AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i122_Arsenical_Resistance_Pump_mthe_reg_300.orf -o122_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 RTH00327 145 M.thermo #2 RTH00304 59 M.thermo #3 RTH00038 21 M.thermo #4 RTH00238 60 M.thermo #5 RTH00622 179 M.thermo #6 RTH01753 54 M.thermo #7 RTH01251 22 M.thermo Motif number 1 ATCTGTTAAAATGATATAGTATTATGATAA 1 24 1 ATGATATAGT 0.794829 -122 ACCTCTGATTATTTTATATATCAGTATCGT 1 84 1 ATTTTATATA 0.863889 -62 ATCGTCATATAAGATATAGATATTATCAAG 1 109 1 AAGATATAGA 0.95347 -37 AGATATTATCAAGTTATTAAAGGGCCAGAT 1 126 1 AAGTTATTAA 0.826835 -20 TTAATTTATTTTTCATTTATTT 5 3 1 AATTTATTTT 0.676348 -177 CCTGACCTGAATTTTATTGAAATAAATGAA 5 22 0 ATTTTATTGA 0.940359 -158 GAACCATGGAAAGTTATATATACTGGCAAT 5 121 1 AAGTTATATA 0.936906 -59 AATATATTCAAATTTATGGATATAAAGGTA 5 158 0 AATTTATGGA 0.91227 -22 CATAAATTTGAATATATTGA 5 170 1 AATATATTGA 0.912591 -10 TTAACATGACATGTTGTAGATTCT 6 5 0 ATGTTGTAGA 0.86596 -50 ********** Masking position 5 Map Score: 6.16133 Number of sites scoring better than the average of aligned sites = 259 Number in coding regions = 207 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 2 CTCCATGAATCTGTTAAAATGATATAGTAT 1 16 1 CTGTTAAAAT 0.867647 -130 TTAAATATCTATGTTATCATAATACTATAT 1 37 0 ATGTTATCAT 0.558693 -109 ATGCTGTTATCATCACACTTCAA 2 4 1 CTGTTATCAT 0.836779 -56 CAGGTTGAACCTGTTAACATGACATGTTGT 6 18 0 CTGTTAACAT 0.564878 -37 ********** Masking position 5 Map Score: 5.53264 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 27 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 3 CTTTCCTCCATGAATCTGTTA 1 1 1 CTTTCCTCAT 0.959362 -145 AGCCCAGAAACACACCTCTGATTATTTTATA 1 71 1 CACACCTCGA 0.985812 -75 CTGTTATCATCACACTTCAATTTGATAACCA 2 14 1 CACACTTCAT 0.957586 -46 GATAACCAGTCATTCCTCAAAAGGAGGGTTT 2 37 1 CATTCCTCAA 0.986045 -23 GCGGATCATGCACTCATCGAACTCATCTGAT 4 21 0 CACTCATCAA 0.957586 -40 CATTTCACCTCAAATTCCAGGTTG 6 41 0 TTCACCTCAA 0.914697 -14 ATCATACCTCCTTAGGGTGCTG 7 10 0 CATACCTCTT 0.945748 -13 ******** ** Masking position 7 Map Score: 4.06234 Number of sites scoring better than the average of aligned sites = 422 Number in coding regions = 395 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 4 ATCTGGCCCTTTAATAACTTG 1 135 0 TCTGGCCCTT 0.972207 -11 TTGAGGAATGACTGGTTATCAAATTGAAGT 2 27 0 ACTGGTTATC 0.86743 -33 ACCTTGCGGATCATGCACTCATCGAACTCA 4 27 0 TCATGCACTC 0.936479 -34 CAGGCAATCTTCTGGCTCCTGACCTGAATT 5 39 0 TCTGGCTCCT 0.938762 -141 AAGGAAGAATTCAGGCAATCTTCTGGCTCC 5 50 0 TCAGGCAATC 0.983763 -130 AGTTATATATACTGGCAATCCCAATTTACC 5 132 1 ACTGGCAATC 0.983329 -48 ********** Masking position 5 Map Score: 1.66626 Number of sites scoring better than the average of aligned sites = 523 Number in coding regions = 491 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 5 TTATGATAACATAGATATTTAAATATAGCC 1 45 1 ATAGATATTT 0.948975 -101 ATATGACGATACTGATATATAAAATAATCA 1 89 0 ACTGATATAT 0.816946 -57 CATATAAGATATAGATATTATCAAGTTATT 1 114 1 ATAGATATTA 0.935489 -32 CAAGGTTTAAGTGGATATTT 4 51 1 GTGGATATTT 0.929069 -10 CCTGAATTTTATTGAAATAAATGAAAAATA 5 17 0 ATTGAAATAA 0.828991 -163 TCATCGAACCATGGAAAGTTATATATACTG 5 116 1 ATGGAAAGTT 0.850708 -64 ATTCAAATTTATGGATATAAAGGTAAATTG 5 153 0 ATGGATATAA 0.961659 -27 ********** Masking position 5 Map Score: 1.81314 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 175 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 6 ********** No masking Map Score: -8.36008e-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 7 ********** No masking Map Score: -8.36008e-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: -8.36008e-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