Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d3pzwa2 ---CHHHC-CHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEECCCCCCCCCCCHHHCCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCHHHCHHHHHHHHHHCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCEECCHHHHHHHCCCCCHHHHCEECCCCEEECCCCHHHCCCCCHHHCHHHHHHHHHHCCCCCCCEECCCCCCCCCCCHHHHCCCCCCCCHHHCCCCCCCHHHHHHCCCEEEEECHHHHHHHHHHHHCCC--CCCCCEEEEEEEECCCCCEEEEEEEEECCCCCCCCCCCCCEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHIIIIIIIHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCHHHHHHHHHHHCCCCCCHHHHHCCCHH-HHHHHHHHHHCCCCHHHHCHHHHHHHCCCEEECCCCCCCEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHCCHHHHHHHHHHHHCCCHHHCCCCCCCC-CCCHHHHHHHHHHHHHHHCHHHHHHHCCHHHHHCCCCCCCCCCCCCCC-CCCCHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC >P1;d3v98a2 CCCCHHHCCCHHHHHHHHHHHHHHH--------HHCCEECCCCCCCCEECCCCHHHCC------HHHCCC----------------------------------CCCCCCHHHHHHHHHH--HCCCHHHCCCCCC-CCCCHHHHHHHHCCCCC---HHHHHHHH-----------------------------HCCCHHHHHHHHHHCCCCCCCEECCCCCCCCCCCHHHHC--------CCCCC-CCCHHHHHHCCCEEEEECHHHC--CCCCCCCCCCCCCCCCCCEEEEEECCCCCEEEEEEECCCCCCC--------CCCEECCC-CCHHHHHHHHHHHHHHHHHHHHHIIIIIIIHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHHHHCCCCCCHHHCCCCCCCCHHHHHHHHHHCCCCCHHHCHHHHHHHCCCCCC--C-------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHCCHHHHHHHHHHHHCCCCCCHHH-CCCCCCCCHHHHHHHHHHHHHHHCHHHHHHHCCHHHHHCCHHHCCCCCCCCCCCCCC--------CCCHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHC----------CCCCCCCCCC------HHH--CCCCCCC PSA >P1;d3pzwa2 ---12970-69856980665077123948951598242020320200020375a9151320046b7300010110107509647900554a9000048152b0a585021040132016501410450088830853083063004004c01702690074035240054008254642030450200464570034260000000000001104006605070b265861681807073b40803b2719601a52200101003300210530172b--7030000000001367730200000010045bb2a8a27341132399a1720201000000100000100000000300000000000011100650001200120030000000200001020700002000044-20010004205a02022110242045050048279282606100a20000200010040047005400422088574068071026007101470001069382018-054392014000000000001000000000001000000012022101-78a485162058653100040002022000000010000201340110060867810a57703701860375087027404720848834500203040402000070966120300000000 >P1;d3v98a2 6020253087785567074215713--------7506024136300200418307501------680008----------------------------------6456100542036006--7060751275264-20a61820470054006---80053016-----------------------------4055350002000001001205307812a3050749206--------92041-c340660076310000206105--b07207437808020000000000167530100000050929b--------81110126-176200000000000000000100001020000000000001110053000000012003100000000031103a911003010001600240033006804163000252068120445--9-------702400002002400600250043005210666810460500260050014400321970-a01730533840030000000000010000000000000000000000145016638--------7064860060000200001000102000425ab0220050466-306383046014404750770265067218----------b1a0303001------064--0000010 Translating the sequences ---CHHHC-CHHHHHHHHHHHHHHH**********CC**CEECCCCC**CCCCHHHCC*********CCC**********************************CHHHCHHHHHHHHHH***HHHHHHHHCCCCC*CCCCHHHHHHHHCCCEE***HHHHHH*******************************HHHCHHHHHHHHHHCCCCCCCEECCCCCCCCCCCHHHHC********HHCCC*CCCHHHHHHCCCEEEEECHHHH**HHHHHHCCC--CCCCCEEEEEEEECCCCCEEEEEEEEECCCCC********EEE**CCC*HHHHHHHHHHHHHHHHHHHHHHH*******HHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCHHHHHHHHHHHCCCCCCHHHHHCCCHH-HHHHHHHHHHCCCCHHHHCHHHHHHHCCCEEE**C*******CCCCCHHHHHHHHHHHHHHHHHHHHHHH*CCCHHHHHCCHHHHHHHHHHHHCCCHHH****CCCC-CCCHHHHHHHHHHHHHHHCHHHHHHHCCHHHHHCC***CCCCCCCCCC-CCC********HCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC*CCCCHHHHHHHHHHHHHHHHHHHHHHHHHC**********CCCCCCCCCC***********CCCCCCC ***CHHHC*CHHHHHHHHHHHHHHH--------HHCCEEC**CCCCCEECCCCHHHCC------HHHCCC----------------------------------C***C*HHHHHHHHHH--H***HHH*CCCCC-CCCCHHHHHHHHCCC**---HHHHHHHH-----------------------------H**CHHHHHHHHHHCCCCCCCEECCCCCCCCCCCHHHHC--------**CCC-CCCHHHHHHCCCEEEEECHHH*--******CCC**CCCCC**EEEEEECCCCCEEEEEEE**CCCCC--------***EECCC-**HHHHHHHHHHHHHHHHHHHHH*******HHHHHHHHHHHHHHCCCCCHHHHHHHHH*CCHHHHHHHHHHHCCCCCCHHH**CCC***HHHHHHHHHHCCCC*HHHCHHHHHHHCCC***--C-------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHCCHHHHHHHHHHHHCCC***HHH-CCCC*CCCHHHHHHHHHHHHHHHCHHHHHHHCCHHHHHCCHHHCCCCCCCCCC*CCC--------*C*HHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHC----------CCCCCCCCCC------HHH--CCCCCCC 48484.tem _________________________________ ---CHHHC-CHHHHHHHHHHHHHHH--------HHCCEECEECCCCCEECCCCHHHCC------HHHCCC----------------------------------CHHHCHHHHHHHHHHH--HHHHHHHHCCCCC-CCCCHHHHHHHHCCCEE---HHHHHHHH-----------------------------HHHCHHHHHHHHHHCCCCCCCEECCCCCCCCCCCHHHHC--------HHCCC-CCCHHHHHHCCCEEEEECHHHH--HHHHHHCCC--CCCCCEEEEEEEECCCCCEEEEEEEEECCCCC--------EEEEECCC-HHHHHHHHHHHHHHHHHHHHHHH*******HHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCHHHHHHHHHHHCCCCCCHHHHHCCCHH-HHHHHHHHHHCCCCHHHHCHHHHHHHCCCEEE--C-------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHCCHHHHHHHHHHHHCCCHHHHHH-CCCC-CCCHHHHHHHHHHHHHHHCHHHHHHHCCHHHHHCCHHHCCCCCCCCCC-CCC--------HCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHC----------CCCCCCCCCC------HHH--CCCCCCC Structural block scores 0 2 - 3.0 P 75.0 2.7 4 6 H 5.0 H 6.0 3.3 10 24 H 5.0 H 5.3 4.5 25 32 - 3.0 P 5.5 75.0 33 34 H 3.0 P 8.5 6.0 35 36 C 5.0 H 3.0 3.0 37 38 E 3.0 P 1.0 1.0 40 41 E 3.0 P 1.5 2.0 42 46 C 5.0 H 0.8 2.2 47 48 E 3.0 P 1.0 0.0 49 52 C 5.0 H 3.8 4.0 53 55 H 5.0 H 6.8 4.0 56 57 C 5.0 H 3.0 0.5 58 63 - 3.0 P 2.5 75.0 64 66 H 3.0 P 7.2 4.7 67 69 C 5.0 H 0.0 2.7 70 103 - 3.0 P 3.7 75.0 105 107 H 3.0 P 4.3 5.0 109 119 H 4.6 H 2.1 2.4 120 121 - 3.0 P 0.5 75.0 122 129 H 4.0 M 2.8 3.5 130 134 C 5.0 H 5.4 4.8 136 139 C 5.0 H 3.5 4.6 140 147 H 5.0 H 1.6 2.8 148 150 C 5.0 H 5.5 3.0 151 152 E 3.0 P 4.0 3.0 153 155 - 3.0 P 2.7 75.0 156 163 H 4.5 M 3.5 2.9 164 192 - 3.0 P 3.0 75.0 193 195 H 3.7 M 1.0 3.0 197 206 H 5.0 H 0.8 1.0 207 213 C 5.0 H 0.3 0.6 214 215 E 5.0 H 2.0 4.0 216 226 C 5.0 H 4.0 4.0 227 230 H 5.0 H 5.0 3.8 232 239 - 3.0 P 4.2 75.0 240 241 H 3.0 P 7.8 5.5 242 244 C 5.0 H 2.7 1.7 246 248 C 5.0 H 6.8 6.5 249 254 H 5.0 H 4.6 3.2 255 257 C 5.0 H 3.0 3.3 258 262 E 5.0 H 0.4 0.4 264 267 H 4.5 M 1.5 3.0 268 269 - 3.0 P 1.0 75.0 270 275 H 3.0 P 1.7 4.6 276 278 C 5.0 H 6.8 4.7 279 280 - 3.0 P 75.0 4.0 281 285 C 5.0 H 2.0 2.0 286 293 E 4.5 M 0.1 0.0 294 298 C 5.0 H 5.2 4.4 299 307 E 4.6 H 0.3 0.7 308 312 C 5.0 H 4.1 6.3 313 320 - 3.0 P 6.8 75.0 321 325 E 3.0 P 2.2 2.2 326 328 C 5.0 H 7.0 3.0 330 352 H 4.8 H 0.7 0.7 353 359 * 1.0 P 0.4 0.4 360 373 H 5.0 H 0.2 0.2 374 378 C 5.0 H 2.2 1.6 379 388 H 4.8 H 0.6 0.3 389 390 C 5.0 H 1.5 2.0 391 401 H 5.0 H 0.2 0.4 402 407 C 5.0 H 1.7 4.1 408 412 H 4.2 M 0.4 0.8 413 415 C 5.0 H 0.0 0.3 416 417 H 3.0 P 4.0 0.5 419 428 H 5.0 H 0.9 1.2 429 432 C 5.0 H 4.4 4.5 433 436 H 4.5 M 1.2 2.5 438 444 H 5.0 H 2.4 3.3 445 447 C 5.0 H 1.7 1.0 448 450 E 3.0 P 4.0 4.3 451 452 - 3.0 P 4.5 75.0 454 460 - 3.0 P 3.6 75.0 461 465 C 5.0 H 2.5 2.6 466 489 H 4.9 H 1.5 1.5 490 492 C 5.0 H 5.3 4.0 493 497 H 5.0 H 4.4 3.8 498 499 C 5.0 H 4.0 3.0 500 511 H 5.0 H 2.4 1.9 512 514 C 5.0 H 2.3 1.3 515 520 H 3.0 P 3.2 3.7 522 525 C 5.0 H 2.8 4.6 527 529 C 5.0 H 3.0 2.7 530 544 H 5.0 H 1.3 1.2 546 552 H 5.0 H 0.1 0.1 553 554 C 5.0 H 0.0 0.0 555 559 H 5.0 H 0.2 0.0 560 561 C 5.0 H 0.0 0.0 562 564 H 3.0 P 0.0 0.0 565 574 C 5.0 H 0.9 1.1 576 578 C 5.0 H 8.5 5.7 579 586 - 3.0 P 3.9 75.0 589 596 H 4.8 H 1.6 3.8 597 599 C 5.0 H 0.7 0.0 600 613 H 5.0 H 0.4 0.4 614 629 C 5.0 H 2.4 3.6 631 634 C 5.0 H 4.1 3.0 635 659 H 5.0 H 3.8 3.6 661 670 - 3.0 P 3.4 75.0 671 680 C 5.0 H 1.3 3.0 681 686 - 3.0 P 4.7 75.0 687 689 H 3.0 P 1.0 3.3 690 691 - 3.0 P 1.5 75.0 692 698 C 5.0 H 0.0 0.1 >>>>>>