AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i054_ecoli_mtub_100.orf -o054_ecoli_mtub_100.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -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 = 0.58 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 cstC 300 acetylornithine delta-aminotransferase #2 argG 300 argininosuccinate synthetase #3 argD 85 acetylornithine delta-aminotransferase #4 pabA 31 p-aminobenzoate synthetase, component II #5 yhfG 104 orf, hypothetical protein #6 argC 153 N-acetyl-gamma-glutamylphosphate reductase #7 argH 60 argininosuccinate lyase #8 ppa 300 inorganic pyrophosphatase #9 argI 161 ornithine carbamoyltransferase 1 #10 argC 193 argC #11 argH 79 argH #12 ppa 137 ppa Motif number 1 GATTTTACGTCCCGTCTCGGTACACCAAATC 2 18 0 CCCGTCTCGT 0.929377 -283 GTTCTTTTGTACCGGAGCCGCC 4 20 1 ACCGGAGCGC 0.987416 -12 CTTCTGCTCTCCCGGCGTAACCCGGATTTGC 5 41 1 CCCGGCGTAC 0.884985 -64 TACTATCATGACCAGAGGTGTGTCAACA 6 8 0 ACCAGAGGGT 0.780203 -146 GTTTTGTTGGCCGGAGGCGCAGCTTTCCGG 7 10 1 GCCGGAGGGC 0.960284 -51 CTCGTCGGGGTAGTTATTATT 8 1 1 CTCGTCGGGT 0.924258 -300 AAAATCCATAACCGTAGCCGCATTTTTCATA 8 152 0 ACCGTAGCGC 0.970645 -149 CCCCCTTCGACTCGGCGCAGCTAGTGGACAT 10 17 1 CTCGGCGCGC 0.985694 -177 AACTTCGAGTCCCATCGGCGCCGCCCGGCGG 10 117 1 CCCATCGGGC 0.966663 -77 ATCGGCGCCGCCCGGCGGTGTGTCAAGTCCC 10 130 1 CCCGGCGGGT 0.996312 -64 TGTGTCAAGTCCCGGCGCAGTCACCGCGGAA 10 148 1 CCCGGCGCGT 0.996294 -46 CACCGCCACGCCCGTCGGCGTGCGATTCTGC 11 40 1 CCCGTCGGGT 0.99128 -40 ATTCTGCCGAACCGGCCGGGCGACGCTGCCA 12 35 1 ACCGGCCGGC 0.961157 -103 TCGAGCCGGTACCGTGGCAGCGTCGCCCGGC 12 49 0 ACCGTGGCGC 0.936948 -89 CTGCCACGGTACCGGCTCGACTAGGGTGTCC 12 60 1 ACCGGCTCAC 0.789971 -78 ******** ** Masking position 3 Map Score: 24.004 Number of sites scoring better than the average of aligned sites = 2929 Number in coding regions = 2775 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 2 CGAAATTTACTGGAAATTACTGCGCCATTCTGA 1 12 0 TGAAATTTGC 0.944674 -289 ATTTTACTTCTGCATAACATTGCGTTTTTTATT 1 70 1 TGATAACTGC 0.740316 -231 GCATATAAAGTGAATACGTTTGCGATGTGGGTG 1 112 0 TGATACGTGC 0.938357 -189 GAAAGTGAACTGGATATTCATTCACATGATTAG 2 95 0 TGATATTTTC 0.920731 -206 TTTCATTTGTTGAATACTTTTGCCTTCTCCTGC 2 124 1 TGATACTTGC 0.970656 -177 GTGTGTTTTTTGTAAAATAATGCGCTTAAGGGA 2 159 0 TGAAAATTGC 0.809035 -142 CCGCTCTCACTGAATTTTTATGCAAAATAAATG 2 235 0 TGATTTTTGC 0.973239 -66 TGCCATTTAGTGATTTTTTATGCATATTTTGTG 3 19 1 TGTTTTTTGC 0.854455 -67 AAATACTGCATGAATATTGATACTATCATGACC 6 26 0 TGATATTTAC 0.741305 -128 TCAACGTTAGTGTATTTTTATTCATAAATACTG 6 51 0 TGATTTTTTC 0.920731 -103 TTCCTTATTTTGAAATTCAATGCCGGAAAGCTG 7 30 0 TGAATTCTGC 0.843612 -31 ATCACAAGTTTGTAATCGCTTTCATCTCACTAT 8 122 1 TGAATCGTTC 0.695361 -179 GCTACGGTTATGGATTTTCCTGCTCTGTATACC 8 165 1 TGATTTTTGC 0.973239 -136 TGTCTTCGCTTGTTTTCGTCTTCATTTTCCTTT 8 215 0 TGTTTCGTTC 0.439717 -86 CCATATAAATTGAATTTTAATTCATTGAGGCGT 9 121 1 TGATTTTTTC 0.920731 -41 GGAATGAGTTTGCAAACTGTTGCATAACG 10 175 1 TGAAACTTGC 0.939505 -19 ** ***** *** Masking position 11 Map Score: 18.3862 Number of sites scoring better than the average of aligned sites = 357 Number in coding regions = 309 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 3 GGAAATTACTGCGCCATTCTGAC 1 1 0 GGCATCTGAC 0.986611 -300 TTTCTCGCGCGGGCAATCTTGCCCGCGCTTCTG 5 14 1 GGCATTTGCC 0.986609 -91 CATGTGTCACGGGAAATTCAGCCTAGTTGGGTC 10 45 1 GGAATCAGCC 0.929312 -149 GGGCGTGGCGGTGCGATTCTGCGTCTGCTCGCG 11 20 0 GGCATCTGCG 0.995734 -60 GCCCGTCGGCGTGCGATTCTGCGTCTGCTCGCC 11 49 1 GGCATCTGCG 0.995734 -31 GAGCTCTCCTGCCTTTCCGGTCC 12 1 1 GGCCTCTGCC 0.994327 -137 TGCCTTTCCGGTCCCATTCTGCCGAACCGGCCG 12 20 1 GCCATCTGCC 0.990863 -118 CGAACCGGCCGGGCGACGCTGCCACGGTACCGG 12 42 1 GGCACCTGCC 0.994193 -96 * ** ** ***** Masking position 11 Map Score: 13.8263 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 153 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 4 TGGTTATAACTCCTTGATTTCCAGTTAGCCTC 1 164 1 TCTTGTTTCC 0.867235 -137 CTTTTGCCTTCTCCTGCTCTCCCTTAAGCGCA 2 140 1 CCCTGTCTCC 0.987389 -161 TTTCTGATTGCCATTTAGTGAT 3 1 1 TTCTGTTGCC 0.968169 -85 CTTGCCCGCGCTTCTGCTCTCCCGGCGTAACC 5 31 1 CTCTGTCTCC 0.983822 -74 CACCTTCTTATGTCTGGTTGCCAGGTTAAACG 6 122 0 TTCTGTTGCC 0.968169 -32 CGAATGTCTTCGCTTGTTTTCGTCTTCATTTT 8 220 0 CCTTGTTTCG 0.858572 -81 TAATACTCGGCACTTGTTTGCCACATATTTTT 8 266 1 CCTTGTTGCC 0.975099 -35 TGCGATTCTGCGTCTGCTCGCGGGAGAACCG 11 10 0 CTCTGTCGCG 0.973254 -70 TGCGATTCTGCGTCTGCTCGCCACAGAAAA 11 60 1 CTCTGTCGCC 0.9917 -20 * **** ***** Masking position 5 Map Score: 10.5657 Number of sites scoring better than the average of aligned sites = 933 Number in coding regions = 898 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 5 GTTTGCGATGTGGGTGAATAAAAAGAATAA 1 98 0 TGGGTGAATA 0.795784 -203 AAGTGCATATAAAGTGAATACGTTTGCGAT 1 119 0 AAAGTGAATA 0.97511 -182 ATATGCATTTAAAGTGCATATAAAGTGAAT 1 130 0 AAAGTGCATA 0.974616 -171 GCCAGTGATAAAAGTGCATAAACGGCGGAG 1 193 0 AAAGTGCATA 0.974616 -108 CACCAGCCGTAAGGTGAATGTTTTACGTTT 6 97 1 AAGGTGAATG 0.956034 -57 CAGACATAAGAAGGTGAATAGCCCCG 6 138 1 AAGGTGAATA 0.974619 -16 ACACTTCAAAAAAGTAAATAAAACGTTAAT 8 94 1 AAAGTAAATA 0.813946 -207 CCTTCAGATCAGAGTGCATGGGACAACGGG 12 109 0 AGAGTGCATG 0.924887 -29 ********** Masking position 8 Map Score: 7.35615 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 100 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 6 GTCAGAATGGCGCAGTAATTTCC 1 4 1 AGAATGGCGC 0.986195 -297 CCGGTACAAAAGAACCGCGCTATT 4 5 0 AGAACCGCGC 0.984018 -27 CCGGGAGAGCAGAAGCGCGGGCAAGATTGC 5 26 0 AGAAGCGCGG 0.933852 -79 GAGCAGACGCAGAATCGCACCGCCACGCCC 11 23 1 AGAATCGCAC 0.988626 -57 GAGCAGACGCAGAATCGCACGCCGACGGGC 11 49 0 AGAATCGCAC 0.988626 -31 CCGGTTCGGCAGAATGGGACCGGAAAGGCA 12 20 0 AGAATGGGAC 0.912411 -118 ********** Masking position 4 Map Score: 5.85804 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 113 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 ATGGCGCAGTAATTTCCAGTAAATTTCGTC 1 17 1 AATTTCCAGT 0.667257 -284 ATAACTCCTTGATTTCCAGTTAGCCTCCGC 1 169 1 GATTTCCAGT 0.923368 -132 GCCTTCTCCTGCTCTCCCTTAAGCGCATTA 2 145 1 GCTCTCCCTT 0.814311 -156 GATGAGCCTGGATTTCCGCTCTCACTGAAT 2 253 0 GATTTCCGCT 0.58041 -48 TTTCTGATTGCCATTTAGTGATTTT 3 6 1 GATTGCCATT 0.369635 -80 TGATTTCTCGCGCGGGCAATC 5 2 1 GATTTCTCGC 0.853561 -103 GCGCGGGCAAGATTGCCCGCGCGAGAAATC 5 12 0 GATTGCCCGC 0.965094 -93 CCGCGCTTCTGCTCTCCCGGCGTAACCCGG 5 36 1 GCTCTCCCGG 0.881557 -69 GCGTAACCCGGATTTGCCGCTTATACTTGT 5 55 1 GATTTGCCGC 0.896254 -50 CGGAGGCGCAGCTTTCCGGCATTGAATTTC 7 22 1 GCTTTCCGGC 0.957736 -39 ACGGTTATGGATTTTCCTGCTCTGTATACC 8 168 1 ATTTTCCTGC 0.541386 -133 AACTAGGCTGAATTTCCCGTGACACATGTC 10 43 0 AATTTCCCGT 0.890057 -151 GAAAACGTGCGTTTTCCCTCACATGACATA 10 79 0 GTTTTCCCTC 0.881502 -115 CGGTTCTCCCGCGAGCAGACGC 11 3 1 GTTCTCCCGC 0.961243 -77 GAGCTCTCCTGCCTTTCCGGTC 12 3 1 GCTCTCCTGC 0.89853 -135 ********** Masking position 3 Map Score: 8.47229 Number of sites scoring better than the average of aligned sites = 3023 Number in coding regions = 2836 Number in noncoding regions = 187 Number of orfs with sites within 600 bp upstream = 202 Fraction of orfs with sites within 600 bp upstream = 0.0324446 Motif number 8 CGTTTATGCACTTTTATCACTGGCTGGCACGAA 1 199 1 CTTTTCACGG 0.991351 -102 TGAACGTGTCCATTTGCCACAAGTATAAGCGGC 5 70 0 CTTTCCACAG 0.978469 -35 GTAAATAAAACGTTAATCACAAGTTTGTAATCG 8 107 1 CTTATCACAG 0.975286 -194 TCTTCATTTTCCTTTTTCACCAGTTTTAAGACG 8 197 0 CTTTTCACAG 0.986466 -104 TTCATTGAGGCGTTAGCCACAGGAGGGATCT 9 141 1 CTTACCACGG 0.980671 -21 AGCTAGTGGACATGTGTCACGGGAAATTCAGCC 10 35 1 CTGTTCACGG 0.968378 -159 * *** **** ** Masking position 9 Map Score: 4.80732 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 46 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 TTACTGGAAATTACTGCGCCATTCTGAC 1 9 0 TTACTGCGCC 0.533158 -292 ATTTCCAGTTAGCCTCCGCCGTTTATGCAC 1 180 1 AGCCTCCGCC 0.968764 -121 TGAATACTTTTGCCTTCTCCTGCTCTCCCT 2 134 1 TGCCTTCTCC 0.674176 -167 CGGGCAAGATTGCCCGCGCGAGAAATCA 5 9 0 TGCCCGCGCG 0.965302 -96 CGGGCAATCTTGCCCGCGCTTCTGCTCTCC 5 23 1 TGCCCGCGCT 0.933055 -82 TTGATGCCTCCCTGAACGTGTCCA 5 91 0 TGCCTCCCTG 0.746324 -14 CGGAAAGCTGCGCCTCCGGCCAACAAAAC 7 10 0 CGCCTCCGGC 0.843018 -51 CCACTGACATTGCCTCCACCTTTGTGACAA 9 56 1 TGCCTCCACC 0.954764 -106 GACTCGAAGTTGCGTCCGCGAAAACGTGCG 10 98 0 TGCGTCCGCG 0.987644 -96 CATTCCGCGGTGACTGCGCCGGGACTTGAC 10 151 0 TGACTGCGCC 0.945471 -43 GGTGCGATTCTGCGTCTGCTCGCGGGAGAA 11 14 0 TGCGTCTGCT 0.835092 -66 CGTGCGATTCTGCGTCTGCTCGCCACAGAA 11 58 1 TGCGTCTGCT 0.835092 -22 GCAGGTCCAATGCGTCCGTGGACACCCTAG 12 80 0 TGCGTCCGTG 0.919905 -58 ********** Masking position 2 Map Score: 8.00015 Number of sites scoring better than the average of aligned sites = 2917 Number in coding regions = 2799 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 10 TCTGCATAACATTGCGTTTTTTATTCTTTTTA 1 78 1 ATGCGTTTTT 0.786299 -223 GGAAGAGTTTAGTGTGTTTTTTGTAAAATAAT 2 171 0 ATGTGTTTTT 0.814044 -130 ATGCAAAATAAATGAGTTTTCATTTAATCATC 2 217 0 ATGAGTTTTA 0.974254 -84 TTCCGCTCTCACTGAATTTTTATGCAAAATAA 2 238 0 ATGAATTTTA 0.95977 -63 ATTGCCATTTAGTGATTTTTTATGCATATTTT 3 17 1 ATGATTTTTA 0.878806 -69 GCTCAACGTTAGTGTATTTTTATTCATAAATA 6 54 0 ATGTATTTTA 0.897264 -100 GCTTTCCGGCATTGAATTTCAAAATAAGGAAA 7 32 1 ATGAATTTCA 0.863696 -29 ATCCATATAAATTGAATTTTAATTCATTGAGG 9 119 1 ATGAATTTTA 0.95977 -43 GTCACCGCGGAATGAGTTTGCAAACTGTTGCA 10 167 1 ATGAGTTTGA 0.909509 -27 * ******** * Masking position 7 Map Score: 4.31032 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 78 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 11 ACGTGTCCATTTGCCACAAGTATAAGCGGC 5 70 0 TTGCCACAAG 0.94252 -35 TGTTGACACACCTCTGGTCATG 6 3 1 TTGACACACC 0.977756 -151 CGGCACTTGTTTGCCACATATTTTTAAAGG 8 273 1 TTGCCACATA 0.940663 -28 GATACTCTTATTGTCACACACCACTGACAT 9 36 1 TTGTCACACA 0.97603 -126 GCATAAATCTTTGTCACAAAGGTGGAGGCA 9 66 0 TTGTCACAAA 0.947567 -96 GCGCCGGGACTTGACACACCGCCGGGCGGC 10 136 0 TTGACACACC 0.977756 -58 ********** Masking position 6 Map Score: 3.50315 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 44 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 12 GTATTCAACAAATGAAAGTGAACTGGATATT 2 110 0 AATGAAATGA 0.839287 -191 AGAGCAGGAGAAGGCAAAAGTATTCAACAAA 2 129 0 AAGGCAAAGT 0.927964 -172 ATTTCAAAATAAGGAAACAGAGTT 7 47 1 AAGGAAAAGA 0.984371 -14 ACTGGTGAAAAAGGAAAATGAAGACGAAAAC 8 206 1 AAGGAAATGA 0.971229 -95 CATATTTTTAAAGGAAACAGAC 8 289 1 AAGGAAAAGA 0.984371 -12 TGGGACCGGAAAGGCAGGAGAGCTC 12 5 0 AAGGCAGAGA 0.95023 -133 ******* *** Masking position 6 Map Score: 2.8375 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 20 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 13 AATCAAGGAGTTATAACCAAACCATATGCA 1 153 0 TTATAACCAA 0.974772 -148 AAATGTGAAATTATAACCACAAAATATGCA 3 39 0 TTATAACCAC 0.957749 -47 CGCGAACATCTTTTAACCAATAATAACTAC 8 20 0 TTTTAACCAA 0.938626 -281 GTGCCGAGTATTATAGCCAACTCGCGCCGA 8 249 0 TTATAGCCAA 0.957746 -52 ********** Masking position 5 Map Score: 0.368896 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 6 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 14 TTCCAGTTAGCCTCCGCCGTTTATGCACTT 1 182 1 CCTCCGCCGT 0.823957 -119 TGATTTCTCGCGCGGGCAATCTTGCC 5 7 1 CTCGCGCGGG 0.567774 -98 CGCTTCTGCTCTCCCGGCGTAACCCGGATT 5 39 1 CTCCCGGCGT 0.956687 -66 AAAGCTGCGCCTCCGGCCAACAAAAC 7 7 0 CTCCGGCCAA 0.796553 -54 TTATAGCCAACTCGCGCCGAATGTCTTCGC 8 239 0 CTCGCGCCGA 0.968553 -62 CTCGAAGTTGCGTCCGCGAAAACGTGCGTT 10 96 0 CGTCCGCGAA 0.884112 -98 CCATCGGCGCCGCCCGGCGGTGTGTCAAGT 10 128 1 CGCCCGGCGG 0.941344 -66 CGGTTCTCCCGCGAGCAGACGCAGA 11 6 1 CTCCCGCGAG 0.556782 -74 GACGCAGAATCGCACGCCGACGGGCGTGGC 11 44 0 CGCACGCCGA 0.948862 -36 GTGGCAGCGTCGCCCGGCCGGTTCGGCAGA 12 37 0 CGCCCGGCCG 0.793988 -101 AGGTCCAATGCGTCCGTGGACACCCTAGTC 12 78 0 CGTCCGTGGA 0.75324 -60 ********** Masking position 1 Map Score: 7.43912 Number of sites scoring better than the average of aligned sites = 2706 Number in coding regions = 2583 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 15 GGCTGGCACGAACCCTGCAATCTACATTTA 1 220 1 AACCCTGCAA 0.925066 -81 GGTACACCAAATCCCAGCAG 2 1 0 ATCCCAGCAG 0.984707 -300 GATCACTATAATGCCTGCAGATTTTACGTC 2 38 0 ATGCCTGCAG 0.963031 -263 AGCGTAATAAAACCCACCAGCCGTAAGGTG 6 83 1 AACCCACCAG 0.96862 -71 AGATCCCTCCTGTGGCTAACGC 9 150 0 ATCCCTCCTG 0.950649 -12 ********** Masking position 1 Map Score: 0.267626 Number of sites scoring better than the average of aligned sites = 327 Number in coding regions = 302 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727