Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1cmwa6 --CCHHHHHHHHHCCCCCCCCCCCCCCCCCCCC------------CCCHHHHHCCCCCCCCCCCCCCCCCHHHH----CCC------CCCCCHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCC--CHHHCCCCCC---------------------------CC >P1;d1ul1x1 --CCHHHHHHHHHHHHCCCC--CCCCCCC----------------C-CCHHHHC-C---------CCHHHHHCCCCCCCCCCCCCC-CC-CHHHHHC--CCCCCHHHCCCCCCCCCHHHHHHHCCCC--CCC-CHHHHC-CHHHHHCCCCCCCCCCCCCCCCCCCCCCC >P1;d3h7ia2 CCCCHHHHHHHHHHHCCHHHCCCCCCCCCCHHHHCCCCCCCCCCCHHHHHHHHH--------CHHHHHHHCC-----------HHHHHHHHHHHHHHCH-HH-------------CCHHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCCCHHHHHHHC----------- >P1;d3orya2 --CCHHHHHHHHHHHCCCCCC-CCCCCCC----------------HHHHHHHHHHH---------CCCCCCC----HHHCCCCCCC-CHHHHHHHHHC-CCCCC--CCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCC------------------ >P1;d5hmla2 CC-CHHHHHHHHHHHCCHHHCCCCCC----------------CCCHHHHHHHHHHHC-----CHHHHHHHCCCCCCCHHHHHHHCCHHHHHHHHHHHCHHHH-------------HHHHHHCCCHHHHHH-------HHHHHHHHHC---------------------- PSA >P1;d1cmwa6 --1788455322203349a090634423b8530------------850157159520059b1984640224317----539------6125507517785a7587989a6aa8a57797567636669--70a629885a---------------------------aa >P1;d1ul1x1 --268625001300461950--8309908----------------7-a048205-4---------540840485275c73631aa0-53-7028532--4a79679838777871757740773078--675-615951-966993897b938977797989a8aa989 >P1;d3h7ia2 b7c577463044004017776000021457028438b93735a08682044008--------6383066308-----------9912600550056109-94-------------45b855687788978598566c626770694949943922a75----------- >P1;d3orya2 --2875261018003019507-8006c07----------------7a505800564---------9205804----88416159a0-80560164439-3987a--b78746891747233563156696369815471785365177839------------------ >P1;d5hmla2 17-68616101400306ba7b18109----------------809785026005616-----3055018507075a67105201816810550144019663-------------677732775795166-------667457887a---------------------- Translating the sequences --CCHHHHHHHHH**CCCCCCCCCCCCCC****------------***HHHHH*********C**CC*******----*CC------C****HHHHHC*CCCCC***CCCCCCCCCHHHHHHHHHHC*--C*********---------------------------** --CCHHHHHHHHHHH*CCCC--CCCCCCC----------------*-**HHHH*-*---------CCHHH*********CC***CC-C*-*HHHHH*--CCCCC***CCCCCCCCCHHHHHHH***C--CC*-****H*-*HHHHHC**C******************* **CCHHHHHHHHHHHCC***CCCCCCCCC****************HHHHHHHHH--------C****HHHCC-----------*****HHHHHHHHHC*-**-------------C*HHHHHHHHH***CC******HHHHHHHH*C**C********----------- --CCHHHHHHHHHHHCCCCCC-CCCCCCC----------------HHHHHHHHH**---------CC***CC----***CC***CC-CHHHHHHHHHC-CCCCC--*CCCCCCCCCHHHHHHHH**C**CC******HHHHHHHHH***C*------------------ **-CHHHHHHHHHHHCC***CCCCCC----------------***HHHHHHHHH***-----C****HHHCC************CC**HHHHHHHHHC****-------------*HHHHH***HH****-------HHHHHHHHHC---------------------- 47807.tem _________________________________ --CCHHHHHHHHHHHCCCCCCCCCCCCCC----------------HHHHHHHHH**------C**CCHHHCC**--***CC***CC-CHHHHHHHHHC*CCCCC--*CCCCCCCCCHHHHHHHHHHC**CC******HHHHHHHHHC**C*------------------ Structural block scores 0 1 - 3.8 M 75.0 75.0 9.2 75.0 4.0 2 3 C 4.8 H 4.0 4.0 8.8 5.0 40.5 4 14 H 4.9 H 3.8 2.6 3.5 3.0 2.7 15 28 C 4.5 M 4.9 14.9 2.9 9.3 20.8 29 44 - 4.2 M 57.2 75.0 5.6 75.0 62.0 45 53 H 4.4 M 4.6 12.4 3.6 4.5 3.7 54 55 * 2.5 P 3.5 39.5 75.0 5.0 3.5 56 61 - 4.4 M 4.4 75.0 75.0 75.0 63.5 63 64 * 3.0 P 6.0 75.0 5.5 75.0 2.5 65 66 C 3.8 M 5.0 4.5 1.5 5.5 2.5 67 69 H 3.8 M 1.3 4.0 5.0 4.3 4.7 70 71 C 3.8 M 3.5 2.0 4.0 2.0 3.5 72 73 * 3.0 P 4.0 6.5 75.0 75.0 3.5 74 75 - 3.8 M 75.0 4.5 75.0 75.0 7.8 76 78 * 2.7 P 51.7 8.2 75.0 6.7 4.7 79 80 C 4.1 M 6.0 4.5 75.0 3.5 2.5 81 83 * 2.7 P 75.0 4.8 53.0 5.0 1.0 84 85 C 4.1 M 75.0 5.2 5.0 5.2 4.5 88 96 H 4.5 M 3.7 11.7 2.4 3.2 2.2 99 103 C 4.0 M 7.1 7.3 47.6 7.5 33.0 104 105 - 3.8 M 8.0 8.0 75.0 75.0 75.0 107 115 C 4.2 M 8.6 6.1 67.1 6.3 67.3 116 125 H 4.5 M 6.2 4.7 7.0 3.9 6.1 127 128 * 2.5 P 42.0 75.0 8.0 7.5 3.5 129 130 C 4.3 M 41.0 6.5 6.5 4.5 40.5 131 136 * 2.2 P 5.9 16.8 7.8 5.5 75.0 137 145 H 4.3 M 52.6 13.7 5.2 4.8 6.4 147 148 * 3.0 P 75.0 8.0 6.5 7.5 75.0 151 168 - 4.1 M 67.8 8.2 48.0 75.0 75.0 >>>>>>