AlignACE version 2.2 July 7, 1998 alignACE -z/skink1/amcguire/genomes/ecoli.fna -a/home/amcguire/alignace/lib/ORF_ecoli.txt -b/home/amcguire/alignace/lib/bimes_ecoli.txt -k0 -l300 -joxyR.reg -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 = 146 Input sequences: #1 dps 298 bp dps 167 1-504 CDS #2 gor 71 bp gor 450 1-1353 CDS #3 katG 300 bp katG 726 1-2181 CDS #4 oxyR 266 bp oxyR 305 1-918 CDS Motif number 1 ATGGTTATGCATAACCATGCAGAAATGTAAAT 1 9 0 ATAAAGCGAA 0.949714 -290 ATGGTTATGCATAACCATGCAGAATTTCTCGCTA 1 25 1 ATAAAGCGAA 0.949714 -274 GGTGTAGAGGAAAAGTAGCGAGAAATTCTGCATG 1 40 0 AAAAACGGAA 0.936867 -259 AATTCGATATATAAAGACGGTGTAGAGGAAAAGT 1 58 0 ATAAAGGGTA 0.930953 -241 AATTTTCGGAATAAATATGCTTTTGCATAATTCG 1 86 0 ATAAAGCTTT 0.520799 -213 ACTAATAGTGGTAACAAGCGTGAAAAACAAAACT 1 182 0 GTAAACGGAA 0.959455 -117 TTATGTCCCAGTAATTAACGAGATTAAGTATAGC 1 255 0 GTAAACGGAT 0.947283 -44 TACAATCGCGGTAATCAACGATAAGGACACTTTG 2 46 1 GTAAACGTAA 0.859841 -26 ATGAGGGCGGGAAAATAAGGTTATCAGCCTTGTT 3 53 1 GAAAAGGTAT 0.8247 -248 TATCCTTCAAGTAATGAGGGAGAAAACAAGGCTG 3 77 0 GTAAAGGGAA 0.976692 -224 CAAATGCTTTATAAAAAAGGGTTTTAGCTTCATA 3 109 0 ATAAAGGTTT 0.726332 -192 TTTGCCATAAAAAAGCCCGGCGATAAGCCAGGCT 4 34 0 AAAACGGGAT 0.744221 -233 TTTTTATGGCAAAAAAAAGCGGATCCTGGAGATC 4 55 1 AAAAAGCGAT 0.891354 -212 TCGAATAACTAAAGCCAACGTGAACTTTTGCGGA 4 87 0 AAAGACGGAA 0.683984 -180 **** * ** *** Masking position 3 Map Score: 10.8373 Number of sites scoring better than the average of aligned sites = 1335 Number in coding regions = 1126 Number in noncoding regions = 209 Number of orfs with sites within 600 bp upstream = 231 Fraction of orfs with sites within 600 bp upstream = 0.0371025 Motif number 2 TATTTATCTGCTCGCCAGGAATTTTCGGAA 1 109 0 CTCGCCAGGA 0.92195 -190 GAGATTAAGTATAGCACCGGCTATGTGTTC 1 240 0 ATAGCACCGG 0.904567 -59 GTAATAGGTGCCAGCAATGGCTGCAA 2 7 0 CCAGCAATGG 0.914876 -65 AAAATGCTGCCTCGAAATGAGGGCGGGAAA 3 37 1 CTCGAAATGA 0.923489 -264 AACGCTGTGTATCGTAACGGTAACACTGTA 3 266 1 ATCGTAACGG 0.932498 -35 TTGAGAAACTCTCGAAACGGGCAGTGACTT 4 122 1 CTCGAAACGG 0.974238 -145 ATAATTGCTCACAGAAACGGAGCGGCACCT 4 165 0 ACAGAAACGG 0.864956 -102 GATAGGTAGAATAGCAATGAACGATTATCC 4 214 0 ATAGCAATGA 0.935511 -53 TATTCTACCTATCGCCATGAACTATCGTGG 4 231 1 ATCGCCATGA 0.960322 -36 TCCATCCTCCATCGCCACGATAGTTCATGG 4 245 0 ATCGCCACGA 0.979403 -22 ********** Masking position 4 Map Score: 7.35569 Number of sites scoring better than the average of aligned sites = 1765 Number in coding regions = 1666 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 3 TAGATATATTGATAAGAACAATTCTTATTT 1 134 0 GATAAGAACA 0.907304 -165 GATTCAATGAGTTAGATATATTGATAAGAA 1 146 0 GTTAGATATA 0.730306 -153 CTATTAGTGTGATAGGAACAGCCAGAATAG 1 208 1 GATAGGAACA 0.961598 -91 GGTAATCAACGATAAGGACACTTTGTC 2 55 1 GATAAGGACA 0.96663 -17 CATATTGTTGGTTAAAGAGATGTAGATCAA 3 185 0 GTTAAAGAGA 0.875901 -116 GATACACAGCGTTAGAGAGAAGTTATAATT 3 249 0 GTTAGAGAGA 0.947524 -52 CAGAATGCTTGATAGGGATAATCGTTCATT 4 199 1 GATAGGGATA 0.970492 -68 AGTTCATGGCGATAGGTAGAATAGCAATGA 4 224 0 GATAGGTAGA 0.961597 -43 ********** Masking position 4 Map Score: 6.56262 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 61 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 4 ATAACCATGCAGAATTTCTCGCTACTTTTC 1 35 1 AGAATTTCTC 0.963448 -264 TCTGCTCGCCAGGAATTTTCGGAATAAATA 1 103 0 AGGAATTTTC 0.772174 -196 CAGATAAATAAGAATTGTTCTTATCAATAT 1 129 1 AGAATTGTTC 0.963449 -170 TAATTCAATTATAACTTCTCTCTAACGCTG 3 243 1 ATAACTTCTC 0.882161 -58 ATTTATACATATAAATGTTC 4 1 0 ATAAATGTTC 0.927337 -266 ATTCGAGTTGAGAAACTCTCGAAACGGGCA 4 115 1 AGAAACTCTC 0.919762 -152 ATTCTGACTGATAATTGCTCACAGAAACGG 4 175 0 ATAATTGCTC 0.963449 -92 CTTGATAGGGATAATCGTTCATTGCTATTC 4 206 1 ATAATCGTTC 0.903941 -61 ********** Masking position 4 Map Score: 5.38033 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 177 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 GTTATGCATAACCATGCAGAAATGTAAAT 1 8 0 AATGCAGAAA 0.837661 -291 GTAGAGGAAAAGTAGCGAGAAATTCTGCATGG 1 39 0 AAGCGAGAAA 0.981355 -260 TAAAGATTCAATGAGTTAGATATATTGATAAG 1 148 0 AAGTTAGATA 0.770888 -151 AATAGTGGTAACAAGCGTGAAAAACAAAACTA 1 181 0 AAGCGTGAAA 0.965047 -118 TGTTACCACTATTAGTGTGATAGGAACAGCCA 1 200 1 AAGTGTGATA 0.902064 -99 GTGTGATAGGAACAGCCAGAATAGCGGAACAC 1 214 1 AAGCCAGAAT 0.943286 -85 GAGGGAGAAAACAAGGCTGATAACCTTATTTT 3 64 0 AAGGCTGATA 0.935414 -237 CCTTCAAGTAATGAGGGAGAAAACAAGGCTGA 3 76 0 AAGGGAGAAA 0.981355 -225 GTGAGCAATTATCAGTCAGAATGCTTGATAGG 4 183 1 AAGTCAGAAT 0.913627 -84 * ********* Masking position 4 Map Score: 5.3857 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 284 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 6 AATTCCTGGCGAGCAGATAAATAAGAATTG 1 116 1 GAGCAGATAA 0.925184 -183 CAGAATAGCGGAACACATAGCCGGTGCTAT 1 230 1 GAACACATAG 0.961077 -69 GTGATCACAAATTTTAAACAGA 3 3 1 GATCACAAAT 0.854516 -298 ATTTTAAACAGAGCACAAAATGCTGCCTCG 3 21 1 GAGCACAAAA 0.958909 -280 AAGAGATGTAGATCAAATTGATCTTAATTA 3 171 0 GATCAAATTG 0.817245 -130 CTGTAGAGGGGAGCACATTG 3 291 1 GAGCACATTG 0.981336 -10 ********** Masking position 5 Map Score: 0.226706 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 145 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 7 ********** No masking Map Score: -4.02005e-14 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: -4.02005e-14 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: -4.02005e-14 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