AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i081_PTS_cellobiose_specific_Transport_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 celC 50 PEP-dependent phosphotransferase enzyme III for cellobiose, arbutin, and salicin #2 celB 84 PEP-dependent phosphotransferase enzyme II for cellobiose, arbutin, and salicin #3 celA 298 PEP-dependent phosphotransferase enzyme IV for cellobiose, arbutin, and salicin #4 osmE 201 activator of ntrL gene Motif number 1 ATTTAAATTGCGGTTTTTAAGGGTATTTTTCT 2 63 1 CGGTTTTAAG 0.928236 -22 TTGTTACTCAAGCTTTCAGACGAATTGA 3 7 0 AGCTTTCGAG 0.955688 -292 GCGCAATGGCCGGTTTCCGTTGTTACTCAAGC 3 26 0 CGGTTTCGTG 0.994054 -273 GCCATTGCGCCGGTTTTTTTTGGCCTGAGTTC 3 48 1 CGGTTTTTTG 0.913034 -251 AAAGTCATGTTGGTTTCGCAAGTTACCCAGAG 3 212 1 TGGTTTCCAG 0.972874 -87 CTGTCGCTTGTCGTTTCAGTAGCAACGGGTTA 4 51 0 TCGTTTCGTG 0.84746 -151 CCATTCAGCCCGCTGTCGCTTGTCGTTTCAGT 4 63 0 CGCTGTCCTG 0.960011 -139 GAAACGGCTCCGCTTTCAGAGGATTCCTGTAT 4 108 0 CGCTTTCGAG 0.994021 -94 ATACATTGGGCGCTTTTTCAAGCCCGTGAACG 4 139 0 CGCTTTTCAG 0.976464 -63 ******* ** * Masking position 6 Map Score: 9.26872 Number of sites scoring better than the average of aligned sites = 920 Number in coding regions = 866 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 2 TCGATGCCGGTACGGGTAATCGTGC 1 5 1 TGCCGGTAGG 0.993172 -46 CGGGTAATCGTGCCGGTAAGAAAAGAGAGGA 1 23 1 TGCCGGTAGA 0.979454 -28 AATTTAAATATTGCGGTATTGATTTATGAAA 2 41 0 TTGCGGTATG 0.849397 -44 GCGAATTATTTGCCCGAAATGTGAAGAGGGT 3 92 1 TGCCCGAATG 0.914418 -207 ACTTTTTTTGTGGCTGAAAGGAGTATACGGT 3 186 0 TGGCTGAAGG 0.993306 -113 GCGGAGTGTCTGGCTGACAGATAATCGTCGA 3 265 1 TGGCTGACGA 0.919116 -34 TTGTCTTTTCTGTCTGGAGGGGTTCA 4 6 0 TGTCTGGAGG 0.927589 -196 AAGCGACAGCGGGCTGAATGGTGGTTAAAAC 4 74 1 GGGCTGAAGG 0.971967 -128 TTTCAGAGGATTCCTGTATGACGTTTTAACC 4 96 0 TTCCTGTAGA 0.905455 -106 ******** ** Masking position 4 Map Score: 8.07203 Number of sites scoring better than the average of aligned sites = 1881 Number in coding regions = 1769 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 3 ATGAAATAACTCTTTGACGGGAAAATTTAAA 2 16 0 TCTTGACGGG 0.985693 -69 AAAAACCGGCGCAATGGCCGGTTTCCGTTGT 3 35 0 GCATGGCCGG 0.950913 -264 GCGCCGGTTTTTTTTGGCCTGAGTTCTTAAT 3 54 1 TTTTGGCCTG 0.962596 -245 AAATTGTTTCTCCTTGACCTGTGGTTATGAC 3 121 0 TCTTGACCTG 0.994992 -178 CAATAGTATTTCTTTGACCTTATAAATTGTT 3 144 0 TCTTGACCTT 0.956875 -155 GGAGTATACGGTATAGACCTGAGCAATAGTA 3 167 0 GTTAGACCTG 0.888677 -132 CACTCCGCAAGCCTTAACCTGCTTCCATGCT 3 242 0 GCTTAACCTG 0.961922 -57 CGGAGCCGTTTCGTTCACGGGCTTGAAAAAG 4 128 1 TCTTCACGGG 0.929533 -74 ** ******** Masking position 8 Map Score: 6.66486 Number of sites scoring better than the average of aligned sites = 1166 Number in coding regions = 1057 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 4 GTGCCGGTAAGAAAAGAGAGGAACGATGT 1 32 1 GAAAAGAGGA 0.986635 -19 TCTTTGACGGGAAAATTTAAAATAAA 2 5 0 GAAAATAAAA 0.916711 -80 AATTCGCGAAGATAATTAAGAACTCAGGCCAA 3 67 0 GATAATAGAA 0.930027 -232 TTATTTGCCCGAAATGTGAAGAGGGTCATAAC 3 97 1 GAAATGAAGA 0.906951 -202 CTGGCTGACAGATAATCGTCGATGAGGGCAGT 3 274 1 GATAATTCGA 0.816677 -25 CCTCCAGACAGAAAAGACAAAACTTCCTTAAA 4 17 1 GAAAAGAAAA 0.957863 -185 CAGCGTGTTAGATAAGCCTGGAATACATTGGG 4 161 0 GATAAGTGGA 0.961035 -41 ****** **** Masking position 4 Map Score: 0.627016 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 198 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 5 ATTTTCCCGTCAAAGAGTTATTTCATAAAT 2 21 1 CAAAGAGTTA 0.966105 -64 ACATTTCGGGCAAATAATTCGCGAAGATAA 3 84 0 CAAATAATTC 0.787165 -215 TTTATAAGGTCAAAGAAATACTATTGCTCA 3 149 1 CAAAGAAATA 0.830649 -150 GTTTCAGTAGCAACGGGTTAGCTTTAAGGA 4 41 0 CAACGGGTTA 0.962187 -161 GCTCCGCTTTCAGAGGATTCCTGTATGACG 4 104 0 CAGAGGATTC 0.95397 -98 AAAAAGCGCCCAATGTATTCCAGGCTTATC 4 153 1 CAATGTATTC 0.85816 -49 TCTTGTTTATCAGCGTGTTAGATAAGCCTG 4 173 0 CAGCGTGTTA 0.917403 -29 ********** Masking position 2 Map Score: 0.404654 Number of sites scoring better than the average of aligned sites = 673 Number in coding regions = 584 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 6 CGGTTTTTAAGGGTATTTTTCT 2 73 1 GGGTATTTTT 0.899927 -12 CGAAACCAACATGACTTTTTTTGTGGCTGA 3 200 0 ATGACTTTTT 0.909465 -99 TCGTCGATGAGGGCAGTTTT 3 289 1 GGGCAGTTTT 0.967773 -10 GTTAGCTTTAAGGAAGTTTTGTCTTTTCTG 4 25 0 AGGAAGTTTT 0.979184 -177 GGATTCCTGTATGACGTTTTAACCACCATT 4 90 0 ATGACGTTTT 0.957481 -112 ********** Masking position 7 Map Score: 0.328787 Number of sites scoring better than the average of aligned sites = 338 Number in coding regions = 273 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 7 ********** No masking Map Score: 1.82142e-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: 1.82142e-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 9 ********** No masking Map Score: 1.82142e-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