AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i121_Acriflavin_Resistance_pump_ecoli_hinf_reg_300.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 acrB 22 acridine efflux pump #2 acrA 141 acridine efflux pump #3 acrE 300 transmembrane protein affects septum formation and cell membrane permeability #4 HI0885 191 thiol:disulfide interchange protein (dsbD) #5 HI0886 111 H. influenzae predicted coding region HI0886 #6 HI0887 187 phosphoribosylaminoimidazolecarboxamide formyltransferase (purH) #7 HI0888 95 phosphoribosylamine--glycine ligase (purD) #8 HI0889 123 serine hydroxymethyltransferase (serine methylase) (glyA) #9 HI0890 58 conserved hypothetical protein #10 HI0891 40 conserved hypothetical protein #11 HI0892 108 ATP-dependent RNA helicase (rhlB) #12 HI0893 241 transcriptional repressor (Bm3R1) #13 HI0894 79 lipoprotein, putative Motif number 1 TCAACCCGCGTCAAAATAAAACAGTAGAAT 3 114 1 TCAAAATAAA 0.870474 -187 GCACATAAACACAAAAAAAGATTAATATTC 3 140 0 ACAAAAAAAG 0.847945 -161 TACTATTCCTCAAAAAACCAAAAGCGCGT 3 282 0 TCAAAAAACC 0.712174 -19 ATAGCATACGCCAAAATAAGTATAAGGATG 4 15 0 CCAAAATAAG 0.899209 -177 AACATTATTGTAACAATAAAAAAGTGCGGT 4 68 1 TAACAATAAA 0.454845 -124 GAAAATCAGGTAAAAAATCACCGCACTTTT 4 87 0 TAAAAAATCA 0.626839 -105 ATGATTTAGATCACAAAAAGGAAAATCAGG 4 107 0 TCACAAAAAG 0.821666 -85 TTACCAAAAGTAAAAAATAA 5 1 0 TAAAAAATAA 0.742209 -111 AATTCATCTTTAAACAAAAGGAAAGCAA 5 94 1 TAAACAAAAG 0.639069 -18 TAAATGTGGGCAAAAATAAGGATAAAATTA 6 27 0 CAAAAATAAG 0.868519 -161 TAAAGTGCGGTAAAAATACGATAAATTTCA 6 75 0 TAAAAATACG 0.901912 -113 ATTAAATAGTTAAAAATAAGCGATGAGAAT 6 154 0 TAAAAATAAG 0.940333 -34 GAATTGCAGGTAAAAAATAGCCGTACTTTT 7 46 1 TAAAAAATAG 0.901173 -50 TATGCCTAATTTAAAAAAAGTACGGCTATT 7 61 0 TTAAAAAAAG 0.684056 -35 AAAAAATAAGCGGCGATATT 9 49 0 AAAAAATAAG 0.76181 -10 GTCCGATTTGCCAAAAATCG 10 31 1 CCAAAAATCG 0.750735 -10 ACCGCACTTATAAAAATTAACCGATAGGGT 11 28 0 TAAAAATTAA 0.690419 -81 GGAAAAATCCTCAAAAAAAGCACCGCACTT 11 49 0 TCAAAAAAAG 0.964886 -60 TAAAATGCAGTCAAAATTAACCGCACTTTT 12 44 0 TCAAAATTAA 0.750751 -198 AAGTAGGATATAAAAAATAGGAATATAAAA 12 69 0 TAAAAAATAG 0.901173 -173 AAGTTAAAAAACAAAAAACGTAACAATACT 12 142 0 ACAAAAAACG 0.764907 -100 TTTTAACTTGCCAAAAAACAAAAAATAAAT 12 163 1 CCAAAAAACA 0.679664 -79 AGCTCCGTTATAAAAATAACAACAA 13 6 0 TAAAAATAAC 0.708647 -74 ********** Masking position 6 Map Score: 19.3029 Number of sites scoring better than the average of aligned sites = 941 Number in coding regions = 594 Number in noncoding regions = 347 Number of orfs with sites within 600 bp upstream = 370 Fraction of orfs with sites within 600 bp upstream = 0.0594282 Motif number 2 TTGGGTAAATAACGCGCTTTTGGTTTTTTG 3 271 1 AACGCGCTTT 0.934816 -30 GTAAAAAATCACCGCACTTTTTTATTGTTA 4 78 0 ACCGCACTTT 0.994942 -114 TCGTATTTTTACCGCACTTTAAGAAATTAT 6 84 1 ACCGCACTTT 0.994942 -104 ATCTAACTATCCCCCTCTTTACAAAAGAGG 7 14 1 CCCCCTCTTT 0.968124 -82 ACCTGCAATTCCCCCTCTTTTGTAAAGAGG 7 27 0 CCCCCTCTTT 0.968124 -69 CAAAAAAAGCACCGCACTTATAAAAATTAA 11 38 0 ACCGCACTTA 0.972507 -71 GTCAAAATTAACCGCACTTTTCATCATTAA 12 35 0 ACCGCACTTT 0.994942 -207 AAATAAAATGAACGCTCATTCATTTTTGAG 12 189 1 AACGCTCATT 0.860976 -53 ********** Masking position 9 Map Score: 12.9754 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 116 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 3 GTTGCTATAAATCGTTAAATAAATAATATATAT 3 13 1 ATTTAATAAA 0.83775 -288 GTAGTGAATGTATCTTAGGTAAATAATATATAT 3 38 0 TATTAGTAAA 0.559368 -263 AAAACCTCGTAAATTGAAATATATATTGATGTA 3 68 0 AATGAATATA 0.610028 -233 CACAAAAAGGAAAATCAGGTAAAAAATCACCGC 4 93 0 AATCAGTAAA 0.947908 -99 CGGGTAGTTAAACAATAATTAAAATTGAAAAAT 5 36 0 AAATAATAAA 0.819214 -76 CTTTTGTTTAAAGATGAATTAAAACGGCGTCAT 5 81 0 AATGAATAAA 0.878573 -31 AAAATTATGAAACTACAACTAAA 6 1 0 AAACAATAAA 0.830958 -187 AAATACGATAAATTTCAGGCATAAAAAAGCCCA 6 59 0 AATCAGCATA 0.652712 -129 AAATATAGAAAAGATTAAATATAATTTCTTAAA 6 101 0 AATTAATATA 0.736712 -87 AATCTTTTCTATATTTAAGCAAACGTTTGCGTT 6 118 1 ATTTAACAAA 0.71154 -70 AAAGAGGGGGATAGTTAGATAAA 7 1 0 ATTTAGTAAA 0.869996 -95 AAAGAGGGGGAATTGCAGGTAAAAAATAGCCGT 7 37 1 AAGCAGTAAA 0.840813 -59 TTAGGAATGAAATTTTAATTAAATTTTTATCCA 8 55 1 AATTAATAAA 0.928276 -69 ATTTTTATCCATAAACAGTTAAACTATCTGCCA 8 77 1 ATACAGTAAA 0.717653 -47 CGCACTTTTCATCATTAAATAAACGCGTGGACT 12 20 0 ATTTAATAAA 0.837749 -222 TAGGAATATAAAATGCAGTCAAAATTAACCGCA 12 49 0 AAGCAGCAAA 0.716178 -193 CCAAAAAACAAAAAATAAATAAAATGAACGCTC 12 173 1 AAATAATAAA 0.819214 -69 CGGAGCTTTAAACATGAGTCAAACTCAACATCA 13 29 1 AATGAGCAAA 0.817519 -51 ** **** **** Masking position 7 Map Score: 10.757 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 210 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 4 ACATCGACGAATGATAATTTGTAGGATAGC 3 201 1 ATGATAATTT 0.630211 -100 AGAATTGAGTATAAAAATATAGATGCTCGA 4 172 0 ATAAAAATAT 0.901373 -20 AAAAATAAGGATAAAATTATGAAACTACAA 6 16 0 ATAAAATTAT 0.815172 -172 ACCGCACTTTAAGAAATTATATTTAATCTT 6 94 1 AAGAAATTAT 0.788667 -94 CATCACTTAAATGAAATTAATTCATCATAA 8 20 0 ATGAAATTAA 0.844968 -104 CATTTAAGTGATGAAAATTTAGGAATGAAA 8 37 1 ATGAAAATTT 0.936379 -87 AAATTTAGGAATGAAATTTTAATTAAATTT 8 51 1 ATGAAATTTT 0.884068 -73 CTGTTTATGGATAAAAATTTAATTAAAATT 8 65 0 ATAAAAATTT 0.869384 -59 TAATCAACGAAAGAAAATAAA 9 2 0 AAGAAAATAA 0.788867 -57 CACCGCACTTATAAAAATTAACCGATAGGG 11 29 0 ATAAAAATTA 0.775553 -80 AAGCTCCGTTATAAAAATAACAACAA 13 7 0 ATAAAAATAA 0.826289 -73 CAAGAAAATATGTGAGCGTTT 13 69 0 AAGAAAATAT 0.878102 -11 ********** Masking position 6 Map Score: 9.92983 Number of sites scoring better than the average of aligned sites = 365 Number in coding regions = 268 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 5 AGGTAAAAAATCACCGCACTTTTTTATTGT 4 80 0 TCACCGCACT 0.995693 -112 TATCGTATTTTTACCGCACTTTAAGAAATT 6 82 1 TTACCGCACT 0.988339 -106 AGGTAAAAAATAGCCGTACTTTTTTTAAAT 7 53 1 TAGCCGTACT 0.928063 -43 CTCAAAAAAAGCACCGCACTTATAAAAATT 11 40 0 GCACCGCACT 0.990489 -69 CAGTCAAAATTAACCGCACTTTTCATCATT 12 37 0 TAACCGCACT 0.993353 -205 ********** Masking position 8 Map Score: 5.65327 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 70 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 ATAAACGCAGCAATGGGTTTATTAACTTTTG 2 81 1 CATGGGTTTA 0.95502 -61 CCCAAAAAGGCAACGCGTTAACTCGCAGAAA 3 245 0 CACGCGTTAA 0.984197 -56 TATTGTTTAACTACCCGTTAAAGATTAATAT 5 52 1 CACCCGTTAA 0.983931 -60 ATAGGGTTTCCTATCGGTTAATCT 11 4 0 CATCGGTTAA 0.975113 -105 ATAGGAAACCCTATCGGTTAATTTTTATAAG 11 21 1 CATCGGTTAA 0.975113 -88 GGGCTTCAGTCCACGCGTTTATTTAATGATG 12 13 1 CACGCGTTTA 0.97092 -229 * ********* Masking position 8 Map Score: 5.01137 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 37 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 GCTATGGTACATACATTCACAAATGTATGTAAA 2 37 0 ATAATCCAAA 0.946215 -105 ATCTCAAGGCACATAAACACAAAAAAAGATTAA 3 145 0 ACAAACCAAA 0.803315 -156 CAAAAGCGCGTTATTTACCCAAAAAGGCAACGC 3 260 0 TTATTCCAAA 0.710946 -41 TACTATTCCTCAAAAAACCAAAAG 3 287 0 ACTTTCCAAA 0.943714 -14 GATGCTCGAAATTCTATCACAAAGAAATTTGAA 4 148 0 ATTTACCAAA 0.898509 -44 GTATAAAAATATAGATGCTCGAAATTCTATCAC 4 161 0 ATAATCCGAA 0.690503 -31 ATTGAAAAATACTTTTTACCAAAAGTAAAAAAT 5 13 0 ACTTTACAAA 0.829827 -99 GTTTTAATTCATCTTTAAACAAAAGGAAAGCAA 5 89 1 ATCTTACAAA 0.661384 -23 TTTTATCCTTATTTTTGCCCACATTTATGTGGG 6 30 1 ATTTTCCACA 0.762283 -158 AAGATTAAATATAATTTCTTAAAGTGCGGTAAA 6 91 0 ATATTCTAAA 0.603077 -97 AATCTTTTCTATATTTAAGCAAACGTTTGCGTT 6 118 1 ATATTACAAA 0.893165 -70 AGCGATGAGAATTATAACGCAAACGTTTGCTTA 6 133 0 ATTTACCAAA 0.898509 -55 CATTTTTAGGAAAAATCCTCAAAAAAAGCACCG 11 54 0 AAAATCCAAA 0.797641 -55 CCACAAGATGAATGATGAACAAAGTAGGATATA 12 87 0 AATATACAAA 0.501984 -155 ATAAGGAGCAATAATTGCTCAAAAATGAATGAG 12 203 0 ATATTCCAAA 0.966381 -39 CATGAGTCAAACTCAACATCAAAGACCAAAACG 13 41 1 ACTAAACAAA 0.510985 -39 *** ** * **** Masking position 13 Map Score: 7.51912 Number of sites scoring better than the average of aligned sites = 454 Number in coding regions = 342 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 8 GTCAATGGTCAAAAGTTAATAAACCCATTG 2 91 0 AAAAGTTAAT 0.855683 -51 AAACACAAAAAAAGATTAATATTCTACTGT 3 134 0 AAAGATTAAT 0.940908 -167 TAACTCGCAGAAAGAAAAATACAGTTCGCT 3 228 0 AAAGAAAAAT 0.861172 -73 TAGATCACAAAAAGGAAAATCAGGTAAAAA 4 101 0 AAAGGAAAAT 0.836148 -91 ACTTTTTACCAAAAGTAAAAAATAA 5 6 0 AAAAGTAAAA 0.504727 -106 ACGGGTAGTTAAACAATAATTAAAATTGAA 5 40 0 AAACAATAAT 0.549552 -72 ACTACCCGTTAAAGATTAATATGACGCCGT 5 61 1 AAAGATTAAT 0.940908 -51 CCTTTTGTTTAAAGATGAATTAAAACGGCG 5 85 0 AAAGATGAAT 0.900165 -27 TAAATATAGAAAAGATTAAATATAATTTCT 6 105 0 AAAGATTAAA 0.764824 -83 CTATTTAATGAAAGGAAAATACA 6 175 1 AAAGGAAAAT 0.836148 -13 TTTATGGATAAAAATTTAATTAAAATTTCA 8 62 0 AAAATTTAAT 0.531874 -62 CCAAAAAACAAAAAATAAATAAAATGAACG 12 173 1 AAAAATAAAT 0.85846 -69 ATAATTGCTCAAAAATGAATGAGCGTTCAT 12 196 0 AAAAATGAAT 0.8032 -46 ********** Masking position 3 Map Score: 9.55962 Number of sites scoring better than the average of aligned sites = 339 Number in coding regions = 222 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 9 GTCCGATTTCAAATTGGTCAATGGTCAAAA 2 107 0 AAATTGGTCA 0.822043 -35 GACCAATTTGAAATCGGACACTCGAGGTTT 2 118 1 AAATCGGACA 0.919615 -24 CAGGCATAAAAAAGCCCACATAAATGTGGG 6 47 0 AAAGCCCACA 0.837493 -141 GATTTTTGGCAAATCGGACAAGGTACTTCA 10 20 0 AAATCGGACA 0.919615 -21 ATTTTTAGGAAAAATCCTCAAAAAAAGCAC 11 56 0 AAAATCCTCA 0.822043 -53 AGGTAAGCCGTAAACCCACAAGATGAATGA 12 105 0 TAAACCCACA 0.857165 -137 ATAAATAAAATGAACGCTCATTCATTTTTG 12 187 1 TGAACGCTCA 0.737958 -55 TAAGGAGCAATAATTGCTCAAAAATGAATG 12 205 0 TAATTGCTCA 0.824597 -37 ATCAAAGACCAAAACGCTCACATATTTTCT 13 58 1 AAAACGCTCA 0.964695 -22 ********** Masking position 3 Map Score: 1.81638 Number of sites scoring better than the average of aligned sites = 716 Number in coding regions = 620 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 10 ATATTTCAATTTACGAGGTTTTAATTCTGCCTCT 3 79 1 TACGGTTTAA 0.990076 -222 TGTTTTATTTTGACGCGGGTTGAAAGAGGCAGAA 3 103 0 TACGGTTGAA 0.973356 -198 TATTAATCTTTAACGGGTAGTTAAACAATAATTA 5 48 0 TACGTGTTAA 0.874417 -64 AAGATTAATATGACGCCGTTTTAATTCATCTTTA 5 72 1 TACGGTTTAA 0.990071 -40 TCCATATCATTATGATGAATTAATTTCATTTAA 8 10 1 TATGGATTAA 0.824486 -114 GTTATTTTTATAACGGAGCTTTAAACATGAGTCA 13 16 1 TACGGTTTAA 0.990087 -64 * *** * ***** Masking position 11 Map Score: 1.49537 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 46 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 11 TAGTTAAAAATAAGCGATGAGAATTATAAC 6 148 0 TAAGCGATGA 0.974094 -40 TAATTTCATTTAAGTGATGAAAATTTAGGA 8 31 1 TAAGTGATGA 0.90777 -93 GATTATATGGTTAGCGGCGATTAATATCGC 9 27 1 TTAGCGGCGA 0.973647 -32 AAAAAATAAGCGGCGATATTAATCGC 9 43 0 TAAGCGGCGA 0.989358 -16 ********** Masking position 3 Map Score: 0.280705 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 59 Number in noncoding regions = 1 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: 1.83563e-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 13 ********** No masking Map Score: 1.83563e-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 14 ********** No masking Map Score: 1.83563e-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