Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1chma1 CCCCEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEECC---------------HHHHHHHHCCCCCCCCCCCEEEECC-----CCEEEEEEHHH------------CCHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHCCC------------CEEEECHHHHHHHC--- >P1;d1pv9a1 -----------------------------CHHHHHHCCCCEEEECC---------------HHHHHHHHCCCCC---CCCEEEEEC-----CEEEEEEEHHH------------HHHHHHHCCC-CEEEEC------CCCHHHHHCCCCCEEEECCC-CCHHHHHHHHHCCCC-------------EEEECHHHHHHHHCC- >P1;d1wl6a1 ---------------CCCCHHHHHHHHHHHHHHCCC-CEEEEEECCCCCEEECCEECCCCCCHHHHHHHCCC----CCCCEEEEEECCCCCEEEEEEECCCCHHHHHHHCCCCHHHHHHHHHCCCEEEE-----HHHHHHHHHHHHCCCCEEECCCCCC-HHHHHHHHHHHHHHHCCHHHCCCCCCEEECCHHHHHHHHHCC PSA >P1;d1chma1 8764144238aa4491558984064007602830675905000010---------------550042000060739b220000025-----94000000362------------5050123031620000055462000300440077083000067308a614630272067------------06032008206823--- >P1;d1pv9a1 -----------------------------03820884906200014---------------7600642050519---730200059-----972200024a2------------3a70585082-604506------8375007507a071001026-079812330485007-------------613704810774469- >P1;d1wl6a1 ---------------c94646304610550084064-3000000014366679b745917024004100006----214000000045787241000026659821778891102b6029704065022-----1850663025103618000005842-a3028106500550571898a2700a5244026404613789 Translating the sequences ***************CCCCHHHHHHHHHHHHHHHHHCCCCEEEECC---------------HHHHHHHHCCCCC**CCCCEEEE*C-----C*EEEEEEHHH------------**HHHHHCCCCEEEEEC*****HHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHCCC------------CEEEECHHHHHHH*--- -----------------------------*HHHHHHCCCCEEEECC---------------HHHHHHHHCCCCC---CCCEEEEEC-----CEEEEEEEHHH------------HHHHHHHCCC-*EEEEC------***HHHHHCCCCCEEEECCC-CCHHHHHHHHH*CCC-------------EEEECHHHHHHHH*C- ---------------CCCCHHHHHHHHHHHHHH***-C**EEEECC****************HHHHHHHCCC----CCCCEEEEE*******EEEEEE****************HHHHHHH*CCCEEEE-----**HHHHHHHHH*CCCCEEE*CCCCC-HHHHHHHHHH***************CEEE*CHHHHHHHH*C* 53092.tem _________________________________ ---------------CCCCHHHHHHHHHHHHHHHHHCCCCEEEECC---------------HHHHHHHHCCCCC--CCCCEEEEEC-----CEEEEEEEHHH------------HHHHHHHCCCCEEEEEC---**HHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHCCC------------CEEEECHHHHHHHH*C- Structural block scores 0 14 - 4.0 M 5.7 75.0 75.0 15 18 C 4.0 M 4.8 75.0 7.9 19 35 H 4.2 M 4.1 45.8 3.3 36 39 C 4.2 M 4.8 4.8 19.5 40 43 E 5.0 H 0.0 0.5 0.0 44 45 C 5.0 H 0.5 2.5 0.5 46 60 - 4.0 M 75.0 75.0 5.7 61 68 H 4.9 H 2.0 3.1 1.4 69 73 C 4.6 H 2.6 4.0 31.2 74 75 - 4.0 M 6.0 75.0 75.0 76 79 C 4.8 H 3.9 21.2 1.8 80 84 E 4.8 H 0.4 1.4 0.0 86 90 - 4.0 M 75.0 75.0 6.2 92 98 E 4.7 H 0.6 1.9 1.0 99 101 H 4.0 M 3.7 5.5 5.7 102 113 - 4.0 M 75.0 75.0 5.1 114 120 H 4.7 H 2.3 5.5 5.4 121 124 C 4.5 M 2.5 21.2 2.5 125 129 E 4.6 H 0.4 3.0 16.8 131 133 - 4.0 M 4.7 75.0 75.0 134 135 * 2.7 P 4.0 75.0 4.5 136 144 H 4.6 H 1.2 12.2 3.1 145 149 C 4.8 H 4.4 4.9 3.6 150 153 E 4.8 H 0.8 0.5 0.0 154 159 C 4.7 H 4.0 15.0 15.7 160 169 H 4.9 H 4.2 4.3 3.5 170 172 C 4.0 M 4.3 2.3 3.3 173 184 - 4.0 M 75.0 75.0 4.8 186 189 E 4.8 H 2.8 4.2 3.8 191 198 H 4.9 H 3.6 4.4 3.2 >>>>>>