Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ee8a2 CCHHHHHHHHHHHHHHHCCCEEE-EEECCCCC---CEE---C-HHHHC-CEEEEEEEEECCEEEEEECC---------CEEEEEECCCCCEEECC----CCCC-EEEEEEECC----CEEEEECCCCCCEEEEEECCCCCCCCHHHHC >P1;d1k3xa2 CCHHHHHHHHHHHHHHHCCCCCC-EEEECCH-------HHHHHHHHHC-CCCEEEEEEECCEEEEEECC---------CCEEEEECCCCCEEEEEECCCCCCCCEEEEEECCC----EEEEEECCC---EEEEECCCHHHHCHHHH-C >P1;d1k82a2 CCHHHHHHHHHHHHHHHCCCEEE-EEEECCCCCCCCCC---HHHHHCC-CEECCEEEEECCEEEEECCC----------CEEEEECCCCCEEEEECCCCCCCC-CCEEEEECC---CCEEEEECCCCCCEEEEECCC----CHHHCCC >P1;d1r2za2 CCHHHHHHHHHHHHHHHCCCCEE-EEEECCHHHEEECCCHHHHHHHHC-CCCCCEEEEECCEEEEEC-C---------CEEEEEECCCCCEEEEEECCCCCCC-EEEEEEECC---CEEEEEECCCCCCEEEEEEHHHHCCCCCCC-C >P1;d1tdza2 -CHHHHHHHHHHHC-CCCCCCCC-EEEECCC-CCC--CCHHHHHHHHC-CCCC-CEEEECCEEEEEECC---------CEEEEEECCCCC-CEEECCCCCCCC-EEEEEECCC----CEEEEECCCCCCEEEEEEHHHHHHHHHHC-C >P1;d5itqa1 CCHHHHHHHHHHHHHHHCCCCEEEECEEC-CCCCCC-------CCCCEEEEEEEEEEEECCEEEEEEEECCCCCCCCCCEEEEEECCCCEEEEEEEHHHCCCC-EEEEEECCCCCCCEEEEEEECCCCCEEEECCCCCC--------- PSA >P1;d1ee8a2 27666016227803630482206-50619179---204---7-08403-73505404155500001068---------60000030163030559----5185-120203036----4202010254503000065741850550572 >P1;d1k3xa2 67474037306702800563705-4030228-------7048229604-83404503049400001022---------9000002069503043162b773a36320202096----300000105---50400647429718407-7 >P1;d1k82a2 27566028217a045404a1304-50403417064502---7504806-73405304253510003028----------11000201630604007a573684-000002044---b31000203545000212a3d----8320383 >P1;d1r2za2 17565027226703560472306-306044560043167295027304-811053062565101020-4---------7000001046406061563aa3674-000001046---920000305435000100037407646204-3 >P1;d1tdza2 -8567026317705-70483604-4050945-005--45088049504-4450-40425551000306b---------711000115650-031184a29793-200102088----30000306544010102549619410894-3 >P1;d5itqa1 28476076205404520782300850402-b50a14-------7070506204050606b70020404129b0859285210002046204041153772293-00010102897862000010654505074729269--------- Translating the sequences CCHHHHHHHHHHHHHHHCCC*EE-EEE*CCC*---***---*-HHHHC-C****EEEEECCEEEEEECC---------CEEEEEECCCCCEEE**----CCCC-EEEEEE*CC----*EEEEECCCCCCEEEEE*CC****C*HH**C CCHHHHHHHHHHHHHHHCCCC**-EEEECC*-------***HHHHHHC-C****EEEEECCEEEEEECC---------C*EEEEECCCCCEEEEE*CCCCCCC*EEEEEE*CC----*EEEEECCC---EEEEE*CC****C*HH*-C CCHHHHHHHHHHHHHHHCCC*EE-EEEECCC*******---HHHHH*C-C****EEEEECCEEEEE*CC----------*EEEEECCCCCEEEEE*CCCCCCC-**EEEE*CC---**EEEEECCCCCCEEEEE*CC----C*HH**C CCHHHHHHHHHHHHHHHCCCCEE-EEEECC***********HHHHHHC-C****EEEEECCEEEEE*-C---------CEEEEEECCCCCEEEEE*CCCCCCC-EEEEEE*CC---**EEEEECCCCCCEEEEE*******C****-C -CHHHHHHHHHHH*-**CCCC**-EEEECCC-***--****HHHHHHC-C***-*EEEECCEEEEEECC---------CEEEEEECCCCC-*EEE*CCCCCCC-EEEEEE*CC----*EEEEECCCCCCEEEEE*********HH*-C CCHHHHHHHHHHHHHHHCCCCEE*E*EEC-C*****-------***********EEEEECCEEEEEE***********CEEEEEECCCC*EEEEE****CCCC-EEEEEE*CC*****EEEEE*CCCCCEEEE**CC**--------- 81624.tem _________________________________ CCHHHHHHHHHHHHHHHCCCCEE-EEEECCC**********HHHHHHC-C****EEEEECCEEEEEECC---------CEEEEEECCCCCEEEEE*CCCCCCC-EEEEEE*CC---**EEEEECCCCCCEEEEE*CC****C*HH*-C Structural block scores 0 1 C 4.8 H 4.5 6.5 4.5 4.0 41.5 5.0 2 16 H 4.9 H 3.7 3.4 4.0 3.7 8.7 3.5 17 20 C 4.8 H 4.0 5.2 4.6 4.0 5.2 5.0 21 22 E 4.1 M 3.0 2.5 2.0 3.0 2.0 0.0 24 27 E 4.8 H 3.0 1.8 2.2 2.2 2.2 2.2 28 30 C 4.5 M 5.7 4.0 2.7 4.3 6.0 29.5 31 40 * 3.0 P 46.5 53.6 24.9 3.8 24.7 39.5 41 46 H 4.4 M 15.7 4.5 4.0 2.8 4.3 27.3 50 53 * 1.2 P 3.2 2.8 3.0 1.8 21.0 1.5 54 58 E 4.9 H 2.8 2.4 2.8 3.2 3.0 3.4 59 60 C 5.0 H 5.0 6.5 4.0 5.5 5.0 9.2 61 66 E 4.9 H 0.2 0.2 0.7 0.7 0.7 1.0 67 68 C 4.3 M 7.0 2.0 5.0 39.5 8.8 2.5 69 77 - 4.5 M 75.0 75.0 75.0 75.0 75.0 6.1 79 84 E 4.9 H 0.5 0.3 0.7 0.2 0.5 0.8 85 89 C 4.9 H 2.0 4.0 2.0 2.8 3.4 2.4 90 94 E 4.6 H 4.4 2.2 2.0 3.6 16.0 2.0 96 102 C 4.7 H 34.9 6.3 6.2 6.3 6.4 4.7 104 109 E 4.8 H 1.3 1.5 0.3 0.2 0.8 0.3 111 112 C 5.0 H 4.5 7.5 4.0 5.0 8.0 5.0 113 115 - 4.5 M 75.0 75.0 75.0 75.0 75.0 8.0 116 117 * 2.2 P 39.5 39.0 7.2 5.5 39.0 4.0 118 122 E 5.0 H 1.0 0.0 0.6 0.6 0.6 0.2 123 128 C 4.7 H 2.7 38.5 2.8 2.8 3.2 3.3 129 133 E 4.9 H 0.6 1.8 1.0 0.2 0.8 4.6 135 136 C 4.1 M 6.0 5.5 8.2 5.0 6.5 5.5 137 140 * 2.3 P 4.5 5.5 75.0 4.2 5.0 41.2 143 144 H 4.2 M 2.5 2.0 1.0 1.0 8.5 75.0 >>>>>>