AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -iglpR_mthe_opreg_300.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 MTH101 231 unknown #2 MTH853 22 conserved protein #3 MTH855 172 inosine-5'-monophosphate dehydrogenase related protein VIII #4 MTH1142 300 H(2)-dependent N5,N10-methylenetetrahydromethanopterin dehydrogenase #5 MTH1143 104 biotin synthetase (BioB) #6 MTH1145 78 conserved protein #7 MTH1147 38 conserved protein #8 MTH1850 105 fumarate reductase Motif number 1 CAGAAAAATTTTAATTAATAATCATTATAAATTGAAGTTT 1 66 1 TATTAAATAA 0.877388 -166 TTTCTAAATGTTACAAGACAAAAGCTTTAAATAGCAGCTA 1 116 0 TAAAAAATAA 0.960083 -116 CCTACAGAATTAATAAGAGAAACTTTTGAAGGCTGATGGG 3 13 0 TAAAAAAGAA 0.88392 -160 AACTTCAGTGTGACATCAAAAGAATCATAAGCACCCACCT 3 50 0 TAATAAATAA 0.988014 -123 CACAGATCCGTGATATTAATATCTTAATAATTATGATTAT 4 58 1 TAATATATAA 0.888623 -243 CCATATAATATTATATGAAAATAATCATAATTATTAAGAT 4 78 0 TAATAAATAA 0.987985 -223 CAAAGGAGGATAAAATGAAAACATTGCTTAAATTGACTTA 4 140 1 TAATAAATTA 0.960191 -161 TTGATAATTTTCAAATCAAAAAACTTATAAGGAGAATTTA 4 202 0 TAATAAATAA 0.98798 -99 AAAAATATATTTATATTGGAAACCGATTAATCTGTACTAC 4 241 1 TAATGAATAA 0.959752 -60 TCTGTACTACTAATAATATAAGTAGTATTACAGAAATGGA 4 271 1 TAAAAAATTA 0.874709 -30 TAAAAATTACTTGGATAAAAAAATAAATAAATTTTTCTGG 5 24 0 TGATAAATAA 0.959873 -81 TTCAGCTGCTTGGGATTGAAAAGTCAGTAAATTGAAGTGT 5 63 0 TGATGAATAA 0.874142 -42 GATTATCAGTTAAAATCACAAACCTTAATATGTGTTGATA 8 30 1 TAATAAAATA 0.736372 -76 GCTGACTCATATGAAAAACTTCAGAATGAACTGAAT 8 80 0 TAATAAAGAA 0.963023 -26 * * ** * ** *** Masking position 11 Map Score: 17.3799 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 36 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 2 GAAGTACCTGCAGGTACATATATCCACTGTG 1 19 0 CAGTACATAT 0.669183 -213 TATGTACCTGCAGGTACTTCACATTTGCCAC 1 30 1 CAGTACTTCA 0.543713 -202 ACATTTGCCACATGAACAGAAAAATTTTAAT 1 50 1 CAGAACAGAA 0.984059 -182 CATAAGCACCCACCTACAGAATTAATAAGAG 3 34 0 CACTACAGAA 0.932922 -139 TTCAGTGTGACATCAAAAGAATCATAAGCAC 3 56 0 CACAAAAGAA 0.720406 -117 GCTATCCATAAATGAACTGATTACTGGTATA 3 136 0 AAGAACTGAT 0.929918 -37 TGAAGCAGCTCAGCCACAGATCCGTGATATT 4 44 1 CACCACAGAT 0.790654 -257 TTTCAATCCCAAGCAGCTGAAACTGGTGTTA 5 82 1 AACAGCTGAA 0.901664 -23 AGGCCCCATCAAAGAACAGCAGAGAAAAACA 6 11 1 AAGAACAGCA 0.91297 -68 ATATAACAGGAAACAGCTGATCAAAA 6 63 1 AACAGCTGAT 0.809337 -16 ACATGGAACGCATGAACTTAAGGGAAAGAGC 7 13 1 CAGAACTTAA 0.913858 -26 AACTTAAGGGAAAGAGCAGAAA 7 27 1 AAGAGCAGAA 0.943702 -12 AAAACTTCAGAATGAACTGAATTTTAATTGT 8 71 0 AAGAACTGAA 0.966287 -35 ** ******** Masking position 2 Map Score: 8.15997 Number of sites scoring better than the average of aligned sites = 701 Number in coding regions = 615 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 3 ATAATGATTATTAATTAAAATTTTTCTGTTCAT 1 61 0 TAATTAATTT 0.954051 -171 ATAATCATTATAAATTGAAGTTTTTTTAGAAAA 1 83 1 TAATTAATTT 0.953351 -149 GTCATCTACATTAATATCAGTTTCTAAATGTTA 1 143 0 TAATACATTT 0.932935 -89 CCACTGCATGTGAACTTCAGTGTGACATCAAAA 3 69 0 TAACTCATGT 0.873577 -104 GTTTCCAATATAAATATATTTTTTGATAATTTT 4 231 0 TAATAATTTT 0.84196 -70 GATAAAAAAATAAATAAATTTTTCTGGGATTTT 5 18 0 TAATAATTTT 0.84196 -87 GAAAAGTCAGTAAATTGAAGTGTAAAAATTACT 5 53 0 TAATTAATGT 0.909668 -52 TTTAACACCAGTTTCAGCTGCTTG 5 91 0 TAACACATTT 0.919835 -14 AACTTCAGAATGAACTGAATTTTAATTGTTTAT 8 67 0 TAACTAATTT 0.944829 -39 * **** ** *** Masking position 4 Map Score: 5.82911 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 22 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 AAACTTCAATTTATAATGATTATTAATTAAAAT 1 73 0 TTAAATGTAT 0.932464 -159 TCCACCAATATTAAATAGGTCATCTACATTAAT 1 161 0 TTAATAGTAT 0.905977 -71 AAGAGAAACTTTTGAAGGCTGATGGGAA 3 6 0 TTTAAGGTAT 0.972468 -167 ACTCAAAATATTTAAATGAACATCCATATACCA 3 110 1 TTTAATGAAT 0.712171 -63 TCATATAATATTATATGGATAATGGATGGTAAA 4 100 1 TTAATGGTAT 0.972468 -201 ATCAAAAAACTTATAAGGAGAATTTATTCACCT 4 195 0 TTAAAGGGAT 0.945252 -106 TCTGCTGTTCTTTGATGGGGCCT 6 1 0 TTTATGGGCT 0.782641 -78 CTGTTTCCTGTTATATGGTTCATACTGTTTATG 6 46 0 TTAATGGTAT 0.972468 -33 GTCTGTATTGTTTAAAAGATTATCAGTTAAAAT 8 13 1 TTTAAAGTAT 0.905976 -93 TGAACTGAATTTTAATTGTTTATCAACACATAT 8 57 0 TTTATTGTAT 0.932455 -49 *** **** * ** Masking position 5 Map Score: 7.83625 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 66 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 TGCAGGTACTTCACATTTGCCACATGAACA 1 38 1 TCACATTTGC 0.800114 -194 TAGATCACCTTCGGTAGAACTGCC 1 218 0 TCACCTTCGG 0.988893 -14 TCATAAGCACCCACCTACAGAATTAATAAG 3 36 0 CCACCTACAG 0.920953 -137 ACACTGAAGTTCACATGCAGTGGTTCTGTG 3 79 1 TCACATGCAG 0.926254 -94 TTATACCACATCCGGTGCTATCCAT 3 158 0 CCACATCCGG 0.936377 -15 TTCATTTTATCCTCCTTTGGGAAGCCTTTA 4 129 0 CCTCCTTTGG 0.913021 -172 GAGAATTTATTCACCTGTGGCAATTTCAGG 4 181 0 TCACCTGTGG 0.946564 -120 ********** Masking position 6 Map Score: 2.84827 Number of sites scoring better than the average of aligned sites = 369 Number in coding regions = 354 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 ********** No masking Map Score: -1.27654e-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 7 ********** No masking Map Score: -1.27654e-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 8 ********** No masking Map Score: -1.27654e-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