Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1nbwb- --------------CCCEEEEECCCCC-----------CHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHCCCCEEEEECCCCEEEEEECCCCCCCCCEEE-ECC-CCHHHHHHHHHHHHHHHHCCCCCCCC-------------------------------------- >P1;d1uc4b- CCEEEEEECCCCCCCCEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHCCCCEEEEECCCCCEEEEECCCCCCCCCEEECCHHHCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEC >P1;d2d0ob1 ------------CCCCCEEEEEEC-------------CCHHHHHHHHHHHHHCCCCEEEEEEC-CCCHHHHHHHHHHCCCCCEEEEECC-CEEEEEECCCCCCCCCEEE-ECC-CCHHHHHHHHHHHHHHHCCCCCC----------------------------------------- PSA >P1;d1nbwb- --------------9600201203719-----------29a015102500783a0503346478088125001400440424000000380600002084569513162-328-277a304200200011149692372b-------------------------------------- >P1;d1uc4b- 71053376095296740000000000054165002724061005102400651b06020000043051150001007200020000000101000034b36484221405300206391035002000210365a0a60894759617472795376237604752599450230737 >P1;d2d0ob1 ------------c96600000008-------------603a2072013007729142524548-8670351026005805250000036-8300003393659613430-448-48773034002100321495828----------------------------------------- Translating the sequences --------------CCCEEEEECCCCC-----------CHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHCCCCEEEEECCCCEEEEEECCCCCCCCCEEE-ECC-CCHHHHHHHHHHHHHHH*CCCCCCCC-------------------------------------- ************CCCC*EEEEECCCCC**********C*HHHHHHHHHHHH*CCC*EEEEECCCCCCHHHHHHHHHHHCCCCEEEEECCCC*EEEEECCCCCCCCCEEE*****CCHHHHHHHHHHHHHHHCCCCCCCCC************************************** ------------CCCCCEEEEE*C-------------CCHHHHHHHHHHHHHCCCCEEEEE*C-CCCHHHHHHHHHH*CCCCEEEEECC-CEEEEEECCCCCCCCCEEE-ECC-CCHHHHHHHHHHHHHHHCCCCCC----------------------------------------- 52968.tem _________________________________ ------------CCCCCEEEEECCCCC----------CCHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHCCCCEEEEECCCCEEEEEECCCCCCCCCEEE-ECC-CCHHHHHHHHHHHHHHHCCCCCCCCC-------------------------------------- Structural block scores 0 11 - 4.0 M 75.0 4.0 75.0 12 16 C 4.4 M 33.0 5.2 6.7 17 21 E 5.0 H 1.0 0.0 0.0 22 26 C 4.2 M 4.0 0.0 46.6 27 36 - 4.0 M 75.0 3.2 75.0 37 38 C 4.0 M 38.5 2.0 3.0 39 51 H 4.9 H 3.7 2.3 3.3 52 55 C 4.8 H 4.6 4.6 4.0 56 60 E 5.0 H 3.2 0.4 3.6 61 66 C 4.7 H 5.8 2.0 18.0 67 77 H 4.9 H 1.9 1.5 2.7 78 81 C 5.0 H 2.5 0.5 3.0 82 86 E 5.0 H 0.0 0.0 0.0 87 90 C 4.8 H 2.8 0.2 23.0 91 96 E 4.8 H 1.3 0.7 1.0 97 105 C 5.0 H 4.6 4.9 5.0 106 108 E 5.0 H 3.0 1.7 2.3 111 112 C 4.0 M 5.0 0.0 6.0 114 115 C 5.0 H 4.5 3.0 6.0 116 130 H 5.0 H 2.1 1.7 2.2 131 139 C 4.6 H 5.9 5.4 29.0 140 177 - 4.0 M 75.0 4.9 75.0 >>>>>>