Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ewqa4 CCCCCCCCC---CCCHHHHHHHHHHHHCCCCEEEEEECCEEECCHHHHHHHHHHHCCCCCCEECC-CCEEC-CEEEHHHHHHHHHHHHC-CCCEEEEEECCCHHHCCCCCCEEEEEEECCCC >P1;d1wb9a4 -----CCCCCHHHCCHHHHHHHHHHHHCCCCEEEEEECCEEEEEHHHHHHHHHHHCCCCEEECCCCCCCEEEEEEEHHHHHHHHHHHHHCCCCEEEEEECCCHHHCCCCCCEEEEEEECC-- PSA >P1;d1ewqa4 95051a596---7118105200712363682000002a8502000620250072091a476573a-21402-01013841971065037-c350000324166980bb416060553227b7 >P1;d1wb9a4 -----a5947694176102103612761693000022a6600003a105501920a19356473b88651220103473299216503947210000224566882a7307060353254-- Translating the sequences *****CCCC---*CCHHHHHHHHHHHHCCCCEEEEEECCEEE**HHHHHHHHHHHCCCC**EECC-CCEE*-*EEEHHHHHHHHHHHH*-CCCEEEEEECCCHHHCCCCCCEEEEEEECC** -----CCCC***HCCHHHHHHHHHHHHCCCCEEEEEECCEEEEEHHHHHHHHHHHCCCCEEE*CC*CC*EE*EEEEHHHHHHHHHHHHH*CCCEEEEEECCCHHHCCCCCCEEEEEEECC-- 55271.tem _________________________________ -----CCCC---HCCHHHHHHHHHHHHCCCCEEEEEECCEEEEEHHHHHHHHHHHCCCCEEEECC-CCEEE-EEEEHHHHHHHHHHHHH-CCCEEEEEECCCHHHCCCCCCEEEEEEECC-- Structural block scores 0 4 - 3.0 P 4.0 75.0 5 8 C 5.0 H 7.6 7.1 9 11 - 3.0 P 75.0 7.3 13 14 C 5.0 H 1.0 4.0 15 26 H 5.0 H 2.9 2.9 27 30 C 5.0 H 4.8 4.8 31 36 E 5.0 H 0.3 0.7 37 38 C 5.0 H 9.2 8.2 39 43 E 4.2 M 1.4 1.2 44 54 H 5.0 H 2.2 3.3 55 58 C 5.0 H 6.1 5.9 59 62 E 3.5 M 6.2 5.5 63 64 C 5.0 H 6.8 7.2 66 67 C 5.0 H 1.5 7.0 68 70 E 3.7 M 2.0 2.7 72 75 E 4.5 M 0.5 1.0 76 88 H 4.8 H 4.2 4.6 90 92 C 5.0 H 6.8 3.3 93 98 E 5.0 H 0.8 0.7 99 101 C 5.0 H 3.7 5.0 102 104 H 5.0 H 7.7 7.3 105 110 C 5.0 H 5.7 4.9 111 117 E 5.0 H 3.0 2.7 118 119 C 5.0 H 4.5 4.5 120 121 - 3.0 P 9.2 75.0 >>>>>>