Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2h5na1 ----------------CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCHH-HHHHHHHCCC-HHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCCC---HHHHHHHHCC--------------- >P1;d2ou3a1 CCCCHHHHHHHHHHHCCC--------CCCCHHHHHHC-CHHHHHHHCC--CCHHHHHHHHHHHHHCCCC----HHHHHHHHHCCCCCCHHHHHCCCCCCCCHHHHHHHHHHHHHCCC--CCHHHHHHC--CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCC PSA >P1;d2h5na1 ----------------9b9a9999a9270677100000200240074697967914620361035090889619711750782859-5036004707-87105100000010009b4906aa257306711760803a07---1860362078--------------- >P1;d2ou3a1 aaa79b26720564185a--------a3284710011-101010012c--1496027401920560704----a502740591806440670164077033363002000200012b--09a227202--0960909620671065158437866874885559a45b Translating the sequences ----------------CC********CCCCHHHHHHH*HHHHHHHHCC**CCHHHHHHHHHHHHHHCCC****HHHHHHH**CCHH-HHHHHHHCCC-HHHHHHHHHHHHHH**CCC**CHHHHHHHH**HHHHCCCCC*---HHHHHHHH**--------------- ****************CC--------CCCCHHHHHH*-*HHHHHHHCC--CCHHHHHHHHHHHHH*CCC----HHHHHHHHHCC****HHHHH*CCC****HHHHHHHHHHHHHCCC--C*HHHHHH*--****CCCCCH***HHHHHHHHHH*************** 158682.tem _________________________________ ----------------CC--------CCCCHHHHHHH-HHHHHHHHCC--CCHHHHHHHHHHHHHHCCC----HHHHHHHHHCCHH-HHHHHHHCCC-HHHHHHHHHHHHHHHHCCC--CHHHHHHHH--HHHHCCCCCH---HHHHHHHHHH--------------- Structural block scores 0 15 - 3.0 P 75.0 6.2 16 17 C 5.0 H 10.2 7.8 18 25 - 3.0 P 9.4 75.0 26 29 C 5.0 H 3.8 5.9 30 36 H 4.7 H 2.1 2.0 38 45 H 4.8 H 1.9 0.5 46 47 C 5.0 H 5.0 7.2 48 49 - 3.0 P 8.0 75.0 50 51 C 5.0 H 7.5 2.5 52 65 H 4.9 H 3.4 3.6 66 68 C 5.0 H 5.7 3.7 69 72 - 3.0 P 6.0 75.0 73 81 H 4.6 H 5.0 4.7 82 83 C 5.0 H 5.0 4.5 84 85 H 3.0 P 7.0 3.0 87 93 H 4.4 M 2.6 3.4 94 96 C 5.0 H 4.7 3.7 98 113 H 4.4 M 1.4 1.4 114 116 C 5.0 H 8.2 4.8 117 118 - 3.0 P 4.5 75.0 120 127 H 4.5 M 5.5 4.3 128 129 - 3.0 P 4.0 75.0 130 133 H 3.0 P 3.5 3.8 134 138 C 5.0 H 4.3 5.2 140 142 - 3.0 P 75.0 4.7 143 152 H 4.6 H 4.1 4.7 153 167 - 3.0 P 75.0 6.8 >>>>>>