Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1j1va- -----------------------------CC---HHHHHHHHHHHCCCCHHHHHCCCCCHHHHHHHC-C-CHHHHHCC--CCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCC--- >P1;d1l8qa1 -----------------CHHHHHHHHHHHHH---HCCHHHHHHHHHCCCHHHHCCCCCCCCCHHHHHHC-CHHHHHHC--CCHHHHHHHCCCCCCCHHHHHHHHHHHCCC--CCHHHHHHHHHHHHHHHHC >P1;d2jrta1 CCCCCCCCCCEEECCC-------------CCEEECCCCCC-CCCC-----------CCC----HHHHHHHHHHHHC--CCCCHHHHHHHC-CCCHHHHHHHHHHHCCCCCCCC--CHHHHHHHHHC----- >P1;d6enia- CC-------------CCHHHHHHHHHHHHHH---HHHHHHHHHHHHCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH-CCC-HHHHHHHHHHHH---HCC--HHHHHHHHHHHC---- PSA >P1;d1j1va- -----------------------------28---177007200833818482045969578022002-0-0004510c--46256008304727465046116217513864992572275039606b--- >P1;d1l8qa1 -----------------d8986566465467---3040162009429195a302485947902201300-00034018--063640163182859942383142037249--8724740350273076601 >P1;d2jrta1 a699775345817048-------------975031a5006-6a15-----------a06----9943220030102--800525101920-8066930580248104859976--7a735721743----- >P1;d6enia- bc-------------7698547456655666---58246517805978718512784286a43845936650221112871738506750-805-974165148719---816--685275148422---- Translating the sequences -----------------------------**---H**HHHHHHHH*CCCHHHH***CCC***HHHH*-*-*HHHHH**--CCHHHHHHHC*CCC*HHHHHHHHHHHH****C***HHHHHHHHHHH**--- -----------------**************---H**HHHHHHHH*CCCHHHH***CCC***HHHHHH*-*HHHHH**--CCHHHHHHHC*CCC**HHHHHHHHHHH***--C**HHHHHHHHHHH***** ****************-------------***********-****-----------CCC----HHHHH***HHHH*--**CCHHHHHHHC-CCC*HHHHHHHHHH******CC--*HHHHHHHHH*----- **-------------****************---H**HHHHHHHH*CCCHHHH****CC***HHHHHH***HHHHH****CCHHHHHHH*-CCC-HHHHHHHHHHHH---*CC--HHHHHHHHHHH*---- 48295.tem _________________________________ **-------------*-**************---H**HHHHHHHH*CCCHHHH***CCC***HHHHHH***HHHHH****CCHHHHHHHC*CCC*HHHHHHHHHHHH****CC**HHHHHHHHHHH**--- Structural block scores 0 1 * 3.5 M 75.0 75.0 8.2 12.0 2 14 - 4.3 M 75.0 75.0 5.3 75.0 17 30 * 3.1 M 65.0 6.7 65.4 5.9 31 33 - 4.3 M 75.0 75.0 2.7 75.0 35 36 * 1.0 P 7.0 2.0 7.8 5.0 37 44 H 4.3 M 2.5 2.8 12.9 4.5 46 48 C 4.3 M 5.7 6.3 75.0 7.3 49 52 H 4.3 M 3.5 4.6 75.0 3.8 53 55 * 2.3 P 6.0 4.7 75.0 5.7 56 58 C 4.8 H 6.7 6.0 5.5 4.7 59 61 * 2.3 P 5.0 5.3 75.0 6.8 62 67 H 4.7 H 13.5 1.3 17.0 5.3 68 70 * 1.8 P 25.0 25.0 0.7 5.7 71 75 H 4.9 H 2.0 1.4 1.2 1.2 76 79 * 2.9 P 40.6 39.8 39.5 4.5 80 81 C 5.0 H 5.0 3.0 2.5 4.0 82 88 H 5.0 H 3.4 3.3 2.9 4.9 91 93 C 5.0 H 5.3 5.0 4.7 4.3 95 106 H 4.8 H 3.7 3.8 3.7 5.2 107 110 * 2.3 P 4.5 22.5 7.8 58.2 111 112 C 4.3 M 6.5 41.5 6.5 3.5 113 114 * 3.5 M 5.5 4.5 75.0 75.0 115 125 H 4.9 H 4.2 3.2 5.1 4.7 126 127 * 2.9 P 8.8 6.5 75.0 38.5 128 130 - 4.3 M 75.0 2.3 75.0 75.0 >>>>>>