AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i057_bsub_mtub_300.orf -o057_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 aroI 275 shikimate kinase #2 tyrA 48 prephenate dehydrogenase #3 trpE 215 anthranilate synthase #4 aroB 61 3-dehydroquinate synthase #5 aroF 69 chorismate synthase #6 cheR 236 methyl-accepting chemotaxis proteins (MCPs) methyltransferase #7 ndk 115 nucleoside diphosphate kinase #8 gerCA 162 heptaprenyl diphosphate synthase component I #9 mtrB 21 tryptophan operon RNA-binding attenuation protein (TRAP) #10 mtrA 187 GTP cyclohydrolase I #11 hbs 300 non-specific DNA-binding protein HBsu #12 aroC 111 3-dehydroquinate dehydratase #13 sigX 203 RNA polymerase ECF-type sigma factor (sigma-X) #14 resD 80 two-component response regulator #15 resC 135 essential protein similar to cytochrome c biogenesis protein #16 resA 131 essential protein similar to cytochrome c biogenesis protein #17 ypuL 91 similar to hypothetical proteins #18 dacB 122 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5*) #19 ypuI 54 similar to hypothetical proteins from B. subtilis #20 ypuG 280 similar to hypothetical proteins #21 yqhS 86 similar to 3-dehydroquinate dehydratase #22 yqhR 226 yqhR #23 yqeG 300 similar to hypothetical proteins #24 aroA 235 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase #25 ytxJ 23 alternate gene name: csb40; similar to general stress protein #26 ytxH 27 alternate gene name: csb40; similar to general stress protein #27 ytxG 161 alternate gene name: csb40; similar to general stress protein #28 murC 249 UDP-N-acetyl muramate-alanine ligase #29 ytpS 159 ytpS #30 ytpP 234 similar to thioredoxin H1 #31 aroA 54 aroA Motif number 1 TCATACAGAAAAAGACCCTTCCATCGAAGA 1 34 1 AAAGACCCTT 0.687157 -242 CTTCGACGCAAAAAAGCGTTAAAACCTTCC 1 88 0 AAAAAGCGTT 0.871151 -188 AAAACAGAACAAAAACCGGCGGCGTTATAT 6 43 0 AAAAACCGGC 0.871257 -194 TTTCTTCACAGAAAAGCCCCTTTCTAAGGG 10 55 1 GAAAAGCCCC 0.874754 -133 CTTGAAATATGAAAAGCCCCTTAGAAAGGG 10 72 0 GAAAAGCCCC 0.874754 -116 TAACACATATAAAAAGCCATATCAAGCATT 11 90 0 AAAAAGCCAT 0.70958 -211 AGTTTTTCTTAAAAAGCCGTTTAATTGTCT 11 171 1 AAAAAGCCGT 0.965476 -130 AAAGAGCCCTTTAAGGCTCT 12 1 1 AAAGAGCCCT 0.834435 -111 AGCAACTAAAAAAGAGCCTTAAAGGGCTCT 12 13 0 AAAGAGCCTT 0.831817 -99 GTTCCATAAGAAACACCCGCTGACTGAGCG 13 40 1 AAACACCCGC 0.866711 -164 GCTATTAAAAAAACACCCGCTCAGTCAGCG 13 57 0 AAACACCCGC 0.866711 -147 AAATCTAAAAAAAACGCCGTTT 17 3 0 AAAACGCCGT 0.708776 -89 GAAGCGGGAGAAAAAGCCTTTGCTTCTGGT 20 103 0 AAAAAGCCTT 0.93939 -178 ATTGTACAGGAAACACCGCTAAACCTCTAG 22 62 1 AAACACCGCT 0.561872 -165 AAAAAAGCGTCCAGATATCAT 24 2 1 AAAAAGCGTC 0.894128 -234 TTTTTACAAAAAAAAGCGCCAGATGATATC 24 24 0 AAAAAGCGCC 0.895896 -212 TTTTTTTGTAAAAAACCCTTGAACATTGCC 24 40 1 AAAAACCCTT 0.873147 -196 TAAAAAGCAGTGATCTCACTG 27 2 1 AAAAAGCAGT 0.799928 -160 TCAGATAAATAAAAAGCAGTGAGATCACTG 27 18 0 AAAAAGCAGT 0.799928 -144 GAAAACGGGTAAACAGCAGTATATCCTGCA 27 127 1 AAACAGCAGT 0.626285 -35 CGCGGCGGCTGAAAAGCCTCCCTTAGCGGC 28 167 0 GAAAAGCCTC 0.872677 -83 CGAATCATGTGAAAAGCCGCTAAGCCCTTG 29 36 1 GAAAAGCCGC 0.92519 -124 GTGGTATACTAAAAACCGTCCCAGAAAACT 29 118 1 AAAAACCGTC 0.789499 -42 ********** Masking position 3 Map Score: 22.462 Number of sites scoring better than the average of aligned sites = 1589 Number in coding regions = 1260 Number in noncoding regions = 329 Number of orfs with sites within 600 bp upstream = 234 Fraction of orfs with sites within 600 bp upstream = 0.0375843 Motif number 2 TATGATAAATAGGAAGGGAGGAATGGCG 1 5 0 AGAGGAGGAT 0.465179 -271 GAAAAACAATAAAGGCGGAAGGTTTTAACGCTTT 1 72 1 AAGGGAAGGT 0.762165 -204 GAATGAGAAGATGGCATGAGAGGATAAAATACTA 3 168 0 AGGTGAGAGA 0.852882 -48 TCCTTGCCATAAGGAGTGAGAGCA 3 202 1 AGGTGAGAGA 0.852882 -14 GAAAATGTGGAGAATATGAGAAAACTGTCGAGGG 4 31 1 AAATGAGAAA 0.856427 -31 CGTTAATGCGATGAAGGGAGAAGAAGTC 5 52 1 AGAGGAGAAA 0.752423 -18 ATGCTCGCAAACAGCGGGAGGATACAGCCAATTC 8 38 1 AAGGGAGGAA 0.865638 -125 GGATGAAAAAAGGAAAAAAAGGAATATTC 11 6 1 AAAGGAAAAA 0.834777 -295 TGTTTGTCCAACAAAGTGAAGAATTTCTGTATGT 11 124 0 AAATGAAGAT 0.554478 -177 CTGTCTCAGAAAAAAATGAGAGCAAGTAAGAGAA 11 201 0 AAATGAGAGA 0.905994 -100 AAAACAAGGTAAAGATTGAAAGGATTTGAGACGA 12 88 1 AAGTGAAAGA 0.905994 -24 TGTCGTATGAATAGCTTGAAAAGTTACATTACAA 13 156 0 AAGTGAAAAT 0.715832 -48 AAATCGTGAGAAAGTTTGAGAACTGTGTCGCTTT 14 18 0 AAGTGAGAAT 0.775552 -63 TCACGATTTGATAAAATGAAAGTAACAGAAGGAA 14 43 1 AAATGAAAGA 0.875405 -38 AATGAAAGTAACAGAAGGAAAGCAGGGGGAAAAC 14 57 1 AAGGGAAAGA 0.918014 -24 ACTCTCCCTGAAAAAGGGAGAGTAAACG 18 5 0 AAAGGAGAGA 0.918014 -118 CATAGAAGGGATAAAAGGAAAAAAGAACGCCCGG 20 44 1 AAAGGAAAAA 0.834777 -237 TTCCTGTACAATAGAGTGAAAGGAAATGGTTAGC 22 40 0 AAGTGAAAGA 0.905994 -187 CTCTAGATTGACAGGCTGAAAAAATTGCCATAGC 22 86 1 AAGTGAAAAA 0.856427 -141 AGCTGCGAGTAAAATTTGAAAATAACGGGTATAA 22 139 0 AAATGAAAAA 0.813037 -88 TGAAAGAAAGAAAAAGGGAAGGGTGCGGGTT 23 280 1 AAAGGAAGGT 0.700259 -21 GCTATCCTACATGATGTGAGGGCAATGTTCAAGG 24 56 0 AGATGAGGGA 0.741214 -180 ATGTGCAGGGAAAGGATGAAAAAA 24 222 1 AAGTGAAAAA 0.856427 -14 AAGAACATAAACAACTGGAGGGATATGAA 30 216 1 AAAGGAGGGT 0.762165 -19 * ** ****** * Masking position 9 Map Score: 20.6745 Number of sites scoring better than the average of aligned sites = 870 Number in coding regions = 679 Number in noncoding regions = 191 Number of orfs with sites within 600 bp upstream = 199 Fraction of orfs with sites within 600 bp upstream = 0.0319627 Motif number 3 ATAACATATTTTTCAGCAAAAAG 5 2 0 TTCAGAAAAA 0.949402 -68 AATTGTATTGTTTCAATAAAAAAATCAGCTTT 6 159 0 TTCAAAAAAA 0.961909 -78 AATTTCTTAATATCTACAAAAA 7 1 0 TTCTAAAAAA 0.802831 -115 TTAAACGGCTTTTTAAGAAAAACTGCACTCTG 11 163 0 TTTAAAAAAA 0.630531 -138 TCTAAACCTGTCTCAGAAAAAAATGAGAGCAA 11 210 0 TTCAGAAAAA 0.95009 -91 TAATAGAAATTTTCAAAAAAAAGTTGTACGTG 12 50 1 TTCAAAAAAA 0.962828 -62 CACTGGCGGATCACGGTAAAAACGCTTTCTAA 16 23 1 TACGGAAAAA 0.761824 -109 AAAAATGAAATGTCAATAAAAAAGCTCACACT 22 180 0 TTCAAAAAAA 0.962837 -47 AGCAAAAAAATTTCGACAAAAATTGGGTTTCT 23 203 0 TTCGAAAAAA 0.954519 -98 TCAAAATGATTGTCGAAAAAAATCGAACTTGC 23 251 0 TTCGAAAAAA 0.955211 -50 CAAGGGTTTTTTACAAAAAAAAGCGCCAGATG 24 29 0 TACAAAAAAA 0.841143 -207 AAGATTAAGCTATCAGCAGAAACCAAGCCGCT 29 69 0 TTCAGAGAAA 0.749964 -91 AATGGACGAGTATCGATAAAAAACATGTAAGA 30 188 1 TTCGAAAAAA 0.95519 -47 * **** ***** Masking position 8 Map Score: 14.5003 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 180 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 4 GAAGGGTCTTTTTCTGTATGATAAATAGGA 1 25 0 TTTCTGTATG 0.892087 -251 TTGTACAACATTTCTGCAGGTATTTTAATA 1 118 0 TTTCTGCAGG 0.77474 -158 AAAAGAAAGACTTCTTTTGGGTAGAATAAA 3 122 0 CTTCTTTTGG 0.744159 -94 AAAAGAAGTCTTTCTTTTGGGTTTATTTGT 3 134 1 TTTCTTTTGG 0.94427 -82 AGCCAATTCTTTTTTTTATGCTATAATGAT 8 63 1 TTTTTTTATG 0.765495 -100 AAGTGAAGAATTTCTGTATGTAGAGTAACA 11 115 0 TTTCTGTATG 0.892087 -186 TCAGCGGGTGTTTCTTATGGAACAAGATTC 13 33 0 TTTCTTATGG 0.682828 -171 GAGCGGAAATTTTCTTTATGCGGCCTTTCT 15 41 1 TTTCTTTATG 0.936657 -95 TCAGGGAGAGTTTTTTTATGTTTGCTTCCA 18 28 1 TTTTTTTATG 0.765495 -95 AACCTGCCTATTTCTTTAGGATTGCTAACC 22 17 1 TTTCTTTAGG 0.970299 -210 TTGCTCAGTTTTTCTTTAGGCGCAAGTTCG 23 230 1 TTTCTTTAGG 0.970299 -71 ACATGATTCGTTTTTTTTGGCGGATTTATG 29 16 0 TTTTTTTTGG 0.789044 -144 ********** Masking position 5 Map Score: 9.50832 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 233 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 5 CGCCTTTATTGTTTTTCCAGCTGACTCTTCG 1 58 0 GTTTTTCCAC 0.436179 -218 CAGACCTCTGCCTTTCCCAACGATCTAAAAT 6 121 1 CCTTTCCCAC 0.974371 -116 GTATGTATAGGCTTTCACACTGCACACCGAA 7 75 0 GCTTTCACAT 0.836212 -41 GCTGGCTGTCCCCGCTGTTAAAAGC 8 5 1 GCTGTCCCCC 0.915759 -158 GCCTTTCACCTCCTCCCAAAAG 11 289 0 CCTTTCACCC 0.855434 -12 GTTTTCCCCCTGCTTTCCTTC 14 70 0 GTTTTCCCCT 0.754873 -11 GTATTTAATCGCTGTCCCAATCTTCGGCGGG 15 74 1 GCTGTCCCAT 0.891721 -62 TGCCCCCTTCCCCCTATTGCAGATC 16 117 0 CCCTTCCCCT 0.871159 -15 TGTATAATCCTTTTCCAGTATGATAAAAT 21 9 1 CCTTTTCCAT 0.817587 -78 CTAACCATTTCCTTTCACTCTATTGTACAGG 22 41 1 CCTTTCACTT 0.725474 -186 CCATAGCCTTGCTTTTCCTACATGCATTATA 22 113 1 GCTTTTCCTC 0.809503 -114 AACCCGCACCCTTCCCTTTTTCTTTCTTT 23 282 0 CCCTTCCCTT 0.809988 -19 TTTTTTCATCCTTTCCCTGCACATTCATTT 24 216 0 CCTTTCCCTC 0.957294 -20 CCTTTAATAAGCTTTCCCATCAGATAAATAA 27 36 0 GCTTTCCCAC 0.97743 -126 TGTAAGATTGGCTTTCCCATTATCATTATCA 30 104 0 GCTTTCCCAT 0.968432 -131 ********* * Masking position 5 Map Score: 12.595 Number of sites scoring better than the average of aligned sites = 473 Number in coding regions = 402 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 6 GCGTTATATGTTGCCGGCTCTGTTGCTTAT 6 22 0 TTGCCGGCTC 0.71353 -215 AGAACAAAAACCGGCGGCGTTATATGTTGC 6 38 0 CCGGCGGCGT 0.828395 -199 CACTTTGCTTTTAGCGGGGCATATGTGCTA 10 127 1 TTAGCGGGGC 0.85131 -61 AATGTATTCATTGGTGGAGGACATAGAAC 10 169 1 TTGGTGGAGG 0.465007 -19 ACCCGCTCAGTCAGCGGGTGTTTCTTATGG 13 43 0 TCAGCGGGTG 0.902712 -161 ACCCGCTGACTGAGCGGGTGTTTTTTTAAT 13 54 1 TGAGCGGGTG 0.680255 -150 GTCCCAATCTTCGGCGGGGCCATACGCGGG 15 87 1 TCGGCGGGGC 0.925316 -49 GCTCAGAGCACTGGCGGATCACGGTAAAAA 16 15 1 CTGGCGGATC 0.678904 -117 CGAGAGCTTTTTGGTGGCTTATACTATAGG 20 212 1 TTGGTGGCTT 0.745427 -69 CTCACACTTTTTGGCAGCTGCGAGTAAAAT 22 158 0 TTGGCAGCTG 0.712877 -69 AAAGCCTCCCTTAGCGGCGTATTTTATATG 28 155 0 TTAGCGGCGT 0.892926 -95 ATTTGCGACCGCGGCGGCTGAAAAGCCTCC 28 176 0 GCGGCGGCTG 0.848969 -74 TTCGTTTTTTTTGGCGGATTTATGGGAGT 29 10 0 TTGGCGGATT 0.879074 -150 AAACAAGGGCTTAGCGGCTTTTCACATGAT 29 39 0 TTAGCGGCTT 0.917616 -121 AAGCCCTTGTTTAGCGGCTTGGTTTCTGCT 29 57 1 TTAGCGGCTT 0.917616 -103 TCCTGCCGTGTCGGCGGGTGTCGTGGGTAC 31 28 0 TCGGCGGGTG 0.960704 -27 ********** Masking position 7 Map Score: 7.4588 Number of sites scoring better than the average of aligned sites = 1749 Number in coding regions = 1597 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 7 TACTTCGACGCAAAAAAGCGTTAAAACCTT 1 90 0 CAAAAAAGCG 0.927425 -186 AAAATGGCTACAACAAAGCGCACTATAAGC 1 165 1 CAACAAAGCG 0.888934 -111 CTTAGAAATACACAAGAGTGTGTATAAAGC 3 25 1 CACAAGAGTG 0.749088 -191 AGTAGTCTTACTTAAAAGCGTTAATGCGAT 5 34 1 CTTAAAAGCG 0.750068 -36 TAAAGGTTTACATTAAAGTGAATAAAGGGT 6 74 1 CATTAAAGTG 0.715012 -163 AATGTTTGTCCAACAAAGTGAAGAATTTCT 11 130 0 CAACAAAGTG 0.915964 -171 GACAAACATTCCTCAGAGTGCAGTTTTTCT 11 150 1 CCTCAGAGTG 0.747195 -151 ATTCATACGACAAAAAAGTGAACGGAGGGG 13 178 1 CAAAAAAGTG 0.94566 -26 GTTTCCTGTACAATAGAGTGAAAGGAAATG 22 46 0 CAATAGAGTG 0.780318 -181 CTCGCAGCTGCCAAAAAGTGTGAGCTTTTT 22 164 1 CCAAAAAGTG 0.925322 -63 GTTATCCACACCAAAAAGTGGATAACTTGT 23 94 1 CCAAAAAGTG 0.925322 -207 TATAATTTGTCTAAAGAGTGATGTAATAAG 23 136 1 CTAAAGAGTG 0.852645 -165 TACTTTATCACTTAAAAGCGTTTGGGTAAT 24 99 1 CTTAAAAGCG 0.750068 -137 ********** Masking position 5 Map Score: 9.85887 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 220 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 8 ATACACAAGAGTGTGTATAAAGCAATTAGA 3 32 1 GTGTGTATAA 0.958604 -184 AAGAAATAAAGTGTATGTAAGCTAGATGCA 10 31 0 GTGTATGTAA 0.778341 -157 CCACTTTTTGGTGTGGATAACAGAACGATT 23 85 0 GTGTGGATAA 0.957802 -216 TGTGAGTATCGTGTTTATAATTTGTCTAAA 23 121 1 GTGTTTATAA 0.863334 -180 AGAGTGGATAGTGTGTGTAAATTTATCCAC 23 164 1 GTGTGTGTAA 0.957802 -137 TCTTCACCAGGTGTGGATAAATTTACACAC 23 176 0 GTGTGGATAA 0.957802 -125 ACTTAAAAGCGTTTGGGTAATAAAGTAGAG 24 108 1 GTTTGGGTAA 0.835761 -128 ATAAAGTAGAGTTTTTATAAAATTTTTTGT 24 127 1 GTTTTTATAA 0.590983 -109 ********** Masking position 9 Map Score: 4.17918 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 17 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 9 TACATTAAAGTGAATAAAGGGTTGAATGGC 6 82 1 TGAATAAAGG 0.626903 -155 GGATGAAAAAAGGAAAAAAAGGA 11 4 1 TGAAAAAAGG 0.922729 -297 GGGAATAAAGATAAAAAGGGCAGGCCAAAC 15 114 1 ATAAAAAGGG 0.626065 -22 CATAGGAATTTGAAAAAGCTTGTTTGTTAA 17 35 1 TGAAAAAGCT 0.761515 -57 TTGTTAAGGTTGAAAAAAGTAAGATAATAC 17 58 1 TGAAAAAAGT 0.771134 -34 AAACTCTCCCTGAAAAAGGGAGAGTAAACG 18 11 0 TGAAAAAGGG 0.976917 -112 CTTATGATGATGAAAAAGCGCGATTCATTA 19 16 0 TGAAAAAGCG 0.91881 -39 GAGTGATACTTGAAAATGGTGAGATG 20 265 1 TGAAAATGGT 0.653075 -16 TTTGAAAGAAAGAAAAAGGGAAGGGTGCGG 23 278 1 AGAAAAAGGG 0.950406 -23 TTATGATTGAAGAAAACGGGTAAACAGCAG 27 116 1 AGAAAACGGG 0.817433 -46 ********** Masking position 6 Map Score: 3.12891 Number of sites scoring better than the average of aligned sites = 1147 Number in coding regions = 981 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 10 CCCTGTCAGGAAGCCCATGCTCTTGAAATAT 10 92 0 AACCCATGCT 0.770847 -96 TTAAAGCGTCAATCCCTTGCTCGTCAAGGAT 11 59 0 AACCCTTGCT 0.963603 -242 TTGAAACCCCTCCGTTCACTTTTTT 13 189 0 AACCCTCCGT 0.90859 -15 AAACATAAAAAAACTCTCCCTGAAAAAGGGA 18 20 0 AACTCTCCCT 0.937013 -103 GCGGGAGAAAAAGCCTTTGCTTCTGGTTTTC 20 99 0 AACCTTTGCT 0.675958 -182 TTTACATGAGAAACCCTCGCGAAAAGGAGAG 21 61 1 AACCCTCGCG 0.904604 -26 ACAATCTCTCCTTTTCGCGAGGG 21 74 0 AACTCTCCTT 0.807597 -13 GACTCAAGCTCTTCCTTCCCTGC 25 8 0 AACTCTTCCT 0.88664 -16 CGGCGGCTGAAAAGCCTCCCTTAGCGGCGTA 28 164 0 AAGCCTCCCT 0.875209 -86 AAAAGCCGCTAAGCCCTTGTTTAGCGGCTTG 29 47 1 AACCCTTGTT 0.881936 -113 AATAAAAATCCCTCCTTATGTATATCC 30 7 1 AACCCTCCTT 0.944275 -228 ** ******** Masking position 2 Map Score: 5.1116 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 173 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 11 GAGGTGATCAAATATCACCTCTTTAGTCT 2 10 1 AAATATCACC 0.946887 -39 AGATATTAAGAAATTTCTCCGCCCCGGATT 7 18 1 AAATTTCTCC 0.946887 -98 AAATATCACCCTTGTCCCCA 8 153 0 AAATATCACC 0.946887 -10 AACGCTTTCTAAATTTCACATAACCTTCAA 16 43 1 AAATTTCACA 0.837289 -89 TAGTGTGTGTAAATTTATCCACACCTGGTG 23 172 1 AAATTTATCC 0.7339 -129 ATCCATCTGTAAATTTCACCCTCATGTACA 30 34 1 AAATTTCACC 0.970814 -201 ********** Masking position 6 Map Score: 1.61778 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 51 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 12 TTGCCTGAATGACATTCATTGTACAACATTT 1 135 0 GACTTCATTG 0.880977 -141 TCCCCAAATTCACATTTATTTCTTAATCTAT 8 128 0 CACTTTATTT 0.707193 -35 TTCCTTCTGTTACTTTCATTTTATCAAATCG 14 46 0 TACTTCATTT 0.792156 -35 TATATCATTGCACGTTCATTTCACATTTCTT 16 78 0 CACTTCATTT 0.960993 -54 TTTCAAGTATCACTCTCATTGCCGGAAAAAC 20 249 0 CACCTCATTG 0.921897 -32 GATTTTTTTCGACAATCATTTTGAAAGAAAG 23 259 1 GACATCATTT 0.78884 -42 CCTTTCCCTGCACATTCATTTTTTATTTTGT 24 206 0 CACTTCATTT 0.960993 -30 CCCAGTATATGACGCTCATTTCAATTTGCGA 28 198 0 GACCTCATTT 0.936878 -52 CTGTAAATTTCACCCTCATGTACACGATGTT 30 40 1 CACCTCATGT 0.849444 -195 *** ******* Masking position 6 Map Score: 2.79683 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 115 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 13 TAATTCCATTCCTTAGGAGGATTTCGCCGA 1 254 1 CCTTAGGAGG 0.957455 -22 ATGAAAAGCCCCTTAGAAAGGGGCTTTTCT 10 64 0 CCTTAGAAAG 0.970538 -124 TCCTTTGAAAGCGACACAGTT 14 2 1 CCTTTGAAAG 0.894288 -79 TTTTAGTGTACCATAGAAGGGATAAAAGGA 20 33 1 CCATAGAAGG 0.936902 -248 CTCTAGTGCTTCTTAGAAAGGAAAACCAGA 20 79 1 TCTTAGAAAG 0.843352 -202 GTACCAGGCACCATAGGAAGC 31 2 0 CCATAGGAAG 0.939272 -53 ********** Masking position 4 Map Score: 1.05003 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 20 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 14 GTTTTCTCATATTCTCCACATTTTCTCTAA 4 26 0 ATTCTCCACA 0.938579 -36 TATTAAGAAATTTCTCCGCCCCGGATTGAT 7 21 1 TTTCTCCGCC 0.887169 -95 ATTCTCCACCCCATCATTAT 7 106 0 ATTCTCCACC 0.948595 -10 ATACACTTTATTTCTTCACAGAAAAGCCCC 10 45 1 TTTCTTCACA 0.939229 -143 ACATACAGAAATTCTTCACTTTGTTGGACA 11 124 1 ATTCTTCACT 0.745432 -177 TTTATTATCATTTCTTCACAGTTCAGTCTG 11 244 0 TTTCTTCACA 0.939229 -57 TGTGTGTAAATTTATCCACACCTGGTGAAG 23 175 1 TTTATCCACA 0.732442 -126 AAAAATTGGGTTTCTTCACCAGGTGTGGAT 23 188 0 TTTCTTCACC 0.949145 -113 ********** Masking position 5 Map Score: 4.03619 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 118 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 15 TAACGCTTTTAAGTAAGACTACTATAACATA 5 26 0 AAGTAAGATA 0.838119 -44 AAATGAGAGCAAGTAAGAGAAAGACAATTAA 11 191 0 AAGTAAGAAA 0.966545 -110 GATAAAATGAAAGTAACAGAAGGAAAGCAGG 14 52 1 AAGTAACAAA 0.807611 -29 AACCTTCAAAAAGTAAGAAATGTGAAATGAA 16 64 1 AAGTAAGAAT 0.819962 -68 AGGTTGAAAAAAGTAAGATAATACTTGAGGT 17 64 1 AAGTAAGAAA 0.966545 -28 GGTATAATGCATGTAGGAAAAGCAAGGCTAT 22 115 0 ATGTAGGAAA 0.779779 -112 ATCATTTTGAAAGAAAGAAAAAGGGAAGGGT 23 273 1 AAGAAAGAAA 0.819962 -28 ATTCTCCGTTATGTAAGAAAATCCTTTAATA 27 58 0 ATGTAAGAAA 0.9381 -104 GATAAAAAACATGTAAGAACATAAACAACTG 30 202 1 ATGTAAGACA 0.801006 -33 ******** ** Masking position 5 Map Score: 2.67619 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 41 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802