AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifarR_ecoli_bsub_100.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 farR 108 transcriptional regulator of succinylCoA synthetase operon #2 ybgA 218 similar to transcriptional regulator (GntR family) #3 treP 192 phosphotransferase system (PTS) trehalose-specific enzyme IIBC component #4 treA 70 trehalose-6-phosphate hydrolase #5 nagA 181 N-acetylglucosamine-6-phosphate deacetylase Motif number 1 ATACAAATACAATACAAATAATTTCAATCA 1 29 0 AATACAAATA 0.932613 -80 TCCTGTAAATAATACAAATACAATACAAAT 1 40 0 AATACAAATA 0.932613 -69 GTATCTCATTAATACGAATTTAACCATTAT 1 84 0 AATACGAATT 0.924439 -25 TAAATTGGTCATAACAAATATGGTGCTTGT 2 34 0 ATAACAAATA 0.914034 -185 GATACTTGTCATTACGAATTTAGCACCGCC 2 65 1 ATTACGAATT 0.930809 -154 TCCTTCTTTTATAACAAATTTTCAGAAATT 2 115 0 ATAACAAATT 0.929074 -104 TCAATGAAAAAGAACGGATTGCATACAGAA 2 186 1 AGAACGGATT 0.890791 -33 ACAAGTTATAAAAACGGATACGGAGGGGTT 3 170 1 AAAACGGATA 0.947643 -23 GCTTGAACCTAAAACAGATTTTATAAAAGG 5 77 1 AAAACAGATT 0.945432 -105 ********** Masking position 4 Map Score: 11.3371 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 157 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 2 ATAAATTCATCCTGTAAATAATACAAATAC 1 49 0 CCTGTAAATA 0.625249 -60 AGATTTGTATCCTTCTTTTATAACAAATTT 2 124 0 CCTTCTTTTA 0.92334 -95 GGATACAAATCTTTCATATTGGGAGGGCAA 2 142 1 CTTTCATATT 0.933537 -77 GTATGCAATCCGTTCTTTTTCATTGAGACC 2 182 0 CGTTCTTTTT 0.764574 -37 AGAGGCTCACCCTGCTTTTTAATGTCATAT 3 11 1 CCTGCTTTTT 0.849657 -182 AACCTTGTCTGTTTCATATATTCCAGACTA 3 68 1 GTTTCATATA 0.682123 -125 GTAGTCAACACTTTTTTATAGCGCTTTCAT 3 100 0 CTTTTTTATA 0.910447 -93 GTGTTGACTACCTGTATATACAGGAATACA 3 119 1 CCTGTATATA 0.940042 -74 GTTTTTATAACTTGTATATACAACTTATAA 3 155 0 CTTGTATATA 0.921154 -38 CCTCCGTATCCGTTTTTATAACTTGTATAT 3 166 0 CGTTTTTATA 0.852005 -27 GCTCACAATACTTTCATTTTATCACTTTCG 5 46 1 CTTTCATTTT 0.899752 -136 GTTTTCCCCCCTTTTATAAAATCTGTTTTA 5 86 0 CTTTTATAAA 0.628684 -96 AATTTGAATACCTTTATTTTACTCTTTTTC 5 143 0 CCTTTATTTT 0.897097 -39 ********** Masking position 3 Map Score: 8.34171 Number of sites scoring better than the average of aligned sites = 720 Number in coding regions = 552 Number in noncoding regions = 168 Number of orfs with sites within 600 bp upstream = 188 Fraction of orfs with sites within 600 bp upstream = 0.030196 Motif number 3 CCTCAAAGAGATAGACAAGCACCATATTTG 2 20 1 ATAGACAAGC 0.887504 -199 CGGATTGCATACAGAATGGGGAGAATGAA 2 200 1 ACAGAATGGG 0.900029 -19 AATATATGAAACAGACAAGGTTACCCTAAA 3 60 0 ACAGACAAGG 0.979189 -133 TTCATATATTCCAGACTAGGATGAAAGCGC 3 80 1 CCAGACTAGG 0.984727 -113 AAATTGAAAACGGGAAAAGGGAACGTTCAA 4 31 0 CGGGAAAAGG 0.907861 -40 TCGGGGCAGCCCGGAACAGGAGGAACATAT 5 12 0 CCGGAACAGG 0.972301 -170 GACTAGTGATCTAGACCAGCTGAGGTGTTT 5 112 0 CTAGACCAGC 0.943605 -70 TATTCAAATTCCAGAAAGGCGGATCATCT 5 163 1 CCAGAAAGGC 0.963521 -19 ********** Masking position 5 Map Score: 5.38346 Number of sites scoring better than the average of aligned sites = 932 Number in coding regions = 829 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 4 TTTCAATCAAGTGAAATTGATCACATA 1 8 0 GTGAAATTGA 0.912754 -101 CATTATGCCCGATAAATTCATCCTGTAAAT 1 60 0 GATAAATTCA 0.962806 -49 GGGCATAATGGTTAAATTCGTATTAATGAG 1 80 1 GTTAAATTCG 0.969001 -29 TGACAAGTATCATAAATTGGTCATAACAAA 2 46 0 CATAAATTGG 0.903977 -173 TAAGGGCGGTGCTAAATTCGTAATGACAAG 2 69 0 GCTAAATTCG 0.948283 -150 CACCACCATATTTAAATTGAAAACGGGAAA 4 44 0 TTTAAATTGA 0.840254 -27 GCCCGAAAGTGATAAAATGAAAGTATTGTG 5 49 0 GATAAAATGA 0.875911 -133 ********** Masking position 5 Map Score: 2.16174 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 161 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 5 TCTATCTCTTTGAGGGGGTGTCAC 2 5 0 TGAGGGGGTG 0.989506 -214 AAACGGATACGGAGGGGTTGGC 3 181 1 GGAGGGGTTG 0.995994 -12 GTGGGGAGCGGGACGTGTTGAACGTTCCCT 4 14 1 GGACGTGTTG 0.983592 -57 CTAGACCAGCTGAGGTGTTTTCCCCCCTTT 5 102 0 TGAGGTGTTT 0.963177 -80 ********** Masking position 3 Map Score: 1.88692 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 52 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 6 ********** No masking Map Score: 1.41641e-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: 1.41641e-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 TGAATTTATCGGGCATAATGGTTAAATTCG 1 70 1 GGGCATAATG 0.922766 -39 CATATTGGGAGGGCAAATGGTATTATGGTC 2 156 1 GGGCAAATGG 0.964183 -63 CATACAGAATGGGGAGAATGAA 2 207 1 GGGGAGAATG 0.979368 -12 CAAGTGGGGAGCGGGACGTGTTGAA 4 6 1 GGGGAGCGGG 0.987292 -65 AATTGAAAACGGGAAAAGGGAACGTTCAAC 4 30 0 GGGAAAAGGG 0.948668 -41 AGCAAGCTCGGGGCAGCCCGGAACAGGAGG 5 19 0 GGGCAGCCCG 0.966626 -163 TTATAAAAGGGGGGAAAACACCTCAGCTGG 5 97 1 GGGGAAAACA 0.858296 -85 ********** Masking position 5 Map Score: 1.96576 Number of sites scoring better than the average of aligned sites = 859 Number in coding regions = 747 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 9 ********** No masking Map Score: 1.41641e-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 10 ********** No masking Map Score: 1.41641e-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: 1.41641e-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