AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00271_ecoli_reg_100.orf -o00271_ecoli_100.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 TTATACGTCTGGATGTCTAAACTAGCATGAAT 3 66 0 GGATGTAAAC 0.996446 -38 TTAGACATCCAGACGTATAAAAACAGGAATCC 3 78 1 AGACGTAAAA 0.881402 -26 CGCCAATTATGGATGTGTAAACATCTGGACGG 5 64 1 GGATGTAAAC 0.996446 -173 GTAAACATCTGGACGGCTAAAATCCTTCGTCT 5 80 1 GGACGTAAAA 0.986981 -157 TAAGTGACCGGGGTGGAGAAACGCAGCCAACG 5 127 0 GGGTGGAAAC 0.938681 -110 AAGCTCCCGGGGATGAATAAACTTGCCGCCTT 5 166 1 GGATGTAAAC 0.996446 -71 CAATACATCTGGACATCTAAACTTCTTTGCGT 6 186 0 GGACATAAAC 0.957762 -91 TAGAATATAAGAATGACTAAAAGGAGAGAAA 7 10 0 GAATGTAAAA 0.9001 -147 TCAGCTATCTGGATGTCTAAACGTATAAGCGT 7 114 1 GGATGTAAAC 0.996446 -43 ***** ***** Masking position 9 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 CAACAGTTTGAGCTAACCAAATTCTCTTTAG 2 23 1 AGCTACCAAA 0.876596 -33 ATGCTAGTTTAGACATCCAGACGTATAAAAA 3 70 1 AGACTCCAGA 0.995593 -34 AAATCTCCAGAGATGTGTTCA 4 119 0 AAATTCCAGA 0.960421 -11 GAAGGATTTTAGCCGTCCAGATGTTTACACA 5 77 0 AGCCTCCAGA 0.993465 -160 AAAGAAGTTTAGATGTCCAGATGTATTGACG 6 190 1 AGATTCCAGA 0.994683 -87 AGATAGCTGAAGATAACCAGAAAATTTGCCA 7 93 0 AGATACCAGA 0.987862 -64 TTATACGTTTAGACATCCAGATAGCTGAAGA 7 111 0 AGACTCCAGA 0.995593 -46 **** ****** Masking position 9 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 CACAACAGTTTGAGCTAACCAAATTCTCTT 2 21 1 TGAGCTAACC 0.963059 -35 TTCTAACTCCTGAACACATCTCTGGAGATT 4 109 1 TGAACACATC 0.969331 -21 GCGTATAGATTGAGCAAATCCCAAATAGCC 6 160 0 TGAGCAAATC 0.978741 -117 GCGTATGTAGTGAGGTAATCAGGTT 7 142 1 TGAGGTAATC 0.883987 -15 CAATAGTTACTGAACTGATCCGATGAGTTA 8 29 1 TGAACTGATC 0.944977 -132 TTGTTCAACATTAACTCATCGGATCAGTTC 8 40 0 TTAACTCATC 0.803908 -121 GAGTTAATGTTGAACAAATCTCATGTTGCG 8 53 1 TGAACAAATC 0.979153 -108 TAATAAAAATTCAACAAACCATACTGGCAT 8 112 0 TCAACAAACC 0.836421 -49 ********** Masking position 3 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 CATAAAGCAGAAAATTTTCGCAAATGGC 3 9 0 AAAATTTTCG 0.848757 -95 AACTAGCATGAATATTCGCGGGCGCATCCT 3 49 0 AATATTCGCG 0.890248 -55 CAGCCTTAGCAATCTTTGCGATTGGTCAGT 4 31 1 AATCTTTGCG 0.971379 -99 TTCGGCATGAATAATTTGCGCTTGAGGAAT 5 24 1 ATAATTTGCG 0.963453 -213 TTACACATCCATAATTGGCGGTTACTGTAT 5 54 0 ATAATTGGCG 0.937217 -183 GGGGATGAATAAACTTGCCGCCTTCCCTAA 5 174 1 AAACTTGCCG 0.858433 -63 CCTGTACGGTAAACTATGCGGGTTTACGGT 6 73 0 AAACTATGCG 0.910709 -204 GACATCTAAACTTCTTTGCGTATAGATTGA 6 177 0 CTTCTTTGCG 0.806187 -100 AGATAACCAGAAAATTTGCCAATGTCGAGC 7 84 0 AAAATTTGCC 0.879546 -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 5 TAGCAATCTTTGCGATTGGTCAGTGATGCT 4 37 1 TGCGATTGGT 0.958044 -93 TCAATCAGAGGGGGATTTGTCTAGAATAGA 4 68 1 GGGGATTTGT 0.983926 -62 AACGGCTATTTGGGATTTGCTCAATCTATA 6 157 1 TGGGATTTGC 0.983926 -120 TGAAGTTCCCTGGGCTTTGTCGGTGAAATG 6 253 0 TGGGCTTTGT 0.983926 -24 CCACGCAACATGAGATTTGTTCAACATTAA 8 56 0 TGAGATTTGT 0.971591 -105 ********** Masking position 6 Map Score: 2.6204 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 57 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 TGAAGAATTGGCATAAAGCAGAAAATTTTCG 3 19 0 GCATAAGCAG 0.952141 -85 ATTCGCGGGCGCATCCTGAAGAATTGGCATA 3 35 0 GCATCCGAAG 0.975046 -69 TGCTAAGGCTGCTTATGGCAGGGAGATAAGG 4 11 0 GCTTATGCAG 0.93857 -119 CGCAAATTATTCATGCCGAAGTGAAGGACTT 5 13 0 TCATGCGAAG 0.931444 -224 AATAATTTGCGCTTGAGGAATATACAGTAAC 5 33 1 GCTTGAGAAT 0.822411 -204 ATCCCCGGGAGCTTACTGAAGTAAGTGACCG 5 149 0 GCTTACGAAG 0.980828 -88 TGTCGAGCCTGCATGTTGAAGGTGAGAAAGT 7 61 0 GCATGTGAAG 0.978942 -96 ****** **** Masking position 10 Map Score: 2.43532 Number of sites scoring better than the average of aligned sites = 673 Number in coding regions = 607 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 7 AGAAAATCCACACAACAGTTTGAGCTA 2 8 1 CCACACAACA 0.984195 -48 GAAACGCAGCCAACGCACCATAAATTTAAA 5 112 0 CAACGCACCA 0.981142 -125 TAAATTGAGACCAGACCACACAGTTGATGT 6 35 1 CCAGACCACA 0.922487 -242 CGGTGAAATGTCAGGCACCAGAGTAAACAT 6 233 0 TCAGGCACCA 0.925648 -44 AAAGCGACCACCACGCAACATGAGATTTGT 8 66 0 CCACGCAACA 0.989891 -95 AATAAAAATTCAACAAACCATACTGGCATA 8 111 0 CAACAAACCA 0.836565 -50 ********** Masking position 3 Map Score: 2.68827 Number of sites scoring better than the average of aligned sites = 496 Number in coding regions = 467 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 8 GAATATTCGCGGGCGCATCCTGAAGAATTGGC 3 38 0 GGGGATCCTG 0.982259 -66 GTCGGGATTCCTGTTTTTATACG 3 91 0 TCGGTTCCTG 0.98228 -13 CATCCATAATTGGCGGTTACTGTATATTCCTC 5 47 0 TGGGTTACTG 0.986824 -190 ATTCATCCCCGGGAGCTTACTGAAGTAAGTGA 5 152 0 GGGGTTACTG 0.994109 -85 GGTAAACTATGCGGGTTTACGGTCAGTACCCA 6 64 0 GCGGTTACGG 0.98112 -213 *** * ****** Masking position 8 Map Score: 1.8323 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 84 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 GCATGAATATTCGCGGGCGCATCCTGAAGA 3 44 0 TCGCGGGCGC 0.969849 -60 CGTTTCTCCACCCCGGTCACTTACTTCAGT 5 136 1 CCCCGGTCAC 0.986353 -101 GTTTATTCATCCCCGGGAGCTTACTGAAGT 5 158 0 CCCCGGGAGC 0.995381 -79 TTACACGATGTCACGGTAACGCCTGTACGG 6 94 0 TCACGGTAAC 0.913974 -183 ACCGACAAAGCCCAGGGAACTTCATCAC 6 259 1 CCCAGGGAAC 0.978868 -18 CGTTTAGACATCCAGATAGCTGAAGATAAC 7 107 0 TCCAGATAGC 0.820058 -50 ********** Masking position 5 Map Score: 2.0122 Number of sites scoring better than the average of aligned sites = 552 Number in coding regions = 498 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 10 AGTAGGCATTACTTCTTAATA 1 91 0 GTAGGCATTA 0.836354 -11 ATCCTGAAGAATTGGCATAAAGCAGAAAAT 3 24 0 ATTGGCATAA 0.833113 -80 AGATGTTTACACATCCATAATTGGCGGTTA 5 60 0 ACATCCATAA 0.826816 -177 AGTTTACCGTACAGGCGTTACCGTGACATC 6 88 1 ACAGGCGTTA 0.944326 -189 TCACGCCGACAGGTGCATTACACGATGTCA 6 111 0 AGGTGCATTA 0.771449 -166 CGTTAAAATTATATGCATTATCACGCCGAC 6 131 0 ATATGCATTA 0.917116 -146 CAAATCCCAAATAGCCGTTAAAATTATATG 6 146 0 ATAGCCGTTA 0.846412 -131 AGATGTATTGACGTCCATTAACACAATGTT 6 208 1 ACGTCCATTA 0.859646 -69 AACAAACCATACTGGCATAAACGCATCTGT 8 100 0 ACTGGCATAA 0.887875 -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 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 Motif number 12 ********** 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 13 ********** 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