Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2w4ra- --CCCCCHHHCEEEECCCCCEEEEHHHEEEECCCEEEECCHHHHHCEEEECCC---CCCC-CCEEEEEEEECC--CCCEEEEEEEECC-EEEEEECHHHEEEEECC--EEECCCCHHHCCCCCCCCCHHHHCCCCCCC >P1;d3ga3a1 CCCCCCCHHHEEEEECCCCCEEEEHHHCEEECCCEEECCCCHHHHCEEEECCCCCCEECC-CCEEEEEEEEC---CCCEEEEEEEECC-EEEEEECHHHEEEEECCCCEEECCCCHHHCCCCCCEECCCC-------- >P1;d4a2va- ---------CCEEEECCCCCEEEEHHHEEEECCCEEEECCCHHHHHEEEEECC--CCCCCCCEEEEEEEEECCCCCCCEEEEEEEECCEEEEEEECHHHEEEC-----CCCCHHHHHHCCCCCCCCCHHHHHHHCCCC PSA >P1;d2w4ra- --666052760300026154701603202304783000137805640736976---9a28-508330302067--2735004102389-16000061600104056--944427618600090670639825849a97 >P1;d3ga3a1 78927951430401036365600406403103761100237904840535737842782a-52414000105---2623001002189-850000306002012788776561871850405053331a6-------- >P1;d4a2va- ---------75401015245400207300105962000197702720536847--5845916022114020659a0535003003159147000052800105-----633505602752ba178065940495347a Translating the sequences --CCCCCHHHCEEEECCCCCEEEEHHHEEEECCCEEEECC*HHHHCEEEECCC---CCCC-CCEEEEEEEECC--CCCEEEEEEEECC-EEEEEECHHHEEEEECC--EEECCCCHHHCCCCCCCCCHHHH***CCCC **CCCCCHHH*EEEECCCCCEEEEHHH*EEECCCEEE*CCCHHHHCEEEECCC**C**CC-CCEEEEEEEEC---CCCEEEEEEEECC-EEEEEECHHHEEEEECC**EEECCCCHHHCCCCCC**C***-------- ---------*CEEEECCCCCEEEEHHHEEEECCCEEEECCCHHHH*EEEE*CC--CCCCC*C*EEEEEEEECC**CCCEEEEEEEECC*EEEEEECHHHEEE*-----***C***HHHCCCCCCCCCHHHH***CCCC 254142.tem _________________________________ --CCCCCHHHCEEEECCCCCEEEEHHHEEEECCCEEEECCCHHHHCEEEECCC--CCCCC-CCEEEEEEEECC--CCCEEEEEEEECC-EEEEEECHHHEEEEECC--EEECCCCHHHCCCCCCCCCHHHH***CCCC Structural block scores 0 1 - 4.0 M 75.0 7.5 75.0 2 6 C 4.0 M 4.6 6.4 75.0 7 9 H 4.0 M 5.0 2.7 52.3 11 14 E 5.0 H 0.8 1.2 1.2 15 19 C 5.0 H 3.6 4.6 3.4 20 23 E 5.0 H 3.5 2.5 1.5 24 26 H 5.0 H 1.7 3.3 3.3 27 30 E 4.8 H 1.2 1.0 0.2 31 33 C 5.0 H 6.3 5.3 6.7 34 37 E 4.8 H 0.8 0.5 0.5 38 40 C 4.7 H 3.7 4.0 5.7 41 44 H 5.0 H 4.8 5.2 4.0 46 49 E 5.0 H 4.0 3.2 3.5 50 52 C 4.7 H 7.3 5.7 6.3 53 54 - 4.0 M 75.0 6.0 75.0 55 59 C 4.4 M 20.9 5.9 6.2 61 62 C 4.5 M 2.5 3.5 3.0 63 70 E 5.0 H 2.4 1.2 1.5 71 72 C 4.5 M 6.5 40.0 5.5 73 74 - 4.0 M 75.0 75.0 9.8 75 77 C 5.0 H 4.0 3.3 2.7 78 85 E 5.0 H 1.9 0.9 1.5 86 87 C 5.0 H 8.5 8.5 7.0 89 94 E 5.0 H 1.2 2.2 1.8 96 98 H 5.0 H 2.3 2.0 3.3 99 103 E 4.6 H 1.0 1.0 16.2 104 105 C 4.0 M 5.5 7.5 75.0 106 107 - 4.0 M 75.0 7.5 75.0 108 110 E 4.0 M 5.7 6.0 4.0 111 114 C 4.2 M 4.8 5.5 4.0 115 117 H 5.0 H 5.0 4.7 3.0 118 126 C 4.8 H 3.1 2.6 5.7 127 130 H 4.0 M 5.5 23.1 4.5 131 133 * 2.7 P 5.7 75.0 6.0 134 137 C 4.0 M 8.9 75.0 6.1 >>>>>>