AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -imodE_mthe_opreg_100.orf -g0.495 -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 = 0.495 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MTH150 75 conserved protein #2 MTH809 138 molybdenum cofactor biosynthesis protein MoaC #3 MTH922 67 unknown #4 MTH923 21 unknown #5 MTH925 32 conserved protein #6 MTH927 139 ferredoxin #7 MTH1550 40 molybdenum cofactor biosynthesis MoaA #8 MTH1551 139 molybdopterin-guanine dinucleotide biosynthesis protein B related #9 MTH1567 235 catalytic subunit of nitrate reductase (flp) #10 MTH1861 300 molybdenum cofactor biosynthesis MoaB Motif number 1 GCCACCGGCTCCATGAATATATACTAGAAG 1 13 1 CCATGAATAT 0.912268 -63 TTATCATCACTCATGAATTTCTTTGATGGA 2 13 0 TCATGAATTT 0.980886 -126 AAGAATTCACCCATGTATTTTAGAATCCAT 2 46 1 CCATGTATTT 0.985687 -93 TTATCATCACTCATGAATTTCTTTGATGGA 2 71 0 TCATGAATTT 0.980886 -68 AAGAATTCACCCATGTATTTTAGAATCCAT 2 104 1 CCATGTATTT 0.985687 -35 TCATGAATTTCTTTGATGGA 2 129 0 TCATGAATTT 0.980886 -10 ATGGATATCCTCACGTATTTCCTGAAAAAT 6 24 0 TCACGTATTT 0.91981 -116 ATCCCCATCTACAGGTATTTTAACGTATTT 9 15 0 ACAGGTATTT 0.883523 -221 TGATTTACATCCAGGTATTTAGTTAAATTA 9 216 0 CCAGGTATTT 0.980014 -20 CGGGTAGGGTCCAGGACTTTTAAAACTTAT 10 76 1 CCAGGACTTT 0.91648 -225 GACCAAATCGTCATAAATTTTTATTACTTT 10 163 1 TCATAAATTT 0.801724 -138 ********** Masking position 3 Map Score: 20.9782 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 71 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 2 AATCCATCAAAGAAATTCATGAGTGATGA 2 9 1 AAAGAATTCA 0.977271 -130 TGATGATAATGAAAGAATTCACCCATGTATT 2 34 1 GAAAAATTCA 0.96255 -105 AGAATCCATCAAAGAAATTCATGAGTGATGA 2 67 1 AAAGAATTCA 0.977271 -72 TGATGATAATGAAAGAATTCACCCATGTATT 2 92 1 GAAAAATTCA 0.96255 -47 AGAATCCATCAAAGAAATTCATGA 2 125 1 AAAGAATTCA 0.977271 -14 AGGTAATCTGAAAGTAATTCAGCACACCTTT 3 43 0 AAAGAATTCA 0.977271 -25 CCTGAAAAATAAAAAAATTGAAA 6 3 0 AAAAAATTGA 0.968867 -137 GGATACTCTTATAAAAATTGAATTTAATAAG 9 41 1 ATAAAATTGA 0.917111 -195 GATAAGACTGAAAAGAAATGATAATGTGGTG 9 101 1 AAAAAAATGA 0.782826 -135 GTATTTAGTTAAATTAATTGAACTATCTTCA 9 201 0 AAATAATTGA 0.847955 -35 GAGAAAAGTAATAAAAATTTATGACGATTTG 10 166 0 ATAAAATTTA 0.78897 -135 AATTATGGATGTAACAATTTATTTATGTGGG 10 263 0 GTAAAATTTA 0.676385 -38 **** ****** Masking position 6 Map Score: 17.2388 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 37 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 3 GAACTATGGTGCTTCTAGTATATATTCATGGAGC 1 20 0 GCTCTGATAA 0.946073 -56 TTCTTTGATGGATTCTAAAATACATGGGTGAATT 2 49 0 GATCTAATAA 0.984467 -90 TTCTTTGATGGATTCTAAAATACATGGGTGAATT 2 107 0 GATCTAATAA 0.984467 -32 GGTATCAGATCCTGGTTTAAA 4 1 0 GATCTGTTAA 0.933459 -21 ATATTCCACAGGTCCATATATAAATCTTTCTTAA 6 111 0 GGTCAAATAA 0.908899 -29 ACTTTATCATGATGCACAGATAAAGGTTATGAGT 8 97 1 GATCAAATAA 0.94629 -43 TGTAGATGGGGATACTCTTATAAAAATTGAATTT 9 32 1 GATCTTATAA 0.919081 -204 TTTACATCCAGGTATTTAGTTAAATTAATTGAAC 9 209 0 GGTTTATTAA 0.73749 -27 TCCCAGATGCTGATTTAAATAACCTAACG 10 6 1 GATCTATTAA 0.966329 -295 TATAAATAGTGCTGTTAATATATAGTAAACGGGT 10 47 1 GCTTTAATAA 0.861189 -254 *** ** * *** * Masking position 11 Map Score: 9.75411 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 51 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 AATCCATCAAAGAAATTCATG 2 1 1 ATCCATCAAA 0.952624 -138 TCATTATCATCACTCATGAATTTCTTTGATG 2 15 0 CCTCATGAAT 0.914252 -124 TGTATTTTAGAATCCATCAAAGAAATTCATG 2 59 1 ATCCATCAAA 0.952624 -80 TCATTATCATCACTCATGAATTTCTTTGATG 2 73 0 CCTCATGAAT 0.914252 -66 TGTATTTTAGAATCCATCAAAGAAATTCATG 2 117 1 ATCCATCAAA 0.952624 -22 GCACTGGAAACGCTCCTGAAAGGTGTGCTGA 3 25 1 CCTCCTGAAA 0.942832 -43 ATCCTCACGTATTTCCTGAAAAATAAAAAAA 6 17 0 ATTCCTGAAA 0.90813 -123 TTCTTAATGGACCTCATGAAAACAGTACTGT 6 87 0 ACTCATGAAA 0.981775 -53 TTTCAGTCTTATCCCATCAAATTTCCTTATT 9 83 0 ACCCATCAAA 0.979218 -153 AATGTGGTGCAACTCATAAAATTAGATGAAT 9 123 1 ACTCATAAAA 0.892863 -113 * ********* Masking position 7 Map Score: 11.2974 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 163 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 5 AATTCTTTCATTATCATCACTCATGAATTTC 2 22 0 TTATCTCACT 0.987546 -117 AATTCTTTCATTATCATCACTCATGAATTTC 2 80 0 TTATCTCACT 0.987546 -59 TAGGACAGTTCACTGCACTGGAAACGCTC 3 9 1 TTCACGCACT 0.980192 -59 CCCCTTCATGTTATCTTCAGTGTCCTTTTTA 8 59 1 TTATCTCAGT 0.97098 -81 CCTCTTCACCTCACTCTCTACTCAT 8 125 0 TTCACTCACT 0.986584 -15 ACATTATCATTTCTTTTCAGTCTTATCCCAT 9 97 0 TTCTTTCAGT 0.839767 -139 TTACTATATATTAACAGCACTATTTATAAAG 10 44 0 TTAACGCACT 0.976178 -257 ***** ***** Masking position 9 Map Score: 8.10988 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 51 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 TAGGACAGTTCACTGCACTGGAAACG 3 6 1 CAGTCACTGC 0.984901 -62 ATAATGTTTCAGTCACCTGCTTGACTGAGC 7 21 0 CAGTACCTGC 0.987774 -20 GTTCAGCCTCAAGTTCCCTTCCATCTATTCT 8 16 1 AAGTCCCTTC 0.976461 -124 CTAAATTTAACAGTCCCCTTCATGTTATCTT 8 45 1 CAGTCCCTTC 0.996285 -95 ATGTTATCTTCAGTGTCCTTTTTATGGTGAA 8 66 1 CAGTTCCTTT 0.888256 -74 GATTTCAGTACAGTACCTTGCCACATATACA 9 159 0 CAGTCCTTGC 0.984901 -77 **** ****** Masking position 4 Map Score: 5.92853 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 139 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 AATATATACTAGAAGCACCATAGTTCTAAT 1 28 1 AGAAGCACCA 0.961865 -48 GAATTCTTTCATTATCATCACTCATGAATT 2 24 0 ATTATCATCA 0.902809 -115 GAATTCTTTCATTATCATCACTCATGAATT 2 82 0 ATTATCATCA 0.902809 -57 AATAGCACCAGTATAATGGC 5 23 0 AATAGCACCA 0.95888 -10 ATCATGATAAAGTTTCACCATAAAAAGGAC 8 80 0 AGTTTCACCA 0.977693 -60 TTTTTATAAGAGTATCCCCATCTACAGGTA 9 28 0 AGTATCCCCA 0.968757 -208 TAATTTTATGAGTTGCACCACATTATCATT 9 117 0 AGTTGCACCA 0.981293 -119 ********** Masking position 1 Map Score: 6.18637 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 88 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 ATTTCTTTGATGGATTCTAAAATACATGGG 2 55 0 TGGATTCTAA 0.907827 -84 ATTTCTTTGATGGATTCTAAAATACATGGG 2 113 0 TGGATTCTAA 0.907827 -26 AACATGAAGGGGACTGTTAAATTTAGAATA 8 41 0 GGACTGTTAA 0.877782 -99 CCCATCTACAGGTATTTTAACGTATTTCAA 9 12 0 GGTATTTTAA 0.950809 -224 GTAGGGTCCAGGACTTTTAAAACTTATTCT 10 79 1 GGACTTTTAA 0.958917 -222 AACTTATTCTGGTCTTTTAAATTGGAATTG 10 99 1 GGTCTTTTAA 0.958918 -202 TGTCAGAAAGGGGATTATAATCATTTTCGG 10 201 1 GGGATTATAA 0.92976 -100 ********** Masking position 9 Map Score: 2.90085 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 66 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 TTTAAACCAGGATCTGATACC 4 7 1 CCAGGATCTG 0.963908 -15 TCCACATGAAGCTCAGTCAAG 7 2 1 CCACATGAAG 0.873448 -39 TCCAGGTTCAGCCTCAAGTTC 8 2 1 CCAGGTTCAG 0.98209 -138 TCCCAGATGCTGATTTAAATAA 10 3 1 CCAGATGCTG 0.974519 -298 ATTTAAAAGACCAGAATAAGTTTTAAAAGT 10 91 0 CCAGAATAAG 0.940241 -210 ********** Masking position 3 Map Score: 0.00702525 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 147 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 10 ********** No masking Map Score: 2.75223e-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: 2.75223e-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 12 ********** No masking Map Score: 2.75223e-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