Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1vl4a- -------CHHHHHHHHHHHHCCCC-EEEEEEEEEEEEEEEEECCE-EEEEEE-CCEEEEEEEECCEEEEE-CCCC---CHHHHHHHHHHHHHCC----CCCCCCCC----CCCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHH-CCCCEEEEEEEEEEEEEE-EEEEECCCCEECCCEEEEEEEEEEEECCC-CCEEEEEEEEECCHHHCC--CCHHHHHHHHHHHCCCCCCCCCC-CCEEECHHHHHHHHHHHHHHHCHHHHHCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCEEEEECCEECCCCCCCCCC---C-CCCCCEECCEECCCEEEECCCCCCHHHHHHHHCCEEEEEEEECHHH-HCCCCCCEEEEEEEEEEEECCEEEEEEEEEEEEEEHHHHHHCEEEECCCCEECCCEEECCEEECCCEEE-- >P1;d1vpba- -----CCCCCCCHHHHHHHHCCCCCEEEEEEEEEEEEEEEEC--CCCC-----CCEEEEEEEECCEEEEEEECCCC--CHHHHHHHHHHHHCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCHHHCCHHHHHHHHHHHHHCCCCCCCCEEEE-EEEEEEEEEEEEEEECCCEEEEEEEEEEEEEEEEEECC-CCCCEEE-EEEECCHHHCC-CCCHHHHHHHHHC-CCCCCCCC-EEEEEEECCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCEECCCCCCHHHHHHHCCCCCCC------CCCCEEECCCCCCHHHHHHCCCEEEEEEEEEE---EEECCCCCEEEEEEEEEEEEC-CCCCEEEEEEEEEEHHHHHHCEEEECCCCCCCCCEECCCEEEEEEEEEEC >P1;d5njcb- CCHHHHCCHHHHHHHHHHHHHCCCCEEEEEEEEEEEEEEEEECCEEEEEEEEEEEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHHC-CCCCCCCCCCCCHHHCCC-CCCCCCCCC--CCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEEEEEEEEECCCCEEEEEEEEEEEEEEEEEEECCEEEEEEEEEEECCHHHCCCHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECHHHHHHHHHCHHHHCCHHHHHCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCEECCCCCCHHHHHHHCCCCCCCCC----CCCCEECCCCCCCC-CHHHHHCCEEEEEEEEC----CCCCCCCEEEEEEEEEEECC-CEEEEEEEEEEEEEHHHHHHCCCEECCCCCCCCCEECCCEEEEEEEEECC PSA >P1;d1vl4a- -------717701650261085b0-4010205525212031361a-467545-42604030159251034-2791---825800550274188a----9650171b----6a25a0703214056176761451056027203-93a502501204031313-3100012a061423100020202020619-661313122000106508--130064005101503a0760879-2300011000040040014000042045840205b35864002540101010325501302110330010532300480304300030104---b-53200009b703000010326a3527500540660000020592ba-3062650606080300105a0732300290304620170053033005321017300000000650806-- >P1;d1vpba- -----806a421062018203550710103044434081154--7458-----84003010104722271618825--6057404720470385a5481341074820166b5780511097198275770151046007303b52840620-00503001513011014b05255640402030504051-ca82511-50301108606-3930064016302-22b17415-861000001110340041016005052036850003a33765101640202000234403503110a1003066240056030201002111053295a2203------4100030537a56296006809600002306b---591654507050201031059-03532017030483028006404300531265433100000057040539 >P1;d5njcb- 790782370590054018407b607101060324331302055084582672683605020167535162738714880056005500750-949447203002672004-a04a05022--22a054970272014004200833a40550400404122105000044a03302010402040201043ba46151603021012a4057064007200720152061630743603000132101a003203a004052026740003904763000730203020446321201000720040642200560504200030300232a57010009----70000209037373-6016506400002408c----71486507062501010060-73421048040472058004604100633163441000000046050607 Translating the sequences -------CHHHHHHHHHHHHCCCC-EEEEEEEEEEEEEEEEECCE-EEEEEE-CCEEEEEEEECCEEEEE-*CCC---CHHHHHHHHHHHH*CC----CCCCCC**----CCCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHH-CCCCEEEEEEEEEEEEEE-EEEEECCCCEE***EEEEEEEEEEEECCC-CCEEEEEEEEECCHHHCC--CCHHHHHHHHHHHCCCCCCCCC*-**EEECHHHHHHHHHHHHHH*CHHHHHCCCCCCCCCCCCCCCCCCCCEEE*CCCCCCCCCCCCCCCCCCCCCEEEEECCEECCCCCC****---C-CCCCC******CCC*EEECCCCCCHHHHHHHHCCEEEEEEEEC***-*CCCCCCEEEEEEEEEEEEC**EEEEEEEEEEEEEHHHHHHCEEEECCCC**CCCEE*CCEEE***EEE-- -----*CC****HHHHHHHHCCCCCEEEEEEEEEEEEEEEE*--****-----CCEEEEEEEECCEEEEEEECCCC--CHHHHHHHHHHHH*CCCCCCCCCCCCHHHCCCCCCCCCCCCCCCHHHCCHHHHHHHHHHHHH***CCCCCEEEE-EEEEEEEEEEEEEEECCC*EEEEEEEEEEEEEEEEECC-CCC*EEE-EEEECCHHHCC-*CCHHHHHHHHH*-CCCCCCCC-EEEEEEEC***HHHHHHHHHH*CCHHHHHCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCEECCCCCCHHHHHHHCCCCCCC------CCCCEEECCCCCCHHHHHH**C*EEEEEEEE*---***CCCCCEEEEEEEEEEEEC-C***EEEEEEEEEEHHHHHHCEEEECCCCCCCCCEECCCEEEEEEEEE*C ******CCHHHHHHHHHHHH*CCCCEEEEEEEEEEEEEEEEECCE*EEEEEE***EEEEEEEECCEEEEEEECCCC***HHHHHHHHHHH*-CCCCCCCCCCCCHHHCCC-CCCCCCCCC--***CCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEEEEEEEEECCCCEEEEEEEEEEEEEEEEE**CC**EEEEEEEEECCHHHCC****HHHHHHHHHHHCCCCCCCCCEEEEEEECHHHHHHHHH*HHHHCCHHHHHCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCEECCCCCCHHHHHHHCCCCCCC**----CCCCEE*CCCCCC*-*HHHHHCCEEEEEEEEC----*CCCCCCEEEEEEEEEEE*C-CEEEEEEEEEEEEEHHHHHHC**EECCCCCCCCCEECCCEEEEEEEEE*C 111283.tem _________________________________ -----*CCHHHHHHHHHHHHCCCCCEEEEEEEEEEEEEEEEECCE*EEEEEE-CCEEEEEEEECCEEEEEEECCCC--CHHHHHHHHHHHH*CCCCCCCCCCCCHHHCCCCCCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEEEEEEEEECCCCEEEEEEEEEEEEEEEEECCCCCCEEEEEEEEECCHHHCC-*CCHHHHHHHHHHHCCCCCCCCCEEEEEEECHHHHHHHHHHHHHHCCHHHHHCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCEECCCCCCHHHHHHHCCCCCCC**----CCCCEEECCCCCCHHHHHHHHCCEEEEEEEEC----*CCCCCCEEEEEEEEEEEEC-CEEEEEEEEEEEEEHHHHHHCEEEECCCCCCCCCEECCCEEEEEEEEE*C Structural block scores 0 4 - 4.0 M 75.0 75.0 6.2 6 7 C 4.5 M 41.0 3.0 5.0 8 19 H 4.7 H 3.0 3.0 3.0 20 24 C 4.6 H 19.9 4.0 6.3 25 41 E 4.9 H 2.1 2.5 2.0 42 43 C 4.0 M 3.5 75.0 2.5 46 51 E 4.0 M 5.2 52.2 5.0 53 54 C 4.0 M 3.0 6.0 5.5 55 62 E 5.0 H 2.4 0.6 2.5 63 64 C 5.0 H 5.5 5.5 6.0 65 71 E 4.7 H 12.9 3.0 3.9 72 75 C 4.8 H 23.0 5.8 5.0 76 77 - 4.0 M 75.0 75.0 8.0 79 90 H 4.9 H 3.2 3.3 2.8 92 103 C 4.7 H 28.9 4.7 3.7 104 106 H 4.0 M 29.2 4.7 5.0 107 121 C 4.6 H 18.4 4.5 17.5 122 124 H 4.0 M 3.7 6.0 4.8 125 126 C 5.0 H 4.0 4.5 2.5 127 142 H 4.8 H 3.4 3.1 2.6 143 147 C 4.8 H 20.5 6.1 5.7 148 167 E 4.9 H 5.2 5.2 1.6 168 171 C 4.8 H 3.4 4.1 4.6 172 188 E 4.8 H 1.5 2.6 1.3 189 194 C 4.0 M 17.2 18.7 6.5 195 203 E 4.8 H 1.4 10.2 2.1 204 205 C 5.0 H 0.5 1.0 0.5 206 208 H 5.0 H 3.7 4.7 5.5 209 210 C 5.0 H 4.0 3.0 2.5 213 214 C 4.0 M 2.0 6.0 5.0 215 225 H 4.8 H 2.0 8.8 2.2 226 234 C 4.9 H 4.6 12.1 3.2 235 241 E 4.4 M 12.7 2.1 1.7 243 256 H 4.6 H 1.0 1.6 2.6 257 258 C 4.5 M 0.0 2.5 2.0 259 263 H 5.0 H 2.0 2.0 1.8 264 283 C 5.0 H 3.7 3.5 3.0 284 286 E 5.0 H 0.3 0.7 1.0 287 308 C 5.0 H 1.8 2.4 2.2 309 313 E 5.0 H 1.8 2.2 1.8 314 315 C 5.0 H 4.0 3.0 3.0 316 317 E 5.0 H 1.5 1.5 2.5 318 323 C 5.0 H 1.7 0.8 1.5 324 330 H 4.0 M 32.9 1.9 1.4 331 337 C 4.9 H 13.8 4.5 3.4 338 339 * 2.7 P 0.0 75.0 4.5 340 343 - 4.0 M 6.9 75.0 75.0 344 347 C 4.8 H 0.8 1.2 1.8 348 350 E 4.7 H 0.3 1.0 0.7 351 356 C 5.0 H 4.9 6.1 4.8 357 364 H 4.4 M 2.9 3.9 12.0 365 366 C 4.5 M 6.0 7.5 5.0 367 374 E 5.0 H 0.9 1.4 1.8 376 379 - 4.0 M 24.8 57.5 75.0 381 386 C 4.8 H 3.2 3.5 4.0 387 398 E 4.9 H 2.4 2.0 2.3 402 414 E 4.8 H 2.6 3.0 3.0 415 420 H 5.0 H 2.2 2.7 2.8 422 425 E 4.5 M 1.5 1.8 1.2 426 434 C 4.8 H 2.4 3.2 3.3 435 436 E 5.0 H 0.0 2.0 0.5 437 439 C 4.7 H 0.0 0.0 0.0 440 448 E 4.7 H 2.8 2.3 2.3 >>>>>>