Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2f48a- CHHHHHHCCCCCCCCHHHHCCHHHEEEEECCCCCCCCCHHHHHHHCCCCCCCCEEEEECCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCHHHHCCCEEEECHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCEEHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHCCCEECCHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCHHHCCHHHHHHHHHHHHHHHHCHHHHCCCCHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCHHHCEEEEEEHHHH-EEEEEECCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHCCCCHHHHHHCC >P1;d5xz7a1 -------------------------------------------------------------------CCEEEEEECCCCCCCHHHHHHHHHHHHHHCC--CEEEEECCCHHHHHHCCEEEECHHHHCCCCCCCCC-CCCCCCCHHHHCCCHHHHHHHHHCCCCCEEEEEECHHHHHHHHHHHHHCC----CCEEEEEECCCCCCCC--CCCCCCCHHHHHHHHHHHHHHHHHHHHHHC-CEEEEEECCCCCCHHHHHHHHHCCCCEEECCCC-----CC---CHHHHHHHHHHHHHCCCCCCEEEEECCCC------------------------------------------------------------------------------CHHHHHHHHHCCC-----------CCCEEEEECHHHHHCCCCCHHHHHHHHHHHHHHHHHC-CCCCCEEEEEECC-------EEEEEEHHHHHC----------------CCCH--HHHHHHHHHCC----------------------------------- PSA >P1;d2f48a- 88436502629041061052609302056688050453596059406012320040566a1a1519920300000012100000000000030035127905010045005000635243058a406622010107006063210577940550180066190400000020100000010001046582a0000000000100013a10100000000012002300710660365653000000002100000000001020010100010456814076005600520250187824000000000002003204500630160127458507a372751271027407a70391047016400210030025024001130130100400153047406524788509290413422106602533000000000000000000000031100000034034815605000000010-001351377711003133082944005304722950146150532761415989a60441030042329 >P1;d5xz7a1 -------------------------------------------------------------------1820000019630000000031003202959--14010024002001734064076a30791346140-20614a07308662077017103427030000004590061015005209----6030000001010307--004400003000520293068129505664-20100101079000000400330a011000123-----a3---60651056155447883710000003101------------------------------------------------------------------------------5066038406631-----------b262512304750379503960371035003200500-76343200014a9-------813014077009----------------4066--82265047628----------------------------------- Translating the sequences *******************************************************************CCEEEEEECCCCCCCHHHHHHHHHHHHHHHC**CEEEEECCC*HHHH*CCEEEECHHHHHHHCCCCCC*CCCCCCC****HHHHHHHHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHH****CCEEEEEEEECCCCCC**CCCCCEEHHHHHHHHHHHHHHHHHHHHHHC*CEEEEEECCCCCCHHHHHHHHHHCCCEE*CHHH*****CC***HHHHHHHHHHHHHHCCCCCEEEEEECCHH******************************************************************************HHHHHHHHHHHHH***********CCCEEEEEE*HHHHCCCCCHHHHHHHHHHHHHHHHHH*CCCCCEEEEEECC*******EEEEEEHHHH-E****************CCC***HHHHHHHHHHH*********************************** -------------------------------------------------------------------CCEEEEEECCCCCCCHHHHHHHHHHHHHH*C--CEEEEECCCHHHHHHCCEEEECHHHH***CCCCCC-CCCCCCCHHHH***HHHHHHHHH*CCCCEEEEEECHHHHHHHHHHHHH**----CCEEEEEE**CCCCCC--CCCCC**HHHHHHHHHHHHHHHHHHHHHHC-CEEEEEECCCCCCHHHHHHHHH*CCCEEEC***-----CC---*HHHHHHHHHHHHHCCCCC*EEEEECC**------------------------------------------------------------------------------*HHHHHHHHH***-----------CCCEEEEE*HHHHHCCCCCHHHHHHHHHHHHHHHHH*-CCCCCEEEEEECC-------EEEEEEHHHH**----------------CCCH--HHHHHHHHH**----------------------------------- 53784.tem _________________________________ -------------------------------------------------------------------CCEEEEEECCCCCCCHHHHHHHHHHHHHHHC--CEEEEECCCHHHHHHCCEEEECHHHHHHHCCCCCC-CCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHH----CCEEEEEEEECCCCCC--CCCCCEEHHHHHHHHHHHHHHHHHHHHHHC-CEEEEEECCCCCCHHHHHHHHHHCCCEEECHHH-----CC---HHHHHHHHHHHHHHCCCCCEEEEEECCHH------------------------------------------------------------------------------HHHHHHHHHHHHH-----------CCCEEEEEEHHHHHCCCCCHHHHHHHHHHHHHHHHHH-CCCCCEEEEEECC-------EEEEEEHHHH-E----------------CCCH--HHHHHHHHHHH----------------------------------- Structural block scores 0 66 - 3.0 P 3.9 75.0 67 68 C 5.0 H 1.0 4.5 69 74 E 5.0 H 0.5 0.3 75 81 C 5.0 H 0.6 2.7 82 96 H 4.9 H 0.8 1.7 98 99 - 3.0 P 8.0 75.0 101 105 E 5.0 H 1.2 1.0 106 108 C 5.0 H 3.0 2.0 109 114 H 4.3 M 1.8 1.7 115 116 C 5.0 H 4.0 3.5 117 120 E 5.0 H 2.2 2.5 122 128 H 4.1 M 5.2 5.2 129 134 C 5.0 H 0.7 3.0 136 142 C 5.0 H 2.4 3.4 143 159 H 4.1 M 3.8 3.6 160 163 C 5.0 H 3.5 3.0 164 169 E 5.0 H 0.0 0.0 171 185 H 4.7 H 0.5 2.9 186 189 - 3.0 P 5.2 75.0 190 191 C 5.0 H 5.2 3.0 192 199 E 4.5 M 0.0 0.5 200 205 C 5.0 H 0.3 1.8 206 207 - 3.0 P 6.8 75.0 208 212 C 5.0 H 0.4 1.6 213 214 E 3.0 P 0.0 0.0 215 236 H 5.0 H 1.9 3.3 240 245 E 5.0 H 0.0 0.3 246 251 C 5.0 H 0.5 2.8 252 261 H 4.8 H 0.1 1.0 262 264 C 5.0 H 0.7 3.8 265 267 E 4.3 M 0.7 0.3 269 271 H 3.0 P 0.3 2.0 272 276 - 3.0 P 4.6 75.0 277 278 C 5.0 H 2.5 6.8 279 281 - 3.0 P 4.3 75.0 282 295 H 4.9 H 2.4 3.9 296 300 C 5.0 H 4.2 5.4 301 306 E 4.7 H 0.0 0.0 307 308 C 5.0 H 0.0 2.0 309 310 H 3.0 P 0.0 0.5 311 388 - 3.0 P 2.8 75.0 389 401 H 4.4 M 2.2 3.7 402 412 - 3.0 P 5.1 75.0 413 415 C 5.0 H 4.3 6.5 416 421 E 4.7 H 2.2 2.2 422 426 H 4.6 H 2.8 3.8 427 431 C 5.0 H 2.2 4.8 432 449 H 4.9 H 0.0 2.4 451 455 C 5.0 H 1.0 4.6 456 461 E 5.0 H 0.5 1.2 462 463 C 5.0 H 2.0 9.8 464 470 - 3.0 P 3.9 75.0 471 476 E 5.0 H 0.8 2.8 477 480 H 5.0 H 0.2 3.5 483 498 - 3.0 P 2.7 75.0 499 501 C 5.0 H 3.7 3.3 503 504 - 3.0 P 6.5 75.0 505 515 H 4.6 H 3.3 4.5 516 550 - 3.0 P 3.7 75.0 >>>>>>