AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i030_ecoli_mtub_100.orf -o030_ecoli_mtub_100.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 glpD 189 sn-glycerol-3-phosphate dehydrogenase (aerobic) #2 glpK 22 glycerol kinase #3 glpF 300 facilitated diffusion of glycerol #4 lpdA 202 lpdA #5 glpK 49 glpK #6 Rv3697c 250 hypothetical protein Rv3697c Motif number 1 GTAATCTGCAAGGCGTGCCGC 3 2 0 AGGCGTGCCG 0.548905 -299 CGATGCTTGTAGGCATGCTGTAAACTTATC 3 226 0 AGGCATGCTG 0.768359 -75 TACCACCCGAGCCCCCGCCGTCTAAGCTTT 4 16 0 GCCCCCGCCG 0.965247 -187 GTACCCATCGCGCCGCGCTGCGGTGCGGGT 4 43 1 CGCCGCGCTG 0.954482 -160 CTTGACGATGACCCGCACCGCAGCGCGGCG 4 53 0 ACCCGCACCG 0.905526 -150 TGCGGGTCATCGTCAAGCTGTGCTTGACTG 4 66 1 CGTCAAGCTG 0.939312 -137 CGTGAGGAGGAGCCGAGCAGTCAAGCACAG 4 83 0 AGCCGAGCAG 0.988357 -120 CTCGGCTCCTCCTCACGCCGCTGCGCGGCG 4 96 1 CCTCACGCCG 0.949539 -107 CGACGATGCACGCCGCGCAGCGGCGTGAGG 4 106 0 CGCCGCGCAG 0.953703 -97 CGTGCATCGTCGCCGAGCTGTGTTGGACTG 4 124 1 CGCCGAGCTG 0.99596 -79 CGTGAGGAGGAGCCGAGCAGTCCAACACAG 4 141 0 AGCCGAGCAG 0.988357 -62 CTCGGCTCCTCCTCACGCCGCTGCGCGGCG 4 154 1 CCTCACGCCG 0.949539 -49 CGACGATGCACGCCGCGCAGCGGCGTGAGG 4 164 0 CGCCGCGCAG 0.953703 -39 CGTGCATCGTCGCCGAGCTAGGTTATGGGC 4 182 1 CGCCGAGCTA 0.934006 -21 CGGCGTCGGACCCGCCGCTGCGGTGGACCA 5 11 1 CCCGCCGCTG 0.87438 -39 CGTCGTTTCAACGCCCGCAGTATGTCGTCA 6 63 0 ACGCCCGCAG 0.917865 -188 GTTTTGCGCTCCTCGCGCTGGCGTCGTTTC 6 84 0 CCTCGCGCTG 0.988222 -167 AGCAATTCGGAGGCGAGCTGCCCTAACGTT 6 111 0 AGGCGAGCTG 0.976888 -140 AAGCTCTGGCGGCCGAGCCTCCTCCAAACG 6 146 1 GGCCGAGCCT 0.786935 -105 ********** Masking position 8 Map Score: 41.8287 Number of sites scoring better than the average of aligned sites = 5521 Number in coding regions = 5341 Number in noncoding regions = 180 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 2 GCGGCACGCCTTGCAGATTACGGTT 3 5 1 CACGCCTGCA 0.857073 -296 CACCCGAGCCCCCGCCGTCTAAGCTTTCCCC 4 12 0 CCCGCCGCTA 0.897657 -191 ACGGCGGGGGCTCGGGTGGTACCCATCGCGC 4 25 1 CTCGGGTGTA 0.931512 -178 TGACCCGCACCGCAGCGCGGCGCGATGGGTA 4 44 0 CGCAGCGGGC 0.873076 -159 TGCTTGACTGCTCGGCTCCTCCTCACGCCGC 4 86 1 CTCGGCTCTC 0.977921 -117 CACGCCGCTGCGCGGCGTGCATCGTCGCCGA 4 109 1 CGCGGCGGCA 0.988694 -94 TCCAACACAGCTCGGCGACGATGCACGCCGC 4 120 0 CTCGGCGCGA 0.996349 -83 TGTTGGACTGCTCGGCTCCTCCTCACGCCGC 4 144 1 CTCGGCTCTC 0.977921 -59 CACGCCGCTGCGCGGCGTGCATCGTCGCCGA 4 167 1 CGCGGCGGCA 0.988694 -36 CATAACCTAGCTCGGCGACGATGCACGCCGC 4 178 0 CTCGGCGCGA 0.996349 -25 CCACCGCAGCGGCGGGTCCGACGCCG 5 6 0 GGCGGGTCGA 0.791295 -44 TTTTGCGCTCCTCGCGCTGGCGTCGTTTCAA 6 82 0 CTCGCGCGGC 0.865577 -169 GTTAGGGCAGCTCGCCTCCGAATTGCTTGCG 6 114 1 CTCGCCTCGA 0.982131 -137 TTGGAGGAGGCTCGGCCGCCAGAGCTTGCGC 6 142 0 CTCGGCCCCA 0.979772 -109 TCAAGATCCACACGGGGCCGCAAGTCGGCAG 6 194 0 CACGGGGCGC 0.958842 -57 ******* *** Masking position 3 Map Score: 25.0387 Number of sites scoring better than the average of aligned sites = 2861 Number in coding regions = 2761 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 3 CGCACAGTTTACGTCGAAGCGGCAGATAAACG 1 49 1 ACGTCGAGCG 0.765611 -141 GCTAATATGTTCGATAACGAACATTTATGAGC 1 143 1 TCGATAAGAC 0.933654 -47 TCATTCACTTTCGTTAAAGCTCATAAATGTTC 1 161 0 TCGTTAAGCC 0.88332 -29 TAAATTTGTTGCGCGAATGATCTAACAAACAT 3 93 1 GCGCGAAGAC 0.886635 -208 AATAAATGGCGCGATAACGCTCATTTTATGAC 3 146 1 GCGATAAGCC 0.964838 -155 CGCTCATTTTATGACGAGGCACACACATTTTA 3 163 1 ATGACGAGCC 0.929132 -138 TGTAAACTTATCGTTAACGAGCAAAAACGAGA 3 206 0 TCGTTAAGAC 0.842835 -95 CCTACAAGCATCGTGGAGGTCCGTGACTTTCA 3 243 1 TCGTGGAGTC 0.839216 -58 CAAGCACAGCTTGACGATGACCCGCACCGCAG 4 60 0 TTGACGAGAC 0.953512 -143 GCGCAGCGGCGTGAGGAGGAGCCGAGCAGTCA 4 90 0 GTGAGGAGAC 0.965913 -113 ACACAGCTCGGCGACGATGCACGCCGCGCAGC 4 115 0 GCGACGAGCC 0.994133 -88 GCGCAGCGGCGTGAGGAGGAGCCGAGCAGTCC 4 148 0 GTGAGGAGAC 0.965913 -55 ACCTAGCTCGGCGACGATGCACGCCGCGCAGC 4 173 0 GCGACGAGCC 0.994133 -30 TATGTCGTCATCGAGGTCGATCGTAGTGCGCA 6 41 0 TCGAGGTGAC 0.881437 -210 TGTCAACGTTTGGAGGAGGCTCGGCCGCCAGA 6 150 0 TGGAGGAGCC 0.928794 -101 GTGGATCTTGACGACAAGGACGCTGTTTGGGC 6 214 1 ACGACAAGAG 0.697377 -37 ******* ** * Masking position 9 Map Score: 21.4747 Number of sites scoring better than the average of aligned sites = 2341 Number in coding regions = 2217 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 4 TGATATGTATAACATTATGGCGTTTATCTGC 1 70 0 AACATTATGC 0.975668 -120 ACATTGAAAAAACATTTTAGAGTGATATGTA 1 92 0 AACATTTTGA 0.979599 -98 TTCGTTATCGAACATATTAGCAAAGAATCGC 1 133 0 AACATATTGC 0.94905 -57 TTCGATAACGAACATTTATGAGCTTTAACGA 1 152 1 AACATTTAGA 0.962597 -38 CAAATTTATTAACATTTTCGATTGATGTGGA 3 70 0 AACATTTTGA 0.979599 -231 GCATACAACAAACATTAACTCTTCAGGATCC 3 276 1 AACATTAATC 0.770394 -25 ******** ** Masking position 5 Map Score: 3.30346 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 133 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 5 TCTTTACAAACAAGTGGGCAAATTTACCGC 1 22 1 CAAGTGGGCA 0.976109 -168 CTCCACGATGCTTGTAGGCATGCTGTAAAC 3 231 0 CTTGTAGGCA 0.964994 -70 ACGCCCGCAGTATGTCGTCATCGAGGTCGA 6 53 0 TATGTCGTCA 0.930299 -198 CACGGGGCCGCAAGTCGGCAGTCGACCAGC 6 185 0 CAAGTCGGCA 0.990952 -66 AAACAGCGTCCTTGTCGTCAAGATCCACAC 6 212 0 CTTGTCGTCA 0.979843 -39 ********** Masking position 5 Map Score: 2.84616 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 174 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 TAGATCATTCGCGCAACAAATTTATTAACAT 3 86 0 GCGCAACAAT 0.934486 -215 CGTGACTTTCACGCATACAACAAACATTAAC 3 264 1 ACGCATACAC 0.906472 -37 AGCCCATAACCTAGCTCGGCGA 4 191 0 GCCCATAACT 0.894811 -12 CGATCGTAGTGCGCATACATCAGATGCTAAC 6 25 0 GCGCATACAC 0.986793 -226 AGCGCGAGGAGCGCAAAACGTTAGGGCAGCT 6 95 1 GCGCAAAACT 0.963284 -156 GCCAGAGCTTGCGCAAGCAATTCGGAGGCGA 6 125 0 GCGCAAGCAT 0.96717 -126 GTCCAAAATCGCCCAAACAGCGTCCTTGTCG 6 225 0 GCCCAAACAC 0.976221 -26 ********* * Masking position 5 Map Score: 2.11205 Number of sites scoring better than the average of aligned sites = 990 Number in coding regions = 934 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 7 CGTCGAAGCGGCAGATAAACGCCATAATGTTATA 1 60 1 GCAAACGCCA 0.795078 -130 GAACATATTAGCAAAGAATCGCGCTTTAGGTAAC 1 121 0 GCAATCGCGC 0.990667 -69 ACAATCAGATGGAATAAATGGCGCGATAACGCTC 3 134 1 GGAATGGCGC 0.882067 -167 GGGCTCGGGTGGTACCCATCGCGCCGCGCTGCGG 4 32 1 GGCATCGCGC 0.994841 -171 GCGCTGCGGTGCGGGTCATCGTCAAGCTGTGCTT 4 57 1 GCCATCGTCA 0.932108 -146 TGACTGCTCGGCTCCTCCTCACGCCGCTGCGCGG 4 90 1 GCCCTCACGC 0.944566 -113 GCCGCTGCGCGGCGTGCATCGTCGCCGAGCTGTG 4 112 1 GGCATCGTCG 0.938811 -91 GGACTGCTCGGCTCCTCCTCACGCCGCTGCGCGG 4 148 1 GCCCTCACGC 0.944566 -55 GCCGCTGCGCGGCGTGCATCGTCGCCGAGCTAGG 4 170 1 GGCATCGTCG 0.938811 -33 TGCATGTAATCGTCCATGATGGTCC 5 35 0 GCAATCGTCC 0.971591 -15 CGCGCTGGCGTCGTTTCAACGCCCGCAGTATGTC 6 67 0 TCCAACGCCC 0.889112 -184 CCTAACGTTTTGCGCTCCTCGCGCTGGCGTCGTT 6 86 0 TGCCTCGCGC 0.924906 -165 CCACGGTCCAAAATCGCCCAAACAGCGTC 6 232 0 GTAATCGCCC 0.932292 -19 ** ******** Masking position 10 Map Score: 14.1089 Number of sites scoring better than the average of aligned sites = 3761 Number in coding regions = 3592 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 8 AACAAACATGCATCATGTACAATCAGATGG 3 116 1 CATCATGTAC 0.922703 -185 TGCCTACAAGCATCGTGGAGGTCCGTGACT 3 241 1 CATCGTGGAG 0.981228 -60 GCGCGGCGTGCATCGTCGCCGAGCTGTGTT 4 118 1 CATCGTCGCC 0.9923 -85 GCGCGGCGTGCATCGTCGCCGAGCTAGGTT 4 176 1 CATCGTCGCC 0.9923 -27 TGCGGTGGACCATCATGGACGATTACATGC 5 29 1 CATCATGGAC 0.98719 -21 AGTATGTCGTCATCGAGGTCGATCGTAGTG 6 45 0 CATCGAGGTC 0.957082 -206 ********** Masking position 3 Map Score: 7.08921 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 172 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 9 GAACTTAAAATGTGTGTGCCTCGTCATAAA 3 170 0 TGTGTGTGCC 0.862171 -131 GCCGCGCTGCGGTGCGGGTCATCGTCAAGC 4 54 1 GGTGCGGGTC 0.940263 -149 ATCGTCAAGCTGTGCTTGACTGCTCGGCTC 4 74 1 TGTGCTTGAC 0.934688 -129 GTCGCCGAGCTGTGTTGGACTGCTCGGCTC 4 132 1 TGTGTTGGAC 0.975485 -71 CGGCGTCGGACCCGCCGCTGC 5 2 1 GGCGTCGGAC 0.948185 -48 GACCCGCCGCTGCGGTGGACCATCATGGAC 5 19 1 TGCGGTGGAC 0.976799 -31 TTGCGCAAGCTCTGGCGGCCGAGCCTCCTC 6 140 1 TCTGGCGGCC 0.912627 -111 AACGTTGACATCCGCTGGTCGACTGCCGAC 6 172 1 TCCGCTGGTC 0.920819 -79 ********** Masking position 4 Map Score: 2.53632 Number of sites scoring better than the average of aligned sites = 1369 Number in coding regions = 1325 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 10 ********** No masking Map Score: 2.11274e-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: 2.11274e-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 12 ********** No masking Map Score: 2.11274e-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