AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -intrC_mgen_opreg_300.orf -g0.317 -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 = 0.317 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MG062 300 PTS system, fructose-specific IIABC component (fruA) #2 MG063 94 1-phosphofructokinase (fruK) #3 MG064 255 conserved hypothetical protein Motif number 1 TCTAAAAAACAATTAGCTACAGCTTTTAAAATTAG 1 32 0 ATAGCACAGT 0.989561 -269 TTTAGAACAAACTGAATCAAAGAATTTGAAATTGT 1 61 1 ATAATAAAGT 0.741707 -240 TGCTGTTAACAATGAAAGACAATTTCAAATTCTTT 1 79 0 ATAAAACAAT 0.987498 -222 TGTTAACAGCATTTAACAACAAAATTGAATAAAAA 1 103 1 ATAACACAAT 0.989173 -198 ATTGAATAAAAATAAAAAACAGACCCTGATGGTCT 1 126 1 ATAAAACAGC 0.926979 -175 TTTATAATAAATTTAACAACAAACTGGGAGCGTAC 1 253 0 ATAACACAAT 0.989173 -48 ACCACCAGGTATTAAAACACTATTTTTTTGCTTGT 2 46 0 ATAAAACTAT 0.893674 -49 GATGGTAAAAAGAAAGCGAAAGCCTAAGCTTAATT 3 20 1 AAAGCAAAGT 0.794375 -236 AAGATAGCAAAGTAAGAAAAAAGATCATACTAAAG 3 92 0 ATAGAAAAAT 0.941259 -164 TACTTTGCAAACTCAAAAACAAGATTAAAGATAGC 3 119 0 ATAAAACAAT 0.987497 -137 TTGCAAAGTAATTTAGCTACAGCTTTAGTTGAAAA 3 144 1 ATAGCACAGT 0.989561 -112 CAGTTCTTTTAAAAAAAGACAATGTTATCTACAAG 3 198 0 AAAAAACAAT 0.941631 -58 CTAATAAATTAGTCAGAGACAAATTTAAAAATCAG 3 230 0 ATAGAACAAT 0.986891 -26 * * *** **** * Masking position 9 Map Score: 20.9683 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 58 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 2 ACATTAGACTAATTTTAAAAGCTGTAGCTA 1 24 1 AATTTTAAAA 0.952287 -277 ATTGTCTTTCATTGTTAACAGCATTTAACA 1 91 1 ATTGTTAACA 0.946743 -210 TATTTATAATAAATTTAACAACAAACTGGG 1 260 0 AAATTTAACA 0.918735 -41 AATTAGTTGCATATTTATAATAAATTTAAC 1 271 0 ATATTTATAA 0.851578 -30 AACAATCTGGATAGTTAAAATATTACGCGA 3 54 0 ATAGTTAAAA 0.969127 -202 CATACTAAAGATTGTTAAAACAATCTGGAT 3 72 0 ATTGTTAAAA 0.969118 -184 AACATTGTCTTTTTTTAAAAGAACTGATTT 3 207 1 TTTTTTAAAA 0.844938 -49 AGTCAGAGACAAATTTAAAAATCAGTTCTT 3 225 0 AAATTTAAAA 0.952298 -31 ********** Masking position 7 Map Score: 7.75647 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 237 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 3 TCTGTTTTTTATTTTTATTCAATTTTGTTG 1 119 0 ATTTTTATTC 0.901954 -182 CGAAAGCCTAAGCTTAATTCGCGTAATATT 3 36 1 AGCTTAATTC 0.946738 -220 TGTTTTAACAATCTTTAGTATGATCTTTTT 3 80 1 ATCTTTAGTA 0.91846 -176 CTTTAGTATGATCTTTTTTCTTACTTTGCT 3 92 1 ATCTTTTTTC 0.936403 -164 TTACTTTGCTATCTTTAATCTTGTTTTTGA 3 112 1 ATCTTTAATC 0.955664 -144 ATTTAGCTACAGCTTTAGTTGAAAACAGAA 3 154 1 AGCTTTAGTT 0.959476 -102 CAAGTTCCACAGCTTTATTTCTGTTTTCAA 3 172 0 AGCTTTATTT 0.966584 -84 ********** Masking position 1 Map Score: 4.46137 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 121 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 TTTTATTCAATTTTGTTGTTAAATGCTGTT 1 107 0 TTTTGTTGTT 0.838242 -194 GGTCTGTTTTTTATTTTTATTCAATTTTGT 1 121 0 TTATTTTTAT 0.692894 -180 CAATTGATTATTATGTTGATTTAAACAAGC 2 22 1 TTATGTTGAT 0.954556 -73 TAAAACACTATTTTTTTGCTTGTTTAAATC 2 39 0 TTTTTTTGCT 0.957254 -56 GTAAGGGGATTAATGTTGCTATTGTA 2 79 1 TAATGTTGCT 0.928087 -16 ATCTTTTTTCTTACTTTGCTATCTTTAATC 3 102 1 TTACTTTGCT 0.971941 -154 TGTAGCTAAATTACTTTGCAAACTCAAAAA 3 135 0 TTACTTTGCA 0.877922 -121 ********** Masking position 6 Map Score: 2.68061 Number of sites scoring better than the average of aligned sites = 310 Number in coding regions = 283 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 5 TAAGACAGAATTTACATTAGACTAA 1 6 1 CAGAATTTAC 0.880891 -295 CAATTAGCTACAGCTTTTAAAATTAGTCTA 1 28 0 CAGCTTTTAA 0.954939 -273 TCATTGTTAACAGCATTTAACAACAAAATT 1 99 1 CAGCATTTAA 0.968776 -202 CATTTAACAACAAAATTGAATAAAAATAAA 1 112 1 CAAAATTGAA 0.878902 -189 CCCTTACCACCAGGTATTAAAACACTATTT 2 56 0 CAGGTATTAA 0.86821 -39 TACAATAGCAACATTAATCCCCTTACCA 2 77 0 CAACATTAAT 0.713421 -18 TTTTTACCATCAAATATTAA 3 1 0 CAAATATTAA 0.859923 -255 AACTCAAAAACAAGATTAAAGATAGCAAAG 3 115 0 CAAGATTAAA 0.91555 -141 TAGTTGAAAACAGAAATAAAGCTGTGGAAC 3 169 1 CAGAAATAAA 0.920847 -87 TAGTCAGAGACAAATTTAAAAATCAGTTCT 3 226 0 CAAATTTAAA 0.916698 -30 ********** Masking position 7 Map Score: 7.14143 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 307 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 TTTTTTAGAACAAACTGAATCAAAGAATTT 1 58 1 CAAACTGAAT 0.978604 -243 CAATGAAAGACAATTTCAAATTCTTTGATT 1 75 0 CAATTTCAAA 0.815856 -226 ATTTAACAACAAAATTGAATAAAAATAAAA 1 113 1 AAAATTGAAT 0.803507 -188 AATTTAACAACAAACTGGGAGCGTACTCAA 1 249 0 CAAACTGGGA 0.916915 -52 ATTGTTAAAACAATCTGGATAGTTAAAATA 3 62 0 CAATCTGGAT 0.904595 -194 AATTACTTTGCAAACTCAAAAACAAGATTA 3 127 0 CAAACTCAAA 0.968712 -129 GCTTTAGTTGAAAACAGAAATAAAGCTGTG 3 165 1 AAAACAGAAA 0.75047 -91 TAGTCAGAGACAAATTTAAAAATCAGTTCT 3 226 0 CAAATTTAAA 0.816076 -30 ********** Masking position 3 Map Score: 1.80827 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 277 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 7 ********** No masking Map Score: -3.24418e-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: -3.24418e-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 9 ********** No masking Map Score: -3.24418e-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