Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1kzqa1 C-CCCEEEEECCC-CCEEE-EEEECCC-CCEEEEECCCCCEEECHHHHCCCCCCCEECCCCCCCCCCCCCHHHCCCCCCHHHEECCCCCCCCCCEEEECCHHHCCCCCEEEEEEEECCCHHH-CEEEEEEECCC >P1;d1kzqa2 CCEEECCEEECCCCCCEEEEEEEECCCCCCEEEEECCCCEEEECCCC-----CEEECCCCCCCC--CEEEHHHCCCCCCCCCEEEECCC--CCEEEEECCCCCCCCCCEEEEEEEEECCCCCEEEEEEEEECC- PSA >P1;d1kzqa1 a-a2742217045-76475-7060249-41200030289070005500746a030034b195009a814605620760639007373940376003050268300784230000014b6575-00004020535 >P1;d1kzqa2 90526a2205061d763510306034a35250100047a06020965-----420034a608b1--84440661076078600a87033--8a004060588000986470000020489a543010503041- Translating the sequences C-***EEEEECCC-CCEEE-EEEECCC-CCEEEEECCCC*EEECHHH*****C**EECCCCCCC**C***HHHCCCCCCHHHEE**CCC**CC*EEEECCHHHCCCCCEEEEEEEE*CCHHH-*EEEEEEECC* C*EEE**EEECCC*CCEEE*EEEECCC*CCEEEEECCCCEEEEC***-----CEEE*CCCCCCC--CEEEHHHCCCCCC***EEEECCC--CCEEEEECC***CCCCCEEEEEEEEECC****EEEEEEEECC- 74877.tem _________________________________ C-EEEEEEEECCC-CCEEE-EEEECCC-CCEEEEECCCCEEEECHHH-----CEEEECCCCCCC--CEEEHHHCCCCCCHHHEEEECCC--CCEEEEECCHHHCCCCCEEEEEEEEECCHHH-EEEEEEEECC- Structural block scores 2 9 E 3.8 M 4.4 4.1 10 12 C 5.0 H 3.0 2.3 14 15 C 5.0 H 6.5 6.5 16 18 E 5.0 H 5.3 3.0 20 23 E 5.0 H 3.2 2.2 24 26 C 5.0 H 5.0 5.8 28 29 C 5.0 H 2.5 3.5 30 34 E 5.0 H 1.0 1.2 35 38 C 5.0 H 4.8 5.4 39 42 E 4.5 M 1.8 2.0 44 46 H 3.0 P 3.3 6.7 47 51 - 3.0 P 5.5 75.0 53 56 E 3.5 M 1.5 1.2 57 63 C 5.0 H 4.4 5.9 64 65 - 3.0 P 9.8 75.0 67 69 E 3.0 P 3.7 4.0 70 72 H 5.0 H 3.7 4.0 73 78 C 5.0 H 3.5 3.5 79 81 H 3.0 P 4.0 4.7 82 85 E 4.0 M 4.2 6.4 86 88 C 5.0 H 5.3 2.0 89 90 - 3.0 P 1.5 75.0 91 92 C 5.0 H 6.5 9.2 93 97 E 4.6 H 1.6 2.0 98 99 C 5.0 H 1.0 2.5 100 102 H 3.0 P 5.7 5.3 103 107 C 5.0 H 3.8 4.6 108 116 E 4.8 H 1.1 1.4 117 118 C 5.0 H 8.8 6.0 119 121 H 3.0 P 5.7 8.2 123 130 E 4.8 H 0.8 1.5 131 132 C 5.0 H 4.0 2.5 >>>>>>