Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d3nwaa- CCCCCCCCCEEECCCCCCCEEECCCCCCCCCCCCC--------------------------CCCCEEEEEEEEEECC---CCEEEEEEEEEEEEEEECEECCCEECCCCEEEEEECC---HHHHHHCHHHHCEEECEEEEEECCEEEEEEHHHCCCCEEECCCCCCCCCCCEEECCCCCCCCCCCCCCCCCEEEEEEEEEEEEEEE-CCCCC-CEEECCCCEECCCCCCCCCCCHHHCCCCCCHHHEEEEEEECCCCCCCCCCCCCCEEEEEEECCCCEEEEECCCCCCCCCCEEEEEEEEEEEEEECC--------CEEEEEECCCCEEEEEECC-CCCHHHCCCCHHHHHHHHHHHHHHHHHHCCCCEEECCCCEEEEECCCEEEEEEEEEEHHHCCCCCCHHHHHHCCCCC---CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---CHHHHHHHHHC--CCEEEEECC----CCEEEEECEEECHHHEEECCCCCCC-----CCCCEEECCCEEEEECCCCCEEEEEECHHHEEECCCCCEEECCCCCEEEEEEC--CEEEEEECCEEEEEEEHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHHHHHCHHHHHCCCCCCCC-------- >P1;d5mdmc- ---------------------------CEEEEEECCCCCCCEECCCCCCCCCCCCCCCCCC--CEEEEEEEEEECCCCCCCEECEEEEEEEEEEEEEECCCCCCCEEEEEEEEECCCHHHHHHHHHHHHCCCCCCCCCCC-----CCCCC----------CC----------------------------CEEEEEEEEEEEECCEEECCCCCCEECC-----CCHHHEECC------------------------------------CCEECCCCCEEEEECCCCCC--CCCCCCCEEEEEEEEEECCC--CCCHHH-EEEECC---CCCCEEHHHCEE---CCCCC---------------------------CCEEECCCCCEEECCC------CCCCCCCCCHHH-CCCCCCCCCCC-C-CCCCC-----CCCCC----------CHHHHHHHHHHHHHHHHHHCCCCCCHHHHHCCCCCCCEEEEEEEEECCEEEEEEEEEEEEEECCCEECCCEEECCCCCCC----EEECCCCCEEECC------EEECHHHCEEEC------------CEEECCHHHCCCCCCCCCC----------------------------------------------------------------------------- >P1;d6tita- ---------------------------CEEEEEECCCCCCCEECCCCCCCCCCCCCCCCCC--CCEEEEEEEEECCHHHHCCCCEEEEEEEEEEEEECCCCCCCCCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCC-----CCCCC----------CC----------------------------CCCEEEEEEEEEECCCEECCCCCCEECC-----CCHHHEECC------------------------------------CEEECCCCCCEEEECC-CCC--CCCCCCCEEEEEEEEECCCCHHHCCCCC-EEEECC---CCCCEECCCCEE---EEECC---------------------------EEEEECCCCCEEEECC------HH-----HHHHHCCCCCCCCCCCCCC-CCCCCC----HHHCC----------HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHCCCCCCCEEEEEEEEECCEEEEEEEEEEEEEECCCEECCCEEEE-CCCCC----EEECCCCCEEECC------EEECHHHCEEEC------------CEEECHHHHCC--------CC---------------CCCHHHHCCCCCCCCCCCCHHHHHHCCCC------------------CCCEEECCEEEEC PSA >P1;d3nwaa- 2506198340200570918634817847a25958b--------------------------93b3340000003119---622518010000401300616865654a367130004---3500271024601030105061ab8533141537826329065bb6996551020189624063955a248010020103306050-73604-403063a2505000000557a169242418b9304035713523057775589440100020440000040532552010043233026040046b--------6303010883300040945-0112a50200330263057007502754078502303910102084200000000125844854b538505715375---520514b6274058415712755757447847616716552831874473168---4244101643a--62000614b----a40013706605171030476050b-----95891012200000359a6943700006701024726312825b806450300--201000570713601479749895a89a8b899a8b789699796688578989a8589633766736665556686979-------- >P1;d5mdmc- ---------------------------63600002526060060a1513201601247385--c1554307020007104942701103003200202278969571545356450778206801823679828547308-----46176----------66----------------------------5643434003075220000001020000-----006b52147------------------------------------4206034b100000364735--90582a03605020004597--806269-010204---000206048012---2601a---------------------------3500102320002055------81701a450031-09607bc1513-0-0082a-----aa64a----------5801461562026003225594915221001001100400000012b95100010000102073451a614022844a5a----35600430282ab------33000000131b------------9314008101253a9667a----------------------------------------------------------------------------- >P1;d6tita- ---------------------------631000036470601401170421010404a02a--a2713608030054019120501000003000204478872474510032250659404601553478719150029-----6815a----------88----------------------------a242314013055020000003030000-----005b3315a------------------------------------7105021b00200032-a16--83595c0572603000842638001688-000102---300005019003---26119---------------------------5400103200000035------5a-----218508075089c180301-207304----88108----------7a557616530550042035a7402011001010100100000003b60010000000000075340a601031-0b598----3170073017059------03000000040b------------73100023039--------ba---------------a339106251604106020046017607c------------------9230337aa2916 Translating the sequences ***************************C******C--------------------------**CCEEEEEEEEE*CC---CCE*EEEEEEEEEEEEEC**CCC**C***EEEEE*CC---HHHHHH*HHH*C***C************************CC****************************CEEEEEEEEEEEE**E-*CCCC-CEE*C*****CC*****CC*************************************EEE**CCCCEEEE*CCCCC**CCC****EEEEEEEEEECC--------C*EEEE*C*******EECC-C*****CCCC****************************CEEEE*CCC*EEEE********CCCCCC*HHHHHCCCCC---CCCCCC*CC********HHH************HHHHHHHHHHHHHHHHHHH**---CHHHHH****C--**EEEEE**----**EEEEE*EEE****EE*CC***CC-----****EEECCC**EEECC******EEECHHH*EE*C*************EEE*C--*******CC*******************CCC****CCCCCCCCCCC*HHHHH*CCCC******************CCC**-------- ---------------------------CEEEEEECCCCCCCEECCCCCCCCCCCCCCCCCC--C*EEEEEEEEECCC***C*ECEEEEEEEEEEEEE*CCCCCCC*EEEEEEEECCCHHHHHHHHHHHH*CCCCCCCCCC-----CCCCC----------CC----------------------------CEEEEEEEEEEEECCEEECCCCCCEECC-----CCHHHEECC------------------------------------C*EECCCCC*EEEECCCCCC--CCCCCCCEEEEEEEEEECCC--*CC***-EEEECC---CCCCEE***CEE---CCCCC---------------------------C*EEECCCCCEEE*CC------CCCCCC***HHH-CCCCCCCCCCC-C-CCCCC-----***CC----------*HHHHHHHHHHHHHHHHHHCCCCCCHHHHHCCCCCCCEEEEEEEEECCEEEEEEEEEEEEEECCCEECCCEEECCCCCCC----EEECCCCCEEECC------EEECHHHCEEEC------------CEEECCHHHCC****CC**----------------------------------------------------------------------------- ---------------------------CEEEEEECCCCCCCEECCCCCCCCCCCCCCCCCC--CCEEEEEEEEECC****CC*CEEEEEEEEEEEEECCCCCCCCCEEEEEEE*CCCHHHHHHHHHHHHHCCCCCCCCCC-----CCCCC----------CC----------------------------C**EEEEEEEEEECC*EECCCCCCEECC-----CCHHHEECC------------------------------------CEEECCCCCCEEEECC-CCC--CCCCCCCEEEEEEEEE*CCC***CC**C-EEEECC---CCCCEECC*CEE---***CC---------------------------*EEEECCCCCEEEECC------**-----HHHHHCCCCCCCCCCCCCC-CCCCC*----HHHCC----------HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHCCCCCCCEEEEEEEEECCEEEEEEEEEEEEEECCCEECCCEEE*-CCCCC----EEECCCCCEEECC------EEECHHHCEEEC------------CEEEC*HHHCC--------**---------------CCC****CCCCCCCCCCC*HHHHH*CCCC------------------CCC********** 161008.tem _________________________________ ---------------------------CEEEEEECCCCCCCEECCCCCCCCCCCCCCCCCC--CCEEEEEEEEECCC***CCECEEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCHHHHHHHHHHHHHCCCCCCCCCC-----CCCCC----------CC----------------------------CEEEEEEEEEEEECCEEECCCCCCEECC-----CCHHHEECC------------------------------------CEEECCCCCCEEEECCCCCC--CCCCCCCEEEEEEEEEECCC--*CC**C-EEEECC---CCCCEECC*CEE---CCCCC---------------------------CEEEECCCCCEEEECC------CCCCCC*HHHHHCCCCCCCCCCCCCC-CCCCC*----HHHCC----------HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHCCCCCCCEEEEEEEEECCEEEEEEEEEEEEEECCCEECCCEEECCCCCCC----EEECCCCCEEECC------EEECHHHCEEEC------------CEEECCHHHCC****CC****---------------CCC****CCCCCCCCCCC*HHHHH*CCCC------------------CCC**-------- Structural block scores 0 26 - 4.0 M 4.1 75.0 75.0 28 33 E 4.0 M 6.6 1.5 0.7 34 40 C 4.1 M 65.9 3.0 3.7 41 42 E 4.0 M 75.0 3.0 2.5 43 60 C 4.0 M 75.0 3.3 2.7 61 62 - 4.0 M 6.0 75.0 75.0 63 64 C 4.5 M 7.2 6.8 6.2 65 73 E 5.0 H 1.1 2.9 3.1 74 76 C 4.3 M 3.7 2.3 3.0 77 79 * 2.7 P 75.0 1.7 3.3 80 81 C 4.5 M 4.0 6.5 1.5 84 96 E 5.0 H 1.4 0.9 0.5 97 105 C 4.3 M 4.8 6.1 5.7 106 113 E 4.5 M 4.3 4.1 2.1 114 116 C 4.7 H 1.3 4.0 3.7 117 129 H 4.6 H 19.2 4.5 4.1 130 139 C 4.2 M 1.6 5.4 4.2 140 144 - 4.0 M 7.4 75.0 75.0 145 149 C 4.0 M 3.2 4.8 6.1 150 159 - 4.0 M 4.6 75.0 75.0 160 161 C 5.0 H 3.0 6.0 8.0 162 189 - 4.0 M 5.2 75.0 75.0 191 202 E 4.8 H 1.3 3.2 2.5 203 204 C 4.0 M 2.5 2.0 1.0 205 207 E 4.0 M 27.3 0.0 0.0 208 213 C 4.8 H 15.3 0.5 1.0 214 215 E 5.0 H 1.5 0.0 0.0 216 217 C 4.5 M 3.0 0.0 0.0 218 222 - 4.0 M 4.1 75.0 75.0 223 224 C 5.0 H 2.5 0.0 0.0 225 227 H 4.0 M 0.0 7.5 6.5 228 229 E 4.0 M 0.0 1.5 2.0 230 231 C 5.0 H 5.0 5.5 7.8 232 267 - 4.0 M 4.8 75.0 75.0 269 271 E 4.7 H 0.3 2.7 2.0 272 277 C 4.5 M 1.7 3.2 2.4 278 281 E 5.0 H 0.0 0.0 0.5 282 287 C 4.7 H 3.2 4.7 16.2 288 289 - 4.0 M 3.5 75.0 75.0 290 296 C 4.4 M 1.4 4.9 6.1 297 306 E 4.9 H 2.2 2.0 3.1 307 309 C 4.7 H 30.8 7.0 4.0 310 311 - 4.0 M 75.0 75.0 5.5 313 314 C 4.0 M 75.0 3.0 0.5 315 316 * 2.7 P 75.0 4.0 7.0 319 322 E 5.0 H 1.0 0.8 0.2 323 324 C 4.5 M 4.0 2.0 1.0 325 327 - 4.0 M 4.7 75.0 75.0 328 331 C 4.0 M 1.0 0.5 0.8 332 333 E 5.0 H 4.5 3.0 2.5 334 335 C 4.0 M 4.5 2.0 0.5 338 339 E 4.0 M 1.0 1.5 1.5 340 342 - 4.0 M 5.8 75.0 75.0 343 347 C 4.2 M 1.0 3.9 3.8 348 374 - 4.0 M 3.4 75.0 75.0 376 379 E 4.8 H 0.8 1.5 1.2 380 384 C 4.6 H 2.8 1.4 1.0 385 388 E 4.8 H 0.0 0.5 0.0 389 390 C 4.0 M 0.0 5.0 4.0 391 396 - 4.0 M 3.3 75.0 75.0 397 402 C 4.0 M 6.2 4.6 52.6 404 408 H 4.6 H 5.0 1.8 3.2 409 422 C 4.6 H 18.8 14.7 4.5 424 428 C 4.4 M 3.8 4.1 2.4 430 433 - 4.0 M 4.5 75.0 75.0 434 436 H 4.0 M 3.3 9.0 5.7 437 438 C 4.0 M 6.0 7.2 4.0 439 448 - 4.0 M 5.8 75.0 75.0 449 467 H 4.9 H 4.5 3.1 3.9 468 473 C 4.2 M 40.5 5.5 4.8 474 478 H 5.0 H 2.2 1.0 0.4 479 485 C 4.1 M 24.9 0.4 0.4 486 494 E 4.6 H 3.4 0.8 0.4 495 496 C 4.0 M 75.0 10.2 8.8 497 510 E 4.6 H 13.8 0.7 0.1 511 513 C 4.0 M 3.0 4.7 5.0 514 515 E 5.0 H 1.5 3.0 2.0 516 518 C 4.7 H 3.7 5.8 5.5 519 521 E 4.0 M 3.7 2.0 1.3 522 528 C 4.0 M 55.2 6.3 15.6 529 532 - 4.0 M 7.8 75.0 75.0 533 535 E 5.0 H 0.7 4.7 3.7 536 540 C 4.6 H 0.8 1.4 2.0 541 543 E 5.0 H 1.0 4.0 2.7 544 545 C 5.0 H 7.0 11.0 7.0 546 551 - 4.0 M 6.6 75.0 75.0 552 554 E 5.0 H 0.0 2.0 1.0 556 558 H 5.0 H 4.3 0.0 0.0 560 562 E 4.7 H 2.0 1.7 1.3 564 575 - 4.0 M 4.5 75.0 75.0 577 579 E 5.0 H 2.7 2.7 1.3 580 581 C 4.0 M 0.0 0.0 0.0 582 584 H 4.0 M 50.7 3.0 1.7 585 586 C 4.0 M 0.5 1.5 6.0 587 590 * 2.7 P 1.2 6.9 75.0 591 592 C 4.0 M 3.5 6.0 75.0 593 596 * 2.7 P 4.2 41.9 43.0 597 611 - 4.0 M 6.7 75.0 75.0 612 614 C 4.0 M 9.2 75.0 5.5 615 618 * 2.7 P 9.1 75.0 4.0 619 629 C 4.0 M 8.0 75.0 2.5 631 635 H 4.0 M 7.4 75.0 2.2 637 640 C 4.0 M 8.1 75.0 6.4 641 658 - 4.0 M 5.7 75.0 75.0 659 661 C 4.0 M 7.7 75.0 4.7 662 663 * 2.7 P 8.0 75.0 1.5 664 671 - 4.0 M 75.0 75.0 6.1 >>>>>>