Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1f86a- -CCEEEEEEECCCCEECCCCEEEEEEECC-CCCEEEEEEEECCCCCEEC-CCCCCCCCCCEEEEEEECHHHHHHHCCCC--CCCCCEEEEEEECCCCCCEEEEEEEEECCEEEEEEEEEC >P1;d2g2na- -CCEEEEEEECCCCEECCCCEEEEEEECC--CCEEEEEEEECCCCCEEC-CCCCCCCCCCEEEEEEECHHHHHHHCCCC--CCCCCEEEEEEE-CCCCCCEEEEEEEECCEEEECCCC-- >P1;d2h6ua- CCCEECCEEECCCCEECCCCEEEEEEECCCCCCEEEEEEEECCCCCCCC-CCCCCCCCCCEEEEEEECHHHHHHHCCCC--CCCCCEEEEEEE-CCCCCCEECCEEECCCCEECCCCC-- >P1;d3qvaa1 --CEEEEEEECCCCEECCCCEEEEECC--------CCEEEECC-CCEEC-CCC-CCCCCCCEEEEEECHHHHHHHCC---CCCCCCEEEEEEC------CEECCEEEECCEEEECCC--- >P1;d4q14a- -CEEEEEEEECCCCEECCCCEEEEEEECC-CCCEEEEEEEECCCCCCCCCCCCCHHHCCCEEEEEEEEHHHHHHHCCCCCCCCCCEEEEEEEE-CCCCCEEEEEEEEECCEEEECCCC-- PSA >P1;d1f86a- -400202030354a43048040402320b-8882571246605960315-80077a70664402010203700683a49--063730424250068682603020503277271636467 >P1;d2g2na- -320102040445873047040101345b--b91751354605940507-5001a8a0755502000302710874a49--072830416160-67394402000203167262551f-- >P1;d2h6ua- a010301030445a530480401011248a6872751254506b60406-90086a60656301030103800884a48--072740214160-854863110003023663636439-- >P1;d3qvaa1 --401010305359640660303034e--------73274508-80509-503-b8706768020103015106659---3194850516171------4220003022a5263653--- >P1;d4q14a- -140302030435953027060102205b-8774621371604a60509740055a506586000103006005a69308a171640415250-96584613110401067373781e-- Translating the sequences -CCEEEEEEECCCCEECCCCEEEEEEECC-CCCEEEEEEEECCCCCEEC-CCCCCCCCCCEEEEEEECHHHHHHHCCCC--CCCCCEEEEEEE*CCCCC*EEEEEEEECCEEEE****** -CCEEEEEEECCCCEECCCCEEEEEEECC--CCEEEEEEEECCCCCEEC-CCCCCCCCCCEEEEEEECHHHHHHHCCCC--CCCCCEEEEEEE-CCCCCCEEEEEEEECCEEEECCCC-- *CCEE**EEECCCCEECCCCEEEEEEECC*CCCEEEEEEEECCCCC**C-CCCCCCCCCCEEEEEEECHHHHHHHCCCC--CCCCCEEEEEEE-CCCCCCEE**EEE*CC*EE*CCCC-- --CEEEEEEECCCCEECCCCEEEEE**--------**EEEECC-CCEEC-CCC-CCCCCC*EEEEEECHHHHHHHCC---*CCCCCEEEEEE*------CEE**EEEECCEEEECCC--- -C*EEEEEEECCCCEECCCCEEEEEEECC-CCCEEEEEEEECCCCC**C*CCCC***CCCEEEEEEE*HHHHHHHCCCC**CCCC*EEEEEEE-CCCCC*EEEEEEEECCEEEECCCC-- 49472.tem _________________________________ -CCEEEEEEECCCCEECCCCEEEEEEECC-CCCEEEEEEEECCCCCEEC-CCCCCCCCCCEEEEEEECHHHHHHHCCCC--CCCCCEEEEEEE-CCCCCCEEEEEEEECCEEEECCCC-- Structural block scores 1 2 C 4.5 M 2.0 2.5 0.5 39.5 2.5 3 9 E 4.9 H 1.0 1.0 1.0 0.7 1.1 10 13 C 5.0 H 5.6 5.2 5.9 5.5 5.2 14 15 E 5.0 H 3.5 5.0 4.0 5.0 4.0 16 19 C 5.0 H 3.0 2.8 3.0 3.0 2.2 20 26 E 4.9 H 2.1 1.9 1.3 3.9 1.6 27 28 C 4.5 M 5.8 8.2 6.0 75.0 8.2 30 32 C 4.4 M 8.0 31.8 7.0 75.0 7.3 33 40 E 4.8 H 4.1 4.0 3.9 22.2 3.8 41 45 C 4.9 H 4.0 3.6 4.7 18.2 4.1 46 47 E 3.8 M 2.0 2.5 2.0 2.5 2.5 50 59 C 4.8 H 5.2 4.7 5.0 12.2 4.0 60 66 E 4.9 H 1.6 1.7 1.9 2.4 2.1 68 74 H 5.0 H 3.4 3.6 3.9 2.7 3.1 75 78 C 4.8 H 6.6 6.9 6.6 41.0 4.5 79 80 - 4.2 M 75.0 75.0 75.0 39.0 9.2 81 85 C 4.9 H 3.8 4.0 4.0 5.4 3.8 86 92 E 4.9 H 2.4 2.6 2.0 3.0 2.4 94 99 C 4.4 M 6.0 5.5 5.7 63.2 6.3 100 107 E 4.6 H 1.6 0.9 0.9 1.1 1.4 108 109 C 5.0 H 4.5 3.5 4.5 6.2 3.0 110 113 E 4.8 H 4.2 4.2 4.5 4.0 5.0 114 117 C 4.4 M 4.8 8.4 5.5 22.2 7.6 118 119 - 4.5 M 6.5 75.0 75.0 75.0 75.0 >>>>>>