Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1hq1a- -----------------------------CCCHHHHHHHHCC---------------------------------CHHHHHHHHHCCCHHHHH---CHHHCC--HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC--- >P1;d1qb2a- -----------------------------CCCHHHHHHHHHHHHHCHHHHHHHHHCCCCCC-CCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHCCCCHHHHHHCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHC------ >P1;d4xcod- ------------CCCCC-----------CCCCHHHHHHHHHHHHHHH------------HH---------CCCHHHHHHHHHHHCCCCHHHHH---CCCCCC--HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHC >P1;d7epka3 CHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHCCCHHHCCCCHHHHHHHHHHHHHCCHHHHH---CHHHCC--HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCC--- PSA >P1;d1hq1a- -----------------------------d120450064159---------------------------------73a602400520679015---607208--97427500980a17484056017404623753887--- >P1;d1qb2a- -----------------------------b679844756666897577529201607806a-60269b45960584385175048205960383b5126107766b117400880917483054006044414836------ >P1;d4xcod- ------------a5477-----------8801042028404633966------------88---------73988407302600520686015---607307--a9315400780a283a1043026305822861579579 >P1;d7epka3 ab896468655467337204500620164705060034004002726915aa63707006604633760070a67305301300620596018---507307--69307500681b0637105500610660492097a--- Translating the sequences -----------------------------CCCHHHHHHHH**---------------------------------*HHHHHHHH*CCCHHHHH---CHHHCC--HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH****--- -----------------------------CCCHHHHHHHHHHHH*****************-***********HHHHHHHHHHH*CCCHHHHH***CHHH*****HHHHHHHHHCCCCHHHHHHHHHHHHHHHHH*------ ------------*****-----------*CCCHHHHHHHHHHHH***------------**---------***HHHHHHHHHHH*CCCHHHHH---C***CC--HHHHHHHHHH*CCCHHHHHHHHHHHHHHHHH******* *****************************CCCHHHHHHHHHHHH*****************************HHHHHHHHHHH**CCHHHHH---CHHHCC--HHHHHHHHHHCCCC**HHHHHHHHHHHHHHH****--- 47446.tem _________________________________ ------------*****-----------*CCCHHHHHHHHHHHH*****************-***********HHHHHHHHHHH*CCCHHHHH---CHHHCC--HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH****--- Structural block scores 0 11 - 4.3 M 75.0 75.0 75.0 6.9 12 16 * 3.5 M 75.0 75.0 6.7 5.2 17 27 - 4.3 M 75.0 75.0 75.0 2.4 29 31 C 5.0 H 5.5 8.2 3.0 4.0 32 43 H 4.8 H 15.3 6.5 3.0 1.6 44 60 * 3.1 M 75.0 4.9 55.1 5.1 62 72 * 3.2 M 75.0 5.3 56.3 4.2 73 83 H 4.8 H 16.6 4.5 3.5 2.5 85 87 C 4.8 H 2.7 2.3 2.7 2.3 88 92 H 5.0 H 4.4 5.2 4.0 4.8 93 95 - 4.3 M 75.0 6.5 75.0 75.0 97 99 H 4.3 M 3.0 3.0 3.3 3.3 100 101 C 4.3 M 4.0 3.5 3.5 3.5 102 103 - 4.3 M 75.0 6.5 75.0 75.0 104 113 H 4.9 H 5.1 4.7 4.8 4.4 114 117 C 4.8 H 4.6 4.2 5.1 4.6 118 134 H 4.9 H 3.9 3.4 3.7 3.2 135 138 * 2.0 P 6.5 57.8 5.5 6.6 139 141 - 4.3 M 75.0 75.0 7.0 75.0 >>>>>>