Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1d2ta- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCCCCCCCCCCCCHHH-CCCHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCC--------------CHHHHHHHHHHHCC-------HHHHHHHCHHHHC-CCCCC-------------------------CCCHHHHHHHHHCHHHHHCCCCHHHHHHHCCCCHHHHHCCCCCCCCC--------------------------------------------------------CCCCCCCCCCHHHHHHHHHHHHHHHHCHHH--------------------------------------------------------HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHH------HHHHHHHHHCC------------------------------------------------ >P1;d1qhba- ----CCCCCCCCC---HHHHHHHHHHHHHHHHHH-CCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHH-HHHHHHHHCCHHHHHCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCHHHCCCC---CCCCCCCCCCCCCCCC--CCHHHHHHHHHHHHHHHCCCCCHHHCCCHHHHHHHHHHHHHHCCCHHHHCCCCCCCC---HHHHHHCCC----CC-CC-CCCCCCCCCCCCCCCCCCHHHCCCCCCCCCEEECC----EEECCCCHHHHHHCEEEECC-EEEE---CCEEEECCCCCCCC-CHHHHHHHHCCCCCCCCCCEEEEEECCCCHHHHHHHHHHCC------CCHHHHHHHHHHHHH-----CCCCCCCCCCCCCHHHHCCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC---CCCCCCCCCCHHHHHHHHHHHHHHHHCC---CC---------CEEC--------CCEEECC---------CCCCEEECCCCCCEEHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEECCCC----CEEEC---------------------------------------------- >P1;d1qi9a- CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC-----------CHHHCCCCCCCCCCCCCC-CHHHHH-HHHHHHHHCCHHHHCCCCCCCCC-----------------CCHHHCCCCCCCCCCCCC---CCCCCCCCCCCCCCCC--CCHHHHHHHHHHHHHHHHCCCCHHHCC---CCHHHHHHHHHHHCCCCHHH-------------CCCCCCCCCCCC-CHHHHCCCCCCCCCCCCCCCCHHHHCCEEEC------------------------------C-EEEC---CCCCCCCCCCCCCC-CHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCC------CCHHHHHHHHHHHHCCCCCCCCCCHHHHHCC------CCCCCC-CCCHHHHHHHHHHHH-HHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCC----CCCCCCCHHHHC-CHHHHHHHHHHHHHHCHHH-----CCCCCCCCCCCC---CCCCCCCCCCHHHHHHHHHHHHHHHHHCHHHHC---------CCCC--------CCEEECC---------CCCCEEECC-CCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCC----CEEEEECCCCEEECCEECCCCCCCCHHHCC--------------------- >P1;d1vnsa- --------------------------------------------------------------CCCCCCCC----CCCCHHHHHCHHHHHHHHHHHHHHHHHHH-------CCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHH--HCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC--CCCCCCCCCCCCEEEECCCCCCCCCEEEECCCCCCCHHHHCCCCC----CCC---CCCCCCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCC-------------CCCC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HCCCCHHHHHHCCCCC--------------------------------------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHC-CCCCCCCCCCCCCCCEEEEECHHHCCCCEEECCCCCCCCCHHHCCEEECCCCEEEEC--CHHHHHHHHHHHHHHCCCCCHHHHCCHHHHCCCCCCCCCCCCCC----CCCCCCCCHHHCCC-CCEECCCCCC---------CCEECCHHHHHHHHHHHHHHCCCCCCCHHHCC PSA >P1;d1d2ta- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------a5016536720005493-22703650771187b4a7077026404604731b--------------58206403500729-------366005103c104-25038-------------------------83152015003000200020002502762713101132a550105ba--------------------------------------------------------a26634000010000010002001400693--------------------------------------------------------595036204200200000000022005000600530182047166046107------6046315855a------------------------------------------------ >P1;d1qhba- ----da98a9a48---995567437552773298-396660832b0367055a968412000001000105842206528104-3027005515994388052019327858405030b30474715105048013035919---2005032110240030--52400000000000001003120211838715b20840182028160054818bb25---833540119----70-63-930010205204601000000010050871567dc----77570874a424502005d9-8425---01171234821100-02400000000020593053589220011000001100607------334002100100233-----90410540131776862a58178-500341038002300720220011000010000000300000010121846a78215306601840670065016407811873a1908351000000000---0020100000110000000000000003---08---------5528--------7013014---------86340490b3704040130000000000000000000000000000100050010003023451b4c0303012048----73360---------------------------------------------- >P1;d1qi9a- a56794b5b391216538865877767476228502a927174192a-----------644010000020693050-58a006-305500841499308804502a6-----------------c27308157012035839---5005140130540230--422200000000000000020103404---9383052008201a080047-------------0220025b8570-6155200004033034100000000241549------------------------------9-7645---02250015840100-329401400200224681731b6610010000001002419------5250042001000a3600379050520495a------974068-200240024007512-40230011000000200000200010000248----61a290273027-17500820173027206b8-----640100000013---00301000001200000000000000052a116---------6504--------a112034---------604824728-674030000000000000000000000000000200300010000200220261a4a1303030043----32030328040206967058400443a70a--------------------- >P1;d1vnsa- --------------------------------------------------------------4650301a----2314b603500000002000100000000-------9011321000000000000000000010461a92910053937761501429b0950200000000400220064696b226700400530083028--50277065a3700600350052038002267134389180869--3120421233535642553566a3734535401003006604000----015---4120000001231594761020005001200039a3c50405952311010000121200000000001000100042155a-------------5048---06500300000000000000000000010004-0200000100270a38--------------------------------------a303580501000100137832002000000000000000000001102-620680768310603067000000034005064705453305606074084240508--0002000000000000000000000004000464b78130245a----85104128276030-725350663b---------a4111000000150032036360520249412 Translating the sequences ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCC******C*******-**C****CCCCCCCCC******HHHHHHHH**CC--------------C*HHHHHHHHH*CC-------*HHHHHH*HHHH*-CCCCC-------------------------CC*HHHHHHHHH*HHHHH****HHHH***CCCCHHHHH*********--------------------------------------------------------CCCCCCCCCCHHHHHHHHHHHHHHHH****--------------------------------------------------------HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH**HHHH****------***********------------------------------------------------ ----*********---******************-***************************CCCCCCCC****CC*CHHHHH-HHHHHHHH**HHHH****************************************CCCC---CCCCCCCC***CCCCC--CC*HHHHHHHHHHHHHH***CC***CC*****HHHHHHHHHH***************---*********----CC-C*-**CCCCCCCC**CCCCCC****CC***********----****CCC******C******-****---CC****CCCC***C-CHHHHHHHH**CC***CCC******CCC*HHHHHHHHH*CC------**HHHHHHHHHHHH*-----********************C**-*CCHHHHHHHHHHHHHHHHHHHHHHHH***CCCCHHHHHH*************************************************CCCCCCCCCCCC---CCCCCCCCCCHHHHHHHHHHHHHHHH*C---*C---------C***--------CC*EE*C---------**CCEEECC*C*****HHHHHHHHHHHHHHHHH*CCCCHHHHHHHHHHHHHHHHHHH**HHHH***CC*****C***----C*EE*---------------------------------------------- ***********************************************-----------****CCCCCCCC****CC-CHHHHH-HHHHHHHH**HHHH*********-----------------**************CCCC---CCCCCCCC***CCCCC--CC*HHHHHHHHHHHHHH***CC***CC---**HHHHHHHHHH********-------------**********CC-C****CCCCCCCC**CCCCCC****CC****------------------------------*-***C---CCCCCCCCCC***C-CHHHHHHHH**CC***CCC******CCC*HHHHHHHHH*CC------**HHHHHHHHHHHH*CCCCC***********------***C**-*CCHHHHHHHHHHHH-HHHHHHHHHHH***CCCCHHHHHH********----************-*******************-----CCCCCCCCCCCC---CCCCCCCCCCHHHHHHHHHHHHHHHH*C****C---------C***--------CC*EE*C---------**CCEEECC-C*****HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH**HHHH***CC*****C***----C*EE**************************--------------------- --------------------------------------------------------------CCCCCCCC----CC*CHHHHH*HHHHHHHH**HHHH*****-------****************************CCCC***CCCCCCCC***CCCCC**CC*HHHHHHHHHHHHHH***CC***CC*****HHHHHHHHHH**--***************************CC*C****CCCCCCCC--CCCCCC****CC*******************CCC******C****----**C---CCCCCCCCCC***C*CHHHHHHHH*******CCC******CC**HHHHHHH***CC********HHHHHHHHHHHH*CCCCC-------------****---C******HHHHHHHHHHHHHHHHHHHHHHHH*-*CCCCHHHHHH*****--------------------------------------******CCCCCCCCCCCC***CCCCCCCCCCHHHHHHHHHHHHHHHH*C-***C*********C***********CC*EE*C***********CCEEECC*C*****--*HHHHHHHHHHHHHHCCCCCHHHH**HHHH**************----CC*****C******-C*EE******---------******************************** 48317.tem _________________________________ ----*********---******************-************-----------****CCCCCCCC****CC*CHHHHH-HHHHHHHH**HHHH*********---****************************CCCC---CCCCCCCC***CCCCC--CC*HHHHHHHHHHHHHH***CC***CC*****HHHHHHHHHH***************---*************CC-C****CCCCCCCC**CCCCCC****CC***********----****CCC******C******-***C---CCCCCCCCCC***C*CHHHHHHHH**CC***CCC******CCC*HHHHHHHHH*CC------**HHHHHHHHHHHH*CCCCC***********--*******C**-*CCHHHHHHHHHHHHHHHHHHHHHHHH***CCCCHHHHHH********----************-************************CCCCCCCCCCCC---CCCCCCCCCCHHHHHHHHHHHHHHHH*C****C---------C***--------CC*EE*C---------**CCEEECC*C*****HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH**HHHH***CC*****C******-C*EE******---------***********--------------------- Structural block scores 0 3 - 4.3 M 75.0 75.0 7.1 75.0 4 12 * 3.5 M 75.0 9.2 6.2 75.0 13 15 - 4.3 M 75.0 75.0 4.0 75.0 16 33 * 3.5 M 75.0 5.7 5.9 75.0 35 46 * 3.5 M 75.0 4.8 5.4 75.0 47 57 - 4.3 M 75.0 5.6 75.0 75.0 58 61 * 3.5 M 75.0 0.5 3.5 75.0 62 69 C 4.3 M 75.0 0.2 0.4 3.7 70 73 * 3.5 M 75.0 4.8 4.5 75.0 74 75 C 4.3 M 75.0 1.0 2.5 2.5 78 82 H 4.3 M 75.0 3.0 4.9 5.1 84 91 H 4.3 M 75.0 2.8 3.1 0.2 92 93 * 2.3 P 75.0 3.0 2.5 0.0 94 97 H 4.3 M 75.0 6.2 5.2 0.2 98 106 * 2.8 P 75.0 4.0 4.8 33.3 107 109 - 4.3 M 75.0 5.7 75.0 75.0 110 137 * 2.9 P 75.0 3.3 39.3 0.6 138 141 C 4.3 M 75.0 6.0 6.2 5.4 142 144 - 4.3 M 75.0 75.0 75.0 6.7 145 152 C 4.3 M 75.0 1.6 2.0 3.5 153 155 * 2.3 P 75.0 1.0 2.7 4.7 156 160 C 4.3 M 75.0 1.4 1.8 2.4 161 162 - 4.3 M 75.0 75.0 75.0 10.2 163 164 C 4.3 M 75.0 3.5 3.0 4.5 166 179 H 4.3 M 75.0 0.1 0.1 0.6 180 182 * 2.3 P 75.0 1.0 0.7 0.7 183 184 C 4.3 M 75.0 1.5 0.5 5.0 185 187 * 2.3 P 75.0 1.0 2.3 7.0 188 189 C 4.3 M 75.0 4.5 2.0 6.8 190 194 * 3.0 P 75.0 4.8 47.4 3.0 195 204 H 4.3 M 75.0 3.6 2.8 2.3 205 219 * 3.0 P 75.0 4.9 37.0 14.2 220 222 - 4.3 M 75.0 75.0 75.0 2.0 223 235 * 2.9 P 75.0 25.7 20.0 2.0 236 237 C 4.3 M 75.0 3.5 3.5 2.0 240 243 * 2.6 P 75.0 22.5 3.2 2.8 244 251 C 4.3 M 75.0 1.2 1.2 6.1 252 253 * 3.5 M 75.0 2.0 1.5 75.0 254 259 C 4.3 M 75.0 1.2 0.8 2.0 260 263 * 2.3 P 75.0 0.0 0.0 2.2 264 265 C 4.3 M 75.0 0.5 3.0 4.0 266 276 * 3.1 M 75.0 5.9 49.5 5.2 277 280 - 4.3 M 75.0 75.0 75.0 4.2 281 284 * 3.5 M 75.0 6.5 75.0 4.2 285 287 C 4.3 M 5.2 5.0 75.0 0.3 288 293 * 2.3 P 4.7 4.9 75.0 2.5 295 300 * 2.5 P 3.0 4.9 64.0 25.7 302 304 * 1.8 P 26.3 4.7 5.7 25.3 306 308 - 4.3 M 3.0 75.0 75.0 75.0 309 318 C 4.7 H 5.2 2.9 2.7 0.8 319 321 * 1.0 P 5.8 0.7 0.3 2.0 325 332 H 5.0 H 3.2 0.8 2.5 2.0 333 334 * 1.0 P 5.0 0.0 1.0 2.5 335 336 C 4.3 M 6.2 1.0 1.0 0.5 337 339 * 2.3 P 75.0 4.7 4.0 0.7 340 342 C 4.3 M 75.0 2.7 5.3 4.0 343 348 * 2.3 P 75.0 4.8 4.8 5.8 349 351 C 4.3 M 51.7 0.3 0.3 4.7 353 361 H 4.8 H 2.2 0.2 0.3 0.9 363 364 C 5.0 H 5.5 3.5 5.0 1.5 365 370 - 4.3 M 75.0 75.0 75.0 0.5 371 372 * 1.6 P 39.0 3.0 3.5 0.0 373 384 H 4.9 H 3.2 1.1 1.9 0.2 386 390 C 4.3 M 3.6 75.0 3.2 4.7 391 401 * 3.5 M 75.0 2.5 4.5 75.0 402 403 - 4.3 M 75.0 7.0 75.0 75.0 404 410 * 3.5 M 75.0 6.5 45.7 34.6 412 413 * 2.3 P 75.0 7.5 7.0 5.5 416 417 C 4.3 M 5.5 0.0 0.0 1.5 418 441 H 4.8 H 1.2 1.6 4.7 0.0 442 444 * 1.4 P 5.0 0.3 0.0 26.3 445 448 C 5.0 H 3.0 0.0 0.5 0.5 449 454 H 4.9 H 2.9 0.5 0.3 0.5 455 462 * 1.5 P 4.8 0.6 1.9 31.7 463 466 - 4.3 M 75.0 7.1 75.0 75.0 467 478 * 3.5 M 75.0 3.9 4.1 75.0 480 503 * 3.4 M 75.0 4.1 18.6 57.5 504 515 C 4.3 M 75.0 0.8 1.2 0.9 516 518 - 4.3 M 75.0 75.0 75.0 6.0 519 528 C 5.0 H 3.1 0.3 0.4 0.4 529 544 H 5.0 H 0.6 0.1 0.2 0.1 547 550 * 2.9 P 40.5 56.2 3.6 20.8 552 560 - 4.3 M 75.0 75.0 75.0 4.3 562 564 * 2.3 P 75.0 5.0 3.0 3.0 565 572 - 4.3 M 75.0 75.0 75.0 0.9 573 574 C 4.3 M 75.0 3.5 5.8 3.5 576 577 E 4.3 M 75.0 1.5 1.0 2.5 580 588 - 4.3 M 75.0 75.0 75.0 3.4 589 590 * 2.3 P 75.0 7.0 3.0 5.5 591 592 C 4.3 M 75.0 3.5 6.0 3.0 593 595 E 4.3 M 75.0 4.3 4.3 3.7 596 597 C 4.3 M 75.0 5.8 5.0 4.0 600 604 * 2.3 P 75.0 1.6 2.8 3.4 605 621 H 4.9 H 2.2 0.2 0.0 8.9 622 626 C 4.9 H 0.0 0.0 0.0 0.0 627 645 H 4.6 H 2.0 0.4 0.4 2.6 646 647 * 1.0 P 4.0 1.5 1.0 1.0 648 651 H 4.3 M 4.0 3.5 2.5 23.6 652 654 * 2.3 P 2.3 5.5 5.2 75.0 655 656 C 4.3 M 41.0 6.2 5.8 6.5 657 661 * 2.3 P 75.0 1.4 1.8 1.6 663 668 * 2.2 P 3.2 39.5 38.7 3.0 672 673 E 4.3 M 42.8 4.5 1.5 4.0 674 679 * 3.3 M 75.0 62.5 2.8 5.2 680 688 - 4.3 M 75.0 75.0 3.9 75.0 689 699 * 3.5 M 75.0 75.0 4.6 1.6 700 720 - 4.3 M 75.0 75.0 75.0 2.8 >>>>>>