AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i078_ecoli_mtub_300.orf -o078_ecoli_mtub_300.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -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 = 0.58 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 rfbA 57 glucose-1-phosphate thymidylyltransferase #2 rfbB 300 dTDP-glucose 4,6 dehydratase #3 trxA 76 thioredoxin 1 #4 rhoL 140 rho operon leader peptide #5 rho 84 transcription termination factor Rho; polarity suppressor #6 rfe 239 UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase; synthesis of enterobacterial common antigen (ECA) #7 Rv0331 113 hypothetical protein Rv0331 #8 Rv0332 74 hypothetical protein Rv0332 #9 Rv0333 26 hypothetical protein Rv0333 #10 rmlA 29 rmlA #11 rmlD 75 rmlD #12 Rv3463 253 hypothetical protein Rv3463 #13 rmlB 72 rmlB Motif number 1 TTACAGCTACCAGAGCACTGCATGCATGCCT 2 186 0 CAGGCACTGC 0.821488 -115 ATTAATCAAACTGAGAGCCGCTTATTTCACA 2 249 1 CTGGAGCCGC 0.967138 -52 TTTTTAGCGACGGGGCACCCGAACATGAAAT 4 15 0 CGGGCACCCG 0.938775 -126 TCGCTAAAAACTGGACGCCCGGCGTGAGTCA 4 36 1 CTGACGCCCG 0.909862 -105 CACGCCGGTGGGCGCGGCCCCCTACC 8 6 1 CGGGGGCGCG 0.96735 -69 CTGGTGTTTCAGGGGCGCCGGTAGGAGCCGT 8 37 0 AGGGCGCCGG 0.979533 -38 CTGAAAGTTACCGTGTGCGGCGG 9 3 0 CCGGTGCGGC 0.938686 -24 GGTCGGCGAACGGCAGTTAGGAGC 10 4 1 CGGGAACGGC 0.97876 -26 GGCTACCCGACAGGGCGCCGTTACACAAGTA 11 18 0 CAGGCGCCGT 0.910887 -58 TAGCCAACCCCGGCGTGCCCGAGGCGTGCCA 11 44 1 CGGGTGCCCG 0.977528 -32 TCTTCCTTGTCGGTGCACCCGATTCCGGCGC 12 30 1 CGGGCACCCG 0.994664 -224 CGTTTGTAGTCCGAGCACGTGCTGCGCCGGA 12 53 0 CCGGCACGTG 0.868236 -201 CGGACTACAAACGTGAGCCGGTGGTGGAAAT 12 71 1 ACGGAGCCGG 0.784569 -183 ATTTTCAAAACTGGGCACGCCAAACCGGCAC 12 122 1 CTGGCACGCC 0.97517 -132 CAAACCGGCACGGGACACCGCACCGCCAACC 12 142 1 CGGACACCGC 0.960792 -112 GCGTTTTGCGCAGAGCACGGCGATGCGGGTA 12 178 0 CAGGCACGGC 0.979141 -76 GGTGCTATTCCGGTGAGCGCGTGGCCTACGG 12 208 0 CGGGAGCGCG 0.985026 -46 TCTAACCGCTCGGCTCACCGGTGCTATTCCG 12 227 0 CGGTCACCGG 0.962116 -27 GCGAACCCAACTGGTCGCGGCTCCACTCGGT 13 28 1 CTGTCGCGGC 0.910505 -45 *** ******* Masking position 8 Map Score: 32.6094 Number of sites scoring better than the average of aligned sites = 3399 Number in coding regions = 3293 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 2 TATATAAAACAACGGCAGGAAGATTCGCAA 2 13 0 AACGGCAGGA 0.826926 -288 TGGTAGCTGTAAAGCCAGGGGCGGTAGCGT 2 205 1 AAAGCCAGGG 0.854827 -96 TCCAGTTTTTAGCGACGGGGCACCCGAACA 4 21 0 AGCGACGGGG 0.867531 -120 TAGCATGACTCACGCCGGGCGTCCAGTTTT 4 42 0 CACGCCGGGC 0.939774 -99 TTATGCCAAAAACGCCACGTGTTTACGTGG 6 18 1 AACGCCACGT 0.929225 -222 ATAAAAGCAAAACGCCACGTAAACACGTGG 6 32 0 AACGCCACGT 0.929225 -208 CACGCCGGTGGGCGCGGCCC 8 1 1 CACGCCGGTG 0.95689 -74 GGTCGGCGAACGGCAGTTAGGAGCCAGT 10 9 1 AACGGCAGTT 0.667146 -21 GGGTTGGCTACCCGACAGGGCGCCGTTACA 11 24 0 CCCGACAGGG 0.97251 -52 ACGCCTCGGGCACGCCGGGGTTGGCTACCC 11 41 0 CACGCCGGGG 0.992519 -35 TTGAGTCTGGCACGCCTCGGGCACGCCGGG 11 52 0 CACGCCTCGG 0.929075 -24 AATCGGGTGCACCGACAAGGAAGAGAAGGA 12 24 0 ACCGACAAGG 0.814217 -230 GGCACGCCAAACCGGCACGGGACACCGCAC 12 135 1 ACCGGCACGG 0.962179 -119 TTGCGCAGAGCACGGCGATGCGGGTAATGT 12 174 0 CACGGCGATG 0.691326 -80 TCCCGAAACGGAGGGTTGCGA 13 2 1 CCCGAAACGG 0.56203 -71 ********** Masking position 4 Map Score: 14.5267 Number of sites scoring better than the average of aligned sites = 3798 Number in coding regions = 3626 Number in noncoding regions = 172 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 3 TTACCAATCCGCTCTGGAAACAAGGAAAATC 2 96 0 GCTTGGAAAC 0.944967 -205 AAGACAATTAGCGTTTGAATTTTTCGGGTTT 2 125 1 GCGTTGAATT 0.873973 -176 AAAACGGGAAGCGTTGGAAATTACAAGATTC 4 113 0 GCGTGGAAAT 0.977472 -28 AAAGCAAAACGCCACGTAAACACGTGGCGTT 6 28 0 GCCCGTAAAC 0.879273 -212 GCGCAAGACTGCGGCGGAATCTAATATTCCA 7 57 1 GCGCGGAATC 0.994166 -57 GGAACTCGATGCGAAGGAATCAGGCTC 7 97 1 GCGAGGAATC 0.970291 -17 TCCTACCGGCGCCCCTGAAACACCAGACTGT 8 42 1 GCCCTGAAAC 0.936013 -33 AGCACGTGCTGCGCCGGAATCGGGTGCACCG 12 40 0 GCGCGGAATC 0.994166 -214 ACGTGAGCCGGTGGTGGAAATTCCGCGAAGG 12 81 1 GTGTGGAAAT 0.809653 -173 *** ******* Masking position 8 Map Score: 9.17163 Number of sites scoring better than the average of aligned sites = 1052 Number in coding regions = 1018 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 4 GTTACCCACTCGCGCTAAACCCGAAAAATTCA 2 140 0 CGGCAAACCC 0.987895 -161 TATGATGTGACGAGCGTTACCCACTCGCGCTA 2 155 0 CGGCTTACCC 0.996372 -146 GGGGCGGTAGCGTGCATTAATACCTCTATTAA 2 222 1 CGGCTTAATA 0.677117 -79 CATGGATGATCCTGCCATACCATTCACAACAT 5 22 1 CCGCATACCA 0.930416 -63 ACATTAAGTTCGAGATTTACCCCAAGTTTAAG 5 50 1 CGGATTACCC 0.96419 -35 AGGGAAAGTCCGTTCCAAACCCACCAGTCCTG 6 158 0 CGTCAAACCC 0.901123 -82 GTGCCCGAGGCGTGCCAGACTCAAACAC 11 58 1 CGGCAGACTC 0.931071 -18 GCACCGCCAACCCACATTACCCGCATCGCCGT 12 161 1 CCACTTACCC 0.903308 -93 AAACCCTAACCGAGCCTTAACCGAGTGGAGCC 13 46 0 CGGCTTAACC 0.981846 -27 ** ** ****** Masking position 9 Map Score: 6.45852 Number of sites scoring better than the average of aligned sites = 691 Number in coding regions = 648 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 5 TGTTGCGAATCTTCCTGCCGTTGTTTT 2 7 1 GAATTTCCTG 0.970924 -294 CTGGAAACAAGGAAAATCCTGGAAAACTTTG 2 83 0 GGAAATCCTG 0.986883 -218 GGGAATTTCATGTTCGGGTGCC 4 2 1 GGAATTCATG 0.953829 -139 AAACAGGCATGGATGATCCTGCCATACCATT 5 15 1 GGATATCCTG 0.981311 -70 GCGATGTTAGGAAAATTCCTGGAATTTGCTG 6 86 1 GAAATTCCTG 0.979528 -154 **** ****** Masking position 7 Map Score: 2.87967 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 101 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 6 ACTTCAGAGCATGCTGTGAAATAAGCGGCT 2 264 0 ATGCTGTGAA 0.79368 -37 CTCGAACTTAATGTTGTGAATGGTATGGCA 5 34 0 ATGTTGTGAA 0.741371 -51 ATTTGTCTTATGCCAAAAACGCCA 6 5 1 GTCTTATGCC 0.819166 -235 ATTTGCTGGCATGTTATGCAATTTGCATAT 6 109 1 ATGTTATGCA 0.640654 -131 AAACCCACCAGTCCTGTGCAAAAATTAACC 6 144 0 GTCCTGTGCA 0.97697 -96 TTCCGCCGCAGTCTTGCGCAAGGTCTTGGG 7 46 0 GTCTTGCGCA 0.97697 -68 CCGTGGTAGGGGGCCGCGCCCACCGGCGTG 8 11 0 GGGCCGCGCC 0.920408 -64 GTCCGAGCACGTGCTGCGCCGGAATCGGGT 12 46 0 GTGCTGCGCC 0.987444 -208 GCGGTGCGGTGTCCCGTGCCGGTTTGGCGT 12 138 0 GTCCCGTGCC 0.935963 -116 GGCCTACGGCGTTTTGCGCAGAGCACGGCG 12 187 0 GTTTTGCGCA 0.890497 -67 CCGAAACGGAGGGTTGCGAACCCAACTGGT 13 13 1 GGGTTGCGAA 0.856327 -60 ********** Masking position 8 Map Score: 5.69018 Number of sites scoring better than the average of aligned sites = 2655 Number in coding regions = 2500 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 7 TTCGGGTTTAGCGCGAGTGGGTAACGCTCGT 2 147 1 GCCGAGTGGG 0.925541 -154 TGCATGCAGTGCTCTGGTAGCTGTAAAGCCA 2 191 1 GCCTGGTAGC 0.974726 -110 TGTAAAGCCAGGGGCGGTAGCGTGCATTAAT 2 212 1 GGGCGGTAGC 0.83622 -89 TGTTGTGAATGGTATGGCAGGATCATCCATG 5 22 0 GGATGGCAGG 0.771527 -63 TGCCGCGCTGGCGATGTTAGGAAAATTCCTG 6 76 1 GCATGTTAGG 0.871756 -164 TTTTTGCACAGGACTGGTGGGTTTGGAACGG 6 150 1 GGCTGGTGGG 0.986231 -90 CACGCCGGTGGGCGCGGCCCCC 8 2 1 ACCCGGTGGG 0.942286 -73 GCCGGTAGGAGCCGTGGTAGGGGGCCGCGCC 8 21 0 GCGTGGTAGG 0.987156 -54 TGTTTCAGGGGCGCCGGTAGGAGCCGTGGTA 8 33 0 GCCCGGTAGG 0.995347 -42 GTGTAACGGCGCCCTGTCGGGTAGCCAACCC 11 23 1 GCCTGTCGGG 0.935026 -53 CCTCGGGCACGCCGGGGTTGGCTACCCGACA 11 37 0 GCGGGGTTGG 0.919159 -39 CACCGGAATAGCACCGGTGAGCCGAGCGGTT 12 224 1 GCCCGGTGAG 0.942286 -30 CTCGGTTAAGGCTCGGTTAGGGTTTGATCC 13 53 1 GCCGGTTAGG 0.970091 -20 ** ******** Masking position 6 Map Score: 17.2087 Number of sites scoring better than the average of aligned sites = 1749 Number in coding regions = 1670 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 8 TCTATTAATCAAACTGAGAGCCGCTTATTT 2 246 1 AAACTGAGAG 0.923873 -55 CCGTCGCTAAAAACTGGACGCCCGGCGTGA 4 33 1 AAACTGGACG 0.964719 -108 TTAAGATAAAACGGGAAGCGTTGGAAAT 4 123 0 AAACGGGAAG 0.936124 -18 GTGAGTTCTTAAACTTGGGGTAAATCTCGA 5 59 0 AAACTTGGGG 0.949424 -26 CGCCACGTAAACACGTGGCGTTTTTGGCAT 6 20 0 ACACGTGGCG 0.910397 -220 GAAATTTTCAAAACTGGGCACGCCAAACCG 12 119 1 AAACTGGGCA 0.928579 -135 TCCCGAAACGGAGGGTTGCGAACCC 13 6 1 AAACGGAGGG 0.957751 -67 ********** Masking position 3 Map Score: 1.97348 Number of sites scoring better than the average of aligned sites = 771 Number in coding regions = 704 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 9 TCACATCATAGGCATGCATGCAGTGCTCTG 2 177 1 GGCATGCATG 0.986842 -124 CAGGGGCGGTAGCGTGCATTAATACCTCTA 2 220 1 AGCGTGCATT 0.955018 -81 CTTATTTCACAGCATGCTCTGAAGTAATAT 2 269 1 AGCATGCTCT 0.815848 -32 CCGTAAACAGGCATGGATGATCCTGCCAT 5 10 1 GGCATGGATG 0.935141 -75 TTTCTCTGAGAGCATGCATT 6 230 1 AGCATGCATT 0.946184 -10 AGCCAACCCCGGCGTGCCCGAGGCGTGCCA 11 45 1 GGCGTGCCCG 0.984189 -31 GCGTGCCCGAGGCGTGCCAGACTCAAACAC 11 56 1 GGCGTGCCAG 0.958021 -20 ********** Masking position 5 Map Score: 4.29308 Number of sites scoring better than the average of aligned sites = 432 Number in coding regions = 412 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 10 ********** No masking Map Score: -9.4259e-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: -9.4259e-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: -9.4259e-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