Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1zsoa1 --CEEEEEEEEEECEEEEECC-CCCCEEEEEEECCCCCEEE-EEEECCCCCEECCCCCCEECC-CCCCCCCCCCEEEEECCCCCCEEEHHHCCCCEEEEEEEEECEEEEEECCCCCEEEEECC-CCEEEEECCCCCCEEECCCCCC-CEEEEEEEEEEE-- >P1;d5zrta- CEEEEEEEEEEEECEEEEEECCCCCCEEEEEEECCCCCCCCCCEEECHHHCEECCCCCCEECEEEECCCCCCEEEEEEEH-HHCCCCCHHHCCCCEEEEEEEECCEEEEEEECCCCEEEEECCCCCEEEEECCCCCCEEEEECCCCEEEEEEEEEEEEEEC PSA >P1;d1zsoa1 --5110303050450430105-68020102030475a5467-7040415476724b5a73002-2306a766501020294a71010368146535600003073050350400630001036-5430680504846165519848-600047042409-- >P1;d5zrta- 3a40002020304402303048770401020306426452982230224465909cc5a300234609627660002025-a22530238145733200201135020340201660003039173816a0504845155509737560002805251576 Translating the sequences --*EEEEEEEEEECEEEEE*C-CCCCEEEEEEECCCCCEEE-EEEEC***CEECCCCCCEEC*-**CCCCCC**EEEEE****CCEEEHHHCCCCEEEEEEEEECEEEEEE*CCCCEEEEECC-CCEEEEECCCCCCEEE**CCCC-*EEEEEEEEEEE-- **EEEEEEEEEEECEEEEEEC*CCCCEEEEEEECCCCC*****EEECHHHCEECCCCCCEECE*EECCCCCCEEEEEEEH-HHCC***HHHCCCCEEEEEEEE*CEEEEEEECCCCEEEEECC*CCEEEEECCCCCCEEEEECCCC*EEEEEEEEEEEE** 141678.tem _________________________________ --EEEEEEEEEEECEEEEEEC-CCCCEEEEEEECCCCCEEE-EEEECHHHCEECCCCCCEECE-EECCCCCCEEEEEEEH-HHCCEEEHHHCCCCEEEEEEEEECEEEEEEECCCCEEEEECC-CCEEEEECCCCCCEEEEECCCC-EEEEEEEEEEEE-- Structural block scores 0 1 - 3.0 P 75.0 6.8 2 12 E 4.8 H 2.0 1.4 14 19 E 4.7 H 1.3 1.3 22 25 C 5.0 H 4.0 4.5 26 32 E 5.0 H 0.9 0.9 33 37 C 5.0 H 6.3 4.4 38 40 E 3.0 P 5.7 5.3 42 45 E 4.5 M 2.8 1.8 47 49 H 3.0 P 3.3 3.3 51 52 E 5.0 H 6.5 7.0 53 58 C 5.0 H 6.7 8.2 59 60 E 5.0 H 1.5 1.5 64 65 E 3.0 P 2.5 5.0 66 71 C 5.0 H 5.9 5.0 72 78 E 4.4 M 1.4 1.4 81 82 H 3.0 P 8.8 6.2 83 84 C 5.0 H 0.5 3.5 85 87 E 3.0 P 1.3 1.7 88 90 H 5.0 H 5.0 4.0 91 94 C 5.0 H 4.5 4.8 95 103 E 4.8 H 2.3 1.3 105 111 E 4.7 H 2.4 1.6 112 115 C 5.0 H 2.2 3.2 116 120 E 5.0 H 0.2 0.6 121 122 C 5.0 H 4.5 6.0 124 125 C 5.0 H 4.5 5.0 126 130 E 5.0 H 3.4 5.1 131 136 C 5.0 H 4.5 4.3 137 141 E 4.2 M 3.6 3.2 142 145 C 5.0 H 7.2 6.5 147 158 E 4.8 H 3.0 2.8 159 160 - 3.0 P 75.0 6.5 >>>>>>