AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i070_Threonine_Biosynthesis_mthe_reg_300.orf -o070_mthe_300.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 RTH02062 231 M.thermo #2 RTH02064 195 M.thermo #3 RTH01737 64 M.thermo #4 RTH00128 23 M.thermo #5 RTH00136 54 M.thermo #6 RTH02067 22 M.thermo #7 RTH01815 75 M.thermo #8 RTH01404 40 M.thermo #9 RTH00929 25 M.thermo Motif number 1 ATCATGGGCCATCCCCTGGGCACAGCCTCT 1 19 0 ATCCCCTGGG 0.982677 -213 GTCACACTCTCCCCTGGATTATAGGTAA 1 214 0 CTCCCCTGGA 0.998286 -18 AGGTATAATATTCCTCAGGAACTCAACACT 2 24 0 TTCCTCAGGA 0.968297 -172 CAGCGGAATATTCCCCAGGAACACGGAAGG 2 87 0 TTCCCCAGGA 0.996356 -109 CTGGGGAATATTCCGCTGGAGGGGTGCTGG 2 99 1 TTCCGCTGGA 0.992984 -97 CCCAGATAGAGTTCCCTGGAAAACCAGCAC 2 122 0 GTTCCCTGGA 0.990453 -74 CCTGAAGGATTTCCCCTGGAGGGTCAGGGT 2 162 1 TTCCCCTGGA 0.998844 -34 TTAAAGGGGTCTTCCATGGATGACTGCAGC 3 13 0 CTTCCATGGA 0.949285 -52 CCCCGTTTAATTTCCCTGGTTAATTCAGGT 7 12 1 TTTCCCTGGT 0.980713 -64 ********** Masking position 2 Map Score: 22.185 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 248 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 2 GGGCGAGAGGCTGTGCCCAGGGGATGGCCCATG 1 14 1 CGTCCCAGGG 0.985924 -218 ACACATGTAACCGGAATCATGGGCCATCCCCTG 1 31 0 CGGATCAGGG 0.98904 -201 GATTCTTTGCCTGTAATGCCGGGGTGATAAACT 1 77 0 CGTATGCGGG 0.985304 -155 CATAGGTTACCTATAATCCAGGGGAGAGTGTGA 1 208 1 CATATCCGGG 0.992171 -24 CCCGGGCATCACGGGACCCGGGGCCCCTCAAGG 2 51 0 AGGACCCGGG 0.975594 -145 AGGAACACGGAAGGCCTCCCGGGCATCACGGGA 2 68 0 AGGCTCCGGG 0.994593 -128 GGGAGGCCTTCCGTGTTCCTGGGGAATATTCCG 2 81 1 CGTTTCCGGG 0.996012 -115 GGAGGGGTGCTGGTTTTCCAGGGAACTCTATCT 2 116 1 TGTTTCCGGG 0.980072 -80 CCTCCAGGGGAAATCCTTCAGGGCGCTGACACC 2 151 0 AATCTTCGGG 0.817962 -45 TCTCAAACCCTGACCCTCCAGGGGAAATCCTTC 2 165 0 TACCTCCGGG 0.951109 -31 TCGCTGCAGTCATCCATGGAAGACCCCTT 3 7 1 CGTATCCTGG 0.9763 -58 CTCAACCAGCACTCACGGGAGGT 4 7 1 CGCCTCAGGG 0.989979 -17 * ** **** *** Masking position 12 Map Score: 21.6625 Number of sites scoring better than the average of aligned sites = 862 Number in coding regions = 815 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 3 AATATTATACCTTGAGGGGCCCCGGGTCCC 2 42 1 CTTGAGGGGC 0.988699 -154 CCGTGATGCCCGGGAGGCCTTCCGTGTTCC 2 70 1 CGGGAGGCCT 0.96904 -126 GAATATTCCGCTGGAGGGGTGCTGGTTTTC 2 104 1 CTGGAGGGGT 0.993964 -92 GGAACTCTATCTGGGGTGTCAGCGCCCTGA 2 137 1 CTGGGGTGTC 0.953877 -59 AGGATTTCCCCTGGAGGGTCAGGGTTTGAG 2 167 1 CTGGAGGGTC 0.994061 -29 ACCTCCCGTGAGTGCTGGTTGAG 4 8 0 CGTGAGTGCT 0.93971 -16 ********** Masking position 6 Map Score: 5.00164 Number of sites scoring better than the average of aligned sites = 648 Number in coding regions = 619 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 4 ATACTGACCGGTGCAGCATCTAAACCCGAAGAG 1 109 0 GGCAGCTCTA 0.893221 -123 ATTTATTTACCATCAGCGATAAATATTGTTGCC 1 176 1 CTCAGCATAA 0.979868 -56 GTATAATATTCCTCAGGAACTCAACACTCTGTC 2 19 0 CTCAGGACTA 0.987213 -177 TCCCCTGGAGGGTCAGGGTTTGAGATAATTTTA 2 173 1 GTCAGGTTTA 0.903038 -23 CCTTTAACAGATGCAGCCATACACAAGTACTGA 3 36 1 AGCAGCATAA 0.903038 -29 ACTATGACGGCTTAAGCAACAGAAATGACTTAA 5 18 1 CTAAGCACAA 0.896063 -37 TCCCTGGTTAATTCAGGTACATATTGATAAGGT 7 24 1 ATCAGGACAA 0.963082 -52 TTTATAGTCACATCAGGCATTTAATTTATCT 8 20 1 CTCAGGATTA 0.979868 -21 * ***** *** * Masking position 5 Map Score: 2.32655 Number of sites scoring better than the average of aligned sites = 430 Number in coding regions = 393 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 5 TGATGGTAAATAAATATTGTAAGTACCATG 1 161 0 TAAATATTGT 0.954449 -71 CCATCAGCGATAAATATTGTTGCCATAGGT 1 185 1 TAAATATTGT 0.954449 -47 TTAATTCAGGTACATATTGATAAGGTGAAT 7 31 1 TACATATTGA 0.912362 -45 GATGTGACTATAAATCTTTTCAT 8 4 0 TAAATCTTTT 0.869036 -37 CAAAAACCTCCACATATTTTCTGT 9 5 0 CACATATTTT 0.890762 -21 ********** Masking position 5 Map Score: 1.16838 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 8 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 AAAACACATGTAACCGGAATCATGGGCCAT 1 37 0 TAACCGGAAT 0.852138 -195 GATAAACTGATAACTGGAAAAACACATGTA 1 55 0 TAACTGGAAA 0.951019 -177 AGAGATTCTTTGCCTGTAATGCCGGGGTGA 1 83 0 TGCCTGTAAT 0.960181 -149 TATTTATCGCTGATGGTAAATAAATATTGT 1 171 0 TGATGGTAAA 0.689184 -61 TGCCATAGGTTACCTATAATCCAGGGGAGA 1 205 1 TACCTATAAT 0.828893 -27 CAGATAGAGTTCCCTGGAAAACCAGCACCC 2 120 0 TCCCTGGAAA 0.901359 -76 AATGACTTAATAACGGTGATATGA 5 41 1 TAACGGTGAT 0.813991 -14 ACTTTATTCTTACCGGTAAA 7 66 1 TACCGGTAAA 0.967435 -10 ATGCCTGATGTGACTATAAATCTTTTCAT 8 10 0 TGACTATAAA 0.81962 -31 ********** Masking position 9 Map Score: 2.26026 Number of sites scoring better than the average of aligned sites = 558 Number in coding regions = 504 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 7 ********** No masking Map Score: -1.0918e-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: -1.0918e-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: -1.0918e-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