Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2hpua1 -CEEEEECCCCCEEEECCHHHHHHHHCCCCCCCCEEEEEEEECC--CCCCCCCCCCCCEEEEHHHCEEEEECCCCCCC------CCC-CEEEECCHHHHHHHHHH----CCEEEEEHHHCCHHHHCCCCCCCCCCCCCCC---- >P1;d3f0pa2 CCEEEEEC--CEEEEECCHHHHHHHHHHH---CCCEEEEEECCCCCCEEEEEECCCCEEEEECCCCEEEECC---CCCCCCHHHHCHHHCCEECCHHHHHHHHCCCCCCCCCEEEEHHHHHHHHH--------HHHHHHHCCCC PSA >P1;d2hpua1 -4040406c388346453022006404852b8152620401000--88406791394968110261400006680488------962-30001357840341398----30102033a5136301554b67c56026957---- >P1;d3f0pa2 48020317--a865405000100040225---75407040602157570402023850760749a0000107---47aa3864801052020023473068116839c28816014067016505--------6505645777c Translating the sequences -CEEEEEC**C*EEEECCHHHHHHHH******CCEEEEEEEECC--C******CCCC*EEEEHHHCEEEEEC***CCC------*C*-*EEEECCHHHHHHHHHH----CCEEEEEHHH**HHHH***************---- *CEEEEEC--CEEEEECCHHHHHHHHHHH---CC*EEEEEE*CC**CEEEEEECCCCEEEEE***CEEEE*C---CCC******HCH*H**EECCHHHHHHHH******CC*EEEEHHHHHHHHH--------HHHHHHH**** 160387.tem _________________________________ -CEEEEEC--CEEEEECCHHHHHHHHHHH---CCEEEEEEEECC--CEEEEEECCCCEEEEEHHHCEEEEEC---CCC------HCH-HEEEECCHHHHHHHHHH----CCEEEEEHHHHHHHHH--------HHHHHHH---- Structural block scores 2 6 E 5.0 H 1.6 1.2 8 9 - 3.0 P 7.8 75.0 11 15 E 4.6 H 5.0 4.6 16 17 C 5.0 H 4.0 2.5 18 28 H 4.5 M 2.8 1.3 29 31 - 3.0 P 7.2 75.0 32 33 C 5.0 H 3.0 6.0 34 41 E 4.5 M 1.9 2.6 42 43 C 5.0 H 0.0 1.5 44 45 - 3.0 P 75.0 6.0 47 52 E 3.0 P 5.7 2.2 53 56 C 5.0 H 4.2 4.5 57 61 E 4.6 H 5.0 4.0 62 64 H 3.0 P 2.7 7.8 66 70 E 4.6 H 0.8 0.2 72 74 - 3.0 P 4.7 75.0 75 77 C 5.0 H 6.7 7.2 78 83 - 3.0 P 75.0 6.6 89 92 E 4.0 M 0.2 0.5 93 94 C 5.0 H 4.0 2.5 95 104 H 4.6 H 4.7 4.4 105 108 - 3.0 P 75.0 6.6 109 110 C 5.0 H 1.5 8.0 111 115 E 4.6 H 1.2 2.4 116 124 H 4.6 H 3.6 3.3 125 132 - 3.0 P 7.0 75.0 133 139 H 3.0 P 5.0 4.4 140 143 - 3.0 P 75.0 8.4 >>>>>>