AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i069_Serine_Metabolism_ecoli_hinf_reg_100.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 sdaA 183 L-serine deaminase #2 sdaC 300 probable serine transporter #3 HI0288 34 L-serine deaminase (sdaA) #4 HI0289 222 serine transporter (sdaC) Motif number 1 TTAGTTTAATTCATGTGAATAGTTAAGCCAGTCGCC 1 85 1 TATGTGTGAA 0.777491 -99 AAGTCAGATGTCGTTTAATGGGCAAATATTGCCCTT 2 27 1 TGTTTAGGAA 0.936298 -274 CTTTTACTTTTGATTTACAGAGTAAAGCGTTGGGAT 2 70 1 TATTTAGGAA 0.984352 -231 ACCGCCGTAATAATTTGAGGGCGGAAAGATACACAC 2 167 0 TATTTGGCAA 0.983956 -134 GATGGCTTAATCATTTACCGCCGTAATAATTTGAGG 2 183 0 TATTTAGCAA 0.98069 -118 TTTCATTTATTTTTATACGCAATCGGTGTCGT 4 7 1 TATTTTTCAA 0.842673 -216 AAAAGTGCGGTAATTTTCAGCGACAAAAAAATCGGT 4 49 0 TATTTTGGAA 0.971195 -174 TTGAGATTCTCTATTTATTGGCATAACATAATACTC 4 128 1 CATTTAGCAA 0.96127 -95 TTAAATTTGTCAATTTGTAGAGCAAAATCCGCTCCA 4 173 0 CATTTGGGAA 0.973776 -50 * ***** * * ** Masking position 6 Map Score: 6.30351 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 122 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 2 CGCGATTTAACTAATATTGCGATGATTGTCTCA 1 44 0 CTAATAGCGT 0.98875 -140 TTAAACTAATCAAAAACCGCGATTTAACTAATA 1 61 0 CAAAAAGCGT 0.98875 -123 CTATGCGCTGTTATTAGTTCGTTACTGGAAGTC 1 136 1 TTATTATCGT 0.748954 -48 GTTTAATGGGCAAATATTGCCCTTAAATTCTCT 2 39 1 CAAATAGCCT 0.912015 -262 CGCCCTCAAATTATTACGGCGGTAAATGATTAA 2 180 1 TTATTAGCGT 0.901017 -121 AAATTTCTCAAAATTCGTTAAAAATTAAA 3 16 0 CTCAAATCGT 0.892353 -19 TTTTCAGCGACAAAAAAATCGGTGCGATGACGA 4 39 0 CAAAAATCGT 0.966449 -184 AATTTTTTTATAAAAAGTGCGGTAATTTTCAGC 4 64 0 TAAAAAGCGT 0.966449 -159 AGAGCAAATTCTAAAATTGTGATCAAGTTAAAA 4 95 0 CTAAAAGTGT 0.913908 -128 ****** *** * Masking position 6 Map Score: 6.09611 Number of sites scoring better than the average of aligned sites = 728 Number in coding regions = 632 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 3 TCATCGCAATATTAGTTAAATCGCGGTTTT 1 52 1 ATTAGTTAAA 0.953595 -132 GCGGTTTTTGATTAGTTTAATTCATGTGAA 1 74 1 ATTAGTTTAA 0.942058 -110 GAACGCGGCGACTGGCTTAACTATTCACAT 1 97 0 ACTGGCTTAA 0.954117 -87 CCCGGGCTGAACTGGCTAAAAGCTGAATTA 2 257 1 ACTGGCTAAA 0.964294 -44 ATTTCTCAAAATTCGTTAAAAATTAAAGGC 3 13 0 ATTCGTTAAA 0.925482 -22 TTCTCTATTTATTGGCATAACATAATACTC 4 134 1 ATTGGCATAA 0.865151 -89 CAAAGCATAAATTACTTAAATTTGTCAATT 4 194 0 ATTACTTAAA 0.802857 -29 ********** Masking position 9 Map Score: 3.38943 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 157 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 4 TGTAGATGTAAAGATAAGTATAG 1 3 0 AAGATAGTAT 0.869397 -181 TGATTGTCTCAAGTAGTGTTTTGTAGATGTA 1 24 0 AAGTATGTTT 0.805807 -160 TCTATCTTCCAAGTAGATTATTGTATTTGAG 2 108 1 AAGTAATTAT 0.90051 -193 AGATACACACAAGTTATGTATCTATCAGTGA 2 146 0 AAGTTTGTAT 0.973786 -155 ATCAAGTTAAAATTTTTTTATAAAAAGTGCG 4 76 0 AATTTTTTAT 0.850203 -147 ACTTGATCACAATTTTAGAATTTGCTCTTTG 4 100 1 AATTTAGAAT 0.722372 -123 GCTCCAACTAAATTTGAGTATTATGTTATGC 4 148 0 AATTTAGTAT 0.935567 -75 TGACAAATTTAAGTAATTTATGCTTTGGAGC 4 197 1 AAGTATTTAT 0.900511 -26 ***** ***** Masking position 2 Map Score: 2.88407 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 122 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 5 ATCTATCAGTGATCTTGATCTCAAATACAA 2 128 0 GATCTTGATC 0.841071 -173 TTCCCGGGCTGAACTGGCTAAAAGCTGAAT 2 255 1 GAACTGGCTA 0.928405 -46 AAAAAAATTTTAACTTGATCACAATTTTAG 4 88 1 TAACTTGATC 0.923391 -135 CACAATTTTAGAATTTGCTCTTTGAGATTC 4 107 1 GAATTTGCTC 0.985233 -116 AGTTGGAGCGGATTTTGCTCTACAAATTGA 4 170 1 GATTTTGCTC 0.978209 -53 ********** Masking position 5 Map Score: 1.94116 Number of sites scoring better than the average of aligned sites = 268 Number in coding regions = 248 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 GTTGGGATAATCTATCTTCCAAGTAGATTA 2 98 1 TCTATCTTCC 0.971054 -203 ACACAAGTTATGTATCTATCAGTGATCTTG 2 141 0 TGTATCTATC 0.982787 -160 ATAACTTGTGTGTATCTTTCCGCCCTCAAA 2 160 1 TGTATCTTTC 0.982815 -141 AAAAATGAAATCTGTCTATCGGCGATGGCT 2 212 0 TCTGTCTATC 0.971057 -89 ********** Masking position 5 Map Score: 1.43256 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 10 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 GAATAGTTAAGCCAGTCGCCGCGTTCCCTC 1 101 1 GCCAGTCGCC 0.994305 -83 TGACTGGACTTCCAGTAACGAACTAATAAC 1 145 0 TCCAGTAACG 0.947629 -39 TTACTGGAAGTCCAGTCACCTTGTCAGGAG 1 157 1 TCCAGTCACC 0.994838 -27 CATTTTTACGGTCAGGCACCTTCCCGGGCT 2 235 1 GTCAGGCACC 0.977783 -66 ********** Masking position 4 Map Score: 0.64137 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 313 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 CATCTGACTTCTTCCGGGGCGCGCAA 2 5 0 CTTCCGGCGC 0.988586 -296 AGTTATGTATCTATCAGTGATCTTGATCTCAA 2 134 0 CTATCGGATC 0.982244 -167 TTGTGTGTATCTTTCCGCCCTCAAATTATTAC 2 165 1 CTTTCGCCTC 0.980666 -136 TGAAATCTGTCTATCGGCGATGGCTTAATCAT 2 205 0 CTATCGGATG 0.974342 -96 GGTCAGGCACCTTCCCGGGCTGAACTGGCTAA 2 244 1 CTTCCGGCTG 0.970589 -57 ***** * **** Masking position 2 Map Score: 0.257382 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 214 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 AACTAATATTGCGATGATTGTCTCAAGTAGTGTT 1 35 0 GCGATGACTC 0.988297 -149 ACAGAGTAAAGCGTTGGGATAATCTATCTTCCAA 2 86 1 GCGTTGGATC 0.993938 -215 CTGTCTATCGGCGATGGCTTAATCATTTACCGCC 2 197 0 GCGATGGATC 0.993795 -104 AAAAATCGGTGCGATGACGACACCGATTGCGTAT 4 25 0 GCGATGAACC 0.978901 -198 TAGAATTTGCTCTTTGAGATTCTCTATTTATTGG 4 115 1 TCTTTGACTC 0.819035 -108 AGTAATTTATGCTTTGGAGCAAACT 4 208 1 GCTTTGGAAC 0.944017 -15 ******* *** Masking position 5 Map Score: 0.347753 Number of sites scoring better than the average of aligned sites = 653 Number in coding regions = 637 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 ********** No masking Map Score: 1.26009e-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: 1.26009e-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: 1.26009e-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