Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1nyoa- CCCCCCHHHHHHHHCCCCCCCCCHHHCCCCCHHHHCCCCCHHHHHHHHCCCCCCCCCHHHHCC--CCEEECCCCHHHHHHCC---HHHHHHHC--CCCCHHHHHHHHCCCC--CCCCCCCCC--------EEEECCCCC-EEEECCCC----C--CCEECCEE--CCEECCCCCCEEEEECCCCCCCCC--- >P1;d1o70a1 ----------------------------------CCHHHHHHHHHHHH--HCCC-HHHHHHHCCC-CEEEEEECHHHHHHCC--CHHHHC------CHHHHHHHHHHCEEC--CCCCHHHHHHHCCC-CCCCEECCCCCCEEEEEEECCHHHCEEEEEECCEEEEEEEEEEECCCEEEEEECCCCCCCC--- >P1;d1o70a2 ---------------------------CCHHHHHHHCHHHHHHHHHCC--CC---CCCHHHHCCCCEEEEEEECHHHHHHHHHHCHHHHHHHCCHHHHHHHHHHHHCCEEEECCCCCHHHHHHHHHHCCCEEEECCCCEEEEEEEEEC----CEEEEEECCEEEEEEEEEEEECCEEEEEECCCCCCCCCCC PSA >P1;d1nyoa- 9a231710990486269862018403b130030016031053001001291179081274025--89100000066008526---98227504--613a603100000004--932717a01--------883802461-4080719a----e--90502c04--020000503400000031004069--- >P1;d1o70a1 ----------------------------------44b40253045008--8025-604850782a-410000013900a728--07a348------468503500110004--3402175037316b-a62506011a91503070768cb91402030580604044141839502000033000165--- >P1;d1o70a2 ---------------------------720242046182052026005--21---800730756863000000125007504852581274014883385025001300002a530408400640777c406050469406050363a----b5200305a3504043331706000000031000177218 Translating the sequences ***************************CC**HHHHCC***HHHHHHHH**CCCC*CCHHHH*C--CCEEE***CHHHHHHCC---HHHHHHHC--*C**HHHHHHHHC**C--CCCC*****--------EEEECCCCC-EEEE***C----C--**EECCEE--**EE***CCCEEEEE*CCCCCCCC--- ----------------------------------*C*HHHHHHHHHHH--*CCC-**HHHHHCCC-CEEEEEECHHHHHHCC--CHHHH*------CHHHHHHHHHHCEEC--CCCCHHHHHHH***-CC**EECCCCC*EEEEEEEC****CEEEEEECCEEEEEEEEEEECCCEEEEEECCCCCCCC--- ---------------------------CC**HHHH*CHHHHHHHHH**--CC---CC*HHHHCCCC*EEEEEECHHHHHH****CHHHHHHHC****HHHHHHHHH*CEE***CCCCHHHHHHH****CCEEEECCCC**EEEEEEEC----CEEEEEECCEEEEEEEEEEE*CCEEEEEECCCCCCCC*** 82153.tem _________________________________ ---------------------------CC**HHHHCCHHHHHHHHHHH--CCCC-CCHHHHHCCCCCEEEEEECHHHHHHCC--CHHHHHHHC--*CHHHHHHHHHHCEEC--CCCCHHHHHHH***-CCEEEECCCCC*EEEEEEEC----CEEEEEECCEEEEEEEEEEECCCEEEEEECCCCCCCC--- Structural block scores 0 26 - 4.0 M 4.8 75.0 75.0 27 28 C 4.0 M 2.0 75.0 4.5 29 30 * 2.7 P 0.0 75.0 1.0 31 34 H 4.0 M 1.0 57.2 2.5 35 36 C 4.0 M 3.0 7.8 3.5 37 47 H 4.5 M 1.3 2.8 2.7 48 49 - 4.0 M 5.5 75.0 75.0 50 53 C 4.2 M 4.5 3.8 38.2 55 56 C 4.0 M 4.5 3.0 4.0 57 61 H 4.6 H 3.0 4.8 3.4 62 66 C 4.2 M 34.4 19.9 5.6 67 72 E 4.5 M 0.2 0.2 0.0 74 79 H 5.0 H 4.2 4.9 3.2 80 81 C 4.0 M 4.0 5.0 2.0 82 83 - 4.0 M 75.0 75.0 6.5 85 91 H 4.6 H 4.7 26.1 3.9 93 94 - 4.0 M 75.0 75.0 6.0 97 106 H 4.7 H 2.4 2.9 2.7 108 109 E 4.0 M 0.0 0.0 0.0 111 112 - 4.0 M 75.0 75.0 6.2 113 116 C 5.0 H 5.2 2.2 3.0 117 123 H 4.0 M 24.2 3.7 3.1 124 126 * 2.7 P 75.0 6.2 4.7 128 129 C 4.0 M 75.0 8.2 8.2 130 133 E 4.5 M 6.8 3.2 2.8 134 138 C 4.8 H 2.6 4.3 4.6 140 146 E 4.6 H 4.1 3.1 3.3 148 151 - 4.0 M 75.0 10.2 75.0 153 158 E 4.3 M 27.3 1.5 1.7 159 160 C 5.0 H 7.2 6.5 7.8 161 171 E 4.4 M 14.6 2.9 3.0 172 174 C 4.7 H 2.3 5.7 2.0 175 180 E 4.8 H 0.0 0.3 0.0 181 188 C 5.0 H 2.9 2.2 2.4 189 191 - 4.0 M 75.0 75.0 3.7 >>>>>>