AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00670_ctra_reg_100.orf -o00670_ctra_100.ace -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -g0.41 -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 = 0.41 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 folD 117 Methylene Tetrahydrofolate Dehydrogenase #2 glyA 300 Serine Hydroxymethyltransferase #3 lpxC 100 UDP-3-O-Acyl GlcNAc Deacetylase #4 rpoD 148 RNA Polymerase Sigma-66 Motif number 1 AAGCTTTTTTCCTAGTAGGAAGCTT 2 6 1 TTTTTCCTAG 0.993975 -295 AAGCGCCCCATTTTCCCTAGTCGCTTACCA 2 95 0 TTTTCCCTAG 0.987752 -206 GCATCGTTTCTTTTTCTTATAGTTATAGTT 2 141 1 TTTTTCTTAT 0.967008 -160 ATAAATCCTCTTTCTCCTAGAAAGTTTAGA 2 174 1 TTTCTCCTAG 0.974714 -127 TTATCCTTTTTTTTTTTTAGCAAGCAAGCG 3 52 0 TTTTTTTTAG 0.976744 -49 GACGGGAGGGGTTTTTCTAGGCCTAAATCT 4 25 1 GTTTTTCTAG 0.92665 -124 ATCAACAGGCTTTTTTTTATCTAAAAATCC 4 56 1 TTTTTTTTAT 0.905715 -93 AGATTTCTTGTTTTTCTTAAGATAAACTGT 4 88 1 TTTTTCTTAA 0.943252 -61 CTAGGCCGATTTTTCCTTAGTTTTAATTTG 4 124 1 TTTTCCTTAG 0.984286 -25 ********** Masking position 3 Map Score: 15.1939 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 111 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 2 TTTTGTAAACTGATCAAGAGAGGTCTAGAC 1 48 1 TGATCAAGAG 0.99066 -70 TGTAAGAATATGATCAACTGAAGCTGCAAT 2 48 1 TGATCAACTG 0.972323 -253 AAACTTTCTAGGAGAAAGAGGATTTATTTT 2 171 0 GGAGAAAGAG 0.963803 -130 AGTGGGTAGAGGATAAAGAGTGCCTCTGCA 2 246 1 GGATAAAGAG 0.986454 -55 GCAAAACCCTGACAAAGAGACCCCGTATA 3 82 0 TGACAAAGAG 0.969804 -19 GGCCTAAATCTGATCAACAGGCTTTTTTTT 4 44 1 TGATCAACAG 0.987768 -105 GTTTTTCTTAAGATAAACTGTCACTTTCTA 4 97 1 AGATAAACTG 0.898397 -52 ********** Masking position 6 Map Score: 9.14399 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 65 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 3 AAGAAGCTTCCTACTAGGAAAAAAGCTT 2 9 0 CTACTAGGAA 0.936908 -292 TTATGGTAAGCGACTAGGGAAAATGGGGCG 2 92 1 CGACTAGGGA 0.94824 -209 GCTTGGTAATGGTCTTGGAAGCATCGTTTC 2 121 1 GGTCTTGGAA 0.971346 -180 AATCCTCTTTCTCCTAGAAAGTTTAGACTT 2 177 1 CTCCTAGAAA 0.922512 -124 GCCTCTGCAAGGTCTTGCAAGGTTTAATCA 2 267 1 GGTCTTGCAA 0.927 -34 ATCAGATTTAGGCCTAGAAAAACCCCTCCC 4 28 0 GGCCTAGAAA 0.98917 -121 AGGAAAAATCGGCCTAGAAAGTGACAGTTT 4 111 0 GGCCTAGAAA 0.98917 -38 ********** Masking position 10 Map Score: 6.45664 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 62 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 4 CAAGAGAGGTCTAGACTCTTTCCCTCTAAACA 1 62 1 CTAGACCTTC 0.990547 -56 CAGCAAAAGTCAAGAAGCTTCCTACTAGGAAA 2 18 0 CAAGAACTTC 0.968988 -283 TAAGGTGCTTTAATACCATTGCAGCTTCAGTT 2 63 0 TAATACATTC 0.774527 -238 CCCATTTTCCCTAGTCGCTTACCATAAGGTGC 2 87 0 CTAGTCCTTC 0.956037 -214 ACGATGCTTCCAAGACCATTACCAAGCGCCCC 2 116 0 CAAGACATTC 0.98501 -185 TACCTAGTTCTAAAACACTTGCTATC 3 5 0 TAAAACCTTC 0.956905 -96 GCAAAACCCTGACAAAGAGACCC 3 88 0 CAAAACCTGC 0.961606 -13 ****** *** * Masking position 3 Map Score: 4.45377 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 83 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 5 TTCTCTTTCAGTCTTCTAGTTT 1 3 1 CTCTTTCAGT 0.955443 -115 GAGGTCTAGACTCTTTCCCTCTAAACAACC 1 67 1 CTCTTTCCCT 0.9831 -51 AATACCATTGCAGCTTCAGTTGATCATATT 2 54 0 CAGCTTCAGT 0.917204 -247 CCAAGCGCCCCATTTTCCCTAGTCGCTTAC 2 97 0 CATTTTCCCT 0.943791 -204 ATCCTCTACCCACTCTCCCTTATCCTTTAT 2 230 0 CACTCTCCCT 0.970927 -71 ATTTCCACCTCCACTGATTAAACCT 2 286 0 CACCTCCACT 0.977118 -15 CCTAGAAAAACCCCTCCCGTCTTTTCTACT 4 16 0 CCCCTCCCGT 0.967999 -133 ********** Masking position 10 Map Score: 4.12001 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 166 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 6 TCAGCTTTTGTAAACTGATCAAGAGAGGTC 1 43 1 TAAACTGATC 0.95397 -75 TTTGCTGTAAGAATATGATCAACTGAAGCT 2 43 1 GAATATGATC 0.96871 -258 TCCTTTATGGGAATCTAATCTTTTGATGAG 2 208 0 GAATCTAATC 0.969685 -93 TTCTAGGCCTAAATCTGATCAACAGGCTTT 4 39 1 AAATCTGATC 0.981249 -110 ********** Masking position 6 Map Score: 0.992817 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 26 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 GAGTCTAGACCTCTCTTGATCAGTTTACAA 1 50 0 CTCTCTTGAT 0.959666 -68 TGGGAATCTAATCTTTTGATGAGAAAGTCT 2 201 0 ATCTTTTGAT 0.975466 -100 CTAGGTAGTAATTTTTTGATATCGCTTGCT 3 30 1 ATTTTTTGAT 0.978387 -71 AAATCTAGGGATTTTTAGATAAAAAAAAGC 4 64 0 ATTTTTAGAT 0.929979 -85 AAATCCCTAGATTTCTTGTTTTTCTTAAGA 4 80 1 ATTTCTTGTT 0.93739 -69 ********** Masking position 6 Map Score: 2.62662 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 40 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 CTTTCAGTCTTCTAGTTTTAAAAATTCATC 1 15 1 TCTAGTTTTA 0.949119 -103 GCACAAATACTTAGTTAAATGGTTTCACA 1 99 0 CTTAGTTAAA 0.913898 -19 TTCTTTTTCTTATAGTTATAGTTAAAATAA 2 148 1 TATAGTTATA 0.81858 -153 AAAATTACTACCTAGTTCTAAAACACTTGC 3 15 0 CCTAGTTCTA 0.957639 -86 TCTAGGGATTTTTAGATAAAAAAAAGCCTG 4 61 0 TTTAGATAAA 0.68651 -88 TCTAAAAATCCCTAGATTTCTTGTTTTTCT 4 75 1 CCTAGATTTC 0.837633 -74 CCGATTTTTCCTTAGTTTTAATTTGTCAGC 4 129 1 CTTAGTTTTA 0.960793 -20 ********** Masking position 4 Map Score: 0.940256 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 71 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: 1.80721e-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 10 ********** No masking Map Score: 1.80721e-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 11 ********** No masking Map Score: 1.80721e-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