Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2a65a1 -CCCCCCHHHHHHHHHHHHCCHHHHCHHHHHHHHCCCHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHC-CCHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCEECCEEHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCHHHHHHHHHHCCCHHHHCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHCC---CCC-----------HHHHHHHHHHHHHHHHHHHHH--------------------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCCHHHHHHHCHHHHHHHHHHHHHHHHCHHHHHH-------------------------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--------------------------------------------------------------------------------------------- >P1;d3giaa- CCCCCCCHHHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHCCCC--CCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-------------------CCCCC------------------HHHHHHHHHHHHHHHHHHHHHCHHH-HHHHHHHHHHHHHHHHHHHHHHHHH----HCCHHHCC--CCCC----H-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCHHHHHHCHH--------HHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHH-CCCCCCCCCCC-CCCCCHHHHHHHHHHHHHHHHC-------------------------CHHHHHHHHH-HHHHHHHHHHHHHHHHC--HHHHCC-C---------HHHHHHHHHHHHHHHHHHHHHHHHHC-------------------------------------HHHHHHHHHHHHHHHHHHHHHHHHHCCCCC---------------HHHCCCC----------------------------------------------------------------------- >P1;d3ooia1 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CHHHHHHHHHHHCCCCCCCEECCCCEECCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCHHHH---------------CCCCCCC-------CCCCCHHHCCCCHHHHCCCCCEEEEECCCCCEEEEECCCCCCCCEEEECCEEEEC---HHHHHHHHHHHHHC------CCCCCCEEEEECCEEEEEEEEECHHHHCEECCCCCEEEEEEEECCEEEEEEEECCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCCCCCC--------- >P1;d5j4ia- CHHHCCCHHHHHHHHHHHHHCCHHHC-HHHHHCC-CCCCHHHHHHHHHH-HHHHHHHHHHHHHHHCC--CCCCHHHHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-------------------HHHHC------------------HHHHHHHHHHHHHHHHHHHHHCHHH-HHHHHHHHHHHHHHHHHHHHHHHHH----CCCHHHHHHCCCCC----CCCHHHHHHHHHHHHHHHHCCCCHHHHCHHHCC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HCCHHHHHHC-C--------CCCHHHHHHH-CCHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHC------------------HHHHHHHHHHHHHHH-HHCHHHHHHHHHHHHHH--HHHHCHHH---------HHHHHHHHHHHHHHHHHHHHCCC----------------------------------------HHHHHHHHHHHHHHHHHHHHHHC--------------------------CCCCCCCCC--------------------------------------------------------------CCC >P1;d5lt7a1 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCCCCCCCCCCCCCCHHHHHCHHHHHHHHHCCCCCCCCEECCCCEEC-------------CCCCCCC---CCCCC--CCHHHH---------------CCCCCCC-------C-CCCHHHCCCCCCCCCCCCCEEEEECCCCCEEEEECCCCCCCCEEEECCCEEEC---HHHHHHHHHHHHHC------CCCCCCEEEEECCEEEECCCEECHHHHCEECCCCCEEEEEEEECCEEEEEEEECCCCCCCCEEEECCHHHHCCCCEEECCCCCCCCCCEEECCCCCCCCC PSA >P1;d2a65a1 -242065370011000000000000020002003270000030054016300000000000000200346200002001003-55560151002000000000000000000010004205657119059b7672125104610480112199b925180483035004500830141036002700061037004307810450162047071963407503810474579428454021200100010010000000000000568200040044004401610161000000000002144a7027105567220000000000131bb046001100300010000100000-00000002101---527-----------466005701620370032005--------------------0360160031200121004001100300043050960281014606480587114103650072057015305774247349-------------------------736701640093067027404611541143569678--------------------------------------------------------------------------------------------- >P1;d3giaa- 88184251640011000000000000-0000005004200030053005-00210020023004500--0000000001302714440010000010000000000010100030215-------------------a2755------------------b821261058106501600563045-3085147105602810550183038----61879337--3385----9-9245314200000000000010000003005---724510150063004301910230020000-005284037126--------0000300430-28a90254005101600200000000000000100032-07035302013-0051450065018302610450-------------------------8120000000-00002001300400441--0a5081-7---------59405703720480164016104444-------------------------------------560273037126814660362277380705---------------6800562----------------------------------------------------------------------- >P1;d3ooia1 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------a868726544783981891640760433b8074582858703705075a5960003a2a04016---------------6340025-------710308c505003056392070321103335100404480875300000000001---59307621571675------a59702013058500000142004000020105120422403062122000004680948510103175513219a47040b177247515--------- >P1;d5j4ia- 9a853042820110001000128003-0016006-00000350074026-10210050002005112--25000010045034-4320000000012000050061033006120337-------------------77175------------------4731073026103510620262154-0083017106311610562056038----62569306813221----c5b684022300530011010000000004106---726600150045005400700240020000-1261960481-a--------3001422585-7988102611600011010000000-000000020005390059502835b360031004300630364062054------------------8a3698174524005-00002004100200252--06a60ca6---------57724730640360064037218----------------------------------------a6236517423760674078617--------------------------973966a5a--------------------------------------------------------------baa >P1;d5lt7a1 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aa9a79caa6b996063a005358606611968300a30501570443-------------6508285---71089--905026---------------7410067-------8-02068906011022455170402519524200402760757300100000005---77426604860696------93852101705d8220001530100000100042205113030b95210000035606574201031532127aa356030b2991386103386a6a7a Translating the sequences -***CCCHHHHHHHHHHHH***H**C**HHHH*******HHHHHHHHHH**HHHHHHHHHHHH******CCCCHHHHHHHH*-**HHHHHHH*HHHHHHHHHHHHHHHHHHHHH***********************************************HHHHHHHHHHHHHHHHHH**C****HHHHHHHHHHHHHHHHHHHHHHH*********HHH******CC*******HHHHHHHHHHHHHHH*****HHHH*H**CC***C*HHHHHHHHHHHHHHHH**HHHHHHHHH****CHHHHHH**************HHHH******HHHHHHHHHHHHHHHHHHHHHHH-**HHHHHHH**---CCC-----------**HHHHHHHHHHHHHHHH***--------------------***HHHHHHHHCC*HH*HHHHHHHHHHHH****HHHH*******CCCCCCCHHHHHHHCHHHHHHHHHHHHHHH*C******-------------------------C*****HHHHHHHHHHHHHHHHHHHHHH********--------------------------------------------------------------------------------------------- ****CCCHHHHHHHHHHHH***H**C-*HHHH*******HHHHHHHHHH-*HHHHHHHHHHHH****--CCCCHHHHHHHH****HHHHHHH*HHHHHHHHHHHHHHHHHHHHH****-------------------*****------------------*HHHHHHHHHHHHHHHHHH**C***-HHHHHHHHHHHHHHHHHHHHHHH**----***HHH**--**CC----*-*HHHHHHHHHHHHHHH*****HHHH*H**CC---C*HHHHHHHHHHHHHHHH**HHHHHHHHH*-**CHHHHHH***--------***HHHH***-**HHHHHHHHHHHHHHHHHHHHHHH***HHHHHHH***-*CCC****CCC-CCCC*HHHHHHHHHHHHHHHHC-------------------------*HHHHHHH**-HH*HHHHHHHHHHHH**--HHHH**-*---------*HHHHHHH*HHHHHHHHHHHHHHH*C-------------------------------------HHHHHHHHHHHHHHHHHHHHHH***CCCC*---------------*HH**C*----------------------------------------------------------------------- -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------*HHHHHHHHHHHC*C***********************HH******CC***C********HHHH---------------CCCCCCC-------C****HHH****HHHH*C*******************************C*****---HHHHHHHHHHHHH*------**CCCC*****************HH**C**CCCCC********************************************************--------- ****CCCHHHHHHHHHHHH***H**C-*HHHH**-****HHHHHHHHHH-*HHHHHHHHHHHH****--CCCCHHHHHHHH**-*HHHHHHH*HHHHHHHHHHHHHHHHHHHHH****-------------------*****------------------*HHHHHHHHHHHHHHHHHH**C***-HHHHHHHHHHHHHHHHHHHHHHH**----***HHH******CC----***HHHHHHHHHHHHHHH*****HHHH*H**CC---C*HHHHHHHHHHHHHHHH**HHHHHHHHH*-**CHHHHHH*-*--------***HHHH***-**HHHHHHHHHHHHHHHHHHHHHHH-**HHHHHHH*****CCC****CCC*CCCC*HHHHHHHHHHHHHHHH**C------------------*****HHHHHHHH**-HHCHHHHHHHHHHHH**--HHHH****---------*HHHHHHH*HHHHHHHHHHH***----------------------------------------HHHHHHHHHHHHHHHHHHHHHH*--------------------------*C**CCCCC--------------------------------------------------------------*** -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCC****CCC*CCCC*HHHHH*HHHHHHHHH*C*C*************-------------*****CC---C****--**HHHH---------------CCCCCCC-------C-***HHH*********C*******************************C*****---HHHHHHHHHHHHH*------**CCCC*****************HH**C**CCCCC***************************************************************** 161070.tem _________________________________ -***CCCHHHHHHHHHHHH***H**C-*HHHH**-****HHHHHHHHHH-*HHHHHHHHHHHH****--CCCCHHHHHHHH*--*HHHHHHH*HHHHHHHHHHHHHHHHHHHHH****-------------------*****------------------*HHHHHHHHHHHHHHHHHH**C***-HHHHHHHHHHHHHHHHHHHHHHH**----***HHH**--**CC----*-*HHHHHHHHHHHHHHH*****HHHH*H**CC---C*HHHHHHHHHHHHHHHH**HHHHHHHHH*-**CHHHHHH*-*--------***HHHH***-**HHHHHHHHHHHHHHHHHHHHHHH-**HHHHHHH**---CCC****CCC-CCCC*HHHHHHHHHHHHHHHHC*C--------------------***HHHHHHHHCC-HHCHHHHHHHHHHHH**--HHHH**-*---CCCCCCCHHHHHHHCHHHHHHHHHHHHHHH*C******-------------------------C*****HHHHHHHHHHHHHHHHHHHHHH***CCCC*---------------*HH**C**CCCCC----------------------------------------------------------------- Structural block scores 1 3 * 3.0 P 2.7 5.7 75.0 7.8 75.0 4 6 C 4.2 M 3.7 3.7 75.0 2.3 75.0 7 18 H 4.2 M 1.0 1.1 75.0 1.2 75.0 19 21 * 3.0 P 0.0 0.0 75.0 1.0 75.0 23 24 * 3.0 P 0.0 0.0 75.0 0.0 75.0 28 31 H 4.2 M 0.5 0.0 75.0 1.8 75.0 32 33 * 3.0 P 1.5 2.5 75.0 3.0 75.0 35 38 * 3.0 P 1.8 1.5 75.0 0.0 75.0 39 48 H 4.2 M 1.9 1.6 75.0 2.7 75.0 51 62 H 4.2 M 0.0 0.8 75.0 0.8 75.0 63 66 * 3.0 P 0.5 2.2 75.0 2.2 75.0 67 68 - 4.5 M 3.5 75.0 75.0 75.0 75.0 69 72 C 4.2 M 2.0 0.0 75.0 1.8 75.0 73 80 H 4.2 M 0.4 0.5 75.0 1.2 75.0 82 83 - 3.8 M 40.0 4.0 75.0 39.5 75.0 85 91 H 4.2 M 2.6 1.3 75.0 0.7 75.0 93 113 H 4.2 M 0.1 0.3 75.0 1.4 75.0 114 117 * 3.0 P 1.0 2.0 75.0 3.2 75.0 118 136 - 4.5 M 4.6 75.0 75.0 75.0 75.0 137 141 * 3.0 P 3.2 5.9 75.0 5.4 75.0 142 159 - 4.5 M 4.0 75.0 75.0 75.0 75.0 161 178 H 4.2 M 2.5 2.9 75.0 2.6 75.0 179 180 * 3.0 P 4.5 5.5 75.0 4.0 75.0 182 184 * 3.0 P 3.0 3.0 75.0 3.3 75.0 186 208 H 4.2 M 2.5 3.2 75.0 2.7 75.0 209 210 * 3.0 P 5.5 5.5 75.0 5.5 75.0 211 214 - 4.5 M 4.2 75.0 75.0 75.0 75.0 215 217 * 3.0 P 4.3 5.0 75.0 4.3 75.0 218 220 H 4.2 M 4.0 6.3 75.0 6.0 75.0 221 222 * 3.0 P 1.5 5.0 75.0 3.0 75.0 223 224 - 3.8 M 4.5 75.0 75.0 4.5 75.0 225 226 * 3.0 P 2.0 3.0 75.0 2.5 75.0 227 228 C 4.2 M 5.5 6.5 75.0 1.5 75.0 229 232 - 4.5 M 6.2 75.0 75.0 75.0 75.0 236 250 H 4.2 M 1.1 1.4 75.0 2.3 75.0 251 255 * 3.0 P 0.2 0.2 75.0 0.2 75.0 256 259 H 4.2 M 0.0 0.0 75.0 0.0 75.0 262 263 * 3.0 P 0.0 1.5 75.0 2.5 75.0 264 265 C 4.2 M 2.5 2.5 75.0 3.0 75.0 266 268 - 4.5 M 5.3 75.0 75.0 75.0 75.0 271 286 H 4.2 M 1.8 2.1 75.0 2.2 75.0 287 288 * 3.0 P 3.5 5.0 75.0 3.5 75.0 289 297 H 4.2 M 0.0 0.8 75.0 0.9 75.0 300 301 * 3.0 P 1.5 0.0 75.0 1.5 75.0 303 308 H 4.2 M 5.1 4.0 75.0 4.7 75.0 312 319 - 4.5 M 2.8 75.0 75.0 75.0 75.0 320 322 * 3.0 P 0.0 0.0 75.0 1.0 75.0 323 326 H 4.2 M 0.0 0.8 75.0 2.2 75.0 327 329 * 3.0 P 1.7 2.3 75.0 6.0 75.0 331 332 * 3.0 P 5.8 5.0 75.0 8.0 75.0 333 355 H 4.2 M 0.7 2.0 75.0 1.6 75.0 357 358 * 3.0 P 0.0 0.0 75.0 0.0 75.0 359 365 H 4.2 M 0.4 0.1 75.0 0.3 75.0 366 367 * 3.0 P 0.5 1.5 75.0 0.0 75.0 368 370 - 4.0 M 75.0 25.7 75.0 5.7 75.0 371 373 C 4.5 M 4.7 3.3 75.0 1.7 10.0 374 377 * 3.0 P 75.0 2.5 75.0 4.0 9.8 378 380 C 4.2 M 75.0 1.3 75.0 5.3 9.0 382 385 C 4.2 M 57.2 1.5 75.0 2.2 6.0 387 402 H 4.8 H 2.6 2.9 23.5 2.4 4.3 406 425 - 4.0 M 75.0 75.0 4.8 68.4 28.4 426 428 * 3.0 P 3.0 75.0 5.0 6.0 75.0 429 436 H 4.0 M 1.6 1.4 3.8 3.9 30.8 437 438 C 3.8 M 0.0 0.0 6.0 2.5 6.5 440 441 H 4.1 M 1.5 0.0 7.0 0.0 75.0 443 454 H 4.2 M 0.8 1.2 3.1 0.9 15.8 455 456 * 3.0 P 3.5 2.5 75.0 3.5 75.0 457 458 - 4.5 M 2.5 75.0 75.0 75.0 75.0 459 462 H 4.2 M 3.8 3.9 75.0 5.6 75.0 463 464 * 3.0 P 5.0 4.5 75.0 6.2 75.0 467 469 - 4.5 M 3.7 75.0 75.0 75.0 75.0 470 476 C 4.1 M 4.4 65.0 2.9 65.0 3.6 477 483 H 4.2 M 2.4 4.0 75.0 4.3 75.0 485 499 H 4.1 M 3.1 2.7 3.2 7.9 7.5 502 507 * 3.0 P 4.8 75.0 2.3 75.0 2.8 508 532 - 3.8 M 75.0 75.0 2.4 75.0 2.9 534 538 * 3.0 P 3.4 75.0 0.2 75.0 1.0 539 560 H 4.7 H 3.2 3.6 30.2 4.6 30.5 561 563 * 2.4 P 4.0 5.7 30.2 52.3 29.0 564 567 C 4.1 M 7.0 3.8 4.5 75.0 4.0 569 583 - 3.8 M 75.0 75.0 1.9 75.0 3.2 585 586 H 4.2 M 75.0 4.0 2.0 75.0 0.0 587 588 * 2.5 P 75.0 2.5 0.0 42.0 0.0 590 591 * 2.5 P 75.0 38.5 1.0 6.0 0.5 592 596 C 4.2 M 75.0 75.0 1.8 7.6 1.6 597 661 - 3.9 M 75.0 75.0 13.3 72.0 4.0 >>>>>>