Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d3sy7a1 ----------------CCCCCCHHHC-CCCCCCEEEEEEEEEEEEEE---------CEEEEEEEEEEEEECCCCCC-------CCEEEEEEEEEEEEEEEECC----------------------EEEEE-EEEEEEEECCEEEEEEEECCCCCCCCCCCCCCCCCCEEEEEEEECCCCCEEEEEEEEE-----------CCEECCC-C------EECCEEEEEEEEEEECCEEEEEEEEEECCCEEEEEEEEEEEEEEECCEEEEEEEEEEEEEECC-------------------CCCCCCEEEEEEEEEEEEECCEEEEEEEEEEEECCCCCCEECCCCCCCCCCCCCCCCCCCCCCCCC-CEEEEEEEECCCCC-----CCCEEEEEEEEEEEEECCCCCC-----CCHHHHHCCCCC-CEEEEEEEEEEEEECCCCC-CCCEEEEEEEEEEEC---HHHCCCCEEEEEEEEEEECCCC >P1;d3syba- CCCCCCCHHHHHCCCHHHCCCCHHHCCCCCCCCEEEEEEEEEEEEEE-----------CEEEEEEEEEEECCCCCC-------CEEEEEEEEEEEEEC----C----------------------EEEEEEEEEEEEEECCEEEEEEEECCEECCEECCCCCCCCCEEEEEEEEEEEECCEEEEEEECC-EECCCCCCCCCCCCCCCCC------CCCCCEEEEEEE-EECCEEEEEEEEEECCCEEEEEEEEEEEECCCCCCEEEEEEEEEEEEECC------------------CCCCCCCEEEEEEEEEEEEECCEEEEEEEEEEECCCCCCCCCCCCC----CCCCCCCC-CCCCCCCCEEEEEEEEEEHHHHC-----CCCEEEEEEEE-CCCEECCCCCCCHHHCCCCCHHHHHCE-EECCCEEEEEEEEECCCCCCCCCEEEEEEEEE-CC---CCCCCCCEEEEEEEEEEEEECC >P1;d3szva1 ---------------------------CCCCCCEEEEEEEEEEEEEEEC----------CCEEEEEEEEECCCCCC-------CEEEEEEEEEEEEEECC------------------------CCEEEE-EEEEEEEECCEEEEEEEECCCCCCCCCCC-CCCCCEEEEEEEEEEEECCEEEEEEEEEEEECCCCCCCCCCCCCC----CC---CCCCEEEEEEEEECCCCEEEEEEEEEECCCEEEEEEEEEEEECC----CCEEEEEEEEEEECC--------------------CCCCCEEEEEEEEEEEEECCEEE-EEEE-CCCCCCCCCCC--CCC-C--CCCCCCCCCCCCCCCCEEEEEEEEEECCCCC-----CCCEEEEEEEEEEEEEEEC----------------C--EEEEEEEEEEEEEEEECCCCCCCCCEEEEEEEEEEECCC-------CEEEEEEEEEEEEEEE >P1;d5dl5a1 --------------------CCCCCCCCCCCCCEEEEEEEEEEEEEEEC---CCCCCEEEEEEEEEEEEECCCCCC-------CEEEEEEEEEEEEEECC---CCC-CCCCCCCCCCC-CCCCCCEEEEE-EEEEEEEECCEEEEEEEECCEECCEECCCCCCCCCEEEEEEEEEEEECCEEEEEEEEEEEECCCCCC-----CCCCCCC----CCCCCEEEEEEEEEEECCEEEEEEEEEECCCEEEEEEEEEEEEEECCCEEEEEEEEEEEEEECCCCCCCCCCCCCCCCHHHHCCCCCCEEEEEEEEEEEEEECCEEEEEEEEEEEECCCCCCCCCCCCC-CCCCCCCCCC-CCCCCCCCEEEEEEEEEECCCCC----CCCCEEEEEEEEEEEEEEEC----------------CCEE-EEEEEEEEEEEEEECCCCCCCCCEEEEEEEEEEECCCCCCCCCCCEEEEEEEEEEEEEEE >P1;d5dl7a- -----------------------------CCCCEEEEEEEEEEEEEEECCCCCCCCCEEEEEEEEEEEEECCCCCC-------CEEEEEEEEEEEEEECC-HHHHHHCCCCCCCCCCC-CCCCCCEEEEE-EEEEEEEECCEEEEEEEECCEECCEECCCCCCCCCEEEEEEEEECCCCCEEEEEEEEEEEECCCCCCCCCCEECCHHHCCCCCEECCCEEEEEEEEEC-CCEEEEEEEEEECCCEEEEEEEEEEEEECCCCEEEEEEEEEEEEEECC------------------CCCCCCCEEEEEEEEEEEEECCEEEEEEEEEEECCCCCCCC----CC-CCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCEECCEECCCEEEEEEEEEEEEECCC----------------CCCCCCEEEEEEEEEEEEECCCCCCCCEEEEEEEEEEEE-CCCCCCCCCCEEEEEEEEEEEEE-C >P1;d5dl8a- -------------------------CCCCCCCCEEEEEEEEEEEEEEECCC--CCCCEEEEEEEEEEEEECCCEEEEEEECCEEEEEEEEEEEEEEEECC-C---CCCCCCCCCCEECCCCEECCEEEEE-EEEEEEEECCEEEEEEEECCCCCCCCCCCCCCCCCEEEEEEEEEECCCCEEEEEEEEEEEECCCCCCCCCCEEEE----CCEEEECCCEEEEEEEEECCCCEEEEEEEEEECCCEEEEEEEEEEEEEC-CCCEEEEEEEEEEEEECC--------------------CCCCCEEEEEEEEEEEEECCEEEEEEEEEEECCCCCCCCC--CCC-CCCCCCCCCCC-CCCCCCCEEEEEEEEEECCC-C-----CCCEEEEEEEEEEEEEECC----------------C--CCEEEEEEEEEEEEEECCCHHHCCEEEEEEEEEEEECCC------CCEEEEEEEEEEEEE-C PSA >P1;d3sy7a1 ----------------c510930880-23886042532313131326---------5522402040442501047a-------9505032415050533816a----------------------95747-3204040653315175204080100020b332120005240512038b5205030404-----------7030100-9------260105081135447b53341702030550040604145544545b63334443030305338-------------------250050702030514343440225170603082800000000c200a1304020000000000050-05043332615659-----453244041403067050504a-----609205a18057-6050403051344324a8a-672143401040405---b302096240303122334756 >P1;d3syba- 44031100327234288149150ba0623877242333314030649-----------75623031433202047a-------a50403140503055----b----------------------62615012061515641162362011200000010240000004281223156b5305131505-0001655925801021044------800906071205-17c33230702040530020604030546657a96234314010404158------------------7350020805030315351550434060302052500000020020----00000002-0100004030606042054335a-----45235304050-04503038060259b151004404607-80707040605145139794550243514140-04---a403377251414112234745 >P1;d3szva1 ---------------------------54a8707043141214343767----------74120305436011488-------9407041213050463c------------------------341626-26070245781343550031600000012-60000004241533547b522513050230034542925604033----07---50610308122554684333170804046006050514346679----b44520415006308--------------------c15905060500254446c1525-1050-06390100103--601-0--3000200150002320505073432623868-----550263031402054024d----------------b--647071403021414534888656314441201120328-------2030414144365836 >P1;d5dl5a1 --------------------34078071596418052341304011616---bb5a62502020313543001459-------9406050513060614a---807-7021300044c-88603770800-7407041632224272103090000000571001000324142244797225061505400001248-----7200135----4306403051454548833431700040561040406143454549a9013352602050303370203201a80496077433054503040305133543625241703020465000011310002-4014020110-01000040305051330321649----65622532204040340213----------------9637-80404050325343358bb3561141312050204a202d41112050503041435736 >P1;d5dl7a- -----------------------------aa936233231303011413752a435002040405135133217a9-------84072623140304031-a960360260100105b-82405750206-05080235772251651030600005006200020004352501436872440305043002112570450005110500865160710406512464-922351603020520030407143064547b63233022230407228------------------85402603030400240525724060704020526000000----14-04010007000010001303040624322258378ab862452731214040450104----------------a3ca630701040515337138aa664224431505050-50277041210702040532267-6 >P1;d5dl8a- -------------------------6105289353432423040325277b--9384200504041412503057297469a532051615050404132-a---2362503001168a76303840508-16050403453141410020800000205410020004240431256a532206140530000125714301145----ca85460600404034444695451140302036003040415244583-89322232512040604b--------------------580702030406132364a142508040304482500104--160-00310012102-00235503050615024466-7-----554342362604035061b----------------7--769050203142532534799465444331304060537------520103050431457-6 Translating the sequences ----------------*********C-CCCCCCEEEEEEEEEEEEEE---------CEEEEEEEEEEEEECCCCCC-------C*EEEEEEEEEEEEE*****----------------------EEEEE-EEEEEEEECCEEEEEEEECC**CC**CCCCCCCCC*EEEEEEEE***CCEEEEEEEEE-----------CC**CC*-*------**CCEEEEEEEEE**CCEEEEEEEEEECCCEEEEEEEEEEEEE**CC*EEEEEEEEEEEEECC-------------------CCCCCCEEEEEEEEEEEEECCEEEEEEEEEEE*CCCCCC****CCC*CCCCCCCCCCCCCCCCCCC-*EEEEEEEECCCCC-----CCCEEEEEEEEEEEEE*CC***-----********C***-*EEEEEEEEEEEEECCCCC-CCCEEEEEEEEEEEC---***CCCCEEEEEEEEEEE***C *************************C*CCCCCCEEEEEEEEEEEEEE-----------*EEEEEEEEEEECCCCCC-------CEEEEEEEEEEEEE*----*----------------------EEEEE*EEEEEEEECCEEEEEEEECC**CC**CCCCCCCCCEEEEEEEEEE**CCEEEEEEE**-EECCCCCCCCCC**CC***------*CCC*EEEEEEE-**CCEEEEEEEEEECCCEEEEEEEEEEEE*C*CC*EEEEEEEEEEEEECC------------------*CCCCCCEEEEEEEEEEEEECCEEEEEEEEEEECCCCCCCCC**CC----CCCCCCCC-CCCCCCCCEEEEEEEEEE****C-----CCCEEEEEEEE-***EECC********************-EE***EEEEEEEEECCCCCCCCCEEEEEEEEE-*C---***CCCCEEEEEEEEEEEEE*C ---------------------------CCCCCCEEEEEEEEEEEEEEEC----------**EEEEEEEEECCCCCC-------CEEEEEEEEEEEEEECC------------------------C*EEEE-EEEEEEEECCEEEEEEEECC**CC**CCC-CCCCCEEEEEEEEEE**CCEEEEEEEEEEEECCCCCCCCCC**CC----**---*CCCEEEEEEEEE**CCEEEEEEEEEECCCEEEEEEEEEEEE*C----**EEEEEEEEEEECC--------------------CCCCCEEEEEEEEEEEEECCEEE-EEEE-**CCCCCCCCC--CCC-C--CCCCCCCCCCCCCCCCEEEEEEEEEECCCCC-----CCCEEEEEEEEEEEEEE*C----------------C--**EEEEEEEEEEEEEECCCCCCCCCEEEEEEEEEEECCC-------CEEEEEEEEEEEEE** --------------------*****C*CCCCCCEEEEEEEEEEEEEEEC---****CEEEEEEEEEEEEECCCCCC-------CEEEEEEEEEEEEEECC---***-***********-*****CEEEEE-EEEEEEEECCEEEEEEEECC**CC**CCCCCCCCCEEEEEEEEEE**CCEEEEEEEEEEEECCCCCC-----*CC****----**CCCEEEEEEEEE**CCEEEEEEEEEECCCEEEEEEEEEEEEE**CC*EEEEEEEEEEEEECC*******************CCCCC*EEEEEEEEEEEEECCEEEEEEEEEEE*CCCCCCCC**CCC-CCCCCCCCCC-CCCCCCCCEEEEEEEEEECCCCC----*CCCEEEEEEEEEEEEEE*C----------------C***-EEEEEEEEEEEEEECCCCCCCCCEEEEEEEEEEECCC****CCCCEEEEEEEEEEEEE** -----------------------------CCCCEEEEEEEEEEEEEEEC*******CEEEEEEEEEEEEECCCCCC-------CEEEEEEEEEEEEEECC-*****************-*****CEEEEE-EEEEEEEECCEEEEEEEECC**CC**CCCCCCCCCEEEEEEEEE***CCEEEEEEEEEEEECCCCCCCCCC**CC**********CCCEEEEEEEEE*-CCEEEEEEEEEECCCEEEEEEEEEEEEEC*CC*EEEEEEEEEEEEECC------------------*CCCCCCEEEEEEEEEEEEECCEEEEEEEEEEECCCCCCCC----CC-CCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCC******CCCEEEEEEEEEEEEE*CC----------------C*****EEEEEEEEEEEEECCCCCCCC*EEEEEEEEEEE-CC****CCCCEEEEEEEEEEEEE-C -------------------------C*CCCCCCEEEEEEEEEEEEEEEC**--***CEEEEEEEEEEEEECCC***********EEEEEEEEEEEEEECC-*---*******************CEEEEE-EEEEEEEECCEEEEEEEECC**CC**CCCCCCCCCEEEEEEEEEE**CCEEEEEEEEEEEECCCCCCCCCC****----******CCCEEEEEEEEE**CCEEEEEEEEEECCCEEEEEEEEEEEEEC-CC*EEEEEEEEEEEEECC--------------------CCCCCEEEEEEEEEEEEECCEEEEEEEEEEECCCCCCCCC--CCC-CCCCCCCCCCC-CCCCCCCEEEEEEEEEECCC-C-----CCCEEEEEEEEEEEEEECC----------------C--**EEEEEEEEEEEEEECCC***CC*EEEEEEEEEEECCC------CCEEEEEEEEEEEEE-C 310584.tem _________________________________ --------------------*****C*CCCCCCEEEEEEEEEEEEEEEC----***CEEEEEEEEEEEEECCCCCC-------CEEEEEEEEEEEEEECC-**--*-***********-*****CEEEEE-EEEEEEEECCEEEEEEEECC**CC**CCCCCCCCCEEEEEEEEEE**CCEEEEEEEEEEEECCCCCCCCCC**CC***-**--**CCCEEEEEEEEE**CCEEEEEEEEEECCCEEEEEEEEEEEEEC*CC*EEEEEEEEEEEEECC------------------*CCCCCCEEEEEEEEEEEEECCEEEEEEEEEEECCCCCCCCC**CCC-CCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCC-----CCCEEEEEEEEEEEEEECC----------------C****EEEEEEEEEEEEEECCCCCCCCCEEEEEEEEEEECCC-***CCCCEEEEEEEEEEEEE*C Structural block scores 0 19 - 4.4 M 60.9 3.3 75.0 75.0 75.0 75.0 20 24 * 3.4 M 5.6 5.6 75.0 4.4 75.0 75.0 27 32 C 4.8 H 4.5 4.8 5.8 4.3 30.5 4.5 33 47 E 5.0 H 7.6 8.0 3.3 2.6 2.2 2.8 49 52 - 4.2 M 75.0 75.0 75.0 59.1 6.1 42.1 53 55 * 3.4 M 75.0 75.0 75.0 9.0 4.0 6.7 57 69 E 4.8 H 2.6 8.8 14.2 2.3 2.2 2.2 70 75 C 4.8 H 3.8 3.9 3.7 3.2 5.4 2.8 76 82 - 4.5 M 75.0 75.0 75.0 75.0 75.0 7.2 84 97 E 4.9 H 2.7 2.5 2.6 2.6 2.6 2.4 98 99 C 4.2 M 5.5 75.0 7.8 7.2 2.0 2.5 101 102 * 3.4 M 8.2 43.2 75.0 75.0 9.8 42.8 103 104 - 4.1 M 75.0 75.0 75.0 4.0 3.0 75.0 107 117 * 3.4 M 75.0 75.0 75.0 3.0 2.4 2.9 119 123 * 3.4 M 75.0 75.0 75.0 5.0 3.8 3.8 125 129 E 4.9 H 6.4 4.0 3.8 3.0 2.6 3.4 131 138 E 5.0 H 2.4 2.6 3.2 3.6 2.9 2.4 139 140 C 5.0 H 4.0 5.0 7.5 2.5 7.0 4.5 141 148 E 5.0 H 3.0 2.6 2.6 2.5 2.8 1.8 149 150 C 5.0 H 2.0 1.0 2.0 1.5 1.5 1.0 151 152 * 1.0 P 4.0 1.0 3.0 4.5 3.0 4.0 153 154 C 5.0 H 0.5 0.0 0.0 0.0 0.0 0.0 155 156 * 1.0 P 0.0 0.0 0.0 0.0 2.5 0.0 157 165 C 4.9 H 2.7 0.8 9.3 1.6 1.1 1.6 166 175 E 4.9 H 1.9 2.3 2.7 2.2 2.4 2.0 176 177 * 1.0 P 5.5 5.5 5.5 5.5 4.5 5.5 178 179 C 5.0 H 8.2 8.2 8.2 8.0 7.5 7.8 180 191 E 4.8 H 20.2 8.2 1.9 2.5 2.1 2.2 192 201 C 4.5 M 60.7 4.1 4.0 31.5 2.7 2.3 202 203 * 1.4 P 1.5 0.5 2.0 41.0 0.0 1.0 204 205 C 4.5 M 0.5 1.5 3.0 1.0 3.0 4.5 206 208 * 2.9 P 28.0 2.7 75.0 1.3 2.0 75.0 210 211 * 3.4 M 75.0 75.0 3.5 75.0 4.0 11.5 212 213 - 4.1 M 75.0 75.0 75.0 75.0 5.5 6.5 214 215 * 2.2 P 38.5 41.5 40.0 3.5 3.5 5.0 216 218 C 4.8 H 2.3 3.0 2.3 3.3 2.7 2.0 219 227 E 4.9 H 3.0 10.7 2.9 3.0 3.1 2.6 228 229 * 1.4 P 5.5 4.0 5.0 6.0 39.5 5.0 230 231 C 5.0 H 8.2 7.8 6.0 5.5 5.5 7.0 232 241 E 5.0 H 2.3 2.1 2.9 2.2 2.2 2.0 242 244 C 5.0 H 3.3 2.7 3.3 4.0 2.3 3.0 245 257 E 4.9 H 3.2 2.8 3.6 3.1 2.8 3.1 260 261 C 4.5 M 8.8 9.8 75.0 9.8 8.8 8.5 263 275 E 4.9 H 2.7 2.1 3.5 2.3 2.3 2.2 276 277 C 5.0 H 5.5 6.5 4.0 3.0 5.0 7.8 278 295 - 4.5 M 75.0 75.0 75.0 3.9 75.0 75.0 297 302 C 4.8 H 2.0 1.7 17.1 2.8 2.8 15.8 303 315 E 5.0 H 2.8 3.0 3.2 2.6 2.2 2.6 316 317 C 5.0 H 2.0 2.5 6.8 4.0 4.5 5.8 318 328 E 4.8 H 3.1 2.5 15.8 2.5 2.5 2.7 329 337 C 4.8 H 1.1 1.0 1.9 1.8 9.2 2.7 338 339 * 3.4 M 6.2 0.0 75.0 0.5 75.0 75.0 340 342 C 4.7 H 0.7 25.7 2.3 0.7 26.7 2.3 344 362 C 4.8 H 0.8 12.2 8.8 4.9 0.9 5.3 363 372 E 4.9 H 10.1 2.6 3.5 2.3 2.6 2.6 373 377 C 4.4 M 5.2 5.1 5.4 4.4 5.0 19.6 378 382 - 4.4 M 75.0 75.0 75.0 61.2 8.8 75.0 383 385 C 5.0 H 4.0 3.7 3.3 4.3 3.7 4.7 386 399 E 4.8 H 2.9 7.6 2.3 2.2 2.4 3.1 400 401 C 4.5 M 2.5 1.5 8.8 2.0 2.0 6.2 402 417 - 4.2 M 26.4 3.5 75.0 75.0 75.0 75.0 419 422 * 2.5 P 21.8 22.0 40.0 22.8 8.0 40.8 423 436 E 4.8 H 2.7 3.4 2.8 2.9 2.8 2.9 437 445 C 4.7 H 13.9 4.8 5.7 6.0 5.7 5.7 446 456 E 4.9 H 1.9 9.0 1.8 1.7 2.6 2.5 457 459 C 4.4 M 51.7 51.3 4.3 5.5 26.7 5.0 461 463 * 2.7 P 4.8 4.8 75.0 6.5 4.7 75.0 464 467 C 4.5 M 4.2 5.0 56.8 1.2 2.0 39.2 468 480 E 4.9 H 2.6 2.8 3.3 2.8 2.9 2.5 >>>>>>