AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifarR_ecoli_bsub_300.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 0.931893 -80 TCCTGTAAATAATACAAATACAATACAAAT 1 40 0 AATACAAATA 0.931893 -69 GTATCTCATTAATACGAATTTAACCATTAT 1 84 0 AATACGAATT 0.924316 -25 TAAATTGGTCATAACAAATATGGTGCTTGT 2 34 0 ATAACAAATA 0.913133 -185 GATACTTGTCATTACGAATTTAGCACCGCC 2 65 1 ATTACGAATT 0.930094 -154 TCCTTCTTTTATAACAAATTTTCAGAAATT 2 115 0 ATAACAAATT 0.928319 -104 TCAATGAAAAAGAACGGATTGCATACAGAA 2 186 1 AGAACGGATT 0.889677 -33 ACAAGTTATAAAAACGGATACGGAGGGGTT 3 170 1 AAAACGGATA 0.947074 -23 GCTTGAACCTAAAACAGATTTTATAAAAGG 5 77 1 AAAACAGATT 0.944841 -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 GTATTTGTATTATTTACAGGATGAATTTAT 1 49 1 TATTTACAGG 0.620748 -60 AAATTTGTTATAAAAGAAGGATACAAATCT 2 124 1 TAAAAGAAGG 0.921973 -95 TTGCCCTCCCAATATGAAAGATTTGTATCC 2 142 0 AATATGAAAG 0.932338 -77 GGTCTCAATGAAAAAGAACGGATTGCATAC 2 182 1 AAAAAGAACG 0.761106 -37 ATATGACATTAAAAAGCAGGGTGAGCCTCT 3 11 0 AAAAAGCAGG 0.847192 -182 TAGTCTGGAATATATGAAACAGACAAGGTT 3 68 0 TATATGAAAC 0.677953 -125 ATGAAAGCGCTATAAAAAAGTGTTGACTAC 3 100 1 TATAAAAAAG 0.908872 -93 TGTATTCCTGTATATACAGGTAGTCAACAC 3 119 0 TATATACAGG 0.938952 -74 TTATAAGTTGTATATACAAGTTATAAAAAC 3 155 1 TATATACAAG 0.919751 -38 ATATACAAGTTATAAAAACGGATACGGAGG 3 166 1 TATAAAAACG 0.849572 -27 CGAAAGTGATAAAATGAAAGTATTGTGAGC 5 46 0 AAAATGAAAG 0.89801 -136 TAAAACAGATTTTATAAAAGGGGGGAAAAC 5 86 1 TTTATAAAAG 0.624199 -96 GAAAAAGAGTAAAATAAAGGTATTCAAATT 5 143 1 AAAATAAAGG 0.895314 -39 ********** Masking position 8 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 CAAATATGGTGCTTGTCTATCTCTTTGAGG 2 20 0 GCTTGTCTAT 0.894269 -199 TTCATTCTCCCCATTCTGTATGCAATCCG 2 200 0 CCCATTCTGT 0.90612 -19 TTTAGGGTAACCTTGTCTGTTTCATATATT 3 60 1 CCTTGTCTGT 0.980561 -133 GCGCTTTCATCCTAGTCTGGAATATATGAA 3 80 0 CCTAGTCTGG 0.985738 -113 TTGAACGTTCCCTTTTCCCGTTTTCAATTT 4 31 1 CCTTTTCCCG 0.913521 -40 ATATGTTCCTCCTGTTCCGGGCTGCCCCGA 5 12 1 CCTGTTCCGG 0.974061 -170 AAACACCTCAGCTGGTCTAGATCACTAGTC 5 112 1 GCTGGTCTAG 0.947197 -70 AGATGATCCGCCTTTCTGGAATTTGAATA 5 163 0 GCCTTTCTGG 0.96589 -19 ********** Masking position 6 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 TCTATCTCTTTGAGGGGGTGTCAC 2 5 0 TGAGGGGGTG 0.98991 -214 AAACGGATACGGAGGGGTTGGC 3 181 1 GGAGGGGTTG 0.996149 -12 GTGGGGAGCGGGACGTGTTGAACGTTCCCT 4 14 1 GGACGTGTTG 0.98422 -57 CTAGACCAGCTGAGGTGTTTTCCCCCCTTT 5 102 0 TGAGGTGTTT 0.964559 -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 5 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 6 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 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 ********** 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 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