AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i001_Purine_Biosynthesis_aful_reg_100.orf -o001_aful_100.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/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 RAG48649 144 Archaeoglobus_fulgidus #2 RAG48877 172 Archaeoglobus_fulgidus #3 RAG02631 207 Archaeoglobus_fulgidus #4 RAG19986 45 Archaeoglobus_fulgidus #5 RAG29290 201 Archaeoglobus_fulgidus Motif number 1 AGAAGAGAGAATAGTAGGCGAGTCGGGGAGCAAG 1 50 0 ATAGAGCGTC 0.932099 -95 TGTGGTTGTCAAAGGACGCGATACCTGCCGACTC 1 104 0 AAAGAGCTAC 0.977092 -41 CTAAACTTTCAAAGCTGGCAGATCTTTAATT 3 8 0 AAAGTGCATC 0.988886 -200 GATCTTAGAGAAAGGAATCAGACCAGCCCCACCA 3 75 1 AAAGATCACC 0.834255 -133 CCACCAGCTAAAAGAATTCTTTTCAAATTGATGC 3 103 1 AAAGATCTTC 0.958927 -105 TACTAGCACTAAAGAGTGCAGAACATCAACGCTG 3 140 1 AAAGGGCAAC 0.926828 -68 AAAAAGCTTAAAAGATTGCGGTTGATTGCTTACC 3 183 1 AAAGTGCTTG 0.934188 -25 AGTCTTTTTAAAAGGTTGCCCATCTGAAGT 4 7 0 AAAGTGCATC 0.988886 -39 AAAATTGAGGATAGCTTGCTGTTCTCAACTAAGG 5 58 0 ATAGTGCTTC 0.968226 -144 TGCTCTTTAAAAATCAAGCGATTCGGTGTATGAT 5 162 0 AAATAGCTTC 0.921864 -40 **** * ** *** Masking position 3 Map Score: 9.73326 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 214 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 ATGTGTGGGGTTGTAGGTATATACCATCCT 1 10 1 GTTGTGGTAT 0.827479 -135 AGCTCCCCGTCAGGATGGTATATACCTACAA 1 21 0 CAGGAGGTAT 0.876163 -124 TCGGTCAGCAGGGGCGGATATATAATTAATC 2 119 0 GGGGCGATAT 0.954653 -54 ACTTTCAAAGCTGGCAGATCTTTAATT 3 7 0 CTGGCGATCT 0.988651 -201 TTTCCCTAGACAGGACGATCTTAGAGAAAGG 3 59 1 CAGGAGATCT 0.912681 -149 TTTAGCTGGTGGGGCTGGTCTGATTCCTTTC 3 84 0 GGGGCGGTCT 0.987381 -124 TGTCGGCAGCGTTGATGTTCTGCACTCTTTA 3 149 0 GTTGAGTTCT 0.905623 -59 TTTTTAAAAGGTTGCCCATCTGAAGT 4 6 0 GTTGCCATCT 0.876142 -40 TTCCGTTAACCTTGCTGGTATTAGTT 5 6 0 CTTGCGGTAT 0.973669 -196 TTGAGGATAGCTTGCTGTTCTCAACTAAGGG 5 57 0 CTTGCGTTCT 0.966974 -145 ***** ***** Masking position 9 Map Score: 8.12527 Number of sites scoring better than the average of aligned sites = 432 Number in coding regions = 399 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 3 AGCAAGCTCCCCGTCAGGATGGTATATACCTA 1 24 0 CCGTCAGGAG 0.985124 -121 GTAGGCGAGTCGGGGAGCAAGCTCCCCGTCAG 1 39 0 CGGGGAGCAC 0.977253 -106 CTCTCTTCTCCCTTCAGCATCGCGGTCAGGAG 1 75 1 CCTTCAGCAG 0.967728 -70 TTCAGCATCGCGGTCAGGAGTCGGCAGGTATC 1 87 1 CGGTCAGGAC 0.995384 -58 TTTCCGTTTTCGGTCAGCAGGGGCGGATATAT 2 127 0 CGGTCAGCAG 0.995828 -46 CGGTAAGCAATCAACCGCAATC 3 196 0 CGGTAAGCAC 0.987553 -12 ********* * Masking position 6 Map Score: 5.63951 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 75 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 4 TTCGAATGTCTTTAAAGTTTAGAGTTTGATC 2 23 0 TTAAAGTTTA 0.930977 -150 TCGAAAGCCTTACAAATCGTATTTAAGCTTT 2 49 1 TAAAATCGTA 0.866652 -124 GTGTAAAAATAACAAAGCTTAAATACGATTT 2 62 0 AAAAAGCTTA 0.940192 -111 CGTTTTTAATTACAAATTCTACCTGTGTAAA 2 86 0 TAAAATTCTA 0.728324 -87 TCTGCCAGCTTTGAAAGTTTAGGTTTTTCTT 3 20 1 TTAAAGTTTA 0.930687 -188 TGCCGACACGGAAAAAGCTTAAAAGATTGCG 3 172 1 GAAAAGCTTA 0.929615 -36 TTTATAAGTAAAAAAATTTTACTAAAATAAA 5 90 0 AAAAATTTTA 0.882451 -112 TTTTTTTACTTATAAATTTTATCCTTCAGAT 5 105 1 TAAAATTTTA 0.921181 -97 ** ******** Masking position 6 Map Score: 3.41172 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 93 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 5 GAATAGTAGGCGAGTCGGGGAGCAAGCTCC 1 46 0 CGAGTCGGGG 0.995252 -99 ATCGCGGTCAGGAGTCGGCAGGTATCGCGT 1 93 1 GGAGTCGGCA 0.990243 -52 AAGCTTTTTCCGTGTCGGCAGCGTTGATGT 3 162 0 CGTGTCGGCA 0.990877 -46 GATTCAAGTCGGAAAAGTCTTTTT 4 32 0 CAAGTCGGAA 0.961693 -14 AAAAATCAAGCGATTCGGTGTATGATGATA 5 158 0 CGATTCGGTG 0.964413 -44 ********** Masking position 5 Map Score: 3.16658 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 55 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 TACCTGTGTAAAAATAACAAAGCTTAAATA 2 68 0 AAAATAACAA 0.915736 -105 GTAGAATTTGTAATTAAAAACGAGGATTAA 2 95 1 TAATTAAAAA 0.905069 -78 TGTCTAGGGAAAAGTAAAAAAAGAAAAACC 3 41 0 AAAGTAAAAA 0.973901 -167 AAATTTTACTAAAATAAAAATTGAGGATAG 5 78 0 AAAATAAAAA 0.960197 -124 ATAAAATTTATAAGTAAAAAAATTTTACTA 5 97 0 TAAGTAAAAA 0.963013 -105 ********** Masking position 5 Map Score: 3.03296 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 29 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 7 TATATACCTACAACCCCACACAT 1 4 0 CAACCCCACA 0.97717 -141 AGTCGGGGAGCAAGCTCCCCGTCAGGATGG 1 34 0 CAAGCTCCCC 0.902743 -111 CGTCCTTTGACAACCACATAAGGCAGAAGA 1 120 1 CAACCACATA 0.837214 -25 GGTAACCACCCTGATCAAACTC 2 3 1 TAACCACCCT 0.95373 -170 ATTAATTATATATCCGCCCCTGCTGACCGA 2 120 1 TATCCGCCCC 0.878983 -53 GGAATCAGACCAGCCCCACCAGCTAAAAGA 3 88 1 CAGCCCCACC 0.9674 -120 GGTAAGCAATCAACCGCAATCTTTTAAGCT 3 187 0 CAACCGCAAT 0.888335 -21 CTACCTCATTCAACCACCCTTAGTTGAGAA 5 41 1 CAACCACCCT 0.989025 -161 ********** Masking position 2 Map Score: 3.29604 Number of sites scoring better than the average of aligned sites = 937 Number in coding regions = 887 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 8 TGCTGAAGGGAGAAGAGAGAATAGTAGGCGAG 1 62 0 AGAAGAGAAT 0.967348 -83 ATTTGTAATTAAAAACGAGGATTAATTATATA 2 100 1 AAAAGAGGAT 0.98611 -73 CTGCTGACCGAAAACGGAAAATAATCGATGAG 2 139 1 AAAAGAAAAT 0.966874 -34 GGGAAAAGTAAAAAAAGAAAAACCTAAACTTT 3 33 0 AAAAGAAAAA 0.898699 -175 TACTAAAATAAAAATTGAGGATAGCTTGCTGT 5 70 0 AAAAGAGGAT 0.98611 -132 **** ****** Masking position 8 Map Score: 1.24628 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 = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 ACTATTCTCTCTTCTCCCTTCAGCATCGCG 1 69 1 CTTCTCCCTT 0.992714 -76 GCCCCTCTTCTGCCTTATGTGGTTGT 1 129 0 CTTCTGCCTT 0.986673 -16 TCTTTTTTTACTTTTCCCTAGACAGGACGA 3 47 1 CTTTTCCCTA 0.972115 -161 ATCTTTTAAGCTTTTTCCGTGTCGGCAGCG 3 169 0 CTTTTTCCGT 0.949858 -39 ********** Masking position 5 Map Score: 1.15449 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 119 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 TCCTGACGGGGAGCTTGCTCCCCGACTCGC 1 37 1 GAGCTTGCTC 0.588134 -108 TTAAAGTTTAGAGTTTGATCAGGGTGGTTA 2 13 0 GAGTTTGATC 0.97562 -160 TATGATGATAGTGTATGATGGTACTCACAA 5 138 0 GTGTATGATG 0.968132 -64 AAGCGATTCGGTGTATGATGATAGTGTATG 5 151 0 GTGTATGATG 0.968132 -51 GATTTTTAAAGAGCATGAGCAAAAAACAAC 5 181 1 GAGCATGAGC 0.884154 -21 ********** Masking position 6 Map Score: 1.74516 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 52 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 11 ********** No masking Map Score: 1.41641e-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: 1.41641e-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 13 ********** No masking Map Score: 1.41641e-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