Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1akpa- CCCEEEEECCCCCCCCEEEEEEEECCCCCCCCCCEEEECCCCCCCEECHHHCCCCCCC-CCEEEEEEEECCEEECCCCCCCCCCCEEECCCCCCCCEEECCCCCCCCCC-CCCCCC-- >P1;d2cboa- CCCEEEEECCCCCCCCCEEEEEEECCCCCCEEEEEEEEEEECCEEEECHHHCEEEECCCCCCEEEEEECCCEEEEECC-CCCEEEEEECCCC--EEEEEEECCCCCCCCCEECCCCCC PSA >P1;d1akpa- 9b3828096295197427060417a198094130602062974680138717466718-a175626071784260328792a557744179166402041137809908-37165f-- >P1;d2cboa- 98560707537806543606030510657250500020407aa32020282345250699051426020334040228-5666457050593--60202030878720a028050489 Translating the sequences CCCEEEEECCCCCCCCEEEEEEEECCCCCC****EEEE***CC**EECHHHC****CC-CCEEEEEEEECCEEE**CC*CCC***EEECCCC****EEE**CCCCCCCC-**CCCC-- CCCEEEEECCCCCCCC*EEEEEEECCCCCCEEEEEEEEEEECCEEEECHHHCEEEECC*CC*EEEEEE*CCEEEEECC-CCCEEEEEECCCC--EEEEEEECCCCCCCC*EECCCC** 49319.tem _________________________________ CCCEEEEECCCCCCCCEEEEEEEECCCCCCEEEEEEEEEEECCEEEECHHHCEEEECC-CCEEEEEEEECCEEEEECC-CCCEEEEEECCCC--EEEEEEECCCCCCCC-EECCCC-- Structural block scores 0 2 C 5.0 H 7.8 7.3 3 7 E 5.0 H 5.4 4.0 8 15 C 5.0 H 5.4 4.8 16 23 E 4.8 H 3.4 2.9 24 29 C 5.0 H 6.2 3.5 30 40 E 3.7 M 3.0 2.1 41 42 C 5.0 H 5.5 10.5 43 46 E 4.0 M 3.8 1.8 48 50 H 5.0 H 5.3 4.0 52 55 E 3.0 P 5.8 4.0 56 57 C 5.0 H 4.5 3.0 59 60 C 5.0 H 5.8 4.5 61 68 E 4.5 M 4.2 2.5 69 70 C 5.0 H 7.5 3.0 71 75 E 4.2 M 3.0 2.0 76 77 C 5.0 H 5.0 5.0 79 81 C 5.0 H 7.2 5.7 82 87 E 4.0 M 5.3 4.5 88 91 C 5.0 H 4.5 4.2 92 93 - 3.0 P 6.0 75.0 94 100 E 3.9 M 1.7 1.9 101 108 C 5.0 H 5.5 5.3 110 111 E 3.0 P 5.0 5.0 112 115 C 5.0 H 8.6 2.2 116 117 - 3.0 P 75.0 8.5 >>>>>>