AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -imarR_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 marR 268 multiple antibiotic resistance protein; repressor of mar operon #2 marB 31 multiple antibiotic resistance protein #3 prkA 300 serine protein kinase #4 yhbH 179 alternate gene name: yzdC; similar to hypothetical proteins #5 yhbI 159 similar to transcriptional regulator (MarR family) Motif number 1 AGCGAAAAGTATAAGGGGTAAACAAGGATAAA 1 43 1 AAAGGGTAAA 0.91054 -226 GTAAACAAGGATAAAGTGTCACTCTTTAGCTA 1 60 1 AAAGTGTCAC 0.929504 -209 GCCAGGGCAACTAATGTGAAAAGTACCAGCGA 1 207 1 CAAGTGAAAA 0.856245 -62 TTGAAAACGTGACAACGTCACTGAG 2 4 1 AAAGTGACAA 0.972566 -28 ATACGAAAGCAAGCCTGGAAAAGAATAA 3 7 0 AGCTGGAAAA 0.647936 -294 ATCCTGCGGTAAAAATTGATACTAAAAAAGTG 3 37 1 AAATTGATAC 0.52163 -264 ATTGATACTAAAAAAGTGACAATGACACCCAT 3 51 1 AAAGTGACAA 0.972566 -250 AGAGGGGGAGAGACGGTGAAAACAATCATCAT 3 84 0 AACGTGAAAA 0.866363 -217 CGGTCGCAGTCTGCCTTGTCAACGATGTATGA 3 172 1 CGCTTGTCAA 0.677132 -129 CCGCCCTATTCGGACGGGTCACGTTGC 4 6 0 CGAGGGTCAC 0.789945 -174 AACTATTTAGAAAATGGGACAAAATAACCCGC 4 34 0 AAAGGGACAA 0.966796 -146 CATTTTCTAAATAGTTTGTCAATTAAACGTGC 4 50 1 AAGTTGTCAA 0.692585 -130 TATCACGACCACAAATGGTTAAGGAGGGGAAT 4 156 1 AAATGGTTAA 0.650757 -24 TAAATGAAAGAAGATTTGTCAAAGGAAAAATT 5 89 0 AGATTGTCAA 0.915102 -71 TTATTGAGGAATGAGGTGAAAAGGAG 5 144 1 AGAGTGAAAA 0.920449 -16 * ** ******* Masking position 11 Map Score: 10.4 Number of sites scoring better than the average of aligned sites = 782 Number in coding regions = 607 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 201 Fraction of orfs with sites within 600 bp upstream = 0.032284 Motif number 2 GTAAACAAGGATAAAGTGTCACTCTTTAGC 1 60 1 ATAAAGTGTC 0.824875 -209 CGCATTGAACAAAACTTGAACCGATTTAGC 1 101 1 AAAACTTGAA 0.887956 -168 CCGATTTAGCAAAACGTGGCATCGGTCAAT 1 121 1 AAAACGTGGC 0.93484 -148 AGTCAAATGAATGAATTGACCGATGCCACG 1 135 0 ATGAATTGAC 0.829292 -134 TTGAAAACGTGACAACGTCACTG 2 4 1 AAAACGTGAC 0.981804 -28 ATCCTGCGGTAAAAATTGATACTAAAAAAG 3 37 1 AAAAATTGAT 0.859891 -264 ATTGATACTAAAAAAGTGACAATGACACCC 3 51 1 AAAAAGTGAC 0.976706 -250 GACAGCACGGAAAAATTGAAGAGGGGGAGA 3 105 0 AAAAATTGAA 0.860258 -196 AACTATTTAGAAAATGGGACAAAATAACCC 4 36 0 AAAATGGGAC 0.77464 -144 ATCTTTTCAAAAGACTTGTTTCATAATCTG 4 105 1 AAGACTTGTT 0.690476 -75 TAAATGAAAGAAGATTTGTCAAAGGAAAAA 5 91 0 AAGATTTGTC 0.794124 -69 ********** Masking position 4 Map Score: 6.2563 Number of sites scoring better than the average of aligned sites = 748 Number in coding regions = 611 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 3 ATTTGACTTATACTTGCCTGGGCAATATTATC 1 157 1 TACTTGCGGG 0.998159 -112 GGCAAGTAATTAGTTGCAGGGGATAATATTGC 1 178 0 TAGTTGCGGG 0.995528 -91 TGCAACTAATTACTTGCCAGGGCAACTAATGT 1 192 1 TACTTGCGGG 0.997881 -77 CATCTCGTGATACATGCTTTGGTTTCTTAAAA 3 214 0 TACATGCTGG 0.983574 -87 ******* *** Masking position 5 Map Score: 3.6482 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 3 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 4 TGATTCTGTATTTTTCTTTATTATGAACGGTC 3 145 1 TTTTTTTATT 0.932751 -156 GTGATACATGCTTTGGTTTCTTAAAAATAAAG 3 208 0 CTTTTTTCTT 0.970244 -93 CATTTCAGGGCTTTTTTTTATTTAATAAAAGC 5 20 1 CTTTTTTATT 0.986373 -140 CAAGCGTTTTCTTGCTTTTATTAAATAAAAAA 5 33 0 CTTGTTTATT 0.970244 -127 GACAAATCTTCTTTCATTTATTAATATTTTAT 5 101 1 CTTTTTTATT 0.986373 -59 **** ****** Masking position 7 Map Score: 2.97964 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 15 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 TCGCTGATAACCCAGATACACAGGATAACA 1 18 0 CCCAGATACA 0.925182 -251 TGCCGCCATCTCGTGATACATGCTTTGGTT 3 222 0 TCGTGATACA 0.979759 -79 AAATAAGGTACTTTGATACAATCTATGCCG 3 247 0 CTTTGATACA 0.955522 -54 CCTCTATCATGTTTGATACACTATGCAAAT 3 273 0 GTTTGATACA 0.921095 -28 CCATTTGTGGTCGTGATACATACGTATTCC 4 144 0 TCGTGATACA 0.979759 -36 ********** Masking position 6 Map Score: 1.12118 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 83 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 TATCCTTGTTTACCCCTTATACTTTTCGCT 1 43 0 TACCCCTTAT 0.94199 -226 GATGATTGTTTTCACCGTCTCTCCCCCTCT 3 86 1 TTCACCGTCT 0.925416 -215 TCACCGTCTCTCCCCCTCTTCAATTTTTCC 3 97 1 TCCCCCTCTT 0.964991 -204 GAATTCCCCTCCTTAACCATTTG 4 167 0 TTCCCCTCCT 0.985845 -13 AATTTCTTTTTCTCCCGTATTTTTTTCGCA 5 63 0 TCTCCCGTAT 0.850314 -97 CTCCTTTTCACCTCATTCCTCAATAA 5 144 0 TTCACCTCAT 0.956141 -16 ********** Masking position 1 Map Score: 0.609158 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 177 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 7 TTGCATCGCATTGAACAAAACTTGAACCGA 1 95 1 TTGAACAAAA 0.907001 -174 TGAACAAAACTTGAACCGATTTAGCAAAAC 1 106 1 TTGAACCGAT 0.970461 -163 AATAATTTCATTGAACAGATCGCTGGTACT 1 228 0 TTGAACAGAT 0.986473 -41 AAAGCAAGCCTGGAAAAGAATAA 3 4 0 TGGAAAAGAA 0.910522 -297 AACAAGTCTTTTGAAAAGATTTATATTCAT 4 95 0 TTGAAAAGAT 0.970031 -85 ********** Masking position 5 Map Score: 2.18458 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 128 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 AGTGTCACTCTTTAGCTAGCCTTGCATCGC 1 74 1 TTTAGCTAGC 0.790018 -195 GGGGATAATATTGCCCAGGCAAGTATAAGT 1 162 0 TTGCCCAGGC 0.995236 -107 TTCACATTAGTTGCCCTGGCAAGTAATTAG 1 197 0 TTGCCCTGGC 0.989115 -72 TTATTCTTTTCCAGGCTTGCTTTCGT 3 7 1 TTTTCCAGGC 0.950934 -294 TCATACATCGTTGACAAGGCAGACTGCGAC 3 174 0 TTGACAAGGC 0.90153 -127 TTTCATAATCTGGCACAAGCCGGAATACGT 4 123 1 TGGCACAAGC 0.856393 -57 CCCGTATTTTTTTCGCAAGCGTTTTCTTGC 5 50 0 TTTCGCAAGC 0.962399 -110 ********** Masking position 1 Map Score: 3.84972 Number of sites scoring better than the average of aligned sites = 1196 Number in coding regions = 1142 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 9 AACCCAGATACACAGGATAACAACCACCA 1 10 0 CACAGGATAA 0.984368 -259 TAATTAGTTGCAGGGGATAATATTGCCCAG 1 174 0 CAGGGGATAA 0.972855 -95 CAATTTTTACCGCAGGATACGAAAGCAAGC 3 25 0 CGCAGGATAC 0.95022 -276 GAAAAAAATACGGGAGAAAAAGAAATTTTT 5 66 1 CGGGAGAAAA 0.843284 -94 GAAGATTTGTCAAAGGAAAAATTTCTTTTT 5 82 0 CAAAGGAAAA 0.894676 -78 AATAATAGTTCACAAGATAAAATATTAATA 5 119 0 CACAAGATAA 0.955112 -41 ********** Masking position 7 Map Score: 1.59338 Number of sites scoring better than the average of aligned sites = 310 Number in coding regions = 267 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 10 ********** No masking Map Score: 3.03645e-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: 3.03645e-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: 3.03645e-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