AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00400_ctra_reg_100.orf -o00400_ctra_100.ace -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -g0.41 -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 = 0.41 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 tyrS 158 tyrosyl tRNA Synthetase #2 trpB 300 Tryptophan Synthase (Beta Chain) #3 trpC 196 Phosphoribosylanthranilate Isomerase #4 aroA 169 Phosphoshikimate 1-carboxyl vinyltransferase #5 aroG 136 phospho-2-dehydro-3-deoxyheptonate aldolase #6 CT389 181 hypothetical protein #7 aspC 89 Aspartate Aminotransferase #8 eno 161 Enolase #9 tyrB 187 Aromatic AA Aminotransferase #10 infC 300 Initiation Factor 3 Motif number 1 AAAAACGACGCGCTTCTCCAATAGAATATT 1 50 0 CGCTTCTCCA 0.920481 -109 CTTTTCTCCATAAAATTATA 2 291 0 CTTTTCTCCA 0.916226 -10 TATGCTAATCTTCTTGTCTTACTTTTTTCT 3 137 1 TTCTTGTCTT 0.867486 -60 ATTAAACGTTCTCTTCTCTTCAAGAGAAGA 5 15 1 CTCTTCTCTT 0.988082 -122 AAAAAACGCCCTCTTCTCTTGAAGAGAAGA 5 26 0 CTCTTCTCTT 0.988082 -111 CTTTCTATTTCTTTTCTCTTCCCTGTGTGT 5 68 1 CTTTTCTCTT 0.948191 -69 TTTTCCTTGTTTCTTCTCTTAACTCATGAA 5 109 0 TTCTTCTCTT 0.968214 -28 CACTCGAGCGCTCTTCTCCTAAAAATCTTG 6 110 1 CTCTTCTCCT 0.98555 -72 AAAATCTTGTTTTTTCTCTACTTCCGAGTT 6 131 1 TTTTTCTCTA 0.830059 -51 CTCCCTCCGAGCCTTCTCTTTGTATTGCGG 8 65 1 GCCTTCTCTT 0.89577 -97 AACAAGATCCTTGTCTAGAACGGTTAA 8 145 0 TCCTTGTCTA 0.748639 -17 GCCACCCTTCTCCAAGAAGAGGGA 10 287 0 CCCTTCTCCA 0.96878 -14 ********** Masking position 5 Map Score: 16.6745 Number of sites scoring better than the average of aligned sites = 315 Number in coding regions = 314 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 2 ATCCTGTTCTTTTTATAGCAAGGCAAGCGATAGCAG 1 92 0 TTTTAAAGGA 0.981799 -67 AAGCGCCAGCTTTCAAAAGAAAGCCAGGCACGCTGT 2 131 0 TTTCAAAAGA 0.921162 -170 TATCCAAGAGATTTATATCAAAGCAATAGAAAATAA 3 103 0 ATTTAAAAGA 0.796123 -94 AAACATAAAATCTTTCAACAAGATTAATTATAACAA 4 15 1 TCTTAAAGAA 0.921161 -155 ATAAAATCCTTTTCATAACAAAAAAATAGAACTTAT 4 55 1 TTTCAAAAAA 0.878598 -115 ATGTCTATTTTCTAAAAAGGTTAAAAATGAATA 4 147 0 TTTTAAAGGA 0.9818 -23 ATAGAAAGATTTTTCAATGAAAAAAACGCCCTCTTC 5 40 0 TTTTAAAAAA 0.954163 -97 GCTATGATCCTTTTCTACTAAGGGAATCTCCCTCCG 8 38 1 TTTTAAAGGA 0.981622 -124 TACTGTCTTTTTTTCCAGTAAGATGACAGCTTGTTG 9 132 0 TTTTAAAGAA 0.971188 -56 ACAGGTCCGCTCTTTCATAAAAATAATGACTCATAT 10 37 0 TCTTAAAAAA 0.879512 -264 TCGAGAGTTTTTTTGAAATAAAAAAATGTTTTGTAT 10 86 1 TTTTAAAAAA 0.954661 -215 TAAAAAAATGTTTTGTATGAAGGTTCAAAAGGTCTA 10 104 1 TTTTAAAGGC 0.902566 -197 **** * **** * Masking position 7 Map Score: 11.1087 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 157 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 3 TTATTCTGTCGCCAGTTTTTTCTATGATTTT 2 255 1 GCCAGTTTTT 0.901503 -46 TAGCATATCCAAGAGATTTATATCAAAGCAA 3 113 0 AAGAGTTTAT 0.680505 -84 TAATCTTGTTGAAAGATTTTATGTTTTTTT 4 10 0 GAAAGTTTTA 0.897877 -160 TTTTGTTATGAAAAGGATTTTATTTTGTTGT 4 47 0 AAAAGATTTT 0.6192 -123 TAGTCTTCGGAAGAGTTTTTTGCATGATATT 4 109 0 AAGAGTTTTT 0.943496 -61 AAAAGAAATAGAAAGATTTTTCAATGAAAAA 5 52 0 GAAAGTTTTT 0.972343 -85 TAGAGAAAAAACAAGATTTTTAGGAGAAGAG 6 120 0 ACAAGTTTTT 0.833093 -62 CCAGTAAGATGACAGCTTGTTGTCCTAAATC 9 123 0 GACAGTTGTT 0.901454 -65 GTGCGCTATAGAGAGGTTTTATT 9 175 1 GAGAGTTTTA 0.918838 -13 AGGGGCGATCGAGAGTTTTTTTGAAATAAAA 10 78 1 GAGAGTTTTT 0.978546 -223 TCGCGAATGCGAAAGATTGTTTAGGCCAGAA 10 249 1 GAAAGTTGTT 0.931377 -52 ***** ***** Masking position 4 Map Score: 8.09887 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 240 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 4 TGAATATCTTGGAAGCAATCAGCTTGAAAAGCTG 2 82 0 GGAAGAAAGT 0.895116 -219 TAAGATCATACGAGGGAAATAAGTTCTATTTTTT 4 75 0 CGAGGAAAAT 0.982011 -95 AGAGAAGAAACAAGGAAAACAAATCTA 5 120 1 CAAGGAAAAT 0.91489 -17 AAGAATTTTAGGAGGCAATGAAATCCAGAATGAG 6 54 0 GGAGGAAAAT 0.985427 -128 AGGATCATAGCGAGGGATTCAATTCTGTGGTATC 8 15 0 CGAGGATAAT 0.966257 -147 CATGCTCATCGGAGGAAATTAGATAAAACGAGCG 8 100 1 GGAGGAAAGT 0.988643 -62 GCTAATACCCCGAGGGAAGAAACTAGGTTATCAT 9 81 1 CGAGGAAAAT 0.982011 -107 TCTTATGGAAGAAGGAGTGAAGTTTTAGGCGCAA 10 149 1 GAAGGGTAGT 0.814658 -152 AGTCTAGAGCGGAGGCGTCTAGATTACGTCGCGA 10 221 1 GGAGGGTAGT 0.957121 -80 ***** ** ** * Masking position 11 Map Score: 7.59725 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 34 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 5 TATTGATAGGAAAAATACAGAGAGGATCTTCT 1 22 0 AAAAACAGAG 0.943966 -137 CCTTGCTATAAAAAGAACAGGATAGATAAGAT 1 105 1 AAAAACAGGA 0.912329 -54 TTATAGTGTTAAAATCATAGAAAAAACTGGCG 2 264 0 AAAAATAGAA 0.960889 -37 TTTTCTCCATAAAATTATAGTGTTAAAATCAT 2 278 0 AAAAATAGTG 0.769494 -23 GATTTATATCAAAGCAATAGAAAATAAATCAT 3 98 0 AAAGATAGAA 0.923131 -99 CTATTTAAGCAAATTCACAGAAAAAAGTAAGA 3 153 0 AAATACAGAA 0.87533 -44 AAAAAAACATAAAATCTTTCAA 4 1 1 AAAAACATAA 0.773908 -169 TTTTCATAACAAAAAAATAGAACTTATTTCCC 4 64 1 AAAAATAGAA 0.960889 -106 AGGGAAGAGAAAAGAAATAGAAAGATTTTTCA 5 60 0 AAAGATAGAA 0.923131 -77 CTTACTGGAAAAAAAGACAGTAAGCAGCAGTG 9 146 1 AAAAACAGTA 0.925267 -42 **** ****** Masking position 7 Map Score: 7.25476 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 82 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 6 GTCTGCTATCGCTTGCCTTGCTATAAAAAGA 1 90 1 GCTGCCTTGC 0.976353 -69 TATAGCTGCAGCATGCCATGCAAATCAGCTT 2 57 1 GCTGCCATGC 0.540233 -244 TCCTCTTACAGCGTGCCTGGCTTTCTTTTGA 2 124 1 GCTGCCTGGC 0.973904 -177 ATAAAAATAAGCCTTCCTTGCAAGAAATCGA 3 67 0 GCTTCCTTGC 0.990258 -130 ATATACTCGGGCCTTCCTTCCATTTTGG 10 8 0 GCTTCCTTCC 0.983682 -293 ** ******** Masking position 4 Map Score: 7.05057 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 7 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 7 TGGCATGCTGCAGCTATACTTATGTACCAA 2 45 0 CAGCTATACT 0.682229 -256 ATAGATCAAAGCGTAATACTCGATTTCTTG 3 48 1 GCGTAATACT 0.853938 -149 CGACACTCGAGCGCTCTTCTCCTAAAAATC 6 107 1 GCGCTCTTCT 0.931021 -75 GCATGTATGACCGCAATACAAAGAGAAGGC 8 75 0 CCGCAATACA 0.828624 -87 GATAAAACGAGCGAACTGCTTTCATTAACC 8 121 1 GCGAACTGCT 0.880635 -41 CGGTTCGATCCCGCTATGCTCCAATTTCTG 9 12 0 CCGCTATGCT 0.955487 -176 TGCCATTGTTGCGCTCTACCAACTGAGCTA 9 55 1 GCGCTCTACC 0.935614 -133 CCTCTCTATAGCGCACTGCTGCTTACTGTC 9 161 0 GCGCACTGCT 0.98509 -27 GAAGTTTTAGGCGCAATACTTGATAATAAT 10 167 1 GCGCAATACT 0.981257 -134 ********** Masking position 7 Map Score: 5.94 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 81 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 8 TCTCTGTATTTTTCCTATCAATATTCTATTGGAGA 1 31 1 TTCCTAAATT 0.958088 -128 CCATATAAACTTATCTAGCAACATCTTATCTATCC 1 124 0 TTTCTAAATC 0.874147 -35 TAGAACTTATTTCCCTCGTATGATCTTAAATATCA 4 81 1 TTCCTCAATC 0.97445 -89 ATGTCTATTTTCTAAAAAGGTTAAAAATGAAT 4 148 0 TTTCTAAGTT 0.807493 -22 CGTTTTTACGTTTCCTCACACAATTAACTAACCAA 6 11 1 TTCCTCAATT 0.981673 -171 CTGGATTTCATTGCCTCCTAAAATTCTTAGTCAAA 6 60 1 TTCCTCAATT 0.981673 -122 CTTTTCTCAGTGCTCTCTAAAAATTACGCTGGACA 7 11 1 TGTCTCAATT 0.826607 -79 TTTTATCTAATTTCCTCCGATGAGCATGTATGACC 8 93 0 TTCCTCAAGC 0.888313 -69 AACAAGATCCTTGTCTAGAACGGTTAATGAAAGCA 8 137 0 TTTCTAAGTT 0.807493 -25 ACCTAGTTTCTTCCCTCGGGGTATTAGCTCAGTTG 9 74 0 TTCCTCGATT 0.917837 -114 ** **** * *** Masking position 6 Map Score: 4.43903 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 70 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 9 GGAAAAATACAGAGAGGATCTTCTGGAGACAGTTA 1 11 0 AGAGTTTCTG 0.922244 -148 GTTGTTAATGAACAAATATTCTGTTTTAGCAGT 2 9 1 TGAATTTCTG 0.760615 -292 GCAATCAGCTTGAAAAGCTGATTTGCATGGCATGC 2 67 0 TGAATATTTG 0.668948 -234 TATAGAAGTAAGAGCGTCTTTTTTGCGCAGGATTA 2 223 1 AGAGTTTTTG 0.954988 -78 CTGAATAACCTGTGCATGTATTTTGTAAGATAGAT 3 19 1 TGTGTTTTTG 0.935664 -178 CTTCAAGAGAAGAGGGCGTTTTTTTCATTGAAAAA 5 32 1 AGAGTTTTTT 0.824052 -105 TTCTCTTCCCTGTGTGTATGATTTGCTGTTCATGA 5 81 1 TGTGTATTTG 0.837943 -56 AAATCCAGAATGAGTATGCTTGTTGGTTAGTTAAT 6 33 0 TGAGCTGTTG 0.887963 -149 AATATAAAGATGAGACTCTCATCTGTCCAGCGTAA 7 34 0 TGAGTATCTG 0.890477 -56 CGAGTATATATGAGTCATTATTTTTATGAAAGAGC 10 30 1 TGAGTTTTTT 0.9003 -271 TTTTTATGAAAGAGCGGACCTGTTTACCAGGGGCG 10 50 1 AGAGCTGTTT 0.475734 -251 TAAGAAGAAATGTGTAGACCTTTTGAACCTTCATA 10 119 0 TGTGCTTTTG 0.890477 -182 **** * ***** Masking position 14 Map Score: 2.82817 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 192 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 AGACACCTCGTCAAAAAAACGACGCGCTTC 1 64 0 TCAAAAAAAC 0.926669 -95 AAGAATCTATCCATATAAACTTATCTAGCA 1 139 0 CCATATAAAC 0.671037 -20 GCGCCAGCTTTCAAAAGAAAGCCAGGCACG 2 135 0 TCAAAAGAAA 0.639421 -166 CATCTCTTAATCAAATAAAAGGCTTCTTAA 2 189 0 TCAAATAAAA 0.865444 -112 AGTGTTAAAATCATAGAAAAAACTGGCGAC 2 262 0 TCATAGAAAA 0.79955 -39 AGAAAATAAATCATATAAAAATAAGCCTTC 3 82 0 TCATATAAAA 0.898513 -115 AAAATCCTTTTCATAACAAAAAAATAGAAC 4 57 1 TCATAACAAA 0.709407 -113 GATTTTTCAATGAAAAAAACGCCCTCTTCT 5 39 0 TGAAAAAAAC 0.573353 -98 AAATAATGACTCATATATACTCGGGCCTTC 10 23 0 TCATATATAC 0.579173 -278 GTCCGCTCTTTCATAAAAATAATGACTCAT 10 39 0 TCATAAAAAT 0.72909 -262 TTTTTTTATTTCAAAAAAACTCTCGATCGC 10 82 0 TCAAAAAAAC 0.926669 -219 TTTTGAACCTTCATACAAAACATTTTTTTA 10 104 0 TCATACAAAA 0.79955 -197 ********** Masking position 5 Map Score: 3.62876 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 164 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: -6.03718e-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 CAAATATTCTGTTTTAGCAGTTTTGGTACA 2 23 1 GTTTTAGCAG 0.951366 -278 TAAATAGTTGGTTTTAGCCCCTTTGTTAT 3 178 1 GTTTTAGCCC 0.947307 -19 TTGACTAAGAATTTTAGGAGGCAATGAAAT 6 64 0 ATTTTAGGAG 0.898825 -118 AAAAACAAGATTTTTAGGAGAAGAGCGCTC 6 115 0 TTTTTAGGAG 0.939995 -67 ATGTTTACACGATTTAGGACAACAAGCTGT 9 113 1 GATTTAGGAC 0.896985 -75 AAGGAGTGAAGTTTTAGGCGCAATACTTGA 10 160 1 GTTTTAGGCG 0.982451 -141 TGCGAAAGATTGTTTAGGCCAGAAGGAGAA 10 256 1 TGTTTAGGCC 0.840413 -45 ********** Masking position 6 Map Score: 2.11605 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 72 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: -6.03718e-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: -6.03718e-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 15 ********** No masking Map Score: -6.03718e-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