Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1v30a1 CEEEEECCCCCCCCCCHHHHC-----CCEEEEEEEE-EEEEEEEC---CCEEEEE---EEEEEEEEEEEECHHHHHHHCCCHHHH-HEEEEEECCC--------CCCEEEEEECC----CCCCEECCCCCHHHHC---------- >P1;d1vkba1 CEEEEECCCCCCCCCCCHHHHCHHHCCEEEEEEEEECCCCCEEEECCCCEEEEECCCCCCCCCEEEEEEECHHHHHHHHHHCCCCCCCEEEEEEEEEEEECCCCEEEEEEEEECCCCHHHHHCCCCC--CCCCCCCCCCCCCCCC >P1;d1xhsa- -CEEEEECCCCCCCCCCCCC-----CCCEEEEECCC-CCEEEEECC--CCEEEEE---CCCCCCEEEEECCHHHHHHHHHHHCCCCCEEEEEECCC--------CCCEEEEEECCCCC---CCEEECCCCCCC---------CCC PSA >P1;d1v30a1 623000002108a17216106-----b065134130-88010222---9300016---6a650100002078811640482a549-5072260706--------27603011117----a262840661203457---------- >P1;d1vkba1 522000010015c132192075982140403050004520000006a2200100433571540401002027601820292161882032341505034264bb21603000066137713937227--505071a295704648 >P1;d1xhsa- -3400000118795320526-----38185227230-58120141c--9301015---5b240603004049800662179508a33143341606--------3620200124643a---c29327703258---------97a Translating the sequences CEEEEECCCCCCCCCC*HHH*-----CCEEEEEEEE-**EEEEEC---CCEEEEE---*****EEEEEEECHHHHHHH***H***-*EEEEEECCC--------CCCEEEEEECC----**CCEECCCCC****C---------- CEEEEECCCCCCCCCCCHHH*****CC*EEEEEEEE*CC**EEE*C**C*EEEE****CCCCCEEEEEEECHHHHHHHHHH*CCCCC*EEEEE**************EEEEEECCCC*****C**CC--CCCC*C*******CCC -*EEEE*CCCCCCCCCC***-----CCCEEEEE***-CCEEEEECC--CCEEEEE---CCCCC*EEEEE*CHHHHHHHHHHHCCCCCEEEEEECCC--------CCCEEEEEECCCC*---CCEE*CCCCCCC---------CCC 110857.tem _________________________________ CEEEEECCCCCCCCCCCHHH*----CCCEEEEEEEE-CCEEEEECC--CCEEEEE---CCCCCEEEEEEECHHHHHHHHHHHCCCCCEEEEEECCC--------CCCEEEEEECCCC*-**CCEECCCCCCCC*C-------CCC Structural block scores 1 5 E 4.8 H 1.0 0.8 1.4 6 16 C 4.8 H 3.0 2.4 3.3 17 19 H 4.0 M 2.3 3.7 4.3 21 24 - 4.0 M 75.0 6.0 75.0 25 27 C 4.3 M 28.8 1.7 4.0 28 35 E 4.6 H 2.9 1.5 3.6 37 38 C 4.0 M 8.0 3.5 6.5 39 43 E 4.6 H 1.0 0.0 1.6 44 45 C 4.0 M 38.5 3.0 6.8 46 47 - 4.0 M 75.0 6.2 75.0 48 49 C 4.5 M 6.0 1.0 6.0 50 54 E 4.8 H 1.4 1.0 1.4 55 57 - 4.0 M 75.0 3.7 75.0 58 62 C 4.0 M 5.5 3.4 4.5 63 69 E 4.7 H 0.4 1.0 1.9 71 81 H 4.6 H 4.8 3.5 4.8 82 86 C 4.0 M 19.6 5.0 4.9 87 92 E 4.8 H 2.8 2.2 2.7 93 95 C 4.0 M 4.3 3.3 4.0 96 103 - 4.0 M 75.0 5.2 75.0 104 106 C 4.0 M 5.0 3.0 3.7 107 112 E 5.0 H 1.0 0.5 0.8 113 116 C 4.5 M 39.5 4.0 4.2 119 120 * 2.7 P 6.2 2.0 75.0 121 122 C 4.5 M 4.0 6.0 7.2 123 124 E 4.0 M 6.0 4.5 6.0 125 132 C 4.2 M 2.8 21.1 4.2 135 141 - 4.0 M 75.0 5.4 75.0 142 144 C 4.0 M 75.0 6.0 8.8 >>>>>>