Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1hw7a- CCEEEEEEECCCCEEEEEEECHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCEEEEEEECCCCEEEEEE---CCCCCCC--CCCHHHHHC-CEEEEEEEEECCCCCEEEEEECCCCCHHHHHHHHHHHHCCCCEEEEEEEEEECC--EEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCC--HHHHHH-CCHHHHHHHHHC-----CCCCCCCCCCCCCCCCCC >P1;d1vq0a1 --CEEEEEECCCCEEEEEEECHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCEEEEEEECCCEEEEEECCCCCCCCCCCCCCCCHHHHHC-CEEEEEEEECCCCCCEEEEEECCCCCCHHHHHHHHHHHCCCCEEEEEEEEEECC-EEEEEEEEEEEECCC-CCCC-CHHHHHHHHHCCCCHHHHCCC-CCHHHHHHHHHCCCCCCCEEECCEEC--------- >P1;d1vzya1 CCEEEEEEECCCCEEEEEEECHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCCEEEEEEECCCCEEEEECCCCCCCCCCCCCCCCHHHHHCCCCEEEEEEECCCCCEEEEEEECCCCCCHHHHHHHHHHHHCCCEEEEEEEEECCCCCEEEEEEEEEEEC-C-CCCHHHHHHHHHHHCCCCCHHHHHHHCCCHHHHHHHHHCCCCEEEEEEECCC---------- PSA >P1;d1hw7a- 9260554458a7722004050182027006a4b046103500020000000000109571302020417100120102033837072605---268804a--a07134004-a0601002316a7a6553314084950140022016643a370604081a679b--63202050414367aa76797856569259717--892576-279820364027-----84a4759a9aaa99a599 >P1;d1vq0a1 --40213312a82010000405a0034026637035000000010000000000106980501010418140640101011721050602337082855b96732036003-9430202341b7a93644507034040260014004522713030302040688-003000000001346-9088-417307821970280360065-18056004400568099154270608--------- >P1;d1vzya1 8020010301b3403000010270033016538051000000010000000000109a9150404050a150510103020603070504626133b53b777110560033b4302061527a87646561704204037002400442481502030203039834040000000002-8-a08a913750673296155114005662303500340014807245518071---------- Translating the sequences CCEEEEEEECCCCEEEEEEECHHHHHHHH***CCCHHHHHHHHHHHHHHHHHHCCCCCC*EEEEEEEECCCCCEEEEEEECCCCEEEEE*---CCCCCCC--CCCHHHHHC-CEEEEEEEE*CCCCCEEEEEECCCCC*HHHHHHHHHHHCCCCEEEEEEEEEECC--EEEEEEEEEEECCC*CCCHHHHHHHHHHHHCCC--HHHHHH-CCHHHHHHHHHC-----C***CCCCC********* --*EEEEEECCCCEEEEEEECHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH**CCCCCEEEEEEEECCCCCEEEEEEECCC*EEEEECCCCCCCCCCCCCCCCHHHHHC-CEEEEEEEECCCCCCEEEEEECCCCCCHHHHHHHHHHHCCCCEEEEEEEEEECC-*EEEEEEEEEEECCC-CCC*-*HHHHHHHHHCCCCHHHH***-CCHHHHHHHHHCCCC**CEEECC**C--------- CCEEEEEEECCCCEEEEEEECHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEE*CCCCCEEEEEEECCCCEEEEECCCCCCCCCCCCCCCCHHHHHC*C*EEEEEEECCCCC*EEEEEECCCCCCHHHHHHHHHHH*CCCEEEEEEEEE*CC**EEEEEEEEEEEC-C-CCCHHHHHHHHHHH*CCCCHHHHHHH*CCHHHHHHHHHCCCC***EEE*CCC---------- 64397.tem _________________________________ CCEEEEEEECCCCEEEEEEECHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCCCCEEEEEEECCCCEEEEECCCCCCCCCCCCCCCCHHHHHC-CEEEEEEEECCCCCCEEEEEECCCCCCHHHHHHHHHHHCCCCEEEEEEEEEECC-*EEEEEEEEEEECCC-CCCHHHHHHHHHHHHCCCCHHHHHHH-CCHHHHHHHHHCCCC**CEEECCCCC--------- Structural block scores 0 1 C 4.0 M 5.5 75.0 4.0 2 8 E 4.9 H 4.1 2.0 0.9 9 12 C 5.0 H 8.1 5.6 4.9 13 19 E 5.0 H 1.9 0.7 0.6 21 31 H 4.7 H 3.7 3.6 2.7 32 34 C 5.0 H 5.2 3.3 4.3 35 52 H 5.0 H 0.9 0.3 0.1 53 59 C 4.6 H 3.3 3.4 4.4 60 67 E 4.9 H 1.5 1.5 2.2 68 72 C 5.0 H 1.8 3.8 4.3 73 79 E 5.0 H 1.1 1.0 1.0 80 83 C 4.8 H 5.2 2.8 2.2 84 88 E 5.0 H 3.0 2.2 2.4 89 104 C 4.6 H 27.2 5.1 4.9 105 109 H 5.0 H 1.6 1.8 2.2 113 120 E 4.9 H 1.5 2.2 2.6 121 126 C 4.7 H 6.8 7.0 6.8 127 132 E 5.0 H 3.5 4.3 4.8 133 138 C 4.8 H 4.3 1.8 1.7 139 149 H 5.0 H 2.4 2.2 2.4 150 153 C 4.8 H 5.9 3.2 4.5 154 163 E 4.9 H 4.2 1.8 1.3 164 165 C 5.0 H 10.2 8.0 8.5 168 178 E 5.0 H 2.5 0.4 0.4 179 181 C 4.7 H 5.3 4.3 28.3 183 185 C 5.0 H 7.8 5.7 6.2 186 197 H 4.7 H 6.5 10.4 5.2 198 201 C 4.8 H 22.5 4.2 4.2 202 208 H 4.4 M 16.0 2.9 2.4 210 211 C 5.0 H 4.5 4.5 2.5 212 220 H 5.0 H 3.8 2.1 1.7 221 224 C 4.2 M 58.0 4.8 3.2 225 226 * 2.7 P 75.0 9.0 4.5 228 230 E 4.0 M 6.2 3.7 3.7 231 235 C 4.2 M 8.1 4.2 18.2 236 244 - 4.0 M 9.2 75.0 75.0 >>>>>>