Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1qmha2 -----------CEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEEEECC---CCCCEEEEEE----EEEEEEHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCCCCCHHHHHCHHHHHHHCCCEEEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCC---HHHHHHHHHHHHHH-CCCEEEECC-CC--HHHHHHHHHHHHHCCCCCEEEE-CCCCEEEEC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- >P1;d2pqca- CCCCEEEECCCCCEEEEEC-CCCHHHHHHHHHHHHHCEEEEEEECCC-------CCHHHHHHHHHHHHC-CCEEEE-ECC--EEEEEEECCCCCCCCCCCEE---CC----CCHHHHHHHHHHHHCCCCEEEEECC--C--CHHHCCC---HHHHHHHHHCCC--EEEEE-C------CCEEEEEEECCCCCCCCEEE-CCCCCHHHHHHHHHHHHCCCCEEEEEECC-CCC----CHHHHHHHHC-CCCEEEEECCCCCEEEEEECCCCCCCC-EEECCCCHHHHHHHHHHHHHCCCCEEEEEEEE--CCHHHCHHHHHHHHHCCEEEEEEEEEECCEEEEEEEEECC--CCCCCEECHHHHHH-CHHHHHHHHHHHCCCCCEEEECCCHHHHHCCCCHHHHHHHHHHHCCCEEEECCCCEEEECCCCCCCCCCCCCCEECCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHCCCCHHHHHHHHCCEEEEC- >P1;d3nvsa- -CCEEEECCCCEECEEEEC-CCCHHHHHHHHHHHHHCCCEEEEECCC-------CCHHHHHHHHHHHHC-CCEEEE-CCCCCCEEEECCCCCCCCCCCEEEE---CC----CCHHHHHHHHHHCCCCCCEEEEECC--H--HHHHCCC---HHHHHHHHHCCC--EEEECCC------CCCCCEEEEC-CCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHC-CCCCEEE----CCCEEEECCCCCCCCCCEEECCCCHHHHHHHHHHHHHHCC-EEEEECCCCCCCCHHHHHHHHHHHHCCEEEECC---------CEEEEECC--CCCCCEEE---CCC-CCCCHHHHHHHHHHCCCCEEEECCHHHHHCCCCHHHHHHHHHHHCCCEEEECCCEEEEECCC---CCCC---CEECCCCCHHHHHHHHHHHH-CCCCEEEECHHHHHHCCCCHHHHHHHHEE------ >P1;d5u4ha1 -CCEEEEECCCCCEEEEEC-CCCHHHHHHHHHHHHHCCCCEEEECCC-------CCHHHHHHHHHHHHC-CCEEEE-E--CCEEEEE---HHHCCC--CEECHHHHC----CCHH-HHHHHHHHHHHHCEEEEECC--CCCCCCCCCC---HHHHHHHHHCCC--EEEEEC----------CEEEEECCCCCCCCEEE-CCCCCHHHHHHHHHHHCCCCCEEEEE---CCCCCHHHHHHHHHHHHC-CCEEECCCC----CEEEEECCCCCCCC-EEECCCCHHHHHHHHHHHHHHCC-EEEEECCC---HHHCHHHHHHHHHCCCEEEECC---------CEEEEECCCCCCCCCCEECCCCCCCCHHHHHHHHHHHCCCCCEEEEE-CCCCC----CC-CCCHHHHHHCCCEEEEECCEEEEECCC---CCCC---CCEECC-CHHHHHHHHHHHHHCCCEEEEECHHHHHHCCCCHHHHHHCCCCEEEEEC PSA >P1;d1qmha2 -----------3080605353100100120000000164201053013a4a8400274012008003600a071622866244010507---8070961618----07750300200200000003065703000300023794340210564105106603060906047407488180300060430a8174062740b---43100100100000-550101078-23--7406011400340181905364-8a9504011------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- >P1;d2pqca- a464030450a10775280-100100000000000004a40405900-------406003200600450-308053-6ca--110040120350750a7406---04----0001000000000000516020404--7--0048010---310070036070--80806-b------92304030402950620626-04231120000000000103830103025-301----10004104a0-807071847b77304050504970603-8150000000000000000007b030102400--1070010015004408060534763734916001040321--b0802703671012-0110000000000007920405306203311130030007005306070727a53020505450690027975205064000000000000000534010400420400025029106a07050657- >P1;d3nvsa- -574332721850355090-200110000000000006a40505300-------403005000600650-a08181-4b84440306032610518872805---00----0001000000000002714010205--8--3026010---030060045040--7060267------7620005040-330649403030421020000000000206460104076a01051105001500640-7070526----a28301035c260702880702000100000000000303-403024004912000140040056040606218---------83010544--70411536---024-0010000000000108940004504001210130050005004302080722842020511b---6064---15050390000000000000-18020101318104100370182076016------ >P1;d5u4ha1 -a33050408360657060-100130000000000004560202300-------6060050017003a0-607060-8--b620604---086095--140267105----3033-00000000002215030040--bb36141660---820160053080--70536b----------9203051bb30704806-07522430000000000006850205---400410001000500450-606085266----63040401860501-71602000000000000000010-30302504---061053007205507060735b---------73010204152060050604313601120000000000006970601-02326----60-1201610450707093ab460404037---5080---260301-110000000000010686040450610430016016104a080607147 Translating the sequences -----------C*EEE**C*CCCHHHHHHHHHHHHH*CC*EEEECCC*******CCHHHHHHHHHHHH**CCEEE***CCCC*EEEE**---CCCC***EEE----*******HHHHHHHHHHH*CCCC*EEEE****C**C***CC****H*HHHHHHHCCC**EEEEE*C******C***EEEEECCCCCCCC****CC---HHHHHHHHHHHH**-C**EEEECC-CC--HHHHHHHHHHHH**CCC*EEE*-**CC*EEE*------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- *CC*EEE*CCCC*EEEEEC-CCCHHHHHHHHHHHHHC***EEEECCC-------CCHHHHHHHHHHHHC-CCEEEE-*CC--*EEEE*****CCCC****EE---*C----CCHHHHHHHHHHH*CCCCEEEEECC--C--C***CCC---HHHHHHHHHCCC--EEEEE-C------C***EEEEECCCCCCCCEEE-CCCCCHHHHHHHHHHHH*CCC*EEEEECC-CCC----*HHHHHHHHC-CCC*EEE****CC*EEEE*CCCCCCCC-EEECCCCHHHHHHHHHHHHH*CC*EEEEE***--***H**HHHHHHHH*CCEEEE************EEEEECC--CCCCC*E*******-C***HHHHHHHH**CCC*EEE**C********C*****HHHHHHCCCEEEE*CC*EEEECCC***CCCC***C*E*CC*CHHHHHHHHHHH**CCC*EEE*C***HHHCCCCHHHHHH*********- -CC*EEE*CCC***EEEEC-CCCHHHHHHHHHHHHHCCC*EEEECCC-------CCHHHHHHHHHHHHC-CCEEEE-*CCCC*EEEE*****CCCC***EEE---*C----CCHHHHHHHHHH**CCCCEEEEECC--*--****CCC---HHHHHHHHHCCC--EEEE**C------C****EEEEC-CCCCC*EEE*CCCCC*HHHHHHHHHHH*CCC*EEEEECC*CCC*HHHHHHHHHHHHC-CCC*EEE----CC*EEEE*CCCCCCCC*EEECCCCHHHHHHHHHHHHH*CC-EEEEE********H**HHHHHHHH*CCEEEE**---------*EEEEECC--CCCCC*E*---***-C***HHHHHHHH**CCC*EEE**C********C*****HHHHHHCCCEEEE*CC*EEEECCC---CCCC---C*E*CC*CHHHHHHHHHHH*-CCC*EEE*C***HHHCCCCHHHHHH****------ -CC*EEE*CCCC*EEEEEC-CCCHHHHHHHHHHHHHCCC*EEEECCC-------CCHHHHHHHHHHHHC-CCEEEE-*--CC*EEEE---***CCC--*EE*****C----CCHH-HHHHHHHH****CEEEEECC--C**C***CCC---HHHHHHHHHCCC--EEEEE*----------*EEEEECCCCCCCCEEE-CCCCCHHHHHHHHHHH**CCC*EEEE---*CCC*HHHHHHHHHHHHC-CC**E****----*EEEE*CCCCCCCC-EEECCCCHHHHHHHHHHHHH*CC-EEEEE***---**H**HHHHHHHH*CCEEEE**---------*EEEEECC**CCCCC*E********C***HHHHHHHH**CCC*EEE*-C****----C*-***HHHHHHCCCEEEE*CC*EEEECCC---CCCC---C*E*CC-CHHHHHHHHHHH**CCC*EEE*C***HHHCCCCHHHHHH********** 55205.tem _________________________________ -CC*EEE*CCCC*EEEEEC-CCCHHHHHHHHHHHHHCCC*EEEECCC-------CCHHHHHHHHHHHHC-CCEEEE-*CCCC*EEEE*****CCCC***EEE---*C----CCHHHHHHHHHHH*CCCCEEEEECC--C**C***CCC---HHHHHHHHHCCC--EEEEE*C------C***EEEEECCCCCCCCEEE*CCCCCHHHHHHHHHHHH*CCC*EEEEECC*CCC*HHHHHHHHHHHHC-CCC*EEE****CC*EEEE*CCCCCCCC-EEECCCCHHHHHHHHHHHHH*CC-EEEEE***--***H**HHHHHHHH*CCEEEE**---------*EEEEECC--CCCCC*E*******-C***HHHHHHHH**CCC*EEE**C********C*****HHHHHHCCCEEEE*CC*EEEECCC---CCCC---C*E*CC*CHHHHHHHHHHH**CCC*EEE*C***HHHCCCCHHHHHH*********- Structural block scores 1 2 C 4.3 M 75.0 5.0 6.0 6.8 4 6 E 4.3 M 75.0 1.0 2.7 1.7 8 11 C 4.3 M 57.0 4.1 4.0 4.2 13 17 E 4.6 H 3.8 5.8 4.4 4.8 20 22 C 5.0 H 1.3 0.3 0.7 0.3 23 35 H 5.0 H 0.3 0.1 0.2 0.3 36 38 C 4.3 M 3.7 4.8 5.5 3.0 40 43 E 5.0 H 1.5 2.2 2.5 1.0 44 46 C 5.0 H 1.3 3.0 1.0 1.0 47 53 - 4.3 M 5.7 75.0 75.0 75.0 54 55 C 5.0 H 1.0 2.0 2.0 3.0 56 67 H 5.0 H 2.6 2.2 2.1 2.7 70 71 C 5.0 H 5.2 1.5 5.2 3.0 72 75 E 4.8 H 4.0 4.0 4.5 3.2 78 81 C 4.3 M 4.5 43.2 6.9 41.9 83 86 E 5.0 H 1.5 1.2 2.2 2.5 87 91 * 2.5 P 46.4 1.2 2.4 46.6 92 95 C 4.8 H 3.8 4.2 3.5 5.0 96 98 * 1.9 P 5.3 5.8 5.7 50.3 99 101 E 4.5 M 5.0 3.3 4.3 2.0 102 104 - 4.3 M 75.0 75.0 75.0 4.7 107 110 - 4.3 M 4.8 75.0 75.0 75.0 111 112 C 4.3 M 1.5 0.0 0.0 1.5 113 123 H 4.9 H 0.4 0.1 0.1 7.4 125 128 C 4.5 M 3.5 1.5 2.5 1.2 129 133 E 4.9 H 2.0 2.4 1.4 1.6 134 135 C 4.3 M 1.5 2.0 2.5 2.0 136 137 - 4.3 M 0.0 75.0 75.0 75.0 139 140 * 3.5 M 2.5 75.0 75.0 7.2 142 144 * 1.0 P 5.3 4.0 2.7 2.0 145 147 C 4.8 H 2.0 0.3 0.3 4.0 148 150 - 4.3 M 2.0 75.0 75.0 75.0 151 159 H 4.9 H 3.2 2.2 2.0 2.8 160 162 C 5.0 H 1.0 2.3 1.3 2.7 163 164 - 4.3 M 3.0 75.0 75.0 75.0 165 169 E 4.9 H 3.8 4.4 3.0 4.2 172 177 - 4.3 M 4.7 75.0 75.0 75.0 179 181 * 1.9 P 1.0 1.7 2.7 53.0 182 186 E 4.9 H 2.0 2.2 1.8 2.0 187 194 C 4.8 H 4.2 3.0 12.5 4.8 195 197 E 4.3 M 5.0 4.7 2.3 4.7 199 203 C 4.6 H 47.3 2.0 2.0 3.2 204 215 H 4.9 H 0.8 0.2 0.2 0.6 217 219 C 4.5 M 26.7 3.7 3.3 4.7 221 225 E 4.7 H 0.4 0.8 1.0 16.4 226 227 C 4.3 M 7.5 3.5 6.5 75.0 229 231 C 4.8 H 26.7 1.3 0.3 1.3 233 244 H 4.8 H 2.5 20.5 1.9 1.2 247 249 C 4.8 H 6.0 5.0 4.7 4.0 251 253 E 4.5 M 4.7 5.3 4.3 5.0 254 257 * 3.2 M 24.4 7.4 75.0 40.5 258 259 C 4.3 M 7.0 5.0 6.2 75.0 261 264 E 4.8 H 1.5 2.2 1.0 1.8 266 273 C 4.3 M 75.0 3.6 4.3 2.6 275 277 E 4.3 M 75.0 4.7 5.0 4.7 278 281 C 4.3 M 75.0 0.0 0.5 0.5 282 294 H 4.3 M 75.0 0.0 0.1 0.0 296 297 C 4.3 M 75.0 9.2 1.5 0.5 299 303 E 4.3 M 75.0 1.2 1.8 1.6 304 306 * 2.3 P 75.0 1.3 1.3 3.0 307 308 - 4.3 M 75.0 75.0 6.5 75.0 309 311 * 2.7 P 75.0 2.7 1.0 27.0 313 314 * 2.3 P 75.0 0.5 0.5 2.5 315 322 H 4.3 M 75.0 1.8 2.4 2.8 324 325 C 4.3 M 75.0 4.0 2.0 3.5 326 329 E 4.3 M 75.0 3.5 3.5 4.0 330 331 * 2.3 P 75.0 5.5 4.5 8.2 332 340 - 4.3 M 75.0 4.3 75.0 75.0 342 346 E 4.3 M 75.0 1.6 1.8 1.2 347 348 C 4.3 M 75.0 1.5 4.0 2.0 349 350 - 4.3 M 75.0 75.0 75.0 3.0 351 355 C 4.3 M 75.0 4.3 2.6 1.6 358 364 * 2.8 P 75.0 2.9 33.9 3.3 367 369 * 2.3 P 75.0 0.7 0.3 1.0 370 377 H 4.3 M 75.0 0.0 0.0 0.0 378 379 * 2.3 P 75.0 0.0 0.5 0.0 380 382 C 4.3 M 75.0 5.3 5.7 5.0 384 386 E 4.3 M 75.0 1.3 0.0 2.0 387 388 * 2.9 P 75.0 4.0 4.5 38.0 390 397 * 2.9 P 75.0 2.1 1.1 39.1 399 403 * 2.5 P 75.0 0.6 1.0 15.6 404 409 H 4.3 M 75.0 2.5 2.0 2.8 410 412 C 4.3 M 75.0 2.0 0.7 2.3 413 416 E 4.3 M 75.0 4.0 4.2 4.8 418 419 C 4.3 M 75.0 7.8 6.0 7.8 421 424 E 4.3 M 75.0 1.8 1.8 2.0 425 427 C 4.3 M 75.0 3.0 4.5 3.3 428 430 - 4.3 M 75.0 3.7 75.0 75.0 431 434 C 4.3 M 75.0 2.8 4.0 3.2 435 437 - 4.3 M 75.0 7.7 75.0 75.0 442 443 C 4.3 M 75.0 3.0 1.5 0.5 446 456 H 4.3 M 75.0 0.0 0.0 0.1 457 458 * 2.9 P 75.0 0.0 37.5 0.5 459 461 C 4.3 M 75.0 2.7 3.0 4.7 463 465 E 4.3 M 75.0 0.3 0.3 1.3 468 470 * 2.3 P 75.0 2.0 3.3 2.3 471 473 H 4.3 M 75.0 1.3 1.7 2.3 474 477 C 4.3 M 75.0 1.8 2.5 1.8 478 483 H 4.3 M 75.0 3.0 3.0 2.0 484 492 * 3.0 P 75.0 4.5 43.1 4.1 >>>>>>