AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i183_thiamin_biosynthesis_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -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 yjbQ 234 similar to Na+/H+ antiporter #2 tenA 248 transcriptional regulator #3 ywdC 42 alternate gene name: ipa-53r #4 thiD 148 phosphomethylpyrimidine kinase #5 ywbI 105 alternate gene name: ipa-24d; similar to transcriptional regulator (LysR family) #6 yxlA 211 similar to purine-cytosine permease Motif number 1 GCGGTCTCCTCCTTACCGATTGTTT 1 6 1 CTCCTCCTTA 0.94678 -229 AGAACAAAACCTCATTTTTAAAAAACATAA 1 168 0 CTCATTTTTA 0.861969 -67 TATGCTAGTTCTCACTCAGAGAACAAAACC 1 187 0 CTCACTCAGA 0.860338 -48 AATCAGAACCTCCTTTTTAAGTCAGGGTT 1 216 0 CTCCTTTTTA 0.960142 -19 AATTGTTCTGCACCTCTATATTAACACGAA 2 29 0 CACCTCTATA 0.815346 -220 CACTAGGGGTGTCCTTCATAAGGGCTGAGA 2 78 1 GTCCTTCATA 0.916808 -171 GTCTAAAAGTCACACTTTTATCTCAGCCCT 2 98 0 CACACTTTTA 0.840446 -151 GTGACTTTTAGACCCTCATAACTTGAACAG 2 115 1 GACCCTCATA 0.902873 -134 AAATCATTCCCCCTCTGAAAATAAAAAA 2 231 0 CCCCCTCTGA 0.93704 -18 AGCTTCCTCCTCACTCTTTCCTTCCTGAA 3 10 1 CTCACTCTTT 0.799295 -33 ATTGATGCCTCCCTTATATACTTATTGT 5 9 1 CTCCCTTATA 0.980774 -97 GACCGTGATCCCCCCTTTTTTGTTTTTCTG 6 12 1 CCCCCTTTTT 0.857053 -200 TATTTGTAAACCCCCTTATAGTCTGTTAAG 6 141 1 CCCCCTTATA 0.969652 -71 TGCATCGTCCTCCATATTGGATGTTT 6 196 0 GTCCTCCATA 0.835296 -16 ********** Masking position 3 Map Score: 13.6923 Number of sites scoring better than the average of aligned sites = 1260 Number in coding regions = 856 Number in noncoding regions = 404 Number of orfs with sites within 600 bp upstream = 462 Fraction of orfs with sites within 600 bp upstream = 0.0742049 Motif number 2 CTCCTTACCGATTGTTTTATTTATTATGAAGC 1 19 1 ATTTTTATTT 0.853678 -216 GAGTCATCACAAGCTTTTATGTGCAAATTATA 1 61 1 AATTTTATGT 0.796501 -174 TTAAGACCTTATCACTTTATTTTTCATCATCA 1 119 1 ATCTTTATTT 0.903501 -116 CCTTGTTAAAATCGCGTTATGTTTTTTAAAAA 1 152 1 ATCGTTATGT 0.936417 -83 ATATTAACACGAATCCTTATTTGGTCAAGAT 2 10 0 GACCTTATTT 0.874403 -239 TGGAGCGGTATTTGTGTTATTTTACTATGCCA 2 166 1 TTTGTTATTT 0.721402 -83 CGGGAAAGTGGTTTTTTTATTTTCAGAGGGGG 2 219 1 GTTTTTATTT 0.84511 -30 CCCCTACCTAGTTTTCTTATGTAGCATTTTAC 4 21 1 GTTCTTATGT 0.943355 -128 TTGAACCTCCATCATGTTTTGTCTTTCATTAT 4 124 0 ATTGTTTTGT 0.728689 -25 TACCTATAGAGAGACCTTATGTACAATAAGTA 5 29 0 GACCTTATGT 0.917848 -77 GAATAAGAAGTATTCCTTTTGTCTATAGAAAG 5 74 1 TACCTTTTGT 0.612876 -32 TTCAAAAGCGTTCATCTTTTTTACAATTCTTT 6 62 1 TTTCTTTTTT 0.595224 -150 GTTTGGCTGCATATCCTTATTTGTAAACCCCC 6 124 1 ATCCTTATTT 0.94683 -88 CTGTTAAGCTATGACTTTATGTCGATTTCAAA 6 163 1 ATCTTTATGT 0.937599 -49 ** ******** Masking position 7 Map Score: 9.55636 Number of sites scoring better than the average of aligned sites = 740 Number in coding regions = 547 Number in noncoding regions = 193 Number of orfs with sites within 600 bp upstream = 205 Fraction of orfs with sites within 600 bp upstream = 0.0329264 Motif number 3 AGTGATAAGGTCTTAATCCTGTTTAGAAAA 1 105 0 TCTTAATCCT 0.94993 -130 TTATTTTTCATCATCACCCTTGTTAAAATC 1 135 1 TCATCACCCT 0.980563 -100 GTGAGAACTAGCATAACCCTGACTTAAAAA 1 202 1 GCATAACCCT 0.974838 -33 CACACTTTTATCTCAGCCCTTATGAAGGAC 2 88 0 TCTCAGCCCT 0.875053 -161 AGCTTCCTCCTCACTCTTTCC 3 2 1 GCTTCCTCCT 0.957852 -41 GTCTTGAACCTCCATCATGTT 4 138 0 TCTTGAACCT 0.814966 -11 GCGCTTCACCCTTTCTATAGAC 5 94 0 GCTTCACCCT 0.99227 -12 TGCATCGTCCTCCATATTGGA 6 201 0 GCATCGTCCT 0.963059 -11 ********** Masking position 10 Map Score: 6.43415 Number of sites scoring better than the average of aligned sites = 350 Number in coding regions = 290 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 4 TTTATTATGAAGCAAAGTGTTGTGAGTCAT 1 38 1 AGCAAAGTGT 0.965214 -197 AAGGGCTGAGATAAAAGTGTGACTTTTAGA 2 97 1 ATAAAAGTGT 0.836253 -152 AGACCTGCGTAGGGAAGTGGAGCGGTATTT 2 149 1 AGGGAAGTGG 0.977151 -100 TTTCCCGCAAGGAAAAGTGGTTTGGAATTG 2 196 0 GGAAAAGTGG 0.97729 -53 TTTTCCTTGCGGGAAAGTGGTTTTTTTATT 2 210 1 GGGAAAGTGG 0.989792 -39 CTTTTCAGGAAGGAAAGAGTGAGGAGGAAG 3 13 0 AGGAAAGAGT 0.94832 -30 ********** Masking position 5 Map Score: 3.84082 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 160 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 5 ACACTTTGCTTCATAATAAATAAAACAATCGG 1 26 0 TCATAATATA 0.970708 -209 TTTCTCTGTATCACAATATATAGAAGATCTAT 4 84 0 TCACAATATA 0.974567 -65 GTTTTGTCTTTCATTATAGTTAGATTTTCTCT 4 109 0 TCATTATATA 0.911927 -40 ACATAAGGTCTCTCTATAGGTAAAATATATAT 5 39 1 TCTCTATATA 0.944462 -67 TACTTCTTATTCTTAATATATATTTTACCTAT 5 54 0 TCTTAATATA 0.961302 -52 ******** ** Masking position 6 Map Score: 0.829756 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 22 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 TTATGAAGCAAAGTGTTGTGAGTCATCACA 1 42 1 AAGTGTTGTG 0.708172 -193 ATTTTAACAAGGGTGATGATGAAAAATAAA 1 134 0 GGGTGATGAT 0.970822 -101 TGTTAAAATCGCGTTATGTTTTTTAAAAAT 1 155 1 GCGTTATGTT 0.78634 -80 TTTAAAAATGAGGTTTTGTTCTCTGAGTGA 1 176 1 AGGTTTTGTT 0.810805 -59 TTTTAAGTCAGGGTTATGCTAGTTCTCACT 1 201 0 GGGTTATGCT 0.953844 -34 CTTAAAAAGGAGGTTCTGATT 1 224 1 AGGTTCTGAT 0.801301 -11 GAACCTGTTCAAGTTATGAGGGTCTAAAAG 2 119 0 AAGTTATGAG 0.87261 -130 AGGAAGGAAAGAGTGAGGAGGAAGCT 3 7 0 GAGTGAGGAG 0.802491 -36 AACTAGGTAGGGGTTTTGAGATG 4 4 0 GGGTTTTGAG 0.962534 -145 TCTATAGAAAGGGTGAAGCGC 5 95 1 GGGTGAAGCG 0.849138 -11 ********** Masking position 4 Map Score: 2.41746 Number of sites scoring better than the average of aligned sites = 720 Number in coding regions = 600 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 7 GCGGTCTCCTCCTTACCGATTGTTTTATTTATTA 1 11 1 CCTACGTGTT 0.971057 -224 AGGATTAAGACCTTATCACTTTATTTTTCATCAT 1 115 1 CCTATATTAT 0.854237 -120 ATCTCAAAACCCCTACCTAGTTTTCTTATGTAGC 4 12 1 CCTACTTTTT 0.945992 -137 TATAGATCTTCTATATATTGTGATACAGAGAAAA 4 83 1 CTTATTTGAT 0.77351 -66 TTGATGCCTCCCTTATATACTTATTGTACATAAG 5 12 1 CCTATTTTAT 0.950694 -94 CGTGATCCCCCCTTTTTTGTTTTTCTGCCTTATG 6 15 1 CCTTTTTTTT 0.847169 -197 TTGTAAACCCCCTTATAGTCTGTTAAGCTATGAC 6 144 1 CCTATGTGTT 0.983402 -68 GCATCGTCCTCCATATTGGATGTTTTTTTGAAAT 6 187 0 CCTATGTGTT 0.983402 -25 ** *** * **** Masking position 4 Map Score: 2.95567 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 159 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 8 TGCAAATTATAGAAGAAGAATCATTTTCTA 1 82 1 AGAAGAAGAA 0.972148 -153 CACAATATATAGAAGATCTATAGGAATCAT 4 75 0 AGAAGATCTA 0.949258 -74 TGTGATACAGAGAAAATCTAACTATAATGA 4 101 1 AGAAAATCTA 0.892506 -48 ATATATATTAAGAATAAGAAGTATTCCTTT 5 63 1 AGAATAAGAA 0.897805 -43 CTCATAAGGCAGAAAAACAAAAAAGGGGGG 6 21 0 AGAAAAACAA 0.939363 -191 AGAATTGTAAAAAAGATGAACGCTTTTGAA 6 62 0 AAAAGATGAA 0.843744 -150 ********** Masking position 6 Map Score: 1.14659 Number of sites scoring better than the average of aligned sites = 790 Number in coding regions = 690 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 9 ********** No masking Map Score: -2.7829e-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 10 ********** No masking Map Score: -2.7829e-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 11 ********** No masking Map Score: -2.7829e-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