AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -ihipB_mjan_opreg_100.orf -g0.314 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.314 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MJ0271 300 M. jannaschii predicted coding region MJ0271 Motif number 1 ACTTAACATAATGTAAAGTATTATTAACATGATAGAG 1 11 1 ATAAAGATAA 0.989992 -290 AACATGATAGAGGAAAAAGATGGGTAAATTACTTCTC 1 36 1 AGAAAAATAA 0.955428 -265 TTCATCTATTATTAAAAACTCTGTTAAAAATCCGAGA 1 69 0 ATAAAATTAA 0.928007 -232 TAATAGATGAATTAAAAGCAGAGATATTTAAAAAATC 1 95 1 ATAAAGATAT 0.978264 -206 ATAAATCCAAAAAGAAAGGATTAACATAATGGATGAT 1 129 0 AAAAAGACAT 0.834707 -172 CAACTTTTACATTAAAGAAAGCCATAAAATTAAGAAT 1 175 0 ATAAGAATAA 0.975277 -126 ATATAACTATATCTAAAGAAAATGCAACTTTTACATT 1 199 0 ATAAAGACAA 0.986067 -102 AAAAGTTGCCATTAAAAATATAACTATATCTAAAGAA 1 216 0 ATAAAAATAT 0.976483 -85 AAAGCAGTAGATAAAAGATAATATCAAATTCAAAACA 1 252 0 ATAAGAACAA 0.965611 -49 TTATCTACTGCTTTAAAATACACTTAAGGTGAAACT 1 275 1 CTAAAAATAA 0.950331 -26 ** **** * *** Masking position 6 Map Score: 11.3252 Number of sites scoring better than the average of aligned sites = 551 Number in coding regions = 449 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 2 ACTTAACATAATGTAAAGTATTAT 1 3 1 TTAACTATGT 0.985603 -298 TAAAGTATTATTAACATGATAGAGGAAAAAGA 1 24 1 TTAACTATAG 0.984861 -277 CTGCTTTTAATTCATCTATTATTAAAAACTCT 1 84 0 TTCATTTTAT 0.7344 -217 AAAGAAAGGATTAACATAATGGATGATTTTTT 1 124 0 TTAACTATGG 0.990867 -177 GTTCTGATTCTTAATTTTATGGCTTTCTTTAA 1 169 1 TTAATTATGG 0.985623 -132 ATGGCTTTCTTTAATGTAAAAGTTGCATTTTC 1 187 1 TTAATTAAAG 0.940558 -114 ACTTTTGTTTTGAATTTGATATTATCTTTTAT 1 247 1 TGAATTATAT 0.878606 -54 AGTTTCACCTTAAGTGTATTTTAAA 1 286 0 TTCACTAAGT 0.934263 -15 ***** * **** Masking position 4 Map Score: 7.97357 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 191 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 3 AAAAAGATGGGTAAATTACTTCTCGGATTTTTA 1 49 1 GTAAATATCT 0.901844 -252 ATATCTCTGCTTTTAATTCATCTATTATTAAAA 1 89 0 TTTTATTTCT 0.800114 -212 TGGATGATTTTTTAAATATCTCTGCTTTTAATT 1 104 0 TTTAATATCT 0.989076 -197 CATCCATTATGTTAATCCTTTCTTTTTGGATTT 1 131 1 GTTAACCTCT 0.913909 -170 TCTTTTTGGATTTATTTAGTTCTGATTCTTAAT 1 151 1 TTTATTATCT 0.98259 -150 GATTCTTAATTTTATGGCTTTCTTTAATGTAAA 1 174 1 TTTATGCTCT 0.921171 -127 CCATTAAAAATATAACTATATCTAAAGAAAATG 1 212 0 TATAATATCT 0.941946 -89 GATATTATCTTTTATCTACTGCTTTAAAATACA 1 264 1 TTTATTAGCT 0.937462 -37 ***** ** *** Masking position 13 Map Score: 2.98948 Number of sites scoring better than the average of aligned sites = 1230 Number in coding regions = 1113 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 4 TCATCTATTATTAAAAACTCTGTTAAAAAT 1 75 0 TTAAAAACTC 0.869704 -226 GATGATTTTTTAAATATCTCTGCTTTTAAT 1 105 0 TAAATATCTC 0.974418 -196 GAATCAGAACTAAATAAATCCAAAAAGAAA 1 149 0 TAAATAAATC 0.980887 -152 ACTTTTACATTAAAGAAAGCCATAAAATTA 1 180 0 TAAAGAAAGC 0.931425 -121 ATTAAAAATATAACTATATCTAAAGAAAAT 1 213 0 TAACTATATC 0.941672 -88 ********** Masking position 6 Map Score: 1.1681 Number of sites scoring better than the average of aligned sites = 402 Number in coding regions = 356 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 5 AAGTAATTTACCCATCTTTTTCCTCTATCA 1 40 0 CCCATCTTTT 0.976859 -261 CTGCTTTTAATTCATCTATTATTAAAAACT 1 86 0 TTCATCTATT 0.93061 -215 CTAAAGAAAATGCAACTTTTACATTAAAGA 1 194 0 TGCAACTTTT 0.989297 -107 TATTTTTAATGGCAACTTTTGTTTTGAATT 1 233 1 GGCAACTTTT 0.987291 -68 ********** Masking position 4 Map Score: 1.1875 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 183 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 ********** No masking Map Score: 7.91135e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 7 ********** No masking Map Score: 7.91135e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 ********** No masking Map Score: 7.91135e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0