Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d5ybya- -CCEEEEECCCEEEEECCCCCEEEEECCCCC-CCCCEEEEECCE-EEEEEEECCHHHHHH-CCCEEEEEEEEEECCCCEEECCEEEEECCCCCEEEEEECCCCC-EEEEECCCCCCCCCCCCCHH-HCCCCEEEEECCEEEEEEECCCCCCEEEEEEECCCCCCEEEEEEEEEEHHHCCCEEEECCEEEEECCCC--CEEEEEEECCCCEEECCCEECCCCCCCEEEEEEECCCCEEEEEECCEEEEEEEEEE >P1;d6qhja- CCCCEEEECCCEEEEECCCCCEEEECCCCCCCCCCCEEEEECCCCCCEEEEECCHHHHHHCCCCEEEECCCCCCCCCCEEECCEEEEECCCCCEEEEEECCCCEEEEEEECCCCCC-CCCCCCCCCCCCCCEEEEECCEEEEEEECCCCCCEEEEEEECCCCCCEEEEEEEEEEHHHCCCEEEECCEEEEECCCCCCCEEEEEEECCCCEEEEEEEECCCCCCCEEEEEEECCCCEEEEEECCEEEEEEEEEC PSA >P1;d5ybya- -b2304607c3750262b24100001002e3-b17200001726-523022082461049-8629516023601001000254000003282200010107966-15316078013767510074-040000010025400000002854410100202288040546060813295000000020000003680--240200020375762b171500a5a4400002002336300000403011040809 >P1;d6qhja- 9445045059082017216430000110517b936400002425a32502008218203848937516023100001000178000002561230010105775343634066034-65501020202000000002520000000b717130000103283062573170505056000000001100003435cc030200020a5575461716060237000001001453000000312002090709 Translating the sequences -CCEEEEECCCEEEEECCCCCEEEEECCCCC-CCCCEEEEECCE-EEEEEEECCHHHHHH-CCCEEEEEEEEEECCCCEEECCEEEEECCCCCEEEEEECCCC*-EEEEECCCCCC*CCCCCCHH-HCCCCEEEEECCEEEEEEECCCCCCEEEEEEECCCCCCEEEEEEEEEEHHHCCCEEEECCEEEEECCCC--CEEEEEEECCCCEEE***EECCCCCCCEEEEEEECCCCEEEEEECCEEEEEEEEEE *CC*EEEECCCEEEEECCCCCEEEE*CCCCC*CCCCEEEEECC****EEEEECCHHHHHH*CCCEEEE******CCCCEEECCEEEEECCCCCEEEEEECCCCE*EEEEECCCCCC-CCCCCC****CCCCEEEEECCEEEEEEECCCCCCEEEEEEECCCCCCEEEEEEEEEEHHHCCCEEEECCEEEEECCCC**CEEEEEEECCCCEEEEEEEECCCCCCCEEEEEEECCCCEEEEEECCEEEEEEEEE* 418768.tem _________________________________ -CCEEEEECCCEEEEECCCCCEEEEECCCCC-CCCCEEEEECCE-EEEEEEECCHHHHHH-CCCEEEEEEEEEECCCCEEECCEEEEECCCCCEEEEEECCCCE-EEEEECCCCCC-CCCCCCHH-HCCCCEEEEECCEEEEEEECCCCCCEEEEEEECCCCCCEEEEEEEEEEHHHCCCEEEECCEEEEECCCC--CEEEEEEECCCCEEEEEEEECCCCCCCEEEEEEECCCCEEEEEECCEEEEEEEEEE Structural block scores 1 2 C 5.0 H 6.8 4.0 3 7 E 4.6 H 2.6 2.8 8 10 C 5.0 H 7.5 4.7 11 15 E 5.0 H 4.0 3.6 16 20 C 5.0 H 4.1 3.2 21 25 E 4.6 H 0.2 0.2 26 30 C 5.0 H 3.9 2.8 32 35 C 5.0 H 5.4 5.5 36 40 E 5.0 H 0.2 0.4 41 42 C 5.0 H 4.5 3.0 45 51 E 4.4 M 2.0 1.7 52 53 C 5.0 H 5.0 5.0 54 59 H 5.0 H 4.0 3.7 61 63 C 5.0 H 5.3 6.7 64 73 E 3.8 M 3.3 2.5 74 77 C 5.0 H 0.2 0.2 78 80 E 5.0 H 0.7 0.3 81 82 C 5.0 H 4.5 7.5 83 87 E 5.0 H 0.0 0.0 88 92 C 5.0 H 3.4 3.2 93 98 E 5.0 H 0.3 0.8 99 102 C 5.0 H 5.5 4.8 105 109 E 5.0 H 3.2 4.0 110 115 C 5.0 H 3.2 3.2 117 122 C 5.0 H 3.2 2.8 123 124 H 3.0 P 5.5 1.0 127 130 C 5.0 H 1.0 0.5 131 135 E 5.0 H 0.2 0.0 136 137 C 5.0 H 3.5 3.5 138 144 E 5.0 H 0.6 0.3 145 150 C 5.0 H 3.8 4.6 151 157 E 5.0 H 0.6 0.6 158 163 C 5.0 H 4.0 3.7 164 173 E 5.0 H 3.3 3.5 174 176 H 5.0 H 5.3 3.7 177 179 C 5.0 H 0.0 0.0 180 183 E 5.0 H 0.0 0.0 184 185 C 5.0 H 1.0 0.5 186 190 E 5.0 H 0.0 0.2 191 194 C 5.0 H 4.2 3.8 195 196 - 3.0 P 75.0 12.5 198 204 E 5.0 H 1.1 1.0 205 208 C 5.0 H 3.8 5.1 209 216 E 4.2 M 5.1 4.6 217 223 C 5.0 H 4.9 2.6 224 230 E 5.0 H 0.3 0.1 231 234 C 5.0 H 3.5 3.2 235 240 E 5.0 H 0.5 0.0 241 242 C 5.0 H 2.0 2.0 243 252 E 4.8 H 2.6 2.9 >>>>>>