AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00290_mgen_reg_300.orf -o00290_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: MG277 42 conserved hypothetical protein Input sequences: #1 MG267 33 conserved hypothetical protein #2 MG268 150 conserved hypothetical protein #3 MG269 300 conserved hypothetical protein #4 MG274 27 pyruvate dehydrogenase component E1, subunit alpha (pdhA) #5 MG275 82 NADH oxidase (nox) #6 MG335.1 58 M. genitalium predicted coding region MG335.1 #7 MG345 43 isoleucyl-tRNA synthetase (ileS) Motif number 1 GTGATGGTTTTTTATTAAAAATAAACCTTAACCC 2 106 1 TTTTAAAATA 0.991952 -45 TTAGCTTGGTTATATTGAAATTCACTTTTA 3 7 0 TTTTGAAATA 0.982511 -294 TAACTTGGAATGGGTTGAAAGTAAAGTTAGTGAT 3 38 1 TGTTGAAATA 0.927588 -263 CATTAGCAATTTTTTTAAAACTAACTACATCACT 3 105 0 TTTTAAAATA 0.991952 -196 GTTAGATTTGTTTGTTAAAAACCATGGCAATAAA 3 143 1 TTTTAAAACA 0.965022 -158 ATTTCTATGCTAATTTAAAACTAAG 4 2 0 TATTAAAATA 0.933681 -26 AGTGATTCGATCTTTTAAAATTAAGCTTTTG 5 8 0 TTTTAAAATA 0.991952 -75 ATTTTAAAAGTCTTATAAAATTAAATAATCGAAT 6 13 0 TTATAAAATA 0.950647 -46 AGCTATATATTAATAATTAAACATTTTAA 6 40 0 TTTTAATATA 0.974383 -19 TCAGAGTAATTTTATTAATATTTATCTAACTTAC 7 16 0 TTTTAATATA 0.974383 -28 * * ****** * * Masking position 8 Map Score: 18.6925 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 64 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 2 ATAATTGAAATAACTTACTGAAAACTACA 1 15 1 TAACTATGAA 0.762976 -19 AATTTCAATATAACCAAGCTAACTTGGAATGG 3 19 1 TAACAACTAA 0.99004 -282 TACTAGATCCTAACCAGTTTAGTGATGTAGTT 3 85 1 TAACAGTTAG 0.857708 -216 GGTTTTTAACAAACAAATCTAACTTTTCATTA 3 134 0 AAACAACTAA 0.96104 -167 AAGATTGCTAAAACAAAACTAGTAAAGAGGAA 3 187 0 AAACAACTAG 0.904465 -114 ACATAAACACTAACAAAACTAAAGATTGCTAA 3 208 0 TAACAACTAA 0.99004 -93 GCTAATTCTCTAAAGAAGCTAATGATAGCATC 3 274 0 TAAAAACTAA 0.98121 -27 AGCTTAATTTTAAAAGATCGAATCACTACTGC 5 15 1 TAAAGACGAA 0.872246 -68 AAATTATCCTTAAATAGCTTAAAAAATTACTG 5 49 1 TAAAAGTTAA 0.891913 -34 CTTATAAAATTAAATAATCGAATTA 6 4 0 TAAAAACGAA 0.97036 -55 TATTAATAATTAAACATTTTAAAAGTCTTATA 6 30 0 TAAAATTTAA 0.750001 -29 **** ** **** Masking position 3 Map Score: 9.13229 Number of sites scoring better than the average of aligned sites = 250 Number in coding regions = 221 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 3 GTTCTAAATTCTAACAATTATTTAAATC 2 7 0 CTACAATTTT 0.946201 -144 ATCACACTCACTGACAAGTCTTAATGCTGCTC 2 79 0 CTACAAGTTT 0.978257 -72 ACCCAACATATTAAAAAGTGTTTAT 2 136 1 TTAAAAGTTT 0.954656 -15 GTTAGTGATCTTAACAACTATTTACTAGATCC 3 63 1 TTACAACTTT 0.954763 -238 TAACTTTTCATTAGCAATTTTTTTAAAACTAA 3 115 0 TTGCAATTTT 0.967404 -186 TTTTTTCCTCTTTACTAGTTTTGTTTTAGCAA 3 183 1 TTACTAGTTT 0.96672 -118 TAGTTTTGTTTTAGCAATCTTTAGTTTTGTTA 3 198 1 TTGCAATCTT 0.873964 -103 AATCTTTAGTTTTGTTAGTGTTTATGTTAGAC 3 213 1 TTGTTAGTTT 0.756817 -88 AATTAAACATTTTAAAAGTCTTATAAAATTAA 6 23 0 TTAAAAGTTT 0.954656 -36 ** ****** ** Masking position 7 Map Score: 6.57133 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 181 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 4 ACATGATTCGACTCTAATGATGTGATGGTTC 2 35 0 ATCTAATGAT 0.983862 -116 GTTGAAAGTAAAGTTAGTGATCTTAACAACT 3 51 1 AGTTAGTGAT 0.97199 -250 GATCCTAACCAGTTTAGTGATGTAGTTAGTT 3 90 1 ATTTAGTGAT 0.96983 -211 AACACTAACAAAACTAAAGATTGCTAAAACA 3 204 0 AACTAAAGAT 0.856164 -97 TATGATTTAGACTTTAATGATCCTGATGCTA 3 250 1 ATTTAATGAT 0.974852 -51 TTCTCTAAAGAAGCTAATGATAGCATCAGGA 3 270 0 AGCTAATGAT 0.985032 -31 * ********* Masking position 6 Map Score: 5.39285 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 69 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 ACTCTAATGATGTGATGGTTCTAAATTCTAA 2 25 0 TGGATGGTTC 0.993802 -126 ATTTCTGGCCTGACATGATTCGACTCTAATG 2 47 0 TGCATGATTC 0.96848 -104 TGTCAGTGAGTGTGATGGTTTTTTATTAAAA 2 95 1 TGGATGGTTT 0.993313 -56 CAAGCTAACTTGGAATGGGTTGAAAGTAAAG 3 33 1 TGAATGGGTT 0.960833 -268 GGGAGTTTATTGCCATGGTTTTTAACAAACA 3 151 0 TGCATGGTTT 0.993312 -150 ** ******** Masking position 6 Map Score: 4.52106 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 4 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 AACCCATTCCAAGTTAGCTTGGTTATATTG 3 24 0 AAGTTAGCTT 0.927244 -277 TGCTAATGAAAAGTTAGATTTGTTTGTTAA 3 131 1 AAGTTAGATT 0.936722 -170 ACACCATTATGATTTAGACTTTAATGATCC 3 243 1 GATTTAGACT 0.818249 -58 CTTCTTTAGAGAATTAGCTTTCC 3 288 1 GAATTAGCTT 0.960727 -13 CTTAGTTTTAAATTAGCATAGAAATAT 4 10 1 AAATTAGCAT 0.914343 -18 GATCTTTTAAAATTAAGCTTTTG 5 4 0 AATTAAGCTT 0.843344 -79 ACTACTGCACAAATTATCCTTAAATAGCTT 5 39 1 AAATTATCCT 0.764903 -44 CAGATGTAAGTTAGATAAATATTAATA 7 8 1 AAGTTAGATA 0.825515 -36 ********** Masking position 6 Map Score: 4.00658 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 159 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 7 ********** No masking Map Score: 1.11798e-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 8 ********** No masking Map Score: 1.11798e-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 9 ********** No masking Map Score: 1.11798e-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