Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1gkub3 CCCCCCEEEEEEECCHHHHHHHHHHHCCCEEEEECCEEEEEEECCCEEEEEEECCCCCEEECCC----CCCCCCCCC----CCCCCCEEECCCCHHHHHHHHHHHHHHHCEEEECCCCCHHHHHHHHHHHHHHC------CCCEEEECCCCCCCHHHHHHHHCCCCCC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC----CCCCCCCCCHHHHHHHHHHHHCHHH--CEEEEEEEC-------CCCEEECCCCC---------------------------EEEEEEEEEEEEEEEECCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHH-CCCCCCCCCCCCCCCHHHHH---HHHHHHC---------CCCC---CCCCCC---CCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEECCEEEEECCEEEEECHHHHHCC-----CCCCCCCCCC-------EEEEEECCCEEEECCCCCCHHHHHHHHHHH-----------------CCCCCCCHHHHHHHHHHCCCEEEECCEEEECHHHHHHHHHHHHCCCHHHCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCC----------------- >P1;d1i7da- -------CEEEEECCHHHHHHHHCCCCC-CCEEEC--CEEEEC---CCEEEEECCCCCEEECCHHHHCHHHHCCCCCCCCCCCCCCCEEECHH-HHHHHHHHHHHHHHCCEEEEECCCCHHHHHHHHHHHHHCCCCHHHHHC--CEECCCCCCCHHHHHHHHCCCEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHHHHCCCEEECCEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCC------CC--------CCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCCCCEEECEEEEEECHHHHHCCCCHHHCCCEECCCCCCCCCCEEEEEEEEEEEEECCCCCCEEHHHHHHHHHCHHHHCCCHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCEEECCCEEEECHHHHHHHHHCC---HHHHCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHCCCCCC >P1;d1mw9x- ------CCEEEEECCHHHHHHHHCCCC-------------------CCEEEEECCCCCEECCCCHHHHHHHHCCCCCCCCC----CCCEECCC-CHHHHHHHHHHHHCCCEEEECCCCCHHHHHHHHHHHHHHCC---CHHH--EEECCCCCCCHHHHHHHHHCCCCC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-----CCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEECCCCCEEEEEEEEECC---EEC---CCCCHHHHHHHHHHHHHCCEEEEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHH-CCCCCCCCCCCCCCCHHHHH---HHHHHHHHHCC-----HHHCCCCCCCCC-------CCCCCCCCCCC--CHHHCC--------CCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEEECCEEEEEEEEEEEECHHHHHCC------CCCCCCCCCCCCCCEEEEEEEEEEEEECCCCCCCCHHHHHHHHHHC-----------------CCCCCCCHHHHHHHHHHCCCEEEECCEEEECHHHHHHHHHHHHHCHHHHCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHCCCCCCCC PSA >P1;d1gkub3 a788745400000124100300031099184571650501415072130100005730140279----732300518----a7162325248a31631040056007607200000202230000020035306------b156030020210067102700681360--465203011032005100230004201552a----66a0102020010001006237406--545310306-------a1505160756---------------------------707040383663646440530000130010016428050550160043001-00000002082330573027---1068208---------a314---42426a---8a7210000042234830461186962603a067201100110040000000530503022010405c55654401050752027017-----1182385055-------854906052472243510201200520563-----------------700213200710320263900427b7202029304501510476613003393045013303203646362550065025106426----------------- >P1;d1i7da- -------120000123200510061058-82681b--111404---9610001058300510804214992683329300020a905243378-14a006004500760660000001434000001100740904781468--04003040535720761186065176161313003021202100330010000100461a0933000311100000000220471892835601202030117784603030513b9186512a76302345205611860596404045186684535031000001002200632813036016103501761500210203032004511871661180053006a119282053834350035a506121000034348------82--------b07a504400300000000000440306113030302604020514701630003008a9334642965801906895604046030265518427201216003003300630a579036305833001705500710430282300536a82020290041015003---93004041006014305402686182650076128406700550371537208a1915 >P1;d1mw9x- ------66100001276019006620a-------------------a9240310564022019968411960001027708----1715128c-28900730471087083010001122300000100131079---97a3--000030210268107710882980--55220202001300410033101300460047-----a14010121000200042145188393732130505030477590705022378---760---40547a607800560571a040562555743460830010050010007624050730160054001-201000021732405a9019---20191038526-----97021a743623-------50000005083--308607--------b06730360021003100000023060521201010a703020713335220224027------a7a4470180979380815707254453834a20221500610384-----------------600213202600330293800414954020283023003003500931031a602510520340078637137106711720292076055628570053369 Translating the sequences ********EEEEECCHHHHHHHH***CC***EEEC***EEEE******EEEEECCCCCEEECCC----****CCCCC----CCCCCCEEECCC*HHHHHHHHHHHHHH*CEEEECCCCCHHHHHHHHHHHHHHC------*C**EEECCCCCCCHHHHHHHHCCCCCC--CHHHHHHHHHHHHHHHHHHHHHHHHHHH*CC----CCCCCCCCCHHHHHHHHHHHH*HHH--C**EEEEE*-------CC*EEE**CCC---------------------------**EEEEEEEEEEEEEECCCCCCCHHHHHHHHHH**CCCHHHHHHHHHHHHH-CCCCCCCCCCCCCCCHHHHH---HHHHHH*---------CCCC---CCCCCC---CCCCCCCCCCCCCC***HHH**********CCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEECCEEEEEC*EEEEECHHHHHCC-----CCCCCCCCCC-------EEEEEE***EE**CCCCCCHHHHHHHHHHH-----------------CCCCCCCHHHHHHHHHHCCCEEEECCEEEECHHHHHHHHHHHH*C*HHHCHHHHHHHHHHHHHHH*CCCCHHHHHHHHHHHHH***----------------- -------CEEEEECCHHHHHHHHCCCCC-**EEEC--*EEEE*---CCEEEEECCCCCEEECC*HHH*HHHHCCCCCCCCCCCCCCCEEEC**-HHHHHHHHHHHHHHCCEEEE*CCCCHHHHHHHHHHHHH*CC****HHC--*EECCCCCCCHHHHHHHHCCC******HHHHHHHHHHHHHHHHHHHHHHHHHHHH**C***CCCCCCCCCHHHHHHHHHHHHHHHH*CCCCEEEEEEEEEECCCCCEEEEEECCC*******C***CCCCHHHHHHHHHHH**CEEE**EEEEEEEEECCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHH*CCCCCCCCCCCCCCCHHHHH***HHHHHHHHHCC*****CCCCCCCCCCCCC***CCCCCCCCCCCCCC------CC--------CCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEE**CC**EEECEEEEEECHHHHHCC*****CCC**CCCCCCCCCCEEEEEEEEEEEEECCCCCC**HHHHHHHHH*H*****************CCCCCCCHHHHHHHHHHCCCEEE*CCEEEECHHHHHHHHH**---HHHHC*HHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCC**H**CCCCCC ------*CEEEEECCHHHHHHHHCCCC-------------------CCEEEEECCCCCEE*CCCHHH*HHHHCCCCCCCCC----CC*EECCC-*HHHHHHHHHHHH*CCEEEECCCCCHHHHHHHHHHHHHHCC---*HH*--EEECCCCCCCHHHHHHHH*CCCCC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-----CCCCCCCHHHHHHHHHHHHHHHH*CCCCEEEEEEEEEECCCCCEEEEEE*****---**C---CCCCHHHHHHHHHHH**C*EEEEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHH-CCCCCCCCCCCCCCCHHHHH---HHHHHHHHHCC-----***CCCCCCCCC-------CCCCCCCCCCC--*HHHCC--------CCCHHHHHHHHHHHHHHHH*CCCCEEEEEEEEEEEECCEEEEE*EEEEEECHHHHHCC------CCCCCCCCCCCCCCEEEEEEEEEEEEECCCCCCCCHHHHHHHHHH*-----------------CCCCCCCHHHHHHHHHHCCCEEEECCEEEECHHHHHHHHHHHH*CHHHHCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCC**H**CCCCCC 56712.tem _________________________________ ------*CEEEEECCHHHHHHHHCCCCC-**EEEC--*EEEE*---CCEEEEECCCCCEEECCCHHH*HHHHCCCCCCCCCCCCCCCEEECCC-HHHHHHHHHHHHHHCCEEEECCCCCHHHHHHHHHHHHHHCC---*HHC--EEECCCCCCCHHHHHHHHCCCCCC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC---CCCCCCCCCHHHHHHHHHHHHHHHH*CCCCEEEEEEEEEECCCCCEEEEEECCC**---**C---CCCCHHHHHHHHHHH**CEEEEEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHH-CCCCCCCCCCCCCCCHHHHH---HHHHHHHHHCC-----CCCCCCCCCCCCC---CCCCCCCCCCCCCC--*HHHCC--------CCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEECCEEEEECEEEEEECHHHHHCC-----CCCCCCCCCCCCCCCEEEEEEEEEEEEECCCCCCCCHHHHHHHHHHH-----------------CCCCCCCHHHHHHHHHHCCCEEEECCEEEECHHHHHHHHHHHH*CHHHHCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCC**H**CCCCCC Structural block scores 0 5 - 4.0 M 7.4 75.0 75.0 8 12 E 5.0 H 0.0 0.4 0.2 13 14 C 5.0 H 1.5 1.5 1.5 15 22 H 5.0 H 1.0 1.4 3.6 23 27 C 4.2 M 4.4 4.0 18.7 29 30 * 2.7 P 6.0 5.0 75.0 31 33 E 4.0 M 4.3 5.0 75.0 35 36 - 4.0 M 2.5 75.0 75.0 38 41 E 4.0 M 1.5 1.5 75.0 43 45 - 4.0 M 3.0 75.0 75.0 46 47 C 4.0 M 2.0 7.5 9.8 48 52 E 5.0 H 0.2 0.4 2.0 53 57 C 5.0 H 3.0 3.2 3.0 58 60 E 4.7 H 1.7 2.0 1.3 61 63 C 4.7 H 6.0 2.7 6.3 64 66 H 4.0 M 75.0 2.3 6.0 68 71 H 4.0 M 3.8 6.5 4.0 72 86 C 4.5 M 22.9 3.6 22.2 87 89 E 4.7 H 3.0 3.0 2.3 90 92 C 4.3 M 7.5 6.0 7.5 94 107 H 4.9 H 2.8 3.1 4.0 108 109 C 4.5 M 3.5 3.0 4.0 110 113 E 5.0 H 0.5 1.5 1.0 114 118 C 4.8 H 0.8 1.0 0.8 119 132 H 4.9 H 1.3 1.4 0.8 133 134 C 4.5 M 40.5 4.5 8.0 135 137 - 4.0 M 75.0 6.3 75.0 139 140 H 4.0 M 43.2 5.0 8.8 142 143 - 4.0 M 5.5 75.0 75.0 144 146 E 4.7 H 1.0 1.3 0.0 147 153 C 5.0 H 0.7 2.1 1.1 154 161 H 5.0 H 2.9 3.6 3.8 162 167 C 4.3 M 4.0 4.3 5.8 168 169 - 4.0 M 75.0 6.5 75.0 171 198 H 5.0 H 1.8 1.2 1.5 199 201 C 4.0 M 29.2 3.3 3.7 202 204 - 4.0 M 75.0 3.8 75.0 205 213 C 4.8 H 3.1 2.2 18.6 214 229 H 4.9 H 1.9 1.6 1.9 231 234 C 4.2 M 22.2 4.5 5.5 235 244 E 4.5 M 31.3 1.5 2.2 245 249 C 4.4 M 47.3 5.4 4.6 250 255 E 4.5 M 2.8 2.0 3.5 256 258 C 4.0 M 6.0 3.0 2.3 259 260 * 2.7 P 75.0 10.2 7.5 261 263 - 4.0 M 75.0 5.0 75.0 264 265 * 2.7 P 75.0 3.0 6.5 267 269 - 4.0 M 75.0 7.8 75.0 270 273 C 4.0 M 75.0 2.0 3.2 274 284 H 4.0 M 75.0 3.5 4.5 285 286 * 1.9 P 41.0 7.0 6.0 288 301 E 4.8 H 4.3 4.1 4.3 302 308 C 5.0 H 1.7 1.3 2.6 309 320 H 4.8 H 1.5 1.3 1.8 321 323 C 5.0 H 4.3 4.0 3.0 324 336 H 5.0 H 1.9 2.5 2.1 338 352 C 5.0 H 1.5 1.3 1.8 353 357 H 5.0 H 3.8 3.8 5.9 358 360 - 4.0 M 75.0 4.7 75.0 361 369 H 4.7 H 19.4 2.7 3.2 370 371 C 4.0 M 75.0 3.0 4.0 372 376 - 4.0 M 75.0 4.7 75.0 377 389 C 4.5 M 20.9 3.4 10.0 390 392 - 4.0 M 75.0 6.8 75.0 393 406 C 4.8 H 2.8 2.3 17.6 407 408 - 4.0 M 6.0 75.0 75.0 410 412 H 4.0 M 3.3 75.0 4.7 413 414 C 4.0 M 1.0 5.0 3.5 415 422 - 4.0 M 5.0 75.0 75.0 423 425 C 5.0 H 5.5 6.2 5.8 426 441 H 5.0 H 1.1 1.7 1.6 442 446 C 4.8 H 1.6 1.6 1.0 447 458 E 4.8 H 1.4 1.7 1.5 459 460 C 5.0 H 8.8 4.0 8.8 461 465 E 4.6 H 5.0 1.2 1.0 467 472 E 4.8 H 2.2 3.2 2.8 474 478 H 5.0 H 2.2 0.6 1.6 479 480 C 5.0 H 4.0 4.0 4.5 481 485 - 4.0 M 75.0 5.9 75.0 486 500 C 4.5 M 27.5 5.2 10.3 501 513 E 4.6 H 15.4 3.2 4.3 514 521 C 4.5 M 2.4 3.1 4.1 522 532 H 4.8 H 2.2 1.6 2.7 533 549 - 4.0 M 75.0 4.2 75.0 550 556 C 5.0 H 2.1 2.6 2.0 557 566 H 5.0 H 2.1 2.5 2.5 567 569 C 5.0 H 4.0 1.7 3.7 570 573 E 4.8 H 3.2 3.5 2.2 574 575 C 5.0 H 9.2 9.2 7.0 576 579 E 5.0 H 1.0 1.0 1.5 581 592 H 4.8 H 3.2 8.2 2.2 595 598 H 4.8 H 1.0 3.0 3.2 600 614 H 4.9 H 2.6 2.0 2.6 615 619 C 4.8 H 5.0 5.8 6.2 620 639 H 4.7 H 17.4 3.4 3.4 640 641 C 4.0 M 75.0 4.0 5.5 642 643 * 2.7 P 75.0 4.0 5.0 645 646 * 2.7 P 75.0 1.0 3.5 647 652 C 4.0 M 75.0 5.8 4.3 >>>>>>