AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -inarP_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 MJ0649 172 NADH oxidase (nox) #2 MJ0965 38 uroporphyrin-III C-methyltransferase (cobA) #3 MJ1165 238 formylmethanofuran dehydrogenase, subunit E (tungsten) (fwdE) Motif number 1 CTATCCCCTCTTTTATTATTTAATAATCTTATT 1 12 1 TTTATTTTAA 0.979307 -161 AATAATCTTATTCTATTTTTAAGTTATTTTTAG 1 33 1 TTTATTTAAG 0.976991 -140 TAAATTTCTAATATATTACTAAAAATAACTTAA 1 51 0 ATTATTTAAA 0.972301 -122 TTCACAATTATTGTATTAGTTAGAAGTTCTATA 1 85 1 TTTATTTTAG 0.956565 -88 AAGTTATAGCTTCTAATACTAATTTTTATGGG 2 10 0 TTTAATTAAT 0.860148 -29 AAAATAAATATTATAATGATTTAGATTAGAAGA 3 18 0 TTTAATTTTA 0.803146 -221 TCATTATAATATTTATTTTTTATGGTTGTATTT 3 32 1 ATTATTTTAT 0.835005 -207 TTTTTTATGGTTGTATTTTTATATTATTAGCTT 3 47 1 TTTATTTATA 0.972303 -192 TAGAAAAGCTTTATATTGGTAAAGCTAATAATA 3 68 0 TTTATTTAAA 0.989974 -171 AAAATAGAACTTTTATTCATATATGTTGAACTA 3 104 1 TTTATTTATA 0.972306 -135 ATATATGTTGAACTATTTATAAATATGTGAGCA 3 122 1 AATATTTAAA 0.887214 -117 ACTTCATACATAGTATTTATAAATGAAAATCAT 3 189 1 TATATTTAAA 0.956758 -50 ** **** **** Masking position 5 Map Score: 18.1551 Number of sites scoring better than the average of aligned sites = 835 Number in coding regions = 607 Number in noncoding regions = 228 Number of orfs with sites within 600 bp upstream = 210 Fraction of orfs with sites within 600 bp upstream = 0.0337295 Motif number 2 CCTCTTTTATTATTTAATAATCTTATTCTA 1 18 1 TATTTAATAA 0.627469 -155 TACTAAAAATAACTTAAAAATAGAATAAGA 1 38 0 AACTTAAAAA 0.868171 -135 AGTTAGAAGTTCTATAAAAACTTTTTGGTT 1 102 1 TCTATAAAAA 0.942568 -71 CCCATAAAAATTAGTATTAG 2 1 1 CCCATAAAAA 0.955682 -38 TAAAAATACAACCATAAAAAATAAATATTA 3 38 0 ACCATAAAAA 0.912636 -201 TAAAGCTAATAATATAAAAATACAACCATA 3 52 0 AATATAAAAA 0.939896 -187 ATTAGCTTTACCAATATAAAGCTTTTCTAC 3 72 1 CCAATATAAA 0.762063 -167 AATAGTTCAACATATATGAATAAAAGTTCT 3 109 0 CATATATGAA 0.799234 -130 TATGTTGAACTATTTATAAATATGTGAGCA 3 125 1 TATTTATAAA 0.856806 -114 GACACACACCTATATAAAAAAGTTTCTACT 3 156 1 TATATAAAAA 0.945614 -83 TGATGATTTTCATTTATAAATACTATGTAT 3 194 0 CATTTATAAA 0.917904 -45 ********** Masking position 6 Map Score: 10.8831 Number of sites scoring better than the average of aligned sites = 1684 Number in coding regions = 1176 Number in noncoding regions = 508 Number of orfs with sites within 600 bp upstream = 414 Fraction of orfs with sites within 600 bp upstream = 0.0664953 Motif number 3 AATATATTACTAAAAATAACTTAAAAATAGAA 1 43 0 TAAAATAATT 0.929155 -130 TTTTAGTAATATATTAGAAATTTATTTCACAA 1 60 1 ATATAGAATT 0.931752 -113 ATTATTGTATTAGTTAGAAGTTCTATAAAAAC 1 91 1 TAGTAGAATT 0.936522 -82 ATTTTGACACAAAAATGAACTTAACCAAAAAG 1 122 0 AAAATGAATT 0.922535 -51 TTATAGCTTCTAATACTAATTTTTATGGG 2 8 0 TAAACTAATT 0.682465 -31 TTAGTATTAGAAGCTATAACTTATTTTA 2 21 1 AAGTATAATT 0.755497 -18 ATGATTTAGATTAGAAGAATTTACG 3 4 0 TTAAAGAATT 0.934971 -235 ATACAACCATAAAAAATAAATATTATAATGAT 3 31 0 AAAAATAATA 0.666755 -208 TTTTCTACCAAAAATAGAACTTTTATTCATAT 3 94 1 AAATAGAATT 0.926321 -145 GTATGAAGTTTAAGTAGAAACTTTTTTATATA 3 166 0 TAATAGAACT 0.851203 -73 TATAAATACTATGTATGAAGTTTAAGTAGAAA 3 178 0 ATGATGAATT 0.748425 -61 *** ***** ** Masking position 8 Map Score: 6.72483 Number of sites scoring better than the average of aligned sites = 1615 Number in coding regions = 1376 Number in noncoding regions = 239 Number of orfs with sites within 600 bp upstream = 207 Fraction of orfs with sites within 600 bp upstream = 0.0332477 Motif number 4 AACTAATACAATAATTGTGAAATAAATTTC 1 76 0 ATAATTGTGA 0.948543 -97 TTTGATGATCATGATTTTGACACAAAAATG 1 137 0 ATGATTTTGA 0.992054 -36 AAATATTATAATGATTTAGATTAGAAGAAT 3 16 0 ATGATTTAGA 0.980165 -223 ATGTTAGTTGATGATTTTCATTTATAAATA 3 202 0 ATGATTTTCA 0.978981 -37 ********** Masking position 5 Map Score: 2.95863 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 67 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 5 TTTTTAAGTTATTTTTAGTAATATATTAGA 1 48 1 ATTTTTAGTA 0.835188 -125 TCTATAAAAACTTTTTGGTTAAGTTCATTT 1 112 1 CTTTTTGGTT 0.91118 -61 TGGTTAAGTTCATTTTTGTGTCAAAATCAT 1 127 1 CATTTTTGTG 0.945231 -46 ATTTTTTATCCTTTTTGATGATCATGATTT 1 150 0 CTTTTTGATG 0.976513 -23 ATTATTTTTTATCCTTTTTGATG 1 160 0 ATTTTTTATC 0.903463 -13 TTCTAATACTAATTTTTATGGG 2 3 0 AATTTTTATG 0.91236 -36 TATAATATTTATTTTTTATGGTTGTATTTT 3 36 1 ATTTTTTATG 0.970546 -203 TAAAAGTTCTATTTTTGGTAGAAAAGCTTT 3 89 0 ATTTTTGGTA 0.952682 -150 TAAGTAGAAACTTTTTTATATAGGTGTGTG 3 158 0 CTTTTTTATA 0.953577 -81 ********** Masking position 5 Map Score: 11.2391 Number of sites scoring better than the average of aligned sites = 581 Number in coding regions = 440 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 6 ********** No masking Map Score: 5.92755e-14 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: 5.92755e-14 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: 5.92755e-14 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