AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -inarP_mjan_opreg_300.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 0.979848 -161 AATAATCTTATTCTATTTTTAAGTTATTTTTAG 1 33 1 TTTATTTAAG 0.977699 -140 TAAATTTCTAATATATTACTAAAAATAACTTAA 1 51 0 ATTATTTAAA 0.973149 -122 TTCACAATTATTGTATTAGTTAGAAGTTCTATA 1 85 1 TTTATTTTAG 0.957875 -88 AAGTTATAGCTTCTAATACTAATTTTTATGGG 2 10 0 TTTAATTAAT 0.863953 -29 AAAATAAATATTATAATGATTTAGATTAGAAGA 3 18 0 TTTAATTTTA 0.808156 -221 TCATTATAATATTTATTTTTTATGGTTGTATTT 3 32 1 ATTATTTTAT 0.839364 -207 TTTTTTATGGTTGTATTTTTATATTATTAGCTT 3 47 1 TTTATTTATA 0.973152 -192 TAGAAAAGCTTTATATTGGTAAAGCTAATAATA 3 68 0 TTTATTTAAA 0.990287 -171 AAAATAGAACTTTTATTCATATATGTTGAACTA 3 104 1 TTTATTTATA 0.973155 -135 ATATATGTTGAACTATTTATAAATATGTGAGCA 3 122 1 AATATTTAAA 0.890376 -117 ACTTCATACATAGTATTTATAAATGAAAATCAT 3 189 1 TATATTTAAA 0.958062 -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 TAGAATAAGATTATTAAATAATAAAAGAGG 1 18 0 TTATTAAATA 0.677955 -155 TCTTATTCTATTTTTAAGTTATTTTTAGTA 1 38 1 TTTTTAAGTT 0.89193 -135 AACCAAAAAGTTTTTATAGAACTTCTAACT 1 102 0 TTTTTATAGA 0.950207 -71 CTAATACTAATTTTTATGGG 2 1 0 TTTTTATGGG 0.964308 -38 TAATATTTATTTTTTATGGTTGTATTTTTA 3 38 1 TTTTTATGGT 0.929038 -201 TATGGTTGTATTTTTATATTATTAGCTTTA 3 52 1 TTTTTATATT 0.95137 -187 GTAGAAAAGCTTTATATTGGTAAAGCTAAT 3 72 0 TTTATATTGG 0.800586 -167 AGAACTTTTATTCATATATGTTGAACTATT 3 109 1 TTCATATATG 0.832976 -130 TGTTGAACTATTTATAAATATGTGAGCAAG 3 127 1 TTTATAAATA 0.873874 -112 AGTAGAAACTTTTTTATATAGGTGTGTGTC 3 156 0 TTTTTATATA 0.95268 -83 ATACATAGTATTTATAAATGAAAATCATCA 3 194 1 TTTATAAATG 0.933139 -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 TATTCTATTTTTAAGTTATTTTTAGTAATA 1 41 1 TTAAGTTATT 0.592412 -132 GTAATATATTAGAAATTTATTTCACAATTA 1 65 1 AGAAATTTAT 0.664751 -108 TGTATTAGTTAGAAGTTCTATAAAAACTTT 1 96 1 AGAAGTTCTA 0.964587 -77 AACTTAACCAAAAAGTTTTTATAGAACTTC 1 107 0 AAAAGTTTTT 0.588539 -66 AACTTTTTGGTTAAGTTCATTTTTGTGTCA 1 120 1 TTAAGTTCAT 0.732267 -53 AATTAGTATTAGAAGCTATAACTTATTTTA 2 19 1 AGAAGCTATA 0.892924 -20 TTTATATTGGTAAAGCTAATAATATAAAAA 3 62 0 TAAAGCTAAT 0.550102 -177 TTTTTGGTAGAAAAGCTTTATATTGGTAAA 3 78 0 AAAAGCTTTA 0.512077 -161 ATATATGAATAAAAGTTCTATTTTTGGTAG 3 98 0 AAAAGTTCTA 0.926039 -141 CATATTTATAAATAGTTCAACATATATGAA 3 119 0 AATAGTTCAA 0.592624 -120 AAGTTTAAGTAGAAACTTTTTTATATAGGT 3 163 0 AGAAACTTTT 0.540463 -76 ATACTATGTATGAAGTTTAAGTAGAAACTT 3 175 0 TGAAGTTTAA 0.878282 -64 ********** Masking position 4 Map Score: 6.48937 Number of sites scoring better than the average of aligned sites = 3336 Number in coding regions = 2913 Number in noncoding regions = 423 Number of orfs with sites within 600 bp upstream = 345 Fraction of orfs with sites within 600 bp upstream = 0.0554128 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 ACTATCCCCTCTTTTATTATTTAATAA 1 8 1 CCTCTTTTAT 0.795712 -165 AATCTTATTCTATTTTTAAGTTATTTTTAG 1 36 1 TATTTTTAAG 0.684917 -137 ATTTTTAAGTTATTTTTAGTAATATATTAG 1 47 1 TATTTTTAGT 0.915218 -126 TTCTATAAAAACTTTTTGGTTAAGTTCATT 1 111 1 ACTTTTTGGT 0.911618 -62 TTGGTTAAGTTCATTTTTGTGTCAAAATCA 1 126 1 TCATTTTTGT 0.907566 -47 TATTTTTTATCCTTTTTGATGATCATGATT 1 151 0 CCTTTTTGAT 0.94463 -22 ATTATTTTTTATCCTTTTTGAT 1 161 0 TATTTTTTAT 0.96926 -12 CTTCTAATACTAATTTTTATGGG 2 4 0 TAATTTTTAT 0.886665 -35 TTATAATATTTATTTTTTATGGTTGTATTT 3 35 1 TATTTTTTAT 0.96926 -204 ATAAAAGTTCTATTTTTGGTAGAAAAGCTT 3 90 0 TATTTTTGGT 0.96051 -149 TTAAGTAGAAACTTTTTTATATAGGTGTGT 3 159 0 ACTTTTTTAT 0.930417 -80 ********** Masking position 5 Map Score: 13.8563 Number of sites scoring better than the average of aligned sites = 1293 Number in coding regions = 969 Number in noncoding regions = 324 Number of orfs with sites within 600 bp upstream = 267 Fraction of orfs with sites within 600 bp upstream = 0.0428847 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