AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00130_mgen_reg_300.orf -o00130_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 MG254 175 DNA ligase #2 MG272 249 dihydrolipoamide acetyltransferase (pdhC) #3 MG274 27 pyruvate dehydrogenase component E1, subunit alpha (pdhA) #4 MG275 82 NADH oxidase (nox) #5 MG277 42 conserved hypothetical protein #6 MG466 25 ribosomal protein L34 (rpL34) #7 MG468.1 62 ABC transporter, ATP-binding protein #8 MG469 300 chromosomal replication initiator protein (dnaA) Motif number 1 TAAAATATACTAAATATTAAAGTAACAACGC 1 17 1 TAAATATAAA 0.886285 -159 AATATTAAAGTAACAACGCAGATATAGTTCA 1 29 1 TAACAAGCAG 0.775108 -147 AATCAGGATTTTACAAAGAAGTTTTAATTTG 1 118 0 TTACAAGAAG 0.908052 -58 TCCTGATTGGTATCAACTAAGTCAGGATTTT 1 141 1 TATCAATAAG 0.834798 -35 TACTATAAATAAGAAAAATCCTGACT 1 160 0 TAAATAGAAA 0.782111 -16 TACCTAGCTCTAAAAAATAAAGCTAGGTAAC 2 28 0 TAAAAATAAA 0.963812 -222 ACAGCTGCTGTAAAAAGTAAGACAAAATTTT 2 133 1 TAAAAATAAG 0.982593 -117 AATTTTTGTCTAACAACTAAAAAGCCAGTAA 2 158 1 TAACAATAAA 0.960386 -92 TAGTGATCTATAACAAATAAAAAAAGCCAGT 2 193 0 TAACAATAAA 0.960374 -57 ATCACTACTATTAAATTTAAACTTTAAGTAC 2 217 1 TTAAATTAAA 0.660232 -33 CTATGCTAATTTAAAACTAAG 3 1 0 TTAAAATAAG 0.959343 -27 ATTCGATCTTTTAAAATTAAGCTTTTG 4 7 0 TTAAAATAAG 0.959246 -76 AAATTTTATATAAATATTAAGTA 5 3 0 TAAATATAAG 0.942921 -40 AATATTTATATAAAATTTAAGTTATTAAAAA 5 16 1 TAAAATTAAG 0.913727 -27 ****** **** Masking position 10 Map Score: 18.1048 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 211 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 2 AATATTTAGTATATTTTAACTTGC 1 5 0 ATATTTTAAC 0.826024 -171 AAAATATACTAAATATTAAAGTAACAACGC 1 18 1 AAATATTAAA 0.816955 -158 CTAGGTAACTATATTTTAAAAAAGTG 2 7 0 ATATTTTAAA 0.931971 -243 CTTAAAGTTTAAATTTAATAGTAGTGATCT 2 215 0 AAATTTAATA 0.754268 -35 ATTTCTATGCTAATTTAAAACTAAG 3 6 0 TAATTTAAAA 0.681745 -22 CAAAAGCTTAATTTTAAAAGATCGAATC 4 9 1 TAATTTTAAA 0.90531 -74 TTAATAACTTAAATTTTATATAAATATTAA 5 14 0 AAATTTTATA 0.931971 -29 CAAAATTAAAATTTTCTAATAGTGTTCT 7 9 1 AAATTTTCTA 0.918502 -54 AAAAAGAGAGATATTTTCAAGAGGAACAAA 8 16 1 ATATTTTCAA 0.918502 -285 AAGAGGAACAAAATTTTCAATATCATAATA 8 34 1 AAATTTTCAA 0.969418 -267 AAAAAAATCAAAATTTTCAACAACAATTCA 8 79 1 AAATTTTCAA 0.969418 -222 CCAATTTCGAGAATTTTAACTATCATTCTT 8 261 1 GAATTTTAAC 0.735801 -40 ********** Masking position 3 Map Score: 13.4036 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 158 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 3 CACTTTTTTAAAATATAGTTACC 2 2 1 ACTTTTAAAA 0.633637 -248 TGAGGTACCTAGCTCTAAAAAATAAAGCTAGG 2 32 0 AGCTTAAAAA 0.860193 -218 TAAATTAAAGTGATGGAAGACAACAAGAAATG 2 69 1 TGATGAGACA 0.496151 -181 GTGCAACAGCTGCTGTAAAAAGTAAGACAAAA 2 128 1 TGCTTAAAAG 0.859995 -122 GCTTTTTAGTTGTTAGACAAAAATTTTGTCTT 2 151 0 TGTTGAAAAA 0.853443 -99 TTAATAGTAGTGATCTATAACAAATAAAAAAA 2 199 0 TGATTAAACA 0.781808 -51 ATAAAATTTAAGTTATTAAAAATAGTTA 5 25 1 AGTTTTAAAA 0.772436 -18 AATCATTAAGTCATCTAAAAAAATACCCTGAG 7 37 0 TCATTAAAAA 0.879564 -26 AAAATTTTGTTCCTCTTGAAAATATCTCTCTT 8 19 0 TCCTTTAAAA 0.911167 -282 ACCATTATTATGATATTGAAAATTTTGTTCCT 8 37 0 TGATTTAAAA 0.926551 -264 TTGATTTTTTTGCTGTAAGAAACCATTATTAT 8 58 0 TGCTTAGAAA 0.860009 -243 TTGTGTGAATTGTTGTTGAAAATTTTGATTTT 8 82 0 TGTTTTAAAA 0.922883 -219 CAGGAATAGTTCCTGTTGAACGCCAAGAAAAA 8 151 1 TCCTTTAACG 0.624689 -150 TTGTCAAGAATGATAGTTAAAATTCTCGAAAT 8 264 0 TGATGTAAAA 0.842259 -37 TATTCTTCTATAACATTGTCAAGAA 8 286 0 TCTTTAAACA 0.64444 -15 **** ** **** Masking position 10 Map Score: 10.2397 Number of sites scoring better than the average of aligned sites = 713 Number in coding regions = 670 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 GGATTTTTCTTATTTATAGTA 1 165 1 TATTTATAGT 0.870654 -11 AGTTTAAATTTAATAGTAGTGATCTATAAC 2 210 0 TAATAGTAGT 0.921278 -40 ATCGTATTGATAGTACTTAAAGTT 2 236 0 TATTGATAGT 0.938143 -14 TTTAAGTTATTAAAAATAGTTA 5 31 1 TAAAAATAGT 0.790542 -12 ATAATCACCTGATTAATTGTTTC 6 13 1 GATTAATTGT 0.865906 -13 TTAGATGACTTAATGATTGTTT 7 51 1 TAATGATTGT 0.94743 -12 TTCAATATCATAATAATGGTTTCTTACAGC 8 49 1 TAATAATGGT 0.897481 -252 GTGGTTGTGTGAATTGTTGTTGAAAATTTT 8 88 0 GAATTGTTGT 0.763314 -213 ACATTGTCAAGAATGATAGTTAAAATTCTC 8 269 0 GAATGATAGT 0.959755 -32 ********** Masking position 7 Map Score: 4.5015 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 107 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 5 GAAGTTTTAATTTGGAGCAGATAACGGGAA 1 102 0 TTTGGAGCAG 0.981469 -74 CGCACTTGCATTGGCAGCATTTCTTGTTGT 2 88 0 TTGGCAGCAT 0.8979 -162 TGTCTTACTTTTTACAGCAGCTGTTGCACT 2 127 0 TTTACAGCAG 0.942132 -123 AAGGATAATTTGTGCAGTAGTGATTCGATC 4 30 0 TGTGCAGTAG 0.949237 -53 ATATCTTAGCTGCAGTAATTTTTTA 4 68 0 TTAGCTGCAG 0.930895 -15 TTTTGATTTTTTTGCTGTAAGAAACCATTA 8 62 0 TTTGCTGTAA 0.899328 -239 TATTAACTGCTTTGGAGTAATTTCTAACTT 8 229 0 TTTGGAGTAA 0.896534 -72 ********** Masking position 9 Map Score: 2.17855 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 72 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 6 GCAAGTTAAAATATACTAAATAT 1 4 1 AGTTAAAATA 0.691374 -172 GTTTTAAATTAGCATAGAAATAT 3 15 1 AGCATAGAAA 0.8563 -13 ATCCTTAAATAGCTTAAAAAATTACTGCAG 4 54 1 AGCTTAAAAA 0.944071 -29 AAATTACTGCAGCTAAGATAT 4 72 1 AGCTAAGATA 0.919092 -11 TCATTAAGTCATCTAAAAAAATACCCTGAG 7 37 0 ATCTAAAAAA 0.877057 -26 ACCAAAAAAAGAGAGATATT 8 1 1 ACCAAAAAAA 0.923835 -300 GGTTTCTTACAGCAAAAAAATCAAAATTTT 8 66 1 AGCAAAAAAA 0.966381 -235 TTCCTCCCCAACCTAAAACAAAAATACCAG 8 124 1 ACCTAAAACA 0.876769 -177 ********** Masking position 6 Map Score: 3.5184 Number of sites scoring better than the average of aligned sites = 291 Number in coding regions = 260 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 7 ATTGGCAGCATTTCTTGTTGTCTTCCATCA 2 79 0 TTTCTTGTTG 0.977777 -171 AGTTACTGGCTTTTTAGTTGTTAGACAAAA 2 161 0 TTTTTAGTTG 0.873469 -89 TGAAAATTTTGTTCCTCTTGAAAATATCTC 8 23 0 GTTCCTCTTG 0.96772 -278 AAATTTTGATTTTTTTGCTGTAAGAAACCA 8 65 0 TTTTTTGCTG 0.910964 -236 ACCAGGAATAGTTCCTGTTGAACGCCAAGA 8 149 1 GTTCCTGTTG 0.982864 -152 CCTGTATCTAGTTTTTCTTGGCGTTCAACA 8 164 0 GTTTTTCTTG 0.958328 -137 ********** Masking position 3 Map Score: 2.67253 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 74 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 8 TAAAAAATAAAGCTAGGTAACTATATTTTA 2 19 0 AGCTAGGTAA 0.981325 -231 TATTTTTTAGAGCTAGGTACCTCATTTCAT 2 40 1 AGCTAGGTAC 0.982677 -210 ACAACTAAAAAGCCAGTAACTAAACTGGCT 2 170 1 AGCCAGTAAC 0.94518 -80 AAATAAAAAAAGCCAGTTTAGTTACTGGCT 2 180 0 AGCCAGTTTA 0.941078 -70 TAATTTTTTAAGCTATTTAAGGATAATTTG 4 48 0 AGCTATTTAA 0.903175 -35 ********** Masking position 5 Map Score: 0.731223 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 11 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 9 ********** No masking Map Score: -2.81785e-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 10 ********** No masking Map Score: -2.81785e-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: -2.81785e-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