Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1u9la- -CCHHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCC >P1;d1y88a1 ---CCHHHCC----CCHHHHHHHHHCCCCCHHHHHHHCHHHHHHC-CCCHHHHHHHHHHHHHHHC---- >P1;d1z4da1 -----CCCCC---CCCHHHHHHHHHCCCCCHHHHHCCCHHHHHCCCCCCHHHHHHHHHHHHHHCC-CCC >P1;d2z43b1 ---CCHHHCC---CCCHHHHHHHHCCCCCCHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC-CC- >P1;d3ldaa1 CCCCCHHHHCCC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCC-CCC PSA >P1;d1u9la- -5983073038407186a204303739065063006252850380aa0757405601640470187578 >P1;d1y88a1 ---6607508----0777123104719155082038165940572-6083730650172068249---- >P1;d1z4da1 -----05804---607891171047381663550060749402819a078820650081058329-39b >P1;d2z43b1 ---9608506---c157721640590a154064008163a701830a066930650051045437-68- >P1;d3ldaa1 ba6240560259-80687006303646262023006064840271a6077920540462037309-48b Translating the sequences -****HHH*****CCCHHHHHHHHHCCCCCHHHHHHCCHHHH*CCCCCCHHHHHHHHHHHHHH****CC ---CCHHHCC----CCHHHHHHHHHCCCCCHHHHHH*CHHHHH*C-CCCHHHHHHHHHHHHHH*C---- -----***CC---CCCHHHHHHHHHCCCCCHHHHH*CCHHHHHCCCCCCHHHHHHHHHHHHHHCC-CCC ---CCHHHCC---CCCHHHHHHHH*CCCCCHHHHH*CCHHHHH***CCCHHHHHHHHHHHHHHCC-CC- ***CCHHH*C**-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCC-CCC 47794.tem _________________________________ ---CCHHHCC---CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCC-CCC Structural block scores 0 2 - 4.0 M 29.7 75.0 75.0 75.0 9.3 3 4 C 4.1 M 5.5 6.0 75.0 7.5 3.0 5 7 H 4.5 M 3.3 4.0 4.3 4.3 3.7 8 9 C 4.2 M 1.5 4.0 2.0 3.0 1.0 10 12 - 4.0 M 4.0 75.0 75.0 75.0 29.7 13 15 C 4.8 H 5.3 27.3 4.3 6.2 4.7 16 24 H 4.9 H 3.9 3.6 4.2 4.6 3.7 25 29 C 5.0 H 4.6 4.2 4.8 4.1 4.0 30 35 H 4.8 H 2.5 3.5 3.2 3.0 1.8 36 37 C 4.8 H 3.5 3.5 3.5 3.5 3.0 38 42 H 4.9 H 3.6 4.6 3.8 4.3 3.6 43 48 C 4.6 H 6.0 16.3 5.9 4.6 5.2 49 62 H 5.0 H 3.5 3.6 3.9 3.4 3.7 63 64 C 4.2 M 4.5 6.5 5.5 5.0 4.5 66 68 C 4.3 M 6.7 75.0 7.8 29.7 7.8 >>>>>>