AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00630_aful_reg_100.orf -o00630_aful_100.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 AF1342 126 thymidine phosphorylase (deoA-2) #2 AF1588 51 conserved hypothetical protein #3 AF1590 300 A. fulgidus predicted coding region AF1590 #4 AF1638 31 ribulose bisphosphate carboxylase, large subunit (rbcL-2) Motif number 1 TTAAAACCTTTTCAGGTGAGAATTTTTAAA 1 32 1 TTCAGGTGAG 0.941423 -95 TTTTTGTGAGTTCTCGGGAGCAAAGAAGTG 3 54 0 TTCTCGGGAG 0.983376 -247 GAAACCGTCTTTTTTGTGAGTTCTCGGGAG 3 64 0 TTTTTGTGAG 0.966752 -237 ACCCATGCGATTTTAGGGAGATTTTTACTC 3 94 0 TTTTAGGGAG 0.990645 -207 TTATTGCGGAATTTGGTGAGACCTTTATTG 3 144 1 ATTTGGTGAG 0.98049 -157 GAGCGGGAAAACTTAGGGAGGATAAAATTA 3 215 0 ACTTAGGGAG 0.934104 -86 TCTACCCTAGTTTTGGGGGGAAGCGAGCGG 3 239 0 TTTTGGGGGG 0.986562 -62 ********** Masking position 6 Map Score: 8.10784 Number of sites scoring better than the average of aligned sites = 247 Number in coding regions = 222 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 2 TCAGCTTTAAAACCTTTTCAGGTGAGAATT 1 26 1 AACCTTTTCA 0.974757 -101 AAACATAAACAACATTATCTATAACTTCTT 1 59 1 AACATTATCT 0.934013 -68 CATTATCTATAACTTCTTCACGATAGCGAG 1 71 1 AACTTCTTCA 0.96738 -56 AAAGAATATTAACTTTTTCTCGCTATCGTG 1 89 0 AACTTTTTCT 0.985235 -38 GGCTTCAAGCAACCACTTCTTTGCTCCCGA 3 41 1 AACCACTTCT 0.93645 -260 AACTTTATTTACCTCCTTAG 4 1 1 AACTTTATTT 0.846827 -31 ********** Masking position 8 Map Score: 3.68389 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 260 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 3 TCTCACCTGAAAAGGTTTTAAAGCTGACGAC 1 22 0 AAAGTTTTAA 0.968831 -105 TTTTCAGGTGAGAATTTTTAAACATAAACAA 1 40 1 AGAATTTTAA 0.934344 -87 ATATTCTTTCAGAGTTTTTGAAGTTCA 1 110 1 AGAGTTTTGA 0.99003 -17 CAGCAAATATAAAGATTTTGATTTAATGTTA 2 15 0 AAAGTTTTGA 0.971058 -37 ATCAATTTGTAGAGGCTTCAAGCAACCACTT 3 28 1 AGAGCTTCAA 0.924805 -273 GCGATTTTAGGGAGATTTTTACTCGAAACCG 3 87 0 GGAGTTTTTA 0.930125 -214 **** ****** Masking position 7 Map Score: 2.59904 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 231 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 4 TTTATAACATTAAATCAAAATCTTT 2 6 1 AACATTAAAT 0.771877 -46 TTGTGTCAGCAAATATAAAGATTTTGATTT 2 22 0 AAATATAAAG 0.923906 -30 GGCGAGAAATAAAGCCAATCAATT 3 5 1 AGAAATAAAG 0.966525 -296 TCAATAGCGCATCAATAAAGGTCTCACCAA 3 156 0 ATCAATAAAG 0.966065 -145 TAGGGAGGATAAAATTAAAGAAACTCTTTG 3 202 0 AAAATTAAAG 0.96348 -99 TGCTAAGGAGGTAAATAAAGTT 4 3 0 GTAAATAAAG 0.926255 -29 ********** Masking position 6 Map Score: 2.27103 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 96 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 5 AACTTCTTCACGATAGCGAGAAAAAGTTAA 1 81 1 CGATAGCGAG 0.991854 -46 ACAAAAAAGACGGTTTCGAGTAAAAATCTC 3 77 1 CGGTTTCGAG 0.97347 -224 TAGTTTTGGGGGGAAGCGAGCGGGAAAACT 3 232 0 GGGAAGCGAG 0.982841 -69 CCCAAAACTAGGGTAGAGGGACCATCACTC 3 252 1 GGGTAGAGGG 0.974146 -49 CTCTTTTCTACTATTGAGAGTCAAGATTAA 3 279 1 CTATTGAGAG 0.878322 -22 ********** Masking position 8 Map Score: 0.739044 Number of sites scoring better than the average of aligned sites = 524 Number in coding regions = 507 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 GATGTTAAATTGTCGTCAGCTTTAAAACCT 1 11 1 TGTCGTCAGC 0.976364 -116 AAAGTTAATATTCTTTCAGAGTTTTTGAAG 1 103 1 TTCTTTCAGA 0.893157 -24 AAATTTGGGGTTGTGTCAGCAAATATAAAG 2 32 0 TTGTGTCAGC 0.979207 -20 TAAAATCGCATGGGTTCAGCTGCTTCCCTT 3 109 1 TGGGTTCAGC 0.982673 -192 TTCAGCTGCTTCCCTTCAGCATTATTGCGG 3 123 1 TCCCTTCAGC 0.982673 -178 ********** Masking position 6 Map Score: 0.412685 Number of sites scoring better than the average of aligned sites = 440 Number in coding regions = 406 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 7 ********** No masking Map Score: -8.78641e-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: -8.78641e-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 9 ********** No masking Map Score: -8.78641e-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