AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i001_Purine_Biosynthesis_aful_reg_300.orf -o001_aful_300.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 RAG09596 300 Archaeoglobus_fulgidus #3 RAG48877 172 Archaeoglobus_fulgidus #4 RAG02631 207 Archaeoglobus_fulgidus #5 RAG02630 133 Archaeoglobus_fulgidus #6 RAG47432 74 Archaeoglobus_fulgidus #7 RAG19986 45 Archaeoglobus_fulgidus #8 RAG29290 201 Archaeoglobus_fulgidus Motif number 1 TGCTCTGTACATACCACCAATTCTAGCATGATTCCCTA 2 20 1 AACAATCTCA 0.901207 -281 CAAGTCGAAAACATTTTTAACCCTGAAGCTCCAGCAAT 2 172 0 AATAACCTAG 0.662881 -129 CCAGATGCTGAGAGCTTAAAGGCACACAAGTCGAAAAC 2 198 0 AAAAAGCACA 0.778197 -103 CACCCTGATCAAACTCTAAACTTTAAAGACATTCGAAA 3 17 1 AAAAATTTAG 0.547164 -156 AACTTTAAAGACATTCGAAAGCCTTACAAATCGTATTT 3 35 1 AAAAACCTCA 0.927754 -138 TACCTGTGTAAAAATAACAAAGCTTAAATACGATTTGT 3 60 0 AACAAGCTAA 0.974486 -113 AGAAAAACCTAAACTTTCAAAGCTGGCAGATCTTTAAT 4 12 0 AACAAGCTCA 0.981402 -196 TAAAGAGTGCAGAACATCAACGCTGCCGACACGGAAAA 4 149 1 AACAAGCTCG 0.981742 -59 AACGCTGCCGACACGGAAAAAGCTTAAAAGATTGCGGT 4 167 1 AAAAAGCTAA 0.95978 -41 AATCTGCTGAAAAACAAAAAAGTTGGAAAATGAACTTA 5 18 0 AAAAAGTTAA 0.872763 -116 TTATATAACAATATCGCAAATGCTATAGATTTATATAG 6 17 0 AAAAAGCTAG 0.9605 -58 ACTTCAGATGGGCAACCTTTTAAAAAGACTTTT 7 6 1 AACAACTTAA 0.81047 -40 AACTAATACCAGCAAGGTTAACGGAATTAACTA 8 6 1 AACAAGTTCG 0.939233 -196 * * *** *** ** Masking position 9 Map Score: 10.227 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 344 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 2 TTCTCTCTTCTCCCTTCAGCATCGCGGTCA 1 73 1 TCCCTTCAGC 0.95671 -72 GCCCCTCTTCTGCCTTATGTGGT 1 132 0 CCTCTTCTGC 0.864571 -13 TTTTAATTGCCTCCATCCGAAGAAACTTTT 2 59 0 CTCCATCCGA 0.914307 -242 GTAGGACAACGCCCTTCCGAGGCGTTAGCC 2 120 0 GCCCTTCCGA 0.978171 -181 GAAGGGCGTTGTCCTACCGCTAGACTACCC 2 133 1 GTCCTACCGC 0.821013 -168 TTTTAAATAACTCCTCCTGCAACGAACCTT 2 258 1 CTCCTCCTGC 0.960866 -43 ATTCTTTCCCTCCAGAATTATCTAAG 2 285 0 TCCCTCCAGA 0.931437 -16 TATATATCCGCCCCTGCTGACCGAAAACGG 3 126 1 CCCCTGCTGA 0.94892 -47 ATCAGACCAGCCCCACCAGCTAAAAGAATT 4 91 1 CCCCACCAGC 0.963794 -117 TTAAAAGGTTGCCCATCTGAAGT 7 4 0 GCCCATCTGA 0.93663 -42 TATAAATTTTATCCTTCAGATTATTGTGAG 8 115 1 ATCCTTCAGA 0.774346 -87 ********** Masking position 4 Map Score: 8.76414 Number of sites scoring better than the average of aligned sites = 1347 Number in coding regions = 1295 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 3 GGATGGAGGCAATTAAAAACCAATGTGCGC 2 71 1 AATTAAAAAC 0.784344 -230 AAAGGCACACAAGTCGAAAACATTTTTAAC 2 189 0 AAGTCGAAAA 0.971975 -112 TAGAATTTGTAATTAAAAACGAGGATTAAT 3 96 1 AATTAAAAAC 0.784344 -77 GTCTAGGGAAAAGTAAAAAAAGAAAAACCT 4 40 0 AAGTAAAAAA 0.935974 -168 TAACGGCATCAATTTGAAAAGAATTCTTTT 4 112 0 AATTTGAAAA 0.886803 -96 AAAAACAAAAAAGTTGGAAAATGAACTTAC 5 17 0 AAGTTGGAAA 0.882691 -117 TAAGTAAATTAATTCGAAAAATTATTATGT 5 84 1 AATTCGAAAA 0.946365 -50 GATTCAAGTCGGAAAAGTCTTTTTA 7 31 0 AAGTCGGAAA 0.944301 -15 TAAAATTTATAAGTAAAAAAATTTTACTAA 8 96 0 AAGTAAAAAA 0.935974 -106 ********** Masking position 4 Map Score: 7.3693 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 74 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 4 CTTTTATAGGGAATCATGCTAGAATTGGTGGTATG 2 29 0 GAATCTAGAT 0.951403 -272 CGCTGAACCCGAATTTTGCCAGATGCTGAGAGCTT 2 219 0 GAATTTAGTG 0.968476 -82 TTTCCCTCCAGAATTATCTAAGGTTCGTTGCAGGA 2 272 0 GAATTTAGTT 0.978567 -29 AATTTGAAAAGAATTCTTTTAGCTGGTGGGGCTGG 4 97 0 GAATTTAGTG 0.968467 -111 CAATCAACCGCAATCTTTTAAGCTTTTTCCGTGTC 4 176 0 CAATCTAGTT 0.975485 -32 ATTTACTTAAGAATCCTGAAAGTTTATTTTCAGTT 5 58 0 GAATCTAGTT 0.989502 -76 AGTTTTTCACCAATCAATCAAGTTTAATCGACATA 5 109 0 CAATCAAGTT 0.892018 -25 ***** * ** ** Masking position 11 Map Score: 2.92325 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 22 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 CATCCTGACGGGGAGCTTGCTCCCCGACTC 1 35 1 GGGAGCTTGC 0.989695 -110 GCCAGATGCTGAGAGCTTAAAGGCACACAA 2 207 0 GAGAGCTTAA 0.666529 -94 AATTATCTAAGGTTCGTTGCAGGAGGAGTT 2 266 0 GGTTCGTTGC 0.92268 -35 AGTTTGATCAGGGTGGTTACC 3 2 0 GGGTGGTTAC 0.9722 -171 AAAAGATTGCGGTTGATTGCTTACCG 4 192 1 GGTTGATTGC 0.939845 -16 TCTCAACTAAGGGTGGTTGAATGAGGTAGT 8 40 0 GGGTGGTTGA 0.972202 -162 AAAAATTGAGGATAGCTTGCTGTTCTCAAC 8 63 0 GATAGCTTGC 0.92836 -139 ********** Masking position 7 Map Score: 2.57412 Number of sites scoring better than the average of aligned sites = 567 Number in coding regions = 539 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 6 GAGAATAGTAGGCGAGTCGGGGAGCAAGCT 1 48 0 GGCGAGTCGG 0.984058 -97 CCTTCAGCATCGCGGTCAGGAGTCGGCAGG 1 85 1 CGCGGTCAGG 0.987513 -60 AACCAATGTGCGCGGGCCGGGATTCGAACC 2 88 1 CGCGGGCCGG 0.997517 -213 CAATGACAAGCGCGGGTAGTCTAGCGGTAG 2 146 0 CGCGGGTAGT 0.969426 -155 TTAAAAATCAAGCGATTCGGTGTATGATGA 8 160 0 AGCGATTCGG 0.948675 -42 ********** Masking position 4 Map Score: 1.93152 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 45 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 CCTCCATCCGAAGAAACTTTTATAGGGAATC 2 49 0 AAGAACTTTT 0.884088 -252 ACACAAGTCGAAAACATTTTTAACCCTGAAG 2 182 0 AAAAATTTTT 0.823562 -119 CATCAATTTGAAAAGAATTCTTTTAGCTGGT 4 105 0 AAAAAATTCT 0.839696 -103 TTTAATCGACATAATAATTTTTCGAATTAAT 5 91 0 ATAAAATTTT 0.803565 -43 CAACCTTTTAAAAAGACTTTTCCGACTTGAA 7 23 1 AAAAACTTTT 0.622671 -23 ATTTATAAGTAAAAAAATTTTACTAAAATAA 8 91 0 AAAAAATTTT 0.731477 -111 **** ****** Masking position 6 Map Score: 0.747195 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 32 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 8 CTCGCCTACTATTCTCTCTTCTCCCTTCAGCA 1 62 1 ATTCTCTTCT 0.94865 -83 TATATAATTAATCCTCGTTTTTAATTACAAAT 3 100 0 ATCCTCTTTT 0.971427 -73 CTCATCGATTATTTTCCGTTTTCGGTCAGCAG 3 139 0 ATTTTCTTTT 0.963073 -34 AAAGTTTAGGTTTTTCTTTTTTTACTTTTCCC 4 33 1 TTTTTCTTTT 0.865486 -175 CTGAAAGTTTATTTTCAGTTATAATCTGCTGA 5 46 0 ATTTTCTTAT 0.88798 -88 ACAGCAAGCTATCCTCAATTTTTATTTTAGTA 8 70 1 ATCCTCTTTT 0.971427 -132 ****** **** Masking position 5 Map Score: 0.403696 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 82 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 CGGGGAGCAAGCTCCCCGTCAGGATGGTAT 1 31 0 GCTCCCCGTC 0.990478 -114 CGGGGAGCTTGCTCCCCGACTCGCCTACTA 1 43 1 GCTCCCCGAC 0.990522 -102 GCCCGGGTTCGAATCCCGGCCCGCGCACAT 2 93 0 GAATCCCGGC 0.978906 -208 GCCGGGATTCGAACCCGGGCTAACGCCTCG 2 103 1 GAACCCGGGC 0.985192 -198 ********** Masking position 5 Map Score: 0.389733 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 45 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 10 ********** No masking Map Score: 1.66429e-14 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: 1.66429e-14 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: 1.66429e-14 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