Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2w6ka1 CCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCHHHCCEEEEECCCCCCHHHHHHHHHHCCCEEEECHHHHHHHH-HHCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHCCCEEECCCCEECCCEEEEEEEECCCC >P1;d3by5a1 ------CCEEEEEECCCCCHHHHHHHHHHHHHHHCCC---CCEEEECCCCCCCHHHHHHHHHCCCCEEECCHHHHHHHH-HHCCC-CHHHCCCCCCCCHHHHHHHHHHCC----CCCCCCCCEEECCEEEEEECCC--- >P1;d3eeqa1 ------CEEEEEECC-CCCHHHHHHHHHHHHHHHCCC-CCEEEEEECC-----HHHC-CHHHHCCEEEECCHHHHHCCCCCCCCCCC---------CCHHHHHHHHHHC------CCCCEEEEE--CCEEEEEECC--- PSA >P1;d2w6ka1 b945771000003058b05074046103600853a37285050000159a38151057019409250421549307702-7205263a5167528010100000000014409960300561444b6020000313258 >P1;d3by5a1 ------6300005164716385027005301751a29---053000233564672066007709170440769407503-8606a-57a1054ab80671000000006a----90504076233c802000006a--- >P1;d3eeqa1 ------500000008-906254036004700961a18-5501000013-----6605-00750a17045078931882728713798---------b720000001008------b00315338--1030000524--- Translating the sequences ******CEEEEEEECCCCCHHHHHHHHHHHHHH*CCC***CCEEEE*CCCCCCHHHHHHHHHHCCCEEE*CHHHHHHHH-HHCCCCCHHH****CCCCHHHHHHHHHH******C***CCCCEE*CCEEEEEEE*C*** ------C*EEEEEECCCCCHHHHHHHHHHHHHHHCCC---CCEEEECCCCCCCHHHHHHHHH*CCCEEECCHHHHHHHH-HHCCC-CHHH****CCCCHHHHHHHHHHC*----CCCCCCCCEE*CCEEEEEE*CC--- ------CEEEEEE*C-CCCHHHHHHHHHHHHHHHCCC-****EEEECC-----HHH*-*HHHHCC*EEECCHHHHH******CCCCC---------CCHHHHHHHHHHC------CCCC***EE--C*EEEEEECC--- 159664.tem _________________________________ ------CEEEEEEECCCCCHHHHHHHHHHHHHHHCCC-**CCEEEECCCCCCCHHHHHHHHHHCCCEEECCHHHHHHHH-HHCCCCCHHH****CCCCHHHHHHHHHHC*----CCCCCCCCEE*CCEEEEEEECC--- Structural block scores 0 5 - 4.0 M 7.2 75.0 75.0 7 13 E 4.7 H 0.4 1.3 0.0 14 18 C 4.8 H 5.9 4.8 19.6 19 33 H 4.9 H 3.1 3.1 3.1 34 36 C 5.0 H 6.8 7.2 6.5 38 39 * 2.7 P 6.5 75.0 5.0 40 41 C 4.0 M 2.5 2.5 0.5 42 45 E 5.0 H 0.0 0.8 0.0 46 52 C 4.1 M 5.4 4.1 54.1 53 62 H 4.6 H 3.2 3.5 10.4 63 65 C 4.7 H 5.3 5.7 6.2 66 68 E 5.0 H 2.0 2.7 3.0 69 70 C 4.5 M 3.0 3.5 3.5 71 78 H 4.6 H 4.0 4.2 5.8 80 81 H 4.0 M 4.5 7.0 7.5 82 86 C 4.8 H 3.2 19.3 5.6 87 89 H 4.0 M 5.5 6.2 75.0 90 93 * 2.7 P 5.0 4.9 75.0 94 97 C 4.5 M 2.2 6.4 42.1 98 107 H 5.0 H 0.1 0.8 0.3 110 113 - 4.0 M 5.5 75.0 75.0 114 121 C 4.1 M 2.6 3.9 12.3 122 123 E 5.0 H 4.0 2.5 5.5 125 126 C 4.5 M 8.8 10.2 38.0 127 133 E 4.7 H 0.7 0.3 1.1 134 135 C 4.5 M 2.0 8.2 3.0 136 138 - 4.0 M 5.0 75.0 75.0 >>>>>>