AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00051_aquae_reg_300.orf -o00051_aquae_300.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 fabZ 23 (3R)-hydroxymyristoyl-(acyl carrier protein) dehydratase #2 kdsA 264 3-deoxy-d-manno-octulosonic acid 8-phosphate synthase #3 rfaD 300 ADP-L-glycero-D-manno-heptose-6-epimerase #4 timA 300 triose phophate isomerase #5 aq_503 83 hypothetical protein #6 otnA' 30 polysaccharide biosynthesis protein (fragment) #7 mtfB 300 mannosyltransferase B #8 xanB 33 mannose-6-phosphate isomerase/mannose-1-phosphate guanyl transferase #9 kpsU 32 3-deoxy-manno-octulosonate cytidylyltransferase #10 rfbD 89 GDP-D-mannose dehydratase #11 mtfA 263 mannosyltransferase A #12 fba 300 fructose-1,6-bisphosphate aldolase class II #13 fucA1 48 fuculose-1-phosphate aldolase #14 metE 44 tetrahydropteroyltriglutamate methyltransferase #15 aq_1975 37 hypothetical protein #16 rfaG 300 glucosyl transferase I Motif number 1 GCAATATGTATTATAGGCTTTTTAAGCGGTTTC 2 39 1 TTATCTTTTT 0.800424 -226 TACTATGGGATTTTTCCCTTTTTTGGCTCTTCT 2 93 0 TTTTCTTTTT 0.950783 -172 CTCCTCAGCGTTCTTGTTTTCTTTATCGTTTAC 2 147 1 TTCTTTTCTT 0.826069 -118 AAACTTTAGTTTTTCAACCTCTTGAATATAACA 3 27 1 TTTTCCTCTT 0.940931 -274 AATATAACAATTCTGACCTTTTTATTTTCGTGG 3 51 1 TTCTCTTTTT 0.982424 -250 TTCTGAAAGTTTTTCTCCCTTTTTCACTTCTCC 3 113 1 TTTTCCTTTT 0.961595 -188 CCTTTTTCACTTCTCCGCTTTTTCTATCTATGT 3 130 1 TTCTCTTTTT 0.982424 -171 GAAATCGGAATACTCTTCCTCTTTGAATTCCTC 3 173 1 TACTCCTCTT 0.867159 -128 TTCAATTAATTTCTTAACTTTCTGTTCTATTTC 4 168 1 TTCTCTTTCT 0.924503 -133 TAACTTTCTGTTCTATTTCTTTTAATTTCTTTG 4 182 1 TTCTTCTTTT 0.906328 -119 TAGGGAGATGTATTACACCTTTTCGGAGACAGC 5 52 1 TATTCCTTTT 0.780035 -32 AACTTCTTTTTTCTCCTCTTCATCGGATAT 10 8 1 TTTTCCTCTT 0.940931 -82 AAAAGCTTTTTTCTTTTCCTTTCCAAGTTTTTA 11 171 0 TTCTCCTTTC 0.960981 -93 GGATTTCTCCTCCTTTTAGAACTTCTT 14 28 0 TTCTCCTTTT 0.986384 -17 AGTCCGGGAATTCTGAGCTTCTTCCTTTTCGAA 16 108 0 TTCTCTTCTT 0.972649 -193 GTTCTGGGATTTCTTCCCTTTCTTGCACTCCTT 16 161 0 TTCTCTTTCT 0.924503 -140 TTAAGCAGATTTCTTAATTTTTCCCGCTTTTCT 16 256 1 TTCTTTTTTC 0.717342 -45 TTTTTCCCGCTTTTCTTCTTTTCTAAAATTTTT 16 273 1 TTTTCTTTTC 0.867854 -28 **** ****** Masking position 4 Map Score: 24.9555 Number of sites scoring better than the average of aligned sites = 839 Number in coding regions = 780 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 2 GTTATCCTTTCCAGAAATGGAACG 2 5 1 TCCTTTCCAG 0.948328 -260 TTAAGCGGTTTCCTTTACAACGAAAGCATA 2 60 1 TCCTTTACAA 0.857123 -205 TCCCATAGTAACCTTTCCCGTGAGGTTTTT 2 116 1 ACCTTTCCCG 0.877933 -149 ACGATTTCCCACCTTCTCGGGCGTTTCTTC 2 210 1 ACCTTCTCGG 0.920531 -55 AAGCCTTATCACCTTTCAGGAACTGCATAA 3 274 1 ACCTTTCAGG 0.948152 -27 AATGAGGGCTACCTTTGAAGCTTCTTCGTC 4 54 1 ACCTTTGAAG 0.856241 -247 GATGTATTACACCTTTTCGGAGACAGCAGG 5 58 1 ACCTTTTCGG 0.964785 -26 TTTTTTCTTTTCCTTTCCAAGTTTTTACTA 11 168 0 TCCTTTCCAA 0.885366 -96 AATCAAGATTACCTTCAAGATTCTTAATGG 11 204 0 ACCTTCAAGA 0.716502 -60 TAGACACCTAACCTTCACGAAACGAATGTT 12 63 1 ACCTTCACGA 0.857259 -238 GTCCTTACAAACCTTTAAAGATTTTC 13 7 0 ACCTTTAAAG 0.898489 -42 GGATTTCTCCTCCTTTTAGAACTTCTTATT 14 25 0 TCCTTTTAGA 0.766815 -20 CTGAGCTTCTTCCTTTTCGAAGAGTTCGTG 16 99 0 TCCTTTTCGA 0.886547 -202 CCGGACTCGGACCTTTAAAGTAACCGTAAG 16 134 1 ACCTTTAAAG 0.898489 -167 CTTAACGAGTTCCTTTGCAGGTTTGAAAGT 16 231 0 TCCTTTGCAG 0.905594 -70 ********** Masking position 5 Map Score: 15.0354 Number of sites scoring better than the average of aligned sites = 820 Number in coding regions = 779 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 3 AACGCTATTTTAACATTTTCAGG 1 6 0 TTTTTAATTT 0.73453 -18 GAAAAACTAAAGTTTTAAAATATCAGTAATA 3 9 0 ATTTTAATAT 0.914845 -292 CTGTTCTATTTCTTTTAATTTCTTTGGATCTTT 4 189 1 TTTTTAATCT 0.618758 -112 CTTTTTTCCTATTTTTAATGCATGTGTATTATT 5 14 1 ATTTTAACAT 0.921005 -70 ATTGAGAGCTTCTTTTCAACCTTCGAGCGATGG 7 48 1 TTTTTCACTT 0.644668 -253 CATTATCCCAACTTTAAACACATGCTCATTCCT 7 120 0 ATTTAAACAT 0.816278 -181 GAATTTTAGCAGTTTAAAATTATCCCCT 8 6 0 ATTTAAATAT 0.803756 -28 ACAAAACTTTAGTTTAAATTCATAAAAGCA 9 8 0 ATTTAAACAT 0.816278 -25 AATTAGGTTATTTTAAGCTATAATTTTTCAA 11 9 1 TTTTTAATAT 0.904345 -255 TTAAGCTATAATTTTTCAATTATGGGCAAGCTG 11 23 1 ATTTTCATAT 0.866599 -241 TATAATGCTAAATTTTCAAGCATATTTAGGGTA 11 68 1 ATTTTCACAT 0.875733 -196 AAACACGTATTCTTTTAATTTATCCCTTAATAA 11 128 0 TTTTTAATAT 0.904345 -136 ATAAAGCGTTATTTTTCAGACATAGGCGCGCAG 12 19 0 ATTTTCACAT 0.875731 -282 GAAAATCTTTAAAGGTTTGTAAGGACCT 13 6 1 TTTTAAATTT 0.513242 -43 TAGAACTTCTTATTTTAAAATATCTTTT 14 6 0 TTTTTAATAT 0.904344 -39 * ****** *** Masking position 8 Map Score: 11.7236 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 60 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 4 AAACAAGAACGCTGAGGAGGAAAAACCTCACGG 2 133 0 GCTGAGGGAA 0.974383 -132 CTTTTACAAGGCTGAAGGGGCTATTCTCTTTAC 2 179 1 GCTGAGGGCA 0.969032 -86 CTCTAAAAAAGAGCTGGAAGAAACGCCCGAGAA 2 223 0 GAGCTGAGAA 0.744442 -42 ATACAGAACCGCGGACGTGGATATGAAGATAAG 3 213 0 GCGGAGGGAA 0.983882 -88 ATCTTTGACCGCGTAGGGGGAGAGTTTTGTAAG 4 216 1 GCGTAGGGAA 0.894526 -85 GAAAATTAAGGAGGTGGGAGCCATGCCTATGTA 4 256 0 GAGGTGAGCA 0.917699 -45 GTGGAAGGAGAAAGTGGTGTATG 7 1 1 GTGGAGAGAA 0.809841 -300 ATGGTTTGGAGAGTATGTAGTGAGCAAAAGGCT 7 77 1 GAGTAGAGTA 0.478582 -224 TAATGATCATGATGATGAGGTCAGGTGGTATGA 7 148 1 GATGAGGGTA 0.884432 -153 ATGAGAGATGGCTGTGGTGGAGTTGATGTGGAC 7 177 1 GCTGTGGGAT 0.68104 -124 TGGTGGAGTTGATGTGGACGAGAAAATAATCAG 7 191 1 GATGTGCGAA 0.722133 -110 AATTATATCCGATGAAGAGGAGAAAAAAGAAGT 10 12 0 GATGAGGGAA 0.96495 -78 AAGGCTGAGCTCGTAGCAAAATTGCAGAA 16 7 1 GAGCTGAGCA 0.705572 -294 CCAAGAAGGAGCTGACGCAGCTATCAAGGCTTT 16 53 1 GCTGAGAGCA 0.943918 -248 ***** * *** * Masking position 7 Map Score: 9.33371 Number of sites scoring better than the average of aligned sites = 579 Number in coding regions = 543 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 5 TATTACTGATATTTTAAAACTTTAGTTTTTCAA 3 10 1 TTTTAAATTT 0.720572 -291 CACGTGAGTGTATTCTGAAAGTTTTTCTCCCTTT 3 101 1 TTCTAAATTT 0.967231 -200 TTTTCTATTGTATACTCAATTCTTATAGAGGTAA 10 64 0 TTCTAATCTT 0.860005 -26 TGTTTATATATTTAGTAAAAACTTGGAAAGGAAA 11 156 1 TTGTAAACTT 0.91259 -108 GAAGAAATAATCTACTCAAAGCTTAAGAACATAA 11 239 1 TTCTAAACTT 0.967822 -25 GCTAACCCCAAGTTCTGCAAACTTGAGCATACAT 12 100 1 ATCTCAACTT 0.769934 -201 TTGAGCATACATTTGTAAAATTTTTATCTTTGAT 12 122 1 ATGTAAATTT 0.766863 -179 AATAATTTATATGGTATAATTTTGAATAGCTCC 12 278 0 TTGTTAATTT 0.565561 -23 ACCTGAGTGATATCCTAAAAACTT 13 35 1 TTCTAAACTT 0.967822 -14 CCTCCTGAGTTTTACTTAAAATTTATACTTT 15 17 1 TTCTAAATTT 0.967231 -21 TATGCCTGCTTTTTCTGCAATTTTGCTACGAGCT 16 18 0 TTCTCAATTT 0.910949 -283 CGTTAAGCAGATTTCTTAATTTTTCCCGCTTTTC 16 254 1 ATCTAATTTT 0.659336 -47 GCTTTTCTTCTTTTCTAAAATTTTTTATTT 16 281 1 TTCTAAATTT 0.967231 -20 * * ** *** *** Masking position 9 Map Score: 10.5667 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 146 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 ACGCTGAGGAGGAAAAACCTCACGGGAAAG 2 128 0 GGAAAAACCT 0.782986 -137 CCTTACTCTAAAAAAGAGCTGGAAGAAACG 2 231 0 AAAAAGAGCT 0.784101 -34 CTACATAGATAGAAAAAGCGGAGAAGTGAA 3 135 0 AGAAAAAGCG 0.685671 -166 GTTGCATGTCCAAAAGAGCGTATAATGAGG 4 31 1 CAAAAGAGCG 0.577389 -270 CCAAAGACGACGAAGAAGCTTCAAAGGTAG 4 62 0 CGAAGAAGCT 0.899581 -239 CCAGATAATCGTAAGGACCAAAAACGACAA 4 104 1 GTAAGGACCA 0.610327 -197 TTAAAAATAGGAAAAAAGCAA 5 2 0 GAAAAAAGCA 0.793907 -82 GTGGAAGGAGAAAGTGGTGTAT 7 3 1 GGAAGGAGAA 0.610165 -298 TCGAAGGTTGAAAAGAAGCTCTCAATAAGC 7 44 0 AAAAGAAGCT 0.763962 -257 GGTAACATAAGGAATGAGCATGTGTTTAAA 7 111 1 GGAATGAGCA 0.755744 -190 CAGATTTATTGGACAGAGCATGGAATTTAT 7 240 1 GGACAGAGCA 0.700282 -61 GAAAGGAAAAGAAAAAAGCTTTTCCATTAA 11 181 1 GAAAAAAGCT 0.850381 -83 TTGTAGCCCTCTAAGGAGCTATTCAAAATT 12 264 1 CTAAGGAGCT 0.781096 -37 TTAAAGGTTTGTAAGGACCTGAGTGATATC 13 19 1 GTAAGGACCT 0.697968 -30 GCAAAATTGCAGAAAAAGCAGGCATAACCA 16 26 1 AGAAAAAGCA 0.793907 -275 GGCATAACCAAGAAGGAGCTGACGCAGCTA 16 46 1 AGAAGGAGCT 0.942827 -255 TCTTCGAAAAGGAAGAAGCTCAGAATTCCC 16 106 1 GGAAGAAGCT 0.962697 -195 ********** Masking position 7 Map Score: 8.60413 Number of sites scoring better than the average of aligned sites = 1136 Number in coding regions = 1079 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 7 TGCTGGACGTTCCATTTCTGGAAAGGATAAC 2 11 0 TCCATTTCTG 0.883616 -254 ATGGGATTTTTCCCTTTTTTGGCTCTTCTGT 2 91 0 TCCCTTTTTG 0.975258 -174 AAAGTTTTTCTCCCTTTTTCACTTCTCCGCT 3 118 1 TCCCTTTTTA 0.885869 -183 TGTTATGATCTCCCTGACCTGATTATTTTCT 7 211 0 TCCCTGACCG 0.877735 -90 CAAATAAAATTCCCTTATTAAGGGATAAATT 11 114 1 TCCCTTATTA 0.863016 -150 AATCAAAGCATCACTTATTAGACCAATCCGC 12 203 1 TCACTTATTG 0.758253 -98 AGCTCAGAATTCCCGGACTCGGACCTTTAAA 16 122 1 TCCCGGACTG 0.937574 -179 TGGGATTTCTTCCCTTTCTTGCACTCCTTAC 16 159 0 TCCCTTTCTG 0.987252 -142 GTATAACTTCTCCCGTTCTGGGATTTCTTCC 16 177 0 TCCCGTTCTG 0.974263 -124 ********* * Masking position 1 Map Score: 4.5836 Number of sites scoring better than the average of aligned sites = 362 Number in coding regions = 347 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 AATTGTTATATTCAAGAGGTTGAAAAACTA 3 33 0 TTCAAGAGGT 0.926136 -268 TCAGAATACACTCACGTGGTTGTACTGAAA 3 89 0 CTCACGTGGT 0.959866 -212 CTTTGAATTCCTCAAGTGGTCTTATCTTCA 3 193 1 CTCAAGTGGT 0.966097 -108 AAATTGAAAATTAAGGAGGTGGGAGCCATG 4 264 0 TTAAGGAGGT 0.910093 -37 TGATGATGAGGTCAGGTGGTATGAGAGATG 7 157 1 GTCAGGTGGT 0.959922 -144 TTGTAGCCCTCTAAGGAGCTATTCAAAATT 12 264 1 CTAAGGAGCT 0.852052 -37 TTAAGTAAAACTCAGGAGGTTAAAA 15 6 0 CTCAGGAGGT 0.990976 -32 ********** Masking position 4 Map Score: 4.00608 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 146 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 9 GGGATTTTTCCCTTTTTTGGCTCTTCTGTATAT 2 87 0 CCTTTTTCTC 0.947228 -178 TCCTCCTCAGCGTTCTTGTTTTCTTTATCGTTT 2 145 1 CGTTCTTTTC 0.863954 -120 ACAATTCTGACCTTTTTATTTTCGTGGTCCTCT 3 57 1 CCTTTTTTTC 0.960698 -244 TTTTCGTGGTCCTCTTTCAGTACAACCACGTGA 3 75 1 CCTCTTTTAC 0.828654 -226 AGTTTTTCTCCCTTTTTCACTTCTCCGCTTTTT 3 120 1 CCTTTTTTTC 0.960698 -181 GAATACTCTTCCTCTTTGAATTCCTCAAGTGGT 3 180 1 CCTCTTTTTC 0.978469 -121 GCTTCTTCGTCGTCTTTGGCTTCAAATACGTCC 4 73 1 CGTCTTTTTC 0.941446 -228 ATGGCTCCCACCTCCTTAATTTTCAATTTAAGT 4 265 1 CCTCCTTTTT 0.687299 -36 AACTTCTTTTTTCTCCTCTTCATCG 10 3 1 CTTCTTTCTC 0.946077 -87 CTAACTAGATCTTCCTTTACCTCTATAAGAATT 10 48 1 CTTCCTTCTC 0.927971 -42 AATGGAAAAGCTTTTTTCTTTTCCTTTCCAAGT 11 176 0 CTTTTTTTTC 0.927809 -88 GAATTCTGAGCTTCTTCCTTTTCGAAGAGTTCG 16 101 0 CTTCTTCTTC 0.790294 -200 GATTTCTTCCCTTTCTTGCACTCCTTACGGTTA 16 154 0 CTTTCTTCTC 0.873893 -147 ******* *** Masking position 6 Map Score: 14.8216 Number of sites scoring better than the average of aligned sites = 667 Number in coding regions = 617 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 10 TAAAGGAAACCGCTTAAAAAGCCTATAATAC 2 46 0 CGCTAAAAAG 0.953216 -219 TTTAACCTTACTCTAAAAAAGAGCTGGAAGA 2 235 0 CTCTAAAAAG 0.960389 -30 TGAAAAGAAGCTCTCAATAAGCCATCTGTTG 7 35 0 CTCTAATAAG 0.972133 -266 GTTATAATTACCCTAAATATGCTTGAAAATT 11 78 0 CCCTAATATG 0.942552 -186 TTTAATTTATCCCTTAATAAGGGAATTTTAT 11 117 0 CCCTAATAAG 0.981799 -147 **** ****** Masking position 6 Map Score: 0.276823 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 30 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 ATGCAACCACGGAAACCTGGTCAGCAA 4 8 0 GGAAACCTGG 0.946026 -293 AGCAAACCTGCTGTCTCCGAA 5 73 0 GCAAACCTGC 0.98155 -11 TAGGAACCCTGCGCGCCTATGT 12 3 1 GGAACCCTGC 0.959172 -298 CCCAAGTTCTGCAAACTTGAGCATACATTT 12 106 1 GCAAACTTGA 0.784777 -195 TGAGCTCGTAGCAAAATTGCAGAAAAAGCA 16 16 1 GCAAAATTGC 0.694142 -285 GTTCTCACTTTCAAACCTGCAAAGGAACTC 16 225 1 TCAAACCTGC 0.938244 -76 GGAAAAATTAAGAAATCTGCTTAACGAGTT 16 250 0 AGAAATCTGC 0.646502 -51 ********** Masking position 4 Map Score: 0.421072 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 135 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 12 TTAATTGAAGAAAACTGTCCCGGTGTGAAGT 4 146 0 AAAATGTCCC 0.951242 -155 TCATGCTTACAAAACTCTCCCCCTACGCGGT 4 223 0 AAAATCTCCC 0.988384 -78 AAAAGGTGTAATACATCTCCCTACTTTAAAT 5 44 0 ATACTCTCCC 0.933885 -40 GCTCTTAAGAATTCTCCCTACAACATAA 6 8 1 AGAATCTCCC 0.968858 -23 GTATTCAGTTAAAAATCACCCAGAGGGTTAT 7 268 0 AAAATCACCC 0.946423 -33 TTAGCAGTTTAAAATTATCCCCT 8 3 0 AAAATATCCC 0.929394 -31 GGTATTTGTATAACTTCTCCCGTTCTGGGAT 16 184 0 TAACTCTCCC 0.922401 -117 **** ****** Masking position 3 Map Score: 4.56217 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 59 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 13 ********** No masking Map Score: -5.88797e-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 14 ********** No masking Map Score: -5.88797e-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 15 ********** No masking Map Score: -5.88797e-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