Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ygya4 CCCCCCCCCCHHHHHHHHHHHHHHC-CCCCCCEEEEEEEEHHHHC-CCHHHHHHHHHHHCHHHCCCCCCCCCHHHHHHHH--------CCEEE----EEEEC--CCCCCCEEEEEEEECCCCCE-EEEEEEEECCCCEEEEEEECCEEEEEC- >P1;d2iafa1 -----CCCCCCCCHHHHHHHHHHHCCCCCCCCEEEEEEEHHHHHCCCCCCHHHHHHHHCCCCCCC----CCCCCHHHHHCEEEECCCEEEECCHHHHEEEECCCCCCCCC-CCCEEEECCCCCEEEEECEEECC-CCCEEEC------CCCCC PSA >P1;d1ygya4 cc826a7053025003400430173-0a85053010202060082-906202100010002a51aba6871707613974--------90606----0444a--90682810000402288882-220000056995521202248774479- >P1;d2iafa1 -----804440030023008104649208705302010014006236a70015201210056529----9762760495440300752505052a7003034a6717344-10200012799741251100024-5181233------86276 Translating the sequences *****CCCCCHHHHHHHHHHHHHHC-CCCCCCEEEEEEEEHHHHC-CCHHHHHHHHHHHCHHHCC****CCCHHHHHHHH--------**EEE----EEEEC--CCCCCC*EEEEEEECCCCCE-EEEEEEEEC*CCEEEEE******EEEC- -----CCCCC***HHHHHHHHHHHC*CCCCCCEEEEEEE*HHHHC*CC**HHHHHHHH*C***CC----CCC**HHHHH*********EEE******EEEEC**CCCCCC-***EEEECCCCCE*EEE*EEE*C-CC*EEE*------***C* 143548.tem _________________________________ -----CCCCCHHHHHHHHHHHHHHC-CCCCCCEEEEEEEEHHHHC-CCHHHHHHHHHHHCHHHCC----CCCHHHHHHHH--------EEEEE----EEEEC--CCCCCC-EEEEEEECCCCCE-EEEEEEEEC-CCEEEEE------EEEC- Structural block scores 0 4 - 3.0 P 8.2 75.0 5 9 C 5.0 H 5.1 4.0 10 23 H 4.6 H 2.1 1.9 26 31 C 5.0 H 4.8 3.7 32 39 E 4.8 H 1.0 0.9 40 43 H 5.0 H 3.5 2.5 46 47 C 5.0 H 4.5 8.2 48 58 H 4.5 M 1.1 1.7 60 62 H 3.0 P 5.8 5.3 63 64 C 5.0 H 5.8 5.5 65 68 - 3.0 P 9.0 75.0 69 71 C 5.0 H 5.0 7.3 72 79 H 4.2 M 4.6 4.6 80 87 - 3.0 P 75.0 2.6 88 92 E 3.4 M 4.2 3.0 93 96 - 3.0 P 75.0 4.9 97 100 E 5.0 H 3.0 1.5 102 103 - 3.0 P 75.0 8.2 104 109 C 5.0 H 5.5 4.3 111 117 E 4.1 M 0.9 0.6 118 122 C 5.0 H 6.8 6.8 125 132 E 4.5 M 1.1 1.4 135 136 C 5.0 H 7.0 3.0 137 141 E 4.2 M 2.0 3.4 142 147 - 3.0 P 5.0 75.0 148 150 E 3.0 P 5.0 5.3 >>>>>>