Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1nrza- -CEEEEEEEECCCCCHHHHHHHHHHHCCCEEEEECHHHHCCHHHHHHHHHCCCC-CCEEEEECHHHHHHHHCCHHHCCCEEEEEECCHHHHHHHHCCCCCCCEEEEEECCCCCCCEEEECCEEECHHHHHHHHHHHH-CCCEEEECCCCCCC-CCCHHHHHHCCCCC >P1;d3eyea- --CEEEEEECCCCCCCHHHHHHHHHHCCCEEEEECHHHHHCHHHHHHHHHHHHHHCCEEEEECHHHHHHHHH-HCCCCCCEEEEECCHHHHHHHHHCCCCCCEEEECCCCCCCCCEEEECCEEECHHHHHHHHHHHH-CCCEEEECCCCCCC-CCCCC--------- >P1;d3lfja1 CEEEEEEEEECCCCCCCHHHHHHCCCCC-EEEEECHHHHHCHHHHHHHHHCCCC-C--CCCCCHHHHC-CCC-CCCCCEEEEEEECCHHHHHHHHHCCCCCCEEEEEECCCCCCCEECC-CCEECCCCC-CCCCC-CCCCCEEEECCCCCCC-CEEHHHHHHHHCC- >P1;d3p3va- CCCEECCEEECCHHHC-CHHHHCC-CCCCEEEEECHHHHHCHHHHHC-CCCCCC-CCEEEEECHHHHHHHHH-HCCCCCEEEEEECCHHHHHHHHHCCCCCCEEEEEECCCCCCCEECCCCCEECHHHHHHHHHHHHCCCCEEECC-CCCCCCCCCHHHHC------ >P1;d5t5da- --CEEEEEECC-CCCC--CHHHHHHCCCCEEEEECHHHHHC-CHHHHHHHHCC--CCEEEEECC-CCHHHHCC----CCCEEEEECCHHHHHHHHHCCC-CCEEEECCC-----------CCCCC-CHHHHCC------CCEEEECCCCC---CEEHHHHC------ PSA >P1;d1nrza- -07021000027002ba404700750907100001691386a943560584219-c17030031a601721557727912000002304101501559090950000307578b09513a40002770360022056-4a080102441a49-554008303796b8 >P1;d3eyea- --313000003600188201500852906000000570075885279246109549061411218502630c-814982400000330400260044918064000000667ab18411950205a60160051038-5a060000331b59-54705--------- >P1;d3lfja1 305011000036002b710260089280-3000005802948832741664008-c--100320a702-336-63a9565000003507003400459050920000207548825505-400029a20-20540-953b060001523a38-3151830387316- >P1;d3p3va- b305030000351033-3036207-3b05000001791195993176-57206b-91315013075026305-816693200000450520250044903095020000456ba28601a40002890260042006738070500-31a5c282704741------ >P1;d5t5da- --512000014-005c--03500852807200001770193-83266058304--e07020331-90293157----9140000023041044027380-1a3000009-----------d671a-7258200------e0600214517---36409652------ Translating the sequences -**EEEEEEECCCCC**HHHHHHHH*CCCEEEEECHHHH*CHHHHHHHHHCCCC-CCEEEEECHHHHHHHHC*H**CCCEEEEEECCHHHHHHHH*CCCCCCEEEEEECCCCCCCEE**CC*EECHHHHHHHHHHHH-CCCEEEECCCCCCC-CCCHHHH******* --CEEEEEE*CCCCCC*HHHHHHHH*CCCEEEEECHHHHHCHHHHHHHHH*****CCEEEEECHHHHHHHH*-HCCCCC*EEEEECCHHHHHHHHHCCCCCCEEEE**CCCCCCCEE**CC*EECHHHHHHHHHHHH-CCCEEEECCCCCCC-CCC**--------- ***EEEEEEECCCCCC*HHHHHH**CCC-EEEEECHHHHHCHHHHHHHHHCCCC-C--****CHHHH*-**C-*CCCC*EEEEEECCHHHHHHHHHCCCCCCEEEEEECCCCCCCEE**-CCEEC****-*****-**CCCEEEECCCCCCC-C**HHHH******- **CEE**EEECC***C-*HHHH**-CCCCEEEEECHHHHHCHHHHH*-**CCCC-CCEEEEECHHHHHHHH*-HCCCCCEEEEEECCHHHHHHHHHCCCCCCEEEEEECCCCCCCEE**CCCEECHHHHHHHHHHHH*CCCEEE*C-CCCCC*CCCHHHH*------ --CEEEEEE*C-CCCC--*HHHHHHCCCCEEEEECHHHHHC-*HHHHHHH*CC--CCEEEEEC*-**HHHHC*----CC*EEEEECCHHHHHHHHHCCC-CCEEEE**C-----------CC**C-*HHHH**------CCEEEECCCCC---C**HHHH*------ 52728.tem _________________________________ -*CEEEEEEECCCCCC*HHHHHHHHCCCCEEEEECHHHHHCHHHHHHHHHCCCC-CCEEEEECHHHHHHHHC-HCCCCCEEEEEECCHHHHHHHHHCCCCCCEEEEEECCCCCCCEE**CCCEECHHHHHHHHHHHH-CCCEEEECCCCCCC-CCCHHHH*------ Structural block scores 3 9 E 4.7 H 0.4 0.6 0.3 1.1 0.6 10 15 C 4.6 H 3.8 3.0 3.8 2.5 16.1 17 24 H 4.5 M 3.4 2.6 3.2 12.0 12.0 25 28 C 4.6 H 4.0 4.2 21.2 4.9 4.2 29 33 E 5.0 H 0.2 0.0 0.6 0.0 0.4 35 39 H 4.9 H 5.4 3.8 4.8 5.4 4.8 41 49 H 4.7 H 5.6 5.7 5.0 13.6 12.6 50 53 C 4.2 M 4.0 3.8 3.0 4.9 20.5 55 56 C 4.8 H 6.8 4.5 43.8 5.0 7.2 57 61 E 4.5 M 2.0 2.6 15.8 2.0 2.4 63 70 H 4.5 M 3.6 3.1 12.6 2.9 12.5 74 78 C 4.4 M 5.2 4.8 6.7 5.0 47.0 79 84 E 4.8 H 0.3 0.7 0.8 0.3 0.7 85 86 C 5.0 H 2.5 3.0 4.0 4.5 2.5 87 95 H 4.9 H 1.9 1.8 2.0 2.0 2.4 96 101 C 4.9 H 5.3 4.7 4.7 4.2 16.2 102 107 E 4.6 H 1.3 0.7 0.7 1.2 0.5 108 114 C 4.6 H 5.5 6.0 4.9 5.6 65.6 115 116 E 4.5 M 7.0 6.0 5.0 7.0 75.0 117 118 * 2.1 P 2.0 1.0 2.5 0.5 75.0 119 121 C 4.3 M 4.8 4.7 26.3 4.8 31.5 122 123 E 4.5 M 0.0 1.0 0.0 0.0 4.0 125 136 H 4.2 M 3.2 3.4 16.0 3.1 33.2 138 140 C 4.8 H 4.8 5.2 4.8 3.7 29.8 141 144 E 4.9 H 2.2 1.5 1.5 3.0 2.0 145 151 C 4.8 H 4.9 4.6 4.6 15.3 24.0 153 155 C 4.2 M 4.7 5.3 3.0 5.7 4.3 156 159 H 4.5 M 2.8 38.8 3.0 3.8 5.0 161 166 - 3.9 M 7.4 75.0 16.7 75.0 75.0 >>>>>>