Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1r5la2 ------CCHHHHHCCCEEECCCCCCCCCEEEEEEHHHCCCC----CCCHHHHHHHHHHHHHHHCC--CHHHHH------HCEEEEEECCCCCHHHHHHCCHHHHHHHHHHHHCCCCCCEEEEEEECCCHHHHHHHC-CHHHCCHHHHCCEEC-CCCCHHHHHHHCC-CCCCHHHCCCCCC---CHHHHHHHHHCCC--HHHHHHCCC------------ >P1;d4uyba2 ------CCHHHHHHCCCEEE-EECCCCCEEEEEECCCCCHHHHHCCCCHHHHHHHHHHHHHHHHH-HHHHHHHHHCCCCCCEEEEEECCCCCHHHHCHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHHHCCHHHHHCEEECCCCCC-CHHHHCCHHHCCHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCC------------ >P1;d6slda2 CHHHHHHHHHHHCCCCEEEE-EECCCCCEEEEEECCCCCHHHHHHHCCHHHHHHHHHHHHHHHHHCHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHH-CHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHCHHHCCHHHHCCEEECCCCHHHHHHHHCCHHHCCHHHCCCCCCCCCC-CCHHHCCCCHHHCCCCCCCCCCCCCCCHHHCCCC PSA >P1;d1r5la2 ------70670065000000562056401000020430619----61606212403520130015--465056------300100210760686029215970156205321a517060300010123b3188124-156406760283041-68b1693038404-a100550318813---6400751174071--89416736b------------ >P1;d4uyba2 ------34810652000410-12056100000001130205000100538300800231066056-205403853a6606300000006904850128200401240033127526841230000314a316623831454057302720451abb15-203830137300240107330896443047603107804793153884------------ >P1;d6slda2 5a981640230071000000-30045020000121190618703730837401811341261036101200143196605210101106a15395167-11812532042227626832031000202b405910650462068703720421aba059402710257100650206160975b-3521200100003772129284035203940137 Translating the sequences ------CCHHHHHCCCEEE****CCCCCEEEEEE***CC**----CCCHHHHHHHHHHHHHHH**--*HHHHH------*CEEEEEECCCCCHHHHHH*CHHHHHHHHHHHH**CCCCEEEEEEECCC**HHHHH*-CHHHCCHHHHCCEE*-CCCCHHHHHHHCC-**CCHHHCCCCCC---C***HHH***CCC--HHH***CCC------------ ------CCHHHHH*CC*EEE-EECCCCCEEEEEECCCCCHHHHH*CCCHHHHHHHHHHHHHHHHH-HHHHHHHHHCCCCCCEEEEEECCCCCHHHH*H**HHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHH*HHHCCHHHH*CEEECCCCC*-*HHHHCCHHHCCHHHCCCCCCCCCC*CC***CCCCCC*CHHHCCCCCC------------ ********HHHH*CCCEEEE-EECCCCCEEEEEECCCCCHHHHH**CCHHHHHHHHHHHHHHHHH*HHHHHHHHHCCCCCCEEEEEECCCCCHHHHHH-CHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHCHHHCCHHHHCCEEECCCC*HHHHHHHCCHHHCCHHHCCCCCCCCCC-CCHHHCCCC***C***CCCCCC************ 52087.tem _________________________________ ------CCHHHHHCCCEEEE-EECCCCCEEEEEECCCCCHHHHH*CCCHHHHHHHHHHHHHHHHH-HHHHHHHHHCCCCCCEEEEEECCCCCHHHHHH*CHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHCHHHCCHHHHCCEEECCCCCHHHHHHHCCHHHCCHHHCCCCCCCCCC*CCHHHCCCCCC*CHHHCCCCCC------------ Structural block scores 0 5 - 4.0 M 75.0 75.0 6.6 6 7 C 4.0 M 3.5 3.5 2.0 8 12 H 4.8 H 3.8 4.0 2.4 13 15 C 4.7 H 1.7 0.7 0.3 16 19 E 4.5 M 0.0 1.2 0.0 21 22 E 4.0 M 4.0 1.5 1.5 23 27 C 5.0 H 3.0 2.4 2.2 28 33 E 5.0 H 0.5 0.0 0.5 34 38 C 4.4 M 2.6 1.4 3.4 39 43 H 4.0 M 47.0 1.0 3.8 45 47 C 4.7 H 4.3 1.7 3.7 48 64 H 4.9 H 2.1 3.0 3.0 66 74 H 4.6 H 27.9 3.3 1.3 75 80 C 4.2 M 50.5 5.2 4.7 81 86 E 5.0 H 0.7 0.0 0.7 87 91 C 5.0 H 3.8 3.8 4.5 92 97 H 4.8 H 4.5 4.0 5.2 100 113 H 4.9 H 4.0 2.3 3.2 114 117 C 5.0 H 3.5 5.0 4.8 118 124 E 5.0 H 0.6 0.9 0.9 125 129 C 4.6 H 4.1 4.3 3.9 130 136 H 4.7 H 14.1 4.1 3.7 138 140 H 5.0 H 5.0 4.3 4.0 141 142 C 5.0 H 3.0 2.5 3.0 143 146 H 5.0 H 3.8 3.0 4.5 147 148 C 4.5 M 5.5 4.5 4.5 149 151 E 4.7 H 1.7 3.0 2.0 152 156 C 4.6 H 20.3 7.1 6.7 157 163 H 4.6 H 4.7 13.7 4.0 164 165 C 5.0 H 2.0 0.5 1.0 166 168 H 4.0 M 28.8 4.3 4.3 169 170 C 5.0 H 0.0 0.0 0.0 171 173 H 5.0 H 3.3 2.0 3.7 174 183 C 4.7 H 25.5 4.1 4.8 185 186 C 4.0 M 0.0 1.5 4.0 187 189 H 4.0 M 4.3 5.7 1.7 190 195 C 4.2 M 3.3 3.2 0.2 198 200 H 4.0 M 7.0 6.3 5.3 201 206 C 4.5 M 5.8 4.8 4.3 207 218 - 4.0 M 75.0 75.0 3.1 >>>>>>