AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00510_aful_reg_300.orf -o00510_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 AF0045 300 mannosyltransferase A (mtfA) #2 AF1551 65 octaprenyl-diphosphate synthase (ispB) #3 AF1552 28 conserved hypothetical protein #4 AF2176 300 4-hydroxybenzoate octaprenyltransferase (ubiA) Motif number 1 GAACCCGAGCGAGATCGTCGAAGCTAAAATCTT 1 1 1 GAGGGTGCGG 0.990339 -300 AAGCTAAAATCTTCGGGGTTAAGTTCGAAGCAACAGTCGTTGA 1 31 1 CTGAGTGAGA 0.952168 -270 GACAGCTCGTCTTTCAGCATCAGCTCGTCAACGACTGTTGCTT 1 58 0 CTGCGTGCAG 0.9688 -243 TGAAAGACGAGCTGTCGTTTGAGCTGGAAGATAAAGGAATACT 1 85 1 GTGGGTGAGA 0.99232 -216 ACAAAGGTAAGATTCCGGTAGAGTTCGACCCTAACAGATTCAG 1 139 1 GTGGGTGCCA 0.991871 -162 CGGATTATGTCCTTGAGGCTGTGGTTGACCCTGAAGCCTATCT 1 229 0 CTGGGTGCCG 0.996303 -72 CTGTAGGTCTCCTTAAGCACGGGGAAGTCGGGGTAGTAGCGCC 4 56 0 CTGGGAGCGG 0.996832 -245 ATGCGATGGAGTTTCTGGCAAAGGTTGGCAGAGAGATGGAGCT 4 131 1 GTGAGTGCAG 0.974666 -170 TTGGCAGAGAGATGGAGCTTGTGATTGTAAGAACGCCCTATCC 4 155 1 GTGGGTGAAA 0.973304 -146 CCAGCAGGTACATGTTGAAGGCGAAGGGAGAGGGATAGGGCGT 4 187 0 CTGGGAGAGG 0.989955 -114 TCAACATGTACCTGCTGGGAGAGCAGGACGTAGTGCTTATGGA 4 212 1 CTGGGAGCGG 0.996832 -89 ACAGGAGGAAGATTCTGAAGGAGCTTCACGAGAAGGTAATGGG 4 257 1 GTGGGTCCGA 0.977065 -44 * * * * * * * ** * Masking position 13 Map Score: 21.3983 Number of sites scoring better than the average of aligned sites = 519 Number in coding regions = 500 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 2 CGAGCTGATGCTGAAAGACGAGCTGTCGTT 1 74 1 CTGAAAGACG 0.912693 -227 GTCGTTTGAGCTGGAAGATAAAGGAATACT 1 98 1 CTGGAAGATA 0.842061 -203 GTGGTTGACCCTGAAGCCTATCTCCTTTGC 1 222 0 CTGAAGCCTA 0.858819 -79 GGATTATGTCCTTGAGGCTGTGGTTGACCC 1 241 0 CTTGAGGCTG 0.979267 -60 TCTGGAGGCAGCAGTTCTCTG 4 2 1 CTGGAGGCAG 0.967316 -299 AAAGCTTAGTATTGAGTCCGCAGAGAACTG 4 22 0 ATTGAGTCCG 0.762333 -279 TGTAGGTCTCCTTAAGCACGGGGAAGTCGG 4 68 0 CTTAAGCACG 0.927236 -233 CAGGGAGATAATGGAGGATGCAATGAACAT 4 96 1 ATGGAGGATG 0.986103 -205 TGCAATGAACATTGAGGATGCGATGGAGTT 4 114 1 ATTGAGGATG 0.958137 -187 TGGCAGAGAGATGGAGCTTGTGATTGTAAG 4 156 1 ATGGAGCTTG 0.881103 -145 CGTAGTGCTTATGGAGGACAGGAGGAAGAT 4 240 1 ATGGAGGACA 0.95459 -61 TCTGAATCACGCCCATTACCT 4 290 0 CTGAATCACG 0.773664 -11 ********** Masking position 5 Map Score: 10.3577 Number of sites scoring better than the average of aligned sites = 2522 Number in coding regions = 2412 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 3 GCAGTATCGGAACTTCTGCCGGTCTGAATC 1 175 0 AACTTCTGCC 0.96402 -126 GAAGTTCCGATACTGCTCTCGGACACAACA 1 189 1 TACTGCTCTC 0.951384 -112 TTTCTCCTTCTGGCATCTAAATAG 1 287 0 TCCTTCTGGC 0.98787 -14 GTCCGCAGAGAACTGCTGCCTCCAGA 4 7 0 AACTGCTGCC 0.963304 -294 ACAAGCTCCATCTCTCTGCCAACCTTTGCC 4 147 0 TCTCTCTGCC 0.88191 -154 GAACGCCCTATCCCTCTCCCTTCGCCTTCA 4 185 1 TCCCTCTCCC 0.984 -116 AAGCACTACGTCCTGCTCTCCCAGCAGGTA 4 220 0 TCCTGCTCTC 0.983528 -81 TTCAGAATCTTCCTCCTGTCCTCCATAAGC 4 246 0 TCCTCCTGTC 0.965023 -55 CACGCCCATTACCTTCTCGTGAAGCTCCTT 4 274 0 ACCTTCTCGT 0.771783 -27 ********** Masking position 7 Map Score: 9.88156 Number of sites scoring better than the average of aligned sites = 1411 Number in coding regions = 1347 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 4 GTTTGAGCTGGAAGATAAAGGAATACTTGT 1 101 1 GAAGATAAAG 0.871562 -200 ACAGCCTCAAGGACATAATCCGCGACCAGC 1 250 1 GGACATAATC 0.80397 -51 AGACCTACAGGGAGATAATGGAGGATGCAA 4 89 1 GGAGATAATG 0.979348 -212 AGATAATGGAGGATGCAATGAACATTGAGG 4 101 1 GGATGCAATG 0.975712 -200 TGAACATTGAGGATGCGATGGAGTTTCTGG 4 119 1 GGATGCGATG 0.957893 -182 GGTACATGTTGAAGGCGAAGGGAGAGGGAT 4 194 0 GAAGGCGAAG 0.905976 -107 TGGGAGAGCAGGACGTAGTGCTTATGGAGG 4 227 1 GGACGTAGTG 0.94395 -74 AGCTTCACGAGAAGGTAATGGGCGTGATTC 4 278 1 GAAGGTAATG 0.979346 -23 ********** Masking position 3 Map Score: 5.07685 Number of sites scoring better than the average of aligned sites = 1027 Number in coding regions = 974 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 5 CCGAAGATTTTAGCTTCGACGATCTCGCTC 1 17 0 TAGCTTCGAC 0.970876 -284 TCAACGACTGTTGCTTCGAACTTAACCCCG 1 44 0 TTGCTTCGAA 0.919104 -257 CTGAATCTGTTAGGGTCGAACTCTACCGGA 1 152 0 TAGGGTCGAA 0.984552 -149 AGATAGGCTTCAGGGTCAACCACAGCCTCA 1 229 1 CAGGGTCAAC 0.958883 -72 GAAAATGTTATAAGTTCAACACCATGAAAG 2 39 1 TAAGTTCAAC 0.86254 -27 AGATAGATTGGGTCAAAGTTTTTTAAA 3 8 1 TTGGGTCAAA 0.955815 -21 ********** Masking position 6 Map Score: 2.30322 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 71 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 ********** No masking Map Score: -1.80235e-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: -1.80235e-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: -1.80235e-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