AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00271_ecoli_reg_300.orf -o00271_ecoli_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -x5 -e 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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 metG 101 methionine tRNA synthetase #2 metK 55 methionine adenosyltransferase 1 (AdoMet synthetase); methyl and propylamine donor, corepressor of met genes #3 metC 103 cystathionine beta-lyase (beta-cystathionase) #4 def 129 peptide deformylase #5 metE 236 tetrahydropteroyltriglutamate methyltransferase #6 metB 276 cystathionine gamma-synthase #7 metA 156 homoserine transsuccinylase #8 metH 160 B12-dependent homocysteine-N5-methyltetrahydrofolate transmethylase, repressor of metE and metF Motif number 1 ATTCATGCTAGTTTAGACATCCAGACGTATAA 3 66 1 GTTTACATCC 0.995643 -38 GGATTCCTGTTTTTATACGTCTGGATGTCTAA 3 78 0 TTTTACGTCT 0.858297 -26 CCGTCCAGATGTTTACACATCCATAATTGGCG 5 64 0 GTTTACATCC 0.995643 -173 AGACGAAGGATTTTAGCCGTCCAGATGTTTAC 5 80 0 TTTTACGTCC 0.984072 -157 CGTTGGCTGCGTTTCTCCACCCCGGTCACTTA 5 127 1 GTTTCCACCC 0.925796 -110 AAGGCGGCAAGTTTATTCATCCCCGGGAGCTT 5 166 0 GTTTACATCC 0.995643 -71 ACGCAAAGAAGTTTAGATGTCCAGATGTATTG 6 186 1 GTTTATGTCC 0.948668 -91 TTTCTCTCCTTTTAGTCATTCTTATATTCTA 7 10 1 TTTTACATTC 0.880143 -147 ACGCTTATACGTTTAGACATCCAGATAGCTGA 7 114 0 GTTTACATCC 0.995643 -43 ***** ***** Masking position 4 Map Score: 16.1133 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 140 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 2 CTAAAGAGAATTTGGTTAGCTCAAACTGTTG 2 23 0 TTTGGTAGCT 0.872598 -33 TTTTTATACGTCTGGATGTCTAAACTAGCAT 3 70 0 TCTGGAGTCT 0.99543 -34 TGAACACATCTCTGGAGATTT 4 119 1 TCTGGAATTT 0.959012 -11 TGTGTAAACATCTGGACGGCTAAAATCCTTC 5 77 1 TCTGGAGGCT 0.993224 -160 CGTCAATACATCTGGACATCTAAACTTCTTT 6 190 0 TCTGGAATCT 0.994487 -87 TGGCAAATTTTCTGGTTATCTTCAGCTATCT 7 93 1 TCTGGTATCT 0.987417 -64 TCTTCAGCTATCTGGATGTCTAAACGTATAA 7 111 1 TCTGGAGTCT 0.99543 -46 ****** **** Masking position 3 Map Score: 12.5694 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 37 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 3 AAGAGAATTTGGTTAGCTCAAACTGTTGTG 2 21 0 GGTTAGCTCA 0.970117 -35 AATCTCCAGAGATGTGTTCAGGAGTTAGAA 4 109 0 GATGTGTTCA 0.975222 -21 GGCTATTTGGGATTTGCTCAATCTATACGC 6 160 1 GATTTGCTCA 0.982856 -117 AACCTGATTACCTCACTACATACGC 7 142 0 GATTACCTCA 0.904658 -15 TAACTCATCGGATCAGTTCAGTAACTATTG 8 29 0 GATCAGTTCA 0.95533 -132 GAACTGATCCGATGAGTTAATGTTGAACAA 8 40 1 GATGAGTTAA 0.836204 -121 CGCAACATGAGATTTGTTCAACATTAACTC 8 53 0 GATTTGTTCA 0.98319 -108 ATGCCAGTATGGTTTGTTGAATTTTTATTA 8 112 1 GGTTTGTTGA 0.864266 -49 ********** Masking position 10 Map Score: 6.2452 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 228 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 CAGCATCACTGACCAATCGCAAAGATTGCT 4 38 0 GACCAATCGC 0.945829 -92 TTCTATTCTAGACAAATCCCCCTCTGATTG 4 69 0 GACAAATCCC 0.992193 -61 CTAACTCCTGAACACATCTCTGGAGATTT 4 111 1 AACACATCTC 0.929631 -19 GTATAGATTGAGCAAATCCCAAATAGCCGT 6 158 0 AGCAAATCCC 0.967495 -119 ACATTTCACCGACAAAGCCCAGGGAACTTC 6 252 1 GACAAAGCCC 0.979063 -25 GTTAATGTTGAACAAATCTCATGTTGCGTG 8 55 1 AACAAATCTC 0.973065 -106 ********** Masking position 6 Map Score: 3.87774 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 68 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 5 CATAAAGCAGAAAATTTTCGCAAATGGC 3 9 0 AAAATTTTCG 0.84673 -95 AACTAGCATGAATATTCGCGGGCGCATCCT 3 49 0 AATATTCGCG 0.888704 -55 CAGCCTTAGCAATCTTTGCGATTGGTCAGT 4 31 1 AATCTTTGCG 0.970939 -99 TTCGGCATGAATAATTTGCGCTTGAGGAAT 5 24 1 ATAATTTGCG 0.962896 -213 TTACACATCCATAATTGGCGGTTACTGTAT 5 54 0 ATAATTGGCG 0.936286 -183 GGGGATGAATAAACTTGCCGCCTTCCCTAA 5 174 1 AAACTTGCCG 0.856514 -63 CCTGTACGGTAAACTATGCGGGTTTACGGT 6 73 0 AAACTATGCG 0.909424 -204 GACATCTAAACTTCTTTGCGTATAGATTGA 6 177 0 CTTCTTTGCG 0.803722 -100 AGATAACCAGAAAATTTGCCAATGTCGAGC 7 84 0 AAAATTTGCC 0.877872 -73 ********** Masking position 5 Map Score: 4.05165 Number of sites scoring better than the average of aligned sites = 650 Number in coding regions = 565 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 6 GCCAATTCTTCAGGATGCGCCCGCGAATATTC 3 38 1 CAGGATCGCC 0.959417 -66 CGTATAAAAACAGGAATCCCGAC 3 91 1 CAGGAACCCA 0.944026 -13 CTGCCATAAGCAGCCTTAGCAATCTTTGCGAT 4 21 1 CAGCCTAGCA 0.84157 -109 ACTGTATATTCCTCAAGCGCAAATTATTCATG 5 29 0 CCTCAACGCA 0.855679 -208 GAGGAATATACAGTAACCGCCAATTATGGATG 5 47 1 CAGTAACGCA 0.96808 -190 TGGAGAAACGCAGCCAACGCACCATAAATTTA 5 114 0 CAGCCACGCC 0.990843 -123 TCACTTACTTCAGTAAGCTCCCGGGGATGAAT 5 152 1 CAGTAACTCC 0.862512 -85 AATAAACTTGCCGCCTTCCCTAAATTCAAAAT 5 181 1 CCGCCTCCCA 0.944886 -56 TGGGTACTGACCGTAAACCCGCATAGTTTACC 6 64 1 CCGTAACCCC 0.96429 -213 TGACATTTCACCGACAAAGCCCAGGGAACTTC 6 250 1 CCGACAAGCC 0.795248 -27 ****** *** * Masking position 10 Map Score: 3.09304 Number of sites scoring better than the average of aligned sites = 3738 Number in coding regions = 3586 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 7 TATGCCAATTCTTCAGGATGCGCCCGCGAA 3 35 1 CTTCAGGATG 0.924688 -69 AAGTCCTTCACTTCGGCATGAATAATTTGC 5 13 1 CTTCGGCATG 0.986955 -224 GGCTAAAATCCTTCGTCTTTTAAATTTATG 5 94 1 CTTCGTCTTT 0.84379 -143 CGGTCACTTACTTCAGTAAGCTCCCGGGGA 5 149 1 CTTCAGTAAG 0.875718 -88 ACTTAATCCTCTTCGTCAATAAATTGAGAC 6 16 1 CTTCGTCAAT 0.904769 -261 ACTTTCTCACCTTCAACATGCAGGCTCGAC 7 61 1 CTTCAACATG 0.923054 -96 TTCTGGTTATCTTCAGCTATCTGGATGTCT 7 102 1 CTTCAGCTAT 0.910438 -55 ********** Masking position 3 Map Score: 1.67852 Number of sites scoring better than the average of aligned sites = 845 Number in coding regions = 803 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 8 AGTAGGCATTACTTCTTAATA 1 91 0 GTAGGCATTA 0.842632 -11 ATCCTGAAGAATTGGCATAAAGCAGAAAAT 3 24 0 ATTGGCATAA 0.839492 -80 AGATGTTTACACATCCATAATTGGCGGTTA 5 60 0 ACATCCATAA 0.833387 -177 AGTTTACCGTACAGGCGTTACCGTGACATC 6 88 1 ACAGGCGTTA 0.946726 -189 TCACGCCGACAGGTGCATTACACGATGTCA 6 111 0 AGGTGCATTA 0.779563 -166 CGTTAAAATTATATGCATTATCACGCCGAC 6 131 0 ATATGCATTA 0.920548 -146 CAAATCCCAAATAGCCGTTAAAATTATATG 6 146 0 ATAGCCGTTA 0.852374 -131 AGATGTATTGACGTCCATTAACACAATGTT 6 208 1 ACGTCCATTA 0.865176 -69 AACAAACCATACTGGCATAAACGCATCTGT 8 100 0 ACTGGCATAA 0.892431 -61 ********** Masking position 8 Map Score: 0.895843 Number of sites scoring better than the average of aligned sites = 812 Number in coding regions = 722 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 9 ********** No masking Map Score: 2.63855e-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 10 ********** No masking Map Score: 2.63855e-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: 2.63855e-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