Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1cg2a2 --------------------------------------------------------------------CEEEEEEEEEECCCEECCCCHH-HCCCHHHHHH-------------HHHHHHHHHCC------C-----------CCCCEEEECCCC---CCEECCEEEEEEEEEECC--CHHHHCCC--CHHHCCCC-------CCCCCEEECCCC------- >P1;d1fnoa3 --------------------------------------------------------------------CEEEEEEEEEECCCCCHHHCC--CCCCHHHHHH-------------HHHHCCCCCCC------HHHCCCC-----CCEEEECCCCC--------CCEEC-CEEEEECCHHHHHHHHHC--CHHHHHCCCCC--CCCEEEEEEEEEC-------- >P1;d1lfwa2 CEEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCEEEEEEECCEEEEEEE-CCCCCCCC--HHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCEECCCEECEEEEEEEEEECCC------CEEEEEEEEECCCCCHHHHHHHHHHHHCC----------CEEEECC-------CCCCC >P1;d1r3na2 ---------------------------------------------------------------------CEEEEEEEEECCCEECCCCCHHHCCCHHHHHH-------------HHHHHHHHHHH------HCC----------CEEECCCEEEECCCCCEECCEEEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEC-------- >P1;d1vgya2 ---------------------------------------------------------------------CEEEEEEEE-CCCEECCC--HHHCCCHHHHHH-------------HHHHHHHH-CCCCCCCC---------CCCCCEEEEEEEECCCCCCCEECCCEEEEEEEECCCCCCHHHHHHHHHHHHHHC--CC-----CCEEEEEEEEC-------- >P1;d1ysja2 ---------------------------------------------------------------------CEEEEEEEEECCC----------CCCHHHHHH-------------HHHHHHC----------------------CCEEEEEEEECC-CCCCCCCC-EEEEEEEECCCHHHHHHCCCCC-HHHHHHHHHC---CCEEEEEEEEEEC-------- >P1;d1z2la2 --------------------------------------------------------------------CEEEEEEEEEECCCEECCCCCHHHCCCHHHHHH-------------HHHHHHHHHHH------HHC---C-----CCEEECCCEEEECCCCCEECCEEEEEEEEEECCHHHHHHHHHHHHHHHHHHHHHH---CCEEEEEEEEEECC------- >P1;d2q43a2 ---------------------------------------------------------------------CCCEEEEEE-EEECC---------CHHHHHHH-------------HHHHHHHH-HCC--CCC--------CCCCCEEEEEEEEEC---------CEEEEEEEEEEC--CCHHHHHHHHHHHHHHHHHCC-----CEEEEEE-CCHHHCCCCCC PSA >P1;d1cg2a2 --------------------------------------------------------------------60206040606075265b7438-8023065007-------------30371069037------9-----------981070576158---b63114704030306056--71990130--93067253-------808026287960------- >P1;d1fnoa3 --------------------------------------------------------------------200030405010454879a4a--c635056048-------------5057412a841------2850ab9-----60114348917--------45603-413010466960451174--71198028719--a050627273465-------- >P1;d1lfwa2 20302040605a4a7837030340300855630052060202058087039405810883907060716b83050204-06016043--03603100000030017260200033005000610050240660202362a8374010000305054a5------8040300010067060840174036416c----------3060729-------84771 >P1;d1r3na2 ---------------------------------------------------------------------02032302040633548814876131045006-------------50272046007------62b----------08070874817494b730113030103041856a307402930673066106629083071836535537-------- >P1;d1vgya2 ---------------------------------------------------------------------220404030-26645566--677062058406-------------40373047-28019048---------8485060817648135c5a72013703050207007318398038304500662--a0-----91908181897-------- >P1;d1ysja2 ---------------------------------------------------------------------0305020103169----------815054027-------------5048514----------------------c08240634614-a4968729-503203060a888217721775-73069306a3---9050405235766-------- >P1;d1z2la2 --------------------------------------------------------------------2031304020605526388168b8132056016-------------30376044307------748---a-----406060773416365a830104030203031663730470055028405810a71---80a17063534771------- >P1;d2q43a2 ---------------------------------------------------------------------103130303-0345a---------84055008-------------30282058-236--94b--------586533406066388---------b41203040504--631780166035205730672-----8060706-1409a783772 Translating the sequences --------------------------------------------------------------------**EEEEEEEE*CCC********-*CCCHHHHHH-------------HHHHHHHH***------*-----------CC**EE******---****CC*EEEEEEEE*CC--*HHHH***--*HHH****-------*****EEE**C*------- --------------------------------------------------------------------**EEEEEEEE*CCC*******--*CCCHHHHHH-------------HHHH*******------*******-----CCEEEE*****--------CC*E*-*EEEE*CC***HHHHHH*--*HHHH******--***EEEEEEE**C-------- ***********************************************************************EEEEEEE-CCC*****--***CCCHHHHHH*************HHHHHHHH**********************CEEEE**EE*****------*EEEEEEEE*CC***HHHHHH***HHH**----------*EEEE**-------***** ---------------------------------------------------------------------*EEEEEEEE*CCC**********CCCHHHHHH-------------HHHHHHHH***------***----------CEEE***EE*********CC*EEEEEEEE*CC***HHHHHH***HHHHH***********EEEEEEE**C-------- ---------------------------------------------------------------------*EEEEEEEE-CCC*****--***CCCHHHHHH-------------HHHHHHHH-********---------***CCEEEE**EE*********CC*EEEEEEEE*CC***HHHHHH***HHHHH*--**-----**EEEEEE**C-------- ---------------------------------------------------------------------*EEEEEEEE*CCC----------CCCHHHHHH-------------HHHHHH*----------------------CCEEEE**EE**-******CC-EEEEEEEE*CC***HHH*****-HHHHH*****---***EEEEEEE**C-------- --------------------------------------------------------------------**EEEEEEEE*CCC**********CCCHHHHHH-------------HHHHHHHH***------***---*-----CCEEE***EE*********CC*EEEEEEEE*CC***HHHHHH***HHHHH*****---***EEEEEEE**C*------- ---------------------------------------------------------------------***EEEEEE-*****---------C*HHHHHH-------------HHHHHHHH-***--***--------****C*EEEE**EE*---------C*EEEEEEEE*C--**HHHHHH***HHHHH*****-----*EEEEEE-*********** 55031.tem _________________________________ --------------------------------------------------------------------**EEEEEEEE*CCC**********CCCHHHHHH-------------HHHHHHHH****--******---*--***CCEEEE**EE*********CC*EEEEEEEE*CC***HHHHHH***HHHHH*****---***EEEEEEE**C*------- Structural block scores 0 67 - 4.7 H 75.0 75.0 3.5 75.0 75.0 75.0 75.0 75.0 68 69 * 2.2 P 3.0 1.0 8.8 37.5 38.5 37.5 1.0 38.0 70 77 E 4.9 H 2.2 1.5 2.8 1.5 1.6 1.4 1.6 1.6 79 81 C 4.7 H 4.0 3.0 2.0 3.0 4.7 5.3 3.3 2.3 82 91 * 2.6 P 12.9 21.6 17.3 5.4 19.6 75.0 6.2 61.5 92 94 C 4.8 H 1.7 4.7 1.3 1.7 2.7 4.7 2.0 29.0 95 100 H 5.0 H 3.0 3.8 0.0 2.5 3.8 3.0 3.0 3.0 101 113 - 4.7 H 75.0 75.0 1.8 75.0 75.0 75.0 75.0 75.0 114 121 H 4.8 H 3.6 4.3 1.8 3.2 3.5 12.8 3.4 3.5 122 125 * 2.5 P 21.2 22.0 1.5 20.5 21.2 75.0 21.2 21.5 126 127 - 4.3 M 75.0 75.0 1.0 75.0 5.0 75.0 75.0 75.0 128 133 * 3.6 M 64.0 40.0 3.0 40.8 39.5 75.0 40.7 41.6 134 136 - 4.3 M 75.0 7.3 1.7 75.0 75.0 75.0 75.0 75.0 138 139 - 4.5 M 75.0 75.0 6.2 75.0 75.0 75.0 75.0 40.0 140 142 * 3.9 M 75.0 75.0 6.0 75.0 6.7 75.0 75.0 6.3 143 144 C 4.6 H 8.5 3.0 2.0 37.5 2.5 6.2 2.0 3.0 145 148 E 4.7 H 2.0 2.2 0.2 3.8 3.8 3.5 3.0 2.5 149 150 * 1.0 P 6.0 6.0 1.5 7.5 6.5 4.5 7.0 6.0 151 152 E 4.3 M 3.5 5.0 2.5 6.0 6.0 5.0 3.5 5.5 153 161 * 2.7 P 28.8 67.4 36.1 5.2 5.1 13.8 4.7 67.6 162 163 C 4.6 H 2.5 4.5 75.0 1.0 2.0 5.5 0.5 43.2 165 172 E 4.9 H 2.0 10.9 1.0 1.4 2.1 2.4 1.4 1.9 174 175 C 4.8 H 5.5 5.0 3.0 6.5 3.5 9.2 6.0 39.5 176 178 * 1.7 P 52.3 7.0 4.3 6.5 4.0 6.0 4.3 28.0 179 184 H 4.7 H 3.8 3.0 3.3 3.7 5.2 4.2 2.7 3.8 185 187 * 2.1 P 50.0 51.3 2.3 3.0 2.3 29.0 2.3 3.0 188 192 H 4.7 H 5.0 5.2 5.9 4.4 3.4 5.0 5.0 3.8 193 197 * 2.2 P 32.0 3.6 75.0 3.0 32.5 4.5 3.9 3.6 198 200 - 4.6 H 75.0 53.0 75.0 5.7 75.0 75.0 75.0 75.0 201 203 * 2.6 P 52.7 5.2 51.0 3.3 53.0 4.7 6.2 52.7 204 210 E 4.6 H 3.7 3.9 14.1 4.4 4.0 2.7 3.6 13.4 211 212 * 1.7 P 8.0 5.0 75.0 4.0 8.5 6.5 5.5 2.5 215 221 - 4.4 M 75.0 75.0 25.3 75.0 75.0 75.0 75.0 6.4 >>>>>>