Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1lfpa- CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHCHHHHHHHHHHHHCC-CHHHHHHHHHHHHCCCCCCCCEEEEEEEEECCCEEE-EEEEECCHHHHHHHHHHHHHHC-CCEECCCCCCHHHEEEEEEEEEEHHH-----CCHHHHHHHHHHHCCCEEECCC-----CEEEEEECHHHHHHHHHHHHCCCCCCCEEEEEEEECCCEECCCHHHHHHHHHHHHHHHCCCCEEECCCCEECCCCCCCC >P1;d1mw7a- ------------------CCHHHHHHHHHHHHHCCCCCHHHCHHHHHHHHHHHHHCCCHHHHHHHHHHCC--CCCCCCEEEEEEEEECCCEEEEEEEEECCHHHHHHHHHHHHCCCCCCEEECCCCCCCCEEEEEEEEEEHHHHHHCCCCHHHHHHHHHHHCEEEEEEEC-----CEEEEEEEHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCCC-HHHHHHHHHHHHHHHCCCCEEEEEECCC-------- >P1;d5ekza- ----------------CHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCC-----CCEEEEEEEECCCCCEEEEEEEECCHHHHHHHHHHHHHHC-CCEECCCCCC--CEEEEEEEEEECCCCCCCCCCHHHHHHHHHHHCCCEEEEEECCCCCEEEEEEEEHHHHHHHHHHHHHCCCCEEEEEEEEEECCCCCCC-HHHHHHHHHHHHHHHHCCCEEEEEECCC-------- PSA >P1;d1lfpa- 62222347543567836b4433113120000024764537805305102421471a-4874086025502a18ab171432401040159000-01000465b4035305610663-90805996304730541010102167-----056a40461086080442341a-----2000000518503700640473904033033032148337088792045004001304526002101000305929637 >P1;d1mw7a- ------------------a645121230011047584639706705211310624b06795035027409--59607055321004063c01000101045494036405720961a7071186730695053200020327306829162970493058340450555b-----720102054922940260075380503403221403843808-b823860570172069190012011007-------- >P1;d5ekza- ----------------7a542620311002101763473a919704a20750574b05894048018385c-----5063131104003700000000085177058204700642-60600ab737--10441000104350687790a473055109509055065253a767910300072a31880365048330406525340405843807-a645860760271045192015022014-------- Translating the sequences *****************HHHHHHHHHHHHHHHHHHCCCHHHCHHHHHHHHHHHHCC-CHHHHHHHHHH**C*CCCCCCEEEEEEEEECCCEEE-EEEEECCHHHHHHHHHHHHHHC-CCEECCCCCC***EEEEEEEEEEHHH-----CCHHHHHHHHHHHCCCEEE**C-----CEEEEEE*HHHHHHHHHHHH*CCCCCCEEEEEEEECCC**CC*HHHHHHHHHHHHHHHCCCCEEE***C********** ------------------**HHHHHHHHHHHHH**CCCHHHCHHHHHHHHHHHH*CCCHHHHHHHHHHCC--CCCCCCEEEEEEEEECCCEEEEEEEEECCHHHHHHHHHHHH**C*CCEE*CCCCC**CEEEEEEEEEEHHH***CCCCHHHHHHHHHHHC**EEEEEC-----CEEEEEEEHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCCC-HHHHHHHHHHHHHHHCCCCEEEEEECCC-------- ----------------*HHHHHHHHHHHHHHHHHHCCC***CHHHHHHHHHHHHCCCCHHHHHHHH**CCC-----CCEEEEEEEE*CCC*EEEEEEEECCHHHHHHHHHHHHHHC-CCEECCCCCC--CEEEEEEEEEE******CCCCHHHHHHHHHHHCCCEEEEE*******EEEEEEEHHHHHHHHHHHHHCCCC**EEEEEEEECCCCCCC-HHHHHHHHHHHHHHH*CCCEEEEEECCC-------- 75625.tem _________________________________ ----------------*HHHHHHHHHHHHHHHHHHCCCHHHCHHHHHHHHHHHHCCCCHHHHHHHHHHCCC-CCCCCCEEEEEEEEECCCEEEEEEEEECCHHHHHHHHHHHHHHC-CCEECCCCCC**CEEEEEEEEEEHHH***CCCCHHHHHHHHHHHCCCEEEEEC-----CEEEEEEEHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCCC-HHHHHHHHHHHHHHHCCCCEEEEEECCC-------- Structural block scores 0 15 - 4.0 M 4.3 75.0 75.0 17 34 H 4.7 H 2.6 7.1 2.9 35 37 C 5.0 H 5.0 6.0 4.7 38 40 H 4.0 M 6.0 6.3 7.5 42 53 H 5.0 H 2.8 2.8 4.7 54 57 C 4.5 M 22.6 5.4 5.1 58 67 H 4.8 H 4.5 4.2 4.5 68 70 C 4.0 M 4.2 28.0 8.5 72 77 C 4.3 M 6.5 4.5 50.8 78 86 E 4.9 H 2.0 2.2 2.1 87 89 C 5.0 H 5.0 7.2 3.3 90 98 E 4.8 H 8.4 0.3 0.0 99 100 C 5.0 H 5.0 4.5 6.5 101 114 H 4.9 H 4.0 4.2 3.6 117 118 C 5.0 H 4.5 3.5 3.0 119 120 E 5.0 H 4.0 4.0 3.0 121 126 C 4.8 H 5.3 4.2 6.5 127 128 * 2.7 P 5.5 7.5 75.0 130 139 E 5.0 H 1.4 1.5 1.4 140 142 H 4.0 M 4.7 4.0 2.7 143 145 * 2.7 P 75.0 4.7 7.0 146 149 C 4.5 M 38.8 4.5 6.6 150 160 H 5.0 H 4.1 4.5 3.5 161 163 C 4.3 M 4.0 2.7 4.7 164 168 E 4.6 H 2.8 4.0 3.6 170 174 - 4.0 M 75.0 75.0 6.7 176 182 E 4.9 H 0.7 1.4 1.6 183 195 H 4.9 H 3.5 3.8 4.5 196 201 C 4.7 H 3.2 3.2 2.7 202 209 E 5.0 H 1.9 2.0 2.9 210 216 C 4.7 H 4.7 4.9 5.0 218 232 H 5.0 H 2.6 4.4 4.4 233 236 C 4.8 H 3.2 4.8 4.2 237 242 E 4.5 M 0.7 0.8 1.7 243 245 C 4.3 M 1.0 2.3 1.7 246 253 - 4.0 M 5.1 75.0 75.0 >>>>>>