AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00510_aful_reg_100.orf -o00510_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 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 GAAGCTAAAATCTTCGGGGTTAAGTTCGAAGCAACAGT 1 30 1 TCTGGGAGTG 0.856769 -271 CGACAGCTCGTCTTTCAGCATCAGCTCGTCAACGACTG 1 64 0 TCTAGCCGTG 0.853671 -237 CTGAAAGACGAGCTGTCGTTTGAGCTGGAAGATAAAGG 1 84 1 AGTCGTGGTG 0.913205 -217 GACAAAGGTAAGATTCCGGTAGAGTTCGACCCTAACAG 1 138 1 AGTCGGGGTG 0.990768 -163 GCGGATTATGTCCTTGAGGCTGTGGTTGACCCTGAAGC 1 235 0 TCTAGGGGTG 0.99076 -66 CCTGTAGGTCTCCTTAAGCACGGGGAAGTCGGGGTAGT 4 62 0 TCTAGCGGAG 0.965816 -239 GCTTAAGGAGACCTACAGGGAGATAATGGAGGATGCAA 4 81 1 ACTAGGGTAG 0.891304 -220 GATGCAATGAACATTGAGGATGCGATGGAGTTTCTGGC 4 112 1 ACTAGGGGTG 0.996459 -189 GATGCGATGGAGTTTCTGGCAAAGGTTGGCAGAGAGAT 4 130 1 AGTTGGAGTG 0.97172 -171 GTTGGCAGAGAGATGGAGCTTGTGATTGTAAGAACGCC 4 154 1 AGTAGCGGTG 0.989792 -147 CCCAGCAGGTACATGTTGAAGGCGAAGGGAGAGGGATA 4 193 0 ACTTGAGGAG 0.961616 -108 TTCAACATGTACCTGCTGGGAGAGCAGGACGTAGTGCT 4 211 1 ACTTGGGGAG 0.993147 -90 GGAGAGCAGGACGTAGTGCTTATGGAGGACAGGAGGAA 4 229 1 ACTTGCAGAG 0.930756 -72 GACAGGAGGAAGATTCTGAAGGAGCTTCACGAGAAGGT 4 256 1 AGTTGAGGTC 0.844718 -45 CTTCACGAGAAGGTAATGGGCGTGATTCAGA 4 280 1 AGTTGGGGTC 0.9692 -21 ** * *** * * * * Masking position 4 Map Score: 20.5879 Number of sites scoring better than the average of aligned sites = 1364 Number in coding regions = 1298 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 2 ACCGGAATCTTACCTTTGTCTGTAAAGACA 1 128 0 TACCTTTGTC 0.901408 -173 GCAGTATCGGAACTTCTGCCGGTCTGAATC 1 175 0 AACTTCTGCC 0.977492 -126 GAAGTTCCGATACTGCTCTCGGACACAACA 1 189 1 TACTGCTCTC 0.946991 -112 TTTCTCCTTCTGGCATCTAAATAG 1 287 0 TCCTTCTGGC 0.972275 -14 GTCCGCAGAGAACTGCTGCCTCCAGA 4 7 0 AACTGCTGCC 0.972839 -294 TCTCTCTGCCAACCTTTGCCAGAAACTCCA 4 137 0 AACCTTTGCC 0.890516 -164 ACAAGCTCCATCTCTCTGCCAACCTTTGCC 4 147 0 TCTCTCTGCC 0.935389 -154 GAACGCCCTATCCCTCTCCCTTCGCCTTCA 4 185 1 TCCCTCTCCC 0.986581 -116 AAGCACTACGTCCTGCTCTCCCAGCAGGTA 4 220 0 TCCTGCTCTC 0.966089 -81 TTCAGAATCTTCCTCCTGTCCTCCATAAGC 4 246 0 TCCTCCTGTC 0.959926 -55 ********** Masking position 7 Map Score: 12.5479 Number of sites scoring better than the average of aligned sites = 1349 Number in coding regions = 1274 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 3 GAACCCGAGCGAGATCGTCGAAGCTAAAATCTT 1 11 1 GAGATGTCGG 0.984466 -290 CTTTCAGCATCAGCTCGTCAACGACTGTTGCTT 1 58 0 CAGCTGTCAG 0.941584 -243 TTATGTCCTTGAGGCTGTGGTTGACCCTGAAGC 1 235 0 GAGGCGTGGG 0.986594 -66 AATAGTAGTTCAGCTGGTCGCGGATTATGTCCT 1 259 0 CAGCTGTCGG 0.982774 -42 CCTTAAGCACGGGGAAGTCGGGGTAGTAGCGCC 4 56 0 GGGGAGTCGG 0.932648 -245 GACCTACAGGGAGATAATGGAGGATGCAATGAA 4 90 1 GAGATATGGG 0.963526 -211 AATGAACATTGAGGATGCGATGGAGTTTCTGGC 4 117 1 GAGGAGCGAG 0.837455 -184 CAGAGAGATGGAGCTTGTGATTGTAAGAACGCC 4 159 1 GAGCTGTGAG 0.98737 -142 GCAGGACGTAGTGCTTATGGAGGACAGGAGGAA 4 234 1 GTGCTATGGG 0.924948 -67 GCTTCACGAGAAGGTAATGGGCGTGATTCAGA 4 279 1 AAGGTATGGG 0.897227 -22 ***** **** * Masking position 3 Map Score: 7.55313 Number of sites scoring better than the average of aligned sites = 1533 Number in coding regions = 1480 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 4 GAGCGAGATCGTCGAAGCTAAAATCTTCGG 1 17 1 GTCGAAGCTA 0.949506 -284 CGACTGTTGCTTCGAACTTAACCCCGAAGA 1 40 0 TTCGAACTTA 0.946297 -261 TCCGGTAGAGTTCGACCCTAACAGATTCAG 1 152 1 TTCGACCCTA 0.987946 -149 TGAGGCTGTGGTTGACCCTGAAGCCTATCT 1 229 0 GTTGACCCTG 0.967729 -72 CTTTCATGGTGTTGAACTTATAACATTTTC 2 39 0 GTTGAACTTA 0.946304 -27 TTTAAAAAACTTTGACCCAATCTATCT 3 8 0 TTTGACCCAA 0.927739 -21 ********** Masking position 5 Map Score: 3.10065 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 54 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 5 CAACAAAAGCAAAGGAGATAGGCTTCAGGG 1 214 1 AAAGGAGATA 0.927655 -87 TTAGATGCCAGAAGGAGAAA 1 291 1 GAAGGAGAAA 0.972875 -10 CTAAGCTTTTTAAGGCGCTACTACCCCGAC 4 43 1 TAAGGCGCTA 0.943505 -258 TTGGCAGAGAGATGGAGCTTGTGATTGTAA 4 155 1 GATGGAGCTT 0.94769 -146 GGTACATGTTGAAGGCGAAGGGAGAGGGAT 4 194 0 GAAGGCGAAG 0.945776 -107 GGAAGATTCTGAAGGAGCTTCACGAGAAGG 4 263 1 GAAGGAGCTT 0.986566 -38 ********** Masking position 2 Map Score: 3.07169 Number of sites scoring better than the average of aligned sites = 480 Number in coding regions = 458 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 ACTGTTGCTTCGAACTTAACCCCGAAGATT 1 38 0 CGAACTTAAC 0.962675 -263 CTGTTAGGGTCGAACTCTACCGGAATCTTA 1 146 0 CGAACTCTAC 0.934796 -155 GAACTTCTGCCGGTCTGAATCTGTTAGGGT 1 166 0 CGGTCTGAAT 0.909629 -135 ATACTGCTCTCGGACACAACAAAAGCAAAG 1 198 1 CGGACACAAC 0.989267 -103 CACAGCCTCAAGGACATAATCCGCGACCAG 1 249 1 AGGACATAAT 0.800988 -52 CAGTTCTCTGCGGACTCAATACTAAGCTTT 4 22 1 CGGACTCAAT 0.99094 -279 ********** Masking position 9 Map Score: 2.83255 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 205 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 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 Motif number 9 ********** 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