Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1k6ka- ---CCCHHHHHHHHHHHHHHHHHCCCEECHHHHHHHHCCC--HHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCEECHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHC--C----------- >P1;d1khya- --CCCCHHHHHHHHHHHHHHHHCCCCCCCCCCC-CCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHC-CCCCC---------CCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCC-HHHHHHHHHCCCCHHHHHHHHHC-------------- >P1;d1qvra1 --CCCCHHHHHHHHHHHHHHHHCCCCEECHHHHHHHHCCCCCCHHHHHHHCCCCCHHHHHHHHHHHHH-CCCCCC--HHHCCCEECHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHCC---------CCCCHHHHHHHHCCCCCCCCCCCCCCCC >P1;d6azya1 CCCCCCHHHHHHHHHHHHHHHHCCCCEECHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHHHHHH-HCCCCC------CCEECHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCH--HHHHHHHHCCCCHHHHHHHHHHHHC----------- PSA >P1;d1k6ka- ---6319406701770263058440330200000020050--4304600541a072a404840353057404606967968608237205503730368187b37b503002003000418a23006005519056760574258--9----------- >P1;d1khya- --9613a60470275057408836065021000-000062ba03035008409081860363055006-72946---------7408404502830460085393a603020000000419-a5007105819066920470058-------------- >P1;d1qvra1 --960043037126305520375503301000001100558622016006508270751267056407-738619--cb5104542a50590185047017638162001000000001318---------a0293b6037017658b82366375074 >P1;d6azya1 bb1714a505701840372056560540000000010052aa03036006609060950173048107-71758a------b295084065015303420592948503010000001208--303710770907683048007743c----------- Translating the sequences ---CCCHHHHHHHHHHHHHHHH*CCCEECHHHHHHHHCCC--*HHHHHHHHCCCCHHHHHHHHHHHHH**CCCCC******CCEECHHHHHHHHHHHHHHH*CCCCCCCHHHHHHHH*CCC**HHHHHHHHCCCCHHHHHHHHHC--C----------- --CCCCHHHHHHHHHHHHHHHHCCCC**C****-***CCCCCC*HHHHHHH*CCCHHHHHHHHHHHH*-*CCCC---------**CHHHHHHHHHHHHHHH**CCCCCCHHHHHHHH*CCC-*HHHHHHHHCCCCHHHHHHHHHC-------------- --CCCCHHHHHHHHHHHHHHHHCCCCEECHHHHHHHHCCCCCCHHHHHHH*CCCCHHHHHHHHHHHHH-*CCCCC--****CCEECHHHHHHHHHHHHHHH*CCCCCCCHHHHHHHH***C*---------CCCCHHHHHHHH*C**C*********** **CCCCHHHHHHHHHHHHHHHHCCCCEECHHHHHHHH*CCCCCHHHHHHHHCCCCHHHHHHHHHHHHH-*CCCCC------CCEECHHHHHHHHHHHHHHH*CCCCCCCHHHHHHHH*CC*--HHHHHHHHCCCCHHHHHHHHH***C----------- 81923.tem _________________________________ --CCCCHHHHHHHHHHHHHHHHCCCCEECHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHH-*CCCCC--****CCEECHHHHHHHHHHHHHHH*CCCCCCCHHHHHHHH*CCC**HHHHHHHHCCCCHHHHHHHHHC**C----------- Structural block scores 0 1 - 4.3 M 75.0 75.0 75.0 11.5 2 5 C 4.8 H 21.2 4.8 3.8 3.2 6 21 H 5.0 H 4.1 4.6 3.2 4.0 22 25 C 4.8 H 2.8 3.8 3.2 4.0 26 27 E 4.3 M 1.5 2.5 1.5 2.0 29 36 H 4.3 M 0.2 9.5 0.2 0.1 37 42 C 4.5 M 26.5 5.0 4.3 4.7 43 50 H 4.8 H 2.8 2.9 2.5 3.0 51 54 C 4.8 H 4.6 4.2 4.2 3.8 55 67 H 4.9 H 3.7 3.3 3.8 3.5 70 74 C 4.9 H 3.2 19.2 5.4 6.3 75 76 - 4.3 M 7.5 75.0 75.0 75.0 77 80 * 3.5 M 7.5 75.0 7.5 75.0 81 82 C 4.3 M 3.0 75.0 2.0 6.8 83 84 E 4.3 M 5.0 5.5 4.5 7.0 86 100 H 5.0 H 3.9 3.5 4.2 3.1 102 108 C 4.9 H 5.9 4.9 2.9 4.4 109 116 H 5.0 H 0.6 0.2 0.1 0.1 118 120 C 4.3 M 4.3 4.7 1.7 3.3 121 122 * 3.5 M 6.2 42.8 41.5 75.0 123 130 H 4.3 M 2.4 3.2 75.0 3.5 131 134 C 5.0 H 3.8 4.0 5.4 4.0 135 143 H 4.9 H 4.7 3.7 4.3 4.0 145 146 * 3.5 M 75.0 75.0 6.5 3.5 148 158 - 4.3 M 75.0 75.0 4.6 75.0 >>>>>>