Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1kb0a2 CHHHHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCEECCCCCCCCCHHHEEEEEEEECC--CCCCCCCCCEEECCEEEEECHH-HCEEEEECCCC-CEEEEECCCCCHHHHHHCCCCCCCCCCEEECCEEEEECCCCEEEEEECCCCCEEEEEECCCCCCCCCCCCCCCEEECCEEEECCCCCCCCCCCEEEEEECCCCCEEEEEECCCCCCC--------CCCCC------HHHHHHHCCCCHHHCCCCCCEECCCCCCEEEECCCCEEEEECCCEECCCHHHHCCCCCCCCCCCEEEEECCCCCCEEEEEECCCCCCCCCCCCCCCEEEEEEEC-----------------CEEEEEEEECC-CCCEEEEEECCCCCEEEEEECC-CCCCEEEEC-CCCCEEECHHHHCCC-------CCEECCCCCCCCCCCCCCEEECCCCEEEEEEEECCCEEEECCCCCCCCCCCCCCCHHHCCCCCEEECCCCCC----CCCEEEEEEEECCCCEEEEEEEECCCCCCCEEEECCCEEEEECCCCEEEEEECCCCCCC-CEECCCCCCCCCEEEEECCEEEEEEEECCCHHHHHHCCCCC-------------------CCCCCEEEEEEECCCCCCCC >P1;d2ad6a- ---------------CHHHHHHHCCCCCCCCCCCCCCCCCEECCCCCCCCCHHHCEEEEEEECC--CCCCCCCCCEEECCEEEEECCCCCCEEEEECCCCCCEEEEECCCCCHHHHHHCCCCCCCCCCEEECCEEEEECCCCEEEEEECCCCCEEEEEECCC-HHHCCCCCCCCEEECCEEEEECCCHHHCCCCEEEEEECCCCCEEEEEECCCCHHHHCCC-----CCCCCCCHHHCCCCHHHHCCCC--CHHH-HCCCCCCCCCEEECCCCEEEEECCCCCCCCHHHCC---CCCCCCCEEEEEECCCCCEEEEEECCCCCCCCCCCCCCCEEEEEEEC-----------------CEEEEEEEEEC-CCCEEEEEECCCCCEEEEEECCCCCCCEEEECCCCCCEEECHHHCCCCC-----CCEEEECCCCCCCCCCCCCEEECCCCEEEEEEECEEEEEEEC-CCCCC---------CCCCCCCEEEEEEECCCCCCCCCCEEEEEECCCCCCEEEEEEECCCCCCCCEEECCCEEEEECCCCEEEEEECCCCCEEEEEECCCCCCCCCEEEEECCEEEEEEEECCCCCCCHHHHCCCCCCCHHHHHHHHCCCHHHCCCCCCEEEEEEC-------- >P1;d4cvba- -----CCCCCCCCCCHHHHC--CCCCCCCCCCCCCCCCCCEECCCCCCCCCHHHCEEEEEEECC---CCCCCCCEEEECCEEEEECCC-CEEEEEECCCC-CEEEEEECCCCCHHHCCCHHHHCCCCCEEECCEEEEECCCCEEEEEECCCCCEEEEEECCCCHHHCCCCCCCCEEECCEEEECCCCCCCCCCCEEEEEECCCCCEEEEEECCCCCC-----------------------CCCHHHCCCCC--HHHCCCCCCCCCCEEECCCCEEEEECCCCCCCCHHHHCCCCCCCCCCCEEEEECCCCCCEEEEEECCCCCCCCCCCCCCCEEEEEECCCCCCCCCEEEECCCCCCCCEEEEEEECCCCCCCEEEEECCCCCEEEEECCC-CCCCEEEEC-CCCCEEECHHHCCCC-----CCCCEEECCCCCCCCCCCCCEEECCCCEEEEEEECEEEEEEECCC-----------CCCHHHCCCEEEEEEECC---CCCCCEEEEEEECCCCCEEEEEEECCCCCCCEEEECCCEEEEECCCCEEEEEECCCCCEEEEEECCCCCCCCEEEEEECCEEEEEEEEC-CCC-------------HHHHHHHHCCCC-CCCCCCCEEEEEECCC------ >P1;d6zcwa- ------------CCCHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCHHHCEEEEEEECCCCCCCCCCCCCEEECCEEEEEECC-CEEEEEECCCC-CEEEEEECCCCCCC--CCCCCCCCCCCEEECCEEEEECCCCEEEEEECCCCCEEEEEECCC-HHHCCCCCCCCEEECCEEEECCCCHHHCCCCEEEEECCCCCCEEEEEECCCCC--EEEEEECCEEEEEEECC-----CCCCCCCCC--CHHH-HCCCCCCCCEEEECCCCEEEEECCCCCCCCHHHCC---CCCCCCCEEEEECCCCCCEEEEEECCCCCCCCCCCCCCCEEEEEECC-----------------CCEEEEEEEEC-CCCEEEEEECCCCCEEEEEECCCCCCCEEEEC-CCCCEEECHHHCCCCCCCCCCCCCEEECCCCCCCCCCCCCEEECCCCEEEEEEECEEEEEEEC-CCCCC---------CCCCCCCEEEEEEECCC----CCCEEEEEEECCCCEEEEEEEECCCCCCCEEEECCCEEEEECCCCEEEEEECCCCCEEEEEECCCCCCCCCEEEEECCEEEEEEEECCCCCHH-------------HHCHHHHHHCCC-CCCCCEEEEEECC--HHHCC PSA >P1;d1kb0a2 b933840580075032910580578040002000212010002165042940761401110606--1840000000005000000001-01000000250-8300314090759225412300000001004110000004020000401608331437019b2853000100000043100000200100010000003057075300010003229--------79245------9005400610155250250100000100000129340000000000000162003855500000000002046082311100010000000000100016181a-----------------98734000000-0000000000440711305300-704006504-87060654a603416-------62220100030000000000046160000000011000100691727744ab23619461000032546819----49520200003045173313250710000000001050000000202000020560851-4360510000000002089501000001100210394421a-------------------57640000000392909349 >P1;d2ad6a- ---------------2930571284a0000110031302020724504393077073224160b--1620001000008510000000300000030652a83414250a0989048102300000000003600000001030000309708340338005-29500001000000570000011101001200000020850833040200073a30202-----a50064155043452037108c--6315-20000010000004823000000000000015205---6400000000003066030400000001000000000000004031b-----------------99612000000-000000001043050200420071030066035a705053188120529-----350580000000000000000046630000000000010305-62937---------42540100505032054057771000010020060734112104000000000041100000001030100118607221544050000000000228b30100000000000001104a49765343000100650374072300010002-------- >P1;d4cvba- -----a217a0760676101--265440000000102020004175044930770542023902---7a2000000005200000003-00000020560-83202151a2477860408402100000025420000002020000304508331336064017500000000000440000000012033000000030860722032600175b-----------------------6a12a304b05--48501000010000003814000000000000003109067050420000000306707330522000100000000000000505060579095013105a1148663200000000000000000750600000100-503005706-670707025810047-----335307010001000000000002653000000000013040479-----------906383200060704106---c383001000010230424031314000000000000400000001120000107408321234040000000000118a200000000-006-------------006300620661-7175861001000149------ >P1;d6zcwa- ------------7072720350163471001200112010002152042a007304221216099b3450000000007110000003-00000030470-84312230813b51--213321000000028810000000030000427608341347016-16400001000100422000001101100202000040960633010000002--202117b7845729302-----97235203c--6315-10000010110003525100000000000003406---7302000000002063020404000002000000000000004164a-----------------a7303000000-00000000304608122014005502007504-9704061499010651ba885184230000000000000000055150000000000030303-92737---------6066010031303214a----810000000304518240334150000000000403000000030300002075083213350810000000002077100000000000002-------------910650171079-2a32030100100--68438 Translating the sequences ************CCCHHHHHH***CCCCCCCCCCCCCCCCEECCCCCCCCCHHH*EEEEEEECC--CCCCCCCCCEEECCEEEEEC**-**EEEEECCCC-CEEEEE*CCCC*HHH**CCCCCCCCCCEEECCEEEEECCCCEEEEEECCCCCEEEEEECCC****CCCCCCCCEEECCEEEECCCC***CCCCEEEEEECCCCCEEEEEECCCCC**--------*****------******H*CCC***C*******CCCCCC*EEECCCCEEEEECCC**CCCHHH*C***CCCCCCCEEEEECCCCCCEEEEEECCCCCCCCCCCCCCCEEEEEE*C-----------------C*EEEEEEE*C-CCCEEEEEECCCCCEEEEEECC-CCCCEEEEC-CCCCEEECHHH*CCC-------CCEE*CCCCCCCCCCCCCEEECCCCEEEEEEE****EEEEC*CCCCC***********CCCCCEEE****CC----CCC*EEEEEEECCCC*EEEEEEECCCCCCCEEEECCCEEEEECCCCEEEEEECCCCC**-*EECCCCCCCCCEEEEECCEEEEEEEECCC***********-------------------CCCCCEEEEEE*C******* ---------------*HHHHH**CCCCCCCCCCCCCCCCCEECCCCCCCCCHHHCEEEEEEECC--CCCCCCCCCEEECCEEEEECCC*C*EEEEECCCC*CEEEEE*CCCC*HHH**CCCCCCCCCCEEECCEEEEECCCCEEEEEECCCCCEEEEEECCC-HHHCCCCCCCCEEECCEEEE*CCC***CCCCEEEEEECCCCCEEEEEECCCC*******-----*************C**H*CCCC--C*HH-*CCCCCCCC*EEECCCCEEEEECCCCCCCCHHH*C---CCCCCCCEEEEE*CCCCCEEEEEECCCCCCCCCCCCCCCEEEEEE*C-----------------C*EEEEEEE*C-CCCEEEEEECCCCCEEEEEECC*CCCCEEEEC*CCCCEEECHHHCCCC*-----CC*EEECCCCCCCCCCCCCEEECCCCEEEEEEECEEEEEEEC-CCCCC---------C*CCCCCEEEEEEECC****CCCCEEEEEE*CCCC*EEEEEEECCCCCCC*EEECCCEEEEECCCCEEEEEECCCCCEEEEEECCCCCCCCCEEEEECCEEEEEEEECCCCC***************HH*HHH*******CCCCCEEEEEEC-------- -----*******CCCHHHH*--*CCCCCCCCCCCCCCCCCEECCCCCCCCCHHHCEEEEEEECC---CCCCCCC*EEECCEEEEECCC-C*EEEEECCCC-CEEEEE*CCCC*HHH**C****CCCCCEEECCEEEEECCCCEEEEEECCCCCEEEEEECCC*HHHCCCCCCCCEEECCEEEECCCC***CCCCEEEEEECCCCCEEEEEECCCCC*-----------------------C**H**CCC**--HH**CCCCCCCC*EEECCCCEEEEECCCCCCCCHHH*C***CCCCCCCEEEEECCCCCCEEEEEECCCCCCCCCCCCCCCEEEEEE*C*****************C*EEEEEEE*C*CCC*EEEEECCCCCEEEEE*CC-CCCCEEEEC-CCCCEEECHHHCCCC-----*CCCEEECCCCCCCCCCCCCEEECCCCEEEEEEECEEEEEEEC*C-----------**C***CCCEEEEEEECC---*CCCCEEEEEEECCCC*EEEEEEECCCCCCCEEEECCCEEEEECCCCEEEEEECCCCCEEEEEECCCCCCCC*EEEEECCEEEEEEEEC-CCC-------------**HH*HHH****-**CCCCCEEEEEECC*------ ------------CCCHHHHHH**CCCCCCCCCCCCCCCCCEECCCCCCCCCHHHCEEEEEEECC**CCCCCCCCCEEECCEEEEE*CC-C*EEEEECCCC-CEEEEE*CCCC***--*CCCCCCCCCCEEECCEEEEECCCCEEEEEECCCCCEEEEEECCC-HHHCCCCCCCCEEECCEEEECCCC***CCCCEEEEE*CCCCCEEEEEECCCCC--*****************-----C****CCCC--C*HH-*CCCCCCCC*EEECCCCEEEEECCCCCCCCHHH*C---CCCCCCCEEEEECCCCCCEEEEEECCCCCCCCCCCCCCCEEEEEE*C-----------------C*EEEEEEE*C-CCCEEEEEECCCCCEEEEEECC*CCCCEEEEC-CCCCEEECHHHCCCC******CCCEEECCCCCCCCCCCCCEEECCCCEEEEEEECEEEEEEEC-CCCCC---------C*CCCCCEEEEEEECC*----CCCEEEEEEECCCC*EEEEEEECCCCCCCEEEECCCEEEEECCCCEEEEEECCCCCEEEEEECCCCCCCCCEEEEECCEEEEEEEECCCCC**-------------HH*HHH******-CCCCCEEEEEECC--***** 50998.tem _________________________________ -----*******CCCHHHHHH**CCCCCCCCCCCCCCCCCEECCCCCCCCCHHHCEEEEEEECC--CCCCCCCCCEEECCEEEEECCC-C*EEEEECCCC-CEEEEE*CCCC*HHH**CCCCCCCCCCEEECCEEEEECCCCEEEEEECCCCCEEEEEECCC*HHHCCCCCCCCEEECCEEEECCCC***CCCCEEEEEECCCCCEEEEEECCCCC******----*********--***C**H*CCCC**C*HH**CCCCCCCC*EEECCCCEEEEECCCCCCCCHHH*C***CCCCCCCEEEEECCCCCCEEEEEECCCCCCCCCCCCCCCEEEEEE*C-----------------C*EEEEEEE*C-CCCEEEEEECCCCCEEEEEECC*CCCCEEEEC-CCCCEEECHHHCCCC*----*CCCEEECCCCCCCCCCCCCEEECCCCEEEEEEECEEEEEEEC*CCCCC-------**C*CCCCCEEEEEEECC*--*CCCCEEEEEEECCCC*EEEEEEECCCCCCCEEEECCCEEEEECCCCEEEEEECCCCCEEEEEECCCCCCCCCEEEEECCEEEEEEEECCCCC*********----**HH*HHH*******CCCCCEEEEEECC*-***** Structural block scores 0 4 - 4.3 M 6.9 75.0 75.0 75.0 5 11 * 3.5 M 3.4 75.0 5.4 75.0 12 14 C 4.3 M 2.7 75.0 4.0 4.7 15 20 H 4.7 H 4.2 4.3 15.0 3.2 21 22 * 1.6 P 2.5 1.5 38.5 0.5 23 39 C 5.0 H 1.6 2.0 1.4 1.7 40 41 E 5.0 H 0.0 1.0 0.0 0.0 42 50 C 5.0 H 3.7 4.1 4.1 2.9 51 53 H 5.0 H 4.3 4.7 4.7 3.3 55 61 E 5.0 H 1.9 3.6 3.6 2.6 62 63 C 5.0 H 3.0 5.8 1.0 4.5 64 65 - 4.3 M 75.0 75.0 75.0 10.2 66 74 C 4.8 H 1.4 1.1 10.5 1.3 75 77 E 5.0 H 0.0 0.0 0.0 0.0 78 79 C 5.0 H 2.5 6.5 3.5 4.0 80 84 E 5.0 H 0.0 0.2 0.0 0.2 85 87 C 4.3 M 0.3 0.0 1.0 1.0 91 95 E 5.0 H 0.0 0.6 0.4 0.6 96 99 C 5.0 H 1.8 3.2 2.8 2.8 102 106 E 5.0 H 1.4 2.8 1.6 2.4 108 111 C 5.0 H 4.0 4.9 4.4 3.0 113 115 H 4.3 M 4.3 4.3 7.0 27.0 116 117 * 1.6 P 4.5 4.5 2.0 38.5 118 127 C 4.7 H 0.6 0.5 1.5 1.0 128 130 E 5.0 H 0.3 0.0 0.7 0.7 131 132 C 5.0 H 2.5 4.5 4.5 8.0 133 137 E 5.0 H 0.2 0.0 0.4 0.2 138 141 C 5.0 H 1.0 0.2 0.5 0.0 142 147 E 5.0 H 1.0 1.0 0.8 1.2 148 152 C 5.0 H 3.0 4.8 3.4 4.6 153 158 E 5.0 H 3.5 3.5 3.2 3.7 159 161 C 5.0 H 3.3 1.7 3.3 2.3 163 165 H 4.3 M 5.0 5.3 4.3 3.7 166 173 C 5.0 H 0.5 0.1 0.0 0.1 174 176 E 5.0 H 0.0 0.0 0.0 0.3 177 178 C 5.0 H 3.5 6.0 4.0 3.0 179 182 E 5.0 H 0.2 0.0 0.0 0.5 183 186 C 4.8 H 0.5 0.8 0.0 0.5 187 189 * 1.0 P 0.3 0.3 1.0 0.7 190 193 C 5.0 H 0.2 0.8 1.5 0.5 194 199 E 4.9 H 0.5 0.3 0.5 1.0 200 204 C 5.0 H 3.8 4.2 4.2 4.2 205 210 E 5.0 H 1.5 2.0 2.5 1.2 211 215 C 4.9 H 1.0 2.0 2.6 0.4 216 221 * 3.3 M 51.8 2.9 64.4 25.8 222 225 - 4.3 M 75.0 75.0 75.0 6.6 226 234 * 3.0 P 36.3 11.8 75.0 4.4 235 236 - 4.3 M 75.0 2.5 75.0 75.0 237 239 * 3.5 M 3.0 3.7 75.0 75.0 241 242 * 1.0 P 2.0 1.0 5.8 4.5 245 248 C 4.7 H 1.8 5.4 4.6 4.4 249 250 * 3.5 M 3.5 75.0 2.5 75.0 253 254 H 4.3 M 3.5 3.0 6.0 3.0 255 256 * 2.2 P 0.5 38.5 2.5 38.0 257 264 C 4.8 H 0.1 0.1 0.2 0.2 266 268 E 5.0 H 0.3 0.0 0.0 0.0 269 272 C 5.0 H 4.5 4.2 4.0 3.8 273 277 E 5.0 H 0.0 0.0 0.0 0.2 278 285 C 4.8 H 0.0 0.0 0.0 0.0 286 288 H 5.0 H 3.0 2.7 1.3 2.3 291 293 * 3.5 M 5.3 75.0 4.3 75.0 294 300 C 5.0 H 1.4 1.4 1.6 1.7 301 305 E 5.0 H 0.0 0.0 0.0 0.0 306 311 C 4.9 H 3.3 3.0 3.8 2.2 312 317 E 5.0 H 1.3 0.7 2.5 1.3 318 332 C 5.0 H 0.1 0.1 0.1 0.1 333 338 E 5.0 H 2.7 1.2 1.7 1.8 341 357 - 4.3 M 75.0 75.0 3.6 75.0 360 366 E 5.0 H 2.0 1.3 1.6 0.9 370 372 C 5.0 H 0.0 0.0 0.0 0.0 373 378 E 4.9 H 0.0 0.2 0.0 0.5 379 383 C 5.0 H 3.0 2.4 3.6 3.6 384 389 E 4.9 H 2.2 1.3 0.2 1.7 390 391 C 5.0 H 0.0 0.0 0.0 0.0 393 396 C 5.0 H 2.8 1.0 2.0 1.8 397 400 E 5.0 H 2.8 3.0 3.0 3.0 403 406 C 5.0 H 5.2 5.6 5.0 5.0 407 409 E 5.0 H 3.7 2.7 2.3 2.3 411 413 H 5.0 H 5.5 5.7 4.7 6.0 414 417 C 4.8 H 3.5 2.2 2.8 3.0 419 422 - 4.3 M 75.0 75.0 75.0 9.5 424 426 C 4.5 M 27.7 2.7 3.7 4.3 427 429 E 4.8 H 1.3 4.3 2.3 1.7 430 442 C 5.0 H 0.3 0.0 0.2 0.0 443 445 E 5.0 H 0.0 0.0 0.0 0.0 446 449 C 5.0 H 4.2 4.8 4.0 4.0 450 456 E 5.0 H 0.0 0.0 0.0 0.0 458 464 E 4.7 H 0.4 0.6 1.1 0.9 467 471 C 4.4 M 5.2 5.4 61.8 5.6 472 478 - 4.3 M 6.0 75.0 75.0 75.0 479 480 * 3.5 M 3.5 75.0 4.5 75.0 483 487 C 4.7 H 1.4 2.0 2.6 2.6 488 494 E 4.6 H 4.0 2.1 2.6 1.7 495 496 C 5.0 H 5.0 2.5 3.0 2.5 498 499 - 4.3 M 75.0 2.5 75.0 75.0 501 504 C 4.7 H 5.0 3.8 3.5 21.0 505 511 E 4.9 H 0.7 0.4 0.3 0.4 512 515 C 5.0 H 2.5 1.5 1.2 2.5 517 523 E 5.0 H 2.4 1.7 2.0 2.4 524 530 C 5.0 H 1.1 0.6 0.6 0.7 531 534 E 4.8 H 0.0 0.0 0.0 0.0 535 537 C 5.0 H 2.0 2.0 1.3 2.3 538 542 E 5.0 H 0.0 0.0 0.0 0.0 543 546 C 5.0 H 0.5 0.2 0.5 0.8 547 552 E 5.0 H 0.7 0.8 0.5 0.8 553 557 C 5.0 H 3.8 4.4 3.8 4.0 558 563 E 4.5 M 15.7 3.0 2.5 2.8 564 572 C 4.9 H 0.7 0.6 0.4 1.0 573 577 E 5.0 H 0.4 0.8 0.4 0.4 578 579 C 5.0 H 8.5 9.8 9.2 7.0 580 587 E 5.0 H 0.8 0.5 0.2 0.1 588 592 C 4.6 H 0.8 0.0 16.2 0.0 593 601 * 3.2 M 3.8 2.3 75.0 58.6 602 605 - 4.3 M 75.0 6.8 75.0 75.0 606 607 * 3.5 M 75.0 3.5 0.0 75.0 608 609 H 4.3 M 75.0 1.5 4.5 5.0 611 613 H 4.3 M 75.0 0.3 2.7 3.7 614 620 * 2.6 P 75.0 3.6 13.7 14.3 621 625 C 5.0 H 4.4 2.4 5.4 3.5 626 631 E 5.0 H 0.0 0.2 0.2 0.8 632 633 C 4.3 M 6.0 38.5 2.5 0.0 636 640 * 3.5 M 5.0 75.0 75.0 5.8 >>>>>>