AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i070_Threonine_Biosynthesis_mthe_reg_100.orf -o070_mthe_100.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTH02064 195 M.thermo #2 RTH01737 64 M.thermo #3 RTH00128 23 M.thermo #4 RTH00136 54 M.thermo #5 RTH02067 22 M.thermo #6 RTH01815 75 M.thermo #7 RTH01404 40 M.thermo #8 RTH00929 25 M.thermo Motif number 1 AGAGTGTTGAGTTCCTGAGGAATATTATAC 1 22 1 GTTCCTGAGG 0.912425 -174 GAATATTATACCTTGAGGGGCCCCGGGTCC 1 41 1 CCTTGAGGGG 0.942951 -155 GGGCATCACGGGACCCGGGGCCCCTCAAGG 1 51 0 GGACCCGGGG 0.952879 -145 ACACGGAAGGCCTCCCGGGCATCACGGGAC 1 67 0 CCTCCCGGGC 0.990576 -129 GGCCTTCCGTGTTCCTGGGGAATATTCCGC 1 85 1 GTTCCTGGGG 0.991703 -111 AACCAGCACCCCTCCAGCGGAATATTCCCC 1 101 0 CCTCCAGCGG 0.987462 -95 CCCAGATAGAGTTCCCTGGAAAACCAGCAC 1 122 0 GTTCCCTGGA 0.906438 -74 CCAGGGAACTCTATCTGGGGTGTCAGCGCC 1 133 1 CTATCTGGGG 0.920431 -63 CAGGGGAAATCCTTCAGGGCGCTGACACCC 1 150 0 CCTTCAGGGC 0.979567 -46 AAACCCTGACCCTCCAGGGGAAATCCTTCA 1 164 0 CCTCCAGGGG 0.996752 -32 TTAAAGGGGTCTTCCATGGATGACTGCAGC 2 13 0 CTTCCATGGA 0.936342 -52 ACCTCCCGTGAGTGCTGGTTG 3 13 0 CCTCCCGTGA 0.955794 -11 ********** Masking position 9 Map Score: 21.2141 Number of sites scoring better than the average of aligned sites = 2026 Number in coding regions = 1962 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 2 CTGAGGAATATTATACCTTGAGGGGCCCCGGGT 1 36 1 TACCTTGAGG 0.927339 -160 CAGGAACACGGAAGGCCTCCCGGGCATCACGGG 1 69 0 GACCTCCCGG 0.997444 -127 TGGAAAACCAGCACCCCTCCAGCGGAATATTCC 1 103 0 GACCTCCAGC 0.991133 -93 CCCTCCAGGGGAAATCCTTCAGGGCGCTGACAC 1 152 0 GACCTTCAGG 0.994936 -44 ATCTCAAACCCTGACCCTCCAGGGGAAATCCTT 1 166 0 CGCCTCCAGG 0.991081 -30 ATCTGTTAAAGGGGTCTTCCATGGATGACTGCA 2 15 0 GGCTTCCATG 0.932634 -50 ATCAGAAACTTTATTCTTACCGGTAAA 6 59 1 TACTTACCGG 0.873593 -17 * * ******** Masking position 8 Map Score: 3.95491 Number of sites scoring better than the average of aligned sites = 1433 Number in coding regions = 1383 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 3 ATAATATTCCTCAGGAACTCAACACTCTGT 1 20 0 TCAGGAACTC 0.994627 -176 GGAATATTCCCCAGGAACACGGAAGGCCTC 1 83 0 CCAGGAACAC 0.983107 -113 CCTGGTTAATTCAGGTACATATTGATAAGG 6 26 1 TCAGGTACAT 0.979323 -50 ATAAGGTGAATCAGAAACTTTATTCTTACC 6 50 1 TCAGAAACTT 0.970466 -26 TATAGTCACATCAGGCATTTAATTTATCT 7 22 1 TCAGGCATTT 0.950676 -19 ********** Masking position 7 Map Score: 3.5227 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 335 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 4 GTTCCCTGGAAAACCAGCACCCCTCCAGCG 1 112 0 AAACCAGCAC 0.996747 -84 CTCAACCAGCACTCACGGGAGG 3 3 1 CAACCAGCAC 0.996132 -21 ACAAAAACCTCCACATATTTTCTG 8 12 0 AAACCTCCAC 0.989522 -14 ********** Masking position 3 Map Score: 2.47394 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 12 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 5 TCTTCCATGGATGACTGCAGCGA 2 4 0 ATGACTGCAG 0.98652 -61 GTACTTGTGTATGGCTGCATCTGTTAAAGG 2 36 0 ATGGCTGCAT 0.979056 -29 GGCTACTATGACGGCTTAAGCAACAGAAAT 4 14 1 ACGGCTTAAG 0.960077 -41 AGCAACAGAAATGACTTAATAACGGTGATA 4 32 1 ATGACTTAAT 0.937504 -23 GATAAATTAAATGCCTGATGTGACTATAAA 7 20 0 ATGCCTGATG 0.952064 -21 ********** Masking position 6 Map Score: 1.51679 Number of sites scoring better than the average of aligned sites = 337 Number in coding regions = 312 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 6 GGCTTAAGCAACAGAAATGACTTAATAACG 4 26 1 ACAGAAATGA 0.96849 -29 AAATGAGAAATAAGAAGGTCAG 5 4 1 TGAGAAATAA 0.901836 -19 TGAATTAACCAGGGAAATTAAACGGGGT 6 9 0 AGGGAAATTA 0.971756 -67 AGATAAATTAAATGCCTGAT 7 31 0 AGATAAATTA 0.936039 -10 ACAGAAAATATGTGGAGGTT 8 1 1 ACAGAAAATA 0.940958 -25 ********** Masking position 5 Map Score: 0.509778 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 43 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 TGAGGTCAGACAGAGTGTTGAGTTCC 1 7 1 CAGACAGAGT 0.99523 -189 GCTGACACCCCAGATAGAGTTCCCTGGAAA 1 130 0 CAGATAGAGT 0.987091 -66 GTTGCTTAAGCCGTCATAGTAGCCAAA 4 8 0 CCGTCATAGT 0.973293 -47 ********** Masking position 6 Map Score: 0.0293038 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 12 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 8 ********** No masking Map Score: 9.53751e-15 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: 9.53751e-15 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: 9.53751e-15 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