Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1q74a- CCCEEEEEECCCCHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCCHHHCCCCCCCHHHHHHHHHHHHHHHCCCCCCEECCCCCCCCCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHC--CC----CCCCCCCEEEEEECCHHHHHHHHHHCCHHHCCCCCCCCCHHHCCCCCCHHHCCEEEECCHHHHHHHHHHHHHCCCCCEECCCCCEEECC-------------CCCEEECCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCC >P1;d1uana- -CEEEEEEECCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCC--------------HHHHHHHHHHHHHHHCCCEEEEE----EECCCCCCCC---------HHHHHHHHHHHHHHCEEEEEEECCC--CCCHHHHHHHHHHHHHHHHHCCCCCCCC--CCCCCCCEEEEECCCCC----------------------------CC----CCEEEEC-HHHHHHHHHHHHCCHHHHC--------CCHHHHHHHHHHHHHHHHH-CCCCCEEEECCCC-CCCCC--CCCCC--------- >P1;d6ulla- -CCCEEEEECCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCC--------------HHHHHHHHHHHHHHHCCC-CEEC----CCCCCCCCCC---------HHHHHHHHHHHHHHCCCEEEEECCC--CCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEECCCCC-----------------------------C----CCEEEEC-HHHHHHHHHHHHCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH-CCCCCEEEEECCC-CCCCCCCCCC----------- PSA >P1;d1q74a- 77110000001010003300000020155a06030000010103503aa834920066647007304900460063070761300294340102280a1b420271479501320072009150000000046085645014201700550182028--39----9a42802000200305520482388069802485073082752161276b702000406690062025005207010310532500046-------------751020032300010174a12a34b48004500272b1b >P1;d1uana- -302000000101000010001002154694300000006066a1657--------------97618712840171030621411----4060170525---------8714350030006150520000156--073700210050062027201588070a--a9218075111002349----------------------------19----0320240-2821940250041083107--------4368406713720462075-6a17200002068-93a66--58598--------- >P1;d6ulla- -70400000000000000000000322659440200000204625027--------------395048107501710605-1331----7150440945---------9901340010005040610000166--05250024004003500820058828086627227044010000134-----------------------------a----1432240-2a017103600510-200656aa16a2620ad11803610581098-3a37100001065-9395a98696----------- Translating the sequences *CCEEEEEECCCCHHHHHHHHHHHHHHHCCC*EEEEECCCCCCCCCCC**************HHHHHHHHHHHHHH*CCC*CEEC****CCCCCCCCCC*********HHHHHHHHHHHHHHCCCEEEEECCC**CCCHHHHHHHHHHHHHHHHH*C--CC----CCCCCCCEEEEE*CC******************************CC****CCEEEEC*HHHHHHHHHHHH*C*CCC**CCCCC***CC-------------******CCCEEEEE****CCCCCCCCCCCC********* -C*EEEEEECCCCHHHHHHHHHHHHHHHCCCCEEEEE**CCCCCCCCC--------------HHHHHHHHHHHHHHHCCC**EE*----**CCCCCCCC---------HHHHHHHHHHHHHHC**EEEEECCC--CCCHHHHHHHHHHHHHHHHHCCCCCCCC--CCCCCCCEEEEECCCCC----------------------------CC----CCEEEEC-HHHHHHHHHHHHCC****C--------CC******HHHHHHHHHHH-CCCCCEEEE*CCC-CCCCC--CCCCC--------- -CC*EEEEECCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCC--------------HHHHHHHHHHHHHHHCCC-CEEC----CCCCCCCCCC---------HHHHHHHHHHHHHHCCCEEEEECCC--CCCHHHHHHHHHHHHHHHHHCCCCCCCC**CCCCCCCEEEEECCCCC-----------------------------C----CCEEEEC-HHHHHHHHHHHHCC-CCCC*CCCCC**CCC*****HHHHHHHHHHH-CCCCCEEEEECCC-CCCCCCCCCC----------- 102588.tem _________________________________ -CCEEEEEECCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCC--------------HHHHHHHHHHHHHHHCCC*CEEC----CCCCCCCCCC---------HHHHHHHHHHHHHHCCCEEEEECCC--CCCHHHHHHHHHHHHHHHHHCCCCCCCC--CCCCCCCEEEEECCCCC----------------------------CC----CCEEEEC-HHHHHHHHHHHHCC*CCCC*CCCCC**CCC*****HHHHHHHHHHH-CCCCCEEEEECCC-CCCCCCCCCCCC--------- Structural block scores 1 2 C 4.5 M 4.0 1.5 3.5 3 8 E 4.8 H 0.2 0.3 0.7 9 12 C 5.0 H 0.5 0.5 0.0 13 27 H 5.0 H 0.9 0.9 0.9 28 31 C 4.8 H 5.4 5.5 5.5 32 36 E 5.0 H 0.6 0.0 0.4 37 47 C 4.8 H 2.1 4.3 2.5 48 61 - 4.0 M 4.7 75.0 75.0 62 76 H 4.9 H 2.8 4.1 3.4 77 79 C 5.0 H 4.7 3.0 3.7 82 83 E 5.0 H 1.5 2.5 3.0 85 88 - 4.0 M 4.5 75.0 75.0 89 98 C 4.8 H 2.9 3.0 3.9 99 107 - 4.0 M 4.3 75.0 75.0 108 121 H 5.0 H 2.8 2.7 2.3 122 124 C 4.3 M 1.7 3.3 3.3 125 129 E 5.0 H 0.0 0.4 0.2 130 132 C 5.0 H 3.3 4.0 4.3 133 134 - 4.0 M 4.0 75.0 75.0 135 137 C 5.0 H 5.0 3.3 2.3 138 154 H 5.0 H 2.4 2.0 1.9 155 162 C 4.4 M 40.2 4.9 4.9 163 164 - 4.0 M 75.0 75.0 6.0 165 171 C 5.0 H 5.1 5.4 3.4 172 176 E 5.0 H 0.4 1.6 1.0 177 181 C 4.4 M 2.6 3.6 1.6 182 209 - 4.0 M 4.2 75.0 75.0 210 211 C 4.5 M 1.5 5.0 42.8 212 215 - 4.0 M 7.9 75.0 75.0 216 217 C 5.0 H 1.0 1.5 2.5 218 221 E 5.0 H 1.0 2.0 2.8 224 235 H 5.0 H 2.9 3.1 3.0 236 237 C 4.5 M 1.0 0.5 0.5 239 242 C 4.0 M 1.0 2.8 2.0 244 248 C 4.0 M 3.0 75.0 6.8 249 250 * 2.7 P 0.0 75.0 6.2 251 253 C 4.3 M 3.3 4.3 2.7 254 258 * 2.7 P 75.0 5.0 6.8 259 269 H 4.0 M 55.7 3.4 3.7 271 275 C 4.6 H 1.4 5.3 4.9 276 280 E 4.8 H 0.8 0.4 0.2 281 283 C 4.0 M 2.7 4.7 3.7 285 296 C 4.7 H 4.9 18.3 18.7 297 305 - 4.0 M 4.4 75.0 75.0 >>>>>>