Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1m5wa- CCCEEEEECHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCEEEEECCCCCCCCCHHHHHHHHHHC---CCEEEEEECCC------HHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHCCCCEEEEECHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCHHHHHC-CCCEEEEEECHHHHHHHHHHCHHHHHHHHHHHHHHHHC >P1;d6w6aa1 -CCEEEEECHHHHHHHHHHCCC-CCHHHHHHHHHHCCCCEEEECCCCCCCCCCHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCHHHHHHHHCCCEEEECCCCCCC-CCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCHHHHHCCCEEEEECHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHCCCEEEEEECHHHHHHHHHHCHHHHHHHHHHHC----- PSA >P1;d1m5wa- b802000100410670378c39833028005400704030000000142300354006304830---92501010004------750153038150410000206491a516000601643a503800540681a0400000404682050014060400000007008087ba4478238504800720371a0501003705091054005-0730200000820073058590770053015105511f >P1;d6w6aa1 -a05000101300451388799-54037104500608030000000133300117104500810673a2400010101176470300150056050400000009683-60550060860085035207604819020000040617404401707031000100301922889908a317400400530284a02000025023900550046039040000073007307978266005502822----- Translating the sequences *CCEEEEECHHHHHHHH**CCC*CCHHHHHHHHH*CCCCEEEEECCCCCCCCCHHHHHHHHHH*---CCEEEEEECCC------HHHHHHHHHHCCCEEEECCCCCCC*CCCCCCC*HHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHH*CCCEEEEECHHHHH***HHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCHHHHH*-CCCEEEEEECHHHHHHHHHHCHHHHHHHHHHHH***** -CCEEEEECHHHHHHHHHHCCC-CCHHHHHHHHHHCCCCEEEE*CCCCCCCCCHHHHHHHHHHH***CCEEEEEECCC********HHHHHHHHCCCEEEECCCCCCC-CCCCCCCHHHHHHHHHHHHHHHH*CCCEEEEEECCC*****HHHHHCCCEEEEECHHHHHHHH****HHHHHHHHHHHHHHH*CCCEEEEECCCCCCCHHHHHH*CCCEEEEEECHHHHHHHHHHCHHHHHHHHHHH*----- 63892.tem _________________________________ -CCEEEEECHHHHHHHHHHCCC-CCHHHHHHHHHHCCCCEEEEECCCCCCCCCHHHHHHHHHHH---CCEEEEEECCC------HHHHHHHHHHCCCEEEECCCCCCC-CCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHCCCEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCHHHHHH-CCCEEEEEECHHHHHHHHHHCHHHHHHHHHHHH----- Structural block scores 1 2 C 5.0 H 4.0 5.2 3 7 E 5.0 H 0.6 1.2 9 18 H 4.6 H 3.6 3.3 19 21 C 5.0 H 8.2 8.3 23 24 C 5.0 H 3.0 4.5 25 34 H 4.8 H 2.6 2.6 35 38 C 5.0 H 1.8 2.8 39 43 E 4.6 H 0.0 0.0 44 52 C 5.0 H 1.4 1.2 53 63 H 4.8 H 3.0 2.5 64 66 - 3.0 P 75.0 5.3 67 68 C 5.0 H 5.5 6.2 69 74 E 5.0 H 1.2 0.8 75 77 C 5.0 H 1.3 0.7 78 83 - 3.0 P 75.0 4.2 84 93 H 4.6 H 3.3 2.0 94 96 C 5.0 H 3.0 3.0 97 100 E 5.0 H 0.2 0.0 101 107 C 5.0 H 3.1 3.7 109 115 C 5.0 H 2.6 3.1 116 132 H 4.8 H 3.7 3.6 133 135 C 5.0 H 3.8 3.3 136 141 E 5.0 H 0.7 0.3 142 144 C 5.0 H 2.7 3.3 145 154 H 3.8 M 2.6 2.8 155 157 C 5.0 H 3.3 3.3 158 162 E 5.0 H 0.0 0.4 164 191 H 4.4 M 4.4 3.8 192 194 C 5.0 H 3.8 4.8 195 199 E 5.0 H 1.2 0.4 200 206 C 5.0 H 3.6 3.0 207 212 H 4.7 H 2.3 2.3 214 216 C 5.0 H 3.3 4.0 217 222 E 5.0 H 0.3 0.7 224 233 H 5.0 H 3.8 4.3 235 246 H 4.8 H 2.4 3.2 247 251 - 3.0 P 6.9 75.0 >>>>>>