Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1dlja3 CHHHHHHHCCCCCCCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHCCCCEEEEECCCCC---------CCC--CCCCCEECCCHHHHHHHCCEEECCCCCHHHHHHH----HHEECCCCCCCC------------- >P1;d1mv8a3 CHHHHHHHCC----CCCEEEECCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEECHHHHHHCCCCCCCCCCCCHHHHCCCCCCHHHHHHHCCEEEECCCC-CCHHHHHCCCCCCEEEECCCCCCCCCCCCEEECCC PSA >P1;d1dlja3 08702430783a297210000201352b08428a0804830760375b0400010442b---------919--aa2906113627501650300004335b508826----b3031807776a------------- >P1;d1mv8a3 3770162016----2450000000462933308b05016004303a6a26020005202702768a6560591460073037619501630400000151-5068006724bc140001341069846a7110283 Translating the sequences CHHHHHHHCC****CCEEEEECCCCCCCCCCCCCCHHHHHHHHHH*CCCEEEEEC****---------CCC--****CEECCCHHHHHHHCCEEE*CCCC*HHHHHH----HHEE***CCCCC------------- CHHHHHHHCC----CC*EEEECCCCCCCCCCCCCCHHHHHHHHHHHCCC*EEEECHHHH*********CCC**HHHHC**CCCHHHHHHHCCEEEECCCC-**HHHH*******EEEECCCCC************* 52413.tem _________________________________ CHHHHHHHCC----CCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHCCCEEEEECHHHH---------CCC--HHHHCEECCCHHHHHHHCCEEEECCCC-HHHHHH----HHEEEEECCCCC------------- Structural block scores 1 7 H 5.0 H 3.4 3.3 8 9 C 5.0 H 7.5 3.5 10 13 - 3.0 P 6.1 75.0 14 15 C 5.0 H 4.5 3.0 16 20 E 4.6 H 0.2 1.0 21 34 C 5.0 H 4.1 3.5 35 45 H 4.8 H 4.2 3.0 46 48 C 5.0 H 5.5 6.2 49 53 E 4.6 H 1.0 1.6 55 58 H 3.0 P 5.4 2.2 59 67 - 3.0 P 75.0 5.7 68 70 C 5.0 H 6.3 3.7 71 72 - 3.0 P 75.0 5.0 73 76 H 3.0 P 8.0 2.5 78 79 E 3.0 P 3.5 1.5 80 82 C 5.0 H 3.3 5.3 83 89 H 5.0 H 3.7 3.6 90 91 C 5.0 H 1.5 2.0 92 95 E 4.5 M 0.0 0.0 96 99 C 5.0 H 3.8 1.8 101 106 H 4.3 M 4.8 3.2 107 110 - 3.0 P 75.0 4.8 111 112 H 3.0 P 7.2 12.0 113 117 E 3.4 M 2.4 1.0 118 122 C 5.0 H 7.5 1.8 123 135 - 3.0 P 75.0 5.0 >>>>>>