Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1bjta- CCCCCCCCCCCCCCCCCCCHHHHHCEEEEEECHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHCCCCCCCCCCEEECCCCCEEEEECCCCCEEEEECCHHHHHHHHHHCCCCCCEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCC---CCEEHHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCEEEECCCHHHHCCHHHHHHCCEEEE-CCEEEEECCCCCCCCHHHHCCEEEECCCCEEEECCCCHHHHHHHHHHHHC--CC-------CC--CCCCCCCCCCCCEEEEEE----------CCEEEEECEEEEEE----CCEEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCEEEECCCC--CCCEEEECCHHHHHHHHHHCHHHHCCCEEEEECCCEEEECCCCCEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC------CCC-HHHHHHHHHHCC--CCEECC----CCCEECCCCCCCCCCCHHHHCCCHHHHCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC----- >P1;d3ilwa- ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCEEHHHHHHHHHHHCCCC-CCCHHHHHHHHHHCC--CCCCCCCEEEECCCCCCCC--CCCCCCCCCEEEECHHHHHHHCCHHHCCCCEEECCCCCCEEECCCCCCCCHHHHHCEECCCCCCCCEECCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCC-CEEECC-HHHHHHHHHCEEEEEEECEEEEEECCCCCEEEEEEECCCCCCHHHHHHHHHHHHH--CCCCCCEEEEEECCCCCCCCCEEEEECCCCCHHHHHHHHHHHCCCEEEEEE-ECEEEEC-CEEEEC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHH------HCCCHHHHHHHHHHHH--CCC-------------------HHHHHHHHCCCHHHHCHHHHHHHHHHHHHHHHHHHHHHH--HHHCHHHHHHHHHHHHHHHHHHHCCCCCCEEEC >P1;d3ku8a- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCCCCCHHHHHHHHHHHHHHHCHHHHHHHHCCCCHHHHHHHHHH-------CCEECC-------CHHHHHHHCCCCCCCCCCCCCCCEEECCEEECCHHHHHHHHCCCHHHHC------------------------------HHHHHHHHHHHCCHHHHCCCCCCCC--C PSA >P1;d1bjta- a177096187051063002a30220000001288048105200830845200011028748977b0889125002500408685607606800000000004760283028105810530091630002135060103055379633112646404610584045270306214057b624600440053027106410765806322748885568237401611000000002113010000005390a---94140460163049205053015001310160012000110000010477007154007514526604031070034003430340083466-8a4600041000000000020162705b4403000010550050021106--a5-------a1--660403005060804335----------72404020307348----92302030000421137037205502805ba694006706342a7--90302030378107405734236106013705055000110968134085034003200720261054016332631514123232114005114586063a------b27-8a4026301739--001019----645035963687306081032179813589416603742761455177157461450037006603910740273068635----- >P1;d3ilwa- ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------77950010300023210200100152212186a015037016304930226-979501800040016--2100020030677003306--6833556603020150021002109150072660445846003000000000000011007ba4500000000510060031008348187a601810294060000022-010169-9013300560627050202062564b78511000330003042470264064337--6a5092047164435c83903010205791718701730162050125080-202010a-973330-200200230070015004300623155056504304002400832a6047238------8095786027403930--a06-------------------770042017089832778346504521770485176064--02766841222056204601852049240723b >P1;d3ku8a- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------915b17116500200010000013950462371758950284026-------911809-------705802841bb510208607872024b8303017800420171998327------------------------------b73266007503106704237369a--b Translating the sequences **********************************************************************************************************************************************************************************************************************************CCCCCCCCCHHHHHHHHHHHHHCCC---CCEEHHHHHHHHHHH*CCC*CCC*HHHHHHHHHCC**CCCCCCCEEEECCCCCCCC**CCCCCCCCCEEEEC**HHHH*C*HHH**CCEEE*-CC**EEECCCCCCCCHHHH*CEE**CCCC**EECCCCHHHHHHHHHHHH*--CC-------**--*CCCCCCCCC*CEEE***----------**EEEEECEEEEEE----C*EEEEEECCCCCCHHHHHHHHHHHH***CCCCCC**EEEECCCC--CCCEEEE*C****HHHHHH*HHHHCCCEEEEE****EEE*C*C*EEE**CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH*******------*CC-HHHHHHHHHH*C--CC**CC----CC*EECC***CC****HHHHCCCHHHHCHHHHHHHHHHHHHHHHHHHHHH***HHH*HHHHHHHHHHHHHHHHHHH***CC----- ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------****CCCCCCCCCHHHHHHHHHHHHHCCC***CCEEHHHHHHHHHHH*CCC-CCC*HHHHHHHHHCC--CCCCCCCEEEECCCCCCCC--CCCCCCCCCEEEEC**HHHH*C*HHH**CCEEE**CC**EEECCCCCCCCHHHH*CEE**CCCC**EECCCCHHHHHHHHHHHH***CC************CCCCCCCCC-CEEE**-************EEEEECEEEEEE****C*EEEEEECCCCCCHHHHHHHHHHHH*--CCCCCC**EEEECCCC**CCCEEEE*C****HHHHHH*HHHHCCCEEEEE*-**EEE*C-C*EEE*-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH*HH*******------*CC*HHHHHHHHHHH*--CCC-------------------HHHHHHHHCCCHHHHCHHHHHHHHHHHHHHHHHHHHHH*--HHH*HHHHHHHHHHHHHHHHHHHCCCCCC***C ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------*******HHHHHHHHHHHHHHH*HHHHHHHH****HHHHHHHHHH-------******-------*HHHHHHHC**CCC*CC****CC*EECC***CCHHHHHHHHCCCHHHHC------------------------------HHHHHHHHHHH**HHHH*CCCCCC*--C 56719.tem _________________________________ ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------****CCCCCCCCCHHHHHHHHHHHHHCCC---CCEEHHHHHHHHHHH*CCC-CCC*HHHHHHHHHCC--CCCCCCCEEEECCCCCCCC--CCCCCCCCCEEEEC**HHHH*C*HHH**CCEEE*-CC**EEECCCCCCCCHHHH*CEE**CCCC**EECCCCHHHHHHHHHHHH*--CC-------**--*CCCCCCCCC-CEEE**-----------**EEEEECEEEEEE----C*EEEEEECCCCCCHHHHHHHHHHHH*--CCCCCC**EEEECCCC--CCCEEEE*C****HHHHHH*HHHHCCCEEEEE*-**EEE*C-C*EEE*-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH*******------*CC-HHHHHHHHHHHC--CCC*CC----CC*EECC***CCHHHHHHHHCCCHHHHCHHHHHHHHHHHHHHHHHHHHHH*--HHH*HHHHHHHHHHHHHHHHHHHCCCCCC*--C Structural block scores 0 221 - 4.0 M 3.4 75.0 75.0 222 225 * 2.7 P 2.2 7.0 75.0 226 234 C 4.0 M 0.2 0.7 75.0 235 247 H 4.0 M 1.1 1.3 75.0 248 250 C 4.0 M 6.5 1.7 75.0 251 253 - 4.0 M 75.0 5.0 75.0 254 255 C 4.0 M 6.5 5.2 75.0 256 257 E 4.0 M 2.5 3.0 75.0 258 268 H 4.0 M 3.2 3.3 75.0 270 272 C 4.0 M 3.3 3.3 75.0 274 276 C 4.0 M 2.0 8.3 75.0 278 286 H 4.0 M 1.3 1.4 75.0 287 288 C 4.0 M 1.5 3.5 75.0 289 290 - 4.0 M 0.0 75.0 75.0 291 297 C 4.0 M 0.3 0.7 75.0 298 301 E 4.0 M 1.2 2.2 75.0 302 309 C 4.0 M 3.9 3.2 75.0 310 311 - 4.0 M 0.0 75.0 75.0 312 320 C 4.0 M 4.0 4.7 75.0 321 324 E 4.0 M 2.0 1.2 75.0 326 327 * 2.7 P 3.5 2.5 75.0 328 331 H 4.0 M 1.8 0.8 75.0 335 337 H 4.0 M 2.0 3.3 75.0 338 339 * 2.7 P 2.0 2.5 75.0 340 341 C 4.0 M 4.0 3.5 75.0 342 344 E 4.0 M 4.3 4.7 75.0 347 348 C 4.0 M 9.2 4.5 75.0 349 350 * 2.7 P 5.0 6.0 75.0 351 353 E 4.0 M 0.0 2.0 75.0 354 361 C 4.0 M 0.6 0.4 75.0 362 365 H 4.0 M 0.0 0.0 75.0 368 369 E 4.0 M 3.5 1.0 75.0 370 371 * 2.7 P 4.5 0.0 75.0 372 375 C 4.0 M 5.1 8.2 75.0 376 377 * 2.7 P 2.0 2.5 75.0 378 379 E 4.0 M 1.5 0.0 75.0 380 383 C 4.0 M 0.2 0.0 75.0 384 395 H 4.0 M 1.6 1.3 75.0 397 398 - 4.0 M 75.0 3.5 75.0 399 400 C 4.0 M 7.8 4.5 75.0 401 407 - 4.0 M 75.0 5.8 75.0 408 409 * 2.7 P 5.8 0.5 75.0 410 411 - 4.0 M 75.0 5.5 75.0 413 421 C 4.0 M 2.0 1.1 75.0 424 426 E 4.0 M 4.0 0.7 75.0 427 428 * 2.7 P 3.0 7.5 75.0 429 439 - 4.0 M 68.6 9.3 75.0 440 441 * 2.7 P 4.5 4.0 75.0 442 446 E 4.0 M 2.0 2.8 75.0 448 453 E 4.0 M 4.2 3.5 75.0 454 457 - 4.0 M 75.0 7.6 75.0 460 465 E 4.0 M 1.3 1.2 75.0 466 471 C 4.0 M 1.2 1.2 75.0 472 483 H 4.0 M 2.9 3.4 75.0 485 486 - 4.0 M 2.5 75.0 75.0 487 492 C 4.0 M 6.8 5.4 75.0 493 494 * 2.7 P 3.0 2.0 75.0 495 498 E 4.0 M 4.0 4.5 75.0 499 502 C 4.0 M 5.9 6.1 75.0 503 504 - 4.0 M 75.0 5.5 75.0 505 507 C 4.0 M 4.0 4.0 75.0 508 511 E 4.0 M 1.2 0.8 75.0 514 517 * 2.7 P 4.0 6.0 75.0 518 523 H 4.0 M 4.3 4.0 75.0 525 528 H 4.0 M 3.0 2.2 75.0 529 531 C 4.0 M 2.0 1.7 75.0 532 536 E 4.0 M 3.2 3.2 75.0 539 540 * 2.7 P 2.5 1.0 75.0 541 543 E 4.0 M 0.3 1.0 75.0 549 551 E 4.0 M 2.7 3.0 75.0 555 599 H 4.7 H 2.3 2.3 3.3 600 606 * 2.7 P 5.5 4.3 75.0 607 612 - 4.0 M 75.0 75.0 4.7 614 615 C 4.0 M 4.5 4.5 75.0 617 627 H 4.5 M 4.0 4.5 23.5 629 630 - 4.0 M 75.0 75.0 11.5 631 633 C 4.7 H 0.3 5.5 2.0 635 636 C 4.0 M 5.0 75.0 4.0 637 640 - 4.0 M 75.0 75.0 5.2 641 642 C 4.0 M 5.0 75.0 4.5 644 645 E 4.0 M 1.5 75.0 3.0 646 647 C 4.0 M 7.0 75.0 9.8 648 650 * 2.7 P 5.0 75.0 2.0 651 652 C 4.0 M 7.5 75.0 0.5 653 660 H 4.5 M 2.6 2.6 2.8 661 663 C 5.0 H 3.3 5.0 5.7 664 667 H 5.0 H 5.2 5.5 5.5 669 690 H 4.0 M 4.5 4.4 75.0 692 693 - 4.0 M 5.0 75.0 75.0 694 696 H 4.0 M 3.3 3.0 75.0 698 716 H 4.8 H 3.1 3.4 7.6 717 722 C 4.3 M 17.2 3.2 5.0 724 725 - 4.0 M 75.0 2.5 75.0 >>>>>>