Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1hlqa- -----CCC--CCCCCCHHHHHCCCCCCHHHCCCCCCCCCC---CCCCHHHCCCCCCC--CCCEECCC--CCCC-CCEECCCCCCCCCCCC- >P1;d1hpia- --------CEECCCCCHHHHHCCCCCCHHHCC---CCCCC---CCCCHHHCCCCCCCCCC-CEEECC--CCCC-EEEECCCCCCCCCCC-- >P1;d1isua- ------------CCCHHHHHHCCCCCCC-CC-------------CCCHHHCCCEECCCCCCCCCEEC--CCCCCCCCCCCCCCCCCCCCC- >P1;d2hipa- --------CCCCCCC----CCCCCCCCHHHHC--CCCCCC---CCCCHHHCCCEEEEEE-CCEEEECCHHHCC-CCEECCCCCCCCCCCC- >P1;d3h31a- CCCCCCCCCCCCHHHHHHHHHCCCCCCCCCC-------------CCCHHHCCCEECCCCCCCCCEEC--CCC--CCCCCCCCCCCCCCCCC >P1;d5d8va- -----CCCCCCCCCCCHHHHHHCCCCCHHHCCHHHHCCCCCCHHHCCHHHCCCEEEEEEECCEEEEC--CCCC-CCEECCCCCCCCCCCCC PSA >P1;d1hlqa- -----737--506583a6068340142057066a726a06---6a211451340629--b5841414--40ac-310217001341486b- >P1;d1hpia- --------47607393860682503360860a---29718---9b131361530555928-830416--4087-230008001231564-- >P1;d1isua- ------------a338932953804882-59-------------a441371430663a599441317--206c0860417000531666a- >P1;d2hipa- --------5770a57----3236013617617--c27808---9a12155043158536-a720616175068-100215001130473b- >P1;d3h31a- aa2706839b188933760782803090449-------------84215516106719499610517--406--3201380114414558d >P1;d5d8va- -----b22b70089928507726066408706077364763626603134143157d52a9511007--207c-4101270013306557f Translating the sequences -----***--CCCCC*HHHHHCCCCCCHHHCC****CCCC---*CCCHHHCCC**CC--CCCEE**C--CCCC-CCEECCCCCCCCCCCC- --------C**CCCC*HHHHHCCCCCCHHHCC---*CCCC---*CCCHHHCCC**CC**C-CEEE*C--CCCC-**EECCCCCCCCCCC-- ------------CCC*HHHHHCCCCCC*-*C-------------CCCHHHCCCEECC**CCC**EEC--CCCC*CC**CCCCCCCCCCCC- --------C*CCCCC----**CCCCCCHHH*C--**CCCC---*CCCHHHCCCEE****-CCEEEEC****CC-CCEECCCCCCCCCCCC- ********C*CC****HHHHHCCCCCC***C-------------CCCHHHCCCEECC**CCC**EEC--CCC--CC**CCCCCCCCCCCC* -----***C*CCCCC*HHHHH*CCCCCHHHCC****CCCC*****CCHHHCCCEE*****CCEEEEC--CCCC-CCEECCCCCCCCCCCC* 57652.tem _________________________________ -----***C*CCCCC*HHHHHCCCCCCHHHCC--**CCCC---*CCCHHHCCCEECC**CCCEEEEC--CCCC-CCEECCCCCCCCCCCC- Structural block scores 0 4 - 4.5 M 75.0 75.0 75.0 75.0 6.0 75.0 5 7 * 3.4 M 5.7 75.0 75.0 75.0 5.7 5.2 10 14 C 4.4 M 4.8 5.0 33.3 5.9 5.8 5.2 16 20 H 4.5 M 6.1 5.6 5.6 46.0 5.6 5.4 21 26 C 4.9 H 2.3 3.2 5.2 3.2 3.7 4.0 27 29 H 4.1 M 4.0 4.7 27.3 4.7 2.7 5.0 30 31 C 4.4 M 3.0 5.2 42.0 4.0 42.0 3.0 32 33 - 4.1 M 8.2 75.0 75.0 75.0 75.0 3.5 34 35 * 3.0 P 4.5 38.5 75.0 7.2 75.0 5.0 36 39 C 4.3 M 5.6 6.2 75.0 5.8 75.0 5.8 40 42 - 4.5 M 75.0 75.0 75.0 75.0 75.0 3.7 44 46 C 4.8 H 4.5 5.2 6.2 4.5 4.7 3.0 47 49 H 5.0 H 3.3 3.3 3.7 3.7 3.7 2.7 50 52 C 5.0 H 2.7 3.0 2.7 2.3 2.7 2.7 53 54 E 4.1 M 3.0 2.5 3.0 3.0 3.0 3.0 55 56 C 4.1 M 5.5 5.0 4.5 6.5 4.0 10.2 57 58 * 1.9 P 75.0 5.5 7.8 4.5 6.5 3.5 59 61 C 4.6 H 8.2 30.3 7.3 30.8 8.0 8.2 62 65 E 4.2 M 2.5 2.0 2.2 2.2 1.8 0.5 67 68 - 4.5 M 75.0 75.0 75.0 4.0 75.0 75.0 69 72 C 4.6 H 6.8 4.8 5.1 4.8 21.2 5.4 74 75 C 4.5 M 2.0 2.5 7.0 0.5 2.5 2.5 76 77 E 4.1 M 1.0 0.0 2.0 1.0 0.5 0.5 78 89 C 5.0 H 3.9 8.8 3.8 3.0 3.7 3.2 >>>>>>