Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1klxa- -----------------------------------------------CCCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHCC--CCC----CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCHHHHHHC------------------------------------------------------------------------------- >P1;d1ouva1 CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHCCCCCC PSA >P1;d1klxa- -----------------------------------------------9a86974636831873170006467700530370--910----84a4036103600857002001100311170742a55383007205400837145002200610560513a655a60581053037280a804a42------------------------------------------------------------------------------- >P1;d1ouva1 73871194056038675273015204600857132001300301351222a--55185006103500737324000300501360522a44294026104300737325001300501350722a54164016204500726117001300501440521964386007002400827215003300301250414a54383016105400737214003210501350305b7368403610630381818603532781799c Translating the sequences -----------------------------------------------CCCC**HHHHHHHHHHHHHHHCCC**HHHHHH**--*CC----CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCHHHHHH*------------------------------------------------------------------------------- ***********************************************CCCC--**HHHHHHHHHHHHHCCCHHHHHHHHHH**HCC****CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCHHHHHHH******************************************************************************* 81901.tem _________________________________ -----------------------------------------------CCCC--HHHHHHHHHHHHHHHCCCHHHHHHHHHH--HCC----CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCHHHHHHH------------------------------------------------------------------------------- Structural block scores 0 46 - 3.0 P 75.0 3.3 47 50 C 5.0 H 8.4 4.1 51 52 - 3.0 P 8.0 75.0 53 67 H 4.7 H 3.8 3.1 68 70 C 5.0 H 5.3 4.3 71 80 H 4.2 M 3.2 1.4 81 82 - 3.0 P 75.0 2.0 84 85 C 5.0 H 0.5 2.5 86 89 - 3.0 P 75.0 4.6 91 103 H 5.0 H 3.5 2.9 104 106 C 5.0 H 4.0 4.3 107 119 H 5.0 H 1.3 1.9 120 126 C 5.0 H 4.8 4.4 127 139 H 5.0 H 3.1 2.8 140 142 C 5.0 H 3.7 3.0 143 155 H 5.0 H 2.4 2.0 156 162 C 5.0 H 4.4 3.9 163 175 H 5.0 H 4.1 2.9 176 178 C 5.0 H 3.3 3.7 179 185 H 4.7 H 5.6 1.7 186 264 - 3.0 P 75.0 3.6 >>>>>>