AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -itrpR_bsub_opreg_100.orf -g0.435 -x5 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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 pabB 166 para-aminobenzoate synthase (subunit A) #2 trpE 215 anthranilate synthase Motif number 1 TTGTATCATTCCTCTATTTTCT 1 155 0 TTATCATTCC 0.975075 -12 CTAATTGCTTTATACACACTCTTGTGTATTTC 2 29 0 TACACACTCT 0.964023 -187 ATTCTCTAACTCAACTCATTCTAATTGCTTTA 2 49 0 TACTCATTCT 0.994813 -167 TCAGCTCAACTAAACTCATTCTCTGCTACCCT 2 81 0 TACTCATTCT 0.994813 -135 TAGTATTTTATCCTCTCATGCCATCTTCTCAT 2 168 1 TTCTCATGCC 0.989339 -48 TCTCATGCCATCTTCTCATTCTCCTTGCCATA 2 181 1 TTCTCATTCT 0.996012 -35 TGCTCTCACTCCTTATGGCAAG 2 204 0 TTCTCACTCC 0.995097 -12 * ********* Masking position 8 Map Score: 13.2956 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 65 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 2 AAAAAGCCAAAACTCCCGGTTCGCC 1 6 1 GCCAAAACTC 0.952849 -161 CACGAAATATAAAAAAACTCCCGGCGAACC 1 28 0 AAAAAAACTC 0.977875 -139 CCTATTCTCTAACTCAACTCATTCTAATTG 2 54 0 AACTCAACTC 0.984661 -162 GTCTCAGCTCAACTAAACTCATTCTCTGCT 2 86 0 AACTAAACTC 0.99302 -130 ACTATATAACAAATAAACCCAAAAGAAAGA 2 142 0 AAATAAACCC 0.966135 -74 ********** Masking position 6 Map Score: 4.58053 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 59 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 3 AATTTCTCTTCCAAGAATAACATTCGTCGC 1 77 0 CCAAGAATAA 0.920301 -90 ACATTGCTTTACAATTAAAAACAAGTAAAA 1 124 1 ACAATTAAAA 0.863472 -43 ACAATTAAAAACAAGTAAAAAAGAAAATAG 1 134 1 ACAAGTAAAA 0.908633 -33 TACGATAAGAACAGCTTAGAA 2 2 1 ACGATAAGAA 0.916931 -214 TGTGTATAAAGCAATTAGAATGAGTTGAGT 2 43 1 GCAATTAGAA 0.961579 -173 GTTTATTCTACCCAAAAGAAGTCTTTCTTT 2 121 1 CCCAAAAGAA 0.957067 -95 AACAAATAAACCCAAAAGAAAGACTTCTTT 2 135 0 CCCAAAAGAA 0.957067 -81 ACTCCTTATGGCAAGGAGAATGAGAAGATG 2 189 0 GCAAGGAGAA 0.958479 -27 ********** Masking position 4 Map Score: 4.68902 Number of sites scoring better than the average of aligned sites = 1012 Number in coding regions = 861 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 4 AAAGCCAAAACTCCCGGTTCGCCGGGAGTTTT 1 13 1 CCCCGTTCGC 0.967555 -154 GCATCAAATATGCCATGTCTGCGACGAATGTT 1 57 1 TCCATTCTGC 0.946022 -110 GGAAGAGAAATTCACTTTTTTCACTAACAACA 1 95 1 TCACTTTTTC 0.970403 -72 TTGTATCATTCCTCTATTTTCTTTTTTACTT 1 146 0 TCTCTTTTTC 0.970403 -21 CATTCTCTGCTACCCTATTCTCTAACTCAACT 2 65 0 TCCCTTTCTC 0.996297 -151 TATCCTCTCATGCCATCTTCTCATTCTCCTTG 2 176 1 TCCATTTCTC 0.98912 -40 * **** ***** Masking position 8 Map Score: 2.74868 Number of sites scoring better than the average of aligned sites = 420 Number in coding regions = 326 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 5 GTTATTCTTGGAAGAGAAATTCACTTTTTT 1 86 1 GAAGAGAAAT 0.980912 -81 GATAAGAACAGCTTAGAAATACACAAGAGT 2 14 1 GCTTAGAAAT 0.972871 -202 GAATAGGGTAGCAGAGAATGAGTTTAGTTG 2 77 1 GCAGAGAATG 0.940664 -139 GTTTAGTTGAGCTGAGACATTATGTTTATT 2 98 1 GCTGAGACAT 0.988666 -118 CTTTTGGGTAGAATAAACATAATGTCTCAG 2 109 0 GAATAAACAT 0.82511 -107 ********** Masking position 5 Map Score: 0.856405 Number of sites scoring better than the average of aligned sites = 565 Number in coding regions = 508 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 6 ********** No masking Map Score: 8.40873e-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: 8.40873e-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: 8.40873e-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