Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1chua3 CCCCEEEEEEECCCCCCCCCCCHHHHHCCCEEECCCCCCCHHHCC-CCHHHCC----------------HHHHHHHHHHHHHHHCC------CCEEEECCCCC-------CHHHHHHCHHHHHHHHC-----------CCCCCCCCCEEEEEEEEEC------- >P1;d1jnra3 CC-CCCCCEEECCC---CCCCHHHHHCCCCCEECCCCCCHHHHCCHHHHHHCCHHHCC--------CCCHHHHHHHHHHHHHCCCC-------CEEECHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCCCCCEEEEECCCCCCCCCCCC >P1;d1y0pa3 CC-CEEEEEEECCC---CCCCCCHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHCCHHHCEEEEEEHHHHHHCCCHHHHHHHCCC-------CEECCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHCCCCCCCCC-CCCCCCCCCCEEEEEEEEEEEE----- >P1;d2bs2a3 CCCCEEECCCCCCC---CCCCCCHHHHHCCEEECCCCCCCHHHHCCCCHHHCC----------------HHHHHHHHHHHHHCCCCCCCCCCCCEEEECHHHC-------HHHHHHHCHHHHHHHHH----------CCCCCCCCCCEEECCEEEEC------- >P1;d3sfda2 -----------------------------CEEECCCCCCCCCCCCCCCHHHCC----------------HHHHHHHHHHHHHHCCCC-CCCCCCEEEECCCCC-------HHHHHHHCHHHHHHHHH----------CCCCCCCCCCEEE-------------- PSA >P1;d1chua3 98944510000527719b140566006470301138673004621-a520705----------------253017005602753b1------81020002565-------4660674149017505a-----------2912028440202156486------- >P1;d1jnra3 aa-45121020461---4000820386070502017651037515a507646780858--------81356131300320265924-------403010160079309c69a537603630362056627601710776a1403742040110744435a5408 >P1;d1y0pa3 99-64400020473---9630234006300000135060012022829701720571687000000012025229505703a5800-------3516406600942-a0618205610760270197880533906-7023206585100020304829----- >P1;d2bs2a3 aa934500000035---234066800647010204725300261279530607----------------4830173043017693017187840020001418-------5a304660790142047----------51812007730102025488------- >P1;d3sfda2 -----------------------------12120376530045126a630a17----------------a74176026502738301-279662033203426-------69507674685276157----------8380413852123-------------- Translating the sequences CC*CEEE*EEECCC***CCCCC*HHHHCCCEEECCCCCCCHHHCC-CCHHHCC----------------HHHHHHHHHHHHHH*CC------CCEEEEC***C-------*HHHHHHCHHHHHHHH*-----------CCCCCCCCCEEEEEEEEEC------- CC-C****EEECCC---CCCC**HHH*CCC*EECCCCCC*HHHCC***HHHCC*****--------***HHHHHHHHHHHHH*CCC-------CEEE**HHH********HHHHHHH*HHHHHHHH************CCCCCCCCCEEEEE****C******* CC-CEEE*EEECCC---CCCCC*HHHHCCCEEECCCCCCC***CCC**HHH******************HHHH***HHHHHHHCCC-------CEE***HHH****-***HHHHHHH*HHHHHHHHH*********-CCCCCCCCCCEEEEEEEEE***----- CC*CEEE****CCC---CCCCC*HHHH*CCEEECCCCCCCHHH*CCCCHHHCC----------------HHHHHHHHHHHHH*CCC******CCEEEECHHHC-------HHHHHHHCHHHHHHHHH----------CCCCCCCCCCEEE**EEEEC------- -----------------------------CEEECCCCCCC***CCCCCHHHCC----------------HHHHHHHHHHHHHHCCC*-****CCEEEEC***C-------HHHHHHHCHHHHHHHHH----------CCCCCCCCCCEEE-------------- 56425.tem _________________________________ CC-CEEE*EEECCC---CCCCC*HHHHCCCEEECCCCCCCHHHCCCCCHHHCC----------------HHHHHHHHHHHHHHCCC------CCEEEECHHHC-------HHHHHHHCHHHHHHHHH----------CCCCCCCCCCEEEEEEEEEC------- Structural block scores 0 1 C 4.5 M 8.5 10.5 9.0 10.5 75.0 4 6 E 4.1 M 3.3 2.7 2.7 3.0 75.0 8 10 E 4.1 M 0.0 0.7 0.7 0.0 75.0 11 13 C 4.5 M 4.7 3.7 4.7 2.7 75.0 14 16 - 4.5 M 5.7 75.0 75.0 75.0 75.0 17 21 C 4.4 M 4.3 2.4 4.0 3.0 75.0 23 26 H 4.4 M 3.0 4.2 2.5 3.5 75.0 27 29 C 4.5 M 3.7 2.3 1.0 3.7 50.3 30 32 E 4.8 H 1.3 2.3 0.0 1.0 1.7 33 39 C 4.9 H 4.0 2.9 2.1 3.0 3.4 40 42 H 3.8 M 3.3 5.0 1.0 2.7 3.0 43 47 C 4.2 M 18.7 4.3 4.6 4.8 5.1 48 50 H 5.0 H 3.0 5.7 2.7 3.0 4.5 51 52 C 4.5 M 2.5 6.5 4.5 3.5 4.0 53 68 - 4.1 M 75.0 40.1 2.3 75.0 75.0 69 82 H 4.8 H 3.1 2.6 4.0 3.4 4.3 83 85 C 4.8 H 5.2 5.0 2.7 4.0 3.7 86 91 - 3.9 M 75.0 75.0 75.0 5.3 16.7 92 93 C 4.6 H 4.5 39.5 39.0 2.0 4.0 94 97 E 4.6 H 0.5 1.0 4.0 0.5 2.0 99 101 H 3.8 M 4.3 2.3 4.0 2.0 3.0 103 109 - 3.9 M 75.0 6.6 15.2 75.0 75.0 110 116 H 4.9 H 4.7 5.8 3.3 4.9 5.7 118 126 H 4.9 H 4.6 3.4 4.3 3.8 5.2 127 136 - 3.9 M 75.0 3.7 11.7 75.0 75.0 137 146 C 4.9 H 10.7 4.5 3.8 3.4 4.2 147 155 E 4.4 M 3.1 2.3 1.1 2.4 50.7 157 163 - 4.3 M 75.0 5.1 55.1 75.0 75.0 >>>>>>