Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1m2oa4 CEEEEECCCC------------CCEECCCCHHHCCCCCEEEEECCCEEEEEEC----HHHHHHHHHC--HHHCC----------CCHHHHHHHHHHHHHHHHHHH--CCCCCCEEEEEECC----CHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHCC >P1;d1pd0a4 CEEEEC-CCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCEEEEECCCCEEEEECCCCCHHHHHHHHCCCCHHHCCCEECCCCCCC----CCHHHHHHHHHHHHHCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCC--CCCCCHHHHHHHHHHHCCC PSA >P1;d1m2oa4 3701102388------------a378291108105551000010591000000----7300732753--32958----------948707700540385067326--91a6706403021b----5840740383031349193b86278774576776787 >P1;d1pd0a4 250010-1707a800557b81320a42801684058500000129710001001607581053003575077031066604518----b18105002200620073b86b47030100107aa617813840751063263--9b7325964584478786a Translating the sequences CEEEEE*CCC------------CCEECCCCHHHCCCCCEEEEECCCEEEEEEC----HHHHHHHHHC--HHHCC----------****HHHHHHHHHHHHHHHHH--CCCCCCEEEEEECC----*HHHHHHH*CCCCCCC**CCCCCHHHHHHHHHHHHCC CEEEE*-CCC************CC**CCCCHHHCCCCCEEEEECCC*EEEEEC****HHHHHHHH*C**HHHCC**********----**HHHHHHHHHHHHH****CCCCCC*EEEEECC****HHHHHHHHHCCCCCCC--CCCCCHHHHHHHHHHH*CC 82754.tem _________________________________ CEEEEE-CCC------------CCEECCCCHHHCCCCCEEEEECCCEEEEEEC----HHHHHHHHHC--HHHCC--------------HHHHHHHHHHHHHHHHH--CCCCCCEEEEEECC----HHHHHHHHHCCCCCCC--CCCCCHHHHHHHHHHHHCC Structural block scores 1 5 E 4.6 H 1.8 1.2 7 9 C 5.0 H 6.3 2.7 10 21 - 3.0 P 75.0 5.5 22 23 C 5.0 H 6.8 1.0 24 25 E 3.0 P 7.5 7.2 26 29 C 5.0 H 3.2 2.8 30 32 H 5.0 H 3.0 6.0 33 37 C 5.0 H 3.2 3.6 38 42 E 5.0 H 0.2 0.2 43 45 C 5.0 H 4.7 6.0 46 51 E 4.7 H 0.2 0.3 53 56 - 3.0 P 75.0 3.5 57 65 H 4.8 H 3.8 2.8 67 68 - 3.0 P 75.0 6.0 69 71 H 5.0 H 4.7 4.7 72 73 C 5.0 H 6.5 1.5 74 87 - 3.0 P 55.6 24.1 88 104 H 4.5 M 3.7 2.7 105 106 - 3.0 P 75.0 7.2 107 112 C 5.0 H 5.6 6.1 113 118 E 4.7 H 2.5 0.8 119 120 C 5.0 H 6.2 3.5 121 124 - 3.0 P 75.0 7.0 125 133 H 4.6 H 4.3 4.8 134 140 C 5.0 H 3.3 3.0 141 142 - 3.0 P 5.0 75.0 143 147 C 5.0 H 6.1 6.5 148 159 H 4.8 H 6.5 6.2 160 161 C 5.0 H 7.5 8.2 >>>>>>