Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1vq8k1 CCCCCCEECCCEECCCEEEECCCCCEEEEEEEEECCCCCCCCCCCEECCCCEEEEEEEEECC--CC-CCCEEEEEEEECCCCEECCCCCEECCCCCEEEEECCCCCCCCCCCCCEEEHHHHHH-CHHHHCCCCEEE >P1;d1whia- ----------CCCCCCEEEECCCCCEEEEEEEEECC---CCCCC-CCCCCCEEEEEEEEECCCCCCCCCCEEEEEEEECCCCEECCCCCEECCCCCEEEEECCCCCCCCCCCCCCCCCHHHHCCCHHHHHHCCCCC PSA >P1;d1vq8k1 47a1a061622055634050004060820403506a29169a57330000210302036066--a0-59462400000065303168676170a12000005983515177064300600071-084019207536 >P1;d1whia- ----------40477360500040304203046038---9bb37-30300220103043058a570669550400000066026198556271a330000069842031860654006305867046017204724 Translating the sequences **********CEECCCEEEECCCCCEEEEEEEEECC***CCCCC*EECCCCEEEEEEEEECC--CC-CCCEEEEEEEECCCCEECCCCCEECCCCCEEEEECCCCCCCCCCCCCEEEHHHHHH-CHHHH**CCEEE ----------C**CCCEEEECCCCCEEEEEEEEECC---CCCCC-**CCCCEEEEEEEEECC**CC*CCCEEEEEEEECCCCEECCCCCEECCCCCEEEEECCCCCCCCCCCCC****HHHH**CHHHHHHCC*** 50193.tem _________________________________ ----------CEECCCEEEECCCCCEEEEEEEEECC---CCCCC-EECCCCEEEEEEEEECC--CC-CCCEEEEEEEECCCCEECCCCCEECCCCCEEEEECCCCCCCCCCCCCEEEHHHHHH-CHHHHHHCCEEE Structural block scores 0 9 - 3.0 P 4.8 75.0 11 12 E 3.0 P 2.5 2.0 13 15 C 5.0 H 4.7 5.7 16 19 E 5.0 H 2.2 2.8 20 24 C 5.0 H 2.0 1.4 25 33 E 5.0 H 2.4 2.1 34 35 C 5.0 H 8.2 5.5 36 38 - 3.0 P 4.0 75.0 39 43 C 5.0 H 7.5 8.4 45 46 E 3.0 P 1.5 1.5 47 50 C 5.0 H 0.5 1.2 51 59 E 5.0 H 1.7 1.4 60 61 C 5.0 H 6.0 6.5 62 63 - 3.0 P 75.0 7.8 64 65 C 5.0 H 5.2 3.5 67 69 C 5.0 H 6.0 6.7 70 77 E 5.0 H 1.5 1.1 78 81 C 5.0 H 3.5 3.0 82 83 E 5.0 H 1.5 4.0 84 88 C 5.0 H 5.6 5.6 89 90 E 5.0 H 3.5 4.0 91 95 C 5.0 H 4.1 4.9 96 100 E 5.0 H 0.0 0.0 101 113 C 5.0 H 4.7 4.5 114 116 E 3.0 P 1.0 1.3 117 122 H 4.3 M 2.3 4.7 125 130 H 4.3 M 4.0 3.3 131 132 C 5.0 H 3.5 2.0 133 135 E 3.0 P 4.7 4.3 >>>>>>