AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -itrpR_ecoli_opreg_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 Motif number 1 AACGGGCAGTGTATTCACCATGCG 1 1 1 ACGGGCTGAT 0.987754 -91 CCGCTCATTAGGCGGGCTGGGTATCTGATTGCTT 1 37 0 GCGGGCGGAT 0.991756 -55 CCGCCTAATGAGCGGGCTTTTTTTTGAACAAAAT 1 56 1 ACGGGCTTTT 0.965445 -36 CATGCTAACCACCCGGCGAGGTGTGACACACCTC 3 43 1 ACCGGCGGGT 0.975558 -114 ACGGCAGGACTGCCGGGAAGTGATGCGCATCACG 3 106 0 TCCGGGGTAT 0.893056 -51 GATGGTAAAAATCGGGGCTGTATATATTATTTTA 4 38 0 ACGGGGGTTA 0.95951 -116 GATTTTTACCATCGGGGCTTTTTTTCTGTCTTTT 4 59 1 ACGGGGTTTT 0.965445 -95 GAGGGTGATCGACCGGCTGGGATTAGGCGGGGAA 5 72 0 GCCGGCGGTT 0.977438 -112 AGCGAGTACAACCGGGGGAGGCATTTTGCTTCCC 6 44 1 ACGGGGGGAT 0.995953 -46 CGCCATTGTTAGCGGGGGAAGCAAAATGCCTCCC 6 59 0 ACGGGGAGAA 0.898722 -31 * ***** ** ** Masking position 3 Map Score: 10.786 Number of sites scoring better than the average of aligned sites = 790 Number in coding regions = 711 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 2 TTATCCAGAACGGGAGTGCGCC 2 3 0 CGGGAGTGCG 0.908473 -135 CGTACTAGTTAACTAGTTCGATGATTAATT 2 91 0 AACTAGTTCG 0.955403 -47 CGAACTAGTTAACTAGTACGCAAGTTCACG 2 101 1 AACTAGTACG 0.986011 -37 AGAACTAGTGCATTAGCTTATT 3 3 1 AACTAGTGCA 0.970821 -154 TGTACCAGTACACGAGTACAAAAGACAGAA 4 82 0 CACGAGTACA 0.961159 -72 CTCCAGTGAAAAATAGTGCGACTGCGTTGT 4 124 0 AAATAGTGCG 0.95871 -30 TGTACTCGCTAAAGAGTACGATAGCATATC 6 24 0 AAAGAGTACG 0.968252 -66 CGTACTCTTTAGCGAGTACAACCGGGGGAG 6 34 1 AGCGAGTACA 0.961159 -56 ********** Masking position 5 Map Score: 9.03898 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 189 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 AACGGGCAGTGTATTCACCATGCG 1 4 1 GGGCAGTGTT 0.985629 -88 CTCATTAGGCGGGCTGGGTATCTGATTGCTT 1 37 0 GGGCTGGGTT 0.995098 -55 CCTAATGAGCGGGCTTTTTTTTGAACAAAAT 1 59 1 GGGCTTTTTT 0.924156 -33 GCTAACCACCCGGCGAGGTGTGACACACCTC 3 46 1 CGGCGAGGTT 0.971495 -111 CTGATTTCAAGTGCGAGGTGTGTCACACCTC 3 60 0 GTGCGAGGTT 0.866368 -97 GTAAAAATCGGGGCTGTATATATTATTTTAC 4 37 0 GGGCTGTATT 0.95338 -117 TTTACCATCGGGGCTTTTTTTCTGTCTTTTG 4 63 1 GGGCTTTTTT 0.924156 -91 GGTGATCGACCGGCTGGGATTAGGCGGGGAA 5 72 0 CGGCTGGGAT 0.970636 -112 GTGGCGTAAACGGCAATGACTGGTTAGCATA 5 134 1 CGGCAATGAT 0.843928 -50 ********* * Masking position 11 Map Score: 7.75071 Number of sites scoring better than the average of aligned sites = 888 Number in coding regions = 808 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 4 AGCAATCAGATACCCAGCCCGCCTAATGAG 1 38 1 TACCCAGCCC 0.880624 -54 AGGTGTGTCACACCTCGCCGGGTGGTTAGC 3 46 0 CACCTCGCCG 0.992222 -111 AGGTGTGACACACCTCGCACTTGAAATCAG 3 61 1 CACCTCGCAC 0.964623 -96 TGATGCGCATCACTTCCCGGCAGTCCTGCC 3 108 1 CACTTCCCGG 0.847109 -49 GTTGGACTTCGCCTCTATGTTTAT 5 5 1 GACTTCGCCT 0.944721 -179 AAAAAGGCTACACTTCGCCTTTGAAAACTC 5 44 0 CACTTCGCCT 0.983653 -140 TGTAGCCTTTTTCCCCGCCTAATCCCAGCC 5 62 1 TTCCCCGCCT 0.88323 -122 GGAAGCAAAATGCCTCCCCCGGTTGTACTC 6 47 0 TGCCTCCCCC 0.978225 -43 GGAGGCATTTTGCTTCCCCCGCTAACAATG 6 60 1 TGCTTCCCCC 0.958099 -30 ********** Masking position 3 Map Score: 6.73032 Number of sites scoring better than the average of aligned sites = 1804 Number in coding regions = 1669 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 5 TTTTTTGTTATCATGCTAACCACCCGGCGAG 3 32 1 TCATGCTAAC 0.989829 -125 GTGATGCGCATCACGATAAACCAATCGCTGC 3 90 0 TCACGATAAC 0.989829 -67 AAACTCATTATCACGATAAACATAGAGGCGA 5 19 0 TCACGATAAC 0.989829 -165 CGTAATAGATTTATGCTAACCAGTCATTGCC 5 145 0 TTATGCTAAC 0.977372 -39 TCCGCACGTTTATGATATGCTATCGTACTC 6 10 1 TTATGATATC 0.92401 -80 ********* * Masking position 7 Map Score: 3.82375 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 44 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 CCTAATGAGCGGGCTTTTTTTTGAACAAAA 1 59 1 GGGCTTTTTT 0.975747 -33 TGTCGATACCCTTTTTACGTGAACTT 2 122 0 TACCCTTTTT 0.962071 -16 ACTAGTGCATTAGCTTATTTTTTTGTTATC 3 14 1 TAGCTTATTT 0.883909 -143 TTTACCATCGGGGCTTTTTTTCTGTCTTTT 4 63 1 GGGCTTTTTT 0.975747 -91 AGGCGAAGTGTAGCCTTTTTCCCCGCCTAA 5 54 1 TAGCCTTTTT 0.97981 -130 CCACGTTACGGACACTTTTTTACTTTTACT 5 108 0 GACACTTTTT 0.860533 -76 ********** Masking position 6 Map Score: 3.20346 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 255 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 7 GTGACACACCTCGCACTTGAAATCAGCAGC 3 65 1 TCGCACTTGA 0.957498 -92 GATAAACCAATCGCTGCTGATTTCAAGTGC 3 77 0 TCGCTGCTGA 0.97592 -80 CAGATTGTGTTCGCTGTTCAGCGATGA 4 8 0 TCGCTGTTCA 0.944915 -146 GTTGGACTTCGCCTCTATGTTTATCGTG 5 9 1 TCGCCTCTAT 0.856623 -175 AGGCTACACTTCGCCTTTGAAAACTCATTA 5 40 0 TCGCCTTTGA 0.983595 -144 TCGATCACCCTCGCAGTAAAAGTAAAAAAG 5 94 1 TCGCAGTAAA 0.809055 -90 AATATGTCGCCATTGTTAGCGGGGGA 6 74 0 TCGCCATTGT 0.937107 -16 ********** Masking position 1 Map Score: 1.64596 Number of sites scoring better than the average of aligned sites = 1099 Number in coding regions = 1041 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 8 CGGGCAGTGTATTCACCATGCGTAAAGCAATCAG 1 13 1 ATTACGCGTA 0.956384 -79 ACCCTTTTTACGTGAACTTGCGTACTAGTTAACT 2 107 0 CGTACGCGTA 0.997805 -31 AAAAAGTGTCCGTAACGTGGCGTAAACGGCAATG 5 118 1 CGTAGGCGTA 0.996806 -66 CAATGCAGCGTCATGCCGCGTAATAGATTTAT 5 162 0 CGTAGGCGTA 0.996806 -22 GATAGCATATCATAAACGTGCGGA 6 1 0 CATACGCGGA 0.98097 -89 *** * * ***** Masking position 5 Map Score: 2.88729 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 55 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 TGACACACCTCGCACTTGAAATCAGCAGCGA 3 66 1 CGCATTGAAA 0.961605 -91 AATAGTGCGACTGCGTTGTTATGCATTGCAC 4 112 0 CTGCTTGTTA 0.889182 -42 GAGGGCTTCTCTCCAGTGAAAAATAGTGCGA 4 133 0 CTCCGTGAAA 0.963106 -21 GGCTACACTTCGCCTTTGAAAACTCATTATC 5 38 0 CGCCTTGAAA 0.992407 -146 AATATGTCGCCATTGTTAGCGGGGGAAG 6 72 0 CGCCTTGTTA 0.984533 -18 **** ****** Masking position 7 Map Score: 0.337154 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 316 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 10 ********** No masking Map Score: 1.72905e-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: 1.72905e-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: 1.72905e-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