Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ftra1 -CEECCEECCCCCCCCCCCEEEEEEEECCCHHHHHHHHHHHHCCCCCCC--------CCCCEEEEEEE-------EECHHHCCCC----------CCEEEEEEEECCHHHHHHHHHHHHHHHCCCCCCC-EEEECCCH-HHCCCCCCHHHHHHHHHCCCCEEEEECCEEEEECCCC >P1;d1ftra2 CCCC---CCCCCCCCCCCEEEEEEEEEECCHHHHHHHHHHHHHHHCCCCCEECCCHHHCCCCCEEECCCCCCCCCEEECHHHCCCCCCCCCCCCCCEEEEEEEEECCHHHHHHHHHHHHH-HHCCCCCEEEEECCCCCCCCCCCCCCHHHHC------------------------ PSA >P1;d1ftra1 -867b77848b68a798b3442200000554640250067008709429--------91405072456-------6134960016----------3100004001754950361135011810261550-41172259-973867161944106609981655647845215155c >P1;d1ftra2 aa88---858b87b96a20761100000646610560072015307a1b3070348c0107a143850785b738526223222a4a82803b806101101020673810340032005-3047273046132486a4878846062a805------------------------ Translating the sequences -CEE***ECCCCCCCCCC*EEEEEEEE*CCHHHHHHHHHHHH***CCCC--------*CCCEEEEEEE-------EE*HHH*CCC----------C*EEEEEEEECCHHHHHHHHHHHHH*H*CCCCC*-EEEECCCH-HHCCCCCCHHHHH************************ *C**---*CCCCCCCCCCEEEEEEEEEECCHHHHHHHHHHHHHHHCCCC********HCCC**EEE*********EEE*HHHCCC**********CEEEEEEEEECCHHHHHHHHHHHHH-HHCCCCCE*EEE*CCC****CCCCCCHHHH*------------------------ 55112.tem _________________________________ -CEE---ECCCCCCCCCCEEEEEEEEEECCHHHHHHHHHHHHHHHCCCC--------HCCCEEEEEEE-------EEEHHHHCCC----------CEEEEEEEEECCHHHHHHHHHHHHH-HHCCCCCE-EEEECCCH-HHCCCCCCHHHHH------------------------ Structural block scores 2 3 E 3.0 P 6.5 8.0 4 6 - 3.0 P 8.5 75.0 8 17 C 5.0 H 8.3 7.8 18 27 E 4.6 H 1.5 1.5 28 29 C 5.0 H 5.0 5.0 30 44 H 4.6 H 3.3 2.8 45 48 C 5.0 H 6.0 7.5 49 56 - 3.0 P 75.0 4.7 58 60 C 5.0 H 1.7 2.7 61 67 E 3.9 M 4.1 4.5 68 74 - 3.0 P 75.0 7.1 75 77 E 4.3 M 3.3 4.3 78 81 H 4.0 M 4.8 2.2 82 84 C 5.0 H 2.3 4.8 85 94 - 3.0 P 75.0 5.5 96 104 E 4.8 H 0.7 0.7 105 106 C 5.0 H 6.0 6.5 107 119 H 5.0 H 3.0 2.2 121 122 H 4.0 M 0.5 1.5 123 127 C 5.0 H 3.8 4.6 130 133 E 4.5 M 3.2 3.0 134 136 C 5.0 H 3.0 6.0 139 140 H 3.0 P 8.0 7.5 141 146 C 5.0 H 5.2 5.3 147 151 H 4.6 H 3.8 5.1 152 175 - 3.0 P 5.0 75.0 >>>>>>