Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d4gt9a1 -CEEEECCCEEEEEEEEECCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCHHHHHCEEEEEEEEEHHHHHHHCCCCCCEEEECCCCCCCCCCCCCCCCHHHHCC-----------CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCEEEEEEEEEHHHHHHHHHHHCCC-------CCCHHHHHHHHHHHHHHHHHCHHHHHHHHHHCCCCCCCC >P1;d4p5aa- CCCEEE-CCCEEEEEEEECCHHHHHHHHHCCCCC-CHHHHHHHHHHHCCCCHHHHCCEEEEEEEEEHHHHHHHCCCCCCEEEECCCCCCCCCCEEECCCCCCCCEEECCHHHCEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCEEEEEEEECHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCHHHHHHHHHCCCCCC--- PSA >P1;d4gt9a1 -351800440104038274603200321393b5c78614620250035851710360302020100320063028098071a3440575517540011628229b-----------7a3b47484326435570362054037427693644603730261000305040204100600161015-------914400130040006005630530040007220706206 >P1;d4p5aa- b80624-3504072381905173015205939bc-ba35810360064860500360501020400420083038198081a255278751c130001579151646598a466347089822564467137712511540363186947446036402810001050303030006001510446905832404400120054017202720530380044240300--- Translating the sequences -CEEEE*CCEEEEEEEEECCHHHHHHHHHCCCCC*HHHHHHHHHHHHHCCCHHHHHCEEEEEEEEEHHHHHHHCCCCCCEEEECCCCCCCCCC***CCCHHHHC*-----------CCC***HHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCEEEEEEEEEHHHHHHHHHHHCCC-------CCCHHHHHHHHHHHHHHHHHCHHHHHHHHHHCCCCC*** *C*EEE-CC*EEEEEEEECCHHHHHHHHHCCCCC-*HHHHHHHHHHH*CCCHHHH*CEEEEEEEEEHHHHHHHCCCCCCEEEECCCCCCCCCCEEECCC****CE***********CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCEEEEEEEE*HHHHHHHHHHHCCC*******CCCHHHHHHHHHHHHHHHHHCHHHHHHHHH*CCCCC--- 69796.tem _________________________________ -CEEEE-CCEEEEEEEEECCHHHHHHHHHCCCCC-HHHHHHHHHHHHHCCCHHHHHCEEEEEEEEEHHHHHHHCCCCCCEEEECCCCCCCCCCEEECCCHHHHCE-----------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCEEEEEEEEEHHHHHHHHHHHCCC-------CCCHHHHHHHHHHHHHHHHHCHHHHHHHHHHCCCCC--- Structural block scores 2 5 E 4.5 M 3.5 3.0 7 8 C 5.0 H 4.0 4.0 9 17 E 4.8 H 2.8 3.8 18 19 C 5.0 H 5.0 2.5 20 28 H 5.0 H 1.6 2.7 29 33 C 5.0 H 8.2 9.0 35 47 H 4.7 H 3.2 4.5 48 50 C 5.0 H 4.7 4.7 51 55 H 4.6 H 3.4 2.8 57 65 E 5.0 H 0.9 1.3 66 72 H 5.0 H 2.0 2.4 73 78 C 5.0 H 4.5 4.8 79 82 E 5.0 H 5.4 5.4 83 92 C 5.0 H 4.3 5.3 93 95 E 3.0 P 1.3 1.0 96 98 C 5.0 H 2.7 2.0 99 102 H 3.0 P 3.5 5.5 105 115 - 3.0 P 75.0 6.0 116 118 C 5.0 H 6.8 5.0 119 145 H 4.8 H 4.3 4.1 146 149 C 5.0 H 6.0 6.5 150 156 H 5.0 H 3.9 3.9 157 161 C 5.0 H 1.8 2.2 162 170 E 4.8 H 1.6 1.3 171 181 H 5.0 H 1.7 1.5 182 184 C 5.0 H 2.0 2.7 185 191 - 3.0 P 75.0 4.7 192 194 C 5.0 H 4.7 2.7 195 211 H 5.0 H 1.9 2.2 213 222 H 4.8 H 2.1 2.9 223 227 C 5.0 H 3.0 1.4 228 230 - 3.0 P 2.7 75.0 >>>>>>