Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1a0ia2 -----------------------------------------------------------------------------------------CCCCCCCEEEEECCHHHHHHHHHHHC-------CEEEEECCCCEEEEEEEEC----CCEEEEECC----CCCCCHHHHHHCEECHHHHHHHHCCCCC------CCC--EEEEEEEEEEC-CCCCCCHHHHHH-CC----CCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEE--HHHHHHCCCEEEEHHHHHHHHHHHHHHHHHHCC-----------CCEEEECCEEEEC----------CHHHHHHHHHHHHCC-------------------CCCCEEEECC------CCEECCEEE----EEEEEEC---------------------- >P1;d1ckma2 ------------------------------------------------CCCEEEEEEEECCEEEEEEEECHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEECCHHHHHHHHH---------CCEEEEEEECCEEEEEEEEEECC-EEEEEEECCCCCEEECCCCCCCC-----------------C------HHH--CEEEEEEEEEE-CC--------------------------------------CCEEEEEEEEEEEECC-----EECCCCCHHHHHHHHHHHHCCCC----------CCCCCCCEEEECCCEE--------------CCCHHHHHHHHH-HHH-------------HHCCEEEEEEEEC------CCCCCCE----EEEEEEEECCC-------------------- >P1;d1fvia2 -------------------------------------------------------------------------------------------CCCCCCCCEECC--CHHHCC---C-------CEEEEECCCCEEEEEC-------C---CEECC----CCCCCCC--------HHHHHHHH-HHCC------------CCEEEEEECC-CCCHHHHHHHHH-CC----CC---------------------CEEEEEEEECC--C-------CCCCCHHHHHHHHHHHHHHCHHHHHCC---------CEEEEECCCEEEC----------CHHHHHHHHHHHHHC-------------------CCCCEEEECC------CCCCCCCCCCCCCCCCEEECC--------------------- >P1;d1p16a2 ------------------------------------------------CCCCCCCCC-----CCCCEECCHHHHHHHHC-CHHHHCCC--CCCCCCEEEEECCHHHHHCCCC---------CCEEEEEEECCEEEEEEEEEECCCEEEEEEEECCCCEEECCCCCCCCCC--------CCCCCCCC------CCC--CEEEEEEEEEE-CCC-----------------------------------CCCCEEEEEEEEEEEECC-----EECCCCCHHHHHHHHHHHCCHHHHHHHHCHHHHCCCCCCCEEEECC-CC--------------HHHH---HHHHC-CCC-------------CCCCEEEEEEEEC------CCCCCCE----EEEEEEEECCC-------------------- >P1;d1s68a- ------------------------------------------------------------------------------------------CCCCCCCCEECCCHHHHHHHHHHCCCC----CCEEEEECCCCEEEEEEEEC-----CCEEEEECCEECCCCCCCCCCHHH--HHHCHHHHHHHHHHHHHH----CEEEEEEEEEEECC-------------------------------CCCC--CCCCC-CCEEEEEEEEEEEC--CCCEEE--CCHHHHHHHHHHH---------------------CCEECCEEEEECHHHHCCCCCCCCCCHHHHHHHHHHHCHHHHHHCCCCCCCCCCCCCCCEEEEEECCCCCCC----------CCCCCCEEEECHHHCC---------------- >P1;d1x9na3 --------------------------------------------------------------------------------------CCCCCCCCCCEEEECCHHHHHHHCCC---------CCEEEECEECCEEEEEEEC--CCC--CEEEECCCCCCCCC---CCHHHH------HC-CHHHCCC------CCC--CEEEEEEEEEE-CCC--------------------CCCCHHHHCCCCCHHHCCCEEEEEEEEEEEECC-----EECCCCCHHHHHHHHHHHCCCC----------------CCCEEECCEEC--------------CCCHHHHCCCCC-HHH----------------CEEEECEECC------CCCCCCCCC--CCCCEEEEEHHHHHCC--------------- >P1;d1xdna- ----------------------------------------------------------------------------------------CCCCCCCCCCCCC-CHHHHHHHHHCCHHH----CCEEEEEECCCEEEEEEEEEECCE-EEEEEECCCCC-CCCCCCCCHHHH--HHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEEEECCCCCCCCCCCEEECCCCCEEEHHH----CCCCCCCCCCCEEEEEEEEEEEEEECCCCHHHEEE--CCHHHHHHHHHCCC--------------------CCEECCCCEEECHHHHHCCCHHHCCCHHHHCCCC-----------CCCCC----CCCCCEEEEEECCCCCHHHH-------CCCCCCEEEEECCCCCC---------------- >P1;d1xk5a- ------------------------------------------------------------------------------------------CCCCCCEEEEECC-CCCCCHHH----------HEEEEEEECCEEEEEEEEC-----CEEEEECCCCCEEEEECCCCCCCC------CCCCCC-----------CC--CEEEEEEEE---HHH----------------------------------------CEEEEEEEEEECC-----EECCCCCHHHHHHHHHHHCCCCCCCCC------CCCCCCCEEEECCEEE--------------CC-HHHHHHHHC-CC--------------CCCCEEEEEEEEC------CCCCCCE----EEEEEEEECHHHHHHHHCCCCCCCHHHCCCC >P1;d3jsla- CCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCHHHCCC----------------CCHHHHHCC-CCCCCCCEEECCCCCCCCEEECCHHHHHHHHHHHHHHCC-CCCEEEEEEECCEEEEEEEEC----CEEEEEEEC--CCCCEEECCHHHHC-CCCCCCCCCCC-----------CC--CEEEEEEEECC-HHHHHHHHHHHC-CCCCCCCCCHHHHHHHHHCCCCHHHHHHCCCEEEEEEECCCC--------------CCCCCCHHHHHHHHHHHC--------------CCCCCCCEEEC----------CHHHHHHHHHHHHHHHHH-------------CCCCEEEEEEEECCHHHHHHHCCC----CCCCCCEEEEECC-------------------- >P1;d7k72a- CHHHHHHHHHHCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCC-CHHHCCC----------------CCHHHCCCCCCCCCCCCEEECCCCCCCCCEECCHHHHHHHHHHHHHHHHHHCCEEEEEEECCEEEEEEEEC----CEEEEEECC--CCCCEEECCHHHHH-CCCCCCCCCCCCCCC------CCC--EEEEEEEEECC-HHHHHHHHHHHC-C-CCCCCCCHHHHHHHHHCCCCHHHHHCCCCEEEEEEEEEEE--------------CCCCCCHHHHHHHHHHCC--------------CCCCCCCEEEC----------CHHHHHHHHHHHHHHHHH-------------CCCCEEEEEEEECCHHHHHHHCCC----CCCCCCEEEEECC-------------------- PSA >P1;d1a0ia2 -----------------------------------------------------------------------------------------9c250300402726693048106809-------1000002051000000027----702050024----618502004112763730560072a407------155--00000000103-b18575007105-46----40a5304799919663604021530100010001--062055674081414403520650140056206-----------4050540524407----------626405612660484-------------------8260010020------413020356----6100215---------------------- >P1;d1ckma2 ------------------------------------------------a16268242513a361805304a9035501740493060a5a8630001221616870585187---------5700000205031000000406a-83100002690200106064027-----------------5------006--00000010000-46--------------------------------------5750000021000024-----73007540940172057107909----------3288020203307013--------------274696177228-805-------------7414022210112------6430413----6181003566e-------------------- >P1;d1fvia2 -------------------------------------------------------------------------------------------907600201508--717409---1-------7010012050110002-------9---40105----8184061--------75015001-6101------------6100010124-b37696047203-61----5a---------------------80001010104--8-------52835044006204721873561383a---------3060211405606----------548305511640476-------------------9240020033------60303345063a420004052--------------------- >P1;d1p16a2 ------------------------------------------------aa9a99690-----9021a517984077136-00a1091a--8370000312805760666108---------4803011206032000002438987100000067120240370100244--------a0457833------306--20000010020-55b-----------------------------------759341200020000045-----5202634047028205640500741484259608298000415309-44--------------1851---86158-779-------------3717250020200------4250427----5182104266b-------------------- >P1;d1s68a- ------------------------------------------------------------------------------------------814701a14337489118505849219----a4000002030200000024-----86230036604089a391461640--38614a107401740794----60400000010006-------------------------------a038--90506-a3100010001236--887380--1103601710160---------------------50100000113607702823240101037017217668147005451905356762101001000071440a----------69600002031b6298---------------- >P1;d1x9na3 --------------------------------------------------------------------------------------25027116022440800a1027416a---------1800000304031000012--6a9--7030016727522a---302203------81-0650258------806--00000020001-387--------------------81275a30550a759639170000010001037-----8312743055005104620545----------------81302106135--------------285796041050-475----------------6040001016------5702012a6--5351102046772778--------------- >P1;d1xdna- ----------------------------------------------------------------------------------------6b31061491762-798137505928008----5500000201020000000158b7-32041035711-864541300021--3a50370054017203954a2a400000000100002071870870a550505587533048----17038251000013020002002005524595051--00172025004405--------------------a031161233340760182715810400661a17-----------9371b----a1200001010051238705-------73b05000123074182---------------- >P1;d1xk5a- ------------------------------------------------------------------------------------------8529300315507-a52b5128----------3000000043920001048-----540000357082645120000000------87527a-----------72--401000020---883----------------------------------------4000000000030-----7603a3404500810762065192057------7370032305207316--------------04-691037005-3a--------------0708230000023------6060537----5175002030230282092a0396911756d >P1;d3jsla- 8836a3085018306501411415985527894167017403610763572558----------------200121508-a85042873804450431940675940470064037508-803000102030010002057----030420003--68062022013002-00100105076-----------61--80000010102-271166117718-78b4a4276155002600436404300717020103201538--------------60a081014007204901--------------0101921451a----------607401800850695388-------------060304001000041a20960545----b720410001208-------------------- >P1;d7k72a- 8772565169004045013222160606275962251355058008-2770448----------------8000330111c1a291861603650122530265a504800930583069804000002010020001057----160440001--54072012017003-309202650766a37------106--10000010003-481078118616-7-9694254100000200036637104717030103410415--------------619181045015005407--------------01028413317----------638504920840382386-------------071403000000021920880735----7200320001208-------------------- Translating the sequences -----------------------------------------------------------------------------------------*CCCCCC**EEECCHHHHHHHHH***-------CEEEEE**CCEEEEEEEE*----**EEEEECC----CCC*C***********************------*CC--*EEEEEEEE**-************-**----*************************EEEEEEEEE--*************HHHHHHHHHHH*********-----------*C*EE*CC*EE**----------****HHHHHHHHH**-------------------C***EEEE*C------****C****----**EEEE*---------------------- ------------------------------------------------******************************************CCCCCC**EEECCHHHHHHHHH---------CCEEEEEE*CCEEEEEEEE****-**EEEEECC**C***C*CCC***-----------------*------***--*EEEEEEEE**-**--------------------------------------****EEEEEEEEEE*C-----*****CCHHHHHHHHHHH*****----------******C*EE*CC*EE--------------***HHHHHHHH*-***-------------**CC**EEEEEEC------**CCC**----****EEEE*C*-------------------- -------------------------------------------------------------------------------------------CCCCC***EECC--*HHH**---*-------CEEEEE**CCEEEEE*-------*---*EECC----CCC*CCC--------********-****------------**EEEEEE**-************-**----**---------------------**EEEEEEE**--C-------***CCHHHHHHHHHHH***********---------***EE*CC*EE**----------****HHHHHHHHH**-------------------C***EEEE*C------**CCC***********EEE*C--------------------- ------------------------------------------------*********-----*****************-********--CCCCCC**EEECCHHHHH****---------CCEEEEEE*CCEEEEEEEE*******EEEEE*C**C***C*CCC*****--------********------*CC--*EEEEEEEE**-***-----------------------------------******EEEEEEEEEE*C-----*****CCHHHHHHHHHHH*********************C*EE*CC-**--------------**HH---HHHH*-***-------------**CC**EEEEEEC------**CCC**----****EEEE*C*-------------------- ------------------------------------------------------------------------------------------CCCCCC**EE*CCHHHHHHHHH*****----CCEEEEE**CCEEEEEEEE*-----**EEEE*C****CCC*CCC*****--******************----C***EEEEEEEE**-------------------------------****--*****-**EEEEEEEEEE*C--******--CCHHHHHHHHHHH---------------------C*EE*C**EE****************HHHHHHHHH********************CC**EEEEEEC******----------******EEE*C*****---------------- --------------------------------------------------------------------------------------****CCCCCC**EE*C*HHHHHH***---------CCEEEE*E*CCEEEEEEE*--***--*EEEECC**C*CCC---C*****------**-*******------*CC--*EEEEEEEE**-***--------------------*********************EEEEEEEEEE*C-----*****CCHHHHHHHHHHH****----------------*C*EE*CC*E*--------------***HHHH*****-***----------------C**EE*EE*C------**CCC****--****EEEE********--------------- ----------------------------------------------------------------------------------------**CCCCCC*****-CHHHHHHHHH*****----CCEEEEEE*CCEEEEEEEE*****-*EEEEECC**C-CCC*CCC*****--*********************CC***EEEEEEEE****************************----***************EEEEEEEEEE*C********--CCHHHHHHHHH***--------------------C*EE*CC*EE****************HHHH****-----------*****----*CC**EEEEEEC********-------******EEEE*C*****---------------- ------------------------------------------------------------------------------------------CCCCCC**EEECC-*****HHH----------*EEEEEE*CCEEEEEEEE*-----*EEEEECC**C*****CCC*****------******-----------CC--*EEEEEEEE---***----------------------------------------*EEEEEEEEEE*C-----*****CCHHHHHHHHHHH*********------******C*EE*CC*EE--------------**-HHHHHHHH*-**--------------**CC**EEEEEEC------**CCC**----****EEEE*********************** ******************************************************----------------*********-**********CCCCCC**EEECCHHHHHHHHH*******-*CCEEEEEE*CCEEEEEEEE*----**EEEEE*C--C*CC***CC*****-***********-----------CC--*EEEEEEEE**-************-*******************************EEEEEEE****--------------******HHHH********--------------****CC*EE**----------****HHHHHHHHH*****-------------**CC**EEEEEEC********CCC----******EEEE*C*-------------------- **********************************************-*******----------------********************CCCCCC***EECCHHHHHHHHH*********CCEEEEEE*CCEEEEEEEE*----**EEEEECC--C*CC***CC*****-***************------*CC--*EEEEEEEE**-************-*-*****************************EEEEEEEEEE*--------------******HHHH********--------------****CC*EE**----------****HHHHHHHHH*****-------------**CC**EEEEEEC********CCC----******EEEE*C*-------------------- 56091.tem _________________________________ ------------------------------------------------******----------------*********-**********CCCCCC**EEECCHHHHHHHHH*****----CCEEEEEE*CCEEEEEEEE*-**-**EEEEECC**C*CCC*CCC*****--**************------*CC--*EEEEEEEE**-************-**----*************************EEEEEEEEEE*C-----*****CCHHHHHHHHHHH*********-----------*C*EE*CC*EE**----------****HHHHHHHHH*****-------------**CC**EEEEEEC********CCC**--******EEEE*C*****---------------- Structural block scores 0 47 - 4.5 M 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 4.2 5.2 48 53 * 3.8 M 75.0 5.6 75.0 9.8 75.0 75.0 75.0 75.0 5.3 5.0 54 69 - 4.6 H 75.0 3.6 75.0 26.6 75.0 75.0 75.0 75.0 75.0 75.0 70 78 * 3.8 M 75.0 4.5 75.0 5.0 75.0 75.0 75.0 75.0 2.1 1.8 80 89 * 3.6 M 68.4 4.8 75.0 18.2 75.0 45.9 61.8 75.0 5.5 5.7 90 95 C 5.0 H 3.8 2.8 16.2 3.0 3.5 2.8 2.5 4.5 2.8 2.5 96 97 * 1.0 P 2.0 1.5 1.0 1.5 5.8 3.0 5.0 1.5 2.0 2.0 98 100 E 4.3 M 3.0 3.0 2.0 3.7 3.3 4.0 5.0 3.7 4.3 2.7 101 102 C 4.7 H 4.0 3.5 4.0 2.5 5.5 0.0 41.0 3.5 6.5 4.0 103 111 H 4.4 M 4.1 5.4 28.1 4.4 5.0 4.7 5.2 13.3 3.9 4.6 112 116 * 3.5 M 33.4 75.0 60.2 75.0 5.0 75.0 3.6 75.0 3.8 3.8 117 120 - 4.5 M 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 22.8 5.8 121 122 C 4.6 H 38.0 6.0 41.0 6.0 7.2 4.5 5.0 39.0 1.5 2.0 123 128 E 4.8 H 0.3 0.3 0.7 1.2 0.3 0.5 0.3 0.0 0.5 0.3 130 131 C 5.0 H 3.0 2.5 2.5 3.0 1.5 2.0 0.5 3.5 1.5 0.5 132 139 E 4.9 H 0.2 0.5 19.2 0.9 0.5 0.9 0.2 2.0 1.0 1.0 142 143 * 3.8 M 75.0 8.2 75.0 8.5 75.0 8.2 9.8 75.0 75.0 75.0 145 146 * 2.5 P 3.5 5.5 42.0 4.0 41.5 75.0 39.0 40.0 1.5 3.5 147 151 E 4.7 H 1.4 0.2 31.0 0.0 2.2 2.0 1.4 0.8 1.2 1.6 152 153 C 4.5 M 3.0 4.0 2.5 3.0 4.5 3.5 4.0 4.0 1.5 0.5 154 155 * 3.0 P 75.0 4.5 75.0 4.0 3.0 4.5 4.0 3.5 75.0 75.0 158 160 C 4.1 M 5.0 0.3 5.7 2.0 9.2 4.8 6.0 5.0 2.7 3.0 162 164 C 4.5 M 0.7 3.3 2.3 2.7 4.7 51.0 2.7 0.7 1.3 1.0 165 169 * 1.7 P 1.6 31.8 75.0 2.0 3.4 1.4 0.6 0.0 1.2 2.2 170 171 - 4.4 M 6.5 75.0 75.0 75.0 75.0 75.0 75.0 75.0 37.5 39.0 172 185 * 2.4 P 3.9 70.0 12.6 35.0 4.0 29.3 3.4 45.7 22.9 4.5 186 191 - 4.6 H 75.0 75.0 75.0 75.0 28.3 75.0 5.2 75.0 75.0 75.0 193 194 C 4.5 M 5.0 3.0 75.0 3.0 40.5 3.0 7.2 4.5 3.5 3.0 195 196 - 4.5 M 75.0 75.0 75.0 75.0 2.0 75.0 0.0 75.0 75.0 75.0 198 205 E 4.9 H 0.1 0.1 1.1 0.1 0.1 0.2 0.1 0.4 0.2 0.1 206 207 * 1.5 P 1.5 0.0 3.0 1.0 3.0 0.5 0.0 75.0 1.0 1.5 209 220 * 3.0 P 4.2 63.3 4.9 58.0 75.0 57.8 4.9 57.8 4.0 4.2 222 223 * 3.6 M 5.0 75.0 3.5 75.0 75.0 75.0 2.5 75.0 7.5 41.0 224 227 - 4.1 M 75.0 75.0 75.0 75.0 75.0 75.0 6.2 75.0 7.5 7.0 228 252 * 3.1 M 4.3 63.7 63.9 58.2 44.2 16.2 14.2 72.2 2.9 2.4 253 262 E 4.8 H 7.8 0.3 8.2 0.4 0.5 0.2 0.6 0.0 1.7 1.7 265 269 - 4.3 M 3.6 75.0 75.0 75.0 34.6 75.0 5.0 75.0 75.0 75.0 270 274 * 2.6 P 5.0 3.4 33.0 3.0 32.2 4.2 31.2 5.3 75.0 75.0 275 276 C 4.4 M 2.5 4.5 4.0 3.5 1.0 3.5 0.0 3.5 75.0 75.0 277 287 H 4.6 H 2.7 3.3 2.6 3.5 2.3 2.5 2.3 3.0 9.6 10.0 288 296 * 2.6 P 2.7 36.1 4.7 3.2 75.0 43.2 67.2 3.9 10.9 10.8 297 307 - 4.4 M 75.0 42.8 62.6 4.8 75.0 75.0 75.0 42.5 75.0 75.0 311 312 E 4.5 M 2.5 1.5 1.0 3.0 0.5 1.0 2.0 2.5 0.5 0.5 314 315 C 4.8 H 2.5 3.5 2.5 4.5 0.0 3.0 3.5 3.5 5.5 6.0 317 318 E 4.6 H 4.0 2.0 5.5 4.0 1.0 4.0 3.0 3.5 4.5 3.0 319 320 * 3.0 P 3.5 75.0 3.0 75.0 4.5 75.0 3.5 75.0 5.8 4.0 321 330 - 4.5 M 75.0 75.0 75.0 75.0 3.5 75.0 3.7 75.0 75.0 75.0 331 334 * 2.0 P 4.5 39.8 5.0 39.8 0.5 40.0 3.2 38.5 4.2 5.5 335 343 H 4.6 H 3.3 4.9 2.9 27.9 3.1 4.1 11.8 11.2 3.1 3.3 344 348 * 2.6 P 47.4 19.2 47.6 21.2 5.0 18.2 75.0 33.7 6.6 5.4 349 361 - 4.6 H 75.0 75.0 75.0 75.0 3.8 75.0 48.6 75.0 75.0 75.0 362 363 * 2.8 P 75.0 5.5 75.0 5.0 6.5 75.0 42.8 3.5 3.0 3.5 364 365 C 4.7 H 41.5 2.5 42.0 4.0 1.5 40.5 1.5 4.0 1.5 2.5 366 367 * 1.0 P 4.0 1.0 3.0 3.5 0.5 2.0 0.0 2.5 2.0 1.5 368 373 E 4.7 H 0.5 1.2 0.8 0.7 0.2 0.3 0.3 0.3 0.2 0.0 375 382 * 3.2 M 56.9 57.5 57.0 57.0 22.1 57.8 3.9 57.0 4.1 3.8 383 385 C 4.5 M 1.7 2.3 2.0 3.0 75.0 0.7 75.0 3.7 4.7 5.0 386 387 * 3.0 P 1.5 2.0 3.5 4.5 75.0 1.5 75.0 5.0 75.0 75.0 388 389 - 4.1 M 5.5 75.0 2.5 75.0 75.0 8.2 75.0 75.0 75.0 75.0 390 395 * 2.0 P 51.2 27.7 4.2 27.7 16.0 27.3 4.4 28.0 4.2 2.3 396 399 E 4.9 H 0.8 2.0 1.0 1.8 0.5 0.8 0.8 0.5 0.2 0.2 402 406 * 3.5 M 75.0 62.9 75.0 62.3 7.3 6.0 4.4 3.0 61.6 61.6 407 422 - 4.7 H 75.0 75.0 75.0 75.0 75.0 70.8 75.0 5.2 75.0 75.0 >>>>>>