Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2pr9a1 CCCCCCCCCCCCEEEEEEEEEEEEEECCCCCEEEEEEEEEEEEEEECCCCCEEEEEECCC------------CCCCCCEEEECCCCCCC-----CCEEECCCCEEEEEEEEEEC-CCC--CCEEEEEEEEEEC-CCEEEEEEEEEECCCCCCCCEEEEEEEECCCCEEEEEEEEC---CCCEEEHHHCEEEEEEC-CCCCCEEEEEEEEEECCCCCCCCCCCCCEEEEEEEC-CCCCCCCEEEEEEECCCCCCCHHHCEEEEEEEEEEEEEEECC >P1;d3l81a- -----------CEEEEEEEEEEEEEECCCCCEEEEEEEEEEEEEECCCCCCEEEEEECCCCEECCCCCCCCCCCCEECEEEECCCCCCCCHHHHCEEEECCCCEEEEEEEEEECCCCCCCCCEEEEEEEEECCCCCEEEEEEEEEECCCCCCEEEEEEEEEECCCCCEEEEEEECCCCCEEEEE--CCEEEEEECCEECCCEEEEEEEEECCCCC---CCCCCCEEEEEEEECCCCCCCCEEEEEEECC---------EEEEEEEEEEEEEEECC PSA >P1;d2pr9a1 3b2088a07361104000201010200380742713050300020400210604020049------------76091582822700597-----86140001256020060504-c04--200303060662a-a7303040105061869370570203010082045071809---6308257a45000060b-1106751505030416959b9882b24203060204-100040404404080683c184b6043636230504803051 >P1;d3l81a- -----------6502020104040202590624704040205040506ba0304000165062453a98847a6100161714a50437519761203060562812006040638026710030316273685625030403030207883304804050300aa064373804494080613--ab103030480509350202020414989---7a81050204040173000406052060744---------73425130207402051 Translating the sequences ***********CEEEEEEEEEEEEEECCCCCEEEEEEEEEEEEEEECCCCCEEEEEECCC------------CCC**CEEEECCCCCCC-----C*EEECCCCEEEEEEEEEEC-CCC--CCEEEEEEEEEEC-CCEEEEEEEEEECCCCCC**EEEEEEEECCCCEEEEEEEEC---C**EEE**HCEEEEEEC-**CCCEEEEEEEEEECCCC***CCCCCCEEEEEEE*-CCCCCCCEEEEEEECC*********EEEEEEEEEEEEEEECC -----------CEEEEEEEEEEEEEECCCCCEEEEEEEEEEEEEE*CCCCCEEEEEECCC************CCCEECEEEECCCCCCC*****CEEEECCCCEEEEEEEEEEC*CCC**CCEEEEEEEEE*C*CCEEEEEEEEEECCCCCCEEEEEEEEEECCCC*EEEEEEEC***CEEEEE--*CEEEEEEC*EECCCEEEEEEEEE*CCCC---CCCCCCEEEEEEEE*CCCCCCCEEEEEEECC---------EEEEEEEEEEEEEEECC 49447.tem _________________________________ -----------CEEEEEEEEEEEEEECCCCCEEEEEEEEEEEEEEECCCCCEEEEEECCC------------CCCEECEEEECCCCCCC-----CEEEECCCCEEEEEEEEEEC-CCC--CCEEEEEEEEEEC-CCEEEEEEEEEECCCCCCEEEEEEEEEECCCCEEEEEEEEC---CEEEEE--HCEEEEEEC-EECCCEEEEEEEEEECCCC---CCCCCCEEEEEEEE-CCCCCCCEEEEEEECC---------EEEEEEEEEEEEEEECC Structural block scores 0 10 - 3.0 P 5.4 75.0 12 25 E 5.0 H 0.8 1.4 26 30 C 5.0 H 3.6 4.4 31 45 E 4.9 H 2.1 2.5 46 50 C 5.0 H 0.6 5.6 51 56 E 5.0 H 2.0 1.2 57 59 C 5.0 H 4.3 4.0 60 71 - 3.0 P 75.0 5.5 72 74 C 5.0 H 4.3 5.8 75 76 E 3.0 P 5.0 0.0 78 81 E 5.0 H 5.0 3.8 82 88 C 5.0 H 4.3 4.8 89 93 - 3.0 P 75.0 5.6 95 98 E 4.5 M 2.8 1.2 99 102 C 5.0 H 0.8 4.2 103 112 E 5.0 H 2.4 2.3 115 117 C 5.0 H 5.5 3.3 118 119 - 3.0 P 75.0 6.5 120 121 C 5.0 H 1.0 0.5 122 131 E 4.8 H 2.6 3.1 134 135 C 5.0 H 8.8 4.0 136 145 E 5.0 H 1.6 1.8 146 151 C 5.0 H 5.5 4.7 152 161 E 4.6 H 2.5 2.7 162 165 C 5.0 H 2.5 5.2 166 173 E 4.8 H 3.1 3.9 175 177 - 3.0 P 75.0 5.7 179 183 E 4.2 M 3.6 3.6 184 185 - 3.0 P 8.8 75.0 188 193 E 5.0 H 1.0 1.2 196 197 E 3.0 P 1.0 2.5 198 200 C 5.0 H 4.3 4.0 201 210 E 4.8 H 2.4 1.6 211 214 C 5.0 H 7.2 7.5 215 217 - 3.0 P 9.5 75.0 218 223 C 5.0 H 4.9 5.2 224 231 E 4.8 H 1.9 1.4 233 239 C 5.0 H 1.3 1.9 240 246 E 5.0 H 2.9 2.9 247 248 C 5.0 H 3.0 4.0 249 257 - 3.0 P 6.0 75.0 258 272 E 5.0 H 3.1 2.7 273 274 C 5.0 H 3.0 3.0 >>>>>>