AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i184_thi_operon_mthe_reg_300.orf -o184_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 RTH00406 76 M.thermo #2 RTH00703 146 M.thermo #3 RTH00308 35 M.thermo #4 RTH01046 227 M.thermo #5 RTH00600 21 M.thermo #6 RTH00364 23 M.thermo Motif number 1 CGAGATATTATTAACTTTGTAGCGATTTATATCTTTC 1 24 1 TAACTTTAGT 0.933026 -53 TAAAACTGCCTAATCTGTTTAGAGAAAGATATAAATC 1 47 0 TATCTTTAGA 0.895314 -30 CATCTTCAGATAAACATTTATAAGGGAACATCCCCTA 2 36 1 TAACATATGA 0.972953 -111 GAAGAAGTCATCAACTTTTATAAGATAGGGGATGTTC 2 61 0 TAACTTATGA 0.992314 -86 AGTTATATTATAAAGTTTTTTAAGTGAATATAAGTTT 2 99 0 TAAGTTTTGA 0.897918 -48 ACTTTATAATATAACTTTCATAGGCATACATTGTTTA 2 120 1 AAACTTATGT 0.942064 -27 TGAGGTGGTCTGAACTATCAACTGAATTTTCTGCATC 4 32 1 TAACTTAAGT 0.963712 -196 CAACCACTAATGAACTGTTATGAGATATCCCTCATCA 4 69 1 TAACTTATGA 0.992339 -159 AGTGCAGGGAAAATCAGTGATGAGGGATATCTCATAA 4 86 0 AATCATATGA 0.735609 -142 TACCTAGGTTTTAACTATAGTATGAGAACTTTGCTTA 4 177 0 TAACTTGTGA 0.975522 -51 * **** * ** * * Masking position 8 Map Score: 9.47195 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 53 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 2 ATAAAAAAGGAGGGTAATTA 2 1 0 AGGGTAATTA 0.887569 -146 TATCTGAAGATGGGAAAATAAAAAAGGAGG 2 18 0 TGGGAAAATA 0.969696 -129 AACATTTATAAGGGAACATCCCCTATCTTA 2 48 1 AGGGAACATC 0.989233 -99 AAGTTTTTTAAGTGAATATAAGTTTAGAAG 2 94 0 AGTGAATATA 0.859133 -53 CTCAGAGCAGATGGAAAATCAGGAA 4 6 0 ATGGAAAATC 0.96928 -222 AGGTTAGTGCAGGGAAAATCAGTGATGAGG 4 98 0 AGGGAAAATC 0.995121 -130 ********** Masking position 6 Map Score: 5.55265 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 148 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 3 GTTTAGAGAAAGATATAAATCGCTACAAAG 1 38 0 AGATATAAAT 0.881105 -39 TCCCATCTTCAGATAAACATTTATAAGGGA 2 33 1 AGATAAACAT 0.978999 -114 TAACTTTCATAGGCATACATTGTTTA 2 131 1 AGGCATACAT 0.899915 -16 AATCAGAAAATGATAACCAT 3 26 1 TGATAACCAT 0.949516 -10 AACTGTTATGAGATATCCCTCATCACTGAT 4 81 1 AGATATCCCT 0.936868 -147 GTTAAAACCTAGGTAACCATTACTCATGGG 4 199 1 AGGTAACCAT 0.983155 -29 ********** Masking position 5 Map Score: 4.09312 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 207 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 AATCGCTACAAAGTTAATAATATCTCGAGC 1 21 0 AAGTTAATAA 0.968828 -56 TATCTTATAAAAGTTGATGACTTCTTCTAA 2 71 1 AAGTTGATGA 0.954028 -76 AAGTGAATATAAGTTTAGAAGAAGTCATCA 2 85 0 AAGTTTAGAA 0.972509 -62 TCACTTAAAAAACTTTATAATATAACTTTC 2 109 1 AACTTTATAA 0.957087 -38 TTCACCGGACAAGTATATAAGCAAAGTTCT 4 160 1 AAGTATATAA 0.95979 -68 ********** Masking position 4 Map Score: 2.30141 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 24 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 ATAATATCTCGAGCAGGTGAACTG 1 5 0 GAGCAGGTGA 0.992732 -72 GACCACCTCAGAGCAGATGGAAAATCAGGA 4 12 0 GAGCAGATGG 0.996038 -216 TTACTGATTTGATCAGTTGGCTGTCCTTCA 4 127 0 GATCAGTTGG 0.989267 -101 ********** Masking position 5 Map Score: 1.09979 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 15 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 6 CGATTTATATCTTTCTCTAAACAGATTAGG 1 46 1 CTTTCTCTAA 0.889503 -31 TTTATTTTCCCATCTTCAGATAAACATTTA 2 26 1 CATCTTCAGA 0.948355 -121 TATAAGGGAACATCCCCTATCTTATAAAAG 2 54 1 CATCCCCTAT 0.90703 -93 AAGTTGATGACTTCTTCTAAACTTATATTC 2 81 1 CTTCTTCTAA 0.932237 -66 ATTATTTATCCCCTGAATCAGAAAAT 3 7 1 TATCCCCTGA 0.90604 -29 ATGGTTATCATTTTCTGATTCAGGGGAT 3 18 0 CATTTTCTGA 0.919827 -18 ATAGTTCAGACCACCTCAGAGCAGATGGAA 4 20 0 CCACCTCAGA 0.862794 -208 TTTCTGCATCCAACCACTAATGAACTGTTA 4 59 1 CAACCACTAA 0.879616 -169 ********** Masking position 7 Map Score: 1.16068 Number of sites scoring better than the average of aligned sites = 1858 Number in coding regions = 1740 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 7 ********** No masking Map Score: 1.3033e-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 8 ********** No masking Map Score: 1.3033e-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: 1.3033e-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