Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1r1ma- ----------------------CCEEEEEEEEEHHHH---HCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHH-CCCCHHHEEEEECCCCCCCCHHHHHHHHHCCCCCCCCCHHHHHHHHHCHHH-CEEEEEEEEEC--- >P1;d2hqsc2 -----------------------------------CCEEECCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHH-CCCCHHHEEEEECCCCCCCCCCC--------------------CHHHHHHH-CEEEEEC------- >P1;d3oona1 -----------------CCEEEEECCEEEEEEE-----EECCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCC-CHHHHHHHHHHHHHHHC-CCCCHHHEEEEECCCCC--------------------------------CCEEEEEEEEEC----- >P1;d3td3a1 -----------------------CCCEEEEEEE----EEECCCCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHEEEEECCCCCCCCCCC--------------------CHHHHHHH-CEEEEEEEEEE--- >P1;d4rhaa- ------------------------CEEEEEEEEHHHH---CCCCCCCCCHHHHHHHHHHHHHHCC--CEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHH-HCCCHHHEEEEC-CCCCCCCCCCCCCCC------------HHHHHHHCHHH-CEEEEEEEECCCC- >P1;d4zhwa- ---------------------------------CCCCEEECCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHH-HCCCHHHEEEEECCCCCCCCCCC--------------------CHHHHHHH-CEEEEECCC----- >P1;d5wtpa1 CCCHHHHHHHHHHHC--CCCCC--------------------CCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHH-CCCCHHHEEEEEEECCCCCCCCC--------------------CHHHHHHH-CEEEEEEE------ >P1;d6jfwa1 C---HHHHHHHHHCCCCCCEEEEECCEEEEEEEHHHH---CCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHH-CCCCHHHEEEEECCCCCCCCCCC--------------------CHHHHHHH-CEEEEEEEEC---C >P1;d7rjja- --------------------------CCCEECC----CCCCCCCCCCCCCCCHHHHHHHC-CCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHC-CCCCCCCHHHEEEEECCCCCCCCCCC--------------------CHHHHHHH-CCEEEEEEEEEECC PSA >P1;d1r1ma- ----------------------782653325130560---0397627048705770580065059280450400000032389a7057105410610061037-28048940613020266182496056718974a936796267513820340-22000404025--- >P1;d2hqsc2 -----------------------------------c3303085662506a923a20481074057479550202000044885a703410540052025203a-49055a10425030266345958--------------------76901450-0001042------- >P1;d3oona1 -----------------9084974b50320304-----01056735801960392056027405748a37010100167869898-45202400520083038-81078920704031155--------------------------------b44250100028----- >P1;d3td3a1 -----------------------a855618170----502055762604981465046006408405906070100005567374047105500520251027639075920816020355433518--------------------69912440-10030505655--- >P1;d4rhaa- ------------------------6927615280550---06a6618027505720480276159--b35030101013497896047105700520062037-370678506060-1389351c9806b39------------a9423930450-1002023658bab- >P1;d4zhwa- ---------------------------------a46741306768290989348204610661377a3a4020100006689875047005500520030037-07057950234030367363619--------------------79a11440-10030432b----- >P1;d5wtpa1 508981274036206--60706--------------------b562813960382065007005626b040300000147b9697127103610430263038-58086a00505020156453629--------------------79912750-41020313------ >P1;d6jfwa1 a---80174059308b29060537c920200020930---0589429018905710540070047277160300000048976a6045306510710181037-48075a20724010147343728--------------------68903460-4000020744---a >P1;d7rjja- --------------------------992370b----2100678657139b07a406822-5158473210200000046a7887057103300320242-27608066800514020276342629--------------------57902460-10030202165a12 Translating the sequences ----------------------*******EE******---*CCCCCCCCHHHHHHHHHHHHHH**CC**EEEEEE*CCCCCCHHHHHHHHHHHHHHHHHHHHH-CCCCHHHEEEEECCCCCCCC************************HHH*HHH-CEEEEEEE***--- -----------------------------------*****CCCCCCCCCHHHHHHHHHHHHHH**CCC**EEEEE*CCCCCCHHHHHHHHHHHHHHHHHHHHH-CCCCHHHEEEEECCCCCCCCCCC--------------------CHHHHHHH-CEEEEE*------- -----------------************EE**-----**CCCCCCCCCHHHHHHHHHHHHHH**CCC**EEEEE*CCCCCC***-*HHHHHHHHHHHHHHH*-CCCCHHHEEEEECCCCC--------------------------------****EEEEEEE*----- -----------------------******EE**----***CCCCCCCCCHHHHHHHHHHHHHH**CCC*EEEEEE*CCCCCCHHHHHHHHHHHHHHHHHHHHH*CCCCHHHEEEEECCCCCCCCCCC--------------------CHHHHHHH-CEEEEEEE***--- ------------------------*****EE******---CCCCCCCCCHHHHHHHHHHHHHH**--C*EEEEEE*CCCCCCHHHHHHHHHHHHHHHHHHHHH-*CCCHHHEEEE*-CCCCCCCCCC*****------------****HHH*HHH-CEEEEEEE*****- ---------------------------------*******CCCCCCCCCHHHHHHHHHHHHHH**CCC**EEEEE*CCCCCCHHHHHHHHHHHHHHHHHHHHH-*CCCHHHEEEEECCCCCCCCCCC--------------------CHHHHHHH-CEEEEE***----- ***************--*****--------------------CCCCCCC**HHHHHHHHHHHH**CCC*EEEEEE*CCCCCCHHHHHHHHHHHHHHHHHHHHH-CCCCHHHEEEEE**CCCCCCCCC--------------------CHHHHHHH-CEEEEEEE------ *---*************************EE******---CCCCCCCCCHHHHHHHHHHHHHH**CCC*EEEEEE*CCCCCCHHHHHHHHHHHHHHHHHHHHH-CCCCHHHEEEEECCCCCCCCCCC--------------------CHHHHHHH-CEEEEEEE**---* --------------------------***EE**----***CCCCCCCCC***HHHHHHH*-****CCC*EEEEEE*CCCCCCHHHHHHHHHHHHHHHHH*-***CCCCHHHEEEEECCCCCCCCCCC--------------------CHHHHHHH-C*EEEEEE****** 103088.tem _________________________________ -----------------------******EE*********CCCCCCCCCHHHHHHHHHHHHHH**CCC*EEEEEE*CCCCCCHHHHHHHHHHHHHHHHHHHHH-CCCCHHHEEEEECCCCCCCCCCC--------------------CHHHHHHH-CEEEEEEE***--- Structural block scores 0 22 - 4.4 M 72.0 75.0 57.0 75.0 75.0 75.0 13.3 13.8 75.0 23 28 * 3.0 P 4.5 75.0 4.2 5.9 17.5 75.0 75.0 5.4 40.8 29 30 E 4.4 M 3.5 75.0 1.5 4.5 3.0 75.0 75.0 0.0 5.0 31 39 * 3.2 M 26.7 35.7 42.2 34.9 27.2 20.6 75.0 26.6 34.9 40 48 C 4.9 H 4.2 4.2 3.9 3.9 4.4 5.2 20.7 4.2 4.8 49 62 H 4.8 H 4.1 4.4 3.8 3.8 3.9 4.1 3.3 3.3 10.1 63 64 * 1.0 P 7.0 6.0 6.0 6.0 7.0 5.0 5.5 5.5 6.5 65 67 C 4.7 H 3.3 6.7 7.5 4.7 53.8 6.8 6.5 5.3 4.7 69 74 E 4.8 H 1.5 1.5 1.5 2.3 1.5 1.2 1.2 1.5 0.5 76 81 C 5.0 H 2.7 4.0 6.2 3.8 4.0 4.8 5.4 4.7 4.6 82 102 H 4.9 H 3.5 3.3 7.0 2.9 3.4 2.9 3.4 3.5 6.6 104 107 C 4.8 H 3.5 4.5 4.0 4.8 4.0 3.0 5.2 4.8 3.5 108 110 H 5.0 H 7.0 5.5 6.3 5.3 6.7 7.0 5.5 5.8 4.7 111 115 E 4.9 H 2.0 2.2 2.2 3.0 2.4 1.8 2.0 2.6 2.0 116 126 C 4.7 H 4.2 4.6 42.3 3.5 12.2 4.3 3.9 3.6 3.9 127 146 - 4.6 H 5.9 75.0 75.0 75.0 47.6 75.0 75.0 75.0 75.0 148 154 H 4.6 H 2.9 3.6 55.8 4.1 3.4 4.2 4.7 4.3 4.0 157 163 E 4.8 H 1.4 11.7 1.1 1.9 1.9 1.7 1.4 1.3 1.0 164 166 * 3.0 P 2.3 75.0 52.7 5.3 8.2 53.8 75.0 27.7 4.0 167 169 - 4.4 M 75.0 75.0 75.0 75.0 32.3 75.0 75.0 53.5 4.5 >>>>>>