AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00660_ecoli_reg_300.orf -o00660_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 leuO 300 probable transcriptional activator for leuABCD operon #2 ilvI 227 acetolactate synthase III, valine sensitive, large subunit #3 sdhC 300 succinate dehydrogenase, cytochrome b556 #4 BIME45 63 BIME #5 sucC 85 succinyl-CoA synthetase, beta subunit #6 ilvB 105 acetolactate synthase I,valine-sensitive, large subunit #7 ivbL 300 ilvB operon leader peptide #8 ilvL 300 ilvGEDA operon leader peptide #9 ilvG_1 139 acetolactate synthase II, large subunit, cryptic, interrupted #10 ilvM 300 acetolactate synthase II, valine insensitive, small subunit Motif number 1 GTTGACATATTTCAGCATAAATTTTTGCATC 1 13 1 TTCAGATAAA 0.981531 -288 AAACATATAATTCAATACAAATCATCAGGAT 1 90 0 TTCAAACAAA 0.94736 -211 CCAAATCAATATCAAAAAAAATCGCAAAACA 1 116 0 ATCAAAAAAA 0.619986 -185 CAATAAAAAATGCAGAATAAACCAGACATTC 2 35 0 TGCAGATAAA 0.89391 -193 AAATTCTACATTCAATAAAAAATGCAGAATA 2 47 0 TTCAAAAAAA 0.888737 -181 AGCCCACACATTCAGAATAAAATTCTACATT 2 66 0 TTCAGATAAA 0.981531 -162 GGGGTAATAAGAATAAACAGGAGGAAA 2 211 0 ATAAGATAAA 0.684773 -17 ATCACTGTTCAGGATAAAACCCGACAAA 3 8 1 TTCAGATAAA 0.981531 -293 TTATCTGCAATTCAGTACAAAACGTGATCAA 7 183 1 TTCAGACAAA 0.970979 -118 ATAAATATTGTTAAACACAAAACCAACAAGG 7 274 1 TTAAAACAAA 0.781809 -27 AAAATTCAATTTCAGTATGAATGTTGTTCCC 8 128 0 TTCAGATGAA 0.889326 -173 TTGTTGTTTTTTAAAAATAAAATAGTGAGTG 8 162 0 TTAAAATAAA 0.851198 -139 GTTTAATAATTTCAATATAAATTGTTGTTTT 8 183 0 TTCAAATAAA 0.966277 -118 ***** ***** Masking position 7 Map Score: 16.7501 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 129 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 2 CGCCAGGTCTCCGGAACACCCTGCAATCCCGAGC 3 85 1 CCGGAACCGC 0.992809 -216 GAAGGAAATCCCGACGTCTCCAGGTAACAGAAAG 3 219 1 CCGACGCCGG 0.994925 -82 ACCTCTGTGCCCGTAGTCCCCAGGGAATAATAAG 3 256 1 CCGTAGCCGG 0.976191 -45 GGGTGACCGACAATGCCCGGAAGCGATACG 5 7 1 CCGACACCGG 0.992784 -79 CAAAACCCCGCCGGCGCAAACCGGGCGGGGTTTT 6 33 1 CCGGCGACGG 0.942427 -73 AGGTGCTTAAACGAAAAACCCCGCCCGGTTTGCG 6 47 0 ACGAAACCGC 0.871926 -59 TAAGCACCTCCCGGAAAGTCGGCCCAGAAGAAAA 6 72 1 CCGGAACGCC 0.824597 -34 AAAATTCGTGCCGAAATTGCGCGTTCTGCGCGGA 7 56 1 CCGAAACGGT 0.847358 -245 ACAAAAAACCCCGCCGGAGCGAGGTTTCGTCAGT 7 150 0 CCGCCGCGGG 0.955621 -151 GACCCCCGCACCGAAAGGTCCGGGGGTTTTTTTT 9 33 1 CCGAAACCGG 0.992926 -107 GCCATGGATGCCGAAGGCGCTGGCTAACATGAGG 10 119 0 CCGAAGCTGC 0.925809 -182 AACACATCACCCGGAAAGACCAGGTTGAAGCGGC 10 154 1 CCGGAACCGG 0.994756 -147 TTACTGGCGCCAGGCGGCACCAGCGGCCAGACGT 10 253 0 CAGGCGCCGC 0.927875 -48 ****** ** ** Masking position 3 Map Score: 16.9415 Number of sites scoring better than the average of aligned sites = 1373 Number in coding regions = 1297 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 3 AACGAGGAAAAAGGGGACAAAATGCACGCGTTGCA 1 49 1 AAGGACAATC 0.951473 -252 AAATCGGCTGAATCCCACAACTTACAGCAATTTCT 2 126 0 AACCACAATC 0.984703 -102 TTCAGGATAAAACCCGACAAACTATATGTAGGTTA 3 18 1 AACCACAATT 0.934254 -283 TCCAGATGCGAAAACGACACGTTACAACGCTGGGT 3 120 0 AAACACACTC 0.953686 -181 GGACTGGAACAACACACGATTCCAAAACCCCG 6 8 1 AAAAACACTC 0.696922 -98 CTATGCACTAAATACGTCAAAATTCGTGCCGAAAT 7 38 1 AAACTCAATC 0.93013 -263 AAACGTGATCAACCCCTCAATTTTCCCTTGCTGAA 7 202 1 AACCTCAATC 0.935161 -99 GTTAAACACAAAACCAACAAGGTCCCCA 7 283 1 AACCACAATC 0.984703 -18 AACTACGAGGAAGGGAACAACATTCATACTGAAAT 8 116 1 AAGGACAATC 0.951473 -185 TTATTTTTAAAAAACAACAATTTATATTGAAATTA 8 173 1 AAACACAATT 0.929159 -128 AGGTTTTGTAAATAGTACAAGATATTTTTTGGCCG 8 227 0 AAAGACAATT 0.884306 -74 GACAATGAATAACAGCACAAAATTCTGTTTCTCAA 9 93 1 AAAGACAATC 0.97193 -47 ** ** **** * * Masking position 9 Map Score: 13.4772 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 122 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 4 AGGTCTCCGGAACACCCTGCAATCCCGAGC 3 89 1 AACACCCTGC 0.940945 -212 CGCGTCATGCAAAACACTGCTTCCAGATGC 3 146 0 AAAACACTGC 0.870112 -155 ACACGATTCCAAAACCCCGCCGGCGCAAAC 6 24 1 AAAACCCCGC 0.996202 -82 GCTTAAACGAAAAACCCCGCCCGGTTTGCG 6 47 0 AAAACCCCGC 0.996202 -59 CAGATAACAAAAAACCCCGCCGGAGCGAGG 7 160 0 AAAACCCCGC 0.996202 -141 TAACGAACTAAGACCCCCGCACCGAAAGGT 9 22 1 AGACCCCCGC 0.978586 -118 AGGTCAAAAAAAACCCCCGGACCTTTCGGT 9 42 0 AAACCCCCGG 0.966161 -98 ACCCTTACTGATAACCCCGATTTCCTCATG 10 96 1 ATAACCCCGA 0.875972 -205 ********** Masking position 1 Map Score: 13.8286 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 78 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 5 AAGAAACGATAAAATCCTCCATTACAGAGG 2 175 0 AAAATCCTCC 0.86142 -53 TGTTCAGGATAAAACCCGACAAACTATATG 3 16 1 AAAACCCGAC 0.970213 -285 CGGAGGAAGGAAATCCCGACGTCTCCAGGT 3 214 1 AAATCCCGAC 0.92801 -87 CACGATTCCAAAACCCCGCCGGCGCAAACC 6 25 1 AAACCCCGCC 0.995554 -81 CTTAAACGAAAAACCCCGCCCGGTTTGCGC 6 46 0 AAACCCCGCC 0.995554 -60 CACCTCCCGGAAAGTCGGCCCAGAAGAAAA 6 76 1 AAAGTCGGCC 0.920332 -30 AGATAACAAAAAACCCCGCCGGAGCGAGGT 7 159 0 AAACCCCGCC 0.995554 -142 ACGCATCATAAAAATCGGCCAAAAAATATC 8 212 1 AAAATCGGCC 0.951677 -89 ********** Masking position 3 Map Score: 12.6261 Number of sites scoring better than the average of aligned sites = 365 Number in coding regions = 302 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 6 CTGATTGCAGAATAGGTCAG 2 1 1 CTGATTGCAG 0.785002 -227 TCTTTTCACCTTTCCTCCTGTTTATTCTTA 2 201 1 TTTCCTCCTG 0.682883 -27 ACAGCCTATACTGCCGCCAGGTCTCCGGAA 3 71 1 CTGCCGCCAG 0.602966 -230 ATGCAAAACACTGCTTCCAGATGCGAAAAC 3 140 0 CTGCTTCCAG 0.977136 -161 TTCCTCCGGTCTGCTTGCGGGTCAGACAGC 3 192 0 CTGCTTGCGG 0.958626 -109 TCGGGATTTCCTTCCTCCGGTCTGCTTGCG 3 203 0 CTTCCTCCGG 0.945576 -98 ATATTTCGTATCGCTTCCGGGCATTGTCGG 5 17 0 TCGCTTCCGG 0.89192 -69 GTTTCGTCAGTCGCCTGCGGCTGGTAACCG 7 131 0 TCGCCTGCGG 0.808532 -170 ATTTTAGTGGCTGATTCCTGTTTATTTGTG 8 22 1 CTGATTCCTG 0.879059 -279 TGGGCCATACCTGCTTCATGTCTCAATCGA 10 212 1 CTGCTTCATG 0.768134 -89 TTCTGAATTACTGGCGCCAGGCGGCACCAG 10 264 0 CTGGCGCCAG 0.480758 -37 ********** Masking position 10 Map Score: 5.77843 Number of sites scoring better than the average of aligned sites = 3264 Number in coding regions = 2933 Number in noncoding regions = 331 Number of orfs with sites within 600 bp upstream = 218 Fraction of orfs with sites within 600 bp upstream = 0.0350145 Motif number 7 TCAGGATAGGTTTTGCAACGCGTGCATTTT 1 67 0 TTTTGCAACG 0.623161 -234 TGGGCCGACTTTCCGGGAGGTGCTTAAACG 6 68 0 TTCCGGGAGG 0.93267 -38 AGTCCTTTTCTTCTGGGCCGACTTTCCGGG 6 81 0 TTCTGGGCCG 0.946028 -25 AAATTGCGCGTTCTGCGCGGAACACGTATA 7 69 1 TTCTGCGCGG 0.966122 -232 TGGAAAATTTTTCAGCAAGGGAAAATTGAG 7 217 0 TTCAGCAAGG 0.969109 -84 TTTCTCAAGATTCAGGACGGGGAACTAACT 9 120 1 TTCAGGACGG 0.974283 -20 CAACTGTTTTTTCAGGAACGATACAGCGAA 10 63 1 TTCAGGAACG 0.950696 -238 CCCATCACTGTTCAGCATGGTGTCGAGTGC 10 186 0 TTCAGCATGG 0.905081 -115 ********** Masking position 2 Map Score: 4.27845 Number of sites scoring better than the average of aligned sites = 711 Number in coding regions = 665 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 8 AAGAATAAACAGGAGGAAAGGTGAAAAGAA 2 200 0 AGGAGGAAAG 0.944224 -28 GCAAGCAGACCGGAGGAAGGAAATCCCGAC 3 204 1 CGGAGGAAGG 0.995001 -97 AAAACCCCGCCGGAGCGAGGTTTCGTCAGT 7 150 0 CGGAGCGAGG 0.943462 -151 GTTGTTCTGGCGGTGGAATGATGCTCGCAA 8 65 1 CGGTGGAATG 0.95613 -236 AGGATGAACTACGAGGAAGGGAACAACATT 8 110 1 ACGAGGAAGG 0.939106 -191 GCATCTTGTTCGAAGGAATGCCTAAAGAGT 8 268 0 CGAAGGAATG 0.93182 -33 ********** Masking position 8 Map Score: 1.41172 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 118 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 9 TCTAATCAACGAGGAAAAAGGGGACAAAAT 1 42 1 GAGGAAAAAG 0.875239 -259 AACCCCGCCGGCGCAAACCGGGCGGGGTTT 6 36 1 GCGCAAACCG 0.916824 -70 CGCGTTCTGCGCGGAACACGTATACTTTCA 7 75 1 GCGGAACACG 0.984648 -226 CAAAAATGCAGCGGACAAAGGATGAACTAC 8 92 1 GCGGACAAAG 0.887804 -209 TGGCTAACATGAGGAAATCGGGGTTATCAG 10 103 0 GAGGAAATCG 0.910005 -198 CCAGGTTGAAGCGGCACTCGACACCATGCT 10 173 1 GCGGCACTCG 0.967867 -128 CTGGCGCCAGGCGGCACCAGCGGCCAGACG 10 254 0 GCGGCACCAG 0.957553 -47 ********** Masking position 3 Map Score: 1.56363 Number of sites scoring better than the average of aligned sites = 962 Number in coding regions = 905 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 10 GCAGAATAAACCAGACATTCATGTCTGACC 2 25 0 CCAGACATTC 0.986653 -203 AATAGAGAGCCCACACATTCAGAATAAAAT 2 74 0 CCACACATTC 0.944287 -154 GCTCCAGTCCTTTTCTTCTGGGC 6 93 0 CCAGTCCTTT 0.93528 -13 AAAAAAACCCCCGGACCTTTCGGTGCGGGG 9 36 0 CCGGACCTTT 0.907913 -104 GCACCAGCGGCCAGACGTTCTCAAGTTCGT 10 241 0 CCAGACGTTC 0.977457 -60 CCGCCTGGCGCCAGTAATTCAGAAATGTTG 10 270 1 CCAGTAATTC 0.85973 -31 ********** Masking position 8 Map Score: 0.881775 Number of sites scoring better than the average of aligned sites = 438 Number in coding regions = 417 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 11 CATTCAATAAAAAATGCAGAATAAACCAGA 2 40 0 AAAATGCAGA 0.949617 -188 AATTAATCCTAAAATAGAGAGCCCACACAT 2 86 0 AAAATAGAGA 0.962168 -142 ATTAATTAAAAAAATAGAGAAATTGCTGTA 2 109 1 AAAATAGAGA 0.962168 -119 GATGCTCGCAAAAATGCAGCGGACAAAGGA 8 84 1 AAAATGCAGC 0.894634 -217 TTTTAAAAATAAAATAGTGAGTGAAAAAAA 8 155 0 AAAATAGTGA 0.885453 -146 ********** Masking position 5 Map Score: 0.184985 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 46 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 12 ********** No masking Map Score: 4.03831e-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: 4.03831e-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 14 ********** No masking Map Score: 4.03831e-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