AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i125_Multidrug_Resistance_Pump_2_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -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 proV 300 ATP-binding component of transport system for glycine, betaine and proline #2 proX 57 high-affinity transport system for glycine betaine and proline #3 b2680 101 orf, hypothetical protein #4 b2682 123 orf, hypothetical protein #5 emrR 90 regulator of plasmid mcrB operon (microcin B17 synthesis) #6 emrA 126 multidrug resistance secretion protein Motif number 1 TGTTGCATTATTCGCCTGAAACCACAATAT 1 60 1 TTCGCCTGAA 0.974685 -241 ATAGCGAAAAAACGCCTGAATATTGTGGTT 1 79 0 AACGCCTGAA 0.985941 -222 CCCGTGATATAAGGGCTGAGAGCAAATCGA 1 133 0 AAGGGCTGAG 0.954693 -168 ATGCGAGCAAATCGCCGGAATTTCCCGTGA 1 156 0 ATCGCCGGAA 0.981047 -145 GATGGCAAATGTGGCATGAATATTGATGCG 1 181 0 GTGGCATGAA 0.877071 -120 GTTGATGAATATGGGATGAAAGATAGATTG 3 32 0 ATGGGATGAA 0.964108 -70 AATATTATAAATAGACTGAATGAATATCTT 4 81 0 ATAGACTGAA 0.868064 -43 TCGTTACTATATCGGCTGAAATTAATGAGG 5 61 1 ATCGGCTGAA 0.994223 -30 TTCTTAACTCATCGGCTGAGCCGACCTGCT 6 91 0 ATCGGCTGAG 0.990562 -36 ********** Masking position 9 Map Score: 12.4199 Number of sites scoring better than the average of aligned sites = 812 Number in coding regions = 737 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 2 AATAGCTTTTTATCACGCAAATAATT 1 5 1 GCTTTTATCC 0.950573 -296 ATACTCTGTTGCATTATTCGCCTGAAACCACA 1 54 1 GCTTATTCGC 0.942925 -247 CAATATTCAGGCGTTTTTTCGCTATCTTTGAC 1 84 1 GCTTTTTTCC 0.972066 -217 TTGCTCTCAGCCCTTATATCACGGGAAATTCC 1 138 1 CCTTATATCC 0.942329 -163 CAATATTCATGCCACATTTGCCATCAGGGGTT 1 186 1 GCACATTTGC 0.820589 -115 TAGAAAGATTCCTTTATTTGTCTATGTCGATA 1 275 0 CCTTATTTGC 0.969112 -26 GTGACGCCGGGCATTATCACCCTGCCAAAAAA 2 26 1 GCTTATCACC 0.95851 -32 TGTTATTCCTTTTTTTGGCAGGGTGATAA 2 39 0 CCTTTTTTGC 0.942105 -19 AGACTGATGGGCTTCTTAACACCCTTATAAGT 4 40 0 GCTCTTAACC 0.810745 -84 GAATATCTTAACCTTATCAGACTGATGGGCTT 4 58 0 ACTTATCAGC 0.820532 -66 CAATACATTTACTTTATTTGTCACTGTCGTTA 5 35 1 ACTTATTTGC 0.932999 -56 CGCGTCATCTCGCTCAAAAATCC 6 2 1 GCTCATCTCC 0.965124 -125 ** ******* * Masking position 7 Map Score: 13.3148 Number of sites scoring better than the average of aligned sites = 1182 Number in coding regions = 866 Number in noncoding regions = 316 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 3 GAGGCAACCCCTGATGGCAAATGTGGCATG 1 193 0 CTGATGGCAA 0.97282 -108 TAATCATCACCTGATGAACAAAAATA 3 86 1 CTGATGAACA 0.872798 -16 CCTTATCAGACTGATGGGCTTCTTAACACC 4 49 0 CTGATGGGCT 0.9724 -75 GCATGTTGCGATGCTGGCCAGTCATTTTTT 6 47 0 ATGCTGGCCA 0.991814 -80 GCATCGCAACATGCTGGCCTTTTTGGCAAG 6 63 1 ATGCTGGCCT 0.984169 -64 CTGAGCCGACCTGCTTGCCAAAAAGGCCAG 6 76 0 CTGCTTGCCA 0.982533 -51 ********** Masking position 5 Map Score: 4.74162 Number of sites scoring better than the average of aligned sites = 967 Number in coding regions = 927 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 4 GATTTGCTCTCAGCCCTTATATCACGGGAA 1 135 1 CAGCCCTTAT 0.954296 -166 GAATCTGAGGCAACCCCTGATGGCAAATGT 1 199 0 CAACCCCTGA 0.950894 -102 ATCTATCTTTCATCCCATATTCATCAACAT 3 34 1 CATCCCATAT 0.971058 -68 TATTCATCAACATCCGCTATTATTGATTTC 3 51 1 CATCCGCTAT 0.975708 -51 CCAGCTTAATCATCACCTGATGAACAAAAA 3 80 1 CATCACCTGA 0.86388 -22 TCATTAATTTCAGCCGATATAGTAACGACA 5 59 0 CAGCCGATAT 0.975708 -32 CAGGTCGGCTCAGCCGATGAGTTAAGAAGA 6 93 1 CAGCCGATGA 0.973857 -34 ********** Masking position 2 Map Score: 5.89167 Number of sites scoring better than the average of aligned sites = 487 Number in coding regions = 451 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 TCAACTTTCTCGATTTGCTCTCAGCCCTTA 1 124 1 CGATTTGCTC 0.991137 -177 GAAATTCCGGCGATTTGCTCGCATCAATAT 1 162 1 CGATTTGCTC 0.991137 -139 TTGAAATGTGCGATGTGGTTT 3 2 0 CGATGTGGTT 0.961135 -100 TCGGCTGAGCCGACCTGCTTGCCAAAAAGG 6 80 0 CGACCTGCTT 0.986337 -47 TTGTTCTCCACGATCTTCTTAACTCATCGG 6 106 0 CGATCTTCTT 0.968462 -21 ********** Masking position 6 Map Score: 4.08295 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 200 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 TAGGGTAGAAAAAAGTGACTATTTCCATTG 1 238 1 AAAAGTGACT 0.932996 -63 GCAATAGAAAGATTCCTTTATTTG 1 287 0 TAGAAAGATT 0.870263 -14 TATGGGATGAAAGATAGATTGTTGAAATGT 3 23 0 AAGATAGATT 0.897223 -79 GTTAATATTATAAATAGACTGAATGAATAT 4 84 0 TAAATAGACT 0.898777 -40 ATTGTTTTAGAAAAATGATTCTTGTGGG 5 9 0 AAAAATGATT 0.9378 -82 TTATAAAAGAAAAAATGACTGGCCAGCATC 6 38 1 AAAAATGACT 0.959574 -89 ********** Masking position 4 Map Score: 0.543693 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 117 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 7 ********** No masking Map Score: -3.17312e-13 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 TCTTTGACAAAAAATATCAACTTTCTCGATT 1 108 1 AAAATATCAC 0.947819 -193 TTACCCAATGGAAATAGTCACTTTTTTCTAC 1 242 0 GAAATAGTAC 0.924361 -59 TCCATTGGGTAATATATCGACATAGACAAAT 1 261 1 AATATATCAC 0.959435 -40 AGACTGAATGAATATCTTAACCTTATCAGAC 4 68 0 AATATCTTAC 0.915362 -56 CAGTCTATTTATAATATTAACAATCGTTAAG 4 93 1 ATAATATTAC 0.848562 -31 TTTCTAAAACAATACATTTACTTTATTTGTC 5 26 1 AATACATTAC 0.915357 -65 AATTTCAGCCGATATAGTAACGACAGTGACA 5 53 0 GATATAGTAC 0.94071 -38 ******** ** Masking position 4 Map Score: 1.05763 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 107 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 9 ********** No masking Map Score: -3.17312e-13 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 10 ********** No masking Map Score: -3.17312e-13 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: -3.17312e-13 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