Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2d9ba1 CC----CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHCCCCCEEEECCCCCCCCCCCCC-------- >P1;d2dn5a1 --------------CHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHCCCCCEEEECCC------------------ >P1;d2dzqa1 --------------CHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHCCCCCEEEECCC--------CCCCCCCCCC >P1;d2ejea1 CCHHHHCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHCCCCCEEEECCCCC-------CCCCCCCCC PSA >P1;d2d9ba1 a7----b54853571375047102500062294a96270228305736900407711ac1703304609392053017639b0504255507589a2cb4-------- >P1;d2dn5a1 --------------3587036002510071395d6448031a805a47820207500ca061660760788404501816980705249c------------------ >P1;d2dzqa1 --------------16870470034100602a4b72380116204625930205501bd0706605618a8406601821c605031555--------621869c998 >P1;d2ejea1 b79a84857141570477075100630071090c43050118405575b304061109d180321580817204501913970606157519-------6036a895b Translating the sequences **----*********HHHHHHHHHHHHHHH*CCCCCCCCCHHHHHHCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHCCCCCEEEECCC*********C-------- --------------*HHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHCCCCCEEEECCC------------------ --------------*HHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHCCCCCEEEECCC--------*C******** ***************HHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHCCCCCEEEECCC**-------C******** 117773.tem _________________________________ **----*********HHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHCCCCCEEEECCC**------*C******** Structural block scores 0 1 * 3.5 M 8.8 75.0 75.0 9.2 2 5 - 4.3 M 75.0 75.0 75.0 7.9 6 14 * 3.2 M 5.5 67.0 66.8 4.2 15 29 H 5.0 H 2.8 3.0 3.1 3.2 30 39 C 4.9 H 5.2 5.5 4.9 3.5 40 45 H 5.0 H 4.2 5.8 3.2 3.8 46 49 C 5.0 H 4.5 5.2 4.8 6.6 50 53 E 5.0 H 2.8 2.2 1.8 2.5 54 68 C 5.0 H 4.3 4.5 4.7 4.0 69 77 H 5.0 H 3.3 4.2 4.8 3.2 78 82 C 5.0 H 5.9 4.8 4.3 4.0 83 86 E 5.0 H 2.8 3.5 2.2 3.2 87 89 C 5.0 H 5.0 8.5 5.0 5.7 90 91 * 3.5 M 3.5 75.0 75.0 5.0 92 97 - 4.3 M 7.8 75.0 75.0 75.0 100 107 * 3.5 M 75.0 75.0 7.8 6.6 >>>>>>