Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ug8a1 --------------------CHHHHHHHHHHHHHHHHHCCCCCEEECCC-CCCHHHHHHHHHHHHHCCCCEEEEEECCCCCCCEEEEEECCCCCC------------------------ >P1;d1whra1 CCCCCCCHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCCCCEEECCC-CCHHHHHHHHHHHHHC---CCCEEEC--CCC-CCEEEECC-CCCCCCCCCHHHHCCCCCCCCCCCCCCC >P1;d2lrra- ---------CCCCCCCCC-------CCHHHHHHHHHHCC-CCCEEECCCCCCHHHHHHHHHHHHHH---CCEEEEECCCC-CCEEEEECCC---------------------------- PSA >P1;d1ug8a1 --------------------a698207600750580293ab58425063-0876426203900672256605022665a9455001033278a98------------------------ >P1;d1whra1 d8a90a7246302710677581383017107603802b4cc8a51608a-09a6334002300410---5072682--b62-61020444-bb09718640443576b7a988ba87aa >P1;d2lrra- ---------b7c3764a9-------c1813530680283-95852505481888225203300611---806151669a8-8330002379---------------------------- Translating the sequences --------------------*HHHHHHHHHHHHHHHHHCCCCCEEECCC-CC*HHHHHHHHHHHHH***C*EEEEECCCCCCCEEEEE*CCCCCC------------------------ *********************HHHHHHHHHHHHHHHHHCCCCCEEECCC-CCHHHHHHHHHHHHH*---CC*EEE*--CCC-C*EEEECC-CCCC************************ ---------*********-------**HHHHHHHHHH*C-CCCEEECCC*CCHHHHHHHHHHHHHH---CCEEEEECCCC-CCEEEEECCC---------------------------- 82708.tem _________________________________ ---------*********--*HHHHHHHHHHHHHHHHHCCCCCEEECCC-CCHHHHHHHHHHHHHH---CCEEEEECCCCCCCEEEEECCCCCCC------------------------ Structural block scores 0 8 - 4.0 M 75.0 7.2 75.0 9 17 * 2.7 P 75.0 3.6 7.8 18 19 - 4.0 M 75.0 6.0 75.0 21 37 H 4.6 H 4.4 3.6 21.0 38 42 C 4.8 H 7.6 9.5 20.0 43 45 E 5.0 H 3.7 4.0 4.0 46 48 C 5.0 H 3.0 6.2 3.0 50 51 C 5.0 H 4.0 4.5 4.5 52 65 H 4.9 H 3.9 2.6 2.9 66 68 - 4.0 M 4.3 75.0 75.0 69 70 C 4.5 M 3.0 2.5 4.0 71 75 E 4.6 H 3.0 5.0 3.8 76 82 C 4.4 M 6.4 35.8 17.1 83 87 E 4.8 H 0.8 1.4 1.0 88 94 C 4.1 M 6.8 16.4 45.6 95 118 - 4.0 M 75.0 7.0 75.0 >>>>>>