 3.8 555 558 C 4.5 M 3.5 22.2 2.2 559 562 E 5.0 H 0.0 0.2 0.0 563 577 C 4.9 H 2.1 12.5 2.8 579 582 E 5.0 H 0.0 1.2 0.0 583 584 C 5.0 H 0.0 0.0 0.0 585 594 H 5.0 H 0.0 0.1 0.0 595 605 C 4.1 M 2.6 68.4 2.6 607 608 E 4.0 M 3.0 75.0 6.0 610 612 C 4.0 M 7.3 75.0 10.0 614 615 E 4.0 M 3.0 75.0 2.0 617 618 * 2.7 P 3.5 75.0 4.0 621 623 C 5.0 H 4.0 1.0 1.7 624 633 H 4.0 M 24.6 3.8 4.2 634 635 * 2.7 P 4.0 3.0 75.0 636 637 C 4.0 M 5.0 7.0 75.0 638 643 * 2.7 P 3.8 4.2 75.0 644 646 C 4.7 H 2.3 0.7 3.0 647 649 H 4.0 M 6.3 3.3 4.0 651 654 H 4.0 M 25.2 4.5 3.5 655 658 * 2.7 P 75.0 5.2 4.2 659 665 - 4.0 M 75.0 75.0 5.1 667 670 C 4.0 M 75.0 4.8 4.4 >>>>>>