Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d3cb2a1 -CCEEEEEEHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHCEEECCCCCEEECEEEEECCCHHHHHHHHCCCC-CCCHHHEEECC-------CCCCCCHHHHHH-HH-CCHHHHHHHHHHHHHCCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHHCC-CEEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCEEEEEEHHHHC-CCCCCCCCCCCCHHHHC-CHHHHHHHHCCCCCCC-------- >P1;d3ryca1 CCCEEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCCCCC-CCHHHHCEEECCCCCEEECEEEEECCCHHHHHHHHCCCCCCCCHHHEEECC-------CCCCCCHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHCCEEEEEEHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCC-------- >P1;d6rvqa1 -CCEEEEEEHHHHHHHHHHHHHH-----CCC------------------------CCEEEEEECCHHHHH---------CCCCC-EEEECCHHHHCCCCCCCCHHHHHH-HHHHCHHHHHHHHC-------CCCEEEEEEECCCCHHHHHHHHHHHHHHHC--CCEEEEEEEECCHHHC--HHHHHHHHHHHHHHHHHCCEEEEEEHHHHHHCCC-----CCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC PSA >P1;d3cb2a1 -300000001320030013003300740a0448073c6c80416000342c883100100000045500670392714-00278012229-------c10c65174026-20-52396008003300890a80400000020240000000000023066416-4603000021478a4a2931680184046008710652350422813-303975839a0669501-30175007405a3035-------- >P1;d3ryca1 2700000001530030040003100730a054406177-78112000253d962000000000033700580387726700385000049-------750746063007710880087006204510760860300000021050000000010034038317935030000510741281b51680185059208920453451414600550597593b6074730162006500730494049-------- >P1;d6rvqa1 -3500000007800710120266-----70b------------------------c0400000032b40a---------8050a-331200692091950d47272054-00451376037109-------a06000000300300001000000300463--a060000022017739--a834810470065058103805113246057518-----a926765036411440189058316946886ab9 Translating the sequences -CCEEEEEEHHHHHHHHHHHHHHHHHH*CCCCCCCCCC*CC*HHHCEEECCCCCEEECEEEEECCCHHHHHHHHCCCC-CCCHHHEEECC-------CCCCCCHHHHHH-HH-*CHHHHHHHHHHHHHCCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHHCC-CEEEEEEEECCCCCCCCCCHHHHHHHHHHHHHH*CCEEEEEEHHHH*-CCC***CCCCCCHHHH*-*HHHHHHHH*****CC-------- *CCEEEEEEHHHHHHHHHHHHHHHHHH*CCCCCCCCCC-CC*HHHCEEECCCCCEEECEEEEECCCHHHHHHHHCCCC*CCCHHHEEECC-------CCCCCCHHHHH***HHH*HHHHHHHHHHHHHCCCCCCEEEEEEECCC*HHHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHCCEEEEEEHHHHHH******CCCCCCHHHHHHHHHHHHHHHHHHHHCC-------- -CCEEEEEEHHHHHHHHHHHHHH-----CCC------------------------***EEEEECC*HHHH---------CCC**-EEE*C*******CCCCCCHHHHHH-HHHHCHHHHHHHH*-------CCCEEEEEEECCCCHHHHHHHHHHHHHHH*--CCEEEEEEEECC***C--**HHHHHHHHHHHHHHHCCEEEEEEHHHHHHCCC-----CCCCHHHHHHHHHHHHHHHHHHHH********** 52490.tem _________________________________ -CCEEEEEEHHHHHHHHHHHHHHHHHH*CCCCCCCCCC-CC*HHHCEEECCCCCEEECEEEEECCCHHHHHHHHCCCC-CCCHHHEEECC-------CCCCCCHHHHHH-HHHHCHHHHHHHHHHHHHCCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHCCEEEEEEHHHHHHCCC***CCCCCCHHHHHHHHHHHHHHHHHHHHCC-------- Structural block scores 1 2 C 5.0 H 1.5 3.5 4.0 3 8 E 5.0 H 0.0 0.0 0.0 9 26 H 4.8 H 1.7 1.7 18.9 28 37 C 4.3 M 5.5 4.5 54.4 39 40 C 4.0 M 4.0 7.5 75.0 42 44 H 4.0 M 2.3 1.0 75.0 46 48 E 4.0 M 2.3 2.3 75.0 49 53 C 4.0 M 6.7 6.7 75.0 54 56 E 4.0 M 0.3 0.0 29.2 58 62 E 5.0 H 0.0 0.0 0.0 63 65 C 4.7 H 3.0 2.0 1.7 66 73 H 4.5 M 3.8 3.9 40.8 74 77 C 4.0 M 3.5 5.5 75.0 79 81 C 5.0 H 0.7 1.0 4.3 82 84 H 4.0 M 5.0 4.3 28.5 85 87 E 5.0 H 1.7 0.0 2.3 88 89 C 4.5 M 5.5 6.5 1.0 90 96 - 4.0 M 75.0 75.0 3.9 97 102 C 5.0 H 6.2 4.8 6.4 103 108 H 4.8 H 3.3 2.7 3.3 110 113 H 4.2 M 20.5 4.2 2.2 115 127 H 4.6 H 3.1 3.1 25.8 128 133 C 4.5 M 5.2 3.8 40.2 134 140 E 5.0 H 0.3 0.3 0.4 141 144 C 4.8 H 1.5 1.5 0.8 145 160 H 4.9 H 1.3 1.4 1.1 161 164 C 4.2 M 21.5 5.0 40.1 165 172 E 5.0 H 1.4 1.6 1.2 173 182 C 4.3 M 5.9 4.0 19.6 183 197 H 4.9 H 3.6 4.3 3.5 198 199 C 5.0 H 3.0 2.0 1.5 200 205 E 5.0 H 3.2 3.7 3.0 206 211 H 4.7 H 15.2 2.7 4.0 212 214 C 4.0 M 2.0 3.3 4.7 215 217 * 2.7 P 7.0 7.0 75.0 218 223 C 4.7 H 6.1 6.1 29.6 224 243 H 4.6 H 7.1 3.0 3.8 244 245 C 4.0 M 4.0 6.5 7.5 246 253 - 4.0 M 75.0 75.0 7.9 >>>>>>