AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i078_Lipopolysaccharide_Biosynthesis_3_mtub_reg_300.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 0.867312 -60 TAGGGGGCCGCGCCCACCGGCGTG 2 5 0 CGCCCACCGG 0.952888 -70 TGGTGTTTCAGGGGCGCCGGTAGGAGCCGT 2 37 0 GGGGCGCCGG 0.982374 -38 AAAGTTACCGTGTGCGGCGG 3 1 0 TGTGCGGCGG 0.917238 -26 TCCTAACTGCCGTTCGCCGACC 4 3 0 CGTTCGCCGA 0.974607 -27 GCTACCCGACAGGGCGCCGTTACACAAGTA 5 18 0 AGGGCGCCGT 0.877354 -58 GCGCCCTGTCGGGTAGCCAACCCCGGCGTG 5 31 1 GGGTAGCCAA 0.727178 -45 GCACGCCTCGGGCACGCCGGGGTTGGCTAC 5 43 0 GGCACGCCGG 0.994798 -33 GCGTGCCCGAGGCGTGCCAGACTCAAACAC 5 56 1 GGCGTGCCAG 0.970772 -20 AGGAAGAGAAGGATCGCCAGAAAGTA 6 7 0 GGATCGCCAG 0.890435 -247 GCCGGAATCGGGTGCACCGACAAGGAAGAG 6 29 0 GGTGCACCGA 0.97547 -225 CCGAGCACGTGCTGCGCCGGAATCGGGTGC 6 44 0 GCTGCGCCGG 0.980231 -210 GGACTACAAACGTGAGCCGGTGGTGGAAAT 6 72 1 CGTGAGCCGG 0.983848 -182 AATTCCGCGAAGGGCTCCGAGAAATTTTCA 6 99 1 AGGGCTCCGA 0.806637 -155 TTCAAAACTGGGCACGCCAAACCGGCACGG 6 125 1 GGCACGCCAA 0.889031 -129 GGTGCGGTGTCCCGTGCCGGTTTGGCGTGC 6 136 0 CCCGTGCCGG 0.812336 -118 CGGGTAATGTGGGTTGGCGGTGCGGTGTCC 6 154 0 GGGTTGGCGG 0.922554 -100 CGCAGAGCACGGCGATGCGGGTAATGTGGG 6 171 0 GGCGATGCGG 0.872526 -83 GTAGGCCACGCGCTCACCGGAATAGCACCG 6 210 1 CGCTCACCGG 0.987129 -44 CTAACCGCTCGGCTCACCGGTGCTATTCCG 6 227 0 GGCTCACCGG 0.992848 -27 GGATCAAACCCTAACCGAGCCTTAACCG 7 55 0 CCCTAACCGA 0.487109 -18 ********** Masking position 8 Map Score: 38.6435 Number of sites scoring better than the average of aligned sites = 39382 Number in coding regions = 36626 Number in noncoding regions = 2756 Number of orfs with sites within 600 bp upstream = 1212 Fraction of orfs with sites within 600 bp upstream = 0.194668 Motif number 2 GTCTTGCGCAAGGTCTTGGGGTGACTGACCG 1 35 0 AGTCTTGGGG 0.62345 -79 GATTCCGCCGCAGTCTTGCGCAAGGTCTTGG 1 47 0 CGTCTTGCGC 0.952838 -67 GAGCCTGATTCCTTCGCATCGAGTTCC 1 97 0 GTTCCTTCGC 0.717864 -17 CCGTGGTAGGGGGCCGCGCCCACCGGCGTG 2 10 0 GGCCGCGCCC 0.707722 -65 TGGCTCCTAACTGCCGTTCGCCGACC 4 6 0 CGCCGTTCGC 0.955249 -24 TTGTGTAACGGCGCCCTGTCGGGTAGCCAAC 5 21 1 GGCCCTGTCG 0.889846 -55 TGAGTCTGGCACGCCTCGGGCACGCCGGGGT 5 50 0 AGCCTCGGGC 0.943469 -26 TAGTCCGAGCACGTGCTGCGCCGGAATCGGG 6 47 0 AGTGCTGCGC 0.87716 -207 AAATTTCTCGGAGCCCTTCGCGGAATTTCCA 6 95 0 GGCCCTTCGC 0.99151 -159 TGGCGGTGCGGTGTCCCGTGCCGGTTTGGCG 6 139 0 GGTCCCGTGC 0.973108 -115 CCGCATCGCCGTGCTCTGCGCAAAACGCCGT 6 181 1 GGCTCTGCGC 0.959889 -73 AAAACGCCGTAGGCCACGCGCTCACCGGAAT 6 202 1 AGCCACGCGC 0.96162 -52 TAGCACCGGTGAGCCGAGCGGTTAGAGCAAC 6 232 1 GGCCGAGCGG 0.945121 -22 TAACCGAGTGGAGCCGCGACCAGTTGGGTTC 7 30 0 GGCCGCGACC 0.915689 -43 * ********* Masking position 3 Map Score: 14.4072 Number of sites scoring better than the average of aligned sites = 19535 Number in coding regions = 17961 Number in noncoding regions = 1574 Number of orfs with sites within 600 bp upstream = 866 Fraction of orfs with sites within 600 bp upstream = 0.139094 Motif number 3 CACCCCAAGACCTTGCGCAAGACTGCGGCG 1 43 1 CCTTGCGCAA 0.545461 -71 CACGCCGGTGGGCGCGGCCCCCTACCA 2 8 1 GTGGGCGCGG 0.93423 -67 CCACAGTCTGGTGTTTCAGGGGCGCCGGTA 2 45 0 GTGTTTCAGG 0.478202 -30 CTGAAAGTTACCGTGTGCGGCGG 3 4 0 CCGTGTGCGG 0.990979 -23 CTCCTAACTGCCGTTCGCCGACC 4 4 0 CCGTTCGCCG 0.924051 -26 TGTAACGGCGCCCTGTCGGGTAGCCAACCC 5 24 1 CCCTGTCGGG 0.948866 -52 GCCAACCCCGGCGTGCCCGAGGCGTGCCAG 5 46 1 GCGTGCCCGA 0.981387 -30 CGTGCCCGAGGCGTGCCAGACTCAAACAC 5 57 1 GCGTGCCAGA 0.865117 -19 GTCGGTGCACCCGATTCCGGCGCAGCACGT 6 38 1 CCGATTCCGG 0.921992 -216 CCGGCGCAGCACGTGCTCGGACTACAAACG 6 54 1 ACGTGCTCGG 0.667335 -200 TTTCTCGGAGCCCTTCGCGGAATTTCCACC 6 93 0 CCCTTCGCGG 0.974165 -161 TGCCGGTTTGGCGTGCCCAGTTTTGAAAAT 6 122 0 GCGTGCCCAG 0.974652 -132 GTGCGGTGTCCCGTGCCGGTTTGGCGTGCC 6 135 0 CCGTGCCGGT 0.855246 -119 AATGTGGGTTGGCGGTGCGGTGTCCCGTGC 6 149 0 GGCGGTGCGG 0.531831 -105 CATCGCCGTGCTCTGCGCAAAACGCCGTAG 6 184 1 CTCTGCGCAA 0.607101 -70 AATAGCACCGGTGAGCCGAGCGGTTAGAGC 6 230 1 GTGAGCCGAG 0.654224 -24 TCGCAACCCTCCGTTTCGGGA 7 2 0 CCGTTTCGGG 0.954698 -71 GCGAACCCAACTGGTCGCGGCTCCACTCGG 7 28 1 CTGGTCGCGG 0.893517 -45 CGAGCCTTAACCGAGTGGAGCCGCGACCAG 7 38 0 CCGAGTGGAG 0.815188 -35 ********** Masking position 5 Map Score: 20.5336 Number of sites scoring better than the average of aligned sites = 46392 Number in coding regions = 42701 Number in noncoding regions = 3691 Number of orfs with sites within 600 bp upstream = 1378 Fraction of orfs with sites within 600 bp upstream = 0.22133 Motif number 4 TAGGAGCCGTGGTAGGGGGCCGCGCCCACC 2 17 0 GGTAGGGGGC 0.937591 -58 CAGGGGCGCCGGTAGGAGCCGTGGTAGGGG 2 29 0 GGTAGGAGCC 0.995945 -46 GCGAACGGCAGTTAGGAGCCAGTT 4 16 1 GTTAGGAGCC 0.985357 -14 GTGTTTGAGTCTGGCACGCCT 5 65 0 TGTTTGAGTC 0.766823 -11 ACCGGCTCACGTTTGTAGTCCGAGCACGTG 6 63 0 GTTTGTAGTC 0.766821 -191 TGAGCCGAGCGGTTAGAGCAACC 6 241 1 GGTTAGAGCA 0.872219 -13 AGCCTTAACCGAGTGGAGCCGCGACCAGTT 7 36 0 GAGTGGAGCC 0.941956 -37 GCTCGGTTAGGGTTTGATCC 7 63 1 GGTTTGATCC 0.923008 -10 ********** Masking position 7 Map Score: 3.83311 Number of sites scoring better than the average of aligned sites = 2898 Number in coding regions = 2636 Number in noncoding regions = 262 Number of orfs with sites within 600 bp upstream = 215 Fraction of orfs with sites within 600 bp upstream = 0.0345326 Motif number 5 GCGCAAGGTCTTGGGGTGACTGACCGAGTC 1 31 0 TTGGGGTGAC 0.866787 -83 CACGCCGGTGGGCGCGGCCCCCT 2 4 1 GCCGGTGGGC 0.981742 -71 GTCTGGTGTTTCAGGGGCGCCGGTAGGAGC 2 40 0 TCAGGGGCGC 0.958768 -35 CGGCGCCCTGTCGGGTAGCCAACCCCGGCG 5 29 1 TCGGGTAGCC 0.95363 -47 CTGGCACGCCTCGGGCACGCCGGGGTTGGC 5 46 0 TCGGGCACGC 0.969622 -30 TGCGCCGGAATCGGGTGCACCGACAAGGAA 6 32 0 TCGGGTGCAC 0.986372 -222 TGCGGGTAATGTGGGTTGGCGGTGCGGTGT 6 156 0 GTGGGTTGGC 0.960799 -98 CCGGTGCTATTCCGGTGAGCGCGTGGCCTA 6 211 0 TCCGGTGAGC 0.955483 -43 CCGCGACCAGTTGGGTTCGCAACCCTCCGT 7 18 0 TTGGGTTCGC 0.980479 -55 ********** Masking position 10 Map Score: 10.2568 Number of sites scoring better than the average of aligned sites = 4938 Number in coding regions = 4531 Number in noncoding regions = 407 Number of orfs with sites within 600 bp upstream = 348 Fraction of orfs with sites within 600 bp upstream = 0.0558946 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 Motif number 8 ********** 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