Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1t3ta6 ---------CCCCCEEEEEEC-CCCCCCCCC--------------------CCCC-CHHHHHH----HHHHHHHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHCCCEEEEEHHHCCCCCC-----------------------------CCCHHHHHHCCCCC-EEEEEEC---HHHHHHHHHHHHHHC---CCEEEEEEEEC--CCEEEEEECCCCEEEEEEEHHHHCCC-------------------------------CCCCCCCC---------- >P1;d1t3ta7 ------CCCCCCCEEEEEEEC-CCCCCCCCCCHHH-----HH--CCCCCCCCCCCCCHHHHHH----HHHHHHHHHHC---CCCCEEEECCCCHHHHHHHHHHHHHCCEEEEECHHHC----------------------------------CCHHHHHHCCCC--EEEEEEE---HHHHHHHHHHHHHCCCHHH-EEEEEEEEC--CCEEEEEEC--CEEEEEEEHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC >P1;d1vk3a3 -------CCCCCCCEEEEEEC-CCCCCCCCC--------------------CCCC-CHHHHC-----CHHHHHCCC-----CCCCEECCCCCCHHHHHHHHHHHHCCCCEECCHHHCCCCCC-----------------------------C-CHHHHHHCCCCC-C-CEEEC---HHHHHHHHHHHHHCC---CEEEEEE-CCC--CCEEECCCC---CCC-CEEHHHHHCC-------------------------------CCCCC------------- >P1;d1vk3a4 ---------------------------------------------------------------------------------------------------------------------------------------------------------------CCCCCEEEEEEEECCCCHHHHHHHHHHHHHHHHCCCEEECCC-----------------------------------CCCCCCCCHHHHCCCCCCCCCCCCEEEEEECCCCCCCCEEEEEEEC >P1;d2btua2 --------CCCCCCEEEEEECCCCCCCCCCCCCCCCCCC-------------CCCCHHHHHC--CCCCHHHHHHHCC--C--CCCCCEECCCCHHHHHCHHHCC---CEECCCCCCC-CCHHHHHHCCCCC-------------------------CHHHCCCCCEEEEEEEC---CC-----CCHHHH----CCCEEEEEC-EEC--CCCCC--------------------------------------------------------------------- >P1;d2v9ya2 ----CCHHHCCCCCEEEEEECCCCCCCCHHHHHHHHH-HCCCCCCCCCCCCCCCCCHHHHHCCCCCCCHHHHHHHHHCC---CCCEEEECCCCHHHHHCHHHCCC-CEEEEEEHHHCCCCHHHHHHHHHHCCC---------------------HHHHHHHCCCCEEEEEEEC---HHHHHHHHHHHHHCC---CCEEEEEEEEEC--CCEEEECHHHHHCCC-------------------------------------------------------CCCC >P1;d2yyda2 ----CCCCCCCCCCEEEECCC-CC-HHHHHHHHHC-----CCCC------HHHHHHHHHHHH---CCCHHHHHHHHH----CCCCEEEECCCCHHHHHHHHHHHHHCCEEEEEHHHCCCCHHHHHHHHCCCCCHHHHHHHHHHCCCEECCCCHHHHHHHHCCCCCCCEEEEEC---HHHHHCHHHHHH-H--HCCCCEEEEEEECC--CCEEEE-------------------------------------------------------------------- >P1;d2z1ea2 ----CCCCCCCCCCEEEECCC-CCHHHHHHHHHHC-----CCCCC----------CCCCC---C-CCCHHHHHHHHHHHCHHHEEEEECCCCCHHHHHHHHHHHHHCCEEEEEHHHCCCCHHHHHHHHHHC------------------------CCHHHCCCCC-CCEEEEC---HHHHHHHCCCCCCC--CCCCCEEEEEEECCCCCCEEEECCCC----CEEE-------CCCCCCCCC---------------------------------------- >P1;d3c9ua2 --CCCCCCCCCCCCEEEEECC-CCHHHHHHHHHHC-----C-CC---CC-CHHHHHHHHHHHCC-CCCHHHHHHHH-----HHCCEEEEEC-CCHHHHHHHHHHHHCCEEEECHHHCCCCHHHHHHHHHCC--------------------CCHHHHHHHCCCCC-EEEEEEC---HHHC--CC---------CCCEEEEEEEECC--CCEEEC---C----EECC-------CCCCCCC------------------------------------------ >P1;d3qtya2 ----C-CCCCCCCCEEEEECCCCCCCCCHHHHHHHHHCCCCCCCCC-CCHHHCCCCHHHHHHCCCCCCHHHHHHHHHCCC--CCCC-CCCCCCHHHHHCHHHCCC-CCEEEECHHHCCCCHHHH-CCCCCCCC---------------------CCC-CCCCC-CCC-CEEEC---HHHCC-CCCCHHHCC--CCCEEEEEEEECC--CCEEEC-------------------------------------------------------------------- >P1;d3u0oa2 ----CCCCCCCCCCEEEECCC-CC-CCCCCCC---------------------CCCCHHHHH---CCCC-HHHHHCC----CCEEEEEECCCCHHHHHHHHHHHHHCEECC-CC-CCCCCC--C------CCCCCC-CCHHHHHHHCCCC----CHHHHCCCCCCCCEEEEEC---HHHHHHHHHHHH-H--CC-CCCCCEECEEC--CCCCCC-------------------------------------------------------------------- >P1;d5cm7a2 CCCCCCCCCCCCCCEEEEECC-CCHHHHHHHCC--------------------CCCCHHHHHCC-CCCC-CHHHHC-----CCCCEEEECC-CCHHHHHHHHHHHHCCEEEEEHHHCCCCHHHHC-CCHH----------------------HHHHHHHHCCCCC-CEEEEEC---HHHHHHHHC----C--CCCCEEEEEEEECC--CCEEEEEC-C----EECC-------CCCCCCCC----------------------------------------- >P1;d6xepa2 -CCCCCCCCCCCCCEEEEECC-CCHHHHHHHHHHC-----CCCCCCCCCCCHHHHHHHHHHHCC-CCCHHHHHHHC-----CCCCEEEEEC-CCHHHHHHHHHHHHCCEEEECHHHCCCCHHHHHHCCHH----------------------HHHHHHHHCCCCC-EEEEEEC---HHHHHHHHHHHH-H--HCCCEEEEEEEECC--CEEEEC---C----CCC--------------------------------------------------------- PSA >P1;d1t3ta6 ---------064702000002-202410b8a--------------------7558-4771572----04201130643ac730033337078600260004003527300601035042549-----------------------------c0638300403041-0100003---594373037107718---02112013028--96202030676875225440963469-------------------------------a99797a9---------- >P1;d1t3ta7 ------580436a00000000-0475112050411-----97--79796a7528413991462----16300540685---8301122607920023001200040400040404708----------------------------------b72600020104--0000003---59139703620483906a0-023024058--936020209--a6514232014122650495356247657486036617725749679b7794a76796897669 >P1;d1vk3a3 -------50553902000004-000420aaa--------------------82a6-579358-----266046455-----91123229078400230004000619000405025022448-----------------------------9-737201402031-0-00000---483093015006629---0602200-038--85104037b---842-3560473268-------------------------------99abb------------- >P1;d1vk3a4 ---------------------------------------------------------------------------------------------------------------------------------------------------------------380762500100264468912840560374058591201628-----------------------------------801492470894900032b17871000003a508080517505708 >P1;d2btua2 --------1675a13000030600073249306348d55-------------d165026219--9490780164038--3--5022315047200451026005---c100084a20-3260072035225-------------------------70043000000100005---29-----320492----925045020-6a8--85081--------------------------------------------------------------------- >P1;d2v9ya2 ----544950765010000102100742372067007-80927582801c609b340361083834909a205403759---50102050361002700161028-910050306405016000101423908---------------------4730042000000000002---694167025508749---050240450364--920607201610668-------------------------------------------------------b97b >P1;d2yyda2 ----38358085501000001-00-0100330274-----9407------774078027327---692540540055----07020015048700020014007409000304086011074014004782228504501770794150a17921000000205500100005---571494068108-8--28191330030186--720105-------------------------------------------------------------------- >P1;d2z1ea2 ----27146064501000000-0002200530975-----a282a----------70712---7-392650042008407591020137038100010002006508000206375020482055009509------------------------3400103030-0000000---67318601105928--305502302402586424010148a7----9464-------03329b57a---------------------------------------- >P1;d3c9ua2 --5903467075a00000023-0000300420372-----9-4a---91-58106300741483-99196068015-----5301001403-30001002500770901020519401117204400842a--------------------55235000101404-1100004---6844--37---------9160310160299--920205---9----8639-------360778a------------------------------------------ >P1;d3qtya2 ----8-08a0756010000203000755384066102591718763-418208763028108572181690462048490--7112-25035200360047102b-910030527308223016-05523926---------------------595-26430-000-00004---6923a-437007629--a070130250274--560404-------------------------------------------------------------------- >P1;d3u0oa2 ----27535052803000002-00-032165c---------------------c7b277037---4937-0283049----1303012403430000101401950a0200-53-404078--8------732aa0-9048600750608----2472000208500100003---4a0286047206-8--3a-30820250574--c80607-------------------------------------------------------------------- >P1;d5cm7a2 bb7817556075602000012-00001005646--------------------a3912721482-5619-039506-----b103010503-300030044009409100302034000174068-2636----------------------7105200120404-0100004---383176058----4--19150220050397--67120227-8----8819-------011688aa----------------------------------------- >P1;d6xepa2 -e8924426066a00000013-0000100530566-----940829762a79222600311372-66186038404-----7202000502-7002600340085080002050a401028006510b99----------------------4044000516504-0100004---5934a4069019-4--0a160340360299--780116---7----739--------------------------------------------------------- Translating the sequences ---------CCCCCEEEEE*C-CC*******--------------------****-*HHHH**----*HHHHHHH*******C**EEEECCCC*HHHHHHHHHHH*CCEEEE*HHHCCCC**-----------------------------****HHHHHCCCCC-*EEEEEC---HHHHHHHH*HHH***---CCEEEEEEEEC--*C*EEE********************-------------------------------********---------- ------*CCCCCC*EEEEE*C-CC***********-----**--*************HHHH**----*HHHHHHH***---*CCCEEEECCCC*HHHHHHHHHHH*CCEEEE**HH*C----------------------------------***HHHHHCCCC--*EEEEE*---HHHHHHHH*HHH*******-EEEEEEEEC--*C*EEE***--**************************************************************** -------CCCCCCCEEEEE*C-CC*******--------------------****-*HHHH*-----CHHHHH***-----*CCCEE**CCCC*HHHHHHHHHHH*CC*EE**HHHCCCC**-----------------------------*-**HHHHHCCCCC-*-*EEEC---HHHHHHHH*HHH***---C*EEEEE-**C--*C*EE****---***-**********-------------------------------*****------------- ---------------------------------------------------------------------------------------------------------------------------------------------------------------*CCCC***EEEEEC***HHHHHHHH*HHH*****CC*EE***-----------------------------------********************************************** --------CCCCCCEEEEE*C*CC***************-------------*****HHHH*--*CCCHHHHHHH**--*--CCC**EECCCC*HHHH*HHH**---CEE******C-CC***********-------------------------*HHHCCCCC**EEEEEC---**-----**HHH*----CCCEEEEE*-E*C--C****--------------------------------------------------------------------- ----*****CCCCCEEEEE*C*CC*************-*******************HHHH****CCCHHHHHHH****---CCCEEEECCCC*HHHH*HHH***-C*EEEE*HHHCCCC*************---------------------*HHHHH*CCCC**EEEEEC---HHHHHHHH*HHH***---CCEEEEEEEE*C--C*EEE**********-------------------------------------------------------**** ----***CCCCCCCEEEE**C-CC-**********-----****------*******HHHH*---CCCHHHHHHH**----*CCCEEEECCCC*HHHHHHHHHHH*CCEEEE*HHHCCCC***********************************HHHHHCCCCC**EEEEEC---HHHHH*HH*HHH-*--*CCC*EEEEEEECC--C*EEE*-------------------------------------------------------------------- ----***CCCCCCCEEEE**C-CC***********-----*****----------*****---*-CCCHHHHHHH**********EEE*CCCC*HHHHHHHHHHH*CCEEEE*HHHCCCC***********------------------------**HHHCCCCC-**EEEEC---HHHHHHH*******--*CCC*EEEEEEECC**C*EEE*****----****-------*********---------------------------------------- --*****CCCCCCCEEEEE*C-CC***********-----*-**---**-*******HHHH***-CCCHHHHHHH*-----**CCEEEE*C-C*HHHHHHHHHHH*CCEEEE*HHHCCCC***********--------------------****HHHHHCCCCC-*EEEEEC---HHH*--**---------CCCEEEEEEEECC--C*EEE*---*----****-------*******------------------------------------------ ----*-*CCCCCCCEEEEE*C*CC**********************-**********HHHH****CCCHHHHHHH*****--CCC*-**CCCC*HHHH*HHH***-CCEEEE*HHHCCCC****-********---------------------***-**CCC-C**-*EEEC---HHH**-****HH***--CCCEEEEEEEECC--C*EEE*-------------------------------------------------------------------- ----***CCCCCCCEEEE**C-CC-*******---------------------****HHHH*---CCC*-HHHHH**----*C**EEEECCCC*HHHHHHHHHHH*C*E**-**-*CCCC*--*------******-*************----*HHHH*CCCCC**EEEEEC---HHHHHHHH*HHH-*--*C-C****EE*E*C--C*****-------------------------------------------------------------------- *******CCCCCCCEEEEE*C-CC*********--------------------****HHHH***-CCC*-*HHHH*-----*CCCEEEECC-C*HHHHHHHHHHH*CCEEEE*HHHCCCC*****-****----------------------***HHHHHCCCCC-*EEEEEC---HHHHHHHH*----*--*CCCEEEEEEEECC--C*EEE***-*----****-------********----------------------------------------- -******CCCCCCCEEEEE*C-CC***********-----*****************HHHH***-CCCHHHHHHH*-----*CCCEEEE*C-C*HHHHHHHHHHH*CCEEEE*HHHCCCC**********----------------------***HHHHHCCCCC-*EEEEEC---HHHHHHHH*HHH-*--*CCCEEEEEEEECC--C*EEE*---*----***--------------------------------------------------------- 56042.tem _________________________________ ----***CCCCCCCEEEEE*C-CC***********-----*****--**-*******HHHH***-CCCHHHHHHH***---*CCCEEEECCCC*HHHHHHHHHHH*CCEEEE*HHHCCCC***********---------------------***HHHHHCCCCC**EEEEEC---HHHHHHHH*HHH***-*CCCEEEEEEEECC--C*EEE***-*----****----------****------------------------------------------ Structural block scores 0 3 - 4.5 M 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 41.0 75.0 75.0 9.5 26.6 4 6 * 2.9 P 75.0 51.7 75.0 75.0 75.0 4.3 4.7 3.3 2.3 27.7 4.7 4.3 3.3 7 13 C 4.7 H 23.9 4.5 3.9 75.0 15.1 4.6 4.4 3.6 5.1 5.2 3.3 4.1 4.4 14 18 E 4.7 H 0.4 0.0 0.4 75.0 0.6 0.2 0.2 0.2 0.0 0.2 0.6 0.4 0.0 22 23 C 4.8 H 1.0 2.0 0.0 75.0 0.0 0.5 0.0 0.0 0.0 0.0 0.0 0.0 0.0 24 34 * 1.9 P 30.6 2.5 30.7 75.0 3.7 3.5 8.6 3.0 1.9 4.1 30.0 15.6 2.4 35 39 - 4.5 M 75.0 75.0 75.0 75.0 21.3 18.0 75.0 75.0 75.0 3.4 75.0 75.0 75.0 40 44 * 3.6 M 75.0 34.6 75.0 75.0 75.0 6.2 19.0 6.6 34.7 5.8 75.0 75.0 4.6 45 46 - 4.2 M 75.0 8.0 75.0 75.0 75.0 5.0 75.0 75.0 75.0 39.0 75.0 75.0 8.0 47 48 * 3.8 M 75.0 7.5 75.0 75.0 75.0 0.5 75.0 75.0 5.0 2.5 75.0 75.0 4.0 50 56 * 2.3 P 25.6 4.3 25.9 75.0 25.1 4.8 4.7 54.6 3.3 3.7 36.9 35.5 4.0 57 60 H 4.6 H 5.0 5.8 6.0 75.0 2.8 2.5 3.5 21.2 3.0 2.8 4.2 3.0 1.2 61 63 * 2.9 P 28.0 27.7 52.7 75.0 53.0 6.3 52.3 52.3 5.0 6.7 52.3 4.7 4.0 65 67 C 4.4 M 50.0 50.3 50.7 75.0 4.3 4.3 5.7 4.7 6.3 3.3 5.3 4.0 4.3 68 74 H 4.6 H 1.6 2.6 4.4 75.0 3.7 4.4 2.6 2.4 4.3 3.9 13.6 14.4 4.1 75 77 * 2.7 P 4.3 6.3 51.7 75.0 28.7 5.0 28.3 4.0 51.7 5.3 29.3 52.0 51.3 78 80 - 4.3 M 10.0 75.0 75.0 75.0 51.0 53.0 75.0 4.0 75.0 28.0 75.0 75.0 75.0 82 84 C 4.3 M 1.0 1.3 1.3 75.0 2.3 2.0 3.0 1.0 1.3 3.0 2.0 1.3 1.3 85 88 E 4.4 M 4.0 2.8 4.0 75.0 2.8 1.8 1.5 2.8 1.2 21.0 1.8 1.5 1.2 89 92 C 4.6 H 5.2 4.5 4.8 75.0 3.2 2.5 4.8 3.0 20.2 2.5 2.5 20.2 21.0 94 104 H 4.6 H 1.8 1.1 1.4 75.0 8.9 2.5 1.6 1.3 2.0 3.1 1.9 2.2 2.5 106 107 C 4.5 M 5.0 2.0 4.5 75.0 43.8 5.0 4.5 4.0 4.5 5.0 5.2 5.0 4.0 108 111 E 4.5 M 1.5 1.0 1.0 75.0 0.2 1.2 0.8 0.5 0.8 0.8 19.2 0.8 0.5 113 115 H 4.4 M 2.7 3.7 2.3 75.0 5.5 3.3 4.7 5.0 4.7 4.0 27.3 2.3 4.8 116 119 C 4.6 H 2.8 39.5 2.0 75.0 20.0 1.5 0.5 1.5 0.8 3.0 2.8 0.2 0.8 120 130 * 2.8 P 62.5 75.0 62.5 75.0 2.9 2.4 3.4 3.9 3.8 9.9 56.6 17.5 11.3 131 151 - 4.5 M 72.0 75.0 71.9 75.0 75.0 68.2 4.1 75.0 71.7 68.2 14.5 75.0 75.0 152 154 * 3.0 P 3.0 6.8 28.3 75.0 75.0 51.3 4.0 75.0 3.3 51.7 50.7 2.7 2.7 155 159 H 4.4 M 3.0 1.6 2.8 60.6 17.2 2.8 0.0 1.6 1.2 19.4 2.6 1.6 1.8 160 164 C 4.8 H 1.6 16.0 1.2 4.6 0.6 0.4 2.4 1.2 1.8 16.4 3.0 2.0 3.2 165 166 * 2.3 P 37.5 37.5 37.5 2.5 0.0 0.0 0.0 37.5 38.0 0.0 0.0 37.5 37.5 167 171 E 4.8 H 0.2 0.0 15.0 0.6 0.2 0.0 0.2 0.0 0.2 15.0 0.2 0.2 0.2 173 175 - 4.8 H 75.0 75.0 75.0 4.7 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 176 183 H 4.5 M 4.2 4.6 3.5 4.6 48.6 4.4 4.5 4.0 22.8 14.1 4.3 4.1 5.2 185 187 H 4.4 M 2.7 2.0 2.0 3.3 4.3 4.3 3.0 4.7 75.0 2.3 2.7 75.0 3.3 188 190 * 2.8 P 5.3 6.7 5.7 3.0 50.7 6.7 52.7 28.3 75.0 5.7 52.7 51.3 51.3 193 195 C 4.5 M 25.7 28.5 27.0 4.0 5.3 26.7 6.0 3.3 5.3 5.8 29.5 5.0 5.8 196 203 E 4.6 H 1.2 2.0 10.2 30.2 11.5 2.2 1.4 1.6 1.6 1.6 2.8 1.5 2.2 204 205 C 4.3 M 41.5 41.5 41.5 75.0 9.2 5.0 7.0 6.5 9.0 5.5 5.5 8.0 9.0 206 207 - 4.4 M 42.0 42.0 41.5 75.0 75.0 75.0 75.0 5.0 75.0 75.0 75.0 75.0 75.0 210 212 E 4.3 M 0.7 0.7 1.3 75.0 3.0 2.0 0.3 0.3 0.7 1.3 2.0 1.0 0.7 213 215 * 3.0 P 3.0 3.7 7.2 75.0 75.0 3.0 51.7 4.3 51.7 51.3 52.3 3.7 52.0 218 221 - 4.2 M 5.5 5.6 22.2 75.0 75.0 3.2 75.0 75.0 75.0 75.0 75.0 75.0 75.0 222 225 * 3.3 M 3.8 2.8 22.2 75.0 75.0 58.2 75.0 5.8 6.5 75.0 75.0 6.5 23.5 226 235 - 4.3 M 26.2 2.5 25.5 75.0 75.0 75.0 75.0 53.1 53.4 75.0 75.0 52.7 75.0 236 239 * 3.8 M 75.0 5.5 75.0 3.2 75.0 75.0 75.0 6.9 8.1 75.0 75.0 8.1 75.0 240 281 - 4.5 M 62.4 6.3 67.3 3.9 75.0 68.8 75.0 71.8 75.0 75.0 75.0 73.5 75.0 >>>>>>