Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1an9a1 ------------------------------------------------CEEEEECCCHHHHHHHHHHHHHHCCCCCC-CEEEEEEC----CCHHH-----CHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCC--------------------CCCCCCCCEEEEE-EEEEEC-------------------CCCCCC--CCCCCCEEEEECCHHHHCCCCCCCEEEEEEEEEE---------CHHHHHHHHH--HHHHCC------------------CCEEEECCCCCHHHHHHCCCCEEEECCHHHHHHH--CCCC-----------------CCCEEEEEEECCC---------------------------CCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHCCCC---------- >P1;d1c0pa1 --------------------------------------------CCCCCEEEEECCCHHHHHHHHHHHHCC-------CEEEEEEC----CCCCCCCCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCC-------------------------CCCCEEEEEEEEEEC-------------------CHHHHHHHCCCCCCCCCEECCHHHC--CCCC-EEEEEEEEEC---------CHHHHHHHHH--HHHHHC------------------CCEEEECCCCCHHHCCC-CCCEEEECCHHHHHCCCCCCCCCC---------------CCCEEEEEEEEECCCCCCCCCCCC--------CCCCCCCCCEEEEEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHCC----------- >P1;d1cjca2 -----------------------------------------------CCEEEEECCCHHHHHHHHHHHHHCC-----CCEEEEECCCCCCCCHHH--HCCCC---------------CCHHHHHHHHHHHHHHCCCCEEEECC---CCCC-CCCCHHHHHHH--CCEEEECCCCCC---CCC-----CCCC---CCCCCC----------------CCCCCCEE--CCEECCCCCEEECCHHHHCCCCCHHHHHHHHH--HHHHHHHH-HHHHC------------------------------CCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH----------HHHHH-------------------------------------CCCCCCCCCHHHHHHHCCC------------------ >P1;d1i8ta1 -----------------------------------------------CEEEEEECCCHHHHHHHHHHHHH-------CCCEEEECCCCCCCHHHC--EEEEC----------------------------------CEEEECCCCCCEEECCHHHHHHHHCCCCCCCCCCCCEEEECCEEEECCCCHHHHHHHHCCC-CHHHHHHHHHHHCCCCCC----------------------------CCCCCHHHHHHHHHHHHHHHHHCHHHHHHHHCCCHHHCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCHHHHHHHHHCC--CEEECCCCHHHCHHHHHCCEEEEEECCCHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCC------------- >P1;d1lqua2 ----------------------------------------------CCEEEEEECCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHH--HCCCC---------------CCHHHHCCHHHHHHHHCCCCEEEEEC---CCCC-CCCCHHHHHHH--CCEEEECCCCCC---CCC-----CCC----CCCCCC----------------CCCCCCEE--CCEECCCCCEEECCHHHHCCCCCHHHHHHHHH--HHHHHHHH-HHHHHHH--------------------------CCCCCCCC-CHHHHHHHHHHHHCCCCEEHHHHHHHHHHHHH----------HHHHH-------------------------------------CCCCCCCCCHHHHHHHHCC------------------ >P1;d1o94a3 CCCCCCCCCH-HHHHHHHCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHCC-------CEEEE-CC---CCCCHHHHCC-CC---------------CCHHHHHHHHHHHHHHHCCCCEECCCC--------CCCHHHHHCC-CCCEEEECCCCCCC---------HHHHHHHH--------CHHHCHHH---------------------CCCEEEECHHHCC--CCCHHHHHHHHH--HHHHCCCCC------------CCCCCCCCCCCCCCCCCCCCC------------------------------------------------------------------------------------------------------------------------CCCCCCCCCC >P1;d1ps9a3 -CCCCCCCCCCCHHHHHC-CCCCCCCCCCCCCCCCCCCCCC--CCC-CCEEEEECCCHHHHHHHHHHHCCC-------CEEEEEECCCCCCCCHHHHCC-CC---------------CCCCHHHHHHHHHHHHHHHCCEEEECC--------CCCCCCC--C-CCCEEEECCCCCCC---------CCHHHHHC--------C----------------------------CC-CEEECHHHCCCCCCCHHHHHHHHH--HHHHHC---------------------------------------------------------------------------------------------------------------------------------------------------------------------- >P1;d2bi7a1 -----------------------------------------------CCEEEEECCCHHHHHHHHHHHCC-------CCEEEEEECCCCCCHHHC--EEECC--------------------------------CCCCEEECCCCCCEEECCHHHHHHHHCCCCEEECCCCEEEEECCEEEEECCCHHHHHHHCCCCCCHHHHHHHHHHHCCCCCC-----------------------------CCCCHHHHHHHHHCHHHHHHHCHHHHHHHHCCCHHHCCHHHCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHCCCCEEEEECCCCC---HHHHHHCCEEEECCCHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEECHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC >P1;d7m32a2 --------------------------------------------CHHHCEEEEECCCHHHHHHHHHHHHHCCC------CEEEEECCCCCCCHHH--HCCCC---------------CCCCHHHHHHHHHHHHCC-CCEEEEC---CCCCCCCCCHHHHHHCC-EEEEEECCCCCC---CCCCHHHHHHCC---CCCCC------------------CCCCCCCCCCCCCC-CCCEEECHHHHCCCC-CHHHHHHHHH--HHHHHHHH-HHHHHCCCCCCC---------------------CCCCCCCCCHHHHCC------------------------------------------------------------------------------------------------------------------- PSA >P1;d1an9a1 ------------------------------------------------04000030301000000000451575066-05020104----43137-----181094a040206488183840270045007304822b--------------------5961870105444-532126-------------------872920--1049104c04405892185277362002031020---------6044004203--620673------------------a071463606504200687040000027850570--3828-----------------960205223173b---------------------------a3400000008099130000000022006102500653923---------- >P1;d1c0pa1 --------------------------------------------aa5a46000020301000000100549-------05030005----00062583972a1054a040204346a706410600420070057027-------------------------89307237636121a-------------------77a601a2005a1047067059960--59c1-3000010010---------6026003101--520774------------------90714435060043006-7060000019b7057000013738---------------b6030523205040338407505b--------9396787a654000000180981200000000430073035017631f----------- >P1;d1cjca2 -----------------------------------------------7110000202110000031017529-----602000013510006600--44248---------------965752722850171055b3030103---0300-61050620160--010000016045---505-----5109---303237----------------97010306--50305a28100000300433a18286136102--50062017-01859------------------------------704a8924028403730784a170050820360283047----------408a6-------------------------------------9482530966731263081------------------ >P1;d1i8ta1 -----------------------------------------------42300014040000000020254-------b25010005691106401--0557a----------------------------------9825234a71100086770141028208069541335174796502200003004311708-64760473067236548a----------------------------6a2710221104200340061013a70384396505803080355221228453321817200105700250063006c--0616473201863a6227606500003200300855395034b9237117505610673a3020005403247211241043017208512897------------- >P1;d1lqua2 ----------------------------------------------3311000020210000005000610675a91702000004400004501--52148---------------95595272187048127283030000---0300-61040a30273--000000024046---506-----506----903159----------------b5010319--90308a0811000020122393a275178103--50063027-4078369--------------------------79823a06-70485038105831661053740660054048----------40767-------------------------------------a571441855950182038------------------ >P1;d1o94a3 7915907172-46528677a365130030014057218052670a61613000120300000000000405-------04030-37---004405a308-69---------------b38723401510570076240514396--------a270650083-90210000262163---------71175048--------35a31a83---------------------9051000001046--536101002100--00010054b------------702734947777787472a89------------------------------------------------------------------------------------------------------------------------c4547868ab >P1;d1ps9a3 -92380825305761596-977313005023536a825489--089-724000130311000000200504-------070000147850047018316-58---------------957515400310563075190524274--------8061985--4-a1620000174454---------71164077--------4----------------------------b2-603200103529605124003100--610091---------------------------------------------------------------------------------------------------------------------------------------------------------------------- >P1;d2bi7a1 -----------------------------------------------44500013030100000130046-------815020016462103301--0445b--------------------------------9587152336811000756802710470170484414352736b460123000600040195a064970670088304a85b-----------------------------80720321024100760040023a704856935056041841893201056723329371002057001600640091930722374707---6a129715000013300201a35387044aa4271055007304a2870000154002190300510320160082027029b79041013a06 >P1;d7m32a2 --------------------------------------------91470300002022001100210020807------40001164a5206511--37337---------------962459406760630474-9050526---61013951108406768-140000015334---608386146007---60602------------------96104066720305-25000000200360a-6595146104--30002005-200652a5a17b---------------------84713956489588c------------------------------------------------------------------------------------------------------------------- Translating the sequences ------------------------------------------------CEEEEECCCHHHHHHHHHHHH********-CEEEEEEC----CCHHH-----C****************CC**HHHHHHHHHHHH*C*CC--------------------***C*CCCEEEE*-******-------------------CC****--******************************EEE*---------CHHHHHHHHH--HHHH**------------------******************CC*****CC*HHHH**--****-----------------*************---------------------------***********************HHHHHHH***********---------- --------------------------------------------***CCEEEEECCCHHHHHHHHHHHH**-------CEEEEEEC----CC******C*CC***************CC**HHHHHHHHHHHH***CC-------------------------CCC*EEE********-------------------C************************--****-******EEEC---------CHHHHHHHHH--HHHHH*------------------*****************-CC*****CC*HHHH**********---------------************************--------*******************************HHHHHHH**********----------- -----------------------------------------------CCEEEEECCCHHHHHHHHHHHH***-----*CEEEEE*CCCCCCCHHH--*C*CC---------------CC**HHHHHHHHHHHH*C*C*EEE*C---****-****HHHHH**--CCEEEECC****---***-----****---***CC*----------------********--*********EEEC******CCCCHHHHHHHHH--HHHHH***-*****------------------------------*****CC**HHH***************************----------*****-------------------------------------*********HHHHHHH***------------------ -----------------------------------------------C*EEEEECCCHHHHHHHHHHHH*-------*C*EEEE*CCCCCC*HH*--****C----------------------------------C*EEE*C************HHHHH*C*CCC****CC*************************-C*****************----------------------------*CCCCHHHHHHHHH**HHHHH*************************************CC*****CC*HHHH*******--*******************************************************************************HHHHHHH********------------- ----------------------------------------------*C*EEEEECCCHHHHHHHHHHHH**********EEEEEECCCCCCCHHH--*C*CC---------------CC**HH**HHHHHHHH*C*C*EEE*C---****-****HHHHH**--CCEEEECC****---***-----***----***CC*----------------********--*********EEEC******CCCCHHHHHHHHH--HHHHH***-*******--------------------------CC*****C-*HHHH***************************----------*****-------------------------------------*********HHHHHHH***------------------ **********-************************************CCEEEEECCCHHHHHHHHHHHH**-------CEEEE-*C---CCC*HH***C-CC---------------CC**HHHHHHHHHHHH*C*CCEE**C*--------***HHHHH*C-CCCEEEECC*****---------********--------********---------------------****EEEC*****--CCCHHHHHHHHH--HHHH*****------------*********************------------------------------------------------------------------------------------------------------------------------********** -*****************-**********************--***-CCEEEEECCCHHHHHHHHHHH***-------CEEEEEECCCCCCC*HH***C-CC---------------CC**HHHHHHHHHHHH***CCEEE*C*--------*******--C-CCCEEEECC*****---------********--------*----------------------------**-*EEEC******CCCCHHHHHHHHH--HHHHH*---------------------------------------------------------------------------------------------------------------------------------------------------------------------- -----------------------------------------------CCEEEEECCCHHHHHHHHHHH**-------*CEEEEEECCCCCC*HH*--***CC--------------------------------C*CCEEE*C************HHHHH*C*C**E***C**************************CC*****************-----------------------------CCCCHHHHHHHHH**HHHHH*************************************CC*****CC*HHHH*******************---******************************************************************HHHHHHH********************* --------------------------------------------****CEEEEECCCHHHHHHHHHHHH****------*EEEEECCCCCCCHHH--*C*CC---------------CC**HHHHHHHHHHHH*C-CCEEE*C---*********HHHHH*C*-**EEEECC****---************---***CC------------------**************-***EEEC******CC-CHHHHHHHHH--HHHHH***-************---------------------CC*****CC*HHH**------------------------------------------------------------------------------------------------------------------- 51971.tem _________________________________ --------------------------------------------***CCEEEEECCCHHHHHHHHHHHH***-----*CEEEEEECCCCCCCHHH--*C*CC---------------CC**HHHHHHHHHHHH*C*CCEEE*C*--****-****HHHHH*C*CCCEEEECC******-***----***********CC*************************--*********EEEC******CCCCHHHHHHHHH--HHHHH***-*******--------******************CC*****CC*HHHH*******************---********************-----------------------***********************HHHHHHH********------------- Structural block scores 0 43 - 4.4 M 75.0 75.0 75.0 75.0 75.0 5.6 10.9 75.0 75.0 44 46 * 3.6 M 75.0 8.7 75.0 75.0 51.0 5.8 30.7 75.0 4.7 47 48 C 4.5 M 37.5 7.2 4.0 3.0 2.0 3.5 4.5 4.0 3.5 49 53 E 5.0 H 0.8 1.2 0.2 0.8 0.2 0.8 1.0 1.2 0.6 54 56 C 5.0 H 2.0 1.7 1.3 2.7 1.3 1.7 2.0 2.0 1.3 57 68 H 5.0 H 0.4 0.6 1.2 0.8 1.0 0.3 0.8 0.8 0.8 69 71 * 2.3 P 3.7 29.3 5.3 51.3 2.3 26.7 26.3 52.0 2.7 72 76 - 4.3 M 4.8 75.0 75.0 75.0 6.5 75.0 75.0 75.0 61.4 79 84 E 4.7 H 1.3 1.3 0.5 1.0 0.3 14.2 1.3 1.3 1.0 85 91 C 4.6 H 44.4 43.6 2.1 4.0 1.7 33.7 4.0 3.1 4.8 92 94 H 4.2 M 3.7 2.7 2.0 1.7 2.0 3.0 2.7 1.3 2.3 95 96 - 4.0 M 75.0 6.5 75.0 75.0 75.0 6.8 5.5 75.0 75.0 100 101 C 4.7 H 4.5 6.2 6.0 8.8 6.0 7.5 6.5 8.2 5.0 102 116 - 4.4 M 3.8 3.6 75.0 75.0 75.0 75.0 75.0 75.0 75.0 117 118 C 4.5 M 5.5 3.5 7.5 75.0 7.0 7.2 7.0 75.0 7.5 119 120 * 2.2 P 6.0 5.0 6.0 75.0 7.0 7.5 6.0 75.0 3.0 121 132 H 4.5 M 2.3 1.7 3.3 75.0 3.9 2.3 2.3 75.0 4.2 136 137 C 4.5 M 6.8 4.5 1.5 8.5 1.5 2.0 4.5 7.5 4.5 138 140 E 4.4 M 75.0 75.0 1.3 3.0 1.0 3.3 3.7 2.7 3.3 144 145 - 4.4 M 75.0 75.0 75.0 4.0 75.0 75.0 75.0 4.5 75.0 146 149 * 3.2 M 75.0 75.0 0.8 0.2 0.8 75.0 75.0 0.2 2.0 151 154 * 2.5 P 75.0 75.0 3.0 5.0 2.8 23.6 22.2 4.8 4.0 155 159 H 4.3 M 47.8 75.0 1.8 1.6 3.1 2.2 19.6 2.8 3.6 163 165 C 4.4 M 2.7 6.7 25.3 4.7 25.0 3.7 5.8 3.7 26.7 166 169 E 4.4 M 3.2 3.0 0.0 4.8 0.0 0.2 0.5 4.2 0.0 170 171 C 4.3 M 39.5 6.5 0.5 3.0 1.0 1.0 0.5 3.5 0.5 172 177 * 1.7 P 3.2 3.9 27.5 5.5 27.3 15.5 16.5 5.8 27.5 179 181 * 3.2 M 75.0 75.0 3.3 2.3 3.7 75.0 75.0 2.3 4.7 182 185 - 4.0 M 75.0 75.0 75.0 0.5 75.0 75.0 75.0 1.2 4.5 186 196 * 3.0 P 75.0 75.0 29.2 2.5 36.2 23.5 23.5 3.2 23.1 197 198 C 4.3 M 7.5 7.0 2.5 40.5 3.0 75.0 75.0 3.0 1.0 199 223 * 3.4 M 9.6 10.0 49.3 27.3 49.6 52.8 72.2 27.6 55.0 224 225 - 4.0 M 4.5 7.0 75.0 75.0 75.0 75.0 75.0 75.0 6.5 226 234 * 2.9 P 2.6 10.3 3.8 75.0 4.4 43.3 52.2 75.0 10.2 235 237 E 4.5 M 1.0 0.3 0.0 75.0 0.3 0.0 1.7 75.0 0.0 239 244 * 3.2 M 75.0 75.0 1.7 63.5 1.2 14.3 1.8 75.0 1.8 245 248 C 4.6 H 57.8 57.8 5.6 5.1 6.4 22.2 5.0 4.2 22.9 249 257 H 5.0 H 1.9 1.4 3.2 1.3 3.8 0.6 1.2 1.4 3.9 258 259 - 4.4 M 75.0 75.0 75.0 1.5 75.0 75.0 75.0 3.5 75.0 260 264 H 4.9 H 4.2 4.2 2.6 2.2 2.8 0.2 3.2 2.0 1.0 265 267 * 2.1 P 51.0 51.3 2.7 1.3 3.0 3.0 50.3 1.7 1.7 269 275 * 3.3 M 75.0 75.0 24.7 4.9 5.3 75.0 75.0 5.6 3.6 276 283 - 4.0 M 75.0 75.0 75.0 3.4 75.0 48.0 75.0 3.0 32.5 284 301 * 3.2 M 3.8 7.1 75.0 3.6 75.0 6.5 75.0 4.1 75.0 302 303 C 4.4 M 3.5 3.5 75.0 4.0 8.0 75.0 75.0 5.0 6.0 304 308 * 2.2 P 0.8 1.2 5.9 0.6 4.7 75.0 75.0 0.6 5.0 309 310 C 4.5 M 1.0 0.5 5.5 6.0 40.5 75.0 75.0 6.0 5.0 312 315 H 4.4 M 4.5 5.9 3.5 1.8 4.2 75.0 75.0 1.8 7.5 316 334 * 3.3 M 52.8 37.1 3.6 10.9 3.5 75.0 75.0 3.7 71.7 335 337 - 4.0 M 75.0 75.0 2.7 5.7 2.0 75.0 75.0 75.0 75.0 338 357 * 3.4 M 28.8 14.0 40.0 2.6 39.8 75.0 75.0 2.6 75.0 358 380 - 4.1 M 75.0 30.1 75.0 4.4 75.0 75.0 75.0 4.3 75.0 381 403 * 3.2 M 2.1 1.9 47.7 2.9 47.6 75.0 75.0 2.7 75.0 404 410 H 4.4 M 1.6 2.4 4.0 2.4 4.3 75.0 75.0 1.7 75.0 411 418 * 3.3 M 2.6 3.1 48.0 5.0 48.2 75.0 75.0 2.6 75.0 419 431 - 4.3 M 58.8 65.3 75.0 75.0 75.0 23.2 75.0 4.8 75.0 >>>>>>