Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2icga1 CCCHHHHHHHHHHHCCCCC-CCCCCCCHHHHHHHHHHHCC-CCHHHHHHHHHCCCEEECCEEECCCCCCHHHCCCCCCHHHHHHHHHHC-CCCCC--CEEECCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCEEEECCHHHHHHHHHHHHHHCC-------- >P1;d2paga1 ----CHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCC----CCCCCHHHHHHHHHHH-CCCCCCEEEEEEC-CEEEEECC-------CCCEEEECCC----EEEEEECCHHHHHHHCCCCC------------ >P1;d2prva1 ----CCCCHHHHHHHHHHC-EECCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHCCEEECCEEECCCCCC------CCHHHHHHHHHHHHCCCCCCEEEEEECC-CEEEEEECC----CCCCCEEEEECC--CEEEEEEECCHHHHHHHHHHHHHHHHCCCCCCCC PSA >P1;d2icga1 4b8039306602860b370-72064056820750273091-006003200551000304932000017714607753002310452277-84056--00045b912211002535296911000206650a6682752030004002620560287b-------- >P1;d2paga1 ----4a91266047344939974830789406701751a2a0184032002300102238160010066----9281101700670194-703570000045c-83000037-------8230110419----22953182014005410073------------ >P1;d2prva1 ----4490392077158a0-7115207a931770275071a007003100741002002a050101259------511016405404852a04b200001048-920100106----c73130010229--7144843280005003730461387749a696ac Translating the sequences *****HHHHHHHHH*CCCC-CCCCCCCHHHHHHHHHHHCC-CCHHHHHHHHH*CCEEECCEEECCCCCC****CCCCCHHHHHHHHHH*-CCCCC--*EEECC*C*EEEEE******CCC**EEEECCC**C***EEEECCHHHHHHHHHHHHHH**-------- ----CHHHHHHHHHHCCCC*CCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHCC***CC***CCCCCC----CCCCCHHHHHHHHHHH-CCCCC*EEEEE*C-CEEEEE*C-------CCCEEEECCC----EEEEEECCHHHHHHH*****------------ ----C***HHHHHHH***C-**CCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHCCEEECCEEECCCCCC------CC*HHHHHHHHHHH*CCCCC*EEEEECC-CEEEEEEC*----CCCCCEEEE*CC--C*EEEEEECCHHHHHHHHHHHHHH********** 160631.tem _________________________________ ----CHHHHHHHHHHCCCC-CCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHCCEEECCEEECCCCCC----CCCCCHHHHHHHHHHH-CCCCC*EEEEECC-CEEEEEEC*----CCCCCEEEECCC--C*EEEEEECCHHHHHHHHHHHHHH**-------- Structural block scores 0 3 - 4.0 M 5.9 75.0 75.0 5 14 H 4.6 H 4.0 4.8 4.2 15 18 C 4.2 M 5.4 5.0 5.9 20 26 C 4.7 H 3.4 5.4 3.3 27 37 H 5.0 H 3.6 4.4 4.7 38 42 C 4.8 H 17.0 4.8 3.7 43 52 H 4.9 H 2.2 2.2 2.3 53 54 C 5.0 H 0.0 0.5 0.0 55 57 E 4.0 M 1.0 1.3 0.7 58 59 C 5.0 H 6.5 5.5 6.2 60 62 E 4.0 M 1.7 2.3 1.7 63 68 C 5.0 H 2.5 2.2 3.0 69 72 - 4.0 M 2.8 75.0 75.0 73 77 C 4.4 M 4.4 4.2 31.4 78 88 H 4.9 H 3.0 3.2 3.4 90 94 C 5.0 H 4.6 4.4 5.6 96 100 E 4.6 H 15.8 0.8 0.2 101 102 C 4.5 M 8.2 8.8 6.0 105 110 E 4.7 H 1.0 1.0 0.7 113 116 - 4.0 M 4.8 75.0 75.0 117 121 C 4.2 M 3.4 32.6 5.3 122 125 E 5.0 H 0.5 0.5 0.2 126 128 C 4.7 H 5.7 4.7 4.3 129 130 - 4.0 M 5.2 75.0 75.0 133 138 E 4.7 H 4.0 3.7 4.2 139 140 C 5.0 H 1.5 5.0 4.0 141 154 H 4.5 M 2.5 12.5 2.9 155 156 * 2.7 P 9.2 75.0 7.0 157 164 - 4.0 M 75.0 75.0 8.4 >>>>>>