Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1gwea- -----------------------------------------------CCCCCCCCCCCCCCCCCCCCCCCCCC---------CCCCCCC---------------------------------------CCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEECCCCCCCCCCHHH-CCCCEEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECC--EEEEEEEECCCCCCCCCHHHHHHHHHHHCCCCCCC----CCCHHHHHHHHHCCHHHHHHHHHHHC-HHHCCCCHHHCCEECCCCEEEECCCCCEEEEEEEEEECCCCC-------CCCHHHHHHHHHH--------CCCHHHHHHHHHHHCCCCCEEEEEEEEEECCHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCHHHHCCCCCCCCCCCCCCEECC-------CCHHHHHHHHHHHHHHHHHC-CCCHHHCHHHCCCCCCCC-CCCCCCCCCC-CCCCCCCCCCCCC-------------CCCCCC--------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHHCHHHHHHHHHHHH--------CCCCC--------CCCCCCCCCCCCC >P1;d1m7sa- C-------------------------------------------------CC--CCCCCCCCCCCCCCCCCCC---------CCCCCCC---------------------------------------CCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEECCCCCCCCCCHHH-CCCCEEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECC--EEEEEEEECCCCCCCCCHHHHHHHHHHHCCCCCCC----CCCHHHHHHHHHCCHHHHHHHHHHHC-HHHCCCCHHHCCEECCCCEEEECCCCCEEEEEEEEEECCCCC-------CCCHHHHHHHHHH--------CCCHHHHHHHHHHHCCCCCEEEEEEEEECHHHHHHCCCCCCCCCCCCC--CCCEEEEEEEEEEEECCCHHHHCCCCCCCCCCCCCCEEEC-------CCHHHHHHHHHHHHHHHHHC-CCCHHHCHHHCCCCCCCC-CCCCCCCCCC-CCCCCCCCCCCC-------------CCCCC---------CCHHHCCCCCCCCCCCCCCCCC---CCCCCHHHHHHHH-HCCHHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHH-CCHHHHHHHCCC---CCCHHHHH----HHHHCCCC------------- >P1;d1u5ua- ------------------------------------------------------------------------------------CCCCHHHHHHHHHCHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH--CCCCCCCCCCEEEEEEEEEECCCC-CCCCCCCC-CCCCEEEEEEEEECCCC---CCCCCEECCEEEEECCCCCCCCCCEEEEEECCCCCCCCHHHHHHHCCCCCC-------------HHHHHHHCCCHHHHHHHHHHCEE---CCCCHHHCCEECCCCEEEECCCCCEEEEEEEEEECCCCCCHHHCCCCCCHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHC-CEEEEEEEEEEECC--CCCCHHHHCCCCCCCCCCCCCEEEEEEEEEEECC--HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH--HCCCCCC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- >P1;d2xq1a- ---------------------------------------------------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---------------------------------------CCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEECCCCCCCCCCHHHCCCCCEEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECC--EEEEEEEECCCCCCCCCHHHHHHHHHHHCCCCCCC----CCCHHHHHHHHHHCHHHHHHHHHHHC-HHHCCCCCCCCCEECCCCEEEECC-CCEEEEEEEEEECCCCC-------CCC-CCHHHHHC---------CCCHHHHHHHHHC--CCCCEEEEEEEEEC-CCC-CCCCCCCCCCCCCCC-CCCCEEEEEEEEEECCCCHHHHCCCCCCCCCCCCCCEEEC-------CCHHHHHHHHHHHHHHHHHC-CCCHHHCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--------------------------CCCCCCCCCCCCCCCCCC--HHHHCCCCCCCCCC-CCCHHHHHC-CHHHHHCCC--CCHHHHHHHHHCCCCC-CHHHHHCCC----------------------------------- >P1;d3ttva1 CCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCHHHHHHHHCCCCCCCCC--CCCCCCCCCCCCCCCCCCC---------CCCCCCC---------------------------------------CCHHHHHHHHHHHCCCCCCCCCCCCEEEEEEEEEECCCCCCCCCCHHHCCCCCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECC--EEEEEEEECCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCHHHHHHHHHHHC-HHHCCCCHHHCCEECCCCEEEECCCCCEEEEEEEEEECCCCC-------CCCHHHHHHHHHH--------CCCHHHHHHHHHHHHCCCCEEEEEEEEEEHHHCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCHHHHCCCCCCCCCCCCCCEECC-------CCHHHHHHHHHHHHHHHHHHCCCCHHHCHHHCCCCCCCC-CCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--------------CCCCCCH--HHCCCCHHHHHHHH-HCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCHHHHCCCCCCCCCCCCCCHHHCCCCCCCCC PSA >P1;d1gwea- -----------------------------------------------a78923b553777420846992627c---------993842a---------------------------------------816135356677766b24216120000000040404560471030500-3493503000000000035a1200100000010000084--30000101001010012373366006100308927----40000200410061400000001000-230004002100000100000006867120000003042724-------20708606721b6--------4453035206510576730401020000429508714100100004035a4162330010104510a73563010000003320500010-------20300442285355604801-65105246006144a647-26187a9297-728b2167370a8-------------c28397--------a88a7643289b99b58782a72850622810061047607974256004000000370-5950164018003601980054015006--------68603--------c00117049b515 >P1;d1m7sa- b-------------------------------------------------b5--542678570b63883635b---------8a28439---------------------------------------816134456677675824418120000003040405280871030300-758260300000001024681300220001010000053--3000011100301000428436501710210685a----86423210510070210000000000-130002001102010000000008776110010205022946-------1123a51893478--------362003730371078674030102012053731972901010000303--a184540040302721966471011000002220400120-------30300551386355406800-55215638105154a675-3a5869a488-9883c0565809-------------85527---------968837a1a389ab9b6a6719---3311070005105-717a64261005000610480-5890103000002-216600430020---80649505----73088289------------- >P1;d1u5ua- ------------------------------------------------------------------------------------250102500065487a40552274147229937770985076227401843366047--411310422100003140403a81-60270600-63244060000000143---620010010001000245448240001030010102000401332460636-------------a4048001400000200001000---10600020000011000060559670100010001748262670420074920360130725ba1846731027205630777-50105000001524--9927411201013078a71513400601055415--882113010103201b00411908003201001201321375116208--646b638---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- >P1;d2xq1a- ---------------------------------------------------a98721787760b5497252847969b6a23761853a---------------------------------------80622526648767472531812000000003030146047103040048552604000000001135b4100510001010000063--41001103001000001291357008202328858----85323210510052210000001000-041002002101010100100229-a9020000003043857-------218-530a723a---------3453036207710--78401010200206-561-816030200003046-8071430040303510965452002000003320600510-------40300451285315405800-44115028003254a74615818668166b44bb32765a096191a7b--------------------------ba5187a8ab69572837--a3026106014027-697227201-002940470--7702740080023057-00760591a----------------------------------- >P1;d3ttva1 9a44b8775514476175a435414025044a26160055077429a87b83--630788670a53862536b---------9a2743a---------------------------------------8163353656776848264181200000000303047406a201010034393500000000010033a1100101000010000041--41000101000010003292465008112118767515051000400310053200000000000-000004002101000000000102976010000105032014-------00628505622a8--------244202510220000374030100001044822961502010000000352181460030001000273451012000001300100020-------50200451296256304800a240131130021117474-1819589168-939250653809538462495836575153572938879a--------------a5a6358--60543200020003-0028602720160013005509555025500410030128005400940a29079a14829407304a18603300033785a7 Translating the sequences -----------------------------------------------***CC**CCCCCCCCCCCCCCCCCCC---------CCCCCCC---------------------------------------CCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEECCCCCCCCCCHHH-CCCCEEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECC--EEEEEEEECCCCCCCCCHHHHHHHHHHHCCCCCCC----CCCHHHHHHHHHCCHHHHHHHHHHHC-HHHCCCCHHHCCEECCCCEEEECCCCCEEEEEEEEEECCCCC-------CCCHHHHHHHHHH--------CCCHHHHHHHHHHH*CCCCEEEEEEEEEE*CH***CCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCHHHHCCCCCCCCCCCCCCEECC-------CCHHHHHHHHHHHHHHHHHC-CCCHHHCHHHCCCCCCCC-CCCCCCCCCC-CCCCCCCCCCCCC-------------CCCC**--------*****CCCCCCCCCCCCCCCC****CCCCHHHHHHHH**CCHHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHH**CHHHHHHHH****--------*****--------************* *-------------------------------------------------CC--CCCCCCCCCCCCCCCCCCC---------CCCCCCC---------------------------------------CCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEECCCCCCCCCCHHH-CCCCEEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECC--EEEEEEEECCCCCCCCCHHHHHHHHHHHCCCCCCC----CCCHHHHHHHHHCCHHHHHHHHHHHC-HHHCCCCHHHCCEECCCCEEEECCCCCEEEEEEEEEECCCCC-------CCCHHHHHHHHHH--------CCCHHHHHHHHHHH*CCCCEEEEEEEEE***H***CCCCCCCCCCCCC--CCC*EEEEEEEEEE*CCCHHHHCCCCCCCCCCCCCCEE*C-------CCHHHHHHHHHHHHHHHHHC-CCCHHHCHHHCCCCCCCC-CCCCCCCCCC-CCCCCCCCCCCC-------------*CCCC---------******CCCCCCCCCCCCCCCC---*CCCCHHHHHHHH-*CCHHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHH-CCHHHHHHH***---********----********------------- ------------------------------------------------------------------------------------CCCC******************************************HHHHHHHHHH*--CCCCCCCCCCEEEEEEEEEECCCC-CCCCC***-CCCCEEEEEEEEECCCC---CCCCC**CCEEEEE***CC*****EEEEE*CCCCCCCCHHHHHHH****CC-------------HHHHHHH*CCHHHHHHHHHH***---CCCCHHHCCEECCCCEEEECCCCCEEEEEEEEEECCCCC*******CCCHHHH**************CCCHHHHHHHHHHH*C-C*EEEEEEEEEE*C--*CCC****CCCCCCCCCCCCCEEEEEEEEEE*CC--HHH***CCCCCCCCCCC**CC*******CCHHHHHHHHHHHHHHHHH*--*C***C*---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ---------------------------------------------------C**CCCCCCCCCCCCCCCCCCC*********CCCCCCC---------------------------------------CCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEECCCCCCCCCCHHH*CCCCEEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECC--EEEEEEEECCCCCCCCCHHHHHHHHHHHCCCCCCC----CCCHHHHHHHHH*CHHHHHHHHHHHC-HHHCCCC***CCEECCCCEEEECC-CCEEEEEEEEEECCCCC-------CCC-**HHHHH*---------CCCHHHHHHHHH*--CCCCEEEEEEEEE*-C**-CCCCCCCCCCCCCCC-CCCCEEEEEEEEEECCCCHHHHCCCCCCCCCCCCCCEE*C-------CCHHHHHHHHHHHHHHHHHC-CCCHHHCHHHCCCCCCCC*CCCCCCCCCC*CCCCCCCCCCCCC******--------------------------CCCCCCCCCCCCCCCC**--**************-C**HHHHH*-*HHHHHCCC--**HHHHHHHHH**CC*-*HHHHH***----------------------------------- **************************************************CC--CCCCCCCCCCCCCCCCCCC---------CCCCCCC---------------------------------------CCHHHHHHHHHH*CCCCCCCCCCCCEEEEEEEEEECCCCCCCCCCHHH*CCCC*EEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECC--EEEEEEEECCCCCCCCCHHHHHHHHHHHCCCCCCC****CCC*HHHHHHHH*CHHHHHHHHHHHC-HHHCCCCHHHCCEECCCCEEEECCCCCEEEEEEEEEECCCCC-------CCCHHHHHHHHHH--------CCCHHHHHHHHHHH*CCCCEEEEEEEEEE**H**CCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCHHHHCCCCCCCCCCCCCCEECC-------CCHHHHHHHHHHHHHHHHH**CCCHHHCHHHCCCCCCCC-CCCCCCCCCC-CCCCCCCCCCCCC*************CCCC**********--------------CCCCCC*--**CCCCHHHHHHHH-*CCHHHHHHHHHHHHHHH*CC*CHHHHHHHHHHHH*CCHHHHHHHH************************************** 56634.tem _________________________________ --------------------------------------------------CC--CCCCCCCCCCCCCCCCCCC---------CCCCCCC---------------------------------------CCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEECCCCCCCCCCHHH-CCCCEEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECC--EEEEEEEECCCCCCCCCHHHHHHHHHHHCCCCCCC----CCCHHHHHHHHHCCHHHHHHHHHHHC-HHHCCCCHHHCCEECCCCEEEECCCCCEEEEEEEEEECCCCC-------CCCHHHHHHHHHH--------CCCHHHHHHHHHHH*CCCCEEEEEEEEEE*CH**CCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCHHHHCCCCCCCCCCCCCCEECC-------CCHHHHHHHHHHHHHHHHHC-CCCHHHCHHHCCCCCCCC-CCCCCCCCCC-CCCCCCCCCCCCC-------------CCCC---------------CCCCCCCCCCCCCCCC---*CCCCHHHHHHHH-*CCHHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHH*CCHHHHHHHH***---------*------------------------- Structural block scores 0 49 - 4.4 M 71.0 73.7 75.0 75.0 5.1 50 51 C 4.3 M 5.5 8.2 75.0 42.8 5.5 52 53 - 3.8 M 7.2 75.0 75.0 8.5 75.0 54 72 C 4.5 M 5.6 5.7 75.0 5.4 5.5 73 81 - 4.5 M 75.0 75.0 75.0 7.1 75.0 82 88 C 4.8 H 6.5 6.4 22.6 5.8 6.6 89 127 - 4.5 M 75.0 75.0 4.4 75.0 75.0 128 129 C 4.5 M 4.5 4.5 5.5 4.0 4.5 130 139 H 5.0 H 4.9 4.9 3.5 4.8 5.1 140 152 C 4.8 H 3.7 3.7 13.5 3.5 3.8 153 162 E 5.0 H 0.8 1.1 1.2 0.6 0.6 163 172 C 5.0 H 3.0 3.4 11.2 2.6 3.5 173 175 H 4.5 M 1.7 1.0 2.0 1.3 0.3 177 180 C 5.0 H 4.8 5.5 3.8 5.0 4.8 181 189 E 4.9 H 0.9 1.0 1.1 1.1 0.6 190 205 C 4.8 H 1.4 1.8 15.2 2.0 1.3 206 213 E 4.8 H 0.1 0.2 0.9 0.2 0.1 214 215 C 5.0 H 6.0 4.0 4.5 4.5 2.5 216 217 - 4.5 M 75.0 75.0 6.0 75.0 75.0 218 225 E 4.8 H 0.6 0.8 1.2 1.2 0.9 226 234 C 4.9 H 0.6 0.9 0.4 0.2 0.4 235 245 H 4.8 H 3.2 3.4 2.6 3.4 3.5 246 252 C 4.6 H 4.1 4.6 54.9 5.1 4.6 253 256 - 4.5 M 75.0 75.0 75.0 75.0 2.8 257 259 C 4.5 M 1.3 6.0 75.0 5.3 2.0 260 268 H 4.8 H 0.8 1.6 11.4 1.6 0.9 269 270 C 4.4 M 3.5 3.5 2.0 3.5 4.0 271 281 H 5.0 H 0.5 0.3 0.3 0.4 0.2 284 286 H 4.5 M 1.7 1.3 75.0 1.7 0.0 287 290 C 5.0 H 1.0 0.5 1.8 0.5 1.0 291 293 H 4.5 M 1.0 0.7 0.7 1.0 1.0 294 295 C 5.0 H 0.0 1.0 0.0 0.5 0.5 296 297 E 5.0 H 0.0 0.5 0.0 0.5 0.0 298 301 C 5.0 H 0.2 0.0 0.5 0.2 0.0 302 305 E 5.0 H 0.0 0.0 1.5 0.8 0.2 306 310 C 4.9 H 5.4 5.6 5.0 21.1 4.8 311 320 E 5.0 H 0.6 1.0 0.9 0.5 0.7 321 325 C 5.0 H 3.8 4.6 4.4 5.4 2.0 326 332 - 4.5 M 75.0 75.0 3.9 75.0 75.0 333 335 C 5.0 H 3.0 1.3 2.3 3.7 2.0 336 345 H 4.4 M 4.8 5.8 2.8 19.1 4.8 346 353 - 4.5 M 75.0 75.0 6.1 75.0 75.0 354 356 C 5.0 H 4.3 3.7 5.3 4.0 3.3 357 367 H 4.9 H 2.7 2.8 3.0 9.5 1.3 369 372 C 4.8 H 4.0 4.2 21.8 4.8 3.5 373 382 E 4.9 H 1.1 1.4 1.2 1.2 0.9 386 387 * 2.1 P 4.0 5.0 42.0 38.0 5.5 388 407 C 4.8 H 2.5 10.0 3.5 6.2 1.8 408 417 E 5.0 H 1.7 2.5 2.4 2.2 1.4 418 421 C 4.6 H 4.6 4.5 21.2 4.0 2.2 422 425 H 4.9 H 4.2 4.5 23.2 4.0 3.2 426 439 C 4.9 H 1.0 0.9 1.8 1.1 0.6 440 441 E 4.5 M 0.0 0.5 2.0 2.5 0.0 442 443 C 4.4 M 0.5 1.0 1.0 0.5 1.0 444 450 - 4.5 M 75.0 75.0 3.1 75.0 75.0 451 452 C 5.0 H 1.0 1.5 0.5 2.0 2.5 453 469 H 5.0 H 3.5 3.6 2.1 3.2 3.4 472 474 C 4.7 H 4.0 4.0 28.3 3.0 2.0 475 477 H 4.5 M 2.3 4.0 7.8 2.0 1.7 479 481 H 4.5 M 2.0 3.0 52.7 2.7 1.0 482 489 C 4.5 M 5.3 5.4 75.0 5.2 3.4 491 500 C 4.5 M 6.2 7.2 75.0 5.5 5.6 502 514 C 4.5 M 5.6 11.4 75.0 6.1 4.9 515 527 - 4.1 M 75.0 69.8 75.0 43.5 5.4 528 531 C 4.2 M 6.4 4.8 75.0 75.0 3.5 532 546 - 4.1 M 44.0 47.7 75.0 75.0 29.6 547 562 C 4.3 M 7.1 7.8 75.0 7.5 45.2 563 565 - 3.8 M 5.7 75.0 75.0 28.3 52.0 567 570 C 4.1 M 2.5 1.2 75.0 3.9 3.5 571 578 H 4.1 M 2.5 2.2 75.0 2.2 0.6 581 582 C 4.3 M 3.5 4.0 75.0 40.5 1.0 583 597 H 4.4 M 2.5 2.8 75.0 8.0 2.4 598 600 C 4.4 M 3.3 4.0 75.0 3.7 3.3 603 614 H 4.4 M 3.1 1.9 75.0 3.1 2.2 616 617 C 4.3 M 0.5 1.5 75.0 2.5 0.5 618 625 H 4.3 M 3.4 2.4 75.0 12.5 2.4 626 628 * 2.4 P 1.7 25.7 75.0 6.8 4.3 629 637 - 3.9 M 67.3 20.2 75.0 75.0 5.9 639 663 - 3.8 M 27.0 52.8 75.0 75.0 4.2 >>>>>>