AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00770_aful_reg_300.orf -o00770_aful_300.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 AF0033 36 acyl carrier protein synthase (acaA-1) #2 AF0932 41 conserved hypothetical protein #3 AF0933 22 branched-chain amino acid aminotransferase (ilvE) #4 AF1014 126 dihydroxy-acid dehydratase (ilvD) #5 AF1665 147 ornithine cyclodeaminase (arcB) #6 AF1667 158 sulfate adenylyltransferase (sat) #7 AF1669 48 adenylylsulfate reductase, subunit B (aprB) #8 AF1671 64 coenzyme F390 synthetase (ftsA-2) #9 AF1720 182 acetolactate synthase, large subunit (ilvB-1) #10 AF1778 105 stage V sporulation protein (spoVG) #11 AF1779 57 2-hydroxyacid dehydrogenase, putative #12 AF1985 45 ketol-acid reductoisomerase (ilvC) #13 AF2009 101 heme biosynthesis protein (nirJ-2) #14 AF2010 46 A. fulgidus predicted coding region AF2010 #15 AF2011 175 conserved hypothetical protein #16 AF2013 275 coenzyme F390 synthetase (ftsA-3) #17 AF2014 63 sugar transporter, putative #18 AF2100 106 acetolactate synthase, large subunit (ilvB-4) Motif number 1 AACGGAAAAACGTTTTAAATCAGCT 2 5 1 GAAAACGTTT 0.945081 -37 GAAGGGCAGGCAAAATTGTTTTATCTTTCTT 5 25 0 CAAAATGTTT 0.904853 -123 AAATTGAATAGAAAAATTTTTCTTACAGCAT 5 76 1 GAAAATTTTT 0.96006 -72 CTGTCTTCTTGAAAAGTATTAAAGTTAATGT 5 121 0 GAAAATATTA 0.826327 -27 GTAGAAAATTTTTTGAACTCCTTT 6 4 1 GAAAATTTTT 0.96006 -155 TTGAAAATTCGAAAACCTTTAATCATTAAAA 6 82 1 GAAAACTTTA 0.92056 -77 TAAAGGTTTCGAAAAATATTTTAATGATTAA 6 100 0 GAAAATATTT 0.91846 -59 TTTTTTTTTAGAAAAATGTATGAAAAGGTTG 7 16 1 GAAAATGTAT 0.729095 -33 TTAGAAAAAAGAAAAATTTTAGAGCT 8 6 0 GAAAATTTTA 0.799691 -59 TTTCTAAATCTAAAAGTTTTTATTGCATTGC 8 30 1 TAAAATTTTT 0.710156 -35 CTGGGCGAACCAAAACTTTTTAAAGCGCATG 9 69 1 CAAAATTTTT 0.919236 -114 CTCTTTTCCAGAGAACTTTTTCATCACTCCC 9 108 0 GAGAATTTTT 0.868042 -75 GCTTTTGCTTCAAAACCTTTTTATCTTTTCT 11 22 1 CAAAACTTTT 0.88994 -36 GCCTAAATAGTAAAATTTTTATTTTTGTTAG 14 12 1 TAAAATTTTA 0.482435 -35 GAACTGGCGGGAAAACCGTTTTTTAATACTG 16 60 0 GAAAACGTTT 0.945081 -216 TTTATTTGCATAAAATTTTTAGCTTTTTAAT 17 30 1 TAAAATTTTA 0.482435 -34 ATCAACCTTAGCAAACTTTTTAAAATTATAA 18 73 1 GCAAATTTTT 0.86802 -34 ***** ***** Masking position 5 Map Score: 23.9981 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 152 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 2 AAGCATCGGGAAGATTTTGACAAAAAACAAAA 4 44 0 AAGATTGACA 0.913469 -83 CCATCCAACCAAAACTTAAAAAATAATGAAGC 4 93 1 AAAATTAAAA 0.853432 -34 CTATTGAAGGAAAAATTGAATAGAAAAATTTT 5 64 1 AAAATTAATA 0.610238 -84 TAAAAGGCAAAGGAGTTCAAAAAATTTTCTAC 6 11 0 AGGATTAAAA 0.904811 -148 TTTATTTTCGAAGAGTTTGAAAATTGCGCGGT 6 39 1 AAGATTGAAA 0.97324 -120 GCCTTATATAAAGGTTTCGAAAAATATTTTAA 6 107 0 AAGGTTGAAA 0.972697 -52 ACCTTTATATAAGGCTGTGAAAAAAAATACAT 6 124 1 AAGGTGGAAA 0.818776 -35 TAAAAACTTTTAGATTTAGAAAAAAGAAAAAT 8 20 0 TAGATTGAAA 0.845855 -45 GCTGCAAGCTAAGTTTTAAAAACTACTTACCT 9 21 0 AAGTTTAAAA 0.838055 -162 AAAAGATAAAAAGGTTTTGAAGCAAAAGCCAA 11 19 0 AAGGTTGAAG 0.809197 -39 TTTAGTTCCAAAAGGTTAAATATCTGGATGCA 13 24 0 AAAGTTAATA 0.60532 -78 AGGGGCCCGATAGATTTGAACATCGAGGAGAC 15 20 1 TAGATTAACA 0.640767 -156 TTTCGATGTGAAGGTTATAAAACTTATTATTA 15 144 0 AAGGTAAAAA 0.773434 -32 TTTGCAGCAAAAGGCTTTAAAAGCCACTGCCT 16 184 0 AAGGTTAAAA 0.975548 -92 TGAGGGAGGCAGGATTTAAATACTTCACCATC 16 232 0 AGGATTAATA 0.718775 -44 GGAAATTTAAAGAATTAAAAAGCTAAAAATT 17 43 0 AAGATTAAAA 0.976035 -21 GTCAGGCTGCAAGAGTTTAAAACCCATCGAAT 18 38 0 AAGATTAAAA 0.976035 -69 **** ** **** Masking position 6 Map Score: 15.8042 Number of sites scoring better than the average of aligned sites = 287 Number in coding regions = 212 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 3 TTATTTAAGATTTGCCTTTTTTGATAGCATTG 1 11 0 TTTCCTTTTT 0.919854 -26 AAACAAAACATTTATTTGTTTTAATCACAAAA 4 20 0 TTTTTTGTTT 0.824168 -107 AAATAAATGTTTTGTTTTTTGTCAAAATCTTC 4 35 1 TTTTTTTTTT 0.961375 -92 GGCAAAATTGTTTTATCTTTCTTATCTACCAT 5 16 0 TTTATCTTTT 0.819002 -132 TTTGAACTCCTTTGCCTTTTATTTTCGAAGAG 6 22 1 TTTCCTTTTT 0.919854 -137 TAACCTATGATGTATTTTTTTTCACAGCCTTA 6 133 0 TGTTTTTTTT 0.810347 -26 TTTAATTTTTTTTTAGAAAAAT 7 1 1 TTTATTTTTT 0.928857 -48 CTCTAAAATTTTTCTTTTTTCTAAATCTAAAA 8 13 1 TTTTTTTTTT 0.961375 -52 TAGTACAGCTTTTACTTCTTTTCTAAAGGAGT 9 146 1 TTTCTTCTTT 0.794501 -37 TCAAAACCTTTTTATCTTTTCTGGGTTCAATT 11 31 1 TTTTCTTTTT 0.932951 -27 ATAGTAAAATTTTTATTTTTGTTAGCATGTAG 14 18 1 TTTATTTTTT 0.928857 -29 GATTATTTATTCTTTTTGATTAATCGT 18 6 1 TTTTTCTTTT 0.896116 -101 *** ****** * Masking position 9 Map Score: 12.4696 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 60 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 4 AGAGCATCTATTGAAGGAAAAATTGAATAG 5 57 1 TTGAAGGAAA 0.983212 -91 CTACTTACCTTTGTAGGAAA 9 1 0 TTGTAGGAAA 0.976163 -182 AAAGAGTTCATTGTAGTACAGCTTTTACTT 9 133 1 TTGTAGTACA 0.848336 -50 AGAATTTTGATTGCAGGAAACGTTAGATTA 10 37 0 TTGCAGGAAA 0.984383 -69 TAAAAAGGTTTTGAAGCAAAAGCCAAACTC 11 15 0 TTGAAGCAAA 0.975779 -43 ATTTTTACACTTGAAGTAAAGAAGGATAAA 15 89 1 TTGAAGTAAA 0.962997 -87 ACGAATGCGTTTGCAGCAAAAGGCTTTAAA 16 195 0 TTGCAGCAAA 0.977519 -81 ********** Masking position 5 Map Score: 9.10574 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 55 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 CAACCAGAAATGAAGGGTGAAA 3 7 0 AAAATGAAGG 0.671224 -16 AATACTTTTCAAGAAGACAGGACATC 5 132 1 AGAAGACAGG 0.93071 -16 AAATATTTTAATGATTAAAGGTTTTCGAATT 6 87 0 AGATTAAAGG 0.936116 -72 AATGTATGAAAAGGTTGGAGGTGAGTTGA 7 30 1 AGGTTGGAGG 0.916669 -19 TATAAGAATTTTGATTGCAGGAAACGTTAGA 10 40 0 TGATTGCAGG 0.808912 -66 CATCGAGGAGACGGATGAAGGTTATGTAGCT 15 40 1 AGGATGAAGG 0.96783 -136 TGAAGTAAAGAAGGATAAAGGAGCAGGCAGT 15 100 1 AGGATAAAGG 0.949661 -76 AGTTCCAGAAAAGCTGACAGGTTGATTCT 16 9 0 AGCTGACAGG 0.830836 -267 CCCCTCTGTAATGATTAAAGGCAGTGGCTTT 16 166 1 AGATTAAAGG 0.936116 -110 TTCTGTCATGAGGGAGGCAGGATTTAAATAC 16 241 0 AGGAGGCAGG 0.965007 -35 * ********* Masking position 9 Map Score: 5.809 Number of sites scoring better than the average of aligned sites = 522 Number in coding regions = 485 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 AAATAATGAAGCACTTCTAAAACC 4 113 1 GCATCAAACC 0.967546 -14 TTTTCTTACAGCATCTCAAGAAAACTTGACATTA 5 93 1 GCACCAAAAA 0.977926 -55 CAGAGTTAAGGCAATGCAATAAAAACTTTTAGAT 8 37 0 GCATCAAAAA 0.985039 -28 TTAGCTTGCAGCAGTGCAATTACCTTGCCTGGGC 9 41 1 GCATCATACC 0.860905 -142 TGTCTGAGCTGCAGTTCCAGAAAAGCTGACAGGT 16 18 0 GCATCAAAAA 0.985039 -258 ACAGTATCTGGCAGTATTAAAAAACGGTTTTCCC 16 49 1 GCATTAAAAA 0.947259 -227 TTAAACTCTTGCAGCCTGACAAAATCAACCTTAG 18 50 1 GCACTAAAAA 0.923582 -57 *** * * * **** Masking position 9 Map Score: 2.8179 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 44 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 AAAACAATTTTGCCTGCCCTTCGAGAGCAT 5 34 1 TGCCTGCCCT 0.983884 -114 GCAATTACCTTGCCTGGGCGAACCAAAACT 9 56 1 TGCCTGGGCG 0.972574 -127 TCCCACCACCAGCATGCGCTTTAAAAAGTT 9 82 0 AGCATGCGCT 0.891214 -101 AGTGCCCCAGTGCCTGAGCTACATAACCTT 15 57 0 TGCCTGAGCT 0.989551 -119 ACGACAAGACTGCCTGCTCCTTTATCCTTC 15 109 0 TGCCTGCTCC 0.948872 -67 TGCCAGATACTGTCTGAGCTGCAGTTCCAG 16 32 0 TGTCTGAGCT 0.936552 -244 ********** Masking position 5 Map Score: 1.94749 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 96 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 TTTACGATTTTTGTGATTAAAACAAATAAA 4 12 1 TTGTGATTAA 0.914748 -115 AAAAATATTTTAATGATTAAAGGTTTTCGA 6 90 0 TAATGATTAA 0.957484 -69 AATTCAGGCGTAATGAATAAATATCGCATG 13 74 1 TAATGAATAA 0.822839 -28 GTTATAAAACTTATTATTAAGCTTACGACA 15 133 0 TTATTATTAA 0.76737 -43 GGCCCCTCTGTAATGATTAAAGGCAGTGGC 16 164 1 TAATGATTAA 0.957484 -112 TATTTATTCTTTTTGATTAATCGTATTCGA 18 14 1 TTTTGATTAA 0.878657 -93 ACTCGATTTATGATTATAATTTTAAAA 18 90 0 TTATGATTAT 0.859035 -17 ********** Masking position 6 Map Score: 3.36466 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 23 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 9 GAGTTAATCAGCTGATTTAAAACGTTTTTC 2 15 0 GCTGATTTAA 0.874934 -27 ACTCGGCGAGTTAATCAGCTGATT 2 28 0 GGCGAGTTAA 0.919151 -14 AAAGGTTGGAGGTGAGTTGA 7 39 1 GGTGAGTTGA 0.949993 -10 GATGCAGAGTTAAGGCAATGCAA 8 52 0 GCAGAGTTAA 0.899282 -13 ATGAGAGCGTGGTAATTTAATCTAACGTTT 10 20 1 GGTAATTTAA 0.885442 -86 TTGAGAGTAACGAAATTTGAAAGGAGGGTT 10 82 1 CGAAATTTGA 0.777105 -24 ATGGGGCCGCCGAGATTTGAACTCGGGTCA 16 95 1 CGAGATTTGA 0.899274 -181 GGAAATTTAAAGAATTAAAA 17 54 0 GGAAATTTAA 0.909601 -10 ********** Masking position 5 Map Score: 0.995837 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 219 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 10 ********** No masking Map Score: 9.54559e-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: 9.54559e-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 12 ********** No masking Map Score: 9.54559e-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