AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -iarcA_mgen_opreg_300.orf -g0.317 -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 = 0.317 maxlen = 30 weight = 0.8 exclude = 0 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 Motif number 1 CACTTTTTTAAAATATAGTTACCTAGCT 1 7 1 TTAAAATTAG 0.962132 -243 GGTACCTAGCTCTAAAAAATAAAGCTAGGTAA 1 29 0 TTAAAAATAA 0.992396 -221 CAACAGCTGCTGTAAAAAGTAAGACAAAATTT 1 131 1 TTAAAAATAA 0.992396 -119 AAAATTTTTGTCTAACAACTAAAAAGCCAGTA 1 156 1 TTAACAATAA 0.982491 -94 AGTAGTGATCTATAACAAATAAAAAAAGCCAG 1 194 0 TTAACAATAA 0.982491 -56 AGATCACTACTATTAAATTTAAACTTTAAGTA 1 215 1 TTTAAATTAA 0.975822 -35 TTCTATGCTAATTTAAAACTAAG 2 2 0 ATTAAAATAA 0.926159 -26 TGATTCGATCTTTTAAAATTAAGCTTTTG 3 8 0 TTTAAAATAA 0.988904 -75 TTAATATTTATATAAAATTTAAGTTATTAAAA 4 14 1 TTAAAATTAA 0.983357 -29 AAATTTAAGTTATTAAAAATAGTTA 4 28 1 TTTAAAATAG 0.974573 -15 * ****** *** Masking position 7 Map Score: 23.4884 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 93 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 2 TAAAATATAGTTACCTAGCTTTATTTTTTA 1 19 1 TTACCTAGCT 0.989701 -231 ATGAAATGAGGTACCTAGCTCTAAAAAATA 1 40 0 GTACCTAGCT 0.984771 -210 AGCCAGTTTAGTTACTGGCTTTTTAGTTGT 1 170 0 GTTACTGGCT 0.940033 -80 AGCCAGTAACTAAACTGGCTTTTTTTATTT 1 180 1 TAAACTGGCT 0.976261 -70 CTTAGTTTTAAATTAGCATAGAAATAT 2 9 1 TAAATTAGCA 0.810865 -19 CAAATTATCCTTAAATAGCTTAAAAAATTA 3 48 1 TTAAATAGCT 0.938458 -35 ATATCTTAGCTGCAGTAATTT 3 72 0 TATCTTAGCT 0.915602 -11 ********** Masking position 6 Map Score: 6.62433 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 69 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 3 TAGTTACCTAGCTTTATTTTTTAGAGCTAGGT 1 26 1 GCTTTTTTTT 0.896353 -224 ACTTGCATTGGCAGCATTTCTTGTTGTCTTCC 1 83 0 GCAGCTTCTT 0.973456 -167 TGCACTTAGCGCATTCGCACTTGCATTGGCAG 1 101 0 GCATTGCCTT 0.973456 -149 TTTTACAGCAGCTGTTGCACTTAGCGCATTCG 1 116 0 GCTGTGCCTT 0.989963 -134 AACTAAACTGGCTTTTTTTATTTGTTATAGAT 1 187 1 GCTTTTTATT 0.956239 -63 GATAATTTGTGCAGTAGTGATTCGATCTTTTA 3 25 0 GCAGTGTATT 0.986223 -58 ATATCTTAGCTGCAGTAATTTTTTAAGCTA 3 63 0 GCTGCGTATT 0.984307 -20 ***** ** *** Masking position 11 Map Score: 6.28935 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 65 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 4 TTAAAGTGATGGAAGACAACAAGAAATGCT 1 73 1 GGAAGACAAC 0.990249 -177 GCTGTAAAAAGTAAGACAAAATTTTTGTCT 1 139 1 GTAAGACAAA 0.993093 -111 CTTTTTAGTTGTTAGACAAAAATTTTGTCT 1 152 0 GTTAGACAAA 0.98778 -98 ********** Masking position 6 Map Score: 1.73294 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 1 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 5 AAGTGCAACAGCTGCTGTAAAAAGTAAGAC 1 126 1 GCTGCTGTAA 0.992839 -124 GATAATTTGTGCAGTAGTGATTCGATCTTT 3 27 0 GCAGTAGTGA 0.976305 -56 ATATCTTAGCTGCAGTAATTTTTTAAGC 3 65 0 GCTGCAGTAA 0.995926 -18 ********** Masking position 10 Map Score: 0.947659 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 4 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 6 TCTTACTTTTTACAGCAGCTGTTGCACTTA 1 125 0 TACAGCAGCT 0.98307 -125 ATCGAATCACTACTGCACAAATTATCCTTA 3 31 1 TACTGCACAA 0.907013 -52 CTTAAAAAATTACTGCAGCTAAGATAT 3 66 1 TACTGCAGCT 0.905533 -17 ********** Masking position 7 Map Score: 0.511456 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 4 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 7 ********** No masking Map Score: -4.09683e-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: -4.09683e-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 9 ********** No masking Map Score: -4.09683e-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