AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i070_Threonine_Biosynthesis_hpyl_reg_300.orf -o070_hpyl_300.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 RHP00236 132 AE000511 #3 RHP00241 68 AE000511 #4 RHP00243 173 AE000511 #5 RHP00454 53 AE000511 #6 RHP00455 72 AE000511 #7 RHP00458 63 AE000511 #8 RHP00461 148 AE000511 Motif number 1 ACTATAATGCGGTTTAAAATTTTGCCGCAA 1 45 0 GGTTTAAAAT 0.990794 -159 AAATTAAACTGGATTAAAAAGACGATCAAT 1 93 1 GGATTAAAAA 0.973166 -111 CTTCAAACTAGTTTTAAAAAGTCATTATTA 2 101 0 GTTTTAAAAA 0.920612 -32 GGATAAAGGGGTTTTAAAATGCTAAAGGCA 3 32 0 GTTTTAAAAT 0.924384 -37 TTTTAAGGCTGATTTAAAAATTCTGGCGTG 4 11 1 GATTTAAAAA 0.944719 -163 TATAATGCTAGTTTTAAAAATGAAAGGGTA 5 13 1 GTTTTAAAAA 0.920612 -41 CAACAATAGGGGTTTAAAAT 5 44 1 GGTTTAAAAT 0.990794 -10 TTGGAGTTAAGGTTTAAAATTTTAGCGTTA 7 20 1 GGTTTAAAAT 0.990794 -44 CGGTTAAAATGGAGTAAAATTTTTACCCAC 8 62 0 GGAGTAAAAT 0.912801 -87 ********** Masking position 5 Map Score: 20.3027 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 82 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 2 CTTATAATACTATAATGCGGTTTAAAATTTTG 1 51 0 TATAAGCGGT 0.868594 -153 TTAATTTTTGATTTATGCTTATAATACTATAA 1 68 0 ATTTAGCTTT 0.671919 -136 GAATGTAACCTTAAATGGTTTTTTAATGAGAA 1 125 0 TTAAAGGTTT 0.79478 -79 AGCATACCCTAAAAGAGCGAATGTAACCTTAA 1 143 0 AAAAGGCGAT 0.421225 -61 TTTTGACTAGAATAGCGCTTCTATTATTGTTG 2 40 0 AATAGGCTTT 0.83769 -93 ATAGCGCAAAAATAAGGCGATTTTGACTAGAA 2 60 0 AATAAGCGAT 0.680777 -73 AAAGGCATTCTTTAATGTTGGTTGCAGG 3 7 0 TTTAAGTTGT 0.865932 -62 ACTTATTTGGATAAAGGGGTTTTAAAATGCTA 3 38 0 ATAAAGGGTT 0.74623 -31 TTTTAAGGCTGATTTAAAAATTC 4 2 1 TTTAAGCTGT 0.952875 -172 GCATAGAAGAATTAGAGCTGTTTGAAGTTTTT 4 60 1 ATTAGGCTGT 0.948611 -114 TTGAAGTTTTTTTAGCGGGTTTTTCATTGAAT 4 81 1 TTTAGGGGTT 0.94389 -93 AACCGCAAGCTTGAATGGTTATTGCTACAAGC 4 126 1 TTGAAGGTTT 0.762512 -48 TAACATGCTTTTTAGCGCTTGTAGCAATAACC 4 142 0 TTTAGGCTTT 0.964421 -32 TGTATAATGCTAGTTTTAAAAATG 5 3 1 TATAAGCTAT 0.737511 -51 AGTTTTAAAAATGAAAGGGTATCAACAATAGG 5 22 1 ATGAAGGGTT 0.709122 -32 TCCTGAATTAGGGTTTATTTTTTGGAAT 6 7 1 ATTAGGTTTT 0.85567 -66 TGGAATTGGATTTAGCGCTTATCTCTTTAGGC 6 33 1 TTTAGGCTTT 0.935551 -40 GGTTTAAAATTTTAGCGTTAGTCGTTTTAATT 7 30 1 TTTAGGTTAT 0.769121 -34 GTCGTTTTAATTTTAGGGGGTTAT 7 50 1 TTTTAGGGGT 0.596024 -14 GCATGACTTTATTAGGGTGGGTAAAAATTTTA 8 46 1 ATTAGGTGGT 0.856601 -103 GAATTGTTTGTTAAAAGTTTCTTTCAATTATA 8 111 0 TTAAAGTTTT 0.670642 -38 ***** **** * Masking position 12 Map Score: 18.2598 Number of sites scoring better than the average of aligned sites = 3684 Number in coding regions = 3307 Number in noncoding regions = 377 Number of orfs with sites within 600 bp upstream = 244 Fraction of orfs with sites within 600 bp upstream = 0.0391905 Motif number 3 TTAAAAAACCATTTAAGGTTACATTCGCTC 1 131 1 ATTTAAGGTT 0.807986 -73 ACATTCGCTCTTTTAGGGTATGCTACGACT 1 151 1 TTTTAGGGTA 0.902011 -53 AATCGCCTTATTTTTGCGCTATGATTTTCA 2 70 1 TTTTTGCGCT 0.900432 -63 TTTTAAGGCTGATTTAAAAA 4 1 1 TTTTAAGGCT 0.928255 -173 TGCATAGAAGAATTAGAGCTGTTTGAAGTT 4 59 1 AATTAGAGCT 0.690141 -115 TTTGAAGTTTTTTTAGCGGGTTTTTCATTG 4 80 1 TTTTAGCGGG 0.953778 -94 TTAACATGCTTTTTAGCGCTTGTAGCAATA 4 145 0 TTTTAGCGCT 0.987354 -29 TCCTGAATTAGGGTTTATTTTTTGG 6 6 1 AATTAGGGTT 0.915021 -67 TTGGAATTGGATTTAGCGCTTATCTCTTTA 6 32 1 ATTTAGCGCT 0.975901 -41 AGGTTTAAAATTTTAGCGTTAGTCGTTTTA 7 29 1 TTTTAGCGTT 0.979984 -35 GTCGTTTTAATTTTAGGGGGTTAT 7 50 1 TTTTAGGGGG 0.960954 -14 AGCATGACTTTATTAGGGTGGGTAAAAATT 8 45 1 TATTAGGGTG 0.928587 -104 ********** Masking position 4 Map Score: 15.5192 Number of sites scoring better than the average of aligned sites = 1644 Number in coding regions = 1494 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 4 CTTTTTAATCCAGTTTAATTTTTGATTTATGC 1 82 0 CGTTTATTTT 0.876662 -122 AAAATGATTCCTTTTTATTTTTGGATAATTT 1 183 0 CTTTTATTTT 0.951074 -21 ACTAGAATAGCGCTTCTATTATTGTTGGTTGA 2 35 0 CCTTCATTAT 0.824503 -98 CTTATTTTTGCGCTATGATTTTCAATAATAAT 2 76 1 CCTATATTTT 0.973733 -57 TAAAGAATGCCTTTAGCATTTTAAAACCCCTT 3 25 1 CTTAGATTTT 0.95748 -44 AACAGCACCACGCCAGAATTTTTAAATCAGCC 4 17 0 CCCAGATTTT 0.886961 -157 TCATTTTTAAAACTAGCATTATACA 5 4 0 ACTAGATTAT 0.691152 -50 ATTGTTGATACCCTTTCATTTTTAAAACTAGC 5 19 0 CCTTTATTTT 0.977245 -35 AAACGACTAACGCTAAAATTTTAAACCTTAAC 7 25 0 CCTAAATTTT 0.885006 -39 TAGCGTTAGTCGTTTTAATTTTAGGGGGTTAT 7 42 1 CTTTTATTTT 0.951074 -22 TATATTTAACACTTAGGATTTTTA 8 3 0 ATTAGATTTT 0.740199 -146 TTTAACCGGTCATTTTAATTATTTTAGTATAA 8 84 1 CTTTTATTAT 0.873597 -65 ATCGCCAAATCCCTTGAATTGTTTGTTAAAAG 8 126 0 CCTTGATTGT 0.92319 -23 * **** ***** Masking position 8 Map Score: 13.7518 Number of sites scoring better than the average of aligned sites = 620 Number in coding regions = 512 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 5 TTTTAAACCGCATTATAGTATTATAAGCATA 1 56 1 CATTTAGTAT 0.965013 -148 ATTAAAAAACCATTTAAGGTTACATTCGCTC 1 130 1 CATTAAGGTT 0.925513 -74 AAACTCCCTTCAAACTAGTTTTAAAAAGTCA 2 107 0 CAAATAGTTT 0.787735 -26 CTGCAACCAACATTAAAGAATGCCTTTAGCA 3 12 1 CATTAAGAAT 0.947951 -57 CCCCTTTATCCAAATAAGTTTGGTTATA 3 51 1 CAAAAAGTTT 0.820531 -18 TGGGCGTTTGCATAGAAGAATTAGAGCTGTT 4 51 1 CATAAAGAAT 0.905247 -123 TAGCAATAACCATTCAAGCTTGCGGTTATAA 4 122 0 CATTAAGCTT 0.9581 -52 AATATAGTGGCATTGTAGCATGACTTTATTA 8 29 1 CATTTAGCAT 0.9581 -120 TCATTTTAATTATTTTAGTATAATTGAAAGA 8 93 1 TATTTAGTAT 0.730021 -56 **** ****** Masking position 7 Map Score: 4.29854 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 212 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 6 GATTTTCCTTTCATCAAACTCATCTCAAC 2 9 1 TTTCACAAAC 0.976089 -124 ATCAAACTCATCTCAACCAACAATAATAGAA 2 23 1 TCTCACCAAC 0.951812 -110 ACTCCAAACTCCCTTCAAACTAGTTTTAAA 2 113 0 TCCCTCAAAC 0.938154 -20 TTAAAACCCCTTTATCCAAATAAGTTTGGTT 3 45 1 TTTATCAAAT 0.721155 -24 TATAACCAAACTTATTTGGAT 3 58 0 TATAACAAAC 0.911309 -11 CTCTAATTCTTCTATGCAAACGCCCACCAAC 4 46 0 TCTATCAAAC 0.96909 -128 TGAAAGAAACTTTTAACAAACAATTCAAGGG 8 117 1 TTTTACAAAC 0.911286 -32 ***** ***** Masking position 9 Map Score: 1.31774 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 165 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 AAAACTAGTTTGAAGGGAGTTTGGAGT 2 116 1 TGAAGGGAGT 0.970505 -17 TTTAAAATGCTAAAGGCATTCTTTAATGTT 3 20 0 TAAAGGCATT 0.85976 -49 CTTATTTGGATAAAGGGGTTTTAAAATGCT 3 39 0 TAAAGGGGTT 0.954391 -30 GTGGTGCTGTTGGTGGGCGTTTGCATAGAA 4 38 1 TGGTGGGCGT 0.895909 -136 TTTCATTGAATGGAGGGGCTTTATAACCGC 4 102 1 TGGAGGGGCT 0.959202 -72 ATCTCTTTAGGCGAGGGGGTCTTGCTCGGG 6 53 1 GCGAGGGGGT 0.91995 -20 GTGTTAAATATAGTGGCATTGTAGCATGAC 8 23 1 TAGTGGCATT 0.780696 -126 AACAAACAATTCAAGGGATTTGGCGATT 8 131 1 TCAAGGGATT 0.949254 -18 ********** Masking position 10 Map Score: 1.21513 Number of sites scoring better than the average of aligned sites = 577 Number in coding regions = 520 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 8 ********** No masking Map Score: -1.04149e-13 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: -1.04149e-13 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 10 ********** No masking Map Score: -1.04149e-13 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