AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00260_mgen_reg_300.orf -o00260_mgen_300.ace -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -g0.32 -x5 -e 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 = 0.32 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MG001 300 DNA polymerase III, subunit beta (dnaN) #2 MG003 84 DNA gyrase subunit B (gyrB) #3 MG254 175 DNA ligase #4 MG272 249 dihydrolipoamide acetyltransferase (pdhC) #5 MG274 27 pyruvate dehydrogenase component E1, subunit alpha (pdhA) #6 MG275 82 NADH oxidase (nox) #7 MG277 42 conserved hypothetical protein #8 MG377 46 conserved hypothetical protein #9 MG378 28 arginyl-tRNA synthetase (argS) #10 MG395 300 putative lipoprotein Motif number 1 AGCAGTAATAATTACATATGTACA 1 4 1 ATAATAATTA 0.527556 -297 TATATATAACAGAAATTAATGATATTTTACA 1 44 0 AAAATTAATG 0.912015 -257 AATTTCTGTTATATATAATAGTATCTATTTT 1 58 1 AATATAATAG 0.497858 -243 TAATTATAGTAATAATTAATACTCTCTAAAA 1 85 0 ATAATTAATA 0.819469 -216 AGCATAAATGCTTAATTATAGTAATAATTAA 1 97 0 CTAATTATAG 0.757548 -204 AGCATTTATGCTTAATTATAAGCTTTTTATG 1 116 1 CTAATTATAA 0.701508 -185 TTTTTATGAACAAAATTATAGACATTTTAGT 1 139 1 CAAATTATAG 0.842775 -162 AGTTCTTATAATAAATAATAGATATTAAAGA 1 167 1 AAAATAATAG 0.894515 -134 TAGATATTAAAGAAAATAAAAAAATAGAAAT 1 185 1 AAAAATAAAA 0.750835 -116 ATAAAAAAATAGAAATAAATATCATAACCCT 1 200 1 AAAATAAATA 0.797596 -101 TTGATAACCCAGAAATTAATACTTAATCAAA 1 230 1 AAAATTAATA 0.885714 -71 ATACTTAATCAAAAATGAAAATATTAATTAA 1 248 1 AAAATGAAAA 0.905863 -53 GAAAATATTAATTAATAAAAGTGAATTGAAT 1 264 1 ATAATAAAAG 0.911238 -37 ATAACACATTAAAAATGAAAGGTTTT 2 6 0 AAAATGAAAG 0.927905 -79 TGGCATAACAAATAATTATAACACATTAAAA 2 23 0 ATAATTATAA 0.879567 -62 AAAATATACTAAATATTAAAGTAACAACGCA 3 18 1 AATATTAAAG 0.801071 -158 GTTATCTGCTCCAAATTAAAACTTCTTTGTA 3 107 1 CAAATTAAAA 0.892417 -69 ACCTAGCTCTAAAAAATAAAGCTAGGTAACT 4 27 0 AAAAATAAAG 0.801198 -223 ACCTCATTTCATAAATTAAAGTGATGGAAGA 4 58 1 AAAATTAAAG 0.971803 -192 TTTTTGTCTAACAACTAAAAAGCCAGTAACT 4 160 1 AAACTAAAAA 0.615029 -90 GTGATCTATAACAAATAAAAAAAGCCAGTTT 4 191 0 AAAATAAAAA 0.929102 -59 TCGTATTGATAGTACTTAAAGTTTAAATTTA 4 228 0 ATACTTAAAG 0.711098 -22 ATAAAATTTAAGTTATTAAAAATAGTTA 7 25 1 ATTATTAAAA 0.638332 -18 TCACGCATATAGGAATTAAAATTTAATAAGT 8 16 1 AGAATTAAAA 0.721561 -31 TTTGCATCATTAAATATAATTTAAAGTA 9 9 1 ATAAATATAA 0.460597 -20 GGTAAACTAACTAAATTAAAACCAAAAAAAT 10 48 0 CAAATTAAAA 0.892403 -253 CAAAAAAGTTAAAAATGAAAATAGAACTACT 10 88 0 AAAATGAAAA 0.905863 -213 TAATGAAAAAACTAATGAAAGCAAATGCAAC 10 122 0 ATAATGAAAG 0.882881 -179 TAAGCAGAATAAAAATAATTAAATTTATCAG 10 181 1 AAAATAATTA 0.655944 -120 CTTTAGCTTCAAAAATAATTGAGTTCATCTT 10 216 0 AAAATAATTG 0.718306 -85 TCTTAACTTCATTAATTAAAGGTTTTGAAAT 10 266 1 ATAATTAAAG 0.952797 -35 * ********* Masking position 8 Map Score: 33.641 Number of sites scoring better than the average of aligned sites = 886 Number in coding regions = 754 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 2 GTAAAATATCATTAATTTCTGTTATATATA 1 45 1 ATTAATTTCT 0.867568 -256 TTTAGAGAGTATTAATTATTACTATAATTA 1 86 1 ATTAATTATT 0.864089 -215 AGCATAAATGCTTAATTATAGTAATAATTA 1 98 0 CTTAATTATA 0.847804 -203 AGCATTTATGCTTAATTATAAGCTTTTTAT 1 116 1 CTTAATTATA 0.847804 -185 TTGATTAAGTATTAATTTCTGGGTTATCAA 1 230 0 ATTAATTTCT 0.867568 -71 ACTTTTATTAATTAATATTTTCATTTTTGA 1 256 0 ATTAATATTT 0.809211 -45 AGTTACCTAGCTTTATTTTTTAGAGCTAGG 4 27 1 CTTTATTTTT 0.767825 -223 AAAATTTTGTCTTACTTTTTACAGCAGCTG 4 134 0 CTTACTTTTT 0.85427 -116 GATCACTACTATTAAATTTAAACTTTAAGT 4 216 1 ATTAAATTTA 0.841603 -34 CTTAGTTTTAAATTAGCATA 5 1 1 CTTAGTTTTA 0.903208 -27 CAAAAGCTTAATTTTAAAAGATCGAA 6 7 1 CTTAATTTTA 0.964849 -76 TCTTAGCTGCAGTAATTTTTTAAGCTATTT 6 60 0 AGTAATTTTT 0.770903 -23 TACTTAATATTTATATAAAATT 7 3 1 CTTAATATTT 0.860501 -40 TTTTTAATAACTTAAATTTTATATAAATAT 7 17 0 CTTAAATTTT 0.928636 -26 TTAGAAACTTATTAAATTTTAATTCCTATA 8 23 0 ATTAAATTTT 0.899472 -24 TTCTAACGGGATTAATTTTTTTGGTTTTAA 10 34 1 ATTAATTTTT 0.969466 -267 ATTTGCTTTCATTAGTTTTTTCATTAGCTT 10 127 1 ATTAGTTTTT 0.915289 -174 TTTTATTCTGCTTAGTTTTAGATGCAATTA 10 165 0 CTTAGTTTTA 0.903208 -136 AATAAAAATAATTAAATTTATCAGTGAAAA 10 188 1 ATTAAATTTA 0.841603 -113 ********** Masking position 3 Map Score: 25.138 Number of sites scoring better than the average of aligned sites = 385 Number in coding regions = 320 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 3 AATTAATGATATTTTACATATGTACTATGTACA 1 29 0 ATTTTAAATT 0.907675 -272 AATAGTATCTATTTTAGAGAGTATTAATTATTA 1 74 1 ATTTTAAAGA 0.788781 -227 TTTTCCCAAAATTTTATTCAATTCACTTTTATT 1 277 0 ATTTTATAAT 0.698561 -24 AAAACCTTTCATTTTTAATGTGTTATAATTATT 2 11 1 ATTTTTAGTT 0.672024 -74 ACCAATCAGGATTTTACAAAGAAGTTTTAATTT 3 119 0 ATTTTAAAGA 0.787518 -57 CTAAGTCAGGATTTTTCTTATTTATAGTA 3 157 1 ATTTTTTATT 0.86058 -19 AGGTAACTATATTTTAAAAAAGTG 4 2 0 ATTTTAAAAT 0.799681 -248 ACCTAGCTTTATTTTTTAGAGCTAGGTACCTCA 4 31 1 ATTTTTAAGT 0.956639 -219 GGCTTTTTTTATTTGTTATAGATCACTACTATT 4 196 1 ATTTGTAAGT 0.722775 -54 CAAAAGCTTAATTTTAAAAGATCGAATCACTA 6 10 1 AATTTTAAGT 0.813992 -73 TAGCTGCAGTAATTTTTTAAGCTATTTAAGGAT 6 54 0 AATTTTTAGT 0.867973 -29 AATAACTTAAATTTTATATAAATATTAAGTA 7 9 0 ATTTTAAAAT 0.817809 -34 TAACTATTTTTAATAACTTAAATTTTAT 7 25 0 ATTTTTAAAT 0.87397 -18 TAGGAATTAAAATTTAATAAGTTTCTAAAAAT 8 25 1 AATTTATAGT 0.847985 -22 AACGGGATTAATTTTTTTGGTTTTAATTTAGTT 10 38 1 ATTTTTTGTT 0.592288 -263 TTTTGGTTTTAATTTAGTTAGTTTACCTGAGTC 10 52 1 AATTTATAGT 0.882584 -249 TTCACTGATAAATTTAATTATTTTTATTCTGCT 10 183 0 AATTTATATT 0.749891 -118 ****** * ** * Masking position 4 Map Score: 14.8393 Number of sites scoring better than the average of aligned sites = 327 Number in coding regions = 269 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 4 AAATATCATTAATTTCTGTTATATATAATAGTA 1 48 1 AATTTTGATA 0.960176 -253 TATAATTAAGCATTTATGCTTAATTATAAGCTT 1 108 1 CATTTTGTAA 0.862008 -193 AAATGTCTATAATTTTGTTCATAAAAAGCTTAT 1 133 0 AATTTGTATA 0.629157 -168 ATTAAGTATTAATTTCTGGGTTATCAAGGGTTA 1 224 0 AATTTTGTTA 0.969468 -77 TTAATATTTTCATTTTTGATTAAGTATTAATTT 1 242 0 CATTTTGTAA 0.862008 -59 AATTGAATAAAATTTTGGGAAAAA 1 287 1 AATTTGGAAA 0.873566 -14 CCACAAACTAAATTTATGGCATAACAAATAATT 2 37 0 AATTTTGATA 0.960176 -48 CCATAAATTTAGTTTGTGGCAAAAGCTTCTGTA 2 51 1 AGTTTTGAAA 0.814367 -34 TCCAAATTAAAACTTCTTTGTAAAATCCTGATT 3 116 1 AACTTTTTAA 0.490188 -60 CCATCACTTTAATTTATGAAATGAGGTACCTAG 4 52 0 AATTTTGATG 0.765396 -198 AGTAAGACAAAATTTTTGTCTAACAACTAAAAA 4 148 1 AATTTTGTAA 0.955597 -102 ATTTAAGGATAATTTGTGCAGTAGTGATTCGAT 6 31 0 AATTTTGGTA 0.881219 -52 TGCTTTCATTAGTTTTTTCATTAGCTTCTTCTT 10 130 1 AGTTTTTTTA 0.586545 -171 GCACTTGTTAAACTTAGGCTTTAGCTTCAAAAA 10 232 0 AACTTGGTTA 0.782803 -69 GGTTTTGAAATATTTTTGTATTAAA 10 286 1 TATTTTGTTA 0.77164 -15 ***** ** *** Masking position 5 Map Score: 9.5516 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 156 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 5 GCTTAATTATAAGCTTTTTATGAACAAAAT 1 125 1 AAGCTTTTTA 0.739501 -176 TGGGTTATCAAGGGTTATGATATTTATTTC 1 211 0 AGGGTTATGA 0.775774 -90 AACAGTACAGAAGCTTTTGCCACAAACTAA 2 59 0 AAGCTTTTGC 0.950268 -26 TAACCTTGGCAAGGTTATGTTCTACCATTG 3 58 0 AAGGTTATGT 0.78316 -118 TAACCTTGCCAAGGTTAAGATGCGGGTTCG 3 71 1 AAGGTTAAGA 0.818694 -105 GTAATTTTTTAAGCTATTTAAGGATAATTT 6 49 0 AAGCTATTTA 0.739501 -34 AGTAGTTATCAAGCCAATGCAAATTCTAAC 10 11 1 AAGCCAATGC 0.874022 -290 AAACTAATGAAAGCAAATGCAACCATCAAA 10 115 0 AAGCAAATGC 0.823977 -186 GCTAATGAAAAAACTAATGAAAGCAAATGC 10 125 0 AAACTAATGA 0.73867 -176 TAAAAAGAAGAAGCTAATGAAAAAACTAAT 10 137 0 AAGCTAATGA 0.975244 -164 ATTATTTTTGAAGCTAAAGCCTAAGTTTAA 10 228 1 AAGCTAAAGC 0.891943 -73 TCATTAATTAAAGGTTTTGAAATATTTTTG 10 274 1 AAGGTTTTGA 0.912685 -27 ********** Masking position 1 Map Score: 6.77728 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 242 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 GCATTCGCACTTGCATTGGCAGCATTTCTT 4 93 0 TTGCATTGGC 0.993387 -157 CCGTTAGAATTTGCATTGGCTTGATAACTA 10 13 0 TTGCATTGGC 0.993387 -288 TTTTTGATGGTTGCATTTGCTTTCATTAGT 10 113 1 TTGCATTTGC 0.982167 -188 TTGCATTTGCTTTCATTAGTTTTTTCATTA 10 123 1 TTTCATTAGT 0.892006 -178 TCATTAGTTTTTTCATTAGCTTCTTCTTTT 10 135 1 TTTCATTAGC 0.977326 -166 ********** Masking position 5 Map Score: 5.90466 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 14 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 GCAAGTTAAAATATACTAAATA 3 3 1 AAGTTAAAAT 0.895812 -173 AACCTTGCCAAGGTTAAGATGCGGGTTCGA 3 72 1 AGGTTAAGAT 0.91531 -104 TTTTACAAAGAAGTTTTAATTTGGAGCAGA 3 111 0 AAGTTTTAAT 0.803023 -65 CCATCACTTTAATTTATGAAATGAGGTACC 4 55 0 AATTTATGAA 0.587358 -195 ATAGTACTTAAAGTTTAAATTTAATAGTAG 4 221 0 AAGTTTAAAT 0.910987 -29 CTTAGTTTTAAATTAGCATAGAA 5 4 1 AGTTTTAAAT 0.778519 -24 CAAAAGCTTAATTTTAAAAGATCGAATCA 6 10 1 AATTTTAAAA 0.759867 -73 ACCATCAAAAAAGTTAAAAATGAAAATAGA 10 94 0 AAGTTAAAAA 0.878754 -207 TATTCTGCTTAGTTTTAGATGCAATTAAAA 10 162 0 AGTTTTAGAT 0.825147 -139 TTAATTAATGAAGTTAAGAAGCACTTGTTA 10 255 0 AAGTTAAGAA 0.906774 -46 CATTAATTAAAGGTTTTGAAATATTTTTGT 10 275 1 AGGTTTTGAA 0.811518 -26 ********** Masking position 9 Map Score: 7.54702 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 189 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 TTATGATATTTATTTCTATTTTTTTATTTT 1 197 0 TATTTCTATT 0.960534 -104 TATTAATTAATATTTTCATTTTTGATTAAG 1 251 0 TATTTTCATT 0.83392 -50 AACGCAGATATAGTTCAATGGTAGAACATA 3 43 1 TAGTTCAATG 0.637491 -133 TATAGTTACCTAGCTTTATTTTTTAGAGCT 4 24 1 TAGCTTTATT 0.784635 -226 CTAAACTGGCTTTTTTTATTTGTTATAGAT 4 189 1 TTTTTTTATT 0.748754 -61 ATATTTCTATGCTAATTTAAA 5 17 0 TATTTCTATG 0.922461 -11 TAACTATTTTTAATAACTTAAATT 7 29 0 TATTTTTAAT 0.748754 -14 GAGTCAATAGTAGTTCTATTTTCATTTTTA 10 80 1 TAGTTCTATT 0.952552 -221 TAAATTTAATTATTTTTATTCTGCTTAGTT 10 178 0 TATTTTTATT 0.94976 -123 ********** Masking position 5 Map Score: 3.69181 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 90 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 9 ********** No masking Map Score: -2.29973e-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 10 ********** No masking Map Score: -2.29973e-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 11 ********** No masking Map Score: -2.29973e-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