AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -iarcA_aquae_opreg_300.orf -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 aq_194 53 putative protein #2 frdB1 35 fumarate reductase iron-sulfur subunit #3 frdA 295 fumarate reductase flavoprotein subunit #4 purB 41 adenylosuccinate lyase #5 aq_598 99 putative protein #6 lpdA 85 dihydrolipoamide dehydrogenase #7 aq_1356 25 putative protein #8 cydA 116 cytochrome oxidase d subunit I #9 icd 113 isocitrate dehydrogenase #10 leuS' 300 leucyl-tRNA synthetase beta subunit Motif number 1 ATAATAGCCTTTAAAAAGTAAGCTTGTAGA 1 19 1 TTAAAAAGTA 0.899226 -35 CTTATTAATAATATTTCTACAAGC 1 40 0 TTAATAATAT 0.807991 -14 AATTCCGTTTGAAAAATTTATCCCCCAGA 2 10 1 TGAAAAATTT 0.697727 -26 GCTCTACGGATTAATAATTTCTTTGATACT 3 82 1 TTAATAATTT 0.91341 -214 AGGTGGTAAATTAAAAAGAGATGAGTGAAG 3 142 1 TTAAAAAGAG 0.849546 -154 CTCCCACGATTAAAAATTTTATCCCTTTC 5 10 1 TTAAAAATTT 0.953659 -90 TATAGATTTTTTAAAAATAGTATTCACTAA 5 75 0 TTAAAAATAG 0.844808 -25 ATAATTTGCCTTAAAAGGAGGAAGCGA 6 8 0 TTAAAAGGAG 0.657485 -78 TTTTGATATACTAATAATTTGCCTTAAAAG 6 21 0 CTAATAATTT 0.870317 -65 GATTAAACTACTAAAAAGTA 7 16 1 CTAAAAAGTA 0.850232 -10 AAGTGTTGGGTTAATGATTATTAACTTTTA 8 78 1 TTAATGATTA 0.491376 -39 CTCCGGAAGGTTAAAAGTTAATAATCATTA 8 89 0 TTAAAAGTTA 0.745199 -28 ACTTAAAGATTTTACCTCTAGA 9 3 1 TTAAAGATTT 0.818461 -111 GGTTAGGTGTCTAATAAGTTATTGATAAAG 10 26 0 CTAATAAGTT 0.874388 -275 TGCAACATAGCTAAAAAGATTGAAAATCAA 10 131 0 CTAAAAAGAT 0.844182 -170 TAGGTGGGTCCTAATAAGTGATGTTTCGAT 10 184 0 CTAATAAGTG 0.821927 -117 AGCCCTCCAATTAAAAGTTTACTAAAGTAA 10 251 1 TTAAAAGTTT 0.874938 -50 AATTAAAAATTTTATATTGACC 10 289 0 TTAAAAATTT 0.953659 -12 ********** Masking position 4 Map Score: 18.4961 Number of sites scoring better than the average of aligned sites = 531 Number in coding regions = 435 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 2 TTACTTTTTAAAGGCTATTATAAAAGTGT 1 8 0 AAGGATTATA 0.847059 -46 TTTACCACCTAAGTTGATAATATTGAACTCTA 3 120 0 AAGTATAATA 0.839067 -176 GGATAAGTGTAAATACAATAAAGAGAGCTTTG 3 176 0 AAATAATAAA 0.838938 -120 ACATTAACCGAAAGGGATAAAATTTTTAATCG 5 17 0 AAAGATAAAA 0.873731 -83 GCTAAAATTAAAGGCAATTAAAACCCCTTTTC 6 52 1 AAGGATTAAA 0.957121 -34 AAATAGATTAAACTACTAAAAA 7 1 1 AAATATTAAA 0.949336 -25 TTGGTAAGTAAATAAAAACTCTCTGAT 8 6 1 AAGTATAAAA 0.954572 -111 AAAAATCAAAAAGTGTTTTAAATTAACTTGAC 9 43 1 AAGTTTTAAA 0.898403 -71 CACTTCTTCAAAATGAATAAAATTACACTCTA 9 76 1 AAATATAAAA 0.916999 -38 TCAAGGATGGAAATTTTATAAAGGTATACTCA 10 103 0 AAATTATAAA 0.563777 -198 CTCCAATTAAAAGTTTACTAAAGTAAAAACTT 10 255 1 AAGTACTAAA 0.892783 -46 **** ****** Masking position 10 Map Score: 6.61514 Number of sites scoring better than the average of aligned sites = 307 Number in coding regions = 276 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 3 AAGGATGCTCTCACAGAATTAGGAAAATAC 3 18 1 TCACAGAATT 0.954251 -278 AGTAGTAGTATCAAAGAAATTATTAATCCG 3 88 0 TCAAAGAAAT 0.972647 -208 ATGTTTAAAGTCATAGAAATGATAGAATGG 5 45 1 TCATAGAAAT 0.984302 -55 CTGATATACATCATAGAAATTAATTTACAA 8 33 1 TCATAGAAAT 0.984302 -84 ********** Masking position 5 Map Score: 2.80337 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 12 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 4 GTAGCAAAAAGTATTTTCCTAATTCTGTGA 3 28 0 GTATTTTCCT 0.944904 -268 CATCTCTTTTTAATTTACCACCTAAGTTGA 3 135 0 TAATTTACCA 0.69865 -161 ACTTATCCTTGTTTTTTCCTTAATCGTGGG 3 200 1 GTTTTTTCCT 0.885918 -96 GGAGGCACGATTATATACCTTGTAAACAGG 3 228 1 TTATATACCT 0.836604 -68 CTGCTGTTCTTTATTTGCCTGTTTACAAGG 3 245 0 TTATTTGCCT 0.972727 -51 GATATACTAATAATTTGCCTTAAAAGGAGG 6 17 0 TAATTTGCCT 0.941691 -69 AAAAGGGGTTTTAATTGCCTTTAATTTTAG 6 53 0 TTAATTGCCT 0.833848 -33 CAGAGAGTTTTTATTTACTTACCAA 8 6 0 TTATTTACTT 0.862833 -111 ACTTAAAGATTTTACCTCTAGAGATTT 9 8 1 GATTTTACCT 0.889904 -106 TTGACCCGAAGTTTTTACTTTAGTAAACTT 10 265 0 GTTTTTACTT 0.755255 -36 ********** Masking position 6 Map Score: 5.91063 Number of sites scoring better than the average of aligned sites = 477 Number in coding regions = 442 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 AAATTGGGTTTATTCGTAGCAAAAAGTATT 3 43 0 TATTCGTAGC 0.930304 -253 GTTTTTTCCTTAATCGTGGGAGGCACGATT 3 210 1 TAATCGTGGG 0.992593 -86 ACAAGGTATATAATCGTGCCTCCCACGATT 3 221 0 TAATCGTGCC 0.980388 -75 ATAAAATTTTTAATCGTGGGAG 5 3 0 TAATCGTGGG 0.992593 -97 ********** Masking position 4 Map Score: 1.95462 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 12 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 TAAACCCAATTTTGGTTTGATGCTCTACGGATTAATAA 3 61 1 TTTGTTGTTC 0.986037 -235 CCTGCTGTTCTTTATTTGCCTGTTTACAAGGTATATAA 3 238 0 TTTTTTGTAA 0.708869 -58 AGATACAGCGTCTAGCTACCTGCTGTTCTTTATTTGCC 3 256 0 TCTGTTGTTC 0.942855 -40 ATTTTATCCCTTTCGGTTAATGTTTAAAGTCATAGAAA 5 26 1 TTTGTTGTAA 0.961295 -74 TGCCTTTAATTTTAGCATTTTGATATACTAATAATTTG 6 30 0 TTTGATGTTC 0.951527 -56 AACACTTAAAGTTTGATCTTTGTTGTAAATTAATTTCT 8 47 0 GTTGTTGTTA 0.959325 -70 AACTTTAAGTGTTGGGTTAATGATTATTAACTTTTAAC 8 72 1 GTTGTTGTAT 0.724872 -45 TTAAAACACTTTTTGATTTTTGTTATAAATCTCTAGAG 9 26 0 TTTGTTGTTA 0.982095 -88 CTTTATAAAATTTCCATCCTTGATTTTCAATCTTTTTA 10 112 1 TTTCTTGTTC 0.911196 -189 TTTTTAGCTATGTTGCATCATGATTTCAATACATCACA 10 144 1 TGTGATGTTA 0.780821 -157 *** * * ** * * * Masking position 11 Map Score: 2.74506 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 44 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 AGCATCAAACCAAAATTGGGTTTATTCGTA 3 55 0 CAAAATTGGG 0.846369 -241 AAGGAAAAAACAAGGATAAGTGTAAATACA 3 191 0 CAAGGATAAG 0.718722 -105 GGAGGGAAAGGAAAGAAGGGA 4 2 0 GAAAGAAGGG 0.952724 -40 TAGGATATCAGAAGGGAGGGAAAGGAAAGA 4 16 0 GAAGGGAGGG 0.938343 -26 GCTCTCCTCCGAAAGTAGAGTGTAATTTTA 9 93 0 GAAAGTAGAG 0.913759 -21 TTCGTTTCGTGAAGGTTAGGTGTCTAATAA 10 39 0 GAAGGTTAGG 0.909889 -262 CGAGGTTCTGCAAACTTGAGTATACCTTTA 10 87 1 CAAACTTGAG 0.727974 -214 GATTGAAAATCAAGGATGGAAATTTTATAA 10 114 0 CAAGGATGGA 0.795145 -187 TGCCAAGGAGCAAAGTAGGGCTCTGTAGCC 10 225 1 CAAAGTAGGG 0.975636 -76 ********** Masking position 3 Map Score: 2.31527 Number of sites scoring better than the average of aligned sites = 617 Number in coding regions = 570 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 8 TTTCGAACCTCCGGAAGGTTAAAA 8 103 0 GAACCTCCGG 0.993406 -14 CAAGTTTGCAGAACCTCGGGTTAGCGGAAA 10 75 0 GAACCTCGGG 0.996406 -226 ACTAAAGTAAAAACTTCGGGTCAATATAAA 10 271 1 AAACTTCGGG 0.973868 -30 ********** Masking position 3 Map Score: 0.456213 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 = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 TATTCGTAGCAAAAAGTATTTTCCTAATTC 3 33 0 AAAAAGTATT 0.826207 -263 CATCAAACCAAAATTGGGTTTATTCGTAGC 3 53 0 AAATTGGGTT 0.755696 -243 AAAAAACAAGGATAAGTGTAAATACAATAA 3 187 0 GATAAGTGTA 0.606163 -109 AGGGAATAGGATATCAGAAGGGA 4 29 0 GAATAGGATA 0.887952 -13 AACATTAACCGAAAGGGATAAAATTTTTAA 5 20 0 GAAAGGGATA 0.846831 -80 GATTTTTTAAAAATAGTATTCACTAACCAT 5 71 0 AAATAGTATT 0.794232 -29 GCTCCTCCTGAAAAGGGGTTTTAATTGCCT 6 63 0 AAAAGGGGTT 0.91224 -23 AACAAAAATCAAAAAGTGTTTTAAATTAAC 9 40 1 AAAAAGTGTT 0.903306 -74 CTTGGCAACTGAATAGGGTAGGTGGGTCCT 10 202 0 GAATAGGGTA 0.939649 -99 ********** Masking position 2 Map Score: 1.40471 Number of sites scoring better than the average of aligned sites = 533 Number in coding regions = 500 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 10 ********** No masking Map Score: 8.55083e-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 11 ********** No masking Map Score: 8.55083e-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 12 ********** No masking Map Score: 8.55083e-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