Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1c9fa- ---------------------------CCCCCCCCEEEEEEECCCCCCCEEEEC-------CHHHHHHHHHHHCCCCCC------CEEEEECC---CCEEECCCCCC-CCC---------------CCEEEEEEECCCCCCCCCCC------ >P1;d1d4ba1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCEEEEEEC-------CCCCHHHHHHHHHCCCCC-------CEEEECC---CCEEECCCHHHHHCC---------------CCCCCCEECCCCCCCC----CCCCCC >P1;d1f2ri- -----------------CCCCCCCCCCCCCCCCCCEEEEEEECCEEEEEEEEEC-------CHHHHHHHHHHHHCCC----HHHCCCEEEECC---CCCCCCCCCCCCCCC---------------CCCEEEEECC------CCCCCCCCCC >P1;d1ip9a1 ----------------------------CCCCCCCEEEEECCCC--CCEEEEECC----CCCHHHHHHHHHHHHCCC------CE-EEEECCCC-CCCCCCCCHHHHHHHHH--------------CCCCEEEEEC---------------- >P1;d1oeya1 -----------------------------------CEEEEECC---CEECCCC-----CCCCHHHHH-CCCCCCCCC----HHHC-CEEECCCCCCCCEEC-CCCC-CCCHHHCC----------CCEEEEEECC----------------- >P1;d1oeyj- -------------------------------CCEEEEEEEEECCEEEEEEEEECCCCCCCCCHHHHHHHHHHHHCC------CCE-EEEEECCC-CCEEECCCHHHHHC-CCCCC---CCCCCCCCCCCCEEEEEC------CCC-CCCCCC >P1;d1pqsa- ---------------------------------------------CCEEEEECCC----CCCCHHHHHHHHHHCCCCCCCCCCCCCCCEEEECC-CEEEECCCCHHHHHHHHHHHHHC---------CCEEEEECC---------------- >P1;d1wmha- ----------------------------------CEEEEEEEC-C-EEEEEEEC-----CCCHHHHHHHHHHHCCCC----CCCC-EEEEECCC-CCEEECCCHHHHHHHHHHHHHCCC-------CCEEEEEEC----------------- >P1;d1wmhb- ----------------------------------CEEEEEEEC-C-EEEEEEEC--HHHCCCHHHHHHHHHHHCCCC----CCCC-EEEEECCC-CCEEECCCHHHHHHHCCCC----C-------CCEEEEEECC---------------- >P1;d2bkfa1 -------------------------------CCCCEEEEEEEC-C-EEEEEEEC--CHHHCCHHHHHHHHHHHHCCC------CE-EEEEECCC-CCEEEECCHHHHHHHHHHHHHCC--------CEEEEEEEEC---------------- >P1;d2c60a1 ---------------------------------CCEEEEEECCC---CEEEEECC----CC-CHHHHHHHHHHHCC-------CC-EEEECCC---CCEECCCHHHHCCHHHHHHCC--------CCCEEEEEEC----------------- >P1;d2npta1 --------------------------CCCCCCCCCEEEEEEEC-CCEEEEEEEC-------CHHHHHHHHHHHCC------CCCCCEEEEECCC-CCEEEECCHHHHHHHHHHHHHHHCCHHHCCCCCEEEEEEC----------------- >P1;d4d2ka1 ------------------------------C--CCEEEEEEECCCCCEEEEEEC-------CHHHHHHHHHHHCCCC----CC-CCCEEEECC---CCCEECCHHHHHCCC---------------CCCEEEEECC------CCCC------ >P1;d4maca- ------------------------------CCCCCEEEEEECCCCCCEEEEEEC-------CHHHHHHHHHHHHCCC----C--CCCEEEECC---CCCEECCHHHHHHCC---------------CCCEEEEECC------CCCCCCC--- PSA >P1;d1c9fa- ---------------------------9b3a68752303020355a74421525-------619600750277190678------70500037---60671506607-606---------------8403001028b2a191699c------ >P1;d1d4ba1 ab9998a966a7a89b8bc997bb4998b7756876626041479877437615-------37a81463007219a7bb-------1610045---72460978604830a---------------a4220002a8b28357----b7abd6 >P1;d1f2ri- -----------------9a9a199849946953571302014195874250502-------4195037403930808----992180200016---806607558600937---------------6804000007------915315a97c >P1;d1ip9a1 ----------------------------cc9b89317040216b--831314062----903175048302650939------80-40002389-83164058694055009--------------5534000446---------------- >P1;d1oeya1 -----------------------------------33130317---6425a09-----462615503-400860927----4760-603042893b83470-58a2-a6019219----------9720203079----------------- >P1;d1oeyj- -------------------------------8313030210963918443051a7729542619504720583194------740-10014268-630420766a3056-28308---5a87b8520313000035------617-70188d >P1;d1pqsa- ---------------------------------------------8661516086----80929402620165258998b1a205940100046-8734505838204701720886b---------444000303---------------- >P1;d1wmha- ----------------------------------704030417-6-84221405-----b35285016302810909----c4a0-40312277-764440655940650062067394-------a20302052----------------- >P1;d1wmhb- ----------------------------------714020416-a-45352416--4a5062296008402620817----b380-90103258-7754706677007600815----8-------6105030539---------------- >P1;d2bkfa1 -------------------------------615502020217-b-56341618--505825096026303920a0a------80-40314258-8744105649505600700464a--------440504056f---------------- >P1;d2c60a1 ---------------------------------a5040302197---55314183----90-18905840462095-------70-6021599---74740664930601661485b--------a810503057----------------- >P1;d2npta1 --------------------------b8898761703030406-b592542521-------51740262067225------9590600106177-5744205548506701731275053587a72910402049----------------- >P1;d4d2ka1 ------------------------------a--b61304012093855470601-------6182036501740a06----9a-280400127---604306528506709---------------7532000038------a494------ >P1;d4maca- ------------------------------628811405001161745480504-------1192027404a40908----8--808200118---505608518402817---------------7622000009------8482775--- Translating the sequences ---------------------------*******CEEEEEE*C******EEEEC-------CHHHHHHHHHHH*CCC**------**EEEECC---C*EE*CC****-***---------------CC*EEEEE*C**********------ **********************************CEEEEEE*C****EEEEEEC-------C***HHHHHHHH*CCC**-------*EEEECC---C*EE*CC*HHHH***---------------CC****EECC******----****** -----------------*****************CEEEEEE*C****EEEEEEC-------CHHHHHHHHHHH*CCC----******EEEECC---C****CC********---------------CC*EEEEECC------********** ----------------------------******CEEEEE**C*--**EEEEEC*----**CHHHHHHHHHHH*CCC------**-*EEE*CC*-*C****CC*HHHH****--------------CC**EEEE*C---------------- -----------------------------------*EEEEE*C---*EE****-----***CHHHHH-******CCC----****-*EEE*CC***C*EE*-C***-********----------*C**EEEE*C----------------- -------------------------------****EEEEEE*C****EEEEEEC*******CHHHHHHHHHHH*CC------***-*EEEECC*-*C*EE*CC*HHHH*-*****---********CC**EEEE*C------***-****** ---------------------------------------------**EEEEE*C*----**C*HHHHHHHHHH*CCC***********EEE*C*-***EE*CC*HHHH**********---------C*EEEEECC---------------- ----------------------------------CEEEEEE*C-*-*EEEEEEC-----**CHHHHHHHHHHH*CCC----****-*EEEECC*-*C*EE*CC*HHHH***********-------CC*EEEEEC----------------- ----------------------------------CEEEEEE*C-*-*EEEEEEC--*****CHHHHHHHHHHH*CCC----****-*EEEECC*-*C*EE*CC*HHHH******----*-------CC*EEEEECC---------------- -------------------------------***CEEEEEE*C-*-*EEEEEEC--*****CHHHHHHHHHHH*CCC------**-*EEEECC*-*C*EE*CC*HHHH**********--------C**EEEEE*C---------------- ---------------------------------*CEEEEEE*C*---*EEEEEC*----**-*HHHHHHHHHH*CC-------**-*EEE*CC---C*EE*CC*HHH**********--------*CC*EEEEEC----------------- --------------------------********CEEEEEE*C-***EEEEEEC-------CHHHHHHHHHHH*C------******EEEECC*-*C*EE*CC*HHHH******************CC*EEEEEC----------------- ------------------------------*--*CEEEEEE*C****EEEEEEC-------CHHHHHHHHHHH*CCC----**-***EEEECC---C**E*CC*HHHH***---------------CC*EEEEECC------****------ ------------------------------****CEEEEEE*C****EEEEEEC-------CHHHHHHHHHHH*CCC----*--***EEEECC---C**E*CC*HHHH***---------------CC*EEEEECC------*******--- 54277.tem _________________________________ ----------------------------******CEEEEEE*C****EEEEEEC-----**CHHHHHHHHHHH*CCC----******EEEECC*-*C*EE*CC*HHHH*********---------CC*EEEEECC------***------- Structural block scores 0 27 - 4.7 H 72.6 9.1 48.7 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 70.3 75.0 75.0 28 33 * 3.3 M 7.7 7.4 5.3 10.4 75.0 39.5 75.0 75.0 75.0 39.5 64.2 6.5 53.7 29.0 35 40 E 4.7 H 1.7 4.0 1.2 2.3 2.2 1.0 75.0 1.8 1.8 1.0 1.5 1.7 1.5 1.7 43 46 * 2.5 P 6.9 7.8 7.2 42.4 57.8 5.2 41.0 41.0 41.1 41.6 58.0 25.1 6.2 4.5 47 52 E 4.7 H 3.0 4.7 2.7 2.0 5.1 2.8 3.2 2.2 3.3 3.5 3.2 3.3 3.7 3.7 54 58 - 4.4 M 75.0 75.0 75.0 60.4 60.8 6.0 61.2 75.0 33.9 32.0 60.6 75.0 75.0 75.0 59 60 * 3.1 M 75.0 75.0 75.0 4.5 4.0 3.0 4.0 7.2 3.0 5.0 4.5 75.0 75.0 75.0 62 72 H 4.8 H 4.0 4.4 4.0 3.7 9.7 4.0 3.4 3.3 3.5 3.6 4.3 3.4 3.4 4.0 74 76 C 4.8 H 5.0 8.8 5.3 7.0 6.0 29.3 7.3 6.0 5.3 7.0 29.7 51.7 5.5 5.7 77 80 - 4.6 H 41.2 43.2 75.0 75.0 75.0 75.0 7.4 75.0 75.0 75.0 75.0 75.0 75.0 75.0 81 86 * 2.5 P 51.2 62.7 4.8 39.5 16.3 27.0 5.1 17.7 17.8 39.5 39.7 4.8 17.4 29.0 87 90 E 4.8 H 1.2 1.8 0.5 0.5 1.8 1.2 0.2 1.5 1.0 2.0 2.0 1.8 1.2 0.8 91 92 C 4.9 H 5.0 4.5 3.5 5.5 5.0 4.0 2.0 4.5 3.5 3.5 9.0 4.0 4.5 4.5 98 99 E 4.4 M 6.5 5.0 6.0 5.0 5.5 3.0 4.5 4.0 5.5 2.5 5.5 3.0 3.5 5.5 101 102 C 4.9 H 2.5 8.0 6.0 6.5 40.0 6.5 6.5 5.5 6.0 5.5 6.0 5.0 5.5 6.5 104 107 H 4.4 M 22.0 4.5 3.5 4.5 24.5 4.6 3.5 4.8 3.5 4.8 4.5 4.8 4.8 3.5 108 116 * 2.6 P 51.3 51.5 52.1 43.2 19.8 28.0 4.3 3.2 27.2 3.0 4.7 3.7 51.8 51.8 117 125 - 4.5 M 75.0 75.0 75.0 75.0 67.7 14.7 67.9 59.8 67.6 67.8 67.8 5.3 75.0 75.0 126 127 C 4.7 H 6.0 7.2 7.0 5.0 4.5 1.5 39.5 6.2 3.5 4.0 4.5 5.0 6.0 6.5 129 133 E 4.8 H 0.8 0.8 0.8 1.6 2.4 0.6 1.4 2.0 2.6 2.8 2.6 2.0 0.4 0.4 134 135 C 4.3 M 5.0 9.2 3.5 5.0 42.0 4.0 1.5 38.5 6.0 14.2 41.0 42.0 5.5 4.5 136 141 - 4.6 H 5.8 6.1 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 142 144 * 3.9 M 8.0 75.0 5.0 75.0 75.0 4.7 75.0 75.0 75.0 75.0 75.0 75.0 7.8 6.7 145 151 - 4.3 M 66.1 19.3 6.9 75.0 75.0 16.1 75.0 75.0 75.0 75.0 75.0 75.0 64.9 35.1 >>>>>>