Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1jida- CCCCCCCHHHCEEECHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEECCCCCCCCCCCCHHHCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCC------------- >P1;d1kvna- --------CCCEEEECHHHCCCCCHHHHCCCCHHHCCCCCCHHHHHHHHHHHCCCE-EEECCCCCCC----CCCCCCEEEECCC-----------CCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC >P1;d1lnga- -----------CEECHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCC-EEECCCCCHHHC---CCCCCEEECCCC-----------CCHHHHHHHHHHHHCCCC--------------- >P1;d3dlua1 ---------CEEEECHHHHCCCCCC-CCCCCCCCCCC-CCCC-CHHHHHHHCCCEEEEEEEEEECCC---EE---EEEEEEECCC-----------CHHHHHHHHHHHHHHHHHHHC----------- PSA >P1;d1jida- 77633337850130110101362789500404795005705061026005829070-31277531a52937787320101010458856323a6045652003100730462b92------------- >P1;d1kvna- --------75617040200038288a533302975004a02670034017469910-514579919b----8995633000336-----------a4857002400710240576688687a659a7c >P1;d1lnga- -----------24010010035175850030359102670407402600572a290-514696407407---746100050828-----------68347003600610474f--------------- >P1;d3dlua1 ---------d524051200127376-9414047a300-7070-102500641907125342656964---73---5030203065-----------b27500330061024047588----------- Translating the sequences ***********EEECHHHHCCCCCC*CCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEECCCCCCC********CCEEEECCC***********CCHHHHHHHHHHHHHH****------------- --------***EEE**HHHCCCCC****CCCC***CCCCCCHHHHHHHHHH*CCCE-EEECCCCCCC----****CCEEEECCC-----------CC*HHHHHHHHHHHHH***************** -----------*EECHHH*CCCCCC*CCCCCCCCCCCCCCCHHHHHHHHHHCCCC*-EEECCCCC****---***CCEEE*CCC-----------CCHHHHHHHHHHHH****--------------- ---------**EEECHHHHCCCCCC-CCCCCCCCCCC-CCC*-*HHHHHHHCCC*E*EEE****CCC---**---**EEEE*CC*-----------CHHHHHHHHHHHHHH******----------- 69695.tem _________________________________ --------***EEECHHHHCCCCCC*CCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEECCCCCCC**-*****CCEEEECCC*----------CCHHHHHHHHHHHHHH******----------- Structural block scores 0 7 - 4.3 M 4.9 75.0 75.0 75.0 8 10 * 2.7 P 4.3 6.0 75.0 31.2 11 13 E 4.8 H 1.3 2.7 2.0 2.0 15 18 H 4.7 H 0.5 0.5 0.2 0.8 19 24 C 4.9 H 4.5 4.8 3.5 4.3 26 40 C 4.7 H 3.4 3.6 3.0 8.8 41 50 H 4.8 H 2.8 3.2 3.1 9.3 51 54 C 4.7 H 4.5 6.2 5.9 4.2 57 59 E 5.0 H 2.0 3.3 3.3 4.0 60 66 C 4.4 M 5.5 7.4 5.1 5.4 67 68 * 3.5 M 5.5 75.0 3.5 75.0 70 74 * 2.5 P 6.4 21.2 33.4 47.0 75 76 C 4.3 M 1.0 4.5 0.5 2.5 77 80 E 4.8 H 0.5 0.8 1.2 1.2 81 83 C 4.8 H 1.7 4.0 6.0 3.0 85 94 - 4.3 M 5.2 75.0 75.0 75.0 95 96 C 4.7 H 4.5 7.2 7.0 43.2 97 110 H 4.8 H 2.6 2.9 2.9 2.4 111 116 * 2.3 P 29.1 5.3 54.4 5.3 117 127 - 4.3 M 75.0 8.1 75.0 75.0 >>>>>>