AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00051_aquae_reg_100.orf -o00051_aquae_100.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 TACTATGGGATTTTTCCCTTTTTTGGCTCTTC 2 94 0 TTTTTCCTTT 0.973143 -171 TCCCGTGAGGTTTTTCCTCCTCAGCGTTCTTG 2 131 1 TTTTTCCCTC 0.978921 -134 TCTCGGGCGTTTCTTCCAGCTCTTTTTTAGAG 2 224 1 TTCTTCCCTC 0.959763 -41 AAAACTTTAGTTTTTCAACCTCTTGAATATAA 3 26 1 TTTTTCACTC 0.812333 -275 TCTGAAAGTTTTTCTCCCTTTTTCACTTCTCC 3 114 1 TTTCTCCTTT 0.970021 -187 CCCTTTTTCACTTCTCCGCTTTTTCTATCTAT 3 129 1 CTTCTCCTTT 0.943243 -172 AATCGGAATACTCTTCCTCTTTGAATTCCTCA 3 175 1 CTCTTCCTTT 0.905293 -126 TTGCTTTTTTCCTATTTTTAATGCATG 5 6 1 TTTTTCCTTT 0.973143 -78 TTGAGAGCTTCTTTTCAACCTTCGAGCGATGG 7 49 1 CTTTTCACTT 0.607687 -252 AACTTCTTTTTTCTCCTCTTCATCGGATATA 10 10 1 TTTCTCCTTC 0.978921 -80 ATGGAAAAGCTTTTTTCTTTTCCTTTCCAAGT 11 176 0 TTTTTTCTTC 0.733259 -88 GGATTTCTCCTCCTTTTAGAACTTC 14 30 0 TTTCTCCCTT 0.966547 -15 ATGCCTGCTTTTTCTGCAATTTTGCTACGAGC 16 19 0 TTTCTGCTTT 0.7171 -282 AATTCTGAGCTTCTTCCTTTTCGAAGAGTTCG 16 101 0 TTCTTCCTTC 0.963915 -200 GTTCTGGGATTTCTTCCCTTTCTTGCACTCCT 16 162 0 TTCTTCCTTC 0.963915 -139 ATTTGTATAACTTCTCCCGTTCTGGGATTTCT 16 180 0 CTTCTCCTTC 0.959763 -121 GATTTCTTAATTTTTCCCGCTTTTCTTCTTTT 16 263 1 TTTTTCCCTT 0.970021 -38 ******* *** Masking position 5 Map Score: 26.6627 Number of sites scoring better than the average of aligned sites = 1002 Number in coding regions = 918 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 2 CGTTCCATTTCTGGAAAGGATAAC 2 5 0 CTGGAAAGGA 0.937374 -260 TATGCTTTCGTTGTAAAGGAAACCGCTTAA 2 60 0 TTGTAAAGGA 0.830294 -205 AAAAACCTCACGGGAAAGGTTACTATGGGA 2 116 0 CGGGAAAGGT 0.854347 -149 GAAGAAACGCCCGAGAAGGTGGGAAATCGT 2 210 0 CCGAGAAGGT 0.904278 -55 TTATGCAGTTCCTGAAAGGTGATAAGGCTT 3 274 0 CCTGAAAGGT 0.937163 -27 GACGAAGAAGCTTCAAAGGTAGCCCTCATT 4 54 0 CTTCAAAGGT 0.829279 -247 CCTGCTGTCTCCGAAAAGGTGTAATACATC 5 58 0 CCGAAAAGGT 0.957162 -26 TAGTAAAAACTTGGAAAGGAAAAGAAAAAA 11 168 1 TTGGAAAGGA 0.862992 -96 CCATTAAGAATCTTGAAGGTAATCTTGATT 11 204 1 TCTTGAAGGT 0.673331 -60 AACATTCGTTTCGTGAAGGTTAGGTGTCTA 12 63 0 TCGTGAAGGT 0.83045 -238 GAAAATCTTTAAAGGTTTGTAAGGAC 13 7 1 CTTTAAAGGT 0.878325 -42 AATAAGAAGTTCTAAAAGGAGGAGAAATCC 14 25 1 TCTAAAAGGA 0.728401 -20 CACGAACTCTTCGAAAAGGAAGAAGCTCAG 16 99 1 TCGAAAAGGA 0.864368 -202 CTTACGGTTACTTTAAAGGTCCGAGTCCGG 16 134 0 CTTTAAAGGT 0.878325 -167 ACTTTCAAACCTGCAAAGGAACTCGTTAAG 16 231 1 CTGCAAAGGA 0.886663 -70 ********** Masking position 6 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 GAAAAACTAAAGTTTTAAAATATCAGTAATA 3 9 0 ATTTTAATAT 0.942349 -292 CTTTTTTCCTATTTTTAATGCATGTGTATTATT 5 14 1 ATTTTAACAT 0.949892 -70 CATTATCCCAACTTTAAACACATGCTCATTCCT 7 120 0 ATTTAAACAT 0.907684 -181 TTGAATTTATAGGTATTCAGTTAAAA 7 285 0 ATTTATATAT 0.572293 -16 GAATTTTAGCAGTTTAAAATTATCCCCT 8 6 0 ATTTAAATAT 0.894603 -28 ACAAAACTTTAGTTTAAATTCATAAAAGCA 9 8 0 ATTTAAACAT 0.907684 -25 AATTAGGTTATTTTAAGCTATAATTTTTCAA 11 9 1 TTTTTAATAT 0.853338 -255 TTAAGCTATAATTTTTCAATTATGGGCAAGCTG 11 23 1 ATTTTCATAT 0.911096 -241 TATAATGCTAAATTTTCAAGCATATTTAGGGTA 11 68 1 ATTTTCACAT 0.922321 -196 AAACACGTATTCTTTTAATTTATCCCTTAATAA 11 128 0 TTTTTAATAT 0.853338 -136 ATAAAGCGTTATTTTTCAGACATAGGCGCGCAG 12 19 0 ATTTTCACAT 0.922306 -282 TAGAACTTCTTATTTTAAAATATCTTTT 14 6 0 TTTTTAATAT 0.853337 -39 * ****** *** Masking position 8 Map Score: 10.1556 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 49 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 4 TAAAGTTTTAAAATATCAGTAATA 3 2 0 AAAATAGAAT 0.558145 -299 TGATATTTTAAAACTTTAGTTTTTCAACCTCTT 3 17 1 AAATTAGTTT 0.745037 -284 ACGAAAATAAAAAGGTCAGAATTGTTATATTCA 3 49 0 AAAGTAGATT 0.711308 -252 AAGGGAGAAAAACTTTCAGAATACACTCACGTG 3 101 0 AACTTAGATA 0.779455 -200 AATAGAACAGAAAGTTAAGAAATTAATTGAAGA 4 166 0 AAATTAGAAT 0.922297 -135 ATACAAAACTTTAGTTTAAATTCATAAA 9 15 0 AAATTAGTTA 0.79436 -18 TACCTCTATAAGAATTGAGTATACAATAGAAAA 10 65 1 AGATTAGATA 0.856647 -25 AATATGCTTGAAAATTTAGCATTATAAACCAAA 11 61 0 AAATTAGATT 0.939687 -203 CAAGTTCTGCAAACTTGAGCATACATTTGTAAA 12 108 1 AAATTAGATA 0.953673 -193 AAGTTTTTAGGATATCACTCAGGT 13 35 0 AGTTTAGATA 0.549655 -14 AAAGTATAAATTTTAAGTAAAACTCAGGAGG 15 17 0 AATTTAGAAA 0.761499 -21 GCTCGTAGCAAAATTGCAGAAAAAGCAGGCATA 16 19 1 AAATGAGAAA 0.695157 -282 AAAAGCGGGAAAAATTAAGAAATCTGCTTAACG 16 254 0 AAATTAGAAT 0.922297 -47 AAATAAAAAATTTTAGAAAAGAAGAAAAGC 16 281 0 AAATTAGAAA 0.939877 -20 *** ** ** *** Masking position 8 Map Score: 6.83176 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 105 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 5 ATATACAGAAGAGCCAAAAAAGGGAAAAATCCC 2 87 1 GAGAAAAAGG 0.961122 -178 AAACGATAAAGAAAACAAGAACGCTGAGGAGGA 2 145 0 GAAAAGAACG 0.897398 -120 AGAGGACCACGAAAATAAAAAGGTCAGAATTGT 3 57 0 GAAAAAAAGG 0.967795 -244 TCACGTGGTTGTACTGAAAGAGGACCACGAAAA 3 75 0 GTAAAAGAGG 0.847816 -226 AAAAAGCGGAGAAGTGAAAAAGGGAGAAAAACT 3 120 0 GAAAAAAAGG 0.967795 -181 ACCACTTGAGGAATTCAAAGAGGAAGAGTATTC 3 180 0 GAAAAAGAGG 0.979632 -121 GGACGTATTTGAAGCCAAAGACGACGAAGAAGC 4 73 0 GAAAAAGACG 0.944496 -228 ACTTAAATTGAAAATTAAGGAGGTGGGAGCCAT 4 265 0 AAAAAGGAGG 0.739521 -36 CGATGAAGAGGAGAAAAAAGAAGTT 10 3 0 GAGAAAGAAG 0.94409 -87 AATTCTTATAGAGGTAAAGGAAGATCTAGTTAG 10 48 0 GAGAAGGAAG 0.932847 -42 ACTTGGAAAGGAAAAGAAAAAAGCTTTTCCATT 11 176 1 GAAAAAAAAG 0.927664 -88 TAACCGTAAGGAGTGCAAGAAAGGGAAGAAATC 16 154 1 GAGAAGAAAG 0.896685 -147 *** ******* Masking position 7 Map Score: 13.9548 Number of sites scoring better than the average of aligned sites = 641 Number in coding regions = 589 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 6 AAACAAGAACGCTGAGGAGGAAAAACCTCA 2 136 0 GCTGAGGAGG 0.986732 -129 CTTTTACAAGGCTGAAGGGGCTATTCTCTT 2 179 1 GCTGAAGGGG 0.892388 -86 AGAAACGCCCGAGAAGGTGGGAAATCGTAA 2 208 0 GAGAAGGTGG 0.711088 -57 TGTACTGAAAGAGGACCACGAAAATAAAAA 3 69 0 GAGGACCACG 0.639298 -232 ATACAGAACCGCGGACGTGGATATGAAGAT 3 216 0 GCGGACGTGG 0.965863 -85 TTGCTGACCAGGTTTCCGTGGT 4 3 1 GCTGACCAGG 0.911719 -298 ATCTTTGACCGCGTAGGGGGAGAGTTTTGT 4 216 1 GCGTAGGGGG 0.754848 -85 ATTGAAAATTAAGGAGGTGGGAGCCATGCC 4 262 0 AAGGAGGTGG 0.693191 -39 TAATGATCATGATGATGAGGTCAGGTGGTA 7 148 1 GATGATGAGG 0.817086 -153 ATGAGAGATGGCTGTGGTGGAGTTGATGTG 7 177 1 GCTGTGGTGG 0.927443 -124 TGGTGGAGTTGATGTGGACGAGAAAATAAT 7 191 1 GATGTGGACG 0.718921 -110 AATTATATCCGATGAAGAGGAGAAAAAAGA 10 15 0 GATGAAGAGG 0.887349 -75 AAGGCTGAGCTCGTAGCAAAATT 16 4 1 GCTGAGCTCG 0.859812 -297 ********** Masking position 10 Map Score: 6.13309 Number of sites scoring better than the average of aligned sites = 699 Number in coding regions = 637 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 7 GTGGGAAATCGTAAAGAGAATAGCCCCTTC 2 192 0 GTAAAGAGAA 0.656957 -73 CCAGATAATCGTAAGGACCAAAAACGACAA 4 104 1 GTAAGGACCA 0.92685 -197 ATTATTTAAAGTAGGGAGATGTATTACACC 5 41 1 GTAGGGAGAT 0.911474 -43 GATTATGTTGTAGGGAGAATTCTTAAGAG 6 12 0 GTAGGGAGAA 0.924443 -19 GTGGAAGGAGAAAGTGGTGTAT 7 3 1 GGAAGGAGAA 0.948103 -298 TGGAGAGTATGTAGTGAGCAAAAGGCTTGG 7 83 1 GTAGTGAGCA 0.852003 -218 GGTAACATAAGGAATGAGCATGTGTTTAAA 7 111 1 GGAATGAGCA 0.895789 -190 TTGTAGCCCTCTAAGGAGCTATTCAAAATT 12 264 1 CTAAGGAGCT 0.852808 -37 TTAAAGGTTTGTAAGGACCTGAGTGATATC 13 19 1 GTAAGGACCT 0.914256 -30 GGCATAACCAAGAAGGAGCTGACGCAGCTA 16 46 1 AGAAGGAGCT 0.785216 -255 TCTTCGAAAAGGAAGAAGCTCAGAATTCCC 16 106 1 GGAAGAAGCT 0.767283 -195 ********** Masking position 7 Map Score: 5.93419 Number of sites scoring better than the average of aligned sites = 599 Number in coding regions = 568 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 8 TGAAAATGTTAAAATAGCGTT 1 13 1 AAAATAGCGT 0.728779 -11 CTTACTCTAAAAAAGAGCTGGAAGAAACGC 2 230 0 AAAAGAGCTG 0.896537 -35 TACATAGATAGAAAAAGCGGAGAAGTGAAA 3 134 0 GAAAAAGCGG 0.974536 -167 TTGCATGTCCAAAAGAGCGTATAATGAGGG 4 32 1 AAAAGAGCGT 0.914353 -269 CAAAGACGACGAAGAAGCTTCAAAGGTAGC 4 61 0 GAAGAAGCTT 0.767208 -240 AAAGGAAAAGAAAAAAGCTTTTCCATTAAG 11 182 1 AAAAAAGCTT 0.864842 -82 ATAAGTTATTGATAAAGCGTTATTTTTCAG 12 33 0 GATAAAGCGT 0.833127 -268 TTGGCAATTGAATAAAGCGGATTGGTCTAA 12 220 0 AATAAAGCGG 0.876175 -81 CAAAATTGCAGAAAAAGCAGGCATAACCAA 16 27 1 GAAAAAGCAG 0.83233 -274 GCATAACCAAGAAGGAGCTGACGCAGCTAT 16 47 1 GAAGGAGCTG 0.816952 -254 TTAGAAAAGAAGAAAAGCGGGAAAAATTAA 16 269 0 AGAAAAGCGG 0.843028 -32 ********** Masking position 6 Map Score: 6.42569 Number of sites scoring better than the average of aligned sites = 342 Number in coding regions = 326 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 TTAGTTTTTCAACCTCTTGAATATAACAAT 3 32 1 AACCTCTTGA 0.966254 -269 CTTTCAGTACAACCACGTGAGTGTATTCTG 3 88 1 AACCACGTGA 0.971819 -213 ATGAAGATAAGACCACTTGAGGAATTCAAA 3 194 0 GACCACTTGA 0.960106 -107 CCATCTCTCATACCACCTGACCTCATCATC 7 158 0 TACCACCTGA 0.961711 -143 TTTTAACCTCCTGAGTTTTACTTA 15 5 1 AACCTCCTGA 0.97792 -33 ********** Masking position 8 Map Score: 1.81452 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 25 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 TATGTATTATAGGCTTTTTAAGCGGTTTCC 2 43 1 AGGCTTTTTA 0.841113 -222 TAGCCCCTTCAGCCTTGTAAAAGTAAACGA 2 172 0 AGCCTTGTAA 0.947731 -93 AAAGGTGATAAGGCTTTTAACTTCTTGCTT 3 260 0 AGGCTTTTAA 0.909843 -41 GTAGGGGGAGAGTTTTGTAAGCATGACGTA 4 228 1 AGTTTTGTAA 0.685404 -73 AGTGAGCAAAAGGCTTGGTAACATAAGGAA 7 95 1 AGGCTTGGTA 0.907663 -206 TACCCTAAATATGCTTGAAAATTTAGCATT 11 71 0 ATGCTTGAAA 0.757979 -193 AAATCTTTAAAGGTTTGTAAGGACCTGAGT 13 13 1 AGGTTTGTAA 0.943809 -36 CTTCTACGAAAGCCTTGATAGCTGCGTCAG 16 64 0 AGCCTTGATA 0.855678 -237 GTTCCTTTGCAGGTTTGAAAGTGAGAACCT 16 223 0 AGGTTTGAAA 0.912817 -78 ********** Masking position 5 Map Score: 2.88262 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 201 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 11 ********** 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 12 ********** 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 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