AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i070_Threonine_Biosynthesis_hpyl_reg_100.orf -o070_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -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 = 0.39 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RHP01055 203 AE000511 #2 RHP00243 173 AE000511 #3 RHP00454 53 AE000511 #4 RHP00455 72 AE000511 #5 RHP00458 63 AE000511 #6 RHP00461 148 AE000511 Motif number 1 TATGATGAAATTTTTTGCCCTTTGCGGCAA 1 24 1 TTTTTTGCCC 0.938754 -180 TTGCGGCAAAATTTTAAACCGCATTATAGT 1 45 1 ATTTTAAACC 0.972008 -159 ATTGATCGTCTTTTTAATCCAGTTTAATTT 1 93 0 TTTTTAATCC 0.927052 -111 CCTTAAATGGTTTTTTAATGAGAACGATTG 1 119 0 TTTTTTAATG 0.560139 -85 CACGCCAGAATTTTTAAATCAGCCTTAAAA 2 11 0 TTTTTAAATC 0.913073 -163 GTTTGAAGTTTTTTTAGCGGGTTTTTCATT 2 79 1 TTTTTAGCGG 0.852039 -95 ATGGAGGGGCTTTATAACCGCAAGCTTGAA 2 111 1 TTTATAACCG 0.821615 -63 CTTAACATGCTTTTTAGCGCTTGTAGCAAT 2 146 0 TTTTTAGCGC 0.933354 -28 TACCCTTTCATTTTTAAAACTAGCATTATA 3 13 0 TTTTTAAAAC 0.907741 -41 ATTTTAAACCCCTATTGTTG 3 44 0 ATTTTAAACC 0.972008 -10 TAACGCTAAAATTTTAAACCTTAACTCCAA 5 20 0 ATTTTAAACC 0.972008 -44 AATGCCACTATATTTAACACTTAGGATTTT 6 13 0 TATTTAACAC 0.65935 -136 ATGGAGTAAAATTTTTACCCACCCTAATAA 6 54 0 ATTTTTACCC 0.949993 -95 ATTTTACTCCATTTTAACCGGTCATTTTAA 6 72 1 ATTTTAACCG 0.963884 -77 ********** Masking position 5 Map Score: 17.1038 Number of sites scoring better than the average of aligned sites = 2168 Number in coding regions = 1855 Number in noncoding regions = 313 Number of orfs with sites within 600 bp upstream = 208 Fraction of orfs with sites within 600 bp upstream = 0.0334083 Motif number 2 AACACAGCCTTACTATGATGAAATT 1 6 1 AGCCTTACTA 0.674163 -198 GAGCGAATGTAACCTTAAATGGTTTTTTAA 1 131 0 AACCTTAAAT 0.923331 -73 AGTCGTAGCATACCCTAAAAGAGCGAATGT 1 151 0 TACCCTAAAA 0.90221 -53 TTTTTAAATCAGCCTTAAAA 2 1 0 AGCCTTAAAA 0.961966 -173 AACTTCAAACAGCTCTAATTCTTCTATGCA 2 59 0 AGCTCTAATT 0.740853 -115 CAATGAAAAACCCGCTAAAAAAACTTCAAA 2 80 0 CCCGCTAAAA 0.913936 -94 TATTGCTACAAGCGCTAAAAAGCATGTTAA 2 145 1 AGCGCTAAAA 0.978268 -29 CCAAAAAATAAACCCTAATTCAGGA 4 6 0 AACCCTAATT 0.956005 -67 TAAAGAGATAAGCGCTAAATCCAATTCCAA 4 32 0 AGCGCTAAAT 0.966403 -41 TAAAATTTTAAACCTTAACTCCAAGATCAA 5 14 0 AACCTTAACT 0.737794 -50 TAAAACGACTAACGCTAAAATTTTAAACCT 5 29 0 AACGCTAAAA 0.971052 -35 ATAACCCCCTAAAATTAAAACGAC 5 50 0 CCCCCTAAAA 0.954038 -14 AATTTTTACCCACCCTAATAAAGTCATGCT 6 45 0 CACCCTAATA 0.950029 -104 ********** Masking position 7 Map Score: 16.1899 Number of sites scoring better than the average of aligned sites = 2163 Number in coding regions = 1954 Number in noncoding regions = 209 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 3 ATAAATCAAAAATTAAACTGGATTAAAAAGACGA 1 84 1 AATAATGATT 0.784906 -120 ATTATCCAAAAATAAAAAGGAATCATTTT 1 185 1 AATAAGGATC 0.984877 -19 TTTTTCATTGAATGGAGGGGCTTTATAACCGCAA 2 100 1 AATAGGGTTT 0.972181 -74 TAGTTTTAAAAATGAAAGGGTATCAACAATAGGG 3 21 1 AATAAGGATC 0.984877 -33 TAGTCGTTTTAATTTTAGGGGGTTAT 5 48 1 AATTAGGGTT 0.900741 -16 CTAAGTGTTAAATATAGTGGCATTGTAGCATGAC 6 19 1 AATAGGGATT 0.969335 -130 TTTAACAAACAATTCAAGGGATTTGGCGATT 6 128 1 AATAAGGTTT 0.979638 -21 *** ** ** *** Masking position 2 Map Score: 5.35243 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 168 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 4 CATCATAGTAAGGCTGTGTT 1 1 0 AGGCTGTGTT 0.94053 -203 TAATACTATAATGCGGTTTAAAATTTTGCC 1 49 0 ATGCGGTTTA 0.796144 -155 TTTTAAGGCTGATTTAAAAATTCTG 2 6 1 AGGCTGATTT 0.814908 -168 AAGTTTTTTTAGCGGGTTTTTCATTGAATG 2 84 1 AGCGGGTTTT 0.95025 -90 CATTGAATGGAGGGGCTTTATAACCGCAAG 2 105 1 AGGGGCTTTA 0.943424 -69 TATCAACAATAGGGGTTTAAAAT 3 41 1 AGGGGTTTAA 0.846508 -13 TCCTGAATTAGGGTTTATTTTTTGGAATT 4 10 1 AGGGTTTATT 0.720154 -63 TCTTTAGGCGAGGGGGTCTTGCTCGGG 4 56 1 AGGGGGTCTT 0.978442 -17 TTTTAATTTTAGGGGGTTAT 5 54 1 AGGGGGTTAT 0.976192 -10 TGACTTTATTAGGGTGGGTAAAAATTTTAC 6 49 1 AGGGTGGGTA 0.850494 -100 ********** Masking position 1 Map Score: 4.57378 Number of sites scoring better than the average of aligned sites = 1710 Number in coding regions = 1473 Number in noncoding regions = 237 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 5 AGCCTTACTATGATGAAATTTTTTGCCCTTTG 1 16 1 TGTAAATTTT 0.926928 -188 TTGCCCTTTGCGGCAAAATTTTAAACCGCATT 1 38 1 CGCAAATTTT 0.875634 -166 TGAGAACGATTGATCGTCTTTTTAATCCAGTT 1 99 0 TGTGTCTTTT 0.932604 -105 AACAGCACCACGCCAGAATTTTTAAATCAGCC 2 17 0 CGCGAATTTT 0.947402 -157 GTGGTGCTGTTGGTGGGCGTTTGCATAGAAGA 2 38 1 TGTGGCGTTT 0.948581 -136 GAATTAGAGCTGTTTGAAGTTTTTTTAGCGGG 2 68 1 TGTGAAGTTT 0.980943 -106 AAAATTTTAGCGTTAGTCGTTTTAATTTTAGG 5 35 1 CGTGTCGTTT 0.955582 -29 TTGAATTGTTTGTTAAAAGTTTCTTTCAATTA 6 113 0 TGTAAAGTTT 0.952653 -36 ** * ******* Masking position 10 Map Score: 3.83451 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 157 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 TTAAACCGCATTATAGTATTATAAGCATAAA 1 58 1 TTATAGTATA 0.73983 -146 TAATTTCAAGTCGTAGCATACCCTAAAAGAG 1 158 0 TCGTAGCATC 0.965367 -46 TTTTTAGCGCTTGTAGCAATAACCATTCAAG 2 135 0 TTGTAGCAAA 0.948397 -39 AAACTGATCTTAACATGCTTTTTAGCGC 2 156 0 TCTTAACATC 0.840755 -18 AGGTTTAAAATTTTAGCGTTAGTCGTTTTAA 5 29 1 TTTTAGCGTA 0.916994 -35 TATAGTGGCATTGTAGCATGACTTTATTAGG 6 31 1 TTGTAGCATA 0.980389 -118 ATTTTAATTATTTTAGTATAATTGAAAGAAA 6 95 1 TTTTAGTATA 0.877366 -54 TGAAAGAAACTTTTAACAAACAATTCAAGGG 6 117 1 TTTTAACAAC 0.773321 -32 ********* * Masking position 5 Map Score: 2.58691 Number of sites scoring better than the average of aligned sites = 388 Number in coding regions = 310 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 7 ********** No masking Map Score: -1.26944e-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 8 ********** No masking Map Score: -1.26944e-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 9 ********** No masking Map Score: -1.26944e-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