Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1i6ua- CCCCHHHHHHHHHHHHHHCCCCEEEECCCCHHHHHHHHCC-CCCCCCCEEEECCCCCCEEEEECCC-----CCCCEEECCC---CCEECCCCCHHHHHHHCCCCCCCEEEEECCCCC-CHHHHHHCCCCEEEEEEEC >P1;d1seia- CCCHHHHHHHHHHHHHHHCCCCEEEE-ECCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEEECCCCCCCCCCCEEECCCCCCCCEECHHHCCCCC------CCCCEEEEEECCEEEEHHHHHHHCCCEEEEEEEC PSA >P1;d1i6ua- ba54500200550152076859305083069202500612-6381038165373a97020305037-----6085010057---436094860760255205579801000307570-1066039432235000101 >P1;d1seia- 18074027005404701754674140-716820530050034271055043346a851102020415996320860612036c65361648502719------ca61000020a56010042058491012100304 Translating the sequences CCC*HHHHHHHHHHHHHHCCCCEEEE**CCHHHHHHHH**-*CCC***EEEE*CCCC*EEEEE*CC-----CCCCEEECCC---CCEEC***CHHHH******CCCCEEEEE*CC**-*HHHHHH*CCCEEEEEEEC CCCHHHHHHHHHHHHHHHCCCCEEEE-ECCHHHHHHHHHH*HCCCEEEEEEEECCCCEEEEEEECC*****CCCCEEECCC***CCEECHHHC****------CCCCEEEEEECCEE*EHHHHHHHCCCEEEEEEEC 56047.tem _________________________________ CCCHHHHHHHHHHHHHHHCCCCEEEE-ECCHHHHHHHHHH-HCCCEEEEEEEECCCCEEEEEEECC-----CCCCEEECCC---CCEECHHHCHHHH------CCCCEEEEEECCEE-EHHHHHHHCCCEEEEEEEC Structural block scores 0 2 C 5.0 H 9.0 3.0 3 17 H 4.9 H 2.4 3.2 18 21 C 5.0 H 7.0 5.5 22 25 E 5.0 H 2.0 2.2 28 29 C 5.0 H 3.0 3.5 30 39 H 4.6 H 2.7 2.3 42 44 C 5.0 H 4.0 3.3 45 52 E 4.0 M 4.1 3.0 53 56 C 5.0 H 7.4 7.4 57 63 E 4.4 M 1.4 0.9 64 65 C 5.0 H 5.0 2.5 66 70 - 3.0 P 75.0 6.4 71 74 C 5.0 H 4.8 4.0 75 77 E 5.0 H 0.3 2.3 78 80 C 5.0 H 4.0 1.7 81 83 - 3.0 P 75.0 8.2 84 85 C 5.0 H 3.5 4.0 86 87 E 5.0 H 3.0 3.5 89 91 H 3.0 P 6.0 5.7 93 96 H 3.0 P 3.8 4.8 97 102 - 3.0 P 3.7 75.0 103 106 C 5.0 H 6.0 7.5 107 112 E 4.7 H 0.7 0.3 113 114 C 5.0 H 6.0 7.8 115 116 E 3.0 P 3.5 3.0 119 125 H 4.7 H 4.0 3.3 126 128 C 5.0 H 2.3 3.3 129 135 E 5.0 H 1.3 1.0 >>>>>>