Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1pfoa1 CCCCCCCCHHHHHHCCCCCCCCCCCEECCCCCC-CCCEEEEECCCCEEEEEEEEEEEEECCC--CEECCCCCCCCCCCC-CEEECCHHHH----CCCCCCCCCCCCCEEEEECCCCCCC-CCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCC--EEECEEEEEEEECCCHHHHHHHHCCCHHHHHHHCCCCHHHHHCCCCEEEEEEEEEEEEEEEECCCCCHHHHCCC-------CC-CHHHHHHCCCCCCCCEEEEEEEEEEEEEEEEEEEC---CCCC-----CHHHHHHHH--HHCCHHHH--CHHHHHHHHCEEEEEEEEECCCC------CCCCEEEC----CHHHHHHHHHHCCEEECCCCCCEEEEEEEECCCCCCCCCCEEEEEEEEEEEEEC--------------------------------------------------------------------------------------------------------------------- >P1;d2qp2a1 CCHHHHHHHHHHHHH---HHHHHCCCC-----------------------------CCCCCHHHCCEEECCCCCCCCHHHEEEECCCCHHHCHHHEEEECCCEEEEECCCEEEEEE-EEEEEEEEEC--CHHHHHHHHHHCCCCC--------------------------------CCCCCCCHHHHHC-CCHHHHCCCEEEEEEEEEEEEEEEECC-HHHHHHHCCHHHHHHHHHCCCHHHHHHHHH--HCCCEEECEEEEEEEEEEEEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCC-CCCHHHHHHHHHHCEEEEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC-----CCCEEEEECCC---------------------------------------------CCEEEHHHHCCC-----HHHHHHHHHHHH-----HCHHHHHHHCCCCC------------------------------------------------- >P1;d3hvna3 -------CHHHHHHHCCCCCHHHCEECCCCCCC-CCCCEEEEECCEEEEEEEEEEEEEEEEC--EEECCCCCCCCCCCC-CEEECCHHHH----CCCCCCCCCCCCCEEEEEECCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCC-CCCCCCCCCEEEEEEEECCCHHHHHHHCCCCHHHHHHHHCCCHHHHHHCCCEEEEEEEEEEEEEEEECCCCCHHHHCC--------CC--CCCCCCCCCCCCCCEEEEEEEEEEEEEEEEEEEC---CCCC-----CHHHHHHHH--HHCCCCCC--CCCCCHHHHCCEEEEEEECCCCCC-----CCEEEEEE-----HHHHHHHHHHHHCCCCCCCCEEEEEEEEECCCCCCCCEEEEEEEEEEEEEEEC--------------------------------------------------------------------------------------------------------------------- >P1;d6jmpa- ---CHHHHHHHHHHHCCCCHHHHCEEECCCCCC-CEEEEEEECCCEEEEEEEEEEEEEEEEC--CEECCCCCCCCCCCC-CEEECCHHHH----CCCCCCCCCCCCCEEEEEECCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHCCC--CCCCCCCC-CEEEEEECCCHHHHHHHHCCCCHHHHCCCCCCHHHHHCCCCEEEEEEEEEEEEEEEECCCCCHHHHCCC-------CC-CHHHHHHCCCCCCCCEEEEEEEEEEEEEEEEEEEC---CCCC-----CHHHHHHHH--HCCCCCC----HHHHHHHHCEEEEEEEECCCCCC-----CEEEEEEE-----HHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCCCCEEEEEEEEEEEEEEEECEEEEEEEEECCCEEEEEEEEEEEECCCCCEEEEEEECCCCCCCCCC-CEEEEEEECCC----EEEEEEEEEEEEEECCEEEEEEEEEEEECCCCEEEEEEEECCCCEEEEEEEECC >P1;d6nala1 --CHHHHHHHHHHHCCCCCCCCCCCC-CCCCCCCCCCCCCEEECCEEEE-EEEEEEEEEEE---CCCCCHHHHHHCCCC-CEEECCHHHH----CCCCEECCCCCCCEEEEEECCCCC--CEEEEE-CCCHHHHHHHHHHHHHHHHCCCC--CCCCCCCCCEEEEEECCCCCCCC-CCCCCHHHHHHHHCCCHHHHHHCCCEEEEEEEEEEEEEEEECCCCCHHHHCCC-------CC-CHHHHHHCCCCCCCCEEEEEEEEEEEEEEEEEEEC---CCHH-----HHHHHHHHHEECCEECCCCCCCCHHHHHHCCEEEEEEEECCC--------CEEEEEEECCCCHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCCCCEEEEEEEEEEEEEEEC--------------------------------------------------------------------------------------------------------------------- PSA >P1;d1pfoa1 73b4822604500650807567102644577aa-377643486cc44010416546363425--402036046270100-0000028202----416143081703304030506709b-635360850639504800770174029447a45--52804363422102342002120403161049307051900650631000011201002040641961470019-------80-60540384606791000001400001000000106---1006-----105500300--16559726--5861460076040000030041b------79443516----607502712852450306570200001000034235011227021321703168--------------------------------------------------------------------------------------------------------------------- >P1;d2qp2a1 b69721640473466---02950807b-----------------------------7005000000000400120000010232005503858a105251c682100400606624-7143130227--5056006400730517--------------------------------c110006007200-569105584100000010101020206-084026003870363058077694037006--620000000000000000000023670a0627146003100143001b257-9830650164028107142100004197250044016728a55870572044028203-----94100000077---------------------------------------------900200030087-----991274047004-----64003611463526------------------------------------------------- >P1;d3hvna3 -------6137408709070363033a87a1aa-17a571685bd64111616345255441--511004196140100-0003037500----417031091803603000600a2ab352638098046820771156007811994-a06520970644132100123600203072105601a308062a006518320000010000010405609316400c--------b1--9630682706493000001302100000000205---0227-----605810420--0546a46a--b08526006605000100006549-----71543666-----05503720573289130570110003010025255051215021220405259--------------------------------------------------------------------------------------------------------------------- >P1;d6jmpa- ---7328602610580906397103581591a9-6532506228710000324246253652--711003182730000-0000028401----6080420516013160409054197861716087052940573038106602873--06857050-364732500213002020622046008307041a10360423000000102003040960950050047-------80-42940595703493000002302000000000005---203a-----307400601--0765946----95158007604010000106593-----73632565-----0710980174125030633011010200002335503042402021060524620503030408030104051230606b70764467451a42256062-61535070501----02503040301062984523300566607115301020446359063525455c >P1;d6nala1 --8c426602850771916288270b-037186b917576665aa2303-52733335381---400004834510100-0000017600----736065071804504030505c1b--453242-4053740573066001610564b--b270260b072212302135000-10001371048108060871575822000000014002040711a61050026-------80-31630373505484000005301100000000105---1314-----2039005900677009097da398338204508010002106--------53327a15046921840360035706005a360110004010024167191605022155524369--------------------------------------------------------------------------------------------------------------------- Translating the sequences ********HHHHHH*CCCCC***CCE*CCCCCC-CCC*EEEE*CC*EEEEEEEEEEEEE**C--CEECCCCCCCCCCCC-CEEECCHHHH----CCCCCCCCCCCCCEEEEE*CCCCCC-C*EEEECCCCHHHHHHHHHHHHHHHH**C**CC--***C**EEEEEECCCHHHHHHH*CCCHHHHHHH*CCCHHHHHCCCCEEEEEEEEEEEEEEEECCCCCHHHHCCC-------CC-CHHHHHHCCCCCCCCEEEEEEEEEEEEEEEEEEEC---CCCC-----CHHHHHHHH--H*CC****--CHHHHHHHHCEEEEEEEE*CCCC------CC**EEE*----*HHHHHHHHHHCC***CCCCC*EEEEEEEECCCCCCCC**EEEEEEEEEEEEEC--------------------------------------------------------------------------------------------------------------------- ****HHHHHHHHHHH---**HHHCC**-----------------------------********C*E**CCCCCCCC****EEECC**HH*********CCC********EEE***-****EEEEEC--CHHHHHHHHHH*****--------------------------------CCCC***HHHHHC-C*HHHHCCC*EEEEEEEEEEEEEEE*C-***HHHHCC*********C*CHHHHHH***--*CC*EEE*EEEEEEEEEEEEEE****CCCC******HHHHHHHH***CCCC-CC***HHHHHHHHCEEEEEEEECCCCCC*****CC***********HHHHHHHHHHCC-----CCCEEEEE***---------------------------------------------************-----************-----**************------------------------------------------------- -------*HHHHHHHCCCCCHHHC*E*CCCCCC-CCC*EEEE*CCEEEEEEEEEEEEEEEEC--*EECCCCCCCCCCCC-CEEECCHHHH----CCCCCCCCCCCCCEEEEEECCCCCC*CEEEEECCCCHHHHHHHHHHHHHHHHCCC-*CCCCCCCC**EEEEEECCCHHHHHHHCCCCHHHHHHHHCCCHHHHH*CCCEEEEEEEEEEEEEEEECCCCCHHHHCC--------CC--******CCCCCCCCEEEEEEEEEEEEEEEEEEEC---CCCC-----CHHHHHHHH--H*CCCCCC--C****HHHHC*EEEEEEECCCCCC-----CCEEEEEE-----HHHHHHHHHH**CCCCCCCCEEEEEEEEECCCCCCCCEEEEEEEEEEEEEEEC--------------------------------------------------------------------------------------------------------------------- ---*HHHHHHHHHHHCCCC*HHHC*E*CCCCCC-C***EEEE*CCEEEEEEEEEEEEEEEEC--CEECCCCCCCCCCCC-CEEECCHHHH----CCCCCCCCCCCCCEEEEEECCCCCC*C*EEEECCCCHHHHHHHHHHHHHHHHCCC--CCCCCCCC-*EEEEEECCCHHHHHHH*CCC*HHHH***CCCHHHHHCCCCEEEEEEEEEEEEEEEECCCCCHHHHCCC-------CC-CHHHHHHCCCCCCCCEEEEEEEEEEEEEEEEEEEC---CCCC-----CHHHHHHHH--HCCCCCC----HHHHHHHHCEEEEEEEECCCCCC-----C*EEEEEE-----HHHHHHHHH*CCCCCCCCCCEEEEEEEEECCCCCCCCEEEEEEEEEEEEEEE************************************************-***********----****************************************************** --**HHHHHHHHHH*CCCCC***CC*-CCCCCC*CCC***EE*CCEEEE-EEEEEEEEEEE---C**CC******CCCC-CEEECCHHHH----CCCC**CCCCCCCEEEEEECCCCC--CEEEEE-CCCHHHHHHHHHHHHHHHHCCC*--CCCCCCC**EEEEEECCC*****-*CCCCHHHHHHHHCCCHHHHH*CCCEEEEEEEEEEEEEEEECCCCCHHHHCCC-------CC-CHHHHHHCCCCCCCCEEEEEEEEEEEEEEEEEEEC---CC**-----*HHHHHHHH***C**CCCC**C*HHHHHH*CEEEEEEEECCC--------C*EEEEEE*****HHHHHHHHH*CCCCCCCCCCEEEEEEEEECCCCCCCCEEEEEEEEEEEEEEEC--------------------------------------------------------------------------------------------------------------------- 418735.tem _________________________________ --**HHHHHHHHHHHCCCCCHHHCCE*CCCCCC-CCC*EEEE*CCEEEEEEEEEEEEEEEEC--CEECCCCCCCCCCCC-CEEECCHHHH----CCCCCCCCCCCCCEEEEEECCCCCC*CEEEEECCCCHHHHHHHHHHHHHHHHCCC--CCCCCCCC**EEEEEECCCHHHHHHHCCCCHHHHHHHHCCCHHHHHCCCCEEEEEEEEEEEEEEEECCCCCHHHHCCC-------CC-CHHHHHHCCCCCCCCEEEEEEEEEEEEEEEEEEEC---CCCC-----CHHHHHHHH--HCCCCCCC--CHHHHHHHHCEEEEEEEECCCCCC-----CCEEEEEE----*HHHHHHHHHHCCCCCCCCCCEEEEEEEEECCCCCCCCEEEEEEEEEEEEEEEC--------------------------------------------------------------------------------------------------------------------- Structural block scores 0 1 - 3.8 M 5.0 8.8 75.0 75.0 75.0 2 3 * 2.5 P 7.8 8.0 75.0 41.0 10.2 4 14 H 4.5 M 3.5 3.9 23.7 3.7 4.3 15 19 C 4.4 M 4.0 45.4 3.2 3.6 3.8 20 22 H 3.8 M 4.7 4.7 4.0 5.7 6.0 23 24 C 4.4 M 1.0 4.0 1.5 1.5 3.5 27 32 C 4.5 M 7.3 75.0 7.9 5.9 4.2 34 36 C 4.2 M 5.7 75.0 6.2 4.7 5.7 38 41 E 4.3 M 4.8 75.0 5.5 3.2 6.2 43 44 C 4.5 M 12.5 75.0 12.5 7.5 10.5 45 60 E 4.4 M 3.3 52.3 3.6 2.7 7.9 62 63 - 4.5 M 75.0 0.0 75.0 75.0 75.0 65 66 E 4.2 M 1.0 0.0 1.0 1.0 0.0 67 78 C 4.6 H 2.4 0.6 2.2 2.0 2.2 81 83 E 5.0 H 0.0 2.3 1.0 0.0 0.0 84 85 C 5.0 H 1.0 0.0 1.5 1.0 0.5 86 89 H 4.8 H 3.0 3.2 3.0 3.2 3.2 90 93 - 4.5 M 75.0 7.9 75.0 75.0 75.0 94 106 C 4.5 M 3.2 3.3 3.3 2.8 4.0 107 112 E 4.7 H 2.0 2.7 1.5 3.3 2.0 113 118 C 4.4 M 5.6 15.8 5.8 4.3 17.5 121 125 E 4.8 H 3.4 1.6 3.8 3.0 3.2 126 129 C 4.6 H 4.8 40.5 5.2 5.0 21.0 130 145 H 4.8 H 3.6 7.4 3.8 3.5 3.1 146 148 C 4.2 M 5.7 75.0 7.3 6.0 5.0 149 150 - 3.8 M 8.8 75.0 42.8 75.0 43.2 151 158 C 4.2 M 21.8 75.0 3.6 3.9 12.9 159 160 * 2.5 P 3.5 75.0 5.0 39.0 5.8 161 166 E 4.5 M 3.0 75.0 1.8 4.5 2.8 167 169 C 4.5 M 1.7 75.0 1.0 0.7 1.0 170 176 H 4.1 M 1.6 75.0 2.0 1.1 12.0 177 180 C 4.7 H 1.8 3.6 2.5 2.5 0.2 181 188 H 4.5 M 3.0 1.9 3.2 2.6 3.0 189 191 C 4.8 H 4.0 26.7 4.7 3.7 4.7 192 196 H 4.9 H 3.2 4.2 3.7 3.1 4.2 197 200 C 4.6 H 3.5 4.5 4.2 3.0 5.5 201 216 E 5.0 H 0.8 0.4 0.5 0.8 0.8 217 221 C 4.6 H 5.2 18.6 4.6 5.8 5.1 222 225 H 5.0 H 3.0 2.0 2.8 1.2 1.5 226 228 C 4.7 H 3.3 3.7 29.2 3.7 2.7 229 235 - 4.5 M 75.0 3.4 75.0 75.0 75.0 236 237 C 4.8 H 4.0 4.0 6.2 4.0 4.0 240 245 H 4.5 M 3.3 4.8 5.3 4.8 3.3 246 253 C 4.6 H 4.1 20.5 3.9 3.9 3.6 254 272 E 4.9 H 0.4 0.0 0.5 0.4 0.6 274 276 - 4.5 M 75.0 5.3 75.0 75.0 75.0 277 280 C 4.8 H 1.8 4.1 2.8 3.9 2.2 281 285 - 4.5 M 75.0 4.0 75.0 75.0 75.0 287 294 H 5.0 H 1.6 1.5 2.5 2.2 3.2 295 296 - 3.8 M 75.0 0.0 75.0 75.0 3.0 298 304 C 4.3 M 5.7 16.8 6.6 16.0 4.6 305 306 - 3.8 M 75.0 1.5 75.0 75.0 12.0 308 315 H 4.6 H 4.0 3.2 3.4 4.4 4.6 317 324 E 4.9 H 0.9 1.9 0.8 0.6 1.4 325 330 C 4.6 H 15.2 3.5 4.0 4.0 38.7 331 335 - 4.5 M 75.0 2.2 75.0 75.0 75.0 336 337 C 4.4 M 8.0 2.0 4.0 5.0 4.0 338 343 E 4.2 M 3.8 5.8 5.0 4.5 4.8 344 347 - 3.8 M 75.0 6.2 75.0 75.0 4.8 349 358 H 4.9 H 3.7 3.4 3.4 3.7 3.0 359 368 C 4.5 M 3.2 39.2 3.8 2.3 3.8 369 377 E 4.7 H 0.3 9.9 0.7 0.6 0.8 378 385 C 4.5 M 2.2 75.0 3.0 2.6 3.8 386 400 E 4.4 M 2.5 75.0 2.1 2.1 3.1 402 518 - 4.3 M 75.0 51.7 75.0 6.4 75.0 >>>>>>