AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02010_mgen_reg_300.orf -o02010_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 Input sequences: #1 MG040 158 lipoprotein, putative #2 MG042 197 spermidine/putrescine ABC transporter, ATP-binding protein (potA) #3 MG077 233 oligopeptide ABC transporter, permease protein (oppB) #4 MG109 59 serine/threonine protein kinase, putative #5 MG115 24 conserved hypothetical protein #6 MG140 300 conserved hypothetical protein #7 MG142 258 translation initiation factor 2 (infB) #8 MG144 24 conserved hypothetical protein #9 MG148 38 conserved hypothetical protein #10 MG149 75 lipoprotein, putative #11 MG149.1 90 conserved hypothetical protein #12 MG150 89 ribosomal protein S10 (rpS10) #13 MG186 300 lipoprotein, putative #14 MG289 300 high affinity transport system protein P37 #15 MG304 176 ABC transporter, ATP binding protein #16 MG305 87 heat shock protein 70 (dnaK) #17 MG309 53 lipoprotein, putative #18 MG412 120 lipoprotein, putative #19 MG414 64 conserved hypothetical protein #20 MG415 300 conserved hypothetical protein Motif number 1 TTTTAGCTAATTATTTTTAGTAAAAAGAAATCA 1 125 0 TATTTTATAA 0.765065 -34 ATCTGTTTATTTTTTAATAGTAAAAACACAATT 2 34 1 TTTTAAATAA 0.849446 -164 ATTGATAGCCTTTTTCAAACCAATTTTGTTAAA 2 81 0 TTTTCAACAA 0.784988 -117 AATATCTTAATTTTTTACAGCAAAATTGATAGC 2 105 0 TTTTTAACAA 0.951768 -93 AAAATTAAGATATTTTTTATCAAAAATTAGCAT 2 124 1 TTTTTTACAA 0.963161 -74 TTTAAATACTTAATTTTCAATAAAAAACGTTAA 2 175 0 TATTTTATAA 0.883702 -23 CAGCACATGATCTTTATCACTAAATTTATGTTT 3 59 1 TTTTATATAA 0.886206 -175 AATTTGATACTTATTTTCAACAATATCACCTAT 4 13 0 TATTTTACAA 0.935776 -47 TCACTACTAATAATTTAAATTAAGCACTCATAC 6 214 1 TATTTAATAA 0.859536 -87 AACAAGACTTTGTTTATTAACAAGAAAACATTT 7 21 1 TTTTATACAA 0.926486 -238 ACGTAAAAGTTCTCTTTTAACAAAATGTTTTCT 7 43 0 TTCTTTACAA 0.633968 -216 CTTGAGATTTTGATTAAGATCAATTTCAAGTTG 7 94 0 TATTAAACAA 0.847857 -165 AGCTTTGAGGTGTTTTTTATCTAGCTTTAAACC 7 154 0 TTTTTTACTA 0.845817 -105 AACCTTAAGGTGTTTTTCAACTACAGCTTTGAG 7 178 0 TTTTTTACTA 0.845816 -81 TTATTTTGAATTTTTCTAAATAAGCTAACAAAT 10 17 0 TTTTCTATAA 0.668309 -59 GTTATTAACTTAATTTAGAATTAACTAATGACA 11 23 1 TATTTAATTA 0.488436 -68 TATAAATTGTTATTTTTTAACAATTTGAACAAT 13 213 1 TTTTTTACAA 0.962779 -88 AAATTGAATTTGTTTAAAACTAAAACAGACAGG 14 23 1 TTTTAAATAA 0.854585 -278 TCCGAATTACTTTTTTGAATTAAAGCTATTCTT 14 99 0 TTTTTGATAA 0.779643 -202 TCTTAAAAAATATTTTTTAATAAAGATTAATTG 14 132 1 TTTTTTATAA 0.928331 -169 AAGTGAATATTTATTTTTATTAAAAACTTATAT 14 189 1 TATTTTATAA 0.873819 -112 ATTTGTAGTCTATTTTTAACTAATATAAAAAAG 14 226 1 TTTTTTATAA 0.941398 -75 AAAAGTTGAATATTTAAAAACAATTAATTTTGA 14 254 1 TTTTAAACAA 0.903903 -47 GCTGCTTTTTTGTTTTTTATCTACCAAAAAACA 15 57 1 TTTTTTACTA 0.845817 -120 CTCTGACTTATTTTTAAAATTTATAAATAAGCT 15 99 1 TTTTAAATTA 0.551092 -78 AATTACTCAGTAATTATAAACAAAAATTAGCAC 16 43 0 TATTATACAA 0.847475 -45 ACTTTTTTTTTAGATCAATAACAATTAC 16 70 0 TTTTTAACAA 0.951763 -18 AAAATGCATTTCATTTAAATTAATTGGCTTGTG 18 25 1 TATTTAATAA 0.876086 -96 GAAATTTTTCTGATTTGTAACAAT 20 2 0 TATTTGACAA 0.770366 -299 TCAGCACAAATAATTAACAGTAATGATTTAACT 20 236 1 TATTAAATAA 0.773284 -65 * ***** * *** Masking position 5 Map Score: 40.7507 Number of sites scoring better than the average of aligned sites = 471 Number in coding regions = 409 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 2 AGAGATACCAAAAAGTAAATCACAACTATAAAACTAATCCT 1 51 0 AAAAAATAAA 0.97382 -108 TATTTTTAGTAAAAAGAAATCAAAAGATAAAAAAATGTTTG 1 106 0 AAAAAATAAA 0.97382 -53 TTATTTTTTAATAGTAAAAACACAATTTAACCTTGTTTCTA 2 40 1 ATAAAAAAAC 0.611078 -158 TTTCAATAAAAAACGTTAATTAGTATAACAATTTTTTATGC 2 153 0 AAATAATAAA 0.835113 -45 TGATTATTTTATAAAAAAATGATACTAATAACGATTACTAG 3 11 0 ATAAAATAAA 0.933694 -223 ATTTGAAACCAAACATAAATTTAGTGATAAAGATCATGTGC 3 61 0 AAAAAATTAA 0.649382 -173 ACCAGCTTCTAAATCTAAAGCATGATTACAATAAAGCAGGA 3 118 0 AAAAAAGAAA 0.902801 -116 TTACTAAATAGAAATAAAAAAAGAACCTGTTTTTTT 3 208 0 AAAAAATAAC 0.840036 -26 CTGTTTCTATAAAAATAAATCAGGTTTTTAACTATTCAATG 6 160 0 AAAAAATAAA 0.97382 -141 TTTGTTTATTAACAAGAAAACATTTTGTTAAAAGAGAACTT 7 29 1 AACAAAAAAA 0.692791 -230 ATCTAGCTTTAAACCAAAAACACTCAAATAATAACCCCTGC 7 128 0 AAAAAAAAAA 0.967105 -131 TTATTTAGAAAAATTCAAAATAAGCAAATTATAATTAGGTG 10 27 1 AAAAAAAATA 0.874959 -49 GTCATTAGTTAATTCTAAATTAAGTTAATAACTATCTTTTT 11 14 0 AATAAATAAA 0.658153 -77 TGGTTAATAAATAAGTAAATAATTTGGGTAAATTAACTTGG 13 139 0 ATAAAATAAA 0.931873 -162 GAATTTGTTTAAAACTAAAACAGACAGGGAAAATTTAACAT 14 28 1 AAAAAAAAAA 0.967105 -273 TGAATAGCAAAAAATATAAGAATAGCTTTAATTCAAAAAAG 14 82 1 AAATAAGAAA 0.558431 -219 TTGAATATTTAAAAACAATTAATTTTGATAATTAATAATCC 14 259 1 AAAAATTAAA 0.657847 -42 AACATATTCCAAATAAAAAAGAGCAGCACAACAGCTGCTTT 15 24 1 AAAAAAAAAA 0.967105 -153 TATAAATTTTAAAAATAAGTCAGAGCTAAAAATCTGTTTTT 15 83 0 AAAAAGTAAA 0.740496 -94 TCAGTTTTAAATACCCAAAACACCAAAACAAT 15 155 1 ATAAAAAAAA 0.917556 -22 AACAAACTTTAATTAGCACTTTTAGTGTTTGAGT 16 4 1 AAATAATATA 0.54658 -84 CAGTAATTATAAACAAAAATTAGCACTCAAACACTAAAAGT 16 28 0 AAAAAATAAA 0.97382 -60 GTGGTAATAATAAAAATATAAATTTTAAAATTATTGA 17 7 1 ATAAAAAATA 0.725946 -47 AGTGTTAATGACATTGAAAAAAACGGATTAAATAGTTATCA 20 35 1 ACAAAAAAAA 0.747223 -266 TTTACTTCTCAAAAAGAAAACAATTTAAATATTTCATCCGC 20 110 1 AAAAAAAATA 0.874959 -191 CTACAATAAAATACATAAAAGATCCTGAGAAATTAATTAAA 20 150 1 ATAAAAAAAA 0.917556 -151 TCTAAAAATGATAGCGAAATCATTAAAGATAAG 20 278 1 ATAAAATATA 0.770169 -23 *** **** * ** Masking position 8 Map Score: 26.4861 Number of sites scoring better than the average of aligned sites = 383 Number in coding regions = 334 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 3 ATATTTTAATCAATTAAATCTGTTTATTTTTTAA 2 17 1 CATTAACTGT 0.975163 -181 AGTAAAAACACAATTTAACCTTGTTTCTATTTAA 2 52 1 CATTAACTTT 0.887175 -146 CATGCTTTAGATTTAGAAGCTGGTTACTTTTGTT 3 135 1 ATTAAACTGT 0.691912 -99 TATTTAAAAGCTTTTCAATTTGATACTTATTTTC 4 28 0 CTTTAATTGT 0.937046 -32 ACTAGTGGAACCATTAAAACTGCTTATCCAGTGA 6 75 1 CATTAACTGT 0.975163 -226 GATTAAGATCAATTTCAAGTTGGTTGTCTAATTT 7 82 0 ATTTAATTGT 0.928985 -177 AAAGACACCTAATTATAATTTGCTTATTTTGAAT 10 39 0 ATTAAATTGT 0.663727 -37 ACAACTGGACCCATTAAAACTGCTTATCCGGTGA 13 21 1 CATTAACTGT 0.975163 -280 GTTACAAACGAAATTGAATTTGTTTAAAACTAAA 14 13 1 AATTAATTGT 0.968078 -288 TTTATTACTTAGATTCAAGTTGCTGGCAATTAAT 14 157 0 AATTAATTGT 0.968078 -144 TTAAAAACTTATATTCAAATTTGTAGTCTATTTT 14 208 1 AATTAATTTT 0.85863 -93 TTGTTTTTAAATATTCAACTTTTTTATATTAGTT 14 243 0 AATTAATTTT 0.85863 -58 TATTTAAAAACAATTAATTTTGATAATTAATAAT 14 264 1 CATTATTTGT 0.734856 -37 AATTTCAATAATTTTAAAATTTATATTTTTATTA 17 18 0 ATTTAATTTT 0.723749 -36 TCTTTAGAAAAGATTTAATCTGTTTAAAAA 18 101 1 AATTAACTGT 0.971836 -20 TCTTTGATAACTATTTAATCCGTTTTTTTCAATG 20 46 0 CATTAACCGT 0.823755 -255 AGCGGATGAAATATTTAAATTGTTTTCTTTTTGA 20 118 0 AATTAATTGT 0.968078 -183 * *** ** *** * Masking position 7 Map Score: 19.237 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 131 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 TAGTTAGTTATTTTGCAAAAAAGGATTAGTT 1 30 1 TTTTCAAAAA 0.859396 -129 TTGATTTCTTTTTACTAAAAATAATTAGCTA 1 124 1 TTTATAAAAA 0.952547 -35 TTGTGTTTTTACTATTAAAAAATAAACAGAT 2 34 0 ACTATAAAAA 0.627441 -164 CTTGTTTCTATTTAACAAAATTGGTTTGAAA 2 71 1 TTTACAAAAT 0.758187 -127 TAAGATATTTTTTATCAAAAATTAGCATAAA 2 129 1 TTTACAAAAA 0.937758 -69 ATACTTAATTTTCAATAAAAAACGTTAATTA 2 172 0 TTCATAAAAA 0.814802 -26 TTCTTGATTATTTTATAAAAAAATGATACTA 3 25 0 TTTTTAAAAA 0.887549 -209 AACCAGTACCATTTCCAAAAAACTGAGAACC 3 175 1 ATTTCAAAAA 0.617836 -59 AAGTAACTGTTTCTATAAAAATAAATCAGGT 6 176 0 TTCTTAAAAA 0.637205 -125 CAAGACTTTGTTTATTAACAAGAAAACATTT 7 23 1 TTTATAACAA 0.615946 -236 AAAGTTCTCTTTTAACAAAATGTTTTCTTGT 7 40 0 TTTACAAAAT 0.758187 -219 AACTTTTACGTCTTGTAAAATTAGACAACCA 7 65 1 TCTTTAAAAT 0.342173 -194 GAAATTGATCTTAATCAAAATCTCAAGGGCA 7 100 1 TTAACAAAAT 0.584249 -159 GGTGTCTTTCTTTACTAAAAAT 10 64 1 TTTATAAAAA 0.952547 -12 ATTTTCTCAATTAAATAAAAAAACAGTGTAA 11 64 0 TTAATAAAAA 0.900008 -27 TTTTGGTGTATCAACTAAAAACTAAAGCGTT 12 28 0 TCAATAAAAA 0.742764 -62 GCAATTAATCTTTATTAAAAAATATTTTTTA 14 135 0 TTTATAAAAA 0.950898 -166 AATATTTATTTTTATTAAAAACTTATATTCA 14 194 1 TTTATAAAAA 0.950898 -107 AAAAAGTTGAATATTTAAAAACAATTAATTT 14 253 1 ATATTAAAAA 0.484223 -48 TTGTTTTTTATCTACCAAAAAACAGATTTTT 15 66 1 TCTACAAAAA 0.832588 -111 CTCAGTAATTATAAACAAAAATTAGCACTCA 16 40 0 ATAACAAAAA 0.644963 -48 ATTTGCAATTAATAAAAATGCATTTCAT 18 8 1 ATTATAAAAA 0.84001 -113 AGATTAAATCTTTTCTAAAGAGAATTCGAAT 18 91 0 TTTTTAAAGA 0.551061 -30 TCCTGAGAAATTAATTAAAAAATCTTTAATT 20 172 1 TTAATAAAAA 0.899988 -129 AACACTGGGCTTAATTAAAGATTTTTTAATT 20 184 0 TTAATAAAGA 0.579779 -117 **** ****** Masking position 7 Map Score: 22.9087 Number of sites scoring better than the average of aligned sites = 617 Number in coding regions = 528 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 5 CTTCTAGTATTTAGTTAGTTATTTTGCAAAAAAGG 1 19 1 TATATTATTT 0.800521 -140 GTAGTATCAAACATTTTTTTATCTTTTGATTTCTT 1 99 1 AATTTTACTT 0.63523 -60 TGACGGTATTTTAGCTAATTATTTTTAGTAAAAAG 1 131 0 TATATTATTT 0.800521 -28 TTTAAATACTTAATTTTCAATAAAAA 2 182 0 TATATTATTT 0.800521 -16 GATCATGTGCTGATGTTCTTGATTATTTTATAAAA 3 36 0 TATTTTGTTA 0.751951 -198 TAAAAGCTTTTCAATTTGATACTTATTTTCAACAA 4 23 0 TATTATATTA 0.705232 -37 TAAAAATAAATCAGGTTTTTAACTATTCAATGGCG 6 157 0 TATTTTACTA 0.953875 -144 TTGCAACTAATTAATTAGTTAACTAATA 9 21 1 TATATTACTA 0.891966 -18 GGTTTAATTTGTTAGCTTATTTAGAAAA 10 4 1 TATTTTACTT 0.946158 -72 TAATTCTAAATTAAGTTAATAACTATCTTTTTTAG 11 11 0 TATTATACTA 0.807049 -80 AAATCCGTAGTCAATTTATTAACTAACTAGTGAAC 12 56 1 TATTTTACTA 0.953875 -34 TTTACCCAAATTATTTACTTATTTATTAACCATTG 13 148 1 TATATTATTA 0.825251 -153 TCCCCACTCTATAAATTGTTATTTTTTAACAATTT 13 204 1 AATTTTATTT 0.499032 -97 AAATTTACATTAATATAGTTATTTTTTGCAATTTA 13 246 0 TATATTATTT 0.800515 -55 AACAACCAGTTAAGCTTGTTAGCTAAATTTACATT 13 270 0 TATTTTACTA 0.953875 -31 AAAGCTATTCTTATATTTTTTGCTATTCAGAGTTA 14 76 0 TATTTTTCTA 0.701682 -225 AAATAAATATTCACTTTATTACTTAGATTCAAGTT 14 170 0 TATTTTATTA 0.922053 -131 TAAAAACAATTAATTTTGATAATTAATAATCCAGG 14 268 1 TATTATATTA 0.704982 -33 CAGCTGCTTTTTTGTTTTTTATCTACCAAAAAACA 15 55 1 TTTTTTACTA 0.527055 -122 TATTTAAAACTGAGGTTTTTAACTTGTAGCAAACT 15 133 0 TATTTTACTT 0.946158 -44 TCAATAATTTTAAAATTTATATTTTTATTATTACC 17 13 0 TATTATATTT 0.670293 -41 TTAAAATTATTGAAATTTTTGACTGTGCA 17 35 1 TATTTTGCTG 0.43601 -19 GCATTTCATTTAAATTAATTGGCTTGTGAAAAAAC 18 30 1 TATATTGCTT 0.642586 -91 GAATTGACACTCAGGTTATTATTTAGTCTAGTTTT 18 60 0 TATTTTATTA 0.922054 -61 GATGAAATATTTAAATTGTTTTCTTTTTGAGAAGT 20 113 0 TATTTTTCTT 0.666521 -188 * * ** *** *** Masking position 6 Map Score: 26.4091 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 175 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 TAAATACTAGAAGATTAATTA 1 2 0 AAGATTAATT 0.947868 -157 TTTGCAAAAAAGGATTAGTTTTATAGTTGT 1 41 1 AGGATTAGTT 0.921721 -118 GCAATCTAAAGGGATTAATATATTAGTATG 6 242 0 GGGATTAATA 0.620567 -59 GATTTTGATTAAGATCAATTTCAAGTTGGT 7 92 0 AAGATCAATT 0.863041 -167 AAAACACCTTAAGGTTAGTTGTAATGATGC 7 195 1 AAGGTTAGTT 0.67947 -64 TAGGATTAATTTTACTTCAAG 8 14 0 AGGATTAATT 0.954674 -11 ATCAACTGTCAAGATCAATTCCTTGATCAA 13 68 1 AAGATCAATT 0.863041 -233 TTTTTTAATAAAGATTAATTGCCAGCAACT 14 144 1 AAGATTAATT 0.947868 -157 ATTAATTATCAAAATTAATTGTTTTTAAAT 14 265 0 AAAATTAATT 0.566087 -36 TTAATAATCCAGGATTAATAA 14 290 1 AGGATTAATA 0.825147 -11 ATTTATAAATAAGCTTAGTTTGCTACAAGT 15 117 1 AAGCTTAGTT 0.795969 -60 TTTTAACACTGGGCTTAATTAAAGATTTTT 20 189 0 GGGCTTAATT 0.736951 -112 ********** Masking position 7 Map Score: 7.24164 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 106 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 TACTATTAAAAAATAAACAGATTTAATTGATT 2 24 0 AAAAAACAGT 0.966765 -174 CCTGAAACAAAAGTAACCAGCTTCTAAATCTA 3 142 0 AAGAACCAGT 0.879562 -92 TGAGAACCTGAAAAAAACAGGTTCTTTTTTTA 3 198 1 AAAAAACAGT 0.966765 -36 TTTTTTCACTGGATAAGCAGTTTTAATGGTTC 6 82 0 GGAAAGCAGT 0.839636 -219 ATTTATTTTTATAGAAACAGTTACTTTGAAGA 6 181 1 ATAAAACAGT 0.787054 -120 TTGTAAAATTAGACAACCAACTTGAAATTGAT 7 77 1 AGAAACCAAT 0.809822 -182 GAAAAATTCAAAATAAGCAAATTATAATTAGG 10 34 1 AAAAAGCAAT 0.865264 -42 TCAATTAAATAAAAAAACAGTGTAAGTGTACA 11 57 0 AAAAAACAGG 0.797846 -34 TTTTTTCACCGGATAAGCAGTTTTAATGGGTC 13 28 0 GGAAAGCAGT 0.839636 -273 CTCAAAAACAACCAGTTAAGCTTGTTA 13 284 0 AAAAACCAGT 0.964544 -17 GATAAAAAACAAAAAAGCAGCTGTTGTGCTGC 15 46 0 AAAAAGCAGT 0.964544 -131 TTTTATCTACCAAAAAACAGATTTTTAGCTCT 15 71 1 CAAAAACAGT 0.821044 -106 AATGACATTGAAAAAAACGGATTAAATAGTTA 20 41 1 AAAAAACGGT 0.797846 -260 TAGTTATCAAAGAGAACCAATTACATATGCAA 20 67 1 AGAAACCAAT 0.809822 -234 ACTTCTCAAAAAGAAAACAATTTAAATATTTC 20 113 1 AAGAAACAAT 0.648317 -188 *** ****** * Masking position 6 Map Score: 11.3196 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 164 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 GCTGATGTTCTTGATTATTTTATAAAAAAA 3 33 0 TTGATTATTT 0.894272 -201 CGCTACGCCATTGAATAGTTAAAAACCTGA 6 152 1 TTGAATAGTT 0.889762 -149 ACAAAGTCTTGTTATTAGTTGCA 7 4 0 GTTATTAGTT 0.809347 -255 AAGGGCAGGGGTTATTATTTGAGTGTTTTT 7 124 1 GTTATTATTT 0.796471 -135 AGTTAACTAATTAATTAGTTGCAAAAAGTT 9 15 0 TTAATTAGTT 0.796569 -24 AGTGTACACTGTCATTAGTTAATTCTAAAT 11 35 0 GTCATTAGTT 0.820874 -56 CGCTACGCCGTTGAATAGTTATGGGGATTT 13 98 1 TTGAATAGTT 0.889762 -203 TTAACTTGGTGTGATTATTTAAATCCCCAT 13 118 0 GTGATTATTT 0.922722 -183 AAGTAATAAAGTGAATATTTATTTTTATTA 14 181 1 GTGAATATTT 0.913069 -120 TATAAAAAAGTTGAATATTTAAAAACAATT 14 249 1 TTGAATATTT 0.881522 -52 TGACACTCAGGTTATTATTTAGTCTAGTTT 18 61 0 GTTATTATTT 0.796471 -60 AATAAAAATTGTCAATATTTCATTAAATAC 19 22 1 GTCAATATTT 0.787959 -43 AAAAAACGGATTAAATAGTTATCAAAGAGA 20 52 1 TTAAATAGTT 0.775001 -249 AGAAAACAATTTAAATATTTCATCCGCTAC 20 124 1 TTAAATATTT 0.760491 -177 ATCATTACTGTTAATTATTTGTGCTGAAAC 20 233 0 TTAATTATTT 0.783061 -68 ********** Masking position 4 Map Score: 15.9884 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 64 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 CTTTGTTGTTCCTTATTCAATGAATCATACAAATA 6 35 1 CTTTCAAGAT 0.987363 -266 GAAGCTTCATCTTTTTTCACTGGATAAGCAGTTTT 6 90 0 CTTTCACGAT 0.981336 -211 AATGGCGTAGCGTTGATCAAGGAATTGATCGCTAC 6 129 0 CTTTCAAGAT 0.987363 -172 TCTAAACTTTTTGCAACTAATTAATTAGTTA 9 7 1 CTTGCAATAT 0.8677 -32 ACACCAAAATCCGTAGTCAATTTATTAACTAACTA 12 50 1 CGTTCAATAT 0.8677 -40 GATTTTTGATCTTTTTTCACCGGATAAGCAGTTTT 13 36 0 CTTTCACGAT 0.981336 -265 AACGGCGTAGCGTTGATCAAGGAATTGATCTTGAC 13 75 0 CTTTCAAGAT 0.987363 -226 * ** **** * ** Masking position 9 Map Score: 3.13634 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 2 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 10 ATCAAAAGATAAAAAAATGTTTGATACTAC 1 99 0 AAAAAAATGT 0.512292 -60 TTCTTTTTACTAAAAATAATTAGCTAAAAT 1 129 1 TAAAAATAAT 0.56784 -30 TTGTTAAATAGAAACAAGGTTAAATTGTGT 2 59 0 GAAACAAGGT 0.525672 -139 TAATTTTTGATAAAAAATATCTTAATTTTT 2 123 0 TAAAAAATAT 0.75743 -75 AAATTAGCATAAAAAATTGTTATACTAATT 2 147 1 AAAAAATTGT 0.414893 -51 TAATTTTCAATAAAAAACGTTAATTAGTAT 2 168 0 TAAAAAACGT 0.624126 -30 TTATTTTATAAAAAAATGATACTAATAACG 3 19 0 AAAAAATGAT 0.626365 -215 CTTATCCAGTGAAAAAAGATGAAGCTTCCC 6 97 1 GAAAAAAGAT 0.796121 -204 TTCTTGTTAATAAACAAAGTCTTGTTATTA 7 17 0 TAAACAAAGT 0.355843 -242 CTAAAAAAGATAGTTATTAAC 11 2 1 TAAAAAAGAT 0.914793 -89 CTTATCCGGTGAAAAAAGATCAAAAATCAA 13 43 1 GAAAAAAGAT 0.796121 -258 AAAAATTGGGTAACAATGGTTAATAAATAA 13 166 0 TAACAATGGT 0.514519 -135 TAATCTTTATTAAAAAATATTTTTTAAGAT 14 131 0 TAAAAAATAT 0.75743 -170 TTAACTAATATAAAAAAGTTGAATATTTAA 14 241 1 TAAAAAAGTT 0.577014 -60 ATATTCCAAATAAAAAAGAGCAGCACAACA 15 27 1 TAAAAAAGAG 0.519114 -150 GAATTCTCTTTAGAAAAGATTTAATCTGTT 18 95 1 TAGAAAAGAT 0.519114 -26 GAACTAGCAATAAAAATTGTCAATATTTCA 19 14 1 TAAAAATTGT 0.754033 -51 CATATGCAATTAAAAATAGTTTTACTTCTC 20 90 1 TAAAAATAGT 0.656468 -211 AGCCCAGTGTTAAAAATGGTATATTCTATG 20 204 1 TAAAAATGGT 0.913348 -97 AATGGGGTTCTAAAAATGATAGCGAAATCA 20 270 1 TAAAAATGAT 0.878752 -31 ********** Masking position 6 Map Score: 8.74305 Number of sites scoring better than the average of aligned sites = 434 Number in coding regions = 381 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 11 AGTAAATCACAACTATAAAACTAATCCTTT 1 49 0 AACTATAAAA 0.64719 -110 AAAGCATGATTACAATAAAGCAGGATTTAT 3 113 0 TACAATAAAG 0.612895 -121 TTGAATAAGGAACAACAAAGGAAAAGGTTT 6 25 0 AACAACAAAG 0.73198 -276 TTTGTTTATTAACAAGAAAACATTTTGTTA 7 29 1 AACAAGAAAA 0.778266 -230 TTAAACCAAAAACACTCAAATAATAACCCC 7 131 0 AACACTCAAA 0.795441 -128 TTTTAGTTGATACACCAAAATCCGTAGTCA 12 39 1 TACACCAAAA 0.769934 -51 TAACAATTTGAACAATTAAATTGCAAAAAA 13 230 1 AACAATTAAA 0.683421 -71 GAATTTGTTTAAAACTAAAACAGACAGGGA 14 28 1 AAAACTAAAA 0.598709 -273 AAATACCCAAAACACCAAAACAAT 15 163 1 AACACCAAAA 0.919582 -14 TTAGCACTCAAACACTAAAAGTGCTAATTA 16 20 0 AACACTAAAA 0.957719 -68 GTGGTAATAATAAAAATATAAATTT 17 6 1 AATAATAAAA 0.551087 -48 CAAGAACTAGCAATAAAAATTGTCAATA 19 9 1 AGCAATAAAA 0.731095 -56 CAATGTCATTAACACTGAAATTTTTCTGAT 20 21 0 AACACTGAAA 0.795441 -280 TTTCATCCGCTACAATAAAATACATAAAAG 20 141 1 TACAATAAAA 0.845072 -160 ********** Masking position 8 Map Score: 3.20635 Number of sites scoring better than the average of aligned sites = 410 Number in coding regions = 374 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 12 CTCTATAAAAAGTAGTATCAAACATTTTTT 1 88 1 AGTAGTATCA 0.88093 -71 TTTATCAAAAATTAGCATAAAAAATTGTTA 2 139 1 ATTAGCATAA 0.766553 -59 AAAAACGTTAATTAGTATAACAATTTTTTA 2 156 0 ATTAGTATAA 0.914322 -42 AGTAATCGTTATTAGTATCATTTTTTTATA 3 13 1 ATTAGTATCA 0.960071 -221 ATTGTTGAAAATAAGTATCAAATTGAAAAG 4 22 1 ATAAGTATCA 0.833105 -38 TAGTTCCCGTATTTGTATGATTCATTGAAT 6 49 0 ATTTGTATGA 0.774112 -252 GGATTAATATATTAGTATGAGTGCTTAATT 6 231 0 ATTAGTATGA 0.94288 -70 ********** Masking position 7 Map Score: 1.27034 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 6 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 13 ********** No masking Map Score: 5.95678e-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: 5.95678e-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: 5.95678e-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