Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2pbdp- CCCHHHHH-HHHCCC----CEEEEEEEECCCCCEEEEECCCCCHHHCCHHHHHHHHC--CCCCHHHCCCEEECCEEEEEEEEECCCCCCCEEEEEECCCCCCCCCEEEEEECCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCC >P1;d3d9ya- -CHHHHHHCCCHHHC----CCCEEEEEEC--CCCCEEECC--CC-CCCHHHHHHHHHHHHCCCHHHHHCEEECCEEE-CCEEC-C----CEEEEEEC------CEEEEEEECCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHCC >P1;d4qwoa1 CHHHHHHH-HHHCCC----CCCCCEEEECCCCCCEEEECCCCCHHHCCHHHHHHHHH---CCCCC---CCEECCEEEEEEEEECC-CCCCE-EEEECC---CCCCEEEEEECCCEEEEE-CCCCCCHHHHHHHHHHHHHHHHCCCC >P1;d5em0a1 -CHHHHHHHHCCCHHHCCCCCCEEEEEEC--CCCEEEECC--CCCCCCHHHHHHHHHHHHCCCCCCCCCEEECCEEEEEEEEECC----CEEEEEEC------CEEEEEEECCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCC PSA >P1;d2pbdp- 992a5208-802767----202000000147667110018c42037059a1185026--a72870598004009350505602036ab5010104023acb6522100002062000000057c2937501710461024037594 >P1;d3d9ya- -9255205830273a----4053000003--80763140b--70-a05691069006007717505b710501a550-04506-7----40010638------840000000650000010278085830183027107604a475 >P1;d4qwoa1 a6276006-60575b----506100001058817220017a5102605590054027---6aa07---60500555051353516-7a300-004014---876110000104400000-044a0666203630240056018786 >P1;d5em0a1 -7346305840240785745050000003--81622041a--603a2589006402600874940777104005440734a1675----4001055b------70000002085000000058606593023002700650485a3 Translating the sequences *C*HHHHH-H*HC*C----C**EEEEEEC**CC*EEEECC**C***CCHHHHHHHH*--*CCC*****CEEECCEEEEEEEEECC****CEEEEEEC******C*EEEEEECCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCC -CHHHHHH***H**C----CCCEEEEEEC--CCC*EEECC--C*-*CCHHHHHHHHH***CCC*****CEEECCEEE-**EE*-C----CEEEEEEC------C*EEEEEECCCEEEEEEECCCCCHHHHHHHHHHHHHHHHH*CC **HHHHHH-H*HC*C----CCC**EEEEC**CCCEEEECC**C***CCHHHHHHHHH---CCC**---C*EECCEEEEEEEEECC-***CE-EEEEC*---**C*EEEEEECCCEEEEE-*CCCCCHHHHHHHHHHHHHHHH*CCC -CHHHHHH*H**C******CCCEEEEEEC--CCCEEEECC--C***CCHHHHHHHHH***CCC*****CEEECCEEEEEEEEECC----CEEEEEEC------C*EEEEEECCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCC 55770.tem _________________________________ *CHHHHHH*H*HC*C----CCCEEEEEEC**CCCEEEECC**C***CCHHHHHHHHH***CCC*****CEEECCEEEEEEEEECC-***CEEEEEEC*---**C*EEEEEECCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCC Structural block scores 2 7 H 4.9 H 4.6 3.2 3.5 3.5 15 18 - 4.3 M 75.0 75.0 75.0 6.0 19 21 C 4.5 M 1.3 3.0 3.7 3.3 22 27 E 4.8 H 0.0 0.5 0.3 0.0 29 30 * 3.5 M 5.5 75.0 6.5 75.0 31 33 C 4.8 H 6.3 5.0 5.3 5.0 34 37 E 4.8 H 0.5 3.5 1.0 2.0 38 39 C 5.0 H 4.5 5.8 4.0 5.8 40 41 * 3.5 M 8.2 75.0 7.8 75.0 43 45 * 1.4 P 3.3 28.5 2.7 4.5 46 47 C 5.0 H 2.5 2.5 2.5 3.5 48 56 H 4.9 H 4.7 4.1 3.6 3.9 57 59 * 3.1 M 53.5 2.3 75.0 2.7 60 62 C 5.0 H 5.7 5.0 9.0 6.7 63 67 * 1.8 P 5.8 5.7 46.4 5.0 69 71 E 4.8 H 1.3 1.7 1.7 1.3 72 73 C 5.0 H 4.5 5.8 2.5 2.5 74 82 E 4.7 H 2.9 11.1 3.6 4.4 83 84 C 4.7 H 1.5 41.0 3.5 6.0 86 88 * 3.5 M 9.0 75.0 6.8 75.0 90 95 E 4.9 H 1.0 1.7 13.2 1.8 98 100 - 4.3 M 11.5 75.0 75.0 75.0 101 102 * 3.5 M 5.5 75.0 7.5 75.0 105 110 E 5.0 H 0.5 0.0 0.3 0.3 111 113 C 5.0 H 2.7 3.7 2.7 4.3 114 120 E 4.8 H 0.0 0.1 10.7 0.0 121 125 C 5.0 H 7.1 5.0 4.9 5.0 126 142 H 5.0 H 3.0 3.9 3.1 3.2 143 145 C 4.8 H 6.0 5.3 7.0 6.2 >>>>>>