Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d3orsa1 -CCEEEEECCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHCCCC-CCCEEEEEEECCCCHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHCCCCCCCCEECCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCC >P1;d3rg8a- CCEEEEEECCHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHCCCCEEECCCCCCHHHHH-HHHHHHCCCCCCCCEECC----CHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHC-- PSA >P1;d3orsa1 -130000043881472043006106508051354501067559405710550697-9040000011470500150033090400000162a867053036304716d938050162257004600130072018947806731770774596667766a78a >P1;d3rg8a- 81000000258914a006600610660905231350206854a503700671185b1610000015980500240043099600001184b69a44-327305816bb2905127----717600130053017939a0473178247676778855a77-- Translating the sequences -C*EEEEECCHHHHHHHHHHHHHHHHCCC*EEEEECCCCCCHHHHHHHHHH**CC-CC*EEEEEEECCCCHHHHHHHHCCCCEEEEEECCC****H*HHHHHHCCCCCCCCEECC****HHHHHHHHHHHHHHCCC*HHHHHHHHHHHHHHHHHHHHHHH** *CEEEEEECCHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHCC*CCEEEEEE**CCCCHHHHHHHHCCCCEEE***CCCHHHHH-HHHHHHCCCCCCCCEECC----*HHHHHHHHHHHH*CCCHHHHHHHHHHHHHHHHHHHHHHH*-- 52255.tem _________________________________ -CEEEEEECCHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHCC-CCEEEEEEEECCCCHHHHHHHHCCCCEEEEEECCCHHHHH-HHHHHHCCCCCCCCEECC----HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH-- Structural block scores 2 7 E 4.7 H 0.5 0.0 8 9 C 5.0 H 3.5 3.5 10 25 H 5.0 H 3.4 4.0 26 28 C 5.0 H 2.7 3.0 29 34 E 4.7 H 3.8 3.2 35 40 C 5.0 H 3.2 3.5 41 52 H 4.7 H 3.9 3.7 53 54 C 5.0 H 8.0 6.5 56 57 C 5.0 H 4.5 3.5 58 65 E 4.2 M 0.8 0.9 66 69 C 5.0 H 4.0 5.5 70 77 H 5.0 H 1.5 1.6 78 81 C 5.0 H 3.2 6.0 82 87 E 4.0 M 0.2 0.3 88 90 C 5.0 H 6.2 7.8 91 95 H 3.4 M 5.2 6.7 97 102 H 5.0 H 2.7 3.3 103 110 C 5.0 H 5.9 6.1 111 112 E 5.0 H 2.5 3.0 113 114 C 5.0 H 3.5 4.5 115 118 - 3.0 P 4.0 75.0 119 132 H 4.7 H 1.7 2.4 133 135 C 5.0 H 7.0 6.3 136 159 H 4.8 H 5.8 6.1 160 161 - 3.0 P 9.2 75.0 >>>>>>