Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1di0a- ----------CCEEEEEEEECCCHHHHHHHHHHHHHHHHHHHC---CCEEEEEEEECCHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCCC-HHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCHHHHHHHHHH---HHH--HHHHHHHHHHHHHHHHHHCCC >P1;d1kz1a- ---CCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHHCCCHHH--EEEEECCCHHHHHHHHHHHHHHCCCCEEEEEEEEECC-CCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECC-------HHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCC---- >P1;d1nqua- CCCCCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHH-CCCCHHH--EEEEEECCHHHHHHHHHHHHCCCCCCEEEEEEEEECC-CCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECC-------HHHHHHCEEE-CCEEHHHHHHHHHHHHHHHHHHHC- PSA >P1;d1di0a- ----------97130000003633600210261047206751a---76060422607406501940270063b603000000011318a874-58417505730670275171101400221b618739844870274---056--303610450284175487778 >P1;d1kz1a- ---b38824049040000104955800820171014103770505783--0533216606401830750076670100000001239-a8671471184048307711763a210140003076-------48301530148b06230451035003502646---- >P1;d1nqua- 99748074709a0300000068377103400620440047-2806662--0423416206401920070055a6020000000114a-a76805821650465076128716200150003056-------6840512046-748220350035005300126645- Translating the sequences ----------CC**EEEEEECCCHHHHHHHHHHHHHHHHHHHC---****EEEEEECCHHHHHHHHHHHHHCCCCCEEEEEEE**CC*CCC*-HHHHHHHHHHHHHHHHHHCCCEEEEEE**CC*******HHHHHHH---***--HHHHHHHHHHHHHHHHHH*C* ---CCCCCCCCCCCEEEEE*CCCHHHHHHHHHHHHHHHHHHHCCCHHH--EEEEE*CCHHHHHHHHHHHHH*CCCCEEEEEEEEECC-CCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECC-------HHHHHHH****CC**HHHHHHHHHHHHHHH**---- ***CCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHH-*CCCHHH--EEEEEECCHHHHHHHHHHHH*CCCCCEEEEEEEEECC-CCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECC-------HHHHHH****-CC**HHHHHHHHHHHHHHHHHH*C- 52121.tem _________________________________ ---CCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHCCCHHH--EEEEEECCHHHHHHHHHHHHHCCCCCEEEEEEEEECC-CCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECC-------HHHHHHH****CC**HHHHHHHHHHHHHHHHHH*C- Structural block scores 0 2 - 4.0 M 75.0 75.0 8.3 3 13 C 4.2 M 49.5 4.9 4.8 14 19 E 4.8 H 0.0 0.2 0.0 20 22 C 5.0 H 4.0 6.0 5.7 23 41 H 4.9 H 2.8 2.9 6.6 42 44 C 4.3 M 53.5 3.3 4.7 45 47 H 4.0 M 29.3 6.0 4.7 48 49 - 4.0 M 3.0 75.0 75.0 50 55 E 4.8 H 2.3 2.3 2.3 56 57 C 5.0 H 5.5 6.0 4.0 58 70 H 4.9 H 3.1 3.2 2.6 71 75 C 4.8 H 4.7 4.0 4.7 76 84 E 4.8 H 0.2 0.3 0.2 85 86 C 5.0 H 2.0 6.0 7.2 88 90 C 5.0 H 8.5 8.2 7.8 91 110 H 4.9 H 7.6 4.0 4.1 111 113 C 5.0 H 3.0 4.5 2.7 114 121 E 4.8 H 1.2 1.0 1.1 122 123 C 5.0 H 8.8 6.5 5.5 124 130 - 4.0 M 5.7 75.0 75.0 131 137 H 4.9 H 4.6 3.4 3.7 138 141 * 2.7 P 56.2 3.2 21.2 142 143 C 4.0 M 5.5 5.8 5.5 144 145 * 2.7 P 75.0 4.0 5.0 146 163 H 4.8 H 3.8 6.8 2.3 >>>>>>