Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d4ogca3 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCCCC-CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCEECCCCCEECCHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHEECCC----CCCCC-CCCHHHHCCCCCCHHHHHHHHCCCHHHHHCC-HHHHCCCCCCCCCCCCCC-----HHHHHHHHHCCCCCCCCCCCHHHHH--------HHHHCCCC----CCCHHHHHHHHH-CCCCCCCCCCC >P1;d4oo8a3 ---CHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCHHHHHCCCCCCCHHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCHHHHHHHHHCCHHHHHHHHHHCCHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHCCCCCHHHHCCCCCCCCCCCCHHHHCCCCCCCCCCCCHHHCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCC--CCCCCCCCCCCCHHHHHHHHHHHHCCCEEECC--CCEECCCCCHHHHHCCCCCCCCCCIIIIIC-CCC---CCCEEECCC----CCCCCCHHHHHHHHHCCCCCCCHH--HHHHHHHHHHHHHHCC--CCCCCCCCCCCCCCCCCC----------CCCCCCHHHHHCCCCCCCCCHHHHHHCCCCCCCCHHHHHHCCCCCCCCCCCCC-- >P1;d5axwa3 CHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-CCCCCCC-------------CCCC-----------------CCCHHHHHHHCCC---CCCHHHHHHHHHHHHHCCCCCCCC--------------------------------CCCCCCCCCCHHHHHHHCCC-CHHHHHHHHHCCC---CCC----CCCCCCC---HHHHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHCCCC--CCCCCCC------------------------------------------------------------------------------------------------------------------------------------CCCCCCC--CHHHHHHHHCCCCC--CCCCCCCCCCCCHHHHHHHHHHHHHCCEECCCCCCCCCHHHHHHHHHHCCCCCC-CCCHHHHCC-CCCCHHHEECCCCCCCCCCCC-CCCHHHHHHHHHCC-CHHHHC--CHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCHHHCCCCCCCCCCCHHHHHH--------CHHHHHH---CCCCHHHHHHHCCCCC------C-- PSA >P1;d4ogca3 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------db7428-1540305b169441003001210304002200703017ad5320527205701710366043917064008409273820561a----81980-0224012335190921463148559952030-222326685971331815-----9802851a81801942020044004--------40062154----514344012631-9088a262796 >P1;d4oo8a3 ---9787577144627764374115301107a2067418201601625b486970555131125695077168222201004301537950301100200110044242182ca167916805305007503923b70908b07057101389470285026508c271022000000734140a21a2b71503236a519841890175068712800710302200312411050044022465177117504610645517008569501000361b170a60030720809b0059328760004151862c60010003900840140a416202405003161271031228ba383020626689020350700435501522254617508--2029330005300001204003200203140d--47520722540046000565051203a700-4b4---ba080761a----70a140400100262075104678--1483005004200117--6200a18830a220641a----------710610450020360b473000300360cb50230660062880703507459-- >P1;d5axwa3 78b7487688176628763466115503105-8391059-------------a13a-----------------c342150035008---70654200100120052133574a--------------------------------96b3a885300013037404-3003001513688---706----9540304---081006006300820851-268702740161046244--715316b------------------------------------------------------------------------------------------------------------------------------------c284027--52431137715504--027a433004200100003001100504081b7662054700550034001554-705083002-0a184820791553b977150-02020012039107-486006--5480015005000012449305730572a26056910600829909711800350055--------0183016---434336400943395b------c-- Translating the sequences ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------*****C-CCCCC**CCCCCCCCCCCCHHHHHHHHHHHHCCCEECCCCC**CCHHHHHHHHHH***CCCCCCCHHHH****CCCHHHEECCC----CCCCC-CCCHHHH*****C***HHHHH**CHHHHH**-HHHH*CCC*CCCCCCCCC-----******HHHCCCCCCCCCCCHHHHH--------*HHH***C----CCCHHHHHHH**-CCCCCCCCC** ---*HHHHHHHHHHHHHHHHHHHHHHHCCC*******CC*************CCCC*****************CCCHHHHHHH******CCCHHHHHHHHHHHHHCCCCCCCC************************************CCCCCC*HHHHHHCCC*C*HHHHHHHH**C***CCC****CCCCCCC****HHHHHHHHHHHH********HH**HHHHHHHH**CC******CC*************************************************************************************************************************************CCCCCC****HHHHHHC*CCCCC--CCCCCCCCCCCCHHHHHHHHHHHHCCCEE*CC--CC*******HHHHHCCCCCCCCCC*****C-CCC---******CCC----CC*CCCHHHHHHHHHCC*C***HH--*HHHHHHHHHHHHHCC--CCCCCCCCCCCCCCCCCC----------CCCCCCHHHHH*********HHHHHHC***CCCCHHHHHH*CCCCCCCCCCCC-- ****HHHHHHHHHHHHHHHHHHHHHHHCCC*-*****CC-------------CCCC-----------------CCCHHHHHHH***---CCCHHHHHHHHHHHHHCCCCCCCC--------------------------------****CCCCCC*HHHHHHCCC-C*HHHHHHHH**C---CCC----CCCCCCC---*HHHHHHHHHHHH*****-**HH**HHHHHHHH**CC--****CC*------------------------------------------------------------------------------------------------------------------------------------CCCCCC*--*HHHHHH**CCCCC--CCCCCCCCCCCCHHHHHHHHHHHH*CCEECCCCCCCCCHHHHHHHHHHCCCCCC-CCCHHHH*C-CCCCHHHEECCCCCC*CCCCC-CCCHHHHHHHHHCC-CHHHH*--CHHHHHHHHHHHHHCCC*********CCCCCCCCCC**HHHCCCCCCCCCCCHHHHH*--------*HHHHH*---CCCCHHHHHHHCCCCC------C-- 345923.tem _________________________________ ---*HHHHHHHHHHHHHHHHHHHHHHHCCC*-*****CC-------------CCCC-----------------CCCHHHHHHH***---CCCHHHHHHHHHHHHHCCCCCCCC--------------------------------****CCCCCC*HHHHHHCCC-C*HHHHHHHH**C---CCC----CCCCCCC---*HHHHHHHHHHHH*****-**HH**HHHHHHHH**CC--****CC*------------------------------------------------------------------------------------------------------------------------------------CCCCCC*--*HHHHHHC*CCCCC--CCCCCCCCCCCCHHHHHHHHHHHHCCCEECCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHH*C-CCCCHHHEECCCCCC-CCCCC-CCCHHHHHHHHHCC*CHHHHH--CHHHHHHHHHHHHHCCC*CCCCCCCCCCCCCCCCCC**HHHCCCCCCCCCCCHHHHH*-------*HHHHHHC---CCCCHHHHHHHCCCCCCCCCCCC-- Structural block scores 0 2 - 4.0 M 75.0 75.0 8.8 4 26 H 4.0 M 75.0 4.6 5.0 27 29 C 4.0 M 75.0 0.7 1.3 32 36 * 2.7 P 75.0 3.8 4.2 37 38 C 4.0 M 75.0 4.5 7.0 39 51 - 4.0 M 75.0 4.0 75.0 52 55 C 4.0 M 75.0 5.2 6.2 56 72 - 4.0 M 75.0 4.2 75.0 73 75 C 4.0 M 75.0 2.0 6.5 76 82 H 4.0 M 75.0 1.4 2.3 83 85 * 2.7 P 75.0 2.0 2.7 86 88 - 4.0 M 75.0 6.3 75.0 89 91 C 4.0 M 75.0 2.7 4.3 92 104 H 4.0 M 75.0 0.8 1.5 105 112 C 4.0 M 75.0 4.4 4.4 113 144 - 4.0 M 75.0 4.5 75.0 145 148 * 2.7 P 75.0 3.2 7.4 149 154 C 4.0 M 75.0 5.3 5.8 156 161 H 4.0 M 75.0 3.8 2.3 162 164 C 4.0 M 75.0 4.3 2.7 168 175 H 4.0 M 75.0 0.6 1.6 176 177 * 2.7 P 75.0 0.0 7.0 179 181 - 4.0 M 75.0 2.7 75.0 182 184 C 4.0 M 75.0 4.8 4.3 185 188 - 4.0 M 75.0 3.9 75.0 189 195 C 4.0 M 75.0 4.2 3.6 196 198 - 4.0 M 75.0 6.5 75.0 200 211 H 4.0 M 75.0 4.4 2.7 212 216 * 2.7 P 75.0 4.8 3.2 218 219 * 2.7 P 75.0 0.0 4.0 220 221 H 4.0 M 75.0 4.0 7.5 222 223 * 2.7 P 75.0 1.5 1.0 224 231 H 4.0 M 75.0 1.2 2.9 232 233 * 2.7 P 75.0 2.5 4.0 234 235 C 4.0 M 75.0 0.5 4.0 236 237 - 4.0 M 75.0 2.5 75.0 238 241 * 2.7 P 75.0 2.0 4.0 242 243 C 4.0 M 75.0 2.0 3.5 245 376 - 4.0 M 75.0 3.5 75.0 377 382 C 4.0 M 75.0 2.7 4.8 384 385 - 4.0 M 75.0 5.0 75.0 387 392 H 4.0 M 18.8 2.8 2.3 395 399 C 5.0 H 2.6 4.2 3.0 400 401 - 4.0 M 2.5 75.0 75.0 402 413 C 5.0 H 3.3 2.2 3.0 414 425 H 5.0 H 1.2 1.0 0.5 426 428 C 4.7 H 2.3 0.7 1.7 429 430 E 5.0 H 1.5 2.0 2.0 431 439 C 4.2 M 5.2 20.6 5.2 440 449 H 4.5 M 3.2 3.0 2.8 450 459 C 4.6 H 3.9 2.4 10.2 460 463 H 4.0 M 2.5 5.1 2.8 467 470 C 4.5 M 4.5 23.6 4.9 471 473 H 4.0 M 4.3 53.8 4.7 474 475 E 4.0 M 2.5 5.2 3.5 476 481 C 4.0 M 40.4 5.4 5.8 483 487 C 4.4 M 5.2 46.4 4.0 489 491 C 5.0 H 1.3 1.7 0.7 492 500 H 4.4 M 3.1 1.7 2.0 501 502 C 4.5 M 4.5 3.5 3.5 505 509 H 4.2 M 3.6 5.0 4.0 510 511 - 4.0 M 6.5 75.0 75.0 513 525 H 4.7 H 8.8 2.1 1.8 526 528 C 4.7 H 6.7 27.7 2.3 530 547 C 4.1 M 24.0 4.1 4.5 548 549 * 2.7 P 6.5 75.0 3.0 550 552 H 4.0 M 6.5 75.0 2.7 553 563 C 4.5 M 2.5 35.5 4.2 564 568 H 5.0 H 2.4 2.2 2.6 570 576 - 4.0 M 75.0 4.9 75.0 578 583 H 4.3 M 2.3 1.0 2.2 585 587 - 4.0 M 75.0 8.0 75.0 588 591 C 4.8 H 21.2 2.5 3.5 592 598 H 4.9 H 2.9 2.9 3.7 599 610 C 4.2 M 11.0 4.7 41.2 611 612 - 4.0 M 7.5 75.0 75.0 >>>>>>