Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1jlya1 ----CCCCC-EEEEEECCCCCEEEECCCCCCCCCCEEEEECCCCCCCCCEEEEECCCCCCCEEEEECCCCCEEEECCCCCCCEEEEECCCCCCCCCCCCCCEEEEECCCCCCCEEEEEECCCCEEEEEECCC-CCCCCEEEEEECCCCCCCCCCEEEEC- >P1;d1jlya2 CHHHHCCCCCCEEEECC-CCCEEEEEE--ECCEEEEEEEECCCCCHHHCEEEEECCC--CCEEEEECCCCEEEEECH--HHCEEEEECCHHHHC--CHHHCEEEEEEE---CCEEEEEECCCCEEEEEECCCCCCCCCEEEEEECCCC--HHHCEEEEEC PSA >P1;d1jlya1 ----35018-400020343731030137a47050001020764907203020370673c5100010452640010235943000052882317494420000403225ba4453010201116110003557-c61520010326861b8530003037- >P1;d1jlya2 98616502695000304-264100036--17a32002031764a26401020132b8--700002025384002026--730000409304949--441010405037---74300020253531012452a6870520000117924--8203050261 Translating the sequences ----*CCCC-EEEEEEC*CCCEEEE*****CC***EEEEECCCCC***CEEEEECCC**CCEEEEECCCC*EEEEC*****CEEEEECC****C**C***CEEEEE*****CCEEEEEECCCCEEEEEECCC-CCCCCEEEEEECCCC*****CEEEE*- ****HCCCC**EEEE*C-CCCEEEEEE--ECCEEEEEEEECCCCCHHHCEEEEECCC--CCEEEEECCCCEEEEECH--HHCEEEEECCHHHHC--CHHHCEEEEEEE---CCEEEEEECCCCEEEEEECCC*CCCCCEEEEEECCCC--HHHCEEEEE* 50382.tem _________________________________ ----HCCCC-EEEEEEC-CCCEEEEEE--ECCEEEEEEEECCCCCHHHCEEEEECCC--CCEEEEECCCCEEEEECH--HHCEEEEECCHHHHC--CHHHCEEEEEEE---CCEEEEEECCCCEEEEEECCC-CCCCCEEEEEECCCC--HHHCEEEEE- Structural block scores 0 3 - 3.0 P 75.0 6.0 5 8 C 5.0 H 3.5 3.2 10 15 E 4.3 M 1.0 1.3 18 20 C 5.0 H 4.3 4.0 21 26 E 4.3 M 1.3 1.7 27 28 - 3.0 P 8.8 75.0 30 31 C 5.0 H 3.5 8.8 32 39 E 4.2 M 1.0 1.4 40 44 C 5.0 H 5.2 5.9 45 47 H 3.0 P 3.0 3.3 49 53 E 5.0 H 2.4 1.2 54 56 C 5.0 H 4.3 7.2 57 58 - 3.0 P 7.8 75.0 59 60 C 5.0 H 3.0 3.5 61 65 E 5.0 H 0.2 0.4 66 69 C 5.0 H 4.2 4.5 70 74 E 4.6 H 1.0 1.2 77 78 - 3.0 P 7.0 75.0 79 80 H 3.0 P 3.5 5.0 82 86 E 5.0 H 1.4 0.8 87 88 C 5.0 H 8.0 6.0 89 92 H 3.0 P 3.2 4.2 94 95 - 3.0 P 6.5 75.0 97 99 H 3.0 P 0.7 1.7 101 107 E 4.4 M 2.3 2.7 108 110 - 3.0 P 8.7 75.0 111 112 C 5.0 H 4.5 5.5 113 118 E 5.0 H 1.0 0.8 119 122 C 5.0 H 2.2 3.8 123 128 E 5.0 H 0.8 1.8 129 131 C 5.0 H 5.7 5.8 133 137 C 5.0 H 5.3 4.4 138 143 E 5.0 H 1.0 0.3 144 147 C 5.0 H 5.2 5.5 148 149 - 3.0 P 9.8 75.0 150 152 H 3.0 P 2.7 3.3 154 158 E 4.6 H 2.6 2.6 >>>>>>