Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1bg1a2 ---------------------------------------------------------CEEEEEECCCCC-CCCCEEECCCCEEEEEEE--CCCCH-HHCC-------------CCEEEEEECCHHHCCCCCCCCCCEEEEC----------CCEEECCCC-----CCC------------------------------------------CCCEEEEEEEEEEEECCC------CCCCCCCHHHCCCHHHCCCCEEEEEEEEEC----------C---EEEEEEEECCCCEEECCHHHHHHHHHHHHHHHHHCCCCCCCCHHHCCCCEEHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCCCCEECHHHHCCCCCCCCCCCHHHHHHHHHHHHHHC >P1;d1mnna- CCEEEECCCCCEEEECCCCCCCCCCCCHHHCCCCCCCEEEEECCCEEECCCCCCCCCEEEEEEEECCEEECCEEEEECCCCEEEEEEEECCCCCHHHHHHCCEEECCCCEECCEEEEEEEEEECCCC-----CEECEEEECCCHHHCCEECCCCEECCCCCCCCHHHHHHCCCCCHHHHHHHHHHHEEEHHHCCHHHCCCCCHHHHCCCCEEECCEEEEEEEECCCCCCCCCCC--------------CCCCEEEEEEEEEEECCCCCEEECCCCCCEEEEEEEEECCCEEEECCC---HHHCHHHC------------------------------------------------------------------------------------------------- PSA >P1;d1bg1a2 ---------------------------------------------------------603420105836-513000228350100032--66446-7035-------------407050201366668a426012305046----------843440117-----689------------------------------------------94101020570206348a------ab6477ab5631531000020003150628----------b---74573432030000067573024000000003102b656416007923404064016002601451198007895156105302687a905a4705045003750ab4950002301730475568 >P1;d1mnna- 8384771b17140100124738178838311020070651661050020977570505020200230031894100015420000000306208396004210104346340300001020121567-----751902014586992765809113000190170520150150979547814930323147266960ab800024038550320010120101aa17153979--------------84240000000000073e354382a2d702001000120240001266---87131937------------------------------------------------------------------------------------------------- Translating the sequences ---------------------------------------------------------*EEEEEE*CC**-CC**EEECCCCEEEEEEE--CCCCH-HH**-------------**EEEEEE**HHHC*****C**CEEEEC----------CCEEECCCC-----***------------------------------------------***EEEEEEEEEEEECCC------**************HHCC**EEEEEEEEEC----------C---EEEEEEEECCC*EEECCH***HHHHHHHH************************************************************************************************* *********************************************************EEEEEEEECCEE*CCEEEEECCCCEEEEEEE**CCCCH*HHHH*************EEEEEEEEEE***C-----CEECEEEEC**********CC*EECCCC*****HHH******************************************EEE**EEEEEEEE**CCC******--------------**CCEEEEEEEEEEEC**********C***EEEEEEEECCCEEEECC*---HHH*HHH*------------------------------------------------------------------------------------------------- 49417-1.tem _________________________________ ---------------------------------------------------------EEEEEEEECCEE-CCEEEEECCCCEEEEEEE--CCCCH-HHHH-------------EEEEEEEEEEHHHC-----CEECEEEEC----------CCEEECCCC-----HHH------------------------------------------EEEEEEEEEEEEEEECCC--------------------HHCCEEEEEEEEEEEC----------C---EEEEEEEECCCEEEECCH---HHHHHHHH------------------------------------------------------------------------------------------------- Structural block scores 0 56 - 3.0 P 75.0 3.7 57 64 E 4.5 M 2.0 1.4 65 66 C 5.0 H 6.5 1.5 67 68 E 3.0 P 4.5 1.5 70 71 C 5.0 H 3.0 8.5 72 76 E 4.2 M 1.0 1.0 77 80 C 5.0 H 4.5 3.0 81 87 E 5.0 H 0.9 0.0 88 89 - 3.0 P 75.0 1.5 90 93 C 5.0 H 5.0 4.0 96 99 H 4.0 M 3.8 2.5 100 112 - 3.0 P 75.0 2.4 113 122 E 4.2 M 2.2 0.6 123 125 H 3.0 P 6.0 4.0 127 131 - 3.0 P 6.1 75.0 133 134 E 3.0 P 1.5 3.0 136 139 E 5.0 H 2.2 0.8 141 150 - 3.0 P 75.0 6.5 151 152 C 5.0 H 6.0 4.5 153 155 E 4.3 M 3.7 1.7 156 159 C 5.0 H 2.2 0.2 160 164 - 3.0 P 75.0 3.4 165 167 H 3.0 P 7.7 2.3 168 209 - 3.0 P 75.0 4.3 210 224 E 4.1 M 2.7 1.8 225 227 C 5.0 H 7.5 6.2 228 247 - 3.0 P 27.1 54.2 248 249 H 3.0 P 0.5 6.0 250 251 C 5.0 H 0.0 3.0 252 262 E 4.6 H 1.7 0.0 264 273 - 3.0 P 75.0 5.5 275 277 - 3.0 P 75.0 3.0 278 285 E 5.0 H 4.4 0.5 286 288 C 5.0 H 1.0 2.0 289 292 E 4.5 M 0.0 0.2 293 294 C 5.0 H 6.5 4.0 296 298 - 3.0 P 3.3 75.0 299 306 H 4.5 M 0.8 4.9 307 403 - 3.0 P 3.8 75.0 >>>>>>