AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00620_mgen_reg_300.orf -o00620_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 Purged sequences: MG301 30 glyceraldehyde-3-phosphate dehydrogenase (gap) Input sequences: #1 MG210.1 200 conserved hypothetical protein #2 MG211 189 conserved hypothetical protein #3 MG272 249 dihydrolipoamide acetyltransferase (pdhC) #4 MG274 27 pyruvate dehydrogenase component E1, subunit alpha (pdhA) #5 MG275 82 NADH oxidase (nox) #6 MG277 42 conserved hypothetical protein #7 MG304 176 ABC transporter, ATP binding protein #8 MG305 87 heat shock protein 70 (dnaK) #9 MG309 53 lipoprotein, putative #10 MG357 300 acetate kinase (ackA) #11 MG460 172 L-lactate dehydrogenase (ldh) Motif number 1 ATTCACTAATTAACTAACAAAAATTATTAAGGA 1 32 1 TACTAAAAAA 0.870075 -169 TTAGTTTAAAAACTAGTAAAAAAGTGTTAATAC 1 65 0 AATATAAAAA 0.695419 -136 TAAACTAGGATTACACTTAAAAAAGTTAGTTTA 1 90 0 TTCATAAAAA 0.932268 -111 TACTAATAGCTACTTGTAAAAAATTAAAAGTTA 1 141 1 TATTTAAAAA 0.926661 -60 TGCCTAAGATTGAAGTTAAAAATGATGATTTA 2 10 1 TTAATAAAAA 0.903506 -180 GATTTAGAGCTAGCTTTAAAAAAGTTTAAAAGG 2 37 1 TACTTAAAAA 0.957656 -153 AAACAAAAGATAGCACAGAAAAAGCGCAGGAAG 2 142 1 TACAAAAAAA 0.90877 -48 GCTAGGTAACTATATTTTAAAAAAGTG 3 5 0 TAATTAAAAA 0.93881 -245 ATGAGGTACCTAGCTCTAAAAAATAAAGCTAGG 3 32 0 TACTTAAAAA 0.957656 -218 AATTTTTGTCTAACAACTAAAAAGCCAGTAACT 3 158 1 TACACAAAAA 0.891499 -92 TAGTGATCTATAACAAATAAAAAAAGCCAGTTT 3 191 0 TACAAAAAAA 0.90877 -59 TATAAAATTTAAGTTATTAAAAATAGTTA 6 24 1 AATTTAAAAA 0.605524 -19 ATAGAACATATTCCAAATAAAAAAGAGCAGCAC 7 20 1 TTCAAAAAAA 0.802979 -157 TTTTGGTAGATAAAAAACAAAAAAGCAGCTGTT 7 53 0 TAAAAAAAAA 0.871405 -124 AGCTTATTTATAAATTTTAAAAATAAGTCAGAG 7 99 0 TAATTAAAAA 0.93897 -78 CTTAGTTTGCTACAAGTTAAAAACCTCAGTTTT 7 130 1 TAAATAAAAA 0.958133 -47 ACCTCAGTTTTAAATACCCAAAACACCAAAACA 7 152 1 TAATCCAAAA 0.556981 -25 AAACAAAAATTAGCACTCAAACACTAAAAGTGC 8 26 0 TACATAAACA 0.809379 -62 TACTCAGTAATTATAAACAAAAATTAGCACTCA 8 40 0 TTTAAAAAAA 0.694886 -48 GTAATTGTTATTGATCTAAAAAAAAAGT 8 70 1 TTATTAAAAA 0.862786 -18 CTGGATTCTTTATCTATTCAAAAAAA 10 4 0 TACTTCAAAA 0.883269 -297 CTATTAATGTTGCTAATACAAAAAATACAGTTG 10 56 1 TGTATCAAAA 0.525802 -245 TAACAGATGTTAATAATGCAAAAACAGTAGCAA 10 86 0 TATATCAAAA 0.863063 -215 AAGTGAAGATAAAAAGTAAAAAAGAAAACCAAT 10 126 1 AAAATAAAAA 0.735007 -175 TCTTAAACAATGAAAATTAAAAAATGCTATATT 10 180 0 TGAATAAAAA 0.801041 -121 GAAATATTATTAAATCTTAAACAATGAAAATTA 10 194 0 TAATTAAACA 0.660086 -107 TAATTAAATGTTTTAACTAAAAAGAAATATTAT 10 217 0 TTTACAAAAA 0.652482 -84 ATATTTACCTTATTTATTAAAAAATAATACTAA 10 267 0 TATTTAAAAA 0.911774 -34 CAGTGTTGTTTTGTAATCCAAAAAAAGTAAATT 11 49 1 TTTATCAAAA 0.720571 -124 ATAAGGATATTTGAAGTCAAAAAACTGTTGCCT 11 83 0 TTAATAAAAA 0.903506 -90 ** ** * ***** Masking position 10 Map Score: 36.9685 Number of sites scoring better than the average of aligned sites = 807 Number in coding regions = 699 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 2 AGTTAATTAGTGAATTTTAACTGAATATACAA 1 15 0 TATTTTAACT 0.952804 -186 CTTAAAAAAGTTAGTTTAAAAACTAGTAAAAA 1 76 0 TATTTAAAAA 0.867964 -125 CCATTAATTCTAACTTTTAATTTTTTACAAGT 1 152 0 TATTTTAATT 0.92774 -49 CTCTAAATCATCATTTTTAACTTCAATCTTAG 2 14 0 TATTTTAACT 0.952804 -176 TTGTCTTCCATCACTTTAATTTATGAAATGAG 3 60 0 TATTTAATTT 0.678505 -190 TCACTACTATTAAATTTAAACTTTAAGTACTA 3 218 1 TATTTAAACT 0.904565 -32 CTTAGTTTTAAATTAGCATAGAA 4 2 1 TATTTTAAAT 0.975604 -26 CAAAAGCTTAATTTTAAAAGATCGAATCA 5 8 1 TATTTTAAAA 0.933341 -75 TTTAATAACTTAAATTTTATATAAATATTAAG 6 13 0 TATTTTATAT 0.933341 -30 TAGCTCTGACTTATTTTTAAAATTTATAAATA 7 96 1 TATTTTAAAA 0.93334 -81 GTTAAAAACCTCAGTTTTAAATACCCAAAACA 7 145 1 TATTTTAAAT 0.975604 -32 AAAATTTCAATAATTTTAAAATTTATATTTTT 9 22 0 TATTTAAAAT 0.949432 -32 TAATTTAGTATTATTTTTTAATAAATAAGGTA 10 263 1 TATTTTTAAT 0.773848 -38 ATAATATCGCTCATCTTTAAATAACAGTGTTG 11 25 1 TACTTTAAAT 0.835297 -148 TTATTTTGGTTCACTTTAATAAATTTTGCTTT 11 122 0 TATTTAATAA 0.697116 -51 GAGATATACTTCAATTTTATTTTGGTTCACTT 11 138 0 TATTTTATTT 0.818023 -35 * * ******** Masking position 6 Map Score: 21.9119 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 139 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 3 AATAGTGCCATTAATTCTAACTTTTAATTTTTT 1 158 0 TAATTCTATT 0.649489 -43 AAATGATGATTTAGAGCTAGCTTTAAAAAAGTT 2 30 1 TAGAGCTATT 0.967768 -160 CTGCGCTTTTTCTGTGCTATCTTTTGTTTTTCT 2 138 0 TTGTGCTATT 0.936287 -52 GCTCTAAAAAATAAAGCTAGGTAACTATATTTT 3 20 0 AAAAGCTATA 0.828906 -230 GCTTTATTTTTTAGAGCTAGGTACCTCATTTCA 3 36 1 TAGAGCTATA 0.95616 -214 ATATTTCTATGCTAATTTAAAACTAAG 4 10 0 TTATGCTATT 0.901783 -18 GCAGTAATTTTTTAAGCTATTTAAGGATAATTT 5 49 0 TTAAGCTATA 0.828905 -34 TAAAAATAAGTCAGAGCTAAAAATCTGTTTTTT 7 82 0 TAGAGCTAAA 0.734835 -95 TCAAACACTAAAAGTGCTAATTAAAGTTTGTT 8 10 0 AAGTGCTATA 0.914338 -78 TTTTAGTGTTTGAGTGCTAATTTTTGTTTATAA 8 30 1 TAGTGCTATT 0.976378 -58 TTAATAGTTGTTAATGCTATTGTCTTCTGGATT 10 30 0 TAATGCTAGT 0.829444 -271 TGAAAATTAAAAAATGCTATATTATCGCTGTTA 10 170 0 AAATGCTATT 0.901763 -131 * ******* ** Masking position 9 Map Score: 8.18782 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 91 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 ACTTGCATTGGCAGCATTTCTTGTTGTCTTC 3 84 0 GCAGCATTTT 0.972025 -166 ACTTTTTACAGCAGCTGTTGCACTTAGCGCA 3 120 0 GCAGCTGTTC 0.813201 -130 ATATCTTAGCTGCAGTAATTTTTTAAGCT 5 64 0 GCTGCAGTAT 0.936433 -19 CAGCTGTTGTGCTGCTCTTTTTTATTTGGAA 7 30 0 GCTGCTCTTT 0.888091 -147 AAACAAAAAAGCAGCTGTTGTGCTGCTCTTT 7 41 0 GCAGCTGTTT 0.985796 -136 TTTTGTATTAGCAACATTAATAGTTGTTAAT 10 48 0 GCAACATTAT 0.856593 -253 AAAAACAGTAGCAACTGTATTTTTTGTATTA 10 69 0 GCAACTGTAT 0.948594 -232 CGCTGTTATTTCAGCTTTTATTGGTTTTCTT 10 147 0 TCAGCTTTTT 0.807586 -154 GTAAATTCAGGCAACAGTTTTTTGACTTCAA 11 75 1 GCAACAGTTT 0.96296 -98 ********* * Masking position 8 Map Score: 6.72418 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 81 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 5 TAATTTCTGGTAGTTTTCTTTACTAATAGC 1 121 1 TAGTTTTCTT 0.413791 -80 TAAATCATCATTTTTAACTTCAATCTTAGG 2 13 0 TTTTTAACTT 0.817298 -177 CTATCTTTTGTTTTTCTCTTAACCGCATCC 2 125 0 TTTTTCTCTT 0.755424 -65 TTTTAAAATATAGTTACCTAGCTTTATTTT 3 16 1 TAGTTACCTA 0.605721 -234 GCAGCATTTCTTGTTGTCTTCCATCACTTT 3 75 0 TTGTTGTCTT 0.865509 -175 TAAGACAAAATTTTTGTCTAACAACTAAAA 3 150 1 TTTTTGTCTA 0.930895 -100 AATTTAATAGTAGTGATCTATAACAAATAA 3 204 0 TAGTGATCTA 0.56927 -46 TACTTAATATTTATATAAAATTTAAGT 6 8 1 TATTTATATA 0.540493 -35 GCTTTTTTGTTTTTTATCTACCAAAAAACA 7 60 1 TTTTTATCTA 0.947308 -117 AAAACTGAGGTTTTTAACTTGTAGCAAACT 7 133 0 TTTTTAACTT 0.817298 -44 TGAGTGCTAATTTTTGTTTATAATTACTGA 8 40 1 TTTTTGTTTA 0.4159 -48 GAGTAATTGTTATTGATCTAAAAAAAAAGT 8 68 1 TATTGATCTA 0.736175 -20 TCTTCTGGATTCTTTATCTATTCAAAAAAA 10 11 0 TCTTTATCTA 0.77209 -290 GCAACTGTATTTTTTGTATTAGCAACATTA 10 60 0 TTTTTGTATT 0.556654 -241 TCTTTTTTACTTTTTATCTTCACTTATAGG 10 121 0 TTTTTATCTT 0.947346 -180 AACCGAAGAATATTTACCTTATTTATTAAA 10 279 0 TATTTACCTT 0.773962 -22 AGGCAACAGTTTTTTGACTTCAAATATCCT 11 83 1 TTTTTGACTT 0.770115 -90 ATTTATTTATCTAGAGATATACT 11 160 0 TATTTATCTA 0.925102 -13 ********** Masking position 4 Map Score: 11.4114 Number of sites scoring better than the average of aligned sites = 627 Number in coding regions = 532 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 6 ATACTCCTTAATAATTTTTGTTAGTTAATT 1 39 0 ATAATTTTTG 0.673386 -162 CATTTTTAACTTCAATCTTAGGCA 2 5 0 TTCAATCTTA 0.646532 -185 GCTCTAAATCATCATTTTTAACTTCAATCT 2 17 0 ATCATTTTTA 0.588627 -173 GCTAGCTTTAAAAAAGTTTAAAAGGATATC 2 45 1 AAAAAGTTTA 0.58758 -145 GTTGTTAGACAAAAATTTTGTCTTACTTTT 3 145 0 AAAAATTTTG 0.671059 -105 TTGATAGTACTTAAAGTTTAAATTTAATAG 3 224 0 TTAAAGTTTA 0.85163 -26 TAAATTTTATATAAATATTAAGTA 6 5 0 ATAAATATTA 0.65742 -38 TTTTAATAACTTAAATTTTATATAAATATT 6 16 0 TTAAATTTTA 0.883546 -27 AAGCTTATTTATAAATTTTAAAAATAAGTC 7 103 0 ATAAATTTTA 0.941638 -74 AAAGTGCTAATTAAAGTTTGTT 8 3 0 TTAAAGTTTG 0.793305 -85 TAATAAAAATATAAATTTTAAAATTATTGA 9 18 1 ATAAATTTTA 0.941638 -36 AGAAATATTATTAAATCTTAAACAATGAAA 10 198 0 TTAAATCTTA 0.79811 -103 GTTCACTTTAATAAATTTTGCTTTGTCTAA 11 116 0 ATAAATTTTG 0.916507 -57 AGAGATATACTTCAATTTTATTTTGGTTCA 11 141 0 TTCAATTTTA 0.851782 -32 ********** Masking position 4 Map Score: 12.0385 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 64 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 AGTAAAAAAGTGTTAATACTCCTTAATAAT 1 54 0 TGTTAATACT 0.904755 -147 AATAGCTACTTGTAAAAAATTAAAAGTTAG 1 145 1 TGTAAAAAAT 0.649883 -56 CTAAGATTGAAGTTAAAAATGATGATTTAG 2 14 1 AGTTAAAAAT 0.649555 -176 TGCTAATTTTTGTTTATAATTACTGAGTAA 8 44 1 TGTTTATAAT 0.873214 -44 ACTGAGTAATTGTTATTGATCTAAAAAAAA 8 65 1 TGTTATTGAT 0.709852 -23 GTGGTAATAATAAAAATATAA 9 2 1 TGGTAATAAT 0.823519 -52 CATTAATAGTTGTTAATGCTATTGTCTTCT 10 35 0 TGTTAATGCT 0.856244 -266 CAACTATTAATGTTGCTAATACAAAAAATA 10 53 1 TGTTGCTAAT 0.71341 -248 GGATAACAGATGTTAATAATGCAAAAACAG 10 92 0 TGTTAATAAT 0.961207 -209 TAATTTTCATTGTTTAAGATTTAATAATAT 10 194 1 TGTTTAAGAT 0.717799 -107 TGTTACAAATAATTATAATA 11 1 1 TGTTACAAAT 0.862663 -172 ********** Masking position 10 Map Score: 3.93114 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 183 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 AAAAGTTTAAAAGGATATCACTGGAAGTAC 2 56 1 AAGGATATCA 0.931415 -134 AAAGCTAGGTAACTATATTTTAAAAAAGTG 3 11 0 AACTATATTT 0.700268 -239 TAAGCTATTTAAGGATAATTTGTGCAGTAG 5 40 0 AAGGATAATT 0.913888 -43 CTTCACTTATAGGGATAACAGATGTTAATA 10 104 0 AGGGATAACA 0.854574 -197 CTGAAATAACAGCGATAATATAGCATTTTT 10 164 1 AGCGATAATA 0.785936 -137 TTAACCGAAGAATATTTACCTTATTTA 10 284 0 AAGAATATTT 0.724451 -17 TTTAAAGATGAGCGATATTATAATTATTTG 11 16 0 AGCGATATTA 0.874984 -157 TTGTCTAAATAAGGATATTTGAAGTCAAAA 11 94 0 AAGGATATTT 0.9528 -79 AATAAAATTGAAGTATATCTCTAGATAAAT 11 149 1 AAGTATATCT 0.788326 -24 ********** Masking position 5 Map Score: 1.79054 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 79 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 ********** No masking Map Score: 1.32404e-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: 1.32404e-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: 1.32404e-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