AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i078_Lipopolysaccharide_Biosynthesis_3_mtub_reg_100.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -x5 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 = 0.66 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 Rv0331 113 hypothetical protein Rv0331 #2 Rv0332 74 hypothetical protein Rv0332 #3 Rv0333 26 hypothetical protein Rv0333 #4 rmlA 29 rmlA #5 rmlD 75 rmlD #6 Rv3463 253 hypothetical protein Rv3463 #7 rmlB 72 rmlB Motif number 1 CTTGCGCAAGACTGCGGCGGAATCTAATAT 1 54 1 ACTGCGGCGG 0.905662 -60 TAGGGGGCCGCGCCCACCGGCGTG 2 5 0 CGCCCACCGG 0.947633 -70 TGGTGTTTCAGGGGCGCCGGTAGGAGCCGT 2 37 0 GGGGCGCCGG 0.981886 -38 AAAGTTACCGTGTGCGGCGG 3 1 0 TGTGCGGCGG 0.943995 -26 TCCTAACTGCCGTTCGCCGACC 4 3 0 CGTTCGCCGA 0.979226 -27 GCTACCCGACAGGGCGCCGTTACACAAGTA 5 18 0 AGGGCGCCGT 0.912648 -58 GCGCCCTGTCGGGTAGCCAACCCCGGCGTG 5 31 1 GGGTAGCCAA 0.654068 -45 GCACGCCTCGGGCACGCCGGGGTTGGCTAC 5 43 0 GGCACGCCGG 0.997157 -33 GCGTGCCCGAGGCGTGCCAGACTCAAACAC 5 56 1 GGCGTGCCAG 0.97463 -20 AGGAAGAGAAGGATCGCCAGAAAGTA 6 7 0 GGATCGCCAG 0.914552 -247 GCCGGAATCGGGTGCACCGACAAGGAAGAG 6 29 0 GGTGCACCGA 0.976982 -225 CCGAGCACGTGCTGCGCCGGAATCGGGTGC 6 44 0 GCTGCGCCGG 0.979744 -210 GGACTACAAACGTGAGCCGGTGGTGGAAAT 6 72 1 CGTGAGCCGG 0.974721 -182 AATTCCGCGAAGGGCTCCGAGAAATTTTCA 6 99 1 AGGGCTCCGA 0.816919 -155 TTCAAAACTGGGCACGCCAAACCGGCACGG 6 125 1 GGCACGCCAA 0.943795 -129 GGTGCGGTGTCCCGTGCCGGTTTGGCGTGC 6 136 0 CCCGTGCCGG 0.8348 -118 CGGGTAATGTGGGTTGGCGGTGCGGTGTCC 6 154 0 GGGTTGGCGG 0.936123 -100 TTTTGCGCAGAGCACGGCGATGCGGGTAAT 6 176 0 AGCACGGCGA 0.873492 -78 GTAGGCCACGCGCTCACCGGAATAGCACCG 6 210 1 CGCTCACCGG 0.983389 -44 CTAACCGCTCGGCTCACCGGTGCTATTCCG 6 227 0 GGCTCACCGG 0.991479 -27 ********** Masking position 8 Map Score: 38.8312 Number of sites scoring better than the average of aligned sites = 33561 Number in coding regions = 31254 Number in noncoding regions = 2307 Number of orfs with sites within 600 bp upstream = 1118 Fraction of orfs with sites within 600 bp upstream = 0.17957 Motif number 2 AAGATATATGGAACTCGATGCGAAGGAATCAG 1 88 1 GAACTCGGCG 0.797207 -26 GAGCCTGATTCCTTCGCATCGA 1 102 0 GAGCCTGTCC 0.944362 -12 CACGCCGGTGGGCGCGGCCCCCTACCACGGC 2 10 1 GGGCGCGCCC 0.772379 -65 GCGCCGGTAGGAGCCGTGGTAGGGGGCCGCGC 2 22 0 GAGCCGTTAG 0.88977 -53 ACCACGGCTCCTACCGGCGCCCCTGAAACACC 2 34 1 CTACCGGCCC 0.740175 -41 CAGCGGTTATCCACAGTCTGGT 2 63 0 CAGCGGTTCC 0.906191 -12 TGGCTCCTAACTGCCGTTCGCCGACC 4 5 0 CTGCCGTGCC 0.962117 -25 TTGTGTAACGGCGCCCTGTCGGGTAGCCAACC 5 21 1 GCGCCCTCGG 0.807084 -55 CAACCCCGGCGTGCCCGAGGCGTGCCAGACTC 5 48 1 GTGCCCGGCG 0.990696 -28 AGCACGTGCTGCGCCGGAATCGGGTGCACCGA 6 39 0 GCGCCGGTCG 0.980426 -215 CTACAAACGTGAGCCGGTGGTGGAAATTCCGC 6 75 1 GAGCCGGGTG 0.958494 -179 AAATTTCTCGGAGCCCTTCGCGGAATTTCCAC 6 94 0 GAGCCCTGCG 0.99285 -160 GCGGTGTCCCGTGCCGGTTTGGCGTGCCCAGT 6 131 0 GTGCCGGTGG 0.919938 -123 TGGGTTGGCGGTGCGGTGTCCCGTGCCGGTTT 6 143 0 GTGCGGTCCC 0.955917 -111 GCGTGGCCTACGGCGTTTTGCGCAGAGCACGG 6 189 0 CGGCGTTGCG 0.76139 -65 CTATTCCGGTGAGCGCGTGGCCTACGGCGTTT 6 203 0 GAGCGCGGCC 0.987472 -51 CCGGTGAGCCGAGCGGTTAGAGCAACC 6 237 1 GAGCGGTGAG 0.926556 -17 GTTGCGAACCCAACTGGTCGCGGCTCCACTCG 7 25 1 CAACTGGGCG 0.703 -48 AACCCTAACCGAGCCTTAACCGAGTGGAGCCG 7 45 0 GAGCCTTCCG 0.962546 -28 ******* *** Masking position 4 Map Score: 26.6917 Number of sites scoring better than the average of aligned sites = 39546 Number in coding regions = 37047 Number in noncoding regions = 2499 Number of orfs with sites within 600 bp upstream = 1153 Fraction of orfs with sites within 600 bp upstream = 0.185191 Motif number 3 TGGTAGGGGGCCGCGCCCACCGGCGTG 2 8 0 CCGCGCCCAC 0.962733 -67 GCCGGGGTTGGCTACCCGACAGGGCGCCGT 5 28 0 GCTACCCGAC 0.760207 -48 CCCGGCGTGCCCGAGGCGTGCCAGACTCAA 5 52 1 CCGAGGCGTG 0.956124 -24 TGCCGGTTTGGCGTGCCCAGTTTTGAAAAT 6 122 0 GCGTGCCCAG 0.991444 -132 TGGCGGTGCGGTGTCCCGTGCCGGTTTGGC 6 140 0 GTGTCCCGTG 0.807693 -114 ACCCGCATCGCCGTGCTCTGCGCAAAACGC 6 179 1 CCGTGCTCTG 0.815707 -75 TCCGGTGAGCGCGTGGCCTACGGCGTTTTG 6 201 0 GCGTGGCCTA 0.720145 -53 AATAGCACCGGTGAGCCGAGCGGTTAGAGC 6 230 1 GTGAGCCGAG 0.974214 -24 ACGGAGGGTTGCGAACCCAACTGGTCGCGG 7 18 1 GCGAACCCAA 0.895839 -55 CCGAGTGGAGCCGCGACCAGTTGGGTTCGC 7 28 0 CCGCGACCAG 0.897127 -45 CTAACCGAGCCTTAACCGAGTGGAGCCGCG 7 43 0 CTTAACCGAG 0.707982 -30 GGATCAAACCCTAACCGAGCCTTAACCGA 7 54 0 CCTAACCGAG 0.916547 -19 ********** Masking position 7 Map Score: 6.96495 Number of sites scoring better than the average of aligned sites = 22024 Number in coding regions = 20256 Number in noncoding regions = 1768 Number of orfs with sites within 600 bp upstream = 1012 Fraction of orfs with sites within 600 bp upstream = 0.162544 Motif number 4 TTCCGCCGCAGTCTTGCGCAAGGTCTTGGG 1 46 0 GTCTTGCGCA 0.970518 -68 GGTCGGCGAACGGCAGTTAG 4 1 1 GGTCGGCGAA 0.883078 -29 GCGCCCTGTCGGGTAGCCAACCCCGGCGTG 5 31 1 GGGTAGCCAA 0.868724 -45 GTCCGAGCACGTGCTGCGCCGGAATCGGGT 6 46 0 GTGCTGCGCC 0.909758 -208 GGCGTGCCCAGTTTTGAAAATTTCTCGGAG 6 113 0 GTTTTGAAAA 0.371547 -141 GTGCCGGTTTGGCGTGCCCAGTTTTGAAAA 6 123 0 GGCGTGCCCA 0.929999 -131 GGCCTACGGCGTTTTGCGCAGAGCACGGCG 6 187 0 GTTTTGCGCA 0.983099 -67 GTGCTATTCCGGTGAGCGCGTGGCCTACGG 6 208 0 GGTGAGCGCG 0.891143 -46 TGAGCCGAGCGGTTAGAGCAACC 6 241 1 GGTTAGAGCA 0.946682 -13 CCGAAACGGAGGGTTGCGAACCCAACTGGT 7 13 1 GGGTTGCGAA 0.979579 -60 GCTCGGTTAGGGTTTGATCC 7 63 1 GGTTTGATCC 0.653129 -10 ********** Masking position 6 Map Score: 4.72892 Number of sites scoring better than the average of aligned sites = 9497 Number in coding regions = 8730 Number in noncoding regions = 767 Number of orfs with sites within 600 bp upstream = 580 Fraction of orfs with sites within 600 bp upstream = 0.0931577 Motif number 5 ********** No masking Map Score: 1.45904e-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 6 ********** No masking Map Score: 1.45904e-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 7 ********** No masking Map Score: 1.45904e-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