Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1gnla- CCCCCCCCCCCCHHHCCCCCCCCC--------CCCHHHHHHHHHHHHH----HHHHHHHH----HHHHHCCC---------------------------CCCHHHHHHHHHHHHHCCC-----CCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHCCCCC-HHHHHHHHCCCCHHHCC--------CHHHHHHHHHHHHHHHH-----HHHHHHHHHHCCCCC---------------HHHHHHHHHHHHHCCC--CCC-CHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHCCCCCEEEE----CCCCCCCEEEEECCCHHHHHHHHHHHCCC----------CCEEEECHHHHHHHHCHHHHHCCCEEEECCCCHHHHHHHHHHHCC-CEEECCCCCCCCC----HHHHCCEEEEC------CCCCCCCEEECCCCCCCC-CCHHHHHHHHCC-------CCCCCCCCCEEEECCCHHHHHHCHH---------HHHHHHHCCCCCEEEECCCCCCCC-H-HHHHHHHHHHHCCC----------CEEEEECCHHHHHCCCCCCC----------EEC----------------------------------------CEECEEECCCHHHHHHHHHHHHHHHHHCCCC-CHHHCCEEEEEE-C--CCHHHHHHHHHHHHCCCCCCEEECCCCCCCCHHHHHHHHH----HHC--CCCCCCHHHHHHHCC-------------------------------------------------- >P1;d2yivx- ------------------CCHHHC--------CCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHCCEECCCCCCCEECCCCCCCCCCCCC---CCCHHHHHHHHHHHHHHHHH-----HH--HHHHHHHHHHHHHHHHCC------------CCCCCCCCC-HHHHHHHHH---HHCCCCCCC----CHHHHHHHHHHHHHHCC-----CCCCCCCHHHHCCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHHCCC--CCCCCHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHCCCCCEEEEECHHHCCCCCEEEEEECCCHHHHHHHHHHHHHCHHHHHHCCCCCEEEEEEHHHHHHHHHHHC-------CCEEECHHHHHHHHHCCCEEEEEECCCCCCCCHHHHHHHHCCEEEECCC-----CCCCCCCEECCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEECCCHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCEEEECCCCCCCCC-CCHHHHHHHHHHHH---------CCCEEEEEHHHHHHHHHCCCCCHHHHHHH--CCHHHHHHHHHHHHHCCC-----------------------CCCCCCEEEEECCCCHHHHHHHHHHHHHHHCC--CHHHCCEEEEECCC--CCHHHHHHHHHHHHCCC-EEEECCCCCCCCCHHHHHHHHCCCHHHHCCEEEECCCHHHHHHHHHHHHHHHHHHCCCCC------------------------------------ >P1;d3i01m- ------------------CCHHHHHCCCCCCCCCCHHHHHHHHHHHHH----HHHHHHHH----HHHHHHHHCC---CCCCCCCCCCCCCHHHHHHCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHCHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHC-----CCCCCHHHCEEEEECHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCEEEEEECCCCHHHHHHHHHHHHCCCCEEECCCCCHHHCCCCCEEECC------CCCCHHHHHHHHHCCCCCCCCCCCCCCCCHHHCCCCCCCC-------CEEEEEEC---------CCCCEEEEEEECC----HHHCCCCCEEEECCCHHHCCCCEEECEEEEEEEECCCCCHHHHHHHHHCHHHHHHCCCCEEEEEECC-EEEEEEEHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCEEEEEEECCHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCEEEEECHHHHCCCCCCEEECCCCCCCCCCCCHHHHHHHHHHCCCCCCCEEECCCEEECCCCEEHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC-EEEEEEHHHCEEEEEECCCCCCCCCCCCHHHHHHHHCCCCCCCCEEEECHH-HHHCCCCCHHHCHHHHEEECC----HHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCCCCHHHHHHHHHHCCCHHHHCCCCC PSA >P1;d1gnla- b660120010106b4900395041--------5082600200200010----00000200----32027293---------------------------a082910310000000000-----0000139500500340082079117508658b04600625188-49502820a8020551a--------66222001100000000-----000000100009445---------------a800300040013025--982-7595037004400610--------240031015000830640441607----000695200000000020010005306b2----------a000000000000000340382b1040000100240470044020-0000000000205----a5029100002------001289053171340570-707801720581-------72074336a413000026103731a---------700711674506200000100024-a-70600360067068----------40000000000010122b0a----------51c----------------------------------------9120100000000020013014303842a3a-501602010000-0--0000000010000128045020005400001880464155----616--073074287019702-------------------------------------------------- >P1;d2yivx- ------------------470762--------0206003400510664a170104327764947737422031814b80715032aaa8265062---60613000007002200400-----43--008003200400220039------------60a206142-6a1027009---209182bb6----72550034004202300-----662a54020012001870284057-3a0004004301740481044--73157146003000200000--------0000100000000005107327140000005470000000000000000005007704b405819072010000000000000031-------1200000000000000300000000022026200801840a01000008-----7241c9052070304504720260053005015619b691310c23340000000500370024347d321400142056440100000111022312-00400130053005---------53000000010000000200011830870--0292036004500621a4-----------------------d22000000000100000002001300a4292--10250000000000--42500200000000000-000001304030085027102540491020101115616500640070028104a1a187------------------------------------ >P1;d3i01m- ------------------5a026108b115bc4405300520250055----00440373----0571285365---847030240103000010031340640230350076148203681416200200000000100000050172578642368320100102100300310043100000000060661820260065000100000001600600271-----a130145100000055001000000000000000318213247005002510300000049164210000000000000000036068632037001205------507500730161090a2b6560b0202100003407087a-------60100003---------a314000002316----6970746404133320561755240100000002073046300500053042000101101044732-8020001360084503061003001310323051003301000005684087216405720750454679210761a20001231240045001000010100116230010203222769130420527954358400062016205920675182000000253000000001-000010460200000029178400092300500030003722502000037-001251003014201000000----5700640595026005439158700720003721360a5026206849020282960a Translating the sequences ******************CC***C--------CCCHHHHHHHHHHHHH----HHHHHHHH----HHHHHCC*---------------------------CCCHHHHHHHHHHHHH*CC-----*****HHHHHHHHHHHHHHHHHHHHCCCCCCCCC****CCCCC-HHHHHHHH**CCHH*CC--------CHHHHHHHHHHHHHH**-----**HHHHHHHH*CCCC---------------HHHHHHHHHHHHHCCC--CCC-CHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHCCCCCEEEE----*CCCCC*EEEEECCCHHHHHHHHHHH**C----------CCEEEECHHHHHHHHCHH********EE***CHHHHHHHHH**CC-*EEECCCCCCCC*----HHH*C*EEE*C------CCCCCCCEEECCCCCCCC-**HHHHHHHH**-------CCCCCCCC*EEEECCCHHHHHHCHH---------HHHHHHHCCCCCEEEE*CCCCCCC-H-H*HHHHHHHHH***----------CEEEEEC*HHHHHCCCCCCC----------***----------------------------------------C**CEEECCC***HHHHHHHHHHHHHH*CC*-CHHHCCEEEEE*-C--CCHHHHHHHHHHHHCCCCCCEE*CCCCCCCCHHHHHHHHH----HHC--*CCCCCHHHHHHH**-------------------------------------------------- ------------------CCHHHC--------CCCHHHHHHHHHHHHH****HHHHHHHH****HHHHHCC**C***CCC**CCCCCCCC*****---CCC*HHHHHHHHHHHHHH**-----HH--HHHHHHHHHHHHHHHH**------------CCCCCCCCC-HHHHHHHHH---HHCCC****----CHHHHHHHHHHHHHHCC-----CC*****HHH*CCCC*****HHH*-****C**HHHHHHHHHHHCCC--CCCCCHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHCCCCCEEEE*CHHHCCCCCEEEEEECCCHHHHHHHHHHHHHCH*****CCCCC*EEEE*HHHHHHHH*HH*-------**EEECHHHHHHHHH*CC**EEEECCCCCCCC*HHH*HHHCCEEEECC*-----CCCCCCCEE*CCC*****HHHHHHHHHHHHHHHHCCCCCCCCCCCC*EEEECCCHHHHHH*HHC******HHHHHHHHHCCCCC*EEEECCCCCCC**-*CHHHHHHHHHHHH---------CC*EEEE*HHHHHH***CCCCC*******--CCHHHHHHHHHH***CCC-----------------------**CCCCEEE**CCCCHHHHHHHHHHHHHH*CC--CHHHCCEEEEECCC--CCHHHHHHHHHHHHCCC-**EECCCCCCCCCHHHHHHHH****HHHC*EE**CCCHHHHHHHHHHHHHHHHHHCCCCC------------------------------------ ------------------CCHHH*********CCCHHHHHHHHHHHHH----HHHHHHHH----HHHHH****C---CCC**CCCCCCCC********CCCC*HHHHHHHHHHHHHCC*****HH**HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC**HHHH*HHHH*CC**CC*********CHHHHHHHHHHHHH*CC*****CCHHHHHHH*-----*****HHH******CHHHHHHHHHHHHH*****CCCCC**HHHHHHHHHHH************HHHHHHHHHHHH*CCC**E****CHHHCCCCCEEE**------****HHHHHHH*H*****CCCCCC****CHHH*****C**-------*EEEEE**---------CCC*EEEE***CC----HHH****C*EEE*CC******C***C**EEE***CCCCCHHHHHHHHH*HHHHHHCCCC******CC-EEEE***HHHHHHC**C******HHHHHHHH*CCCCCEEEEE**CC****H*HC*HHHHHHHHHHH*********CCEEEEECHHHH**CCCC***C*********CCHHHHHHHHHH***CCC**************************CCC***CCCCCC*************-******HHHC*EEEEECCC**CC*****HHHHHHH*CCCCC**C****C**-HHH*****H***HHH**EECC----HHHHHHHHHHHHHHHHHCCCCC************************************ 56821.tem _________________________________ ------------------CCHHHC--------CCCHHHHHHHHHHHHH----HHHHHHHH----HHHHHCC**C---CCC**CCCCCCCC*****---CCCCHHHHHHHHHHHHHHCC-----HH**HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC-HHHHHHHHH*CCHHCCC****----CHHHHHHHHHHHHHHCC-----CCHHHHHHHH*CCCC*****HHH*-****CHHHHHHHHHHHHHCCC--CCCCCHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHCCCCCEEEE*CHHHCCCCCEEEEEECCCHHHHHHHHHHHHHCH*****CCCCCCEEEECHHHHHHHHCHH*------*EEEEECHHHHHHHHH*CCC*EEEECCCCCCCC*HHH*HHHCCEEEECC*-----CCCCCCCEEECCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCC*EEEECCCHHHHHHCHHC******HHHHHHHHHCCCCCEEEEECCCCCCC*H-HCHHHHHHHHHHHH---------CCEEEEECHHHHHHCCCCCCCC*******--CCHHHHHHHHHH***CCC-----------------------**CCCCEEECCCCCCHHHHHHHHHHHHHH*CC*-CHHHCCEEEEECCC--CCHHHHHHHHHHHHCCCCCCEECCCCCCCCCHHHHHHHHH***HHHC*EECCCCCHHHHHHHHHHHHHHHHHHCCCCC------------------------------------ Structural block scores 0 17 - 4.0 M 3.3 75.0 75.0 18 19 C 5.0 H 6.0 5.5 7.8 20 22 H 4.0 M 3.0 4.3 2.7 24 31 - 4.0 M 75.0 75.0 6.3 32 34 C 5.0 H 4.3 0.7 2.7 35 47 H 5.0 H 1.0 2.7 2.5 48 51 - 4.0 M 75.0 4.6 75.0 52 59 H 5.0 H 0.2 3.8 2.6 60 63 - 4.0 M 75.0 6.0 75.0 64 68 H 5.0 H 2.8 4.6 3.0 69 70 C 4.0 M 5.5 1.0 6.5 71 72 * 1.9 P 39.0 2.0 4.5 74 76 - 4.0 M 75.0 5.5 75.0 77 79 C 4.0 M 75.0 5.0 6.3 80 81 * 2.7 P 75.0 3.0 1.5 82 89 C 4.0 M 75.0 5.8 1.2 90 94 * 2.7 P 75.0 3.8 0.2 95 97 - 4.0 M 75.0 75.0 1.3 98 101 C 4.5 M 23.4 3.2 3.2 102 115 H 4.9 H 1.1 1.3 3.1 116 117 C 4.0 M 0.0 0.0 1.0 118 122 - 4.0 M 75.0 75.0 4.4 123 124 H 4.0 M 0.0 3.5 3.5 125 126 * 2.7 P 0.0 75.0 1.0 127 147 H 4.7 H 3.1 12.3 0.8 148 165 C 4.2 M 4.6 39.2 3.2 167 175 H 4.8 H 4.5 3.9 0.9 177 178 C 4.0 M 1.0 75.0 3.5 179 180 H 4.0 M 2.5 1.0 0.5 181 183 C 4.3 M 5.5 6.0 0.0 184 187 * 2.7 P 75.0 7.8 0.0 188 191 - 4.0 M 75.0 75.0 3.0 193 206 H 4.9 H 1.0 2.1 2.2 207 208 C 4.0 M 0.0 0.0 0.0 209 213 - 4.0 M 75.0 75.0 0.0 214 215 C 4.0 M 0.0 6.0 3.5 216 223 H 4.2 M 0.1 2.9 2.0 225 228 C 4.0 M 5.5 0.8 75.0 229 233 * 2.7 P 75.0 5.0 3.1 234 236 H 4.0 M 75.0 3.0 3.3 239 242 * 2.7 P 75.0 3.4 0.0 244 256 H 4.8 H 2.3 2.8 0.5 257 259 C 4.0 M 2.3 2.7 0.0 260 261 - 4.0 M 75.0 75.0 0.0 262 266 C 4.8 H 20.2 4.6 2.8 267 281 H 4.7 H 2.9 1.1 2.2 282 289 - 4.0 M 75.0 75.0 1.6 290 304 H 4.8 H 1.8 0.1 0.9 305 309 C 4.6 H 3.6 3.2 0.0 310 313 E 4.2 M 3.5 3.5 2.2 316 318 H 4.0 M 50.0 0.0 5.7 319 323 C 5.0 H 4.0 3.2 2.4 324 329 E 4.3 M 0.3 0.0 13.8 330 332 C 4.0 M 0.0 0.0 75.0 333 345 H 4.4 M 2.2 1.5 14.2 348 352 * 2.7 P 75.0 5.7 6.6 353 358 C 4.2 M 51.8 3.2 4.8 359 362 E 4.0 M 0.0 0.2 1.2 364 371 H 4.4 M 0.0 0.0 1.8 373 374 H 4.0 M 3.5 1.5 8.8 376 381 - 4.0 M 4.2 75.0 75.0 383 387 E 4.0 M 0.2 0.6 0.2 389 397 H 4.0 M 2.3 0.0 67.0 399 401 C 4.3 M 0.7 1.0 4.8 403 406 E 4.8 H 0.0 0.0 0.0 407 414 C 4.2 M 0.2 1.8 29.6 416 418 H 4.0 M 75.0 2.7 7.3 420 422 H 4.0 M 5.2 4.0 5.7 423 424 C 4.0 M 5.5 5.2 2.0 425 428 E 4.5 M 0.2 0.2 2.8 429 430 C 4.5 M 1.0 0.0 2.5 432 436 - 4.0 M 75.0 75.0 4.8 437 443 C 4.3 M 2.9 5.1 1.7 444 446 E 4.7 H 3.0 2.3 0.0 447 454 C 4.0 M 3.4 2.9 2.0 455 470 H 4.4 M 21.6 2.6 1.8 471 482 C 4.2 M 27.7 4.9 2.0 484 487 E 5.0 H 2.0 1.0 2.5 488 490 C 4.0 M 0.0 0.0 0.3 491 496 H 5.0 H 3.2 2.5 3.5 498 499 H 4.0 M 5.8 1.0 1.5 501 506 * 2.7 P 75.0 5.4 1.7 507 515 H 4.7 H 19.1 1.9 1.4 516 520 C 5.0 H 4.4 3.0 1.8 521 525 E 4.6 H 0.4 0.0 0.8 526 532 C 4.3 M 1.0 1.4 3.3 538 549 H 4.7 H 3.5 1.8 3.8 550 558 - 4.0 M 75.0 75.0 4.7 559 560 C 4.5 M 39.5 4.0 5.8 561 565 E 4.8 H 0.0 0.0 0.6 567 572 H 4.5 M 0.2 0.2 1.7 573 580 C 4.1 M 12.8 0.4 1.2 581 587 * 2.7 P 75.0 3.9 0.4 588 589 - 4.0 M 75.0 75.0 3.5 590 591 C 4.0 M 3.0 1.0 2.5 592 601 H 4.0 M 68.8 2.9 1.2 602 604 * 2.7 P 75.0 2.7 7.3 605 607 C 4.0 M 75.0 5.2 1.3 608 630 - 4.0 M 75.0 75.0 3.3 631 632 * 2.7 P 75.0 7.8 7.0 633 636 C 4.2 M 3.0 0.5 3.8 637 639 E 4.0 M 0.3 0.0 4.7 640 645 C 4.2 M 0.0 0.2 0.3 646 659 H 4.0 M 2.1 1.5 6.1 661 662 C 4.0 M 6.8 5.5 0.0 666 668 H 5.0 H 2.3 2.3 3.3 669 670 C 4.5 M 1.0 0.0 1.0 671 675 E 5.0 H 0.2 0.0 0.0 676 678 C 4.3 M 25.0 0.0 4.0 679 680 - 4.0 M 75.0 75.0 7.5 681 682 C 5.0 H 0.0 3.0 2.0 683 694 H 4.6 H 0.2 0.6 1.8 695 700 C 4.3 M 3.2 12.5 2.0 701 702 E 4.0 M 1.0 0.0 3.5 703 711 C 4.1 M 1.1 1.2 9.7 712 720 H 4.3 M 4.6 3.3 1.3 721 723 * 2.7 P 75.0 2.7 1.7 724 726 H 4.7 H 27.3 3.3 1.0 729 730 E 4.0 M 37.5 0.5 0.0 731 735 C 4.0 M 4.2 2.8 45.0 736 753 H 4.3 M 39.5 3.0 7.4 754 758 C 4.0 M 75.0 5.5 5.2 759 794 - 4.0 M 75.0 75.0 3.6 >>>>>>