Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2a90a1 ------------------CCCCCCCEEEEC-----CEEEECCHHHHHHHHHHHHCCCCEEC---CCCCCCCCCCEEECCC-CEECC-----CCCEECCCCCCCHHHHCC---- >P1;d2a90a2 -----------------------CEEEECCCCCCCCCEEECC-CHHHHHHHHHHCCCCEEE--HHHHCCCC-CEEEECCCCEEEECC--CCCCCEEECCCC------CCCCCC >P1;d2rsfa1 CCCCCCCCCHHHHHHHHHHCCCCEEEEECC-----CCEEECCCCCHHHHHHHHHHCCCEEEEECC----CC-EEEEECCCCEEECCCCCCCCEEEEEECCCCCCCCC------ PSA >P1;d2a90a1 ------------------a94411002439-----a7346069700720370478854700---47148829a3302067-40629-----a240535564926406a7---- >P1;d2a90a2 -----------------------200200689a29a514609-70273046045594a613--038313c3-422040865404529--816430443b39------888a7a >P1;d2rsfa1 ba8983626794487269556360024518-----b8365077811540230245246514073a----75-31100048210246d2878554032434936a968------ Translating the sequences ------------------*CCCCC*EEE*C-----C*EEECC**HHHHHHHHHHCCCCEE*---C**CCCC*C*EEECCC-*EECC-----CCCEE*CCCCCC****CC---- -----------------------CEEEECC*****CCEEECC-CHHHHHHHHHHCCCCEEE--****CCCC-CEEEECCCCEEE*CC--CCCCCEEECCCC------CC**** *******************CCCC*EEEECC-----CCEEECC*C*HHHHHHHHH*CCCEEE***C----CC-*EEEECCCCEEECCC**CCC**EEE*CCCCC****------ 117839.tem _________________________________ ------------------*CCCCCEEEECC-----CCEEECC*CHHHHHHHHHHCCCCEEE--*C**CCCC-CEEEECCCCEEECCC--CCCCCEEECCCCCC****CC---- Structural block scores 0 17 - 4.0 M 75.0 75.0 6.7 19 23 C 4.0 M 3.8 60.4 4.0 24 27 E 4.8 H 1.5 0.5 2.8 28 29 C 4.5 M 6.0 3.0 4.5 30 34 - 4.0 M 75.0 7.7 75.0 35 36 C 4.5 M 8.8 7.8 9.8 37 39 E 5.0 H 4.3 3.7 4.7 40 41 C 5.0 H 3.0 4.5 3.5 44 53 H 4.9 H 3.0 3.1 2.2 54 57 C 4.8 H 6.2 7.1 4.2 58 60 E 4.7 H 2.3 3.3 3.3 61 62 - 4.0 M 75.0 75.0 3.5 65 66 * 2.7 P 4.0 5.5 75.0 67 70 C 4.5 M 5.5 4.9 40.5 73 76 E 4.8 H 2.0 2.0 0.5 77 80 C 4.8 H 22.0 4.8 3.5 81 83 E 4.7 H 3.3 2.7 1.0 84 86 C 4.3 M 28.7 5.3 7.8 87 88 - 4.0 M 75.0 75.0 5.0 89 93 C 4.2 M 33.3 4.4 5.8 94 96 E 4.7 H 2.7 2.7 1.7 97 102 C 4.5 M 5.2 29.4 4.8 103 106 * 2.7 P 4.0 75.0 8.4 107 108 C 4.0 M 8.8 8.0 75.0 109 112 - 4.0 M 75.0 9.0 75.0 >>>>>>