AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i039_ecoli_mtub_300.orf -o039_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 wcaJ 54 putative colanic acid biosynthsis UDP-glucose lipid carrier transferase #2 cpsG 104 phosphomannomutase #3 gmd 25 GDP-D-mannose dehydratase #4 wcaA 34 putative regulator #5 BIME92 24 BIME #6 wza 300 putative polysaccharide export protein #7 pmmA 101 pmmA #8 Rv3258c 122 hypothetical protein Rv3258c Motif number 1 TGTTATTAGCCCCTTACCCGCAGTGGGGTAAGGGA 1 21 0 CCCCCCCAGG 0.925214 -34 ATAAAATTGGCCGCTTCGGTCAGGGCCAACTATTG 2 61 1 CCGCGGCAGG 0.988547 -44 CGACGCCTGCATTCGCACCGCCCC 5 8 1 TGCCGCCCGC 0.939888 -17 CATCAACGACTGCATGCTGAGAGGGTGTGAAAAAT 6 49 1 TGCCTGGAGG 0.724958 -252 CATCCAGACACGCTACCGCCCCTGGCTTTTTAGCT 6 106 0 CGCCGCCCTG 0.980412 -195 TCTTCCCATGCTGTTCGAGACCGATTCGG 7 5 1 CCCCTGTCGG 0.950572 -97 CTGTTCGAGACCGATTCGGCCCGCGTCGTTCGCGG 7 21 1 CCGCGGCCGG 0.997316 -81 CGGCCCGCGTCGTTCGCGGGCCGATAGGCTGGCGG 7 37 1 CGTCGGCCGT 0.975355 -65 GCGAGCAATCCGGCGGGGCCGCGAG 8 1 0 CGGGGCGCGG 0.986794 -122 CGGGGCGGGTCGGTAGCGCGGCGAGCAATCCGGCG 8 21 0 CGGCGCGCGG 0.998702 -102 GTGGAGCCGTCGGTCGCGGGGCGGGTCGGTAGCGC 8 37 0 CGGCGGGCGG 0.909532 -86 TGAGCGATTCCCGCAGCTCCTCGTGGAGCCGTCGG 8 59 0 CCGCTCTCGG 0.962295 -64 CTGCGGGAATCGCTCACGCGCCGATGGTAACGGTT 8 78 1 CGCCGCCCGT 0.995277 -45 CCGTCCACGCCGCGATGTTTAACCGT 8 107 0 CGTCGCGCGT 0.974287 -16 *** *** *** * Masking position 13 Map Score: 25.1685 Number of sites scoring better than the average of aligned sites = 3474 Number in coding regions = 3299 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 2 CGTTATTTACACCGCGGTTTCGCATTCATTGC 2 23 0 ACCGCGTTCG 0.898925 -82 CAGCTCATAAGCCGGGAGAACAACCT 4 19 1 GCCGGGGACA 0.95794 -16 GGGGCGGTGCGAATGCAGGCGTCG 5 10 0 GCGGTGGATG 0.912294 -15 TAAAAAGCCAGGGGCGGTAGCGTGTCTGGATG 6 109 1 GGGGCGTACG 0.993464 -192 CCAGCCTATCGGCCCGCGAACGACGCGGGCCG 7 37 0 GGCCCGGACG 0.994497 -65 GGCGAGCAATCCGGCGGGGCCGCGAG 8 5 0 CCGGCGGGCG 0.988201 -118 CGGATTGCTCGCCGCGCTACCGACCCGCCCCG 8 24 1 GCCGCGTACG 0.998028 -99 CTACCGACCCGCCCCGCGACCGACGGCTCCAC 8 40 1 GCCCCGGACG 0.997542 -83 CGTTACCATCGGCGCGTGAGCGATTCCCGCAG 8 78 0 GGCGCGGACG 0.998702 -45 GTTAAACATCGCGGCGTGGACGG 8 110 1 GCGGCGGGCG 0.998318 -13 ****** ** ** Masking position 6 Map Score: 21.1131 Number of sites scoring better than the average of aligned sites = 1517 Number in coding regions = 1264 Number in noncoding regions = 253 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 3 ACGTCGCATCAGGCAATGAATGCG 2 5 1 CGCATCAGGC 0.977215 -100 TAAAATTGGCCGCTTCGGTCAGGGCCAACT 2 62 1 CGCTTCGGTC 0.985611 -43 AAATTTAACTGGCATCAGTCCTAAAAAAAT 6 191 0 GGCATCAGTC 0.986966 -110 CGACGCGGGCCGAATCGGTCTCGAACAGCA 7 19 0 CGAATCGGTC 0.99087 -83 CGATTCGGCCCGCGTCGTTCGCGGGCCGAT 7 32 1 CGCGTCGTTC 0.960371 -70 AGCGCGGCGAGCAATCCGGCGGGGCCGCGA 8 12 0 GCAATCCGGC 0.8328 -111 TCCTCGTGGAGCCGTCGGTCGCGGGGCGGG 8 47 0 GCCGTCGGTC 0.985042 -76 AGGAGCTGCGGGAATCGCTCACGCGCCGAT 8 73 1 GGAATCGCTC 0.954264 -50 ********** Masking position 5 Map Score: 9.46136 Number of sites scoring better than the average of aligned sites = 1289 Number in coding regions = 819 Number in noncoding regions = 470 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 4 GCGGGTAAGGGGCTAATAACAGGAACAACG 1 35 1 GGCTAATAAC 0.965051 -20 TTGTTCTCCCGGCTTATGAGCTGGTTTGCT 4 12 0 GGCTTATGAG 0.978852 -23 TGATGAGAAAGGGTTATTACGGAAATTAAC 6 24 0 GGGTTATTAC 0.941173 -277 TACCGCCCCTGGCTTTTTAGCTACCAATAC 6 98 0 GGCTTTTTAG 0.940409 -203 TTCATCCGCAGGCTATTGACAGAATAATTC 6 157 0 GGCTATTGAC 0.983163 -144 ATAGTGCACAGGATAATTACTCTGCCAAAG 6 268 1 GGATAATTAC 0.915208 -33 GCGCGGGCTCCTGACAACCTAGATT 7 87 0 GGCTCCTGAC 0.966658 -15 ********** Masking position 9 Map Score: 5.10576 Number of sites scoring better than the average of aligned sites = 250 Number in coding regions = 224 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 ACCCGCAGTGGGGTAAGGGAAGATCCGACA 1 11 0 GGGTAAGGGA 0.991496 -44 ACCCCACTGCGGGTAAGGGGCTAATAACAG 1 27 1 GGGTAAGGGG 0.994246 -28 GCCTGAAAAAGGGTAACGAT 2 95 1 GGGTAACGAT 0.974845 -10 AGTCGTTGATGAGAAAGGGTTATTACGGAA 6 30 0 GAGAAAGGGT 0.944927 -271 CACGCGCCGATGGTAACGGTTAAACATCGC 8 92 1 TGGTAACGGT 0.974845 -31 ********** Masking position 5 Map Score: 4.09641 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 168 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 6 CGCATCAGGCAATGAATGCGAAACCGCGGTGT 2 15 1 ATGAATGCAA 0.735325 -90 AGGGCCAACTATTGCCTGAAAAAGGGTAACGA 2 82 1 ATGCCTGAAA 0.899899 -23 AACCAGCTCATAAGCCGGGAGAACAACCT 4 16 1 TAGCCGGGGA 0.897305 -19 CTCATCAACGACTGCATGCTGAGAGGGTGTGA 6 47 1 ATGCATGCGA 0.730136 -254 TGGTAGCTAAAAAGCCAGGGGCGGTAGCGTGT 6 102 1 AAGCCAGGGC 0.890081 -199 TATTCTGTCAATAGCCTGCGGATGAAATCAAT 6 161 1 AAGCCTGCGA 0.977275 -140 TATTCAATTAACTGCAAGGTAAATGTGCATGG 6 222 1 ATGCAAGGAA 0.943468 -79 GCAAGGTAAATGTGCATGGCGACATTGCTATT 6 235 1 TTGCATGGGA 0.965499 -66 TCGGTCTCGAACAGCATGGGAAGA 7 3 0 AAGCATGGAA 0.973207 -99 * ******* ** Masking position 8 Map Score: 4.83184 Number of sites scoring better than the average of aligned sites = 1493 Number in coding regions = 1406 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 7 CCGCGGTTTCGCATTCATTGCCTGATGCGA 2 14 0 GCATTCATTG 0.746936 -91 CCTTTTTCAGGCAATAGTTGGCCCTGACCG 2 77 0 GCAATAGTTG 0.898943 -28 CGGTGCGAATGCAGGCGTCG 5 1 0 GCAGGCGTCG 0.997126 -24 CTCTCAGCATGCAGTCGTTGATGAGAAAGG 6 42 0 GCAGTCGTTG 0.985365 -259 GACCGATTCGGCCCGCGTCGTTCGCGGGCC 7 29 1 GCCCGCGTCG 0.96876 -73 AGGCTGGCGGCCAAGAGTCGCAGAAAATCT 7 62 1 CCAAGAGTCG 0.884763 -40 AGCTCCTCGTGGAGCCGTCGGTCGCGGGGC 8 50 0 GGAGCCGTCG 0.943521 -73 ACGAGGAGCTGCGGGAATCGCTCACGCGCC 8 70 1 GCGGGAATCG 0.907317 -53 ********** Masking position 8 Map Score: 3.69815 Number of sites scoring better than the average of aligned sites = 2502 Number in coding regions = 2371 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 8 GTAAATAACGACAAAAATAAAATTGGCCGCT 2 45 1 ACAAAAATAA 0.93457 -60 ATTCAAAAATACAGAGGAATAAT 3 3 1 TCAAAAATAA 0.916156 -23 TGAGAGGGTGTGAAAAATTAAACTAAATCAG 6 66 1 TGAAAAATTA 0.952284 -235 GGCTATTGACAGAATAATTCAGACTGGTCTT 6 146 0 AGAATAATTA 0.842562 -155 CATCAGTCCTAAAAAAATTGATTTCATCCGC 6 178 0 AAAAAAATTA 0.87191 -123 AGTTAATTGAATAAAAATTTAACTGGCATCA 6 204 0 ATAAAAATTA 0.872035 -97 TCTGCCAAAGTGATAAATAAACA 6 288 1 TGATAAATAA 0.768375 -13 ********* * Masking position 6 Map Score: 0.750942 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 114 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 9 CTGCGGGTAAGGGGCTAATAACAGGAACAA 1 33 1 GGGGCTAATA 0.96481 -22 CCTGACCGAAGCGGCCAATTTTATTTTTGT 2 55 0 GCGGCCAATT 0.97764 -50 TGGCTTTTTAGCTACCAATACACTGATTTA 6 89 0 GCTACCAATA 0.809214 -212 GCGTCGTTCGCGGGCCGATAGGCTGGCGGC 7 43 1 CGGGCCGATA 0.971172 -59 CGATAGGCTGGCGGCCAAGAGTCGCAGAAA 7 58 1 GCGGCCAAGA 0.99324 -44 GCAATCCGGCGGGGCCGCGAG 8 2 0 GGGGCCGCGA 0.978041 -121 ********** Masking position 5 Map Score: 2.91973 Number of sites scoring better than the average of aligned sites = 391 Number in coding regions = 368 Number in noncoding regions = 23 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: 1.43773e-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: 1.43773e-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: 1.43773e-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