AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00310_mgen_reg_300.orf -o00310_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 MG272 249 dihydrolipoamide acetyltransferase (pdhC) #2 MG274 27 pyruvate dehydrogenase component E1, subunit alpha (pdhA) #3 MG275 82 NADH oxidase (nox) #4 MG277 42 conserved hypothetical protein #5 MG395 300 putative lipoprotein Motif number 1 CACTTTTTTAAAATATAGTTACCTAGCT 1 7 1 TTAAAATTAG 0.965984 -243 GGTACCTAGCTCTAAAAAATAAAGCTAGGTAA 1 29 0 TTAAAAATAA 0.96758 -221 GTACCTCATTTCATAAATTAAAGTGATGGAAG 1 56 1 TATAAATAAA 0.695692 -194 CAACAGCTGCTGTAAAAAGTAAGACAAAATTT 1 131 1 TTAAAAATAA 0.967581 -119 AAAATTTTTGTCTAACAACTAAAAAGCCAGTA 1 156 1 TTAACAATAA 0.86735 -94 AGTAGTGATCTATAACAAATAAAAAAAGCCAG 1 194 0 TTAACAATAA 0.867349 -56 AGATCACTACTATTAAATTTAAACTTTAAGTA 1 215 1 TTTAAATTAA 0.917067 -35 TCTATGCTAATTTAAAACTAAG 2 1 0 TTAAAACAAG 0.960323 -27 GATTCGATCTTTTAAAATTAAGCTTTTG 3 7 0 TTAAAATAAG 0.953851 -76 TTAATATTTATATAAAATTTAAGTTATTAAAA 4 14 1 TTAAAATTAA 0.967457 -29 AAATTTAAGTTATTAAAAATAGTTA 4 28 1 TTTAAAATAG 0.913451 -15 AACTAACTAAATTAAAACCAAAAAAATTAATC 5 43 0 ATAAAACAAA 0.772209 -258 ATCAAAAAAGTTAAAAATGAAAATAGAACTAC 5 89 0 TAAAAATAAA 0.859881 -212 AAGAAGCTAATGAAAAAACTAATGAAAGCAAA 5 128 0 TAAAAAATAA 0.893641 -173 TTTAGATGCAATTAAAAAGAAGAAGCTAATGA 5 147 0 ATAAAAAAAG 0.736066 -154 TTTAATTGCATCTAAAACTAAGCAGAATAAAA 5 163 1 TTAAAACAAG 0.96033 -138 ATCTTTTCACTGATAAATTTAATTATTTTTAT 5 189 0 TATAAATTAA 0.757019 -112 AAGAAGCACTTGTTAAACTTAGGCTTTAGCTT 5 238 0 TTTAAACTAG 0.924391 -63 TTTAATACAAAAATATTTCAAA 5 289 0 TTAATACAAA 0.664227 -12 * ****** *** Masking position 7 Map Score: 26.662 Number of sites scoring better than the average of aligned sites = 347 Number in coding regions = 302 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 2 CTAAAAAATAAAGCTAGGTAACTATATTTTA 1 19 0 AAGCTAGGTA 0.866428 -231 CAAATAAAAAAAGCCAGTTTAGTTACTGGCT 1 180 0 AAGCCAGTTA 0.935492 -70 ATATTTCTATGCTAATTTAAAACTAAG 2 9 0 ATGCTAATTA 0.865229 -19 GTAATTTTTTAAGCTATTTAAGGATAATTTG 3 48 0 AAGCTATTTA 0.943726 -35 AGTAGTTATCAAGCCAATGCAAATTCTAACG 5 11 1 AAGCCAATGA 0.92119 -290 AATTAAAACCAAAAAAATTAATCCCGTTAGA 5 35 0 AAAAAAATTA 0.811506 -266 TGACTCAGGTAAACTAACTAAATTAAAACCA 5 55 0 AAACTAACTA 0.882299 -246 TGCAACCATCAAAAAAGTTAAAAATGAAAAT 5 97 0 AAAAAAGTTA 0.729475 -204 GCTAATGAAAAAACTAATGAAAGCAAATGCA 5 124 0 AAACTAATGA 0.956604 -177 TAAAAAGAAGAAGCTAATGAAAAAACTAATG 5 136 0 AAGCTAATGA 0.968209 -165 AAGCAGAATAAAAATAATTAAATTTATCAGT 5 182 1 AAAATAATTA 0.945488 -119 TTTAGCTTCAAAAATAATTGAGTTCATCTTT 5 215 0 AAAATAATTA 0.945504 -86 TTTAATACAAAAATATTTCAAAACCTTTAA 5 281 0 AAAATATTTA 0.828279 -20 ********* * Masking position 6 Map Score: 13.3281 Number of sites scoring better than the average of aligned sites = 403 Number in coding regions = 371 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 3 TAAGTGCAACAGCTGCTGTAAAAAGTAAGAC 1 125 1 AGCTGCTTAA 0.943941 -125 ATCGAATCACTACTGCACAAATTATCCTTAA 3 31 1 TACTGCAAAA 0.833875 -52 ATCCTTAAATAGCTTAAAAAATTACTGCAGC 3 54 1 AGCTTAAAAA 0.953404 -29 ATATCTTAGCTGCAGTAATTTTTTAAGC 3 65 0 AGCTGCATAA 0.976891 -18 CAGGTAAACTAACTAAATTAAAACCAAAAAA 5 50 0 AACTAAATAA 0.596903 -251 AGCAAATGCAACCATCAAAAAAGTTAAAAAT 5 103 0 ACCATCAAAA 0.785931 -198 AAAAAGAAGAAGCTAATGAAAAAACTAATGA 5 135 0 AGCTAATAAA 0.779999 -166 TCTTTTTAATTGCATCTAAAACTAAGCAGAA 5 159 1 TGCATCTAAA 0.686747 -142 TCTAAAACTAAGCAGAATAAAAATAATTAAA 5 173 1 AGCAGAAAAA 0.912987 -128 CTTAGGCTTTAGCTTCAAAAATAATTGAGTT 5 222 0 AGCTTCAAAA 0.982361 -79 AGTGCTTCTTAACTTCATTAATTAAAGGTTT 5 260 1 AACTTCATAA 0.90258 -41 ******* *** Masking position 10 Map Score: 7.76591 Number of sites scoring better than the average of aligned sites = 358 Number in coding regions = 341 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 4 TAAATTTAATAGTAGTGATCTATAACAAAT 1 206 0 AGTAGTGATC 0.991978 -44 TAATTTGTGCAGTAGTGATTCGATCTTTTA 3 25 0 AGTAGTGATT 0.9784 -58 AGTAGTTATCAAGCCAATGC 5 1 1 AGTAGTTATC 0.987625 -300 CTGAGTCAATAGTAGTTCTATTTTCATTTT 5 78 1 AGTAGTTCTA 0.945037 -223 ********** Masking position 6 Map Score: 2.64596 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 5 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 5 ACAAGAAATGCTGCCAATGCAAGTGCGAAT 1 91 1 CTGCCAATGC 0.971027 -159 GCCAATGCAAGTGCGAATGCGCTAAGTGCA 1 103 1 GTGCGAATGC 0.971027 -147 AATGCGCTAAGTGCAACAGCTGCTGTAAAA 1 118 1 GTGCAACAGC 0.84221 -132 AGTAGTTATCAAGCCAATGCAAATTCTAAC 5 11 1 AAGCCAATGC 0.989783 -290 AAACTAATGAAAGCAAATGCAACCATCAAA 5 115 0 AAGCAAATGC 0.984284 -186 TAAAAAGAAGAAGCTAATGAAAAAACTAAT 5 137 0 AAGCTAATGA 0.890394 -164 ATTATTTTTGAAGCTAAAGCCTAAGTTTAA 5 228 1 AAGCTAAAGC 0.964596 -73 ********** Masking position 6 Map Score: 6.08297 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 75 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 ********** No masking Map Score: 7.9824e-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 7 ********** No masking Map Score: 7.9824e-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 8 ********** No masking Map Score: 7.9824e-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