Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1oaca1 ---------CCCCCCCCCCCCCCCEEEE-C-CEEEECCEEEEEEEECCCEEEEEEEEEEEC--CEEEEEEEEEEEEEEEEECCCCCCCCCCCEECHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCEEEEEEEEEEEEEEE-EEEEEECC---CCC-CCEEEEEEEEEEEEEECCCCCEEEEEEEECCCCEEEEEEEEECCCEEECCCCCCCCCCHHHHCCCEEEEECCEEEECEEEEEEEEEEECCCCCEEEEEEEEEEEEECC-CC---CCCCEEEEEEEEEECCHHHHCCCCCC--CCEEEEEEEEEECCC-CCEEEEEEEEEEEECCCCCCCCCCCCCCHHHHHCHHHHCCEEEEECCCCCCCCCCCCCCCCCCC--CCHHHHCCCC-CCCCCEEEEEEEEEEEEECCCHHHCCCEEE--EEEEEEEEEECCCCCCCCCCCC--------------C--------------------------------- >P1;d1rjoa1 ------CCCCCCCCCCCCCCCCCCCEEE-CCCEEEECCEEEEEEEECCCEEEEEEEEEEEC--CEEEEEEEEEEEEEEEEECCCCCCCCCCCEEEIIIIICHHHHCCCCCCCCCCCCCCEEECCEEECCCCCEEECCCCEEEEEEEE-EEEEEEECCCC-C--CEEEEEEEEEEEEEEECCCCCEEEEEEEECCCCEEEEEEEEECCCCEECCC-----C----CCCCEEEEECCEEEECEEEEEEEEEEECCCCCCCEEEEEEEEEC--C-CC-CCCCCCCCEEEEEEEECCHHHCEECCCHHHCCEEEEEEEEEECCC-CCEEEEEEEEC------CCCCCCCCCCCHHHHHCHHHHCCEEEEECCCCCCCCCCCCCCCCCC--CCCHHHHHCCC-CCCCCCCEEEEEEEEEEECCCHHHCCCEEE--EEEEEEEEECCCCCCCCCCCCCCC---------------------------------------------- >P1;d1w2za1 CCCCCCCCCCCCCCCCCCCCCCCCEEEE-C-CEEEECCEEEEEEEECCCEEEEEEEEEEECCCCEEEEEEEEEEEEEEEEECCCCCCCCCCCEECHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCEEEEEEEEEEEEECC-CEEEEEEECCCCCCCEEEEEECCEEEEEEEECCCCCEEEEEEECCCCCEEEEEEECCCCCEEECCCCCHHH--CCCC-CCEEEEECCEEEECEEEEEEEEEEECCCCCCCEEEEEEEEEEECC-CC--CCCCCEEEEEEEEECCCHHHHCCCCCC-CCEEEEEEEEEEECCC-CCEEEEEEECC-----CCC-CCCCCCCCHHHHHCHHHHCCEEEEECCCCCCCCCCCCCCCCCCC--CCHHHHHHHC-CCCCCCCEEEEEEEEEEECCCHHHCCCCCC--EEEECEEEEECCCCCCCCCCCCCCCCCC-----CCCC--------------------------------- >P1;d1w7ca1 -------CCCCCCCCCCCCCCCCCCEEECCCCEEEECCEEEEEEEECCCEEEEEEEEEC------CEEEEEEEEEEEEEEEECCCCCCHHHCEEEHHH-HCCCC-CCCCCCCCCCCCCCEEEEEEEEEC-CEEEEEEEEEEEEEEECCCCCEEEEEC-----CEEEEECCEEEEEEEEECCCCCEEEEEEECCCCCEEEEEEECCCCCCEECCC--------CCCHHHCCEEECCEECCCEEEEEEEEEEECCCCCEEEEEEEEEEEEEEECCCCCC-CEEEEEEEEEEECCCCCCCCCCCCHHHCEEEEEEEEEEECCC-CCEEEEEEEEC-----CCCCCCCCCCCCCCCCCCHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCHHHHCCC--CCCCCEEEEEEEEEEEEECCCHHHCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCEEEEEECCCCCCEEEECCCCCCCCCCCCCCCCCHHHCCCCCCEEEEC >P1;d2oqea1 ------CC---CCCCCCCCCCCCCCEEE-C-CEEEECCEEEEEEEECCCEEEEEEEEEEEC--CEEEEEEEEEEEEEEEEECCCCCCCHHHCEECHHHHCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCEEEEEEEEEEEEEEE-EEEEEEECHHH-CCCCEEEEEEEEEEEEEEECCCCCEEEEEEEECCCCEEEEEEECCCCCCEECCC-----CC--CCCCCEEEEECCEEEECEEEEEEEEEEECCCCCCCEEEEEEEEECCCC-CCCCCCCCCCCEEEEEEECCCHHHHCCCCCHHHCCEEEEECCCCCCCCCCCCCEEEEECC------CCCCCCCCCCCHHHHHCHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCEEEEEEEEEEECCCHHHCCC-CC--EEEEEEEEEECCCCCCCCCCCCCCEEEC-HHHHHHCC--------------------------------- PSA >P1;d1oaca1 ---------bb898875727a9250729-c-550505502030404420002026020338--88515005100000000007055a80672120000353004403304648402500302515063a687735044000000362-45035756---ac6-83745533100010102094301000001220100010012150222808065593b508711440400565200030010000000000134600010124373709-9a---897a4395455560630570025074--b12000003555065-654000102031506062091061679581262030023100002337a222000690992861--3003500873-260631200000000020605770177062--120403041340146521597a--------------a--------------------------------- >P1;d1rjoa1 ------ba8a8898885728a4230717-cb43050440002030431000003700043c--a74040032000000000080638814701200001430025045076674150303112150639877755073000010355-74055763995-9--783425141000002041c5200010000030102020202140321914b-----c----42a40250499200020010000000000065302010015484--a-76-9b1891a37556262045065012613694711000002734167-86200010304------2452053889470061020034000003438705100149079484--a4004411854-240413300000000111605770377054--63000405136004652167184b---------------------------------------------- >P1;d1w2za1 9897879549999b986632a648090a-b-4605052070303044100010250004075376502004200000001002056a61661030000141004204508467204470421406044b987664161000000349-560247439958b6a475314020000100020b430101000112000402010205022281b2678a5--2988-120510455100030010000000000076600002152473628-8b--74a785464564730730540122188-7614000001545099-55200020514-----b10-41719894910410100230000013488140000690781809--5002410774-280444300000010130606791367065--5623020402500165205749338b3a-----6509--------------------------------- >P1;d1w7ca1 -------96aa7a9933315983307355a62305035000406062210010330202------a44005000000000003013780560030000-50000-12004008202020201404052a-82314050000000341a621447659-----5313303000000101030c62110101000101010003010702027156--------97066405406873000300100000000001a6502002133471525386279-664638476352264056901513a99403000000754167-84210000437-----901420556a1920130010020000003239a1720012902a447a03230280068--3504032000000001314059702840536803000202133024852047171114244589678385434c3868b7b395881348528854275685 >P1;d2oqea1 ------ba---887985827a8270708-c-430402505040313400000038010527--88512006100000000017057830462040000150004103607658306150411206164a777753262000000463-65024912774-a65214104031000001031953010300011400020206030503258099-----b5--804640350755200010010000001030146300000006481757-761851591a47564362074085012514991711010001556068476200020406------40170639a8341030010043000000358a1310007904a06078740035026907560343700000000021605592177-63--470503030440048410473a256427-5740876b--------------------------------- Translating the sequences ---------CCCCCCCCCCCCCCC*EEE-C-CEEEECCEEEEEEEECCCEEEEEEEEEEEC--CEEEEEEEEEEEEEEEEECCCCCCCCCCCEECHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCEEEEEEEEEEEEEEE-EEEEEE*C---*CC-C*EEEEEEEEEEEEEECCCCCEEEEEEEECCCCEEEEEEE**CCC*EECCC*****C*****CCCEEEEECCEEEECEEEEEEEEEEECCCCC**EEEEEEEEEEECC-CC---CCCCEEEEEEEEE*CCHHHHCCCCC*--CCEEEEEEEEEECCC-CCEEEEEEEE******CCCCCCCCCCCCHHHHHCHHHHCCEEEEECCCCCCCCCCCCCCCCCCC--CCHHHH*CCC-CCCCC**EEEEEEEEEEECCCHHHCCC***--EEEEEEEEEECCCCCCCCCCCC--------------C--------------------------------- ------CCCCCCCCCCCCCCCCCCCEEE-C*CEEEECCEEEEEEEECCCEEEEEEEEEEEC--CEEEEEEEEEEEEEEEEECCCCCCCCCCCEE******C****CCCCCCCCCCCCCCEEE**EEECCCCCEEE****EEEEEEEE-EEEEEEECC**-C--CEEEEEEEEEEEEEEECCCCCEEEEEEEECCCCEEEEEEE**CCCCEECCC-----C----CCCCEEEEECCEEEECEEEEEEEEEEECCCCCCCEEEEEEEEE*--C-CC-CCCCCC**EEEEEEE*CCHHH***CCCHHHCCEEEEEEEEEECCC-CCEEEEEEEEC------CCCCCCCCCCCHHHHHCHHHHCCEEEEECCCCCCCCCCCCCCCCCC--CCCHHHHHCCC-CCCCCCCEEEEEEEEEEECCCHHHCCC***--EEEEEEEEE*CCCCCCCCCCCCCC---------------------------------------------- ******CCCCCCCCCCCCCCCCCC*EEE-C-CEEEECCEEEEEEEECCCEEEEEEEEEEEC**CEEEEEEEEEEEEEEEEECCCCCCCCCCCEECHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCEEEEEEEEEEEEE**-*EEEEEE*C***CCC*EEEEE**EEEEEEEECCCCCEEEEEEE*CCCCEEEEEEECCCCC*EECCC*****--**CC-CCEEEEECCEEEECEEEEEEEEEEECCCCCCCEEEEEEEEEEECC-CC--CCCCCEEEEEEEEECCCHHHHCCCCC*-*C*EEEEEEEEEECCC-CCEEEEEEE*C-----CCC-CCCCCCCCHHHHHCHHHHCCEEEEECCCCCCCCCCCCCCCCCCC--CCHHHHH**C-CCCCCCCEEEEEEEEEEECCCHHHCCC*CC--EEEE*EEEEECCCCCCCCCCCCCC****-----***C--------------------------------- -------CCCCCCCCCCCCCCCCCCEEE*C*CEEEECCEEEEEEEECCCEEEEEEEEE*------*EEEEEEEEEEEEEEE*CCCCCC***CEE*HHH-HCCCC-CCCCCCCCCCCCCCEEEEEEEE*C-C*EEEEEEEEEEEEEE*****EEEE*C-----C*EEEE**EEEEEEEEECCCCCEEEEEEE*CCCCEEEEEEECCCCCCEECCC--------*CC*****EEECCEE**CEEEEEEEEEEECCCCC**EEEEEEEEEEE***CC*CC-C**EEEEEEEEECCC****CCCCCHHHC*EEEEEEEEEECCC-CCEEEEEEEEC-----CCCCCCCCCCCC*****CHHHHCCEEEEECCCCCCCCCCCCCCCCCCC*CCCHHHH*CC--CCCCC**EEEEEEEEEEECCCHHHCCC*CC***EEEEEEEEECCCCCCCCCCCCC*********************************************** ------CC---CCCCCCCCCCCCCCEEE-C-CEEEECCEEEEEEEECCCEEEEEEEEEEEC--CEEEEEEEEEEEEEEEEECCCCCCC***CEECHHHH*CCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCEEEEEEEEEEEEEEE-EEEEEEEC***-CCCCEEEEEEEEEEEEEEECCCCCEEEEEEEECCCCEEEEEEECCCCCCEECCC-----C*--CCCCCEEEEECCEEEECEEEEEEEEEEECCCCCCCEEEEEEEEE**CC-CC*CCCCCC**EEEEEEECCCHHHHCCCCCHHHCCEEEEE*****CCC*CC**EEEEE*C------CCCCCCCCCCCHHHHHCHHHHCCEEEEECCCCCCCCCCCCCCCCCCC*CC*HHHHHCCC*CCCCCCCEEEEEEEEEEECCCHHHCCC-CC--EEEEEEEEEECCCCCCCCCCCCCC****-*******C--------------------------------- 49998.tem _________________________________ ------CCCCCCCCCCCCCCCCCCCEEE-C-CEEEECCEEEEEEEECCCEEEEEEEEEEEC--CEEEEEEEEEEEEEEEEECCCCCCCCCCCEECHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCEEEEEEEEEEEEEEE-EEEEEEECC**-CCCCEEEEEEEEEEEEEEECCCCCEEEEEEEECCCCEEEEEEECCCCCCEECCC-----C--*CCCCCEEEEECCEEEECEEEEEEEEEEECCCCCCCEEEEEEEEEEECC-CC-CCCCCCEEEEEEEEECCCHHHHCCCCCHHHCCEEEEEEEEEECCC-CCEEEEEEEEC-----CCCCCCCCCCCCHHHHHCHHHHCCEEEEECCCCCCCCCCCCCCCCCCC-CCCHHHHHCCC-CCCCCCCEEEEEEEEEEECCCHHHCCC*CC--EEEEEEEEEECCCCCCCCCCCCCC****-----***C--------------------------------- Structural block scores 0 5 - 4.5 M 75.0 75.0 8.0 75.0 75.0 6 24 C 4.8 H 17.7 6.9 6.7 9.7 17.7 25 27 E 5.0 H 6.0 5.0 6.5 5.0 5.0 32 35 E 5.0 H 2.5 2.0 2.8 2.0 1.8 36 37 C 5.0 H 5.0 4.0 3.5 4.0 3.5 38 45 E 5.0 H 1.6 1.1 2.1 2.0 2.0 46 48 C 5.0 H 2.0 1.3 1.7 1.7 1.3 49 59 E 4.9 H 1.6 1.5 1.1 7.8 1.7 61 62 - 4.5 M 75.0 75.0 4.0 75.0 75.0 64 80 E 4.9 H 1.5 1.2 1.2 5.8 1.4 81 91 C 4.6 H 4.6 4.1 4.0 3.0 3.9 92 93 E 5.0 H 1.5 1.5 1.5 1.5 2.0 95 99 H 4.3 M 1.6 1.0 1.0 16.0 1.2 100 118 C 4.9 H 2.6 3.1 3.1 5.1 2.9 119 126 E 4.9 H 2.8 2.4 2.6 2.0 2.6 127 131 C 4.7 H 6.9 6.8 7.9 19.5 7.1 132 146 E 4.8 H 2.3 2.7 2.7 1.4 2.5 148 154 E 4.6 H 4.1 4.9 4.0 4.3 3.9 155 156 C 3.9 M 40.5 6.0 6.0 7.0 4.5 157 158 * 3.0 P 75.0 7.0 7.0 75.0 5.5 160 163 C 4.2 M 25.4 41.5 8.0 39.5 5.9 164 178 E 4.8 H 2.2 2.0 1.5 0.8 1.0 179 183 C 5.0 H 3.6 4.9 4.1 4.7 4.2 184 191 E 4.8 H 0.2 0.1 0.4 0.5 0.6 192 195 C 5.0 H 1.2 1.0 0.8 0.5 1.2 196 202 E 5.0 H 0.3 0.9 1.0 0.6 1.4 203 208 C 4.4 M 2.0 2.0 1.8 1.7 2.2 209 210 E 5.0 H 5.0 5.0 5.0 4.5 6.5 211 213 C 5.0 H 2.7 5.5 4.8 4.0 6.0 214 218 - 3.8 M 5.6 75.0 7.3 75.0 75.0 220 221 - 3.8 M 2.5 75.0 38.5 75.0 40.0 223 227 C 4.3 M 3.4 19.1 18.8 4.6 4.4 228 232 E 4.8 H 1.8 2.2 2.0 3.0 3.0 233 234 C 5.0 H 5.5 9.0 5.0 7.5 5.0 235 238 E 4.8 H 0.5 0.5 0.2 0.8 0.5 240 250 E 5.0 H 0.1 0.1 0.1 0.1 0.2 251 257 C 4.7 H 2.0 2.0 2.7 3.2 2.4 258 268 E 4.8 H 2.5 9.1 2.7 2.5 2.4 269 270 C 4.3 M 4.5 42.8 5.0 3.5 6.0 272 273 C 5.0 H 9.8 6.5 9.8 7.0 6.5 275 280 C 4.5 M 30.8 6.6 18.6 17.8 4.8 281 289 E 4.7 H 5.1 5.2 4.9 4.9 5.3 290 292 C 4.6 H 3.0 3.0 3.3 4.0 3.7 293 296 H 4.3 M 3.0 2.8 2.2 5.0 3.2 297 301 C 4.8 H 2.8 2.6 2.8 2.0 2.6 302 304 H 4.0 M 51.3 6.3 30.0 9.5 6.3 305 306 C 4.4 M 6.2 4.0 3.5 2.0 4.0 307 316 E 4.8 H 2.0 1.7 1.9 1.9 1.9 317 319 C 5.0 H 3.7 4.7 6.0 4.7 4.7 321 322 C 5.0 H 5.5 7.0 5.0 6.0 6.5 323 330 E 4.7 H 0.9 0.8 1.2 1.2 1.0 332 336 - 4.5 M 2.4 75.0 75.0 75.0 75.0 337 348 C 4.9 H 4.3 10.4 10.9 4.4 10.5 349 353 H 4.5 M 3.8 2.8 3.0 1.2 1.6 355 358 H 5.0 H 1.2 1.2 0.8 0.8 1.2 359 360 C 5.0 H 2.0 2.0 1.5 0.0 1.5 361 365 E 5.0 H 0.4 0.6 0.2 0.6 0.0 366 384 C 5.0 H 4.2 7.8 4.0 4.4 3.9 386 388 C 4.6 H 26.0 4.8 26.7 2.7 3.7 389 393 H 4.8 H 1.6 2.0 1.4 2.0 2.0 394 396 C 4.5 M 6.0 5.7 6.0 29.7 5.0 398 404 C 4.7 H 2.9 2.4 3.6 2.4 4.0 405 415 E 5.0 H 0.2 0.3 0.5 0.5 0.3 416 418 C 5.0 H 3.7 3.7 4.0 3.0 3.7 419 421 H 5.0 H 4.7 4.7 5.7 5.3 5.3 422 424 C 5.0 H 5.0 5.7 5.3 4.7 5.0 426 427 C 3.8 M 4.0 4.5 5.5 4.0 4.5 428 429 - 4.5 M 75.0 75.0 75.0 7.0 75.0 430 439 E 4.8 H 1.8 2.2 2.4 1.1 2.6 440 453 C 4.9 H 14.6 4.4 3.6 3.2 3.8 454 457 * 3.0 P 75.0 75.0 8.2 2.8 4.8 458 462 - 3.9 M 75.0 75.0 75.0 6.4 18.2 463 465 * 3.0 P 75.0 75.0 3.7 6.0 7.0 467 499 - 4.5 M 75.0 75.0 75.0 6.0 75.0 >>>>>>