Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1p0za1 -----------------CCCCHHHHHHHHHHHHHHHC----CHHHHHHHH-----CCCHH-HHHHHHHHHHHHCCCCEEEEEEC-----------------------CCCEEECCC--HHHCCCCCCC------CCCHHHHHH------CCCEEEEEEEC----CEEEEEEEEEEEC---CCCCEEEEEEEEEEH---HHCC----------------------------------------------------------------------------------------------------------- >P1;d2basa2 ---------------CHHHHHHHHHHHHHHHHHHHHHHHHC-------CCCCC-------HHHHHHHHHHHCHHHCCEEECCCCCCCCCCEEEEEC----CEEEEEHHHCC---------CCCCCCC--------CHHHHCCC---CCCCCEECCCCCCCCCC----CCEEEEECCC---------CCEEEEECH---HHHCCCC-----------CCC------------------------------------------------------------------------------------------ >P1;d2hjea- ------------CHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCHHHHHHHH--HHHHHHC-HHHCCCEEEEECC-----------------------C-CEEEECC-HHHHHCCC-------HH-HHHHHHHHCC--CCCCCEEEEEEECC----EEEEEEEEEEEEECCCCCCEEEEEEEEEECCCCHHHHHHHHHHCCCC--EEEEEEC-CEEEEECCC-------CCCCCCHHHHHC---------------------CEEEEEEEEECCEEEEEEEEEEEC-------------- >P1;d2p7ja1 --------------------------------------------------CEE-------CC-----------CCEEEEEECCCCCEEECCC--------------HHHCCCCCCCCCCCCCCCCCC--------CCHHHHHC---CCCEEEECC-------C----EEEEEEEEECCCC----CEEEEEEEEEH---HHHCC---------------------------------------------------------------------------------------------------------- >P1;d2p7ja2 ----CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHCCHHHHHHH---CCEEEEEEECC-----------------------CCCEEEEEEECCCCCEEECCCCCCCCCCHHHHHHHCCCCCCCEEEEEEECEECCEECCCCCEEEEEECEEE---CCEEEEEEEEEEEH---HHHHHHC-------------------------------------------------------------------------------------------------------- >P1;d3by8a- -----------------CHHHHHHHHHHHHHHHHHHC----CHHHHHHCC-----CCHHHCCHHHHHHHHHHHCCCCEEEEEEC-----------------------CCCCCCCCC--HHHCCCCCCC------HHHCHHH-H------CCCEEEEECCC----CCCEEEEEEEEEC---CCCCEEEEEEEEEEH---HHHHHHHHC------------------------------------------------------------------------------------------------------ >P1;d3c38a- ------------CHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCCHHHHH--HHHHHCC-HHHCCCEEEEEEC-----------------------C-EEEEECC-CHHHHCCC-------HH-HHHHHHHHCC--CCCCCEEEEECCCC----CCEEEEEEEEEECCCC-CCCCEEEEEEEECCCCHHHHHHHHHHCCCC--EEEEEEC-CEEEEECCC-------CCCCCCHHHHHCCCCCCC--------------CEEEEEEEEEECCEEEEEEEEEEEEC------------- >P1;d3c8ca1 -------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC---------HHHHHHHHCCHHHHH--HCCCEEEEECC----------------------CCC-EEECCC--C---CCCCCCCCHHHCHHHHHHHHHC----CCEECCCEECCCCC----CEEEEEEEEEECCCCCCEEEEEEEEECH---HHHHHHHCCCCCCCCEEEEEEECCCCEEECC-CHHHCC---------CCC-CCC-CCCCCCCCCEEEEE-CCEEEEEEEEECC---CCCEEEEEEECHHHHHHHHHHHHCC >P1;d3li9a- -------CHHHHHHH-CCHHHHHHHHHC-CHHHHHHHHHHHC-CCCC-------CCCCCCC-CHHH-HHHHCCCCCCEEEEEECCC----CCCCCHHHCCCCCCCCCCCCCCEEEECCCC--CCEEEECCCCCCCHHHHHHHHHC----CCEECCCCCCC-------CCCCEEEEEEEEC--CEEEEEEEEECCC---HHHHHHHCCCCCCCCCEEE-CCCCCCCCCCCCCHHHCCCCCHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCEEEEEEEEC---CCCEEEEEEEECCCC---------- >P1;d4xmra1 CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCHHHHHHHHHHHHH-HHHHHH-CCCEEEEECC-----------------------CCC-EEEEEC--C--CCEEECCCCHHHCHHHHHHCCCC----CCEECCCEECCCCC----CEEEEEEEEEEEC--CEEEEEEEEEEEH---HHHHHHHHHCC----CCEEEECCCCCEEEEC-CHHHHC----CCCCCHHHHHHHHHHCC--CCCEEEEE-CCEEEEEEEEEEC-----CEEEEEEEECHHHHC-------- >P1;d6py3a- ----CCHHHHHHHHC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CC---------HHHHHHHHCCHHHHC--CCCCEEEECC-----------------------CCC-EEEECC-------CCCCCCCHHHCHHHHHHHHCC----CCEECCCEECCCCC----CEEEEEEEEEC-----CCCEEEEEEEEH---HHHHHHHCC----CCEEEEEEECCCCEEECC-CHHHCC---------CCHHHHCCCCCCCCCCCEEEEE-CCEEEEEEEEECCCCCCCCEEEEEEEECC-CCC-------- PSA >P1;d1p0za1 -----------------b7545920450161057008----386016005-----65559-40661035338a18030000015-----------------------904100015--7922664081------920660175------36222244726----2650000000031---b96711000000002---952b----------------------------------------------------------------------------------------------------------- >P1;d2basa2 ---------------a9a84377114801740570157248-------a4a48-------5351045006403a100000035805050000126a----79043257149---------4522738--------60682157---8585010373380a537----50110202ba---------811000015---720572b-----------705------------------------------------------------------------------------------------------ >P1;d2hjea- ------------669812650570056005303830471082640250088465a705820--5623774-6831020000027-----------------------8-8100117-50582207-------88-2064018506--81751410407085----63100000103062486883202000000008169003102750b04--0000008-973003007-------981808256028---------------------352171504159861301000039-------------- >P1;d2p7ja1 --------------------------------------------------546-------7a-----------8635302033501034055--------------852150275892863104726--------90156056---497773457-------8----330404055798a----61102020114---96266---------------------------------------------------------------------------------------------------------- >P1;d2p7ja2 ----9a88766766687766287348917860572057016383054007755a9236701800720581---50020000034-----------------------80404010506286804419723604a160053047093452223b533035778247a412030000104---aa822000000002---6105751-------------------------------------------------------------------------------------------------------- >P1;d3by8a- -----------------78435711770171068019----257035007-----462870a0383038329957010000022-----------------------813000014--7821266051------9106601-8------27324344513----1460000000023---7a7611000000033---740675589------------------------------------------------------------------------------------------------------ >P1;d3c38a- ------------8497527502620681032046404710859600700345568505910--7422774-793202010002a-----------------------6-8010117-50882205-------57-1046007407--6354020130609a----65010000113044ac-a74102000000008269003502560a03--000002a-562011006-------9a1607484005194357--------------72402205040387714000010646------------- >P1;d3c8ca1 -------9a078406710541077017306911820570054029538---------5a3057104676049--10500000339----------------------606-101039--9---19168a1303723005404936----71200901512467----6300000000538977622000000020---7500830272804b03300002692200002-768101---------563-500-93890559224062-b945200001609---619010000012850483347786b >P1;d3li9a- -------98426704-804830761084-4604720680076-2929-------7450a50-7404-7205627401000000255----300741842562a10375000000003088--72524207707846102503753----82101404456-------a30001000042b--a810000001020---8411760171523880300-0015020001084592106310652a4741460073067051632326589566240002217---144100101013925---------- >P1;d4xmra1 a86664478047604520750341048136702710560285027263710564730374003203-721672-8000000019-----------------------643-000034--9--8081376180573700520363b----80210523405126----5700000100428--a740000000010---75037504815----3400002476700003-689237----88381640161268475--56004177-b984200000603-----711000025075049-------- >P1;d6py3a- ----b7797138605-50782076037204920730260074038-48---------886026305797028--2021001038-----------------------718-220257-------515bc130472301660482b----50001301801147----6300000120b-----c44000000021---540071078----d31300000392300003-667203---------4407701594102b5a124053-9943100000506901319020010043a-039-------- Translating the sequences -----------------****HHHHHHHHHHHHHHH*----*HH******-----***HH-**HHH*HHH****CCCEEEEE*C-----------------------C*C**E***--****CCC***------***HHHHH*------CC*E******C----****EEEEEEEE*---**C**EEEEEEEEEH---HH**----------------------------------------------------------------------------------------------------------- ---------------***HHHHHHHHHHHHHHHHHHHHH**-------*****-------***HHH*HHH*****CCEEE***C************----*********C*---------**CCC**--------*HHHH***---***CC*E******C***----**EEEEE***---------**EEEEE*H---HHH****-----------***------------------------------------------------------------------------------------------ ------------******HHHHHHHHHHHHHHHHHHHHH***HH**************HH*--HHH*HH*-***CCCEEEEE*C-----------------------C-C**E***-*****CCC-------**-HHHHHHH***--**CC*E******C*----***EEEEEEEE******C**EEEEEEEEE****HHHHHH********--*******-*********-------************---------------------************************-------------- --------------------------------------------------***-------**-----------*C**EEEE**C********--------------***C************CCC**--------**HHHHH*---******E**-------*----*EEEEEEEE****----*EEEEEEEEEH---HHH**---------------------------------------------------------------------------------------------------------- ----**************HHHHHHHHHHHHHHHHHHHHH***HH**************HH***HHH*HHH---*C**EEEEE*C-----------------------C*C**E**********************HHHHHHH**********E******C********EEEEEE*E**---*C**EEEEEEEEEH---HHHHHH*-------------------------------------------------------------------------------------------------------- -----------------*HHHHHHHHHHHHHHHHHH*----*HH******-----***HH***HHH*HHH****CCCEEEEE*C-----------------------C*C******--****CCC***------*HH*HHH-*------CC*E******C----****EEEEEEEE*---**C**EEEEEEEEEH---HHHHHH***------------------------------------------------------------------------------------------------------ ------------******HHHHHHHHHHHHHHHHHHHHH***HH**************HH*--HHH*H**-***CCCEEEEE*C-----------------------C-***E***-*****CCC-------**-HHHHHHH***--**CC*E******C*----***EEEEEEEE*****-C***EEEEEEEE****HHHHHH********--*******-*********-------******************--------------**************************------------- -------***********HHHHHHHHHHHHHHHHHHHHH***HH****---------*HH***HH**HHH**--*CC*EEEE*C*----------------------C*C-*E****--*---CC**********HHHHHHH***----CC*E******C***----*EEEEEEEE******C**EEEEEEEE*H---HHHHHH*************************-******---------***-***-**************-*************---************************* -------********-**HHHHHHHHH*-*HHHHHHHHH***-****-------*******-*HHH-HHH****CCCEEEEE*C**----*****************C*C**E*******--CC***********HHHHHHH***----CC*E******C-------****EEEEE****--C**EEEEEEE***---HHHHHH*************-***************************************************************---***************---------- ******************HHHHHHHHHHHHHHHHHHHHH***HH**************HH***HHH-HHH***-CCCEEEEE*C-----------------------C*C-*E****--*--CC***********HHHHHH****----CC*E******C***----*EEEEEEEE****--C**EEEEEEEEEH---HHHHHH*****----****************-******----*****************--********-*************-----***************-------- ----***********-**HHHHHHHHHHHHHHHHHHHHH***HH*-**---------*HH***HH**HHH**--CCC*EEEE*C-----------------------C*C-*E****-------C**********HHHHHHH***----CC*E******C***----*EEEEEEEE**-----***EEEEEEEEH---HHHHHH***----******************-******---------**********************-*****************************-***-------- 103190.tem _________________________________ -------***********HHHHHHHHHHHHHHHHHHHHH***HH**************HH***HHH*HHH****CCCEEEEE*C*----------------------C*C**E*********CCC**********HHHHHHH***--**CC*E******C***--***EEEEEEEE******C**EEEEEEEEEH---HHHHHH********-****************-******----*****************--********-*************---*************-*---------- Structural block scores 0 6 - 4.5 M 75.0 75.0 75.0 75.0 46.8 75.0 75.0 75.0 75.0 6.4 46.5 7 17 * 3.0 P 69.2 57.3 37.0 75.0 6.7 68.8 37.3 4.8 11.2 3.9 10.8 18 38 H 4.7 H 10.4 3.9 3.2 75.0 4.8 10.8 3.2 3.5 7.3 3.3 3.6 39 41 * 2.3 P 51.0 29.0 3.3 75.0 3.3 50.7 4.3 3.0 4.3 5.0 3.7 42 43 H 4.5 M 7.0 75.0 5.0 75.0 5.5 6.0 7.5 1.0 38.5 1.0 1.5 44 57 * 2.8 P 28.8 50.9 4.3 60.0 4.5 28.7 3.4 50.4 40.1 3.9 55.6 58 59 H 4.4 M 7.0 75.0 5.0 75.0 3.5 7.5 5.0 6.8 7.8 5.5 7.0 60 62 * 2.1 P 26.3 4.3 50.0 30.8 3.0 3.5 50.0 4.0 27.3 1.0 2.7 63 65 H 4.6 H 4.3 1.7 4.3 75.0 3.0 4.7 4.3 1.7 2.7 1.7 2.7 67 69 H 4.6 H 3.7 2.0 6.0 75.0 4.7 4.7 6.0 4.3 3.0 3.3 5.3 70 73 * 2.5 P 5.6 4.4 23.0 58.2 57.5 6.2 23.5 40.8 5.0 22.5 40.0 74 76 C 4.5 M 3.7 0.3 1.0 4.7 0.7 2.7 1.3 2.0 1.7 2.7 1.3 77 81 E 4.8 H 0.0 0.6 0.0 1.6 0.0 0.0 0.2 0.0 0.0 0.0 0.4 85 106 - 4.5 M 75.0 16.3 75.0 48.9 75.0 75.0 75.0 75.0 16.8 75.0 75.0 110 111 * 1.9 P 0.5 42.0 0.5 2.5 2.0 0.0 0.5 38.0 0.0 37.5 38.5 113 121 * 2.4 P 19.6 59.3 11.6 5.4 4.0 19.2 11.9 35.8 18.8 35.1 43.2 122 124 C 4.4 M 5.3 3.7 3.0 3.7 2.7 4.7 2.3 28.3 4.7 5.3 51.7 125 134 * 3.0 P 46.8 61.1 61.6 60.8 4.3 46.5 61.2 4.2 4.1 4.1 4.7 135 141 H 4.7 H 3.1 4.0 3.0 3.7 2.6 12.7 2.6 2.3 2.4 2.4 2.9 142 144 * 2.2 P 51.7 52.3 3.7 52.0 5.3 52.7 3.7 6.0 5.0 6.8 7.2 145 146 - 4.5 M 75.0 41.5 75.0 39.5 3.5 75.0 75.0 75.0 75.0 75.0 75.0 147 148 * 3.6 M 75.0 6.5 4.5 8.0 3.5 75.0 4.5 75.0 75.0 75.0 75.0 149 150 C 4.5 M 4.5 2.5 6.0 7.0 2.0 4.5 4.5 4.0 5.0 4.0 2.5 153 158 * 1.3 P 3.5 4.0 2.0 52.0 3.2 3.5 1.7 2.7 3.0 2.3 2.2 160 162 * 3.2 M 75.0 5.0 51.7 52.7 5.7 75.0 53.5 5.7 75.0 3.0 4.0 163 164 - 4.5 M 38.5 75.0 75.0 75.0 5.5 38.0 75.0 75.0 75.0 75.0 75.0 165 167 * 2.7 P 3.7 51.7 3.3 51.0 5.2 3.3 3.7 52.0 53.5 51.7 52.0 168 175 E 4.8 H 0.4 2.2 0.5 2.6 0.8 0.2 0.8 0.4 0.5 1.0 0.8 176 181 * 2.8 P 41.1 64.2 4.3 30.8 39.9 40.9 17.7 5.3 27.9 27.3 51.9 183 184 * 1.8 P 4.0 75.0 5.5 40.5 5.0 3.5 5.5 4.0 4.5 5.5 8.2 185 193 E 4.8 H 0.1 9.6 0.4 0.9 0.2 0.4 0.3 0.4 0.3 0.1 0.7 195 197 - 4.5 M 75.0 75.0 3.0 75.0 75.0 75.0 3.3 75.0 75.0 75.0 75.0 198 203 H 4.6 H 29.6 3.8 3.2 17.3 4.0 4.8 3.8 3.8 4.5 4.5 2.8 204 211 * 3.3 M 75.0 67.1 3.7 75.0 65.8 49.6 3.3 4.3 3.4 30.4 41.1 213 228 * 3.2 M 75.0 61.7 11.2 75.0 75.0 75.0 11.1 1.8 5.4 2.2 1.5 230 235 * 3.8 M 75.0 75.0 63.7 75.0 75.0 75.0 63.5 3.8 3.5 5.8 4.0 236 239 - 4.5 M 75.0 75.0 41.8 75.0 75.0 75.0 42.4 75.0 2.5 75.0 75.0 240 256 * 3.6 M 75.0 75.0 33.2 75.0 75.0 75.0 8.2 33.7 4.3 4.6 24.5 257 258 - 4.2 M 75.0 75.0 75.0 75.0 75.0 75.0 75.0 2.5 2.5 75.0 6.8 259 266 * 3.9 M 75.0 75.0 75.0 75.0 75.0 75.0 75.0 3.8 3.5 3.8 3.8 268 280 * 3.3 M 75.0 75.0 19.5 75.0 75.0 75.0 13.5 3.7 3.4 3.3 2.8 281 283 - 4.2 M 75.0 75.0 7.3 75.0 75.0 75.0 6.0 75.0 75.0 75.0 3.3 284 296 * 3.3 M 75.0 75.0 13.3 75.0 75.0 75.0 8.0 2.2 1.9 13.3 2.6 299 308 - 4.7 H 75.0 75.0 75.0 75.0 75.0 75.0 75.0 6.2 75.0 61.3 61.2 >>>>>>