Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1cb8a2 -CEEEEECCCEEEEEECCCCEEEEEECCCEEEEECCEEEEECCCEEEEEECCC--CCEEEEECCCC--------CCCEEEEEEE-EC-------------CC-CCEEEEEEECCCHHHCCCCEEC------ >P1;d1egua2 C-CEEEECCCEEEEEECCCCEEEEEECCCCCEEECC-CEEECCCEEEEEEEEC-CEEEEEEECCCCCCCCCHHHHEECC---------------------------------------------------- >P1;d1f1sa3 CEEEEEECCCEEEEEECCCCEEEEEECCCCCEEECC-CEEECCCEEEEEEEEC-CEEEEEEEECCCCEEEECCCC-------------------------------------------------------- >P1;d1hn0a3 -CEEEEECCCEEEEEECCCCEEEEEECCCEECCC-CCEEEECCCEEEEEEECC-CCEEEEEECCCCCCCCCCCCCCEEEEEEEC-CCEEECCCCCCCEEEEE-CCEEEEEEEEC----CCCCEEEEEEECC >P1;d1rwaa2 CEEEEEECCCEEEEEECCCCEEEEEECC--CEEEC--CEEECCCEEEEEEEEC-CEEEEEEECCCCCCC--------EEEEECCCCCCCEEEECC-CEEEECCCCCEEEEEECC--CCCCCCEEEEEEC-- >P1;d1x1ia2 CCEEECCCCCEEEEEECCCCEEEEEECCCCCEEEC--CEEECCCEEEEEEEECCCEEEEEEECCCCCCC-------CEEEEEEC-CCEEEEEECCCEEEEECC-CCEEEEEECC--CCCCCEEEEEEEEC- PSA >P1;d1cb8a2 -6660377b61404037863106040554660503812040532020303605--a1402020556--------7173040205-44-------------85-2819636080239872154250------ >P1;d1egua2 b-762464941407257a63107030647751503a-402023404060436c-a81407051467776154750067b---------------------------------------------------- >P1;d1f1sa3 65653364b31204236654204050547770406a-306065305060426c-b825040434948654763a2-------------------------------------------------------- >P1;d1hn0a3 -7533375920406245a57304030664260a0-81045034505050335a-810202010584436aa7906415040103-74040258b29083625-c9303020506----507636040344a >P1;d1rwaa2 6756237681050445796821304066--66308--600052405050147b-730403010355947--------50301004a706512668-281863a77401050807--b361742802045-- >P1;d1x1ia2 a6576177b21405229854302040556762503--0020334030504339a640303010444728-------83040405-340533804930606425-8304030607--9071661403060f- Translating the sequences -*EEEEECCCEEEEEECCCCEEEEEECCC**EEECC**EEECCCEEEEEE**C--**EEEEECCCC--------***EEEEE**-*C-------------**-*C*EEEEEE*C****CCC*EE*------ C-*EEEECCCEEEEEECCCCEEEEEECCC*CEEECC-CEEECCCEEEEEEEEC-CEEEEEEECCCCCCC**********---------------------------------------------------- C*EEEEECCCEEEEEECCCCEEEEEECCC*CEEECC-CEEECCCEEEEEEEEC-CEEEEEEE*CCCC********-------------------------------------------------------- -*EEEEECCCEEEEEECCCCEEEEEECCC*****-C**EEECCCEEEEEEE*C-C*EEEEEECCCCCCC********EEEEE**-*C***************-*C*EEEEEE*C----CCC*EE******* C*EEEEECCCEEEEEECCCCEEEEEECC--CEEEC--CEEECCCEEEEEEEEC-CEEEEEEECCCCCCC--------EEEEE****C********-********C*EEEEEE*C--**CCC*EE*****-- C*EEE**CCCEEEEEECCCCEEEEEECCC*CEEEC--CEEECCCEEEEEEEEC*CEEEEEEECCCCCCC-------*EEEEE**-*C****************-C*EEEEEE*C--**CCC*EE******- 49863.tem _________________________________ C*EEEEECCCEEEEEECCCCEEEEEECCC*CEEECC-CEEECCCEEEEEEEEC-CEEEEEEECCCCCCC********EEEEE**-*C********-******-*C*EEEEEE*C--**CCC*EE*****-- Structural block scores 2 6 E 4.7 H 4.4 5.0 4.6 4.2 4.6 5.2 7 9 C 5.0 H 8.2 5.7 6.2 5.3 5.0 6.8 10 15 E 5.0 H 2.0 3.2 2.0 2.7 3.0 2.3 16 19 C 5.0 H 6.0 6.6 5.2 6.9 7.5 6.5 20 25 E 5.0 H 1.8 1.8 1.8 1.7 1.7 1.5 26 28 C 4.8 H 4.7 5.7 5.3 5.3 29.0 5.3 31 33 E 4.5 M 1.7 2.0 1.3 3.5 3.0 2.3 34 35 C 4.4 M 5.5 6.8 8.2 41.5 41.5 39.0 38 40 E 5.0 H 1.3 0.7 2.0 3.0 0.0 0.7 41 43 C 5.0 H 3.3 3.0 4.7 4.0 3.7 3.3 44 51 E 4.8 H 1.8 2.9 2.9 2.6 2.8 2.2 55 61 E 4.8 H 2.8 3.6 3.3 0.9 1.6 1.6 62 68 C 4.6 H 34.4 5.4 5.6 4.3 4.7 4.1 69 76 * 3.2 M 48.8 3.5 22.8 6.0 75.0 66.6 77 81 E 4.3 M 1.8 48.7 75.0 2.0 1.8 2.2 82 83 * 2.7 P 2.5 75.0 75.0 1.5 0.0 2.5 87 94 * 3.4 M 75.0 75.0 75.0 4.1 4.2 4.0 96 101 * 3.2 M 52.2 75.0 75.0 4.0 4.7 3.0 106 111 E 4.3 M 5.3 75.0 75.0 1.7 2.3 2.2 114 115 - 4.5 M 6.0 75.0 75.0 75.0 75.0 75.0 116 117 * 3.4 M 7.5 75.0 75.0 75.0 7.2 4.5 118 120 C 4.3 M 2.7 75.0 75.0 4.0 4.7 4.7 122 123 E 4.3 M 3.5 75.0 75.0 4.5 5.0 2.5 124 128 * 3.3 M 60.0 75.0 75.0 2.2 2.2 1.8 129 130 - 4.3 M 75.0 75.0 75.0 7.2 75.0 48.8 >>>>>>