Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1gxja- CCCHHHHHHHHHH--HHCCCEEEEHHHHCCCCHHHHHHHHHHHHHHHHCEEECCHHHHHHHHHHHHHHCCCCCCEEECCCCCC-CCCCCCCHHHCCCEEEEHHHHCCCC-HHHHHHHHHHHCCCEEECCHHHHHHHHHHHCCCCCEEECCCCEECCCCCEECCCC >P1;d3l51b1 C--HHHHHHHHHHHHCCCCCEEEEHHHCCCCCHHHHHHHHHHC-HHHHCEEECCHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCCCHHH----CCCHHHHCCCCCHHHHHHHHHHHCCCEEECCHHHHHHHHCCCCCCCCEEECCCCEECCCCC-CCC-- PSA >P1;d1gxja- d467005102637--85092013004611706a82660072009b54710004439117507510775807a06001156080-82a42b5058190111001510705-b7096000300520000563910440286290a1300035022042a38473a8b >P1;d3l51b1 d--9228203703638607303020162170696167018300-911730005369016505720985b28a15010047772596b73a015b----0400122070a476032001400520000765810550034a9450200016031046818-85c-- Translating the sequences C**HHHHHHHHHH--HHCCCEEEEHHHHCCCCHHHHHHHHHHH*HHHHCEEECCHHHHHHHHHHHHHHCCCCCCEEECCCCCC-CCCCCCCHHH****EEEHHHHCCCC-HHHHHHHHHHHCCCEEECCHHHHHHHHHHHCCCCCEEECCCCEECCCCC*ECC** C--HHHHHHHHHH****CCCEEEEHHH*CCCCHHHHHHHHHH*-HHHHCEEECCHHHHHHHHHHHHH*CCCCCCEEECCCCCC*CCCCCCCHHH----***HHHHCCCC*HHHHHHHHHHHCCCEEECCHHHHHHHH***CCCCCEEECCCCEECCCCC-*CC-- 75553.tem _________________________________ C--HHHHHHHHHH--HHCCCEEEEHHHHCCCCHHHHHHHHHHH-HHHHCEEECCHHHHHHHHHHHHHHCCCCCCEEECCCCCC-CCCCCCCHHH----EEEHHHHCCCC-HHHHHHHHHHHCCCEEECCHHHHHHHHHHHCCCCCEEECCCCEECCCCC-ECC-- Structural block scores 1 2 - 3.0 P 5.0 75.0 3 12 H 5.0 H 3.1 3.6 13 14 - 3.0 P 75.0 4.5 15 16 H 3.0 P 6.5 7.0 17 19 C 5.0 H 3.7 3.3 20 23 E 5.0 H 1.0 1.2 24 27 H 4.5 M 2.8 2.2 28 31 C 5.0 H 3.5 3.5 32 42 H 4.8 H 3.8 3.7 44 47 H 5.0 H 6.9 4.5 49 51 E 5.0 H 0.0 0.0 52 53 C 5.0 H 4.0 4.0 54 67 H 4.9 H 4.1 4.5 68 73 C 5.0 H 5.2 6.3 74 76 E 5.0 H 0.3 0.3 77 82 C 5.0 H 3.3 4.5 84 90 C 5.0 H 6.1 6.7 91 93 H 5.0 H 4.3 5.8 94 97 - 3.0 P 2.8 75.0 98 100 E 3.0 P 0.7 1.3 101 104 H 5.0 H 1.8 1.2 105 108 C 5.0 H 3.0 4.4 110 120 H 5.0 H 3.3 2.1 121 123 C 5.0 H 2.3 2.3 124 126 E 5.0 H 0.0 0.0 127 128 C 5.0 H 5.5 6.5 129 139 H 4.5 M 3.5 3.8 140 144 C 5.0 H 4.7 4.0 145 147 E 5.0 H 0.0 0.0 148 151 C 5.0 H 2.5 2.5 152 153 E 5.0 H 1.0 0.5 154 158 C 5.0 H 5.5 5.4 161 162 C 5.0 H 6.8 8.8 163 164 - 3.0 P 9.8 75.0 >>>>>>