Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1qwza1 CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCEEEEEECCCCC--CCHHHHHHHHHCHHHHHHCCEEEEEECCEEEEEEEEEEEEEECCC--CCCCCCCCCHHHHHHHHHHHHHHCCCCCC-CCCCCCCCEEEEEECCCCC---CCCCEEEEEEEEEEEEE >P1;d1t2wa- ---------------------------CCCCCCCCC---CCCEEEEEHHHCEEEEEECCCCCHHHHHH---------CEEECCCCCCCC--CCEEEEEEECCCCCCCCCCCCHHHCC------CCCEEEEEECCEEEEEEEEEEEEECCC----------------CCCCCCCCC------------CCCCEEEEEEEEEEECCCCEEEEEEEEEEEECC-- >P1;d5yfka- -CCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCEEEEEECCCCCHHHCCCCCCCCCCCCCEEECCCCCCCC-CCEEEEECCCCCC--CCCCHHHHHHHCHHHHHHCCEEEEEECCEEEEEEEEEEEEEEHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEEEECCC-----CCEEEEEEEEEEC-- PSA >P1;d1qwza1 988606410670263086128728871530052028307201000307b1302000011a43740142004469171000000430627901400001002175--830000045016492058244040002202040300001425186--68241509678205720740463050b0b-0a0629230000001238a---2a67510000010454a >P1;d1t2wa- ---------------------------91912a634---74023010460806130100304470093---------1000266a0407--43102000245976772001406408------760402030c84314050172221519----------------95277315a------------786500102103714996551653110001259-- >P1;d5yfka- -7a14595039059200186998778255108605930620300030570501000010a646403521044680800000010805087-0300002020261--6200010440276a20671440200275863201000002251860872041607779205800840272052609c0904191200000030465-----a703000000329-- Translating the sequences *******HHHHHHHH*****HH*****HHHHHHHHC*CCCEEEEEE*CCCCCEEEEECCCCCC***CCCCCCCCCCCCCEEECCCCCCCC*CCEEEEEECCCCC--CC**HHHHHHHCHHHHHHCCEEEEEECCEEEEEEEEEEEEEECC*--**CCCCCCCHHHHHHHHHHHHH*CCCCCC-CCCCCCCCEEEEEE**CCC---C*CCEEEEEEEEEE*** ---------------------------********C---C**EEEEE***C*EEEEECCCCC*HHH**---------C*EE*CCCCCCC--CCEEEEEE*CCCC**CCCC**HHH**------*CCEEEEEECCEEEEEEEEEEEEE*CC----------------*********------------CCCCEEEEEEEE******C***EEEEEEEEE*C-- -******HHHHHHHH*****HH*****HHHHHHHH**CCCEEEEEEECCCCCEEEEE*CCCCCHHHCCCCCCCCCCCCCEEECCCCCCCC-CCEEEEE*CCCCC--CCCCHHHHHHHCHHHHHHCCEEEEEECCEEEEEEEEEEEEEE*******CCCCCCCHHHHHHHHHHHHH*CCCCCC*CCCCCCCCEEEEEEEECCC-----CCEEEEEEEEEEC-- 63817.tem _________________________________ -******HHHHHHHH*****HH*****HHHHHHHHC*CCCEEEEEEECCCCCEEEEECCCCCCHHHCCCCCCCCCCCCCEEECCCCCCCC-CCEEEEEECCCCC--CCCCHHHHHHHCHHHHHHCCEEEEEECCEEEEEEEEEEEEEECC*--**CCCCCCCHHHHHHHHHHHHH*CCCCCC-CCCCCCCCEEEEEEEECCC---C*CCEEEEEEEEEEC-- Structural block scores 1 6 * 2.7 P 5.3 75.0 6.1 7 14 H 4.0 M 3.1 75.0 4.1 15 19 * 2.7 P 3.4 75.0 3.0 20 21 H 4.0 M 7.5 75.0 9.0 22 26 * 2.7 P 5.2 75.0 6.4 27 34 H 4.0 M 2.1 5.2 3.8 37 39 C 4.3 M 3.0 52.3 2.7 40 46 E 4.6 H 0.6 1.4 0.9 47 51 C 4.2 M 4.5 3.6 3.4 52 56 E 5.0 H 0.4 2.2 0.2 57 62 C 4.7 H 4.4 1.8 4.6 63 65 H 4.0 M 1.7 2.3 2.3 66 78 C 4.1 M 2.9 52.9 2.9 79 81 E 4.7 H 0.0 0.7 0.0 82 89 C 4.9 H 3.9 13.6 3.6 91 92 C 5.0 H 2.5 3.5 1.5 93 98 E 4.8 H 0.2 0.5 0.3 99 103 C 4.8 H 3.0 5.4 2.2 104 105 - 4.0 M 75.0 6.5 75.0 106 109 C 4.5 M 2.8 2.2 2.0 110 116 H 4.4 M 1.4 3.3 1.6 118 123 H 4.0 M 4.7 63.7 5.2 124 125 C 5.0 H 3.0 3.0 2.5 126 131 E 5.0 H 1.3 1.5 1.3 132 133 C 5.0 H 2.0 10.2 6.0 134 147 E 4.9 H 1.5 2.6 2.1 148 149 C 4.0 M 4.5 5.0 4.5 151 152 - 4.0 M 75.0 75.0 4.0 153 154 * 2.7 P 7.0 75.0 4.5 155 161 C 4.0 M 3.9 75.0 3.6 162 174 H 4.0 M 4.0 26.9 4.0 176 181 C 4.0 M 4.7 75.0 3.7 183 190 C 4.5 M 4.1 40.8 3.2 191 198 E 4.8 H 0.4 0.9 0.4 199 201 C 4.0 M 7.2 4.0 5.0 202 204 - 4.0 M 75.0 8.0 75.0 207 208 C 4.0 M 6.5 3.5 8.8 209 218 E 4.9 H 1.1 1.8 0.8 220 221 - 4.0 M 7.2 75.0 75.0 >>>>>>