AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00460_ctra_reg_100.orf -o00460_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 gatC 200 Glu-tRNA Gln Amidotransferase (C subunit) #2 glyA 300 Serine Hydroxymethyltransferase #3 lpxC 100 UDP-3-O-Acyl GlcNAc Deacetylase Motif number 1 ATTAAATTGCAAAAAAGATTAAAAGTCAGA 1 42 0 AAAAAAGATT 0.860451 -159 GAGAGAACAAAAAAAGACTTTATTAAATTG 1 63 0 AAAAAGACTT 0.89803 -138 TTTGCGACAGCAAAACGCATCTTTAATAGA 1 91 0 CAAAACGCAT 0.912705 -110 TGCTGTCGCAAAAGACGCTTCAGTAAGAGT 1 109 1 AAAGACGCTT 0.986116 -92 TTTTTACACTAAAAACACTCTTACTGAAGC 1 125 0 AAAAACACTC 0.838481 -76 TCCTACTAGGAAAAAAGCTT 2 1 0 AAAAAAGCTT 0.961378 -300 CAGCAAAAGTCAAGAAGCTTCCTACTAGGA 2 20 0 CAAGAAGCTT 0.961862 -281 ACGATGCTTCCAAGACCATTACCAAGCGCC 2 118 0 CAAGACCATT 0.870866 -183 TTTCTAGGAGAAAGAGGATTTATTTTAACT 2 167 0 AAAGAGGATT 0.861588 -134 TACCTAGTTCTAAAACACTTGCTATC 3 7 0 TAAAACACTT 0.837868 -94 GCAAAACCCTGACAAAGAGAC 3 90 0 CAAAACCCTG 0.858584 -11 ********** Masking position 5 Map Score: 8.75775 Number of sites scoring better than the average of aligned sites = 589 Number in coding regions = 589 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 2 AAAGTCTTTTTTTGTTCTCTCTATTAAAGATGC 1 72 1 TTTTTTCTTA 0.734046 -129 AAAGATGCGTTTTGCTGTCGCAAAAGACGCTTC 1 97 1 TTTCTTCGAA 0.95064 -104 TAAGAGTGTTTTTAGTGTAAAAAAGTACGAAGG 1 132 1 TTTGTTAAAA 0.875348 -69 AAGCTTTTTTCCTAGTAGGAAGCTTCTT 2 6 1 TTTTCTAGAG 0.891477 -295 CTTCTTGACTTTTGCTGTAAGAATATGATCAAC 2 33 1 TTTCTTAAAA 0.932282 -268 ATCGTTTCTTTTTCTTATAGTTATAGTTAAAAT 2 143 1 TTTTTTAGTA 0.961562 -158 AGAAAGAGGATTTATTTTAACTATAACTATAAG 2 156 0 TTTTTTAATA 0.927284 -145 ATAAATCCTCTTTCTCCTAGAAAGTTTAGACTT 2 174 1 TTTTCTAGAA 0.915037 -127 AAGTTTAGACTTTCTCATCAAAAGATTAGATTC 2 195 1 TTTTCTCAAA 0.917689 -106 TTATCCTTTTTTTTTTTTAGCAAGCAAGCGATA 3 49 0 TTTTTTAGAA 0.981192 -52 *** ** *** ** Masking position 8 Map Score: 6.9462 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 234 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 TTTAATAGAGAGAACAAAAAAAGACTTTATTAAATTGCAAAAAA 1 56 0 AGAAAAGATA 0.939051 -145 TTTAGTGTAAAAAAGTACGAAGGATTTTATTCTGCATAAGATCA 1 142 1 AAAAAAGATG 0.992845 -59 TATTCTGCATAAGATCATGATTGACCATGTTTAGGATGGAAG 1 169 1 AAGAAAGATG 0.987601 -32 CACCTTATGGTAAGCGACTAGGGAAAATGGGGCGCTTGGTAATG 2 88 1 TAAGAAGATG 0.931911 -213 TATAACTATAAGAAAAAGAAACGATGCTTCCAAGACCATTACCA 2 124 0 AGAAAAGATG 0.992798 -177 TAGATTCCCATAAAGGATAAGGGAGAGTGGGTAGAGGATAAAGA 2 221 1 TAAAAAGATG 0.980963 -80 GAGTGGGTAGAGGATAAAGAGTGCCTCTGCAAGGTCTTGCAAGG 2 245 1 AGGAAAGCTG 0.954026 -56 TTGCTTGCTAAAAAAAAAAAAGGATAATATACGGGGTCTCTTTG 3 55 1 AAAAAAGATG 0.992946 -46 **** * * ** * * Masking position 10 Map Score: 5.70154 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 50 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 AAGTACGAAGGATTTTATTCTGCATAAGAT 1 154 1 GATTTTATTC 0.959979 -47 GGTCAATCATGATCTTATGCAGAATAAAAT 1 165 0 GATCTTATGC 0.968337 -36 AGCTTCAGTTGATCATATTCTTACAGCAAA 2 43 0 GATCATATTC 0.977493 -258 CTCATCAAAAGATTAGATTCCCATAAAGGA 2 208 1 GATTAGATTC 0.941805 -93 AAAAAAAAAGGATAATATACGGGGTCTCTT 3 67 1 GATAATATAC 0.915126 -34 ********** Masking position 7 Map Score: 2.70532 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 49 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 ********** No masking Map Score: -1.26233e-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 6 ********** No masking Map Score: -1.26233e-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 7 ********** No masking Map Score: -1.26233e-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