Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ccwb- -------------------------------------CCCCCCCCC---HHHHHHHHHHHHHHC--HHHHHCC---HHHHHHHHH------CCC--------HHHCHHHHHHHHHHHCCCEEEC--CCCCCCHH-----HHHHHHHHHHH-CCCCCCEEEECCCCHHHCCHHHHHHHHHHHHHHC-----------------------------------------------------------------------CCCCCCCCHHHHHHHHHHHHHH--HCCCCEEEECCCCCCHHHHHHHHHCCCCEEECCCCCCCCCC-CCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCCCCCCCCC--HHHHHHHHHHHHHHHHHC----CC-------CEEEEEEECCC-CHHHHH-HHHHHHHHHHHHHHHHCCCC---CCEEEEEEECCCCCCCC-CHHHHHHHHHHHHHHHHHHCCCEEECCCCCCCCCCC-CHHHHHHHHHHHHHHHHHCC----CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCC-CCHHHHHHHHHHCCCCCCCCC-----CCC-----CCCCCCEEEECCC-CCEEEEECCCCCCCHHHHHHHHH-HHHHHHHHHCC-----------------CCCH---HHHHHHHHHCCCCCCCCCCC---------------- >P1;d1reqa1 CCCCCCCCCCCCC----------------------CCCC--------CCHHHHHHHHHCCCCCCEECCCCCEECCCCCHHHCCCC------CCCCCCCC----CCCCCCCCCCHHHCCCCEEEEEE--CCCCHH-----HHHHHHHHHHH--CCCCEEEECCCHHHHHCCCCCC---------------------HHHHHHCCCCCCC--CCCHHHHHHHCCCCCCC---------------------------CCEEEECCCCCHHHHHHHHHHHHHHCC-------------------CC-CCCEEEECCCCHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCC-CEECEEEECHHHHHHCCC--HHHHHHHHHHHHHHHHHHHHHCCCCHHHCHHHEEEEEEECC--CHHHHH-HHHHHHHHHHHHHHHCCCCCCHHHHCCCEEEEECHHHCCCCCCCHHHHHHHHHHHHHHHCCCCEEECCCCCCCCCCC-CHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH-CCCC--------CCHHHHHHHCHHHHHHH-----HHHHHHHHHHHH-CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHH-HHHHHHCCCCCHHHHHHHHHHHHHCCCCCHHH---CHHHHHHHHHHCCCCHHHHHHHHCCCCCCC------ >P1;d1reqb1 -------------CCCCHHHCCCCCCCCCHHHHHHCCCC--------CCCCCHHHHHHH---HCEECCCCCEECCCCCCCCCC----------CCCCCC----CCCCCCCCCCCCCCCCCEEEEEE--CCCC-------CCCCCHHHHHC--CCCCEEEEECCC----------------------------------------CCCC-----CCCHHHHCCCCCCC---------------------------CCEEEEECCCCHHHHHHHHHHHHHCCC-------------------CCHHHCCEEEEECHHHHHHHHC--------CCCCCCCCCCCCCCCCC-CCEEEEEECHHHHCCCCC--HHHHHHHHHHHHHHHHHHHHHCCCCHHHHHCCEEEEEEECC--CHHHHH-HHHHHHHHHHHHHHHHHCC-CHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCHH-HHHH--------CCCCCCCCCCHHHHHHH-----HHHHHHHHHHHCCCCCCCCCCCCCCC---CCCCCC---------------------------------------------------------------------------------- >P1;d1uc4a- ---------------------------------------------CCCHHHHHHHCCHHHHCCCCCCCHHHCCCCCCCCCCCCCCEEEECCEEEEECCEEHHHCCHHHHHHHH------------HCCCCCCHHHHHCCCHHHHHHHHHCCCCCHH------HHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCEEECCCCCCCHHHHHHHHHHHHHHCCCEEEECCCC------------------------HHHHHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHCCCCCEEEEEECCCCHHHHHHC--CCCHHHHHHHHHHHHC------CCCEEEEECCCCHHHHCCCCC-CCCHHHHHHHHHHHHHHH------------CCCEEECCCHHHCCCHHHCCCHHHHHHHHHHHHHHC---------CCEEECCCCCCCC--CCHHHHHHHHHHHHCCCCC--CCCEEEECCCHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCC-----HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCHHHCCCCCHHHHHHHHHHHHH--------------------CCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHCCCCEEECCCEEECCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCC >P1;d1xrsa- -------------------------------------CCCCCCCCHHHHHHHHHHHHHHHHHHH--HHHHCEEEHHHHHHHHHHC------CCCCCCCC---CCCHHHHHHHHHHHCCCCCCCH--HHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEC--CCCHHHHHHHHHHHHHCCCCEEEECCCCCHHHCCCCCCCCCCCCCCCCCC-CHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHCCCEEECCCCHHHHHH---CCCHHHHHHHHHHHHHHHHHC---CCEEECCCHHHHCCCCCCCCHHHHHHHHHHHHHHHHHC----CCC----HHHEECEEECCCCCCCCCHH-HHHHHHHHHHHHHCC----------CCCCEEECCCCCCCC-CHHHHHHHHHHHHHHHHHHCCCEEECCCCCCCCCCC-CHHHHHHHHHHHHHHHHHCCCHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHCCCCC--C---------------CCCCCCCCCCHH-HEEECCCCCCCHHHHHHCCC--------------------------------------------------------------------------- PSA >P1;d1ccwb- -------------------------------------280617306---795067105501833--7109406---1a6018205------905--------6810004105403857400000--31020116-----60071053017-507010000200540183506304811740773a-----------------------------------------------------------------------7240600000010091015006--10810000000012010000000000000000000000002-17735045001000000000020053705000000100112000--000000000000000020----20-------30000001000-231000-00010025005710664827---7040000000012a007-669604a20480030001020000000003326951-74610030052027108629----863287687065018203500620043017209-820040014007500000040-----406-----3027502000037-00000160360207791153057-20760186092-----------------a255---6004203600373631112c---------------- >P1;d1reqa1 a99597a959a8b----------------------a885--------a43a764788168a4c4660506050665168913a0a------02a37007----33001005760047730201131--011007-----50161055018--3607000010050003011034---------------------8714a50044000--00001004300670504---------------------------82401000000000000000000543a-------------------04-75040100000000000160100329002100010031018405-502001000110124302--00000000000001004103819180260013010000014--413000-00000001000500761809556010000201000500042316303800240030000000110100000333233-4760163004101501672632863023273120020021015402720-6127--------40047107776046406-----514852684179-345240224854b4792329072870175058-10870481677088217504500565663882---10030003004330001200710340722b------ >P1;d1reqb1 -------------c868a967987583361475218b48--------8a5081850485---417511281613241465069----------358117----56012117619474610310200--0247-------83030045016--680600000006----------------------------------------6003-----38506500430614---------------------------70200010456153005200300362a-------------------574660200000010030132a--------70818700117308502-801000000110035002--1100000000000100410482a170150030000000004--524000-0000000200050057280-68841001000000521017620410371154003000003020000000012294077230143104102510375410473031025530020064006403107-7039--------49002006581168317-----8058307723855834371333a56b---b09529---------------------------------------------------------------------------------- >P1;d1uc4a- ---------------------------------------------a6698747668554570b45a36385020005065129030606b98032008345870240020006------------60052a4076018270760081023291718------5014002000000014001407384013002000003300000000034000000000001003140100001024------------------------760100000000000000240000000182860130040300000030301004300761--a150450191072056------520000010000101639505-220001000000000200------------901000000062081000064022000000000000---------3000000000400--6188224700210030000--0000000000330012a10001162078005304655200202006-----9731371033004002200860901806980072006050075036073940272054027--------------------752616401700485a1870062045015218646026200003bb77320176170705089402407ba225403916a4978a >P1;d1xrsa- -------------------------------------374108074910660262064005601--7206820000000000000------90441298---840001200610483b003100--001000012327371450061025970304617348486046303510691077058236307532861934a810000301--20106602740240043400000030063003354025521692980030-023004100710470066342000000201000000000000211000020000200033---300010000001000000020---00200020330039560473010000000000000320----603----36100000000042839513-320001000000004----------701000000433076-739403600240020010050200100000344481-777005400710571196275218748088535116006600740171065037--------3301600450101--a---------------37254751513b-1026239511000442029c--------------------------------------------------------------------------- Translating the sequences -------------------------------------CC*******---HHHHHHHHHHHH*HC--**HH***---**HHH****------CCC--------***CHHHHHHHHHH*CCCEEE*--**CCCCHH-----*HHHHHHHHHH-CCCCC*EEE*CC**HHHCC**HHHHHHHH*****-----------------------------------------------------------------------*****CCCHHHHHHHHHHHHHH--*CCC*EEE*CC****HHHHH**HHCCC*EEECCCC******-**CCCHHHHHHHHHHHHHHHHH****CC**EEECC****CCCCC--HHHHHHHHHHHHHHHHH*----CC-------CEEEEEEECC*-CHHHHH-HHHHHHHHHHHHHHH**CC*---*****EEEECCCCCCCC-CHHHHHHHHHHHHHHHHHHCCCEEECCCCCCCCCCC-CHHHHHHHHHHHHHHHHHCC----CCCCCCCHHHHHHHHHHHHHHHHHHHHHHH***-****HHHHHHHHCCCC***C*-----***-----***CCC****CCC-CC*****CCCCCC*HHHHHHHHH-**HHHH*****-----------------****---***********CCCC*****---------------- *************----------------------**CC--------C*HHHHHHHHH*****C**CC**CEECCCCCHHHCC*C------CCCCCCCC----CCC*******HHHCCCCEEE***--CCCCHH-----*HHHHHHHHHH--CCCC*EEE*CCHHHHHCC****---------------------***********CC--CCCHHHHHHH******C---------------------------CC*****CCC*HHHHHHHHHHHHHH*C-------------------CC-*CC*EEE*CCC*HHHH**C**CCCHHHHHHHHHHHHHHHHH**C-C*E*EEE*CHHHH**CCC--HHHHHHHHHHHHHHHHHH****CCC****H**EEEEEEECC--CHHHHH-HHHHHHHHHHHHHHH**CC******CCCEEEE*C***CCCCC**HHHHHHHHHHHHHHH*CCCEEECCCCCCCCCCC-CHHHHHHHHHHHHHHHH*CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH-****--------**HHHHHH*C**HHH**-----HHHHHHHHHHH*-CCCCCCCC*CC*****CCCCCCHHHHHHHHHH-**HHHH**************************---***********CCCC***************------ -------------************************CC--------C****HHHHHHH---HC**CC**CEECCCCC***CC----------CCCCCC----CCC**********CCCCEEE***--CCCC-------C****HHHHH*--CCCC*EEE*CC*----------------------------------------**CC-----***HHHH******C---------------------------CC*****CCC*HHHHHHHHHHHHH**C-------------------CCHH*CCEEEE*C**HHHHHHC--------****************C-CCEEEEE*CHHHHCCCCC--HHHHHHHHHHHHHHHHHH****CCC****H*CEEEEEEECC--CHHHHH-HHHHHHHHHHHHHHH**CC-*****CCCEEEE*CCCCCCCCC**HHHHHHHHHHHHHHHHCCCEEECCCCCCCCCCC*C*HHHHHHHHHHHHHHH*CCCCCCCCCCCCCHHHHHHHHHHHHHH**HH-HHHH--------********CC**HHH**-----HHHHHHHHHHHCCCCCCCCCC*CC**---CCCCCC---------------------------------------------------------------------------------- ---------------------------------------------**C*HHHHHH**HHHH**C**CCHH***CCCCC***CC*C***********CC*****CC*HHHHHHH------------***CCCCHH*****CHHHHHHHHH**CCC**------*HHHHHCC**HHHHHHHH**************************CC**CCCHHHHHHH******************------------------------**HHHHHHHHHHHHHHH*CCCC*EEE*CC****HHHHHCC**C**EEEECCCCHHHHHHC--CCCHHHHHHHHHHHH*------C*C*EEEE*CC*HHH*CCCC*-***HHHHHHHHHHHHHHH------------*C*EEE*******C*HHH***HHHHHHHHHHHHHH*---------CC*EE**CCCCCC--CCHHHHHHHHHHHH*****--CC*EE**CCC***CCC*C****HHHHHHHHHHHHH*CCCCCCCCCC-----HHHHHHHHHHHHHHHHHHHH********HHHHHHHH*CCCHHHC******HHHHHHHHHHH--------------------CCCCHHHHHHHHHH***HHHH****************************************CCCC********************* -------------------------------------CC**********HHHHHHHHHHHH*H*--**HHCEE*****HHH***C------CCCCCCCC---*CC*HHHHHHHHHHCCCC****--******HH*****CHHHHHHHHHH*CCCCC*****C*HHHHH****HHHHHHHH***************************C--CCCHHHHHHH******C***************************CC****-C**HHHHHHHHHHHHHHH*CCCC*EEE*CC****HHHHH**HH*CC*EEECCCCHHHHHH---CCCHHHHHHHHHHHHHHHHH*---CCEEE**C*HHH*CCCCC**HHHHHHHHHHHHHHHHH*----CCC----H**EE*EEE*CC**C***HH-HHHHHHHHHHHHH**----------CCC*EEECCCCCCCC-CHHHHHHHHHHHHHHHHHHCCCEEECCCCCCCCCCC-CHHHHHHHHHHHHHHHHHCCC****CCCCCC*HHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHCCCC*--C---------------**CCCCCCCC**-*******CCCC**HHHH***--------------------------------------------------------------------------- 51703.tem _________________________________ -------------------------------------CC------*-C*HHHHHHHHHHHH*HC**CCHHCEECCCCCHHHCC*C------CCCCCCCC---*CCCHHHHHHHHHHCCCCEEE*-***CCCCHH-----CHHHHHHHHHH-CCCCC*EEE*CCHHHHHCC**HHHHHHHH*****----------***********CC--CCCHHHHHHH******C---------------------------CC*****CCCHHHHHHHHHHHHHHH*CCCC*EEE*CC****HHHHHCCHHCCCEEEECCCCHHHHHHC--CCCHHHHHHHHHHHHHHHHH**C-CCEEEEECCHHHHCCCCC--HHHHHHHHHHHHHHHHHH----CCC----H*CEEEEEEECC*-CHHHHH-HHHHHHHHHHHHHHH**CC----**CCCEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCEEECCCCCCCCCCC-CHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHCCCCHHHC*-----HHHHHHHHHHHCCCCCCCCCC-CC*****CCCCCCHHHHHHHHHH-**HHHH*****-----------------****---***********CCCC*****---------------- Structural block scores 0 36 - 4.5 M 75.0 48.1 30.6 75.0 75.0 37 38 C 4.5 M 5.0 6.5 6.0 75.0 5.0 39 44 - 3.8 M 2.8 75.0 75.0 75.0 3.3 49 60 H 4.6 H 3.8 6.6 16.2 6.0 3.1 64 65 * 3.0 P 75.0 6.0 6.0 7.8 75.0 66 67 C 3.8 M 4.0 2.5 1.0 4.5 4.5 68 69 H 3.8 M 4.5 3.0 5.0 5.5 3.0 71 72 E 3.8 M 3.0 2.5 3.5 1.0 1.0 73 77 C 4.0 M 47.3 4.8 2.8 1.0 0.0 78 80 H 3.8 M 2.3 6.0 3.7 4.0 0.0 81 82 C 3.8 M 5.0 6.8 7.5 5.5 0.0 85 90 - 4.5 M 75.0 75.0 75.0 5.4 75.0 91 98 C 4.2 M 48.6 3.7 21.9 3.0 4.6 99 101 - 4.5 M 75.0 75.0 75.0 5.7 75.0 103 105 C 4.3 M 3.0 2.0 3.7 2.0 1.3 106 115 H 3.9 M 2.5 2.3 3.9 23.3 2.2 116 119 C 4.4 M 4.0 4.2 2.8 75.0 3.6 120 122 E 4.1 M 0.0 1.0 1.3 75.0 1.3 125 127 * 3.0 P 26.3 50.3 50.0 2.0 25.0 128 131 C 4.5 M 0.8 0.5 3.2 5.4 0.2 132 133 H 4.5 M 3.5 3.5 75.0 3.5 0.5 134 138 - 3.8 M 75.0 75.0 75.0 3.4 3.4 140 149 H 4.7 H 2.4 2.7 2.2 2.7 2.4 151 155 C 4.6 H 2.6 18.2 19.0 5.2 2.8 157 159 E 4.1 M 0.0 0.0 0.0 75.0 3.7 161 162 C 4.2 M 0.0 0.0 0.0 40.0 6.0 163 167 H 4.3 M 3.6 1.6 61.2 1.0 4.8 168 169 C 4.1 M 4.0 0.5 75.0 1.0 1.5 170 171 * 2.1 P 3.0 0.5 75.0 0.0 4.0 172 179 H 4.2 M 3.5 57.1 75.0 0.6 3.9 180 184 * 3.0 P 5.5 75.0 75.0 3.0 3.6 185 194 - 3.8 M 75.0 75.0 75.0 1.8 4.1 195 205 * 2.8 P 75.0 4.0 61.9 0.5 3.5 206 207 C 4.3 M 75.0 0.0 1.5 0.0 0.5 208 209 - 4.5 M 75.0 75.0 75.0 1.5 75.0 210 212 C 4.2 M 75.0 0.0 75.0 1.3 1.0 213 219 H 4.3 M 75.0 1.1 3.9 0.0 3.6 220 225 * 2.1 P 75.0 3.0 2.3 0.7 1.7 227 253 - 4.2 M 75.0 75.0 75.0 44.9 2.3 254 255 C 4.2 M 75.0 5.0 3.5 75.0 8.5 256 260 * 2.3 P 3.8 1.0 0.6 75.0 15.6 261 263 C 4.0 M 0.0 0.0 3.0 29.3 1.7 264 278 H 4.9 H 6.5 0.6 2.3 0.1 2.4 280 283 C 4.3 M 2.5 58.9 58.9 1.5 1.5 285 287 E 4.2 M 0.0 75.0 75.0 0.0 0.0 289 290 C 4.2 M 0.0 75.0 75.0 4.5 0.5 291 294 * 3.0 P 0.8 75.0 75.0 4.0 0.0 295 299 H 4.2 M 0.2 75.0 75.0 1.6 0.0 300 301 C 3.8 M 0.0 2.0 6.0 1.5 0.0 302 303 H 3.9 M 0.0 41.0 5.0 0.0 1.0 304 306 C 4.0 M 0.0 3.0 2.7 0.0 0.7 307 310 E 4.6 H 0.0 0.2 0.0 1.5 0.5 311 314 C 4.5 M 0.0 0.0 0.2 0.2 0.0 315 320 H 4.3 M 0.3 0.2 1.5 3.3 1.3 322 323 - 3.8 M 4.0 0.5 75.0 75.0 75.0 324 326 C 4.5 M 5.0 1.0 75.0 5.5 1.0 327 343 H 4.4 M 0.7 1.6 16.2 20.0 0.2 344 345 * 2.5 P 0.0 2.0 2.5 75.0 37.5 348 349 C 4.4 M 3.5 2.5 4.0 0.0 0.0 350 354 E 4.3 M 1.0 0.6 0.2 0.2 0.8 355 356 C 4.2 M 0.0 0.0 0.0 0.0 1.5 357 360 H 4.2 M 0.5 0.8 0.5 0.5 1.5 361 365 C 4.7 H 0.6 2.2 2.0 4.6 4.8 366 367 - 4.2 M 75.0 75.0 75.0 40.0 5.0 368 385 H 4.8 H 0.1 0.3 0.4 0.4 0.3 386 389 - 3.8 M 75.0 3.0 3.5 75.0 75.0 390 392 C 4.4 M 25.7 6.0 6.2 75.0 3.0 393 396 - 3.8 M 75.0 2.0 1.5 75.0 75.0 400 406 E 4.5 M 0.1 0.1 0.0 0.1 0.0 407 408 C 4.5 M 0.0 2.5 2.0 3.0 0.0 412 416 H 4.5 M 0.8 0.8 1.2 0.2 4.2 418 432 H 4.9 H 1.8 0.9 0.8 0.5 0.7 433 434 * 2.5 P 5.0 3.5 4.5 37.5 75.0 435 436 C 4.2 M 5.0 4.0 4.0 75.0 75.0 437 440 - 3.8 M 58.0 6.2 24.2 75.0 75.0 441 442 * 3.0 P 3.5 0.5 2.5 75.0 75.0 443 445 C 4.3 M 1.3 0.0 0.3 1.0 2.7 446 449 E 4.6 H 0.0 0.8 0.0 0.0 0.0 450 459 C 4.5 M 10.2 1.4 2.4 16.1 10.5 460 477 H 4.7 H 3.0 1.7 1.6 6.2 1.9 478 480 C 4.8 H 0.7 0.3 1.7 25.0 2.3 481 483 E 4.8 H 0.0 0.7 0.0 0.0 0.3 484 494 C 4.8 H 2.6 1.5 1.6 0.8 2.2 497 513 H 4.8 H 2.6 2.8 2.2 2.5 3.5 514 526 C 4.6 H 27.0 3.6 2.7 13.2 5.0 527 549 H 4.8 H 3.0 5.2 5.9 12.1 3.0 550 557 - 3.9 M 12.0 75.0 75.0 3.8 75.0 558 565 H 4.3 M 2.0 2.9 2.6 3.2 2.1 566 569 C 4.1 M 1.2 5.0 3.8 2.8 1.5 570 572 H 4.0 M 0.0 4.7 5.7 4.0 50.3 575 579 - 4.5 M 75.0 75.0 75.0 5.0 75.0 580 590 H 4.1 M 35.5 4.6 4.6 3.0 62.3 591 600 C 4.2 M 2.4 10.6 4.2 75.0 4.5 602 603 C 4.1 M 0.0 6.5 7.8 75.0 0.5 604 608 * 2.6 P 1.4 7.1 48.5 75.0 4.4 609 614 C 4.7 H 1.8 3.8 6.1 28.3 1.2 615 624 H 4.3 M 4.5 4.3 75.0 3.1 25.9 626 627 * 3.0 P 1.0 0.5 75.0 5.8 75.0 628 631 H 4.2 M 3.5 4.8 75.0 3.8 75.0 632 636 * 3.0 P 5.0 5.8 75.0 3.4 75.0 637 653 - 3.8 M 75.0 4.0 75.0 2.5 75.0 654 657 * 3.0 P 5.6 5.2 75.0 8.2 75.0 658 660 - 4.5 M 75.0 75.0 75.0 4.0 75.0 661 671 * 3.0 P 2.2 1.0 75.0 3.1 75.0 672 675 C 4.2 M 4.8 1.5 75.0 5.2 75.0 676 680 * 3.0 P 3.5 0.6 75.0 4.9 75.0 681 696 - 4.1 M 75.0 30.5 75.0 5.7 75.0 >>>>>>