Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1mixa1 CCCCCCHHHHHC-C-CHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHHHHHHHCCCCCCCCC----CCCCC----HHHCCCHHHC------CCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCC >P1;d2al6a1 ------CCHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHCHHHHHHHHHCCCHHHCCCHHHHHCCC--HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCC >P1;d4yl8a2 --------CHHHHCCCHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHHHHHHHCCCC--CCC-----CCCC----CCCCCCHHHHHHCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCC--- >P1;d5ryoa2 -------CCHHH-CCCHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHHHHHHHCCCCCCCCC----CCCCC----CCCCCC--CC------CHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCC PSA >P1;d1mixa1 8a7a56685056-3-668405730471253027560-6072730040001000042650469706----8a407----1650009613------958019401720670aa17555011500210172a63 >P1;d2al6a1 ------b953a821965730382055017401762047075820030000000123192838103678406513773505700065016618--8740154017005502918445003300710564191 >P1;d4yl8a2 --------5158818765315650583272016374-6033a200200010001622518--91b-----5104----b161005603673a285860176026404605927555012300320481--- >P1;d5ryoa2 -------a4048-4a666514630460262013460-6084721020001110034731469719----ba360----a26003--a3------7480053016205705a17645012300430271a62 Translating the sequences *********HH*-C-CHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHHHHHHHCCCCCCCCC----*CCCC----***CCCHHH*------****HHHHHHHHHHCCCCCHHHHHHHHHHHH**CCCC ------***HHH*CCCHHHHHHHHHHHHHHHH**CC*CCCHHHHHHHHHHHHHHH*CCCCCC*******************CCCHHH*****--*HHHHHHHHHHHH*CCCCCHHHHHHHHHHHHCCCCCC --------*HHH*CCCHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHHHHHHHCCCC--CCC-----CCCC----***CCCHHH********HHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCC--- -------**HHH-CCCHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHHHHHHHCCCCCCCCC----*CCCC----***CCC--**------*HHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCC 47031.tem _________________________________ ------***HHH*CCCHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHHHHHHHCCCCCCCCC----*CCCC----***CCCHHH*****--*HHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCC Structural block scores 0 5 - 4.3 M 7.8 75.0 75.0 75.0 6 8 * 2.3 P 6.3 8.5 51.7 29.8 9 11 H 4.8 H 3.7 7.2 4.7 4.0 13 15 C 4.8 H 28.0 5.3 5.3 6.8 16 31 H 5.0 H 3.6 3.2 3.7 3.2 32 35 C 4.7 H 4.5 3.8 5.0 3.2 37 39 C 5.0 H 4.3 4.7 3.0 4.7 40 55 H 5.0 H 1.4 1.5 1.7 1.6 56 64 C 4.6 H 4.8 3.9 20.8 5.2 65 68 - 4.3 M 75.0 6.2 75.0 75.0 70 73 C 4.3 M 5.4 3.8 2.5 4.9 74 77 - 4.3 M 75.0 5.5 75.0 75.0 78 80 * 1.0 P 4.0 4.0 6.2 6.2 81 83 C 5.0 H 0.0 0.0 0.3 1.0 84 86 H 4.3 M 5.3 3.7 3.7 53.5 87 91 * 3.0 P 60.6 4.4 5.9 60.6 92 93 - 4.3 M 75.0 75.0 5.0 75.0 95 107 H 4.8 H 3.8 3.0 3.8 3.2 108 112 C 5.0 H 5.8 4.0 4.6 4.7 113 124 H 5.0 H 2.1 2.2 2.2 2.3 125 130 C 4.4 M 4.9 4.3 39.7 4.8 >>>>>>