AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -itrpR_ecoli_hinf_100.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 trpE 91 anthranilate synthase component I #2 trpL 137 trp operon leader peptide #3 aroH 156 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (DAHP synthetase, tryptophan repressible) #4 mtr 153 tryptophan-specific transport protein #5 slt 183 soluble lytic murein transglycosylase #6 trpR 89 regulator for trp operon and aroH; trp aporepressor #7 HI0287 116 tryptophan-specific transport protein (mtr) #8 HI0825 145 H. influenzae predicted coding region HI0825 #9 HI0830 37 trp operon repressor (trpR) #10 HI1387 105 anthranilate synthase component I (trpE) #11 HI1388.1 48 H. influenzae predicted coding region HI1388.1 #12 HI1389 52 anthanilate phosphoribosyltransferase (trpD) #13 HI1389.1 36 indole-3-glycerol phosphate synthase / phosphoribosylanthranilate isomerase (trpC) #14 HI1430 179 short chain dehydrogenase/reductase #15 HI1547 217 phospho-2-dehydro-3-deoxyheptonate aldolase (phenylalanine repressible) (aroG) Motif number 1 GTACTAGTTAACTAGTTCGATGATTAATTG 2 90 0 ACTAGTTCGA 0.932095 -48 GAACTAGTTAACTAGTACGCAAGTTCACGT 2 102 1 ACTAGTACGC 0.936915 -36 AGAACTAGTGCATTAGCTTATTT 3 4 1 ACTAGTGCAT 0.938047 -153 GTACCAGTACACGAGTACAAAAGACAGAAA 4 81 0 ACGAGTACAA 0.966943 -73 TCCAGTGAAAAATAGTGCGACTGCGTTGTT 4 123 0 AATAGTGCGA 0.961912 -31 GTACTCGCTAAAGAGTACGATAGCATATCA 6 23 0 AAGAGTACGA 0.894377 -67 GTACTCTTTAGCGAGTACAACCGGGGGAGG 6 35 1 GCGAGTACAA 0.77689 -55 GCACTATTATAGTAGTACACAAGGAAAGTG 7 75 0 AGTAGTACAC 0.837265 -42 GTACTACTATAATAGTGCAAATTTATTTTA 7 87 1 AATAGTGCAA 0.973485 -30 ACACTATTAAACTAGTGCAT 9 1 0 ACTAGTGCAT 0.938047 -37 GCACTAGTTTAATAGTGTAAAATGGGAGCA 9 13 1 AATAGTGTAA 0.645485 -25 GTACTATTAAACTAGTGCAAAAGGAATAAG 10 60 0 ACTAGTGCAA 0.988668 -46 GCACTAGTTTAATAGTACAAAATTTTCCAA 10 72 1 AATAGTACAA 0.971301 -34 GTACTATTAAAGTAGTACAAATAAATTTTG 14 133 0 AGTAGTACAA 0.950409 -47 GTACTACTTTAATAGTACAAATAAGCTCAA 14 145 1 AATAGTACAA 0.971301 -35 GTACTAGTAAACTAGTTCGATATGTTTTTT 15 136 0 ACTAGTTCGA 0.932095 -82 GAACTAGTTTACTAGTACAAAAATAAGTGT 15 148 1 ACTAGTACAA 0.987718 -70 ********** Masking position 6 Map Score: 32.229 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 26 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 2 AATCATCGAACTAGTTAACTAGTACGCAAGTT 2 95 1 CTATTACTAG 0.497082 -43 TCCTTGTGTACTACTATAATAGTGCAAATTTA 7 80 1 CTATATATAG 0.640102 -37 AATTGCGCCACCATTTTCATAGAGAGAAAAAA 8 124 1 CCATTTATAG 0.969273 -22 ATGCACTAGTTTAATAGTGTAAAATGG 9 6 1 CTATTTATAG 0.601083 -32 TCCTTTTGCACTAGTTTAATAGTACAAAATTT 10 65 1 CTATTTATAG 0.601083 -41 TAAAAGCTAATTTTATACGCCACAATAA 13 7 1 CTATTTATAC 0.957854 -30 TTTATTTGTACTACTTTAATAGTACAAATAAG 14 138 1 CTATTTATAG 0.870298 -42 AGTTGTAAAGATAGTTTAATAGGGAATTTGTA 15 92 1 ATATTTATAG 0.900912 -126 ACATATCGAACTAGTTTACTAGTACAAAAATA 15 141 1 CTATTTCTAG 0.598152 -77 *** *** **** Masking position 5 Map Score: 14.283 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 5 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 3 AACGGGCAGTGTATTCACCA 1 1 1 AACGGGCAGT 0.920636 -91 AAGTGTCCGTAACGTGGCGTAAACGGCAAT 5 121 1 AACGTGGCGT 0.883547 -63 GCATATCATAAACGTGCGGA 6 1 0 AACGTGCGGA 0.966294 -89 ACAACATTACAAAGGGGACTAAATGTCCCC 7 22 1 AAAGGGGACT 0.945646 -95 ATATCGATAAAAAGGGGACATTTAGTCCCC 7 35 0 AAAGGGGACA 0.926675 -82 GTACACAAGGAAAGTGCAATATATTTATAT 7 61 0 AAAGTGCAAT 0.828014 -56 AAATGAATGAAAAGTGGGCAAATTTGTCCA 8 30 1 AAAGTGGGCA 0.977271 -116 AGATAAAACAAAAGTGGACAAATTTGCCCA 8 44 0 AAAGTGGACA 0.957638 -102 GACATCAAAAAGTGCGGTAATTTTTAAC 11 9 1 AAAGTGCGGT 0.986032 -40 TTTCTCCTTTAAAGTGCGGTTAAAAATTAC 11 27 0 AAAGTGCGGT 0.986032 -22 ATTGAAATAAAAATTGGGCAGATTATATCA 14 26 1 AAATTGGGCA 0.755205 -154 GTACAGCACAAAAGTGCGGTATTTTTTTAT 15 19 1 AAAGTGCGGT 0.986032 -199 ********** Masking position 2 Map Score: 14.6016 Number of sites scoring better than the average of aligned sites = 434 Number in coding regions = 364 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 4 GGTTAGCATGATAACAAAAAAATAAGCTAATG 3 21 0 ATACAAAAAA 0.679664 -136 CACGAGTACAAAAGACAGAAAAAAAGCCCCGA 4 70 0 AAAAAGAAAA 0.952481 -84 CCCTCGCAGTAAAAGTAAAAAAGTGTCCGTAA 5 101 1 AAAGAAAAAA 0.913153 -83 CAATATATTTATATCGATAAAAAGGGGACATT 7 43 0 ATACATAAAA 0.772919 -74 AATCTTAATAAAATGAATGAAAAGTGGGCAAA 8 20 1 AAAGATGAAA 0.711029 -126 ATTCAGAATTGAATAGATAAAACAAAAGTGGA 8 56 0 GAAAATAAAA 0.624371 -90 CACCATTTTCATAGAGAGAAAAAA 8 132 1 ATAAAGAAAA 0.919565 -14 TTTTTAATCAAAAAGTATAAAAAATAAAAATC 10 20 1 AAAGATAAAA 0.944033 -86 AAAATTTTCCAAAAGGATAAATAAAT 10 90 1 AAAGATAAAT 0.624082 -16 AACCGCACTTTAAAGGAGAAAAA 11 36 1 TAAGAGAAAA 0.773452 -13 TAAAATATAGAAAATTAACAAATC 12 3 1 AAAAAGAAAA 0.952481 -50 ACAAATCCATATACAAAGAAAAACAGGAATAG 12 28 1 ATAAAGAAAA 0.919565 -25 ATACGCCACAATAAGAAGAAAA 13 25 1 ATAGAGAAAA 0.948181 -12 TAAGTAAATAAAAGATAAAAAAATACCGCACT 15 31 0 AAAAAAAAAA 0.867888 -187 *** * ****** Masking position 7 Map Score: 9.58278 Number of sites scoring better than the average of aligned sites = 426 Number in coding regions = 271 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 5 TACGCATGGTGAATACACTGCCCGTT 1 4 0 GAATACGCCC 0.911777 -88 TAAAGCAATCAGATACCCAGCCCGCCTAATGAG 1 35 1 AGATACGCCC 0.967135 -57 TTTGTTCAAAAAAAAGCCCGCTCATTAGGCGGG 1 55 0 AAAAACGCTC 0.914894 -37 CTGTAAAATAATATATACAGCCCCGATTTTTAC 4 35 1 ATATACGCCC 0.964614 -119 TACAAAAGACAGAAAAAAAGCCCCGATGGTAAA 4 63 0 AGAAAAGCCC 0.761451 -91 TTAGGCGGGGAAAAAGGCTACACTTCGCCTTTG 5 51 0 AAAAACACAC 0.79197 -133 CGGGGGAAGCAAAATGCCTCCCCCGGTTGTACT 6 48 0 AAAATCCCCC 0.875339 -42 TTATCGATATAAATATATTGCACTTTCCTTGTG 7 55 1 AAATATGCAC 0.713798 -62 CAAACCCTGTATAATTGCGCCACCATTTTCATA 8 112 1 ATAATCCCAC 0.625704 -34 AGTGCGGTTAAAAATTACCGCACTTTTTGATGT 11 12 0 AAAATCGCAC 0.939365 -37 TTGCTTGATGATATAATCTGCCCAATTTTTATT 14 31 0 ATATACGCCC 0.964614 -149 TAAAAGATAAAAAAATACCGCACTTTTGTGCTG 15 22 0 AAAAACGCAC 0.977566 -196 ***** * **** Masking position 3 Map Score: 7.8237 Number of sites scoring better than the average of aligned sites = 898 Number in coding regions = 755 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 6 CGAGGTGTGTCACACCTCGCCGGGTGGTTA 3 48 0 CACACCTCGC 0.993075 -109 CGAGGTGTGACACACCTCGCACTTGAAATC 3 59 1 CACACCTCGC 0.993075 -98 TACAAGTCTCAGAAATTTGT 3 147 0 TACAAGTCTC 0.907015 -10 GGAAAAAGGCTACACTTCGCCTTTGAAAAC 5 46 0 TACACTTCGC 0.970958 -138 AAACTATCTTTACAACTCTCTTGCAAGCTG 15 79 0 TACAACTCTC 0.963188 -139 ********** Masking position 4 Map Score: 2.80824 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 38 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 7 TGTCCGTAACGTGGCGTAAACGGCAATGAC 5 124 1 GTGGCGTAAA 0.977671 -60 TATGAAAATGGTGGCGCAATTATACAGGGT 8 115 0 GTGGCGCAAT 0.941144 -31 ACATCAAAAAGTGCGGTAATTTTTAACCGC 11 12 1 GTGCGGTAAT 0.977675 -37 CTCCTTTAAAGTGCGGTTAAAAATTACCGC 11 24 0 GTGCGGTTAA 0.915284 -25 TCTTCTTATTGTGGCGTATAAAATTAGCTT 13 14 0 GTGGCGTATA 0.959137 -23 CAGCACAAAAGTGCGGTATTTTTTTATCTT 15 22 1 GTGCGGTATT 0.959137 -196 ********** Masking position 2 Map Score: 2.74424 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 116 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 AGATACCCAGCCCGCCTAATGAGCGGGCTT 1 45 1 CCCGCCTAAT 0.990433 -47 AGCCTTTTTCCCCGCCTAATCCCAGCCGGT 5 65 1 CCCGCCTAAT 0.990433 -119 GCAGCGTCATGCCGCGTAATAGATTTATGC 5 160 0 GCCGCGTAAT 0.990433 -24 CAATGCAGCGTCATGCCGCGTAAT 5 170 0 GCAGCGTCAT 0.938591 -14 ********** Masking position 7 Map Score: 0.991965 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 26 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 9 TAACTAGTACGCAAGTTCACGTAAAAAGGGTATC 2 110 1 GCAATAGTAA 0.92599 -28 GATCACCCTCGCAGTAAAAGTAAAAAAGTGTCCG 5 96 1 GCAGAATAAA 0.613582 -88 GGCGTAAACGGCAATGACTGGTTAGCATAAATCT 5 136 1 GCAAATGTTA 0.666839 -48 TCCGCACGTTTATGATATGCTATCGTA 6 4 1 GCACTAGATA 0.702044 -86 CAAGGAAAGTGCAATATATTTATATCGATAAAAA 7 52 0 GCAATTTATA 0.833732 -65 CTATAATAGTGCAAATTTATTTTAGAGGCATTTT 7 93 1 GCAATATTTA 0.968559 -24 AGCTGACGCAATCTTAATAAAATGAATGAAA 8 8 1 GCAATATAAA 0.942053 -138 TTGATTGCAAGCAATTTCATTTTAATTTTAAAAA 14 102 0 GCAATATTTA 0.968563 -78 GAAATTGCTTGCAATCAAAATTTATTTGTACTAC 14 118 1 GCAAAATTTA 0.941105 -62 CAACTCTCTTGCAAGCTGAATAAAACGAAATAAT 15 63 0 GCAATATAAA 0.942053 -155 CAAGAGAGTTGTAAAGATAGTTTAATAGGGAATT 15 86 1 GTAAAATTTA 0.534138 -132 GTGTAGATTAGCTACATAATTTAAACACAACATT 15 174 1 GCTATATTAA 0.721618 -44 **** * * **** Masking position 14 Map Score: 3.36718 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 195 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 10 AGCAATCAGATACCCAGCCCGCCTAATGAGCG 1 38 1 TACCCCCCGC 0.977398 -54 GTTATCATGCTAACCACCCGGCGAGGTGTGAC 3 38 1 TAACCCCGGC 0.964914 -119 GTGATGCGCATCACTTCCCGGCAGTCCTGCCG 3 107 1 TCACTCCGGC 0.950351 -50 AGAAATTTGTTGCTTCTACGGCAGGACTGCCG 3 125 0 TGCTTACGGC 0.897352 -32 ACTGCGAGGGTGATCGACCGGCTGGGATTAGG 5 79 0 TGATCCCGGC 0.975252 -105 GGAAGCAAAATGCCTCCCCCGGTTGTACTCGC 6 45 0 TGCCTCCCGG 0.953213 -45 GGAGGCATTTTGCTTCCCCCGCTAACAATGGC 6 60 1 TGCTTCCCGC 0.980884 -30 ***** ***** Masking position 1 Map Score: 0.876124 Number of sites scoring better than the average of aligned sites = 782 Number in coding regions = 724 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 11 CGCTCATTAGGCGGGCTGGGTATCTGATTG 1 40 0 GCGGGCTGGG 0.987173 -52 ATGCTAACCACCCGGCGAGGTGTGACACAC 3 44 1 CCCGGCGAGG 0.968754 -113 AGGGTGATCGACCGGCTGGGATTAGGCGGG 5 75 0 ACCGGCTGGG 0.944599 -109 GCGAGTACAACCGGGGGAGGCATTTTGCTT 6 45 1 CCGGGGGAGG 0.991552 -45 GCCATTGTTAGCGGGGGAAGCAAAATGCCT 6 62 0 GCGGGGGAAG 0.957799 -28 ********** Masking position 5 Map Score: 0.649659 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 301 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 12 ********** No masking Map Score: -2.17836e-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 13 ********** No masking Map Score: -2.17836e-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 14 ********** No masking Map Score: -2.17836e-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