AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00520_aful_reg_300.orf -o00520_aful_300.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 AF0242 50 glucose-1-phosphate thymidylyltransferase (graD-1) #2 AF0325 300 glucose-1-phosphate thymidylyltransferase (graD-2) #3 AF0361 59 UDP-glucose 4-epimerase (galE-1) #4 AF1142 221 glucose-1-phosphate cytidylyltransferase (rfbF) #5 AF2009 101 heme biosynthesis protein (nirJ-2) #6 AF2010 46 A. fulgidus predicted coding region AF2010 #7 AF2011 175 conserved hypothetical protein #8 AF2013 275 coenzyme F390 synthetase (ftsA-3) #9 AF2014 63 sugar transporter, putative Motif number 1 TTTGTTCAAAAAGAATAAAAAGCTTTTGAGG 1 21 0 AAGATAAAAA 0.948353 -30 TGGGAGAGGTTAGAGTTAAAACCGACAATAT 2 253 1 TAGATTAAAA 0.762576 -48 TGGGAAAGATTTTAAAATGAGTTGTT 3 44 0 AAGATTTAAA 0.929131 -16 GAAAAATGTTAAAAGGAGAGTTAT 4 208 0 AAATTTAAAA 0.74031 -14 TTAGTTCCAAAAGGTTAAATATCTGGATGCA 5 24 0 AAGGTAAATA 0.675816 -78 ACATGCTAACAAAAATAAAAATTTTACTATT 6 17 0 AAAATAAAAA 0.718409 -30 TCTTTACTTCAAGTGTAAAAATTGAGTGCCC 7 80 0 AAGTTAAAAA 0.937123 -96 TTTCGATGTGAAGGTTATAAAACTTATTATT 7 145 0 AAGGTATAAA 0.903239 -31 CAGTATCTGGCAGTATTAAAAAACGGTTTTC 8 50 1 CAGTTTAAAA 0.794403 -226 TTTGCAGCAAAAGGCTTTAAAAGCCACTGCC 8 185 0 AAGGTTTAAA 0.927801 -91 CAGGATGGTGAAGTATTTAAATCCTGCCTCC 8 229 1 AAGTTTTAAA 0.914101 -47 GGAAATTTAAAGAATTAAAAAGCTAAAAAT 9 44 0 AAGATTAAAA 0.961946 -20 **** ****** Masking position 9 Map Score: 10.5334 Number of sites scoring better than the average of aligned sites = 225 Number in coding regions = 137 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 2 ATTTTGACTCCCTCAAAAGCTTTT 1 4 1 TGACTCCCTC 0.693376 -47 ACTTTTGTCCCTGCCGGCTCTCTGCACAGAA 2 128 1 CGCCGGCTCT 0.947013 -173 CTTTCTATGTCATCCTCCTCCAGATAATCTC 2 207 0 CTCCTCCTCC 0.960223 -94 GCAATGACCGCTGCTGCCCCCAATCCGACGA 4 33 1 CGCTGCCCCC 0.965538 -189 TGTTCAAATCTATCGGGCCCCTCCCTTAATC 7 11 0 TTCGGGCCCC 0.956156 -165 ACATAACCTTCATCCGTCTCCTCGATGTTCA 7 36 0 CTCCGTCTCC 0.910869 -140 AGTGTAAAAATTGAGTGCCCCAGTGCCTGAG 7 69 0 TGAGTGCCCC 0.869374 -107 TACGACAAGACTGCCTGCTCCTTTATCCTTC 7 109 0 CGCCTGCTCC 0.991209 -67 AGTTCAAATCTCGGCGGCCCCATCATTGAAC 8 87 0 TGGCGGCCCC 0.973096 -189 TGAACTCGGGTCACCGGCTCCCAAAGCCGAG 8 112 1 TACCGGCTCC 0.92642 -164 ACCAGGCTACCCTACGGCCCCTCTGTAATGA 8 149 1 CTACGGCCCC 0.980423 -127 TATTTAAATCCTGCCTCCCTCATGACAGAAA 8 242 1 CGCCTCCCTC 0.95276 -34 * ********* Masking position 8 Map Score: 11.1453 Number of sites scoring better than the average of aligned sites = 1023 Number in coding regions = 953 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 3 GAGAATTAGCCTGCAGAGACACTATCACAG 2 16 1 CTGCAGAGAC 0.993248 -285 GTGAACGGTACTGCAAGGATTGTTGTTGAT 2 65 1 CTGCAAGGAT 0.888425 -236 GAAAGAGATACTGCTGAGGAAGAGAGAGAG 2 97 1 CTGCTGAGGA 0.869436 -204 TGCAGAGAGCCGGCAGGGACAAAAGTGCTC 2 124 0 CGGCAGGGAC 0.950243 -177 TGCCGGCTCTCTGCACAGAATAGAGAACCC 2 139 1 CTGCACAGAA 0.962427 -162 TATACTTTTTCTGCACAGGTCAGCGAGGTG 3 13 0 CTGCACAGGT 0.94802 -47 ATTTCTCCAGCTGCAATGACCGCTGCTGCC 4 21 1 CTGCAATGAC 0.927344 -201 CAAGTTCTGTCAGCAGATACTCCCATTTGA 4 148 1 CAGCAGATAC 0.820047 -74 TCTGGAACTGCAGCTCAGACAGTATCTGGC 8 31 1 CAGCTCAGAC 0.907729 -245 AAGCCTTTTGCTGCAAACGCATTCGTTTTT 8 199 1 CTGCAAACGC 0.880499 -77 ********** Masking position 4 Map Score: 5.88045 Number of sites scoring better than the average of aligned sites = 760 Number in coding regions = 710 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 4 GTCATCCTCCTCCAGATAATCTCCAATCTGCA 2 198 0 TCCGATAACT 0.970801 -103 ACACCTGTTTTCGAGAGAATCTTTGCCAGAGG 4 96 1 TCGGAGAACT 0.98011 -126 TTGCCAGAGGTCGGGAAAACCTCCGATAAACA 4 118 1 TCGGAAAACT 0.990941 -104 GAGCTGCAGTTCCAGAAAAGCTGACAGGTTGA 8 15 0 TCCGAAAACT 0.990941 -261 CATTGAACTGGCGGGAAAACCGTTTTTTAATA 8 63 0 GCGGAAAACG 0.970725 -213 TACTTCACCATCCTGAAAAACGAATGCGTTTG 8 212 0 TCCGAAAACG 0.989093 -64 *** ***** ** Masking position 6 Map Score: 5.63873 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 67 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 TCAGCAGTATCTCTTTCCCATCAACAACAA 2 84 0 CTCTTTCCCA 0.987437 -217 TTTAACTCTAACCTCTCCCAAAATCGTCCT 2 243 0 ACCTCTCCCA 0.978771 -58 TCATTTTAAAATCTTTCCCA 3 50 1 ATCTTTCCCA 0.992593 -10 TTTCGAGAGAATCTTTGCCAGAGGTCGGGA 4 104 1 ATCTTTGCCA 0.980387 -118 ********** Masking position 6 Map Score: 1.70282 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 30 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 CGCTTCTGTGATAGTGTCTCTGCAGGCTAA 2 21 0 ATAGTGTCTC 0.786027 -280 GATTTATAAAATATTGTCGGTTTTAACTCT 2 264 0 ATATTGTCGG 0.853111 -37 GCTTACGACAAGACTGCCTGCTCCTTTATC 7 113 0 AGACTGCCTG 0.94216 -63 AGAATCAACCTGTCAGCTTTTCTGGA 8 7 1 AACCTGTCAG 0.854872 -269 ATACTGCCAGATACTGTCTGAGCTGCAGTT 8 36 0 ATACTGTCTG 0.981821 -240 CCGTTTTTTAATACTGCCAGATACTGTCTG 8 46 0 ATACTGCCAG 0.965955 -230 TAGCCTGGTGATCCTCTCGGCTTTGGGAGC 8 128 0 ATCCTCTCGG 0.878991 -148 AAGTATTTAAATCCTGCCTCCCTCATGACA 8 239 1 ATCCTGCCTC 0.948342 -37 ********** Masking position 1 Map Score: 1.73903 Number of sites scoring better than the average of aligned sites = 334 Number in coding regions = 302 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 7 CAATCCAGTGCTCGCTTCTGTGATAGTGTC 2 33 0 CTCGCTTCTG 0.952391 -268 CAAAAGTGCTCTCTCTCTTCCTCAGCAGTA 2 105 0 CTCTCTCTTC 0.812552 -196 TTCCGGGGTTCTCTATTCTGTGCAGAGAGC 2 144 0 CTCTATTCTG 0.920763 -157 CCCCGGAAAAATCCCTCTTGAGATAATTGA 2 166 1 ATCCCTCTTG 0.760817 -135 TCCAGATAATCTCCAATCTGCACCTCAATT 2 190 0 CTCCAATCTG 0.953064 -111 CAAAATCGTCCTCGAACCTTTCTATGTCAT 2 225 0 CTCGAACCTT 0.691556 -76 TCGGTTTTAACTCTAACCTCTCCCAAAATC 2 248 0 CTCTAACCTC 0.849965 -53 TCAGCAGATACTCCCATTTGATTTAAATCA 4 157 1 CTCCCATTTG 0.913888 -65 TTAAATACTTCACCATCCTGAAAAACGAAT 8 219 0 CACCATCCTG 0.907358 -57 TAAATCCTGCCTCCCTCATGACAGAAAGAT 8 246 1 CTCCCTCATG 0.935104 -30 ********** Masking position 9 Map Score: 3.7645 Number of sites scoring better than the average of aligned sites = 1768 Number in coding regions = 1685 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 8 CCAATCTGCACCTCAATTATCTCAAGAGGG 2 178 0 CCTCAATTAT 0.846399 -123 CTAACCTCTCCCAAAATCGTCCTCGAACCT 2 236 0 CCAAAATCGT 0.964691 -65 ACCGTTATTGCCACAATCGTCGGATTGGGG 4 50 0 CCACAATCGT 0.967243 -172 ACCTTTTGGAACTAAATAGTTCATACATAG 5 40 1 ACTAAATAGT 0.826157 -62 ATTCATTACGCCTGAATTGTTCCTATGTAT 5 62 0 CCTGAATTGT 0.950856 -40 GGCCTAAATAGTAAAATTTTTA 6 3 1 CCTAAATAGT 0.969998 -44 ********** Masking position 5 Map Score: 0.812124 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 128 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 9 ********** No masking Map Score: 1.60826e-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 10 ********** No masking Map Score: 1.60826e-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: 1.60826e-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