AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00360_mgen_reg_300.orf -o00360_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 MG077 233 oligopeptide ABC transporter, permease protein (oppB) #2 MG081 55 ribosomal protein L11 (rpl11) #3 MG087 28 ribosomal protein S12 (rpS12) #4 MG090 51 ribosomal protein S6 (rpS6) #5 MG094 49 replicative DNA helicase (dnaB) #6 MG096 182 conserved hypothetical protein #7 MG097 56 uracil DNA glycosylase (ung) #8 MG098 99 Glu-tRNA amidotransferase subunit gatC-related protein Motif number 1 CTAGTAATCGTTATTAGTATCATTTTTTTATAAAA 1 10 1 GTTTTATTTT 0.936321 -224 GCACATGATCTTTATCACTAAATTTATGTTTGGTTT 1 61 1 TTTTCATTTA 0.838802 -173 GATTTAGAAGCTGGTTACTTTTGTTTCAGGTAACCA 1 144 1 CTGTTATTTT 0.819734 -90 TTTGTTTCAGGTAACCAGTACCATTTCCAAAAAACT 1 163 1 GTACCATTTT 0.936092 -71 AACAGGTTCTTTTTTTATTTCTATTTAGTAA 1 213 1 TTTTTATTTT 0.963372 -21 AAATATAACTTTACTCAATGAGTTTTTCCAAAAAGT 4 22 1 TTATCATTTT 0.988085 -30 CAATTTTAGCCATTCAGTTTTGAAAAGAAAA 6 6 1 TTACCATTTT 0.963236 -177 AATGGTAAAATTATTCATTAAACTTTCCTTGTTAGT 6 51 1 TTATCATTTT 0.988085 -132 GTTAGTTGTAGTTTTCAATACTGTTTGTATTTCGAA 6 81 1 GTTTCATTTT 0.964709 -102 TTAAAATATGTTATTTAATTGTCTTTTTTAATTTCA 6 149 1 TTATTATTTT 0.97807 -34 TAAGAAATTTTTGATCAGTTACTTTTACCTAGATAA 7 16 1 TTGTCATTTT 0.975926 -41 TAATAATCACTTAGTTAAATAATTTTACAAGGTTGT 8 58 0 TTATTAATTT 0.82593 -42 TAAGTGATTATTACTTAATTGCACTTTAG 8 81 1 TTATTATCTT 0.875556 -19 *** *** * *** Masking position 7 Map Score: 14.9579 Number of sites scoring better than the average of aligned sites = 287 Number in coding regions = 253 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 2 TCTTGATTATTTTATAAAAAAATGATACTAATA 1 22 0 TTTTAAAAAT 0.921339 -212 AAGTAACCAGCTTCTAAATCTAAAGCATGATTA 1 131 0 CTTTAAATAA 0.875444 -103 TTCTCAGTTTTTTGGAAATGGTACTGGTTACCT 1 171 0 TTTGAAATTA 0.924956 -63 TTACTAAATAGAAATAAAAAAAG 1 221 0 TTATAAATAA 0.853378 -13 CTCCCACATTTTTGGAAAATTTTAAA 2 4 0 TTTGAAAATT 0.912066 -52 ATACTTAATAAAAATATAACTTTACTC 4 5 1 TTATAAAAAT 0.830439 -47 AAAAACTTTTTGGAAAAACTCATTGAGTAAA 4 31 0 TTTGAAAATC 0.791342 -21 AGCCATTCAGTTTTGAAAAGAAAAGTTTAAATT 6 18 1 TTTGAAAAAA 0.974886 -165 TTAAAATGAACTTCGAAATACAAACAGTATTGA 6 95 0 CTTGAAATAA 0.937044 -88 AACTACGAATTTTTTAAAATGAACTTCGAAATA 6 108 0 TTTTAAAAAA 0.948277 -75 ACAATTTATGAAATTAAAAAAGACAATT 6 165 0 TTAGAAATAA 0.924956 -18 TCTATTAAGAAATTTTTGATCAGTTAC 7 5 1 TTAGAAATTT 0.767032 -52 TTGTTTATTGATTAGAAAAACAACAACCTTGTA 8 36 1 ATTGAAAAAA 0.83147 -64 AAACAACAACCTTGTAAAATTATTTAACTAAGT 8 53 1 CTTTAAAAAT 0.855379 -47 *** ***** ** Masking position 7 Map Score: 13.2755 Number of sites scoring better than the average of aligned sites = 579 Number in coding regions = 528 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 3 TCATGTGCTGATGTTCTTGATTATTTTATAAAAAA 1 34 0 ATTTCATTTT 0.674101 -200 TTTATCACTAAATTTATGTTTGGTTTCAAATGAAG 1 71 1 AATTATTGTT 0.797869 -163 GTTGGATTATAAATCCTGCTTTATTGTAATCATGC 1 105 1 AATCCTTTTT 0.848032 -129 CAGCTTCTAAATCTAAAGCATGATTACAATAAAGC 1 122 0 ATTAAATGTT 0.587746 -112 GAAATAAAAAAAGAACCTGTTTTTTTCAGGTTCTC 1 199 0 AAAACTTTTT 0.667999 -35 TGTGGGAGCTAATTAAGCGTTTGTACCACAGCAAA 2 29 1 AATAATTTTA 0.840699 -27 TCATTGAGTAAAGTTATATTTTTATTAAGTAT 4 8 0 AATTATTTAT 0.572552 -44 TTTACCATTAATTTAAACTTTTCTTTTCAAAACTG 6 25 0 ATTAATTTTT 0.889636 -158 AAAGATCTAGAACTACGAATTTTTTAAAATGAACT 6 116 0 AATACTTTTT 0.961657 -67 AAAGACAATTAAATAACATATTTTAAAGATCTAGA 6 140 0 AATAAATTTA 0.758841 -43 TCTATTAAGAAATTTTTGATCAGTTAC 7 3 1 TATAAATTTT 0.622647 -54 TACCTAGATAAATTTAAAGTTTATTT 7 41 1 AATTATTTTT 0.930152 -16 AACAAGTGTCAACTACAGCTTTGTTTTTAA 8 6 0 AATACTTTTT 0.961657 -94 AAAATTATTTAACTAAGTGATTATTACTTAATTGC 8 68 1 AATAAATTTT 0.941492 -32 ** *** *** ** Masking position 11 Map Score: 8.95213 Number of sites scoring better than the average of aligned sites = 579 Number in coding regions = 498 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 4 GATGTTCTTGATTATTTTATAAAAAAATGA 1 30 0 ATTATTTTAT 0.772803 -204 GAAACCAAACATAAATTTAGTGATAAAGAT 1 68 0 ATAAATTTAG 0.755659 -166 ACATTTTTGGAAAATTTTAAA 2 2 0 AAAATTTTAA 0.814637 -54 TAATAAAAATATAACTTTACTCAATGAGTT 4 16 1 ATAACTTTAC 0.936051 -36 TAATTTTACCATTAATTTAAACTTTTCTTT 6 34 0 ATTAATTTAA 0.864683 -149 AGTTTAATGAATAATTTTACCATTAATTTA 6 45 0 ATAATTTTAC 0.964851 -138 TTTTACCTAGATAAATTTAAAGTTTATTT 7 38 1 ATAAATTTAA 0.781351 -19 ACTTAGTTAAATAATTTTACAAGGTTGTTG 8 56 0 ATAATTTTAC 0.964851 -44 ********** Masking position 4 Map Score: 7.98488 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 38 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 AAATAATCAAGAACATCAGCACATGATCTT 1 43 1 GAACATCAGC 0.96285 -191 TTAAGCGTTTGTACCACAGCAAAAT 2 41 1 GTACCACAGC 0.95611 -15 ACAGTATTGAAAACTACAACTAACAAGGAA 6 75 0 AAACTACAAC 0.960734 -108 AAACAAGTGTCAACTACAGCTTTGTTTTTA 8 12 0 CAACTACAGC 0.978874 -88 TTGATTAGAAAAACAACAACCTTGTAAAAT 8 43 1 AAACAACAAC 0.960734 -57 ********** Masking position 3 Map Score: 1.20381 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 28 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 ********** No masking Map Score: -4.80737e-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: -4.80737e-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: -4.80737e-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