Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1mqsa- CCCCCC-CHHHHHCCCCCCCC--CCCCCCCHHHHCCCCCCEEEEECHHHHHHHCCCCC-HHHHHCCEEEEEECCCCCCCEEEEEEEEEECCCHHHHHHHHHHHHH---CCEEEEEEEECCCCCHHHHHHHHH-HHHCCCCHHHEEEEEECCCCCEECCCCCEECCCCCHHHHHHCCC--CCHHHHHHHHHHHHHHHHHHHCCCCEEEECCC-CHHHHHHHHHHHHHHHHHHCC-----CCC--CCEEEEEEHHHCCCC-CCCCCCCCC-CCCCCC--CCCCCCCC--------CCCCCCCCCCCC-CCCCCCHHHHHHHHHHHHHH-CCHHHHHCCC----CCCHHHHHHHHHHHHC-CHHHHHHHHCCCCCHHHHHHCCC--CCC---------CCCCCCCCCCCCCCCCCC-CHHHHHHHHHCCCCCCCHHHHHHHHHH--CCCCCCCCCHHHHCC----------CCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCCCEEEEEECCCCHHHHHHHCCHHHCCCCCCCCCEECCCCCHHHHHHHHHHHHHHC-CC >P1;d3c98a- -CCHHHHHHHHHHHHCHHHHCCC--------------CCCEEEEECHHHHHHHHCCCCHHHHCCCCEEEEEECCCCCCCCCCCCEEEEECCCHHHHHHHHHCCCCHHHCCCCCEEEEECCCCCHHHHHHHHCCHHHH-----CEEEEEECCCCCEECCCCEEECCCCCHHHHHHCHHHCCCCHHHHHHHHHHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEHHHCCCCCCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCEEEEEEECCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC------CCCCCCCCCHHHHHHHHHHCCCCCCC------CCCCCC-------CCCCCCEEEEEEECCEEHHHHHHHHHHHHHHCCCEEEEEECCEECHHHHHHHHCCCCCCCCCC PSA >P1;d1mqsa- 972115-0263024012063a--b6b78477852877276000000870450061008-9605600056423066b09555a21000002155600320070055---410230100002304791463068-20671c36921423331304010204100005374001303250--9738a1047005001000212a310000035a-420340043006301652695-----986--300000010211010-020010000-002200--a1304149--------6636071a1501-70252401600451471587-28627a578a----b646a15733830500-50033028327050420060046--149---------712703911864961340-0000000102066b0491376034206--7593a1001027018----------5383450659f4ba92a8726b04562100000020020990475005104800101056a3a33454054110000000101000101107729a9703000001001046107002503843-7a >P1;d3c98a- -530252017301840055046a--------------c5500000071043006200569504721034223047a08436831000002157800420140066586320600000001705aa046504726029-----3152243030000010310000116a0010000452596296204400400000000070305001235280036005201620572379567006795366010000000001100000101000000010709924060623549a475262403170a104700231054078202630782187380765713115525725850131200120062047416b3134006100300233228789187139603500539a073210000000000242005685076028308059611500400430705021769a837a48933a5aa6b------35823103020120032005870628------612118-------9772101000000000000001001401883770100000001011650052024044859a4 Translating the sequences *CC***-*HHHHH**C****C--**************CCCEEEEECHHHHHHH*CCCC-HHHHHCCEEEEEECCCCCCCEEEEEEEEEECCCHHHHHHHHHHHHH---CCEEEEEEEECCCCCHHHHHHHHH-HHH******HEEEEEECCCCCEECCCC*EECCCCCHHHHHHC**--CCHHHHHHHHHHHHHHHHHHHCCCCEEEECCC-*HHHHHHHHHHHHHHHHHH*C-----CCC--CCEEEEEEHHHCCCC-CCCCCC***-****CC--CC******--------****CCCCC***-**CCCCHHHHHHHHHHHHHH-**HHHHHCCC----CCCHHHHHHHHHHHH*-*HHHHHHHH*CC**HHHHHH***--*CC---------C********CCCCCC***-*HHHHHHHHHCCCCC**HHHHHHHHHH--*********HHHHCC----------CCCCCCCCCCCCC******CCCCCCCCCHHHHHHHH**CCCCCHH******CCEEEC*******CCCCCC*EEEEEECC**HHHHHHH**HHH**CCC****EECC**CHHHHHHHHHHHHHHC-CC -CCHHH*HHHHHHHHCHHHHC**--------------CCCEEEEECHHHHHHHHCCCC*HHH**CCEEEEEECCCCCCC*****EEEEECCCHHHHHHHHH*******CC***EEEEECCCCCHHHHHHHH**HHHH-----*EEEEEECCCCCEECCCCEEECCCCCHHHHHHCHH**CC*HHHHHHHHHHHHHHHHHHCCCCEEEECCC*HHHHHHHHHHHHHHHHHHHHC*****CCC**CCEEEEEEHHHCCCC*CCCCCCHHH*HHHHCC**CCEEEEEE********EEEECCCCCHHH*HHCCCCHHHHHHHHHHHHHH*HHH****CCC****CCCHHHHHHHHHHHHH*HHHHHHHHHHCCHHHHHHHHHHH**HCC*********CHHHHHHHHCCCCCCHHH*HHHHHHHHHHCCCCCHHHHHHHHHHH***HHHHHHHHHHHHHCC**********CCCCCCCCCCCCC------CCCCCCCCCHHHHHHHHHHCCCCC**------CC***C-------CCCCCCEEEEEEECCEEHHHHHHHHHHHHHHCCCEEEEEECCEECHHHHHHHH******C*CC 56815.tem _________________________________ -CCHHH-HHHHHHHHCHHHHC----------------CCCEEEEECHHHHHHHHCCCC-HHHHHCCEEEEEECCCCCCCEEEEEEEEEECCCHHHHHHHHHHHHH---CCEEEEEEEECCCCCHHHHHHHHH-HHHH-----HEEEEEECCCCCEECCCCEEECCCCCHHHHHHCHH--CCHHHHHHHHHHHHHHHHHHHCCCCEEEECCC-HHHHHHHHHHHHHHHHHHHHC-----CCC--CCEEEEEEHHHCCCC-CCCCCCHHH-HHHHCC--CCEEEEEE--------EEEECCCCCHHH-HHCCCCHHHHHHHHHHHHHH-HHHHHHHCCC----CCCHHHHHHHHHHHHH-HHHHHHHHHHCCHHHHHHHHHHH--HCC---------CHHHHHHHHCCCCCCHHH-HHHHHHHHHHCCCCCHHHHHHHHHHHH--HHHHHHHHHHHHHCC----------CCCCCCCCCCCCC------CCCCCCCCCHHHHHHHHHHCCCCCHH------CCEEEC-------CCCCCCEEEEEEECCEEHHHHHHHHHHHHHHCCCEEEEEECCEECHHHHHHHHHHHHHHC-CC Structural block scores 1 2 C 5.0 H 4.5 4.0 3 5 H 3.0 P 2.3 2.3 7 14 H 4.2 M 2.1 3.0 16 19 H 3.0 P 2.8 2.5 21 36 - 3.0 P 15.6 66.7 37 39 C 5.0 H 5.0 7.5 40 44 E 5.0 H 0.0 0.0 46 53 H 4.8 H 3.8 2.6 54 57 C 5.0 H 2.2 1.8 59 63 H 4.2 M 5.2 5.0 64 65 C 5.0 H 0.0 1.5 66 71 E 5.0 H 3.3 2.3 72 78 C 5.0 H 5.4 4.8 79 88 E 4.0 M 2.4 2.1 89 91 C 5.0 H 2.7 2.7 92 104 H 4.4 M 2.5 2.9 105 107 - 3.0 P 75.0 6.3 108 109 C 5.0 H 2.5 2.5 110 117 E 4.2 M 0.8 0.8 118 122 C 5.0 H 1.8 2.6 123 131 H 4.8 H 4.9 5.2 133 136 H 4.5 M 3.8 4.2 137 141 - 3.0 P 6.3 75.0 143 148 E 5.0 H 2.7 2.8 149 153 C 5.0 H 1.6 0.6 154 155 E 5.0 H 0.5 0.0 156 159 C 5.0 H 1.8 1.2 160 162 E 4.3 M 0.0 0.0 163 167 C 5.0 H 3.8 3.7 168 173 H 5.0 H 1.2 0.2 175 176 H 3.0 P 2.5 4.5 177 178 - 3.0 P 75.0 3.5 179 180 C 5.0 H 8.0 7.5 181 199 H 4.9 H 2.3 1.6 200 203 C 5.0 H 3.6 2.5 204 207 E 5.0 H 0.0 1.5 208 210 C 5.0 H 6.2 3.3 212 231 H 4.8 H 2.9 3.3 233 237 - 3.0 P 75.0 3.8 238 240 C 5.0 H 7.7 7.0 241 242 - 3.0 P 75.0 4.5 243 244 C 5.0 H 1.5 3.0 245 250 E 5.0 H 0.2 0.2 251 253 H 5.0 H 1.0 0.0 254 257 C 5.0 H 0.5 0.5 259 264 C 5.0 H 0.5 0.3 265 267 H 3.0 P 0.0 0.0 269 272 H 3.0 P 1.0 0.2 273 274 C 5.0 H 0.0 3.5 275 276 - 3.0 P 75.0 4.5 277 278 C 5.0 H 5.8 5.5 279 284 E 3.0 P 3.5 3.0 285 292 - 3.0 P 75.0 5.9 293 296 E 3.0 P 5.2 3.5 297 301 C 5.0 H 3.9 2.2 302 304 H 3.0 P 2.0 3.8 306 307 H 3.0 P 3.5 3.5 308 311 C 5.0 H 3.2 1.5 312 325 H 5.0 H 3.5 3.7 327 333 H 3.3 M 5.8 4.9 334 336 C 5.0 H 8.5 6.0 337 340 - 3.0 P 75.0 1.5 341 343 C 5.0 H 7.2 4.0 344 356 H 4.8 H 4.0 3.0 358 367 H 4.6 H 2.6 2.6 368 369 C 5.0 H 3.5 8.8 370 380 H 4.1 M 2.5 1.9 381 382 - 3.0 P 75.0 0.0 384 385 C 5.0 H 6.5 3.0 386 394 - 3.0 P 75.0 5.8 396 403 H 3.0 P 3.0 3.2 404 409 C 5.0 H 5.7 5.8 410 412 H 3.0 P 2.3 2.0 414 423 H 4.8 H 0.3 0.2 424 428 C 5.0 H 4.7 2.2 429 440 H 4.5 M 3.8 4.4 441 442 - 3.0 P 75.0 2.5 443 455 H 3.6 M 3.5 2.5 456 457 C 5.0 H 4.5 3.5 458 467 - 3.0 P 75.0 5.2 468 480 C 5.0 H 6.6 7.6 481 486 - 3.0 P 7.8 75.0 487 495 C 5.0 H 4.2 2.8 496 505 H 4.6 H 0.4 1.0 506 510 C 5.0 H 4.4 5.2 511 512 H 3.0 P 6.0 5.0 513 518 - 3.0 P 1.7 75.0 519 520 C 5.0 H 4.0 3.5 521 523 E 3.0 P 0.3 1.3 525 531 - 3.0 P 5.4 75.0 532 537 C 5.0 H 3.5 4.3 538 544 E 4.7 H 0.9 0.1 545 546 C 5.0 H 0.0 0.0 547 548 E 3.0 P 0.5 0.0 549 562 H 4.4 M 2.1 1.9 563 565 C 5.0 H 8.8 4.7 566 571 E 3.7 M 0.5 0.2 572 573 C 5.0 H 0.5 0.0 574 575 E 3.0 P 0.0 0.5 577 590 H 4.1 M 2.9 2.9 593 594 C 5.0 H 8.8 7.2 >>>>>>