AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -irpoN_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 CTAATTTTAAAAGCTGTAGCTAATTGTTTTTTAGA 1 32 1 ACTGTGCTAT 0.987778 -269 ACAATTTCAAATTCTTTGATTCAGTTTGTTCTAAA 1 61 0 ACTTTATTAT 0.70987 -240 AAAGAATTTGAAATTGTCTTTCATTGTTAACAGCA 1 79 1 ATTGTTTTAT 0.985359 -222 TTTTTATTCAATTTTGTTGTTAAATGCTGTTAACA 1 103 0 ATTGTGTTAT 0.987322 -198 AGACCATCAGGGTCTGTTTTTTATTTTTATTCAAT 1 126 0 GCTGTTTTAT 0.915372 -175 GTACGCTCCCAGTTTGTTGTTAAATTTATTATAAA 1 253 1 ATTGTGTTAT 0.987322 -48 ACAAGCAAAAAAATAGTGTTTTAATACCTGGTGGT 2 46 1 ATAGTTTTAT 0.877475 -49 AATTAAGCTTAGGCTTTCGCTTTCTTTTTACCATC 3 20 0 ACTTTGCTTT 0.76699 -236 CTTTAGTATGATCTTTTTTCTTACTTTGCTATCTT 3 92 1 ATTTTTCTAT 0.931755 -164 GCTATCTTTAATCTTGTTTTTGAGTTTGCAAAGTA 3 119 1 ATTGTTTTAT 0.985358 -137 TTTTCAACTAAAGCTGTAGCTAAATTACTTTGCAA 3 144 0 ACTGTGCTAT 0.987778 -112 CTTGTAGATAACATTGTCTTTTTTTAAAAGAACTG 3 198 1 ATTGTTTTTT 0.932183 -58 CTGATTTTTAAATTTGTCTCTGACTAATTTATTAG 3 230 1 ATTGTTCTAT 0.984916 -26 * **** *** * * Masking position 7 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 TAGCTACAGCTTTTAAAATTAGTCTAATGT 1 24 0 TTTTAAAATT 0.950887 -277 TGTTAAATGCTGTTAACAATGAAAGACAAT 1 91 0 TGTTAACAAT 0.945189 -210 CCCAGTTTGTTGTTAAATTTATTATAAATA 1 260 1 TGTTAAATTT 0.916436 -41 GTTAAATTTATTATAAATATGCAACTAATT 1 271 1 TTATAAATAT 0.847698 -30 TCGCGTAATATTTTAACTATCCAGATTGTT 3 54 1 TTTTAACTAT 0.968205 -202 ATCCAGATTGTTTTAACAATCTTTAGTATG 3 72 1 TTTTAACAAT 0.968196 -184 AAATCAGTTCTTTTAAAAAAAGACAATGTT 3 207 0 TTTTAAAAAA 0.841282 -49 AAGAACTGATTTTTAAATTTGTCTCTGACT 3 225 1 TTTTAAATTT 0.950899 -31 ********** Masking position 5 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 0.889076 -182 CGAAAGCCTAAGCTTAATTCGCGTAATATT 3 36 1 AGCTTAATTC 0.939351 -220 TGTTTTAACAATCTTTAGTATGATCTTTTT 3 80 1 ATCTTTAGTA 0.907532 -176 CTTTAGTATGATCTTTTTTCTTACTTTGCT 3 92 1 ATCTTTTTTC 0.927687 -164 TTACTTTGCTATCTTTAATCTTGTTTTTGA 3 112 1 ATCTTTAATC 0.949446 -144 ATTTAGCTACAGCTTTAGTTGAAAACAGAA 3 154 1 AGCTTTAGTT 0.953903 -102 CAAGTTCCACAGCTTTATTTCTGTTTTCAA 3 172 0 AGCTTTATTT 0.96184 -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 GTTTGTTCTAAAAAACAATTAGCTACAGCT 1 43 0 AAAAACAATT 0.803828 -258 TTGCATATTTATAATAAATTTAACAACAAA 1 265 0 ATAATAAATT 0.932219 -36 CTAAAGCGCTAATTAGTTGCATATTTAT 1 283 0 CTAATTAGTT 0.842791 -18 AATCAACATAATAATCAATTGCGCAAGCGT 2 13 0 ATAATCAATT 0.96874 -82 GACAAATTTAAAAATCAGTTCTTTTAAAAA 3 218 0 AAAATCAGTT 0.932291 -38 ACTAATAAATTAGTCAGAGAC 3 245 0 CTAATAAATT 0.919372 -11 ********** Masking position 4 Map Score: 1.71756 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 81 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 AACAGCATTTAACAACAAAATTGAATAAAA 1 107 1 AACAACAAAA 0.837571 -194 ACAAAATTGAATAAAAATAAAAAACAGACC 1 121 1 ATAAAAATAA 0.691841 -180 GCTTGTTTAAATCAACATAATAATCAATTG 2 22 0 ATCAACATAA 0.954341 -73 GATTTAAACAAGCAAAAAAATAGTGTTTTA 2 39 1 AGCAAAAAAA 0.957051 -56 TACAATAGCAACATTAATCCCCTTAC 2 79 0 AGCAACATTA 0.927756 -16 GATTAAAGATAGCAAAGTAAGAAAAAAGAT 3 102 0 AGCAAAGTAA 0.971806 -154 TTTTTGAGTTTGCAAAGTAATTTAGCTACA 3 135 1 TGCAAAGTAA 0.87739 -121 ********** Masking position 5 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 6 TTTTTTAGAACAAACTGAATCAAAGAATTT 1 58 1 CAAACTGAAT 0.97765 -243 CAATGAAAGACAATTTCAAATTCTTTGATT 1 75 0 CAATTTCAAA 0.809059 -226 ATTTAACAACAAAATTGAATAAAAATAAAA 1 113 1 AAAATTGAAT 0.796368 -188 AATTTAACAACAAACTGGGAGCGTACTCAA 1 249 0 CAAACTGGGA 0.913452 -52 ATTGTTAAAACAATCTGGATAGTTAAAATA 3 62 0 CAATCTGGAT 0.900675 -194 AATTACTTTGCAAACTCAAAAACAAGATTA 3 127 0 CAAACTCAAA 0.967331 -129 GCTTTAGTTGAAAACAGAAATAAAGCTGTG 3 165 1 AAAACAGAAA 0.742023 -91 TAGTCAGAGACAAATTTAAAAATCAGTTCT 3 226 0 CAAATTTAAA 0.809285 -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