Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1hwtc1 --------CCCCCCHHHHHHCCCCCCCC----------CCCHHHHHHCCHHHCCCCC---------- >P1;d1pyia1 ---------CCCCCHHHHHHCCCCCCCC----------CCCHHHHHCCC--CCCCCCCCCC--CC-- >P1;d1zmec1 ----------CCCCHHHHHHCCCCCCC-----------CCCHHHHHCCC--CCCCCCCC-------- >P1;d2alca- CCCCCCCCCCCCCCHHHHHCCCCCCCCCCHHHHHHHCCCCCHHHHHHC--CCCCCHHHHCCCCCCCC >P1;d3coqa1 ----------CCCCHHHHHHCCCCCCCC----------CCCHHHHHCCC--CCCCCCC--C--CCCC PSA >P1;d1hwtc1 --------95382012048493904466----------730430475933750704a---------- >P1;d1pyia1 ---------5853043048482803567----------92063057494--8144357976--86-- >P1;d1zmec1 ----------b72021056584a035b-----------750850684b2--9052598b-------- >P1;d2alca- 57a956573a24000103669390704491b41378a2710810676a--2801070007378756a >P1;d3coqa1 ----------a33023058594a04377----------940540686a4--9061488--a--899a Translating the sequences --------*CCCCCHHHHHHCCCCCCCC----------CCCHHHHH*CC***CCCCC---------- ---------CCCCCHHHHHHCCCCCCCC----------CCCHHHHHCCC--CCCCCCC**C--CC-- ----------CCCCHHHHHHCCCCCCC-----------CCCHHHHHCCC--CCCCCCC*-------- *********CCCCCHHHHH*CCCCCCCC**********CCCHHHHH*C--*CCCC*****C**CC** ----------CCCCHHHHHHCCCCCCCC----------CCCHHHHHCCC--CCCCCCC--C--CC** 57701.tem _________________________________ ---------CCCCCHHHHHHCCCCCCCC----------CCCHHHHHCCC--CCCCCCC*-C--CC-- Structural block scores 0 8 - 4.4 M 67.7 75.0 75.0 6.4 75.0 9 13 C 4.8 H 3.6 4.2 19.1 3.3 18.3 14 19 H 4.9 H 3.2 3.8 3.2 2.7 3.8 20 27 C 4.9 H 5.1 4.9 14.6 4.5 5.6 28 37 - 4.5 M 75.0 75.0 75.0 5.7 75.0 38 40 C 5.0 H 3.3 3.7 4.0 2.7 4.3 41 45 H 5.0 H 3.6 4.2 5.4 4.4 4.6 46 48 C 4.4 M 5.7 5.7 5.8 30.5 6.8 49 50 - 4.2 M 5.0 75.0 75.0 38.5 75.0 51 57 C 4.7 H 14.5 4.6 5.4 2.3 5.1 61 62 - 4.5 M 75.0 75.0 75.0 7.5 75.0 63 64 C 4.2 M 75.0 7.0 75.0 6.0 8.5 65 66 - 3.8 M 75.0 75.0 75.0 8.2 9.8 >>>>>>