AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -inarL_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 MJ0033 254 succinate dehydrogenase, flavoprotein subunit (sdhA) #2 MJ0085 134 iron transport periplasmic binding protein, putative (ceuE) #3 MJ0086 36 unspecified methyltransferase #4 MJ0087 23 hemin permease (hemU) #5 MJ0090 80 collagenase (prtC) #6 MJ0091 95 Na+/Ca+ exchanger protein, putative #7 MJ0292 186 conserved hypothetical protein #8 MJ0649 172 NADH oxidase (nox) #9 MJ0965 38 uroporphyrin-III C-methyltransferase (cobA) #10 MJ1165 238 formylmethanofuran dehydrogenase, subunit E (tungsten) (fwdE) Motif number 1 GGCAGTGCATCCGTTTTGATGAACCTTTTAC 1 33 1 CCTTTTGATG 0.831338 -222 CTTCACATGAACCTTTTAGTAAAAGGTTCAT 1 51 0 ACTTTTAGTA 0.698831 -204 AAAATAGTAATATTTTTAATAAGGCACTGGT 1 111 0 TATTTTAATA 0.910836 -144 CTTGTTCTTTTTTTATTTATACTATGCCAAT 1 142 1 TTTATTTATA 0.534435 -113 TAAATCAAAATAGCTTTGATGAAAAAAATAA 1 187 0 TACTTTGATG 0.813164 -68 GAGGGTATCCTATTTTTGGTGATAAAAA 1 237 1 TATTTTGGTG 0.955216 -18 CTTTTTTCTATTTTTTATATAATTTTTAT 2 9 1 TATTTTTATA 0.959618 -126 ATTTTTTATATAATTTTTATGAATATTGATG 2 20 1 TATTTTTATG 0.958029 -115 TTTTAACGATTATTTTTGATAAACTACCGAA 2 54 1 TATTTTGATA 0.969743 -81 TATGAACAAAAATTTTTAATATCTAATATAT 2 89 0 AATTTTAATA 0.803638 -46 TTTTTAATTTTTTATAATTTTTATTT 3 6 1 AATTTTTATA 0.904653 -31 TTTATAATTTTTATTTTGGTGATAAA 3 21 1 TTTTTTGGTG 0.812367 -16 TCTTTTTTATATAATGAGGTC 5 1 1 TCTTTTTATA 0.95115 -80 AGGGTTTTGCTCCTATTGATATGCTCTCAAA 7 27 1 TCTATTGATA 0.862214 -160 CAAGACAACCTCACTTTAATAAAGATTTGAG 7 52 0 TCCTTTAATA 0.542485 -135 TCTTATTTATAACTTTTGGTGATAATAGGCT 7 131 0 AATTTTGGTG 0.894927 -56 ATTTTTAAGTTATTTTTAGTAATATATTAGA 8 47 1 TATTTTAGTA 0.876177 -126 CTTAACCAAAAAGTTTTTATAGAACTTCTAA 8 104 0 AATTTTTATA 0.904654 -69 TTGGTTAAGTTCATTTTTGTGTCAAAATCAT 8 126 1 TCTTTTTGTG 0.928271 -47 TATTTTTTATCCTTTTTGATGATCATGATTT 8 150 0 CCTTTTGATG 0.831338 -23 CTTCTAATACTAATTTTTATGGG 9 3 0 TATTTTTATG 0.958029 -36 TTATAATATTTATTTTTTATGGTTGTATTTT 10 35 1 TATTTTTATG 0.958029 -204 TAGAAAAGCTTTATATTGGTAAAGCTAATAA 10 70 0 TTTATTGGTA 0.517579 -169 ATAAAAGTTCTATTTTTGGTAGAAAAGCTTT 10 89 0 TATTTTGGTA 0.956876 -150 ATATATGTTGAACTATTTATAAATATGTGAG 10 122 1 AATATTTATA 0.693084 -117 TTAAGTAGAAACTTTTTTATATAGGTGTGTG 10 158 0 ACTTTTTATA 0.88602 -81 ACTTCATACATAGTATTTATAAATGAAAATC 10 189 1 TATATTTATA 0.849765 -50 ** ******** Masking position 6 Map Score: 36.1251 Number of sites scoring better than the average of aligned sites = 1305 Number in coding regions = 981 Number in noncoding regions = 324 Number of orfs with sites within 600 bp upstream = 316 Fraction of orfs with sites within 600 bp upstream = 0.0507549 Motif number 2 TTCTTGTTCTTTTTTTATTTATACTATGCCAA 1 140 1 TTTTTTTTAT 0.834296 -115 CAATTTTTTCATTTAGGATTATTTTTTTCATC 1 169 1 ATTTAATTAT 0.950858 -86 CATCAAAGCTATTTTGATTTATAAGTTTTAAA 1 197 1 ATTTTTTTAT 0.868983 -58 CTATTTTTTATATAATTTTTATGAATATTGAT 2 18 1 TATAATTTAT 0.680624 -117 TTGATGTATTTTTAACGATTATTTTTGATAAA 2 45 1 TTTAAATTAT 0.936222 -90 TATATTAGATATTAAAAATTTTTGTTCATATC 2 90 1 ATTAAATTTT 0.555806 -45 TTATCACCAAAATAAAAATTATAAAAAATTAA 3 14 0 AATAAATTAT 0.83681 -23 ACTATCACATTTTTTGAATTATT 4 2 0 TTTTTATTAT 0.901647 -22 ATTTTTTTAAATTTTAAATTATATTTGAAGTA 5 53 0 ATTTTATTAT 0.923509 -28 TTTGCTTAAGTTTAAATATTATTGCAGAATAT 6 35 1 TTTAAATTAT 0.936222 -61 AAAAGTTATAAATAAGATTTATCATTATTAAT 7 145 1 AATAATTTAT 0.737964 -42 ATTTATCATTATTAATCATTATAAATTCCTAA 7 161 1 ATTAAATTAT 0.949682 -26 TCTTATTCTATTTTTAAGTTATTTTTAGTAAT 8 38 1 TTTTTGTTAT 0.572165 -135 TTTAAGTTATTTTTAGTAATATATTAGAAATT 8 50 1 TTTTAAATAT 0.637233 -123 TAGAAATTTATTTCACAATTATTGTATTAGTT 8 74 1 TTTCAATTAT 0.734416 -99 ATTATTTTTTATCCTTTTTGAT 8 161 0 ATTATTTTAT 0.865869 -12 AGCTTCTAATACTAATTTTTATGGG 9 4 0 ACTAATTTAT 0.559333 -35 AACCATAAAAAATAAATATTATAATGATTTAG 10 27 0 AATAAATTAT 0.83681 -212 TATGGTTGTATTTTTATATTATTAGCTTTACC 10 52 1 TTTTTATTAT 0.901647 -187 ATGTTGAACTATTTATAAATATGTGAGCAAGA 10 126 1 ATTTAAATAT 0.698917 -113 TTAGTTGATGATTTTCATTTATAAATACTATG 10 197 0 ATTTTTTTAT 0.868983 -42 ***** ***** Masking position 3 Map Score: 20.0491 Number of sites scoring better than the average of aligned sites = 1627 Number in coding regions = 1120 Number in noncoding regions = 507 Number of orfs with sites within 600 bp upstream = 442 Fraction of orfs with sites within 600 bp upstream = 0.0709926 Motif number 3 TCAGATATTTAAAACTTATAAATCAAAATAG 1 205 0 AAAATTATAA 0.973336 -50 CAATATTCATAAAAATTATATAAAAAATAGA 2 17 0 AAAATTATAT 0.891044 -118 GATATGAACAAAAATTTTTAATATCTAATAT 2 91 0 AAAATTTTAA 0.867402 -44 TCACCAAAATAAAAATTATAAAAAATTAAAA 3 12 0 AAAATTATAA 0.973335 -25 AAAATTTAAAAAAATTTCTAA 5 70 1 AAAATTCTAA 0.980557 -11 AAAAGTTATACATCCAAGGGT 7 1 1 AAAATTATAC 0.926745 -186 TATTATCACCAAAAGTTATAAATAAGATTTA 7 135 1 AAAATTATAA 0.973336 -52 AATTGTGAAATAAATTTCTAATATATTACTA 8 63 0 TAAATTCTAA 0.832318 -110 AAGTTTTTATAGAACTTCTAACTAATACAAT 8 94 0 AGAATTCTAA 0.888323 -79 AAAATAAGTTATAGCTTCTAATACTAATTTT 9 17 0 ATAGTTCTAA 0.730389 -22 CATAAAAAATAAATATTATAATGATTTAGAT 10 25 0 AAATTTATAA 0.822632 -214 TTATATTGGTAAAGCTAATAATATAAAAATA 10 60 0 AAAGTAATAA 0.644596 -179 ATATATGAATAAAAGTTCTATTTTTGGTAGA 10 97 0 AAAATTCTAT 0.918696 -142 CCTATATAAAAAAGTTTCTACTTAAACTTCA 10 164 1 AAAGTTCTAC 0.898204 -75 **** ****** Masking position 3 Map Score: 18.0299 Number of sites scoring better than the average of aligned sites = 561 Number in coding regions = 410 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 4 TAGGATTATTTTTTTCATCAAAGCTATTTT 1 182 1 TTTTTCATCA 0.90413 -73 TTTTTATCACCAAAAATAGGAT 1 243 0 TTTATCACCA 0.987493 -12 ATTGTCACCATTTTAGGCTA 2 125 0 ATTGTCACCA 0.956842 -10 TTTATCACCAAAATAAAAAT 3 27 0 TTTATCACCA 0.987493 -10 ATATAAGCCTATTATCACCAAAAGTTATAA 7 126 1 ATTATCACCA 0.983775 -61 ATAAATAAGATTTATCATTATTAATCATTA 7 152 1 TTTATCATTA 0.832171 -35 TGTCAAAATCATGATCATCAAAAAGGATAA 8 145 1 ATGATCATCA 0.900333 -28 ********** Masking position 7 Map Score: 7.68605 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 80 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 5 TTATTAAAAATATTACTATTTTCTTGTTCTTT 1 120 1 TATTTATTTT 0.960646 -135 TTATTTATACTATGCCAATTTTTTCATTTAGG 1 154 1 TATGAATTTT 0.686354 -101 TTTTTTCATTTAGGATTATTTTTTTCATCAAA 1 172 1 TAGGTATTTT 0.882744 -83 CTTTTTTCTATTTTTTATATAATT 2 3 1 TTTTTATTTT 0.858567 -132 TTTTTATGAATATTGATGTATTTTTAACGATT 2 33 1 TATTTGTATT 0.837274 -102 AATTTTTTATAATTTTTATTTTGGTGATAAA 3 16 1 AATTTATTTT 0.858559 -21 TCATATTGGTTATTGCTATTTTATACTTCAAA 5 30 1 TATTTATTTT 0.960646 -51 TTAGAAATTTTTTTAAATTTTAAATTATATT 5 60 0 TTTTAATTTT 0.494931 -21 AAAGTTTGTTTTTGAATATATTCTGCAATAAT 6 52 0 TTTGTATATT 0.725802 -44 TTGGTGATAATAGGCTTATATTGCCATGGGGA 7 115 0 TAGGTATATT 0.855305 -72 AAGTTATTTTTAGTAATATATTAGAAATTTAT 8 53 1 TAGTTATATT 0.914119 -120 TTTATTTCACAATTATTGTATTAGTTAGAAGT 8 80 1 AATTTGTATT 0.561301 -93 ATCATTATAATATTTATTTTTTATGGTTGTAT 10 31 1 TATTTTTTTT 0.706099 -208 TTTATGGTTGTATTTTTATATTATTAGCTTTA 10 50 1 TATTTATATT 0.950405 -189 ATATGAATAAAAGTTCTATTTTTGGTAGAAAA 10 94 0 AAGTTATTTT 0.771231 -145 ATAGAACTTTTATTCATATATGTTGAACTATT 10 107 1 TATTTATATG 0.708508 -132 **** ****** Masking position 9 Map Score: 13.6975 Number of sites scoring better than the average of aligned sites = 905 Number in coding regions = 575 Number in noncoding regions = 330 Number of orfs with sites within 600 bp upstream = 284 Fraction of orfs with sites within 600 bp upstream = 0.0456152 Motif number 6 GCTACGCTCGGCAGTGCCTC 1 1 0 GCAGTGCCTC 0.995121 -254 GCGTAGCGAGGCAGTGCATCCGTTTTGATG 1 24 1 GCAGTGCATC 0.992483 -231 ATTAGGATTACCAGTGCCTTATTAAAAATA 1 102 1 CCAGTGCCTT 0.965513 -153 AGCAAAATTTTCAGTTCATCCATATTGTAT 6 11 0 TCAGTTCATC 0.924309 -85 ********** Masking position 5 Map Score: 0.889697 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 8 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 AGTGCCTTATTAAAAATATTACTATTTTCT 1 114 1 TAAAAATATT 0.65774 -141 ATATAATTTTTATGAATATTGATGTATTTT 2 27 1 TATGAATATT 0.852162 -108 TTTAATTTTTTATAATTTTTATTTTGGTGA 3 13 1 TATAATTTTT 0.663847 -24 TTTGCTTAAGTTTAAATATTATTGCAGAAT 6 35 1 TTTAAATATT 0.658638 -61 ACCTCACTTTAATAAAGATTTGAGAGCATA 7 46 0 AATAAAGATT 0.855413 -141 TATAATGATTAATAATGATAAATCTTATTT 7 154 0 AATAATGATA 0.248878 -33 ATTAGGAATTTATAATGATTAATAATGATA 7 164 0 TATAATGATT 0.925796 -23 AAATAAATATTATAATGATTTAGATTAGAA 10 20 0 TATAATGATT 0.925796 -219 GCTTTACCAATATAAAGCTTTTCTACCAAA 10 76 1 TATAAAGCTT 0.847628 -163 TTGAACTATTTATAAATATGTGAGCAAGAC 10 129 1 TATAAATATG 0.757742 -110 AAATACTATGTATGAAGTTTAAGTAGAAAC 10 177 0 TATGAAGTTT 0.696402 -62 GATTTTCATTTATAAATACTATGTATGAAG 10 190 0 TATAAATACT 0.74088 -49 ********** Masking position 5 Map Score: 2.19784 Number of sites scoring better than the average of aligned sites = 1237 Number in coding regions = 930 Number in noncoding regions = 307 Number of orfs with sites within 600 bp upstream = 275 Fraction of orfs with sites within 600 bp upstream = 0.0441696 Motif number 8 TTGTTCTTTTTTTATTTATACTATGCCAAT 1 143 1 TTTATTTATA 0.700629 -112 CAAAGCTATTTTGATTTATAAGTTTTAAAT 1 200 1 TTGATTTATA 0.938007 -55 TTTATGAATATTGATGTATTTTTAACGATT 2 35 1 TTGATGTATT 0.845563 -100 ATCACATTTTTTGAATTATT 4 1 0 TTGAATTATT 0.927183 -23 TAAATTATATTTGAAGTATAAAATAGCAAT 5 41 0 TTGAAGTATA 0.866775 -40 TTTTTAAATTTTAAATTATATTTGAAGTAT 5 52 0 TTAAATTATA 0.885036 -29 AAAACAAACTTTAATTAATTTAGTAGGGAT 6 72 1 TTAATTAATT 0.616576 -24 AATAAGATTATTAAATAATAAAAGAGGGGA 8 15 0 TTAAATAATA 0.656465 -158 TATTCTATTTTTAAGTTATTTTTAGTAATA 8 41 1 TTAAGTTATT 0.703243 -132 TTCATATATGTTGAACTATTTATAAATATG 10 119 1 TTGAACTATT 0.748432 -120 GTTGATGATTTTCATTTATAAATACTATGT 10 196 0 TTCATTTATA 0.776256 -43 ********** Masking position 4 Map Score: 3.97467 Number of sites scoring better than the average of aligned sites = 575 Number in coding regions = 444 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 9 TGCCGAGCGTAGCGAGGCAGTGCATCCGTT 1 18 1 AGCGAGGCAG 0.988186 -237 TCTTTATTAAAGTGAGGTTGTCTTGGCAAC 7 58 1 AGTGAGGTTG 0.984695 -129 GGGATACCCGAGCGAGGTTGCCAAGACAAC 7 74 0 AGCGAGGTTG 0.994334 -113 ********** Masking position 5 Map Score: 0.244873 Number of sites scoring better than the average of aligned sites = 3 Number in coding regions = 1 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 10 AGGAAAGAATTAGGATTACCAGTGCCTTAT 1 94 1 TAGGATTACC 0.927732 -161 TCACCAAAAATAGGATACCCTCATCAGATA 1 229 0 TAGGATACCC 0.978313 -26 ATATCAATAGGAGCAAAACCCTTGGATGTA 7 19 0 GAGCAAAACC 0.900367 -168 AAACCCCTATTGGGATACCCGAGCGAGGTT 7 85 0 TGGGATACCC 0.97395 -102 ATATTGCCATGGGGAAAACCCCTATTGGGA 7 100 0 GGGGAAAACC 0.971354 -87 ********** Masking position 5 Map Score: 0.185811 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 38 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 ********** No masking Map Score: -1.73129e-12 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 12 ********** No masking Map Score: -1.73129e-12 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 13 ********** No masking Map Score: -1.73129e-12 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