Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2hj2a1 -------CCCCCCCC---------------------CCCCCC------HHHHHHHHHHHHHHHHHH-HCCCCEEEEEEEEE----------------CCEEEEEEEEECCCCC---CCC-CHHH-HHHHHCCEE-----HHHCEECCCCEEEEEEECCCHHHHHHHCCCC >P1;d2hj2a2 CHHHCCCCCCCCCCC---------------------CCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEEEEEEEC---CCEEEEEEEEEEEEEEECC-CC--HHHHHHHHHHCCHHHHCC--H------HHCC--CCEEEECCCCCCC---------- >P1;d2hj2a3 ----CCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-----CHHHHHHHHHHHHHHHHHHC----CCCCCCEEEEECCC---------CCCCCCEEEEECCCCCCCC--HHHHCCCCCCCCHHHHHH--HHCCCCCCCCCCCCCCCCCC---CCHHHCCCCC--- >P1;d4le5a1 -------C-CCCCCC---------------------CCCCCC------HHHHHHHHHHHHHHHHHH-HCCCCEEEEEEEEE----------------CCEEEEEEEEECCCCCCHHHHHHHHHH-HHHHHCCCCCCCCCCCCCCCHHHCEEEEEEECCC----------- >P1;d4le5a2 --CCCCCCCCCCCCC---------------------CCCCCCHHHCCHHHHHHHHHHHHHHHHHHHCC-CCCCCCCEEEEEEECCCHHHHHCCCCCEEEEEEEECCCCCCCC--HHHHHHHHHH-HHHCCCC--CC-----CCCCCCCCEEEECCCCCCC---------- >P1;d6rk7a2 C-CCCCCCCCCCCCC---------------------CCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEEEECCCC-------CCEEEEEEEEEEECCCCC--HHHHHHHHHH-HHHHHHH--HC-----CCCC--CCEEEECCCCCCC---------- PSA >P1;d2hj2a1 -------ea8a8989---------------------93a634------684016302730461048-50780306080508----------------87203041505080a0---925-2028-106807345-----9859102570605270982589626663696 >P1;d2hj2a2 8a978b8c9a5988a---------------------761801b554213510265048203612767416004571807050626a6---e545141051020203047-17--396048103460054005--9------7116--a051500374633---------- >P1;d2hj2a3 ----87989399a67177257104888271b73204b2625-----53500030012102200466----9009503070504b---------b567056230513830b36--484041040404281017--305076842b0379200637---8130063406--- >P1;d4le5a1 -------b-998889---------------------959534------684016302830384048-41870506090716----------------c45020424160a39066850371027-005908252569755864210940603171985a----------- >P1;d4le5a2 --ba9b8c9a6989b---------------------76170099853046111720373057306726-72075a0706060516577366827155051010201049917--2760471037-10480a0--29-----91053980603004a5255---------- >P1;d6rk7a2 a-b9ac8b9a89a9b---------------------7629407575303400272028103502758506405570807050448ab-------835051020303037817--5930482047-0046007--61-----a032--a072410789632---------- Translating the sequences -------CCCCCCCC---------------------CCCCCC------HHHHHHHHHHHHHHHHH*-*CCCCEEEEEEEEE----------------**EEEEEEEE*CCCC*---***-*HHH-HHHHHCC**-----***C****CCEEEE***CCC*********** ****CC*CCCCCCCC---------------------CCCCCC****CHHHHHHHHHHHHHHHHHH***CCC*EEEEEEEEE******---*********EEEEEEEECC-CC--HHHHHHHHHH**HHHHCC--*------**CC--CCEEEEC**CCC*---------- ----CC***CCCCCC*********************CCCCC-----CHHHHHHHHHHHHHHHHHH*----CC****EEEEE***---------******EEEEE***CCCCC--HHHH********HHHH**--*******CCCC**CC****C---CC********--- -------C-CCCCCC---------------------CCCCCC------HHHHHHHHHHHHHHHHH*-*CCCCEEEEEEEEE----------------**EEEEEEEE*CCCC**HHHHHHHHHH-HHHHHCC*********CCCC***CEEEE***CCC----------- --**CC*CCCCCCCC---------------------CCCCCC****CHHHHHHHHHHHHHHHHHH***-CCC****EEEEE******************EEEEE***CCCCC--HHHHHHHHHH-HHH**CC--**-----CCCC**CCEEEEC**CCC*---------- *-**CC*CCCCCCCC---------------------CCCCCC****CHHHHHHHHHHHHHHHHHH***CCC*EEEEEEEEE******-------*****EEEEEEEECCCCC--HHHHHHHHHH-HHHHH**--**-----CCCC--CCEEEEC**CCC*---------- 55973.tem _________________________________ --**CC*CCCCCCCC---------------------CCCCCC****CHHHHHHHHHHHHHHHHHH***CCCCEEEEEEEEE******------******EEEEEEEECCCCC--HHHHHHHHHH-HHHHHCC--**---**CCCC**CCEEEEC**CCC*---------- Structural block scores 0 1 - 4.3 M 75.0 9.2 75.0 75.0 75.0 42.8 2 3 * 3.4 M 75.0 8.0 75.0 75.0 11.0 10.2 4 5 C 4.3 M 75.0 9.8 7.5 75.0 10.2 11.5 7 14 C 4.8 H 9.7 9.1 7.7 17.2 9.4 9.9 15 35 - 4.5 M 75.0 75.0 4.5 75.0 75.0 75.0 36 41 C 4.9 H 5.9 3.8 16.9 5.8 3.5 4.7 42 45 * 3.4 M 75.0 6.4 75.0 75.0 7.8 6.0 47 64 H 5.0 H 7.2 3.1 1.6 7.5 3.1 2.6 65 67 * 2.1 P 29.3 5.7 52.0 29.0 5.0 6.0 68 71 C 4.5 M 3.8 1.8 39.8 4.0 21.0 2.5 72 80 E 4.6 H 3.3 4.1 3.2 3.8 4.6 4.1 81 86 * 3.1 M 75.0 5.1 40.1 75.0 4.0 6.3 87 92 - 4.3 M 75.0 41.4 75.0 75.0 5.3 75.0 93 98 * 2.2 P 52.5 2.7 5.8 52.8 3.8 16.0 99 106 E 4.7 H 1.9 1.0 3.5 2.2 0.6 1.1 107 111 C 4.7 H 4.7 18.8 4.7 5.7 6.0 5.2 112 113 - 4.3 M 37.5 75.0 75.0 3.0 75.0 75.0 114 123 H 4.4 M 25.3 3.8 2.9 3.9 3.7 4.2 125 129 H 4.6 H 3.0 1.8 3.0 2.8 2.6 2.0 130 131 C 4.1 M 5.0 2.5 4.0 5.0 5.2 3.5 132 133 - 4.1 M 4.5 75.0 75.0 3.5 75.0 75.0 134 135 * 2.3 P 75.0 42.0 1.5 5.5 5.5 3.5 136 138 - 4.1 M 75.0 75.0 4.0 7.0 75.0 75.0 139 140 * 3.4 M 8.5 75.0 7.0 6.5 75.0 75.0 141 144 C 4.4 M 3.8 3.8 4.4 3.2 3.8 3.9 145 146 * 2.7 P 3.5 75.0 5.0 4.5 6.0 75.0 147 148 C 4.8 H 3.5 5.2 5.5 2.0 4.0 5.2 149 152 E 4.5 M 3.2 2.8 2.2 2.5 2.2 3.5 154 155 * 1.9 P 4.5 5.0 75.0 5.0 7.2 7.5 156 158 C 4.8 H 5.0 4.3 28.0 7.8 4.0 6.0 160 169 - 4.2 M 5.9 75.0 24.4 75.0 75.0 75.0 >>>>>>