AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00010_mgen_reg_300.orf -o00010_mgen_300.ace -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -g0.32 -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 = 0.32 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: MG022 29 DNA-directed RNA polymerase, subunit delta (rpoE) MG274 27 pyruvate dehydrogenase component E1, subunit alpha (pdhA) MG301 30 glyceraldehyde-3-phosphate dehydrogenase (gap) Input sequences: #1 MG014 239 ABC transporter, ATP-binding protein #2 MG015 46 ABC transporter, ATP-binding protein #3 MG017 65 ATP-dependent RNA helicase, putative #4 MG018 188 ATP-dependent RNA helicase, putative #5 MG019 41 heat shock protein (dnaJ) #6 MG062 300 PTS system, fructose-specific IIABC component (fruA) #7 MG069 300 PTS system, glucose-specific IIABC component (ptsG) #8 MG109 59 serine/threonine protein kinase, putative #9 MG210.1 200 conserved hypothetical protein #10 MG211 189 conserved hypothetical protein #11 MG272 249 dihydrolipoamide acetyltransferase (pdhC) #12 MG275 82 NADH oxidase (nox) #13 MG277 42 conserved hypothetical protein #14 MG304 176 ABC transporter, ATP binding protein #15 MG305 87 heat shock protein 70 (dnaK) #16 MG309 53 lipoprotein, putative #17 MG407 66 enolase (eno) #18 MG431 59 triosephosphate isomerase (tpiA) #19 MG432 85 conserved hypothetical protein #20 MG460 172 L-lactate dehydrogenase (ldh) Motif number 1 AATTAGCTGTTTTGATTATAAAAACTGTTAAAAT 1 214 0 TTTTAAAAAA 0.700038 -26 TTTGTTTTATTTAGCTGATCAAAAATTAATAATG 3 38 0 TTATACAAAA 0.554783 -28 CTTTGTAGTGCTTGTTCATAAAAAAGTAAACGGT 4 38 0 CTTTAAAAAA 0.860273 -151 AAACATTCCCATTAAAGATAAGAATCAAATTGCG 4 117 1 ATTAAAAGAA 0.626826 -72 TTTGATTCAGTTTGTTCTAAAAAACAATTAGCTA 6 48 0 TTTTTAAAAA 0.725112 -253 TGTTAACAGCATTTAACAACAAAATTGAATAAAA 6 103 1 ATTAACAAAA 0.813482 -198 ACAAAATTGAATAAAAATAAAAAACAGACCCTGA 6 121 1 ATAATAAAAA 0.92971 -180 ATTAGAACTAATAAAATTCCAAAAACAACTAAAA 7 37 0 ATAATCAAAA 0.855021 -264 AAAAATTTCACTTAAAGAACAAAAGAAAGGTCAA 7 98 1 CTTAACAAAA 0.807289 -203 CCACCTATTCCTAGCATTAAAAAAACTATTGCAA 7 226 0 CTAATAAAAA 0.927029 -75 AATTCACTAATTAACTAACAAAAATTATTAAGGA 9 31 1 TTATAAAAAA 0.736475 -170 TTAAACTAGGATTACACTTAAAAAAGTTAGTTTA 9 90 0 ATTATAAAAA 0.917079 -111 TTACAAGTAGCTATTAGTAAAGAAAACTACCAGA 9 126 0 CTAATAAGAA 0.685682 -75 TTACTAATAGCTACTTGTAAAAAATTAAAAGTTA 9 140 1 CTATTAAAAA 0.892767 -61 TGCCTAAGATTGAAGTTAAAAATGATGATTTA 10 9 1 ATTATAAAAA 0.917079 -181 TGATTTAGAGCTAGCTTTAAAAAAGTTTAAAAGG 10 36 1 CTATTAAAAA 0.892767 -154 AAAACAAAAGATAGCACAGAAAAAGCGCAGGAAG 10 141 1 ATAAAAAAAA 0.921251 -49 AGCTAGGTAACTATATTTTAAAAAAGTG 11 5 0 CTATTAAAAA 0.892764 -245 AATGAGGTACCTAGCTCTAAAAAATAAAGCTAGG 11 32 0 CTATTAAAAA 0.892767 -218 AAATTTTTGTCTAACAACTAAAAAGCCAGTAACT 11 157 1 CTAACAAAAA 0.587621 -93 GTAGTGATCTATAACAAATAAAAAAAGCCAGTTT 11 191 0 ATAAAAAAAA 0.921251 -59 TATAGAACATATTCCAAATAAAAAAGAGCAGCAC 14 19 1 ATTAAAAAAA 0.907248 -158 TTTTTGGTAGATAAAAAACAAAAAAGCAGCTGTT 14 53 0 ATAAAAAAAA 0.921251 -124 AAGCTTATTTATAAATTTTAAAAATAAGTCAGAG 14 99 0 ATATTAAAAA 0.896567 -78 GCTTAGTTTGCTACAAGTTAAAAACCTCAGTTTT 14 129 1 CTAATAAAAA 0.927029 -48 TTACTCAGTAATTATAAACAAAAATTAGCACTCA 15 40 0 ATTAAAAAAA 0.907247 -48 AGTAATTGTTATTGATCTAAAAAAAAAGT 15 69 1 ATTTTAAAAA 0.878757 -19 ATTAAATAGAAAAATATTGTTAAT 17 53 0 ATTAAAAAAA 0.907252 -14 GAAAGATTTTATAAGTTTTCAAAAACCATTTTCT 18 34 0 ATATTCAAAA 0.794446 -26 TACTAATAAGATAGTAAATAAGAAATTATTAATT 19 31 1 ATAAAAAGAA 0.667647 -55 ATAAGAAATTATTAATTACCAAAATTATTAAAAT 19 48 1 ATTTACAAAA 0.740818 -38 ATTTACTTTTTTTGGATTACAAAACAACACTGTT 20 47 0 TTTATCAAAA 0.63647 -126 AATAAGGATATTTGAAGTCAAAAAACTGTTGCCT 20 83 0 TTTATAAAAA 0.801255 -90 *** * * ***** Masking position 11 Map Score: 39.6006 Number of sites scoring better than the average of aligned sites = 607 Number in coding regions = 510 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 2 TAATTATTATAACAATTTTAATTTAACCAAAATA 1 172 1 AAATTAATTT 0.924911 -68 TTTGATTATAAAAACTGTTAAAATTCGAGGGGTA 1 204 0 AAATTAAAAT 0.924911 -36 TTTTATAATCAAAACAGCTAATTTT 1 225 1 AAAATAATTT 0.754211 -15 TTTGTCTTTCAACACTATTAAATTTAT 3 4 0 AAATTAAATT 0.924911 -62 TTGAAAGACAAACATTATTAATTTTTGATCAGCT 3 26 1 AAATTAATTT 0.92491 -40 AATCATCAAAAACAGTTTTAAAAAGCGCAATTTG 4 142 0 AAATTAAAAA 0.924911 -47 AGCAAGAATTATAATTAACACTCTAAG 5 4 1 AAATTAATTA 0.924911 -38 AACTGAATCAAAGAATTTGAAATTGTCTTTCATT 6 70 1 AAATGAAATT 0.644189 -231 AACAAAATTGAATAAAAATAAAAAACAGACCCTG 6 120 1 AAAATAAAAA 0.754257 -181 TGCAAGCAAAAATAAAACTAATTTGTTGTTTCTT 7 197 0 AAAATAATTT 0.754211 -104 TTTAAAACTACTAAATTTTATTAACCA 7 284 0 AAATTAAATT 0.924911 -17 AGTTAGTTTAAAAACTAGTAAAAAAGTGTTAATA 9 66 0 AAATTAAAAA 0.924911 -135 GTAAAAAATTAAAAGTTAGAATTAATGGCACTAT 9 156 1 AAATGAATTA 0.644189 -45 TACTTAATATTTATATAAAATTTAAGTTA 13 6 1 AAATTATAAA 0.636243 -37 ACTTATTTTTAAAATTTATAAATAAGCTTAGTTT 14 104 1 AAATTAAATA 0.924911 -73 CTCAAACACTAAAAGTGCTAATTAAAGTTTGTT 15 10 0 AAATTAATTA 0.924911 -78 CAAAAATTTCAATAATTTTAAAATTTATATTTTT 16 22 0 AAATTAAAAT 0.924911 -32 TATATGTTTTAAGATTTCTATTAATTCAAGTAAT 17 11 0 AAATTATTAA 0.636243 -56 TAGAAATCTTAAAACATATAATAATTTTATTAAC 17 25 1 AAAATAATAA 0.754257 -42 TAAATAGAAAAATATTGTTAATAAAATTATTATA 17 41 0 AAATTAATAA 0.924911 -26 ATGGTTTTTGAAAACTTATAAAATCTTTCAT 18 39 1 AAATTAAAAT 0.924911 -21 CACTAAGCTTAATATTACTAATAAGATAGTAAAT 19 16 1 AAATTAATAA 0.924911 -70 ATTAATTACCAAAATTATTAAAATAATTGTTCTT 19 58 1 AAATTAAAAT 0.924911 -28 TGTTACAAATAATTATAATATCGCTCATCTT 20 8 1 AAATTAATAT 0.924911 -165 ATTACAAAACAACACTGTTATTTAAAGATGAGCG 20 32 0 AAATTATTTA 0.636243 -141 TTTGTAATCCAAAAAAAGTAAATTCAGGCAACAG 20 58 1 AAAATAAATT 0.754211 -115 ** * * ****** Masking position 10 Map Score: 38.1008 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 177 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 3 ACACCCCTGATAAGGGTGAGGTCGATGGTTCA 1 89 0 TAAGTGAGGT 0.950482 -151 ATAACTCACTTAAAAATGAAGTTCCTAGAGGG 7 154 1 TAAATGAAGT 0.983569 -147 TGCCTAAGATTGAAGTTAAAAATGAT 10 5 1 TAAGTGAAGT 0.971344 -185 CTATTAAATTTAAACTTTAAGTACTATCAATA 11 224 1 TAAATTAAGT 0.959014 -26 AAATTTTATATAAATATTAAGTA 13 2 0 TAAATTAAGT 0.959014 -41 AATATTTATATAAAATTTAAGTTATTAAAAAT 13 16 1 TAAATTAAGT 0.959014 -27 TTTGGGTATTTAAAACTGAGGTTTTTAACTTG 14 142 0 TAAATGAGGT 0.971344 -35 TGAACCAAAATAAAATTGAAGTATATCTCTAG 20 141 1 TAAATGAAGT 0.983569 -32 **** ****** Masking position 9 Map Score: 10.2483 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 15 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 4 ATTATAAAAACTGTTAAAATTCGAGGGGTAT 1 203 0 CTGTTAAATT 0.88803 -37 TAATTAATCTCTTTAAAATCTTTCAAGAACT 2 21 0 CTTTAAAACT 0.605746 -26 TCTTTCAACACTATTAAATTTAT 3 3 0 CTATTAAATT 0.946252 -63 TTAGCTACAGCTTTTAAAATTAGTCTAATGT 6 24 0 CTTTTAAATT 0.976805 -277 CCAATTAGAACTAATAAAATTCCAAAAACAA 7 43 0 CTAATAAATT 0.767642 -258 TTATTTTGAGCTTTAAAAATTTCACTTAAAG 7 84 1 CTTTAAAATT 0.918857 -217 TTTAAAACTACTAAATTTTATTAACCAA 7 283 0 CTACTAAATT 0.735226 -18 TATTTAAAAGCTTTTCAATTTGATACTTATT 8 31 0 CTTTTCAATT 0.851059 -29 TTAATTCTAACTTTTAATTTTTTACAAGTAG 9 150 0 CTTTTAATTT 0.794041 -51 CAGTGATATCCTTTTAAACTTTTTTAAAGCT 10 48 0 CTTTTAAATT 0.976806 -142 TAGATCACTACTATTAAATTTAAACTTTAAG 11 214 1 CTATTAAATT 0.946252 -36 GTGATTCGATCTTTTAAAATTAAGCTTTTG 12 10 0 CTTTTAAATT 0.976805 -73 CCTTAAATAGCTTAAAAAATTACTGCAGCTA 12 56 1 CTTAAAAATT 0.679997 -27 CTCTGACTTATTTTTAAAATTTATAAATAAG 14 99 1 TTTTTAAATT 0.719383 -78 AATTTCAATAATTTTAAAATTTATATTTTTA 16 21 0 ATTTTAAATT 0.719366 -33 ******** ** Masking position 7 Map Score: 16.6058 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 82 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 TGTAAAACCAAGTTCTTGAAA 2 1 1 TGAAAACCAA 0.861471 -46 TTAATAGTGTTGAAAGACAAACATTATTAAT 3 17 1 TGAAGACAAA 0.984328 -49 CTGTTAACAATGAAAGACAATTTCAAATTCT 6 81 0 TGAAGACAAT 0.898348 -220 AGTGAGTTATTGGAAGTCAAATCATTAGTAA 7 133 0 TGAAGTCAAA 0.888646 -168 AGGGAGTTGATGAAAAAGAAACAACAAATTA 7 182 1 TGAAAAGAAA 0.887251 -119 TGCGGTTAAGAGAAAAACAAAAGATAGCACA 10 128 1 AGAAAACAAA 0.891227 -62 ATTAAAGTGATGGAAGACAACAAGAAATGCT 11 72 1 TGAAGACAAC 0.929069 -178 TGCTGTAAAAAGTAAGACAAAATTTTTGTCT 11 138 1 AGAAGACAAA 0.9397 -112 GCTTTTTAGTTGTTAGACAAAAATTTTGTCT 11 152 0 TGTAGACAAA 0.888646 -98 TTTTGGTAGATAAAAAACAAAAAAGCAGCTG 14 55 0 TAAAAACAAA 0.72237 -122 ATCAATTAGTTGGAAAAGAAAATGGTTTTTG 18 18 1 TGAAAAGAAA 0.887251 -42 ** ******** Masking position 5 Map Score: 8.06711 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 73 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 TGGTTAAATTAAAATTGTTATAATAATTAG 1 171 0 AAAATTGTTA 0.683183 -69 TTTGATTATAAAAACTGTTAAAATTCGAGG 1 208 0 AAAACTGTTA 0.815608 -32 AATTCTTCATAAAACCTTTGTAGTGCTTGT 4 57 0 AAAACCTTTG 0.755388 -132 TGCGCTTTTTAAAACTGTTTTTGATGATTA 4 147 1 AAAACTGTTT 0.844884 -42 TGATGATTACAAAACCATTGATTTAGCAGA 4 168 1 AAAACCATTG 0.905858 -21 AAGCAAAAATAAAACTAATTTGTTGTTTCT 7 198 0 AAAACTAATT 0.347647 -103 TAGCATTAAAAAAACTATTGCAAGCAAAAA 7 219 0 AAAACTATTG 0.949325 -82 TATCAAATTGAAAAGCTTTTAAATAGGGGT 8 37 1 AAAAGCTTTT 0.116393 -23 TTAACTAACAAAAATTATTAAGGAGTATTA 9 41 1 AAAATTATTA 0.724162 -160 AAAGTAAGACAAAATTTTTGTCTAACAACT 11 146 1 AAAATTTTTG 0.745476 -104 AATAGCTTAAAAAATTACTGCAGCTAAGAT 12 61 1 AAAATTACTG 0.520922 -22 TCAGAGCTAAAAATCTGTTTTTTGGTAGAT 14 75 0 AAATCTGTTT 0.291922 -102 TATAAATTTTAAAATTATTGAAATTTTTGA 16 27 1 AAAATTATTG 0.901302 -27 TATTGTTAATAAAATTATTATATGTTTTAA 17 33 0 AAAATTATTA 0.724162 -34 ATTAAATAGAAAAATATTGTTAATAAAAT 17 48 0 AAAAATATTG 0.620617 -19 TAAGTTTTCAAAAACCATTTTCTTTTCCAA 18 27 0 AAAACCATTT 0.772759 -33 CAAAATTATTAAAATAATTGTTCTTAACT 19 67 1 AAAATAATTG 0.473344 -19 TTGAAGTCAAAAAACTGTTGCCTGAATTTA 20 76 0 AAAACTGTTG 0.938979 -97 ********** Masking position 9 Map Score: 7.60277 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 341 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 TATGAAGAATTATTTCAAATAGATTATTTAA 4 76 1 TATTCAAATA 0.651772 -113 TTGTTAAATTTATTATAAATATGCAACTAAT 6 269 1 TATTTAAATA 0.537663 -32 TAGGTGATATTGTTGAAAATAAGTATCAAAT 8 14 1 TGTTAAAATA 0.857384 -46 CTGATATCTATATACTAAATAGTGCCATTAA 9 177 0 TATATAAATA 0.583063 -24 CACTTTTTTAAAATATAGTTACCTA 11 5 1 TTTTAAAATA 0.727285 -245 AGTAGTGATCTATAACAAATAAAAAAAGCCA 11 195 0 TATACAAATA 0.838553 -55 AAATTTAAGTTATTAAAAATAGTTA 13 28 1 TATTAAAATA 0.660526 -15 ATATAGAACATATTCCAAATAAAAAAGAGCA 14 18 1 TATTCAAATA 0.939031 -159 TATTTATAAATTTTAAAAATAAGTCAGAGCT 14 97 0 TTTTAAAATA 0.811809 -80 GTGGTAATAATAAAAATATAAATTTTAA 16 8 1 TAATAAAATA 0.659801 -46 ATAATAATTTTATTAACAATATTTTTCTATT 17 42 1 TATTACAATA 0.550079 -25 CTAAGCTTAATATTACTAATAAGATAGTAAA 19 18 1 TATTCTAATA 0.68414 -68 TGTTACAAATAATTATAATAT 20 1 1 TGTTCAAATA 0.906085 -172 **** ****** Masking position 8 Map Score: 9.09607 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 48 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 TCAACCTCCTGAGTGCAAATCAGGTGCTCT 1 15 1 GAGTGCAAAT 0.934317 -225 TGCATCCTTAGAGTGTTAATTATAATTCTT 5 14 0 GAGTGTTAAT 0.940224 -28 CTAAAGCGCTAATTAGTTGCATA 6 288 0 AAGCGCTAAT 0.936271 -13 ACTAGTAAAAAAGTGTTAATACTCCTTAAT 9 57 0 AAGTGTTAAT 0.9287 -144 CTGCCAATGCAAGTGCGAATGCGCTAAGTG 11 101 1 AAGTGCGAAT 0.945818 -149 CAAACACTAAAAGTGCTAATTAAAGTTTGT 15 12 0 AAGTGCTAAT 0.979485 -76 TTTAGTGTTTGAGTGCTAATTTTTGTTTAT 15 31 1 GAGTGCTAAT 0.982952 -57 ********** Masking position 8 Map Score: 7.66667 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 8 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 9 ATGGGGATGTAGCTCAACTGATAGAGCACCT 1 36 0 AGCCAACTGA 0.791727 -204 AGTTTTTATAATCAAAACAGCTAATTTT 1 222 1 ATCAAACAGC 0.94654 -18 AAATTTTATTAACCAAACAGCTTAGGAAGGG 7 268 0 AACAAACAGC 0.970619 -33 CTTAATGGCTAGCTAAACTGCGAAACTTCCT 10 169 0 AGCAAACTGC 0.972819 -21 GAATGCGCTAAGTGCAACAGCTGCTGTAAAA 11 117 1 AGTCAACAGC 0.832209 -133 TTTGTCTAACAACTAAAAAGCCAGTAACTAA 11 162 1 AACAAAAAGC 0.850987 -88 AAAAGCCAGTAACTAAACTGGCTTTTTTTAT 11 177 1 AACAAACTGG 0.766279 -73 AAAAGATCGAATCACTACTGCACAAATTATC 12 26 1 ATCCTACTGC 0.648338 -57 AAAAAAGAGCAGCACAACAGCTGCTTTTTTG 14 38 1 AGCCAACAGC 0.98269 -139 GTAGATAAAAAACAAAAAAGCAGCTGTTGTG 14 50 0 AACAAAAAGC 0.850987 -127 *** ******* Masking position 7 Map Score: 4.6438 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 38 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 10 CCTGATTTGCACTCAGGAGGTTGAGGGT 1 8 0 ACTCAGGGGT 0.974128 -232 TGGAAGTATAGCTCAGTTGGTTAGAGCACAC 1 117 0 GCTCAGTGGT 0.945179 -123 ATATTTAATGGCGGAAGCGGTGGGATTCGAA 6 166 1 GCGGAAGGGT 0.962345 -135 CTGGGAGCGTACTCAAGTGGTTAAGAGGACA 6 234 0 ACTCAAGGGT 0.959916 -67 GCATCCCTTTGCGCAAGTGGTATTCATGGCG 10 100 0 GCGCAAGGGT 0.991108 -90 CACAGAAAAAGCGCAGGAAGTTTCGCAGTTT 10 155 1 GCGCAGGAGT 0.964431 -35 ******* *** Masking position 5 Map Score: 2.09024 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 2 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 11 TCAAAAATTAATAATGTTTGTCTTTCAACA 3 24 0 ATAATGTTTG 0.701448 -42 TAAAACCTTTGTAGTGCTTGTTCATAAAAA 4 48 0 GTAGTGCTTG 0.889051 -141 AATAGTTTTTTTAATGCTAGGAATAGGTGG 7 230 1 TTAATGCTAG 0.932491 -71 AAATGATGATTTAGAGCTAGCTTTAAAAAA 10 30 1 TTAGAGCTAG 0.956314 -160 GCTCTAAAAAATAAAGCTAGGTAACTATAT 11 23 0 ATAAAGCTAG 0.857344 -227 GCTTTATTTTTTAGAGCTAGGTACCTCATT 11 36 1 TTAGAGCTAG 0.956314 -214 AAAGTGCTAATTAAAGTTTGTT 15 3 0 TTAAAGTTTG 0.84377 -85 ATTAGCACTTTTAGTGTTTGAGTGCTAATT 15 22 1 TTAGTGTTTG 0.895468 -66 ********** Masking position 3 Map Score: 1.98052 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 61 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 12 CATAATCCTAAGGGTATTTAACTAATTATTA 1 150 1 AGGTATTTAA 0.972822 -90 TATTTCAAATAGATTATTTAAGAAGATTTGA 4 86 1 AGATATTTAA 0.822788 -103 GATGGTCTGTTGGATATTTAATGGCGGAAGC 6 153 1 TGGTATTTAA 0.939657 -148 GTAATTTTTTAAGCTATTTAAGGATAATTTG 12 48 0 AAGTATTTAA 0.907104 -35 TATAAAATTTAAGTTATTAAAAATAGTTA 13 24 1 AAGTATTAAA 0.669664 -19 TTTGGTGTTTTGGGTATTTAAAACTGAGGTT 14 151 0 TGGTATTTAA 0.939657 -26 TGTCTAAATAAGGATATTTGAAGTCAAAAAA 20 92 0 AGGTATTTGA 0.916764 -81 *** ******* Masking position 6 Map Score: 1.99594 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 28 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 13 TTATCACTTGCATCCTTAGAGTG 5 29 0 TCACTTGCAT 0.910469 -13 TTTAAAAATTTCACTTAAAGAACAAAAGAA 7 95 1 TCACTTAAAG 0.924806 -206 TTCCAATAACTCACTTAAAAATGAAGTTCC 7 149 1 TCACTTAAAA 0.755833 -152 TAAAAGGATATCACTGGAAGTACGCAGGTT 10 63 1 TCACTGGAAG 0.802696 -127 TTGTCTTCCATCACTTTAATTTATGAAATG 11 62 0 TCACTTTAAT 0.888784 -188 TAGCGCATTCGCACTTGCATTGGCAGCATT 11 97 0 GCACTTGCAT 0.813872 -153 CGTATTGATAGTACTTAAAGTTTAAATTTA 11 228 0 GTACTTAAAG 0.510125 -22 CTATTTTTAATAACTTAAATTTTATATAAA 13 20 0 TAACTTAAAT 0.624774 -23 ATTACTTGAATTAATAGAAAT 17 2 1 TTACTTGAAT 0.823231 -65 TTATTTTGGTTCACTTTAATAAATTTTGCT 20 124 0 TCACTTTAAT 0.888784 -49 ********** Masking position 5 Map Score: 0.952138 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 79 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 14 ********** No masking Map Score: 1.57273e-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: 1.57273e-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