AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i293_mixed_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -x5 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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 metS 300 methionyl-tRNA synthetase #2 yabD 78 similar to hypothetical proteins #3 yabE 155 similar to hypothetical proteins #4 yabF 144 similar to hypothetical proteins #5 yabG 161 yabG #6 veg 210 veg #7 sspF 159 small acid-soluble spore protein (alpha/beta-type SASP) #8 yabH 147 similar to hypothetical proteins #9 purR 55 transcriptional regulator #10 spoVG 193 spoVG #11 gcaD 192 UDP-N-acetylglucosamine pyrophosphorylase #12 prs 22 phosphoribosyl pyrophosphate synthetase #13 ctc 84 general stress protein #14 spoVC 106 thermosensitive mutant blocks spore coat formation (stage V sporulation) #15 spoIIE 300 serine phosphatase #16 yabS 84 similar to hypothetical proteins #17 yabT 88 yabT #18 yacA 103 similar to cell-cycle protein #19 ftsH 97 cell-division protein and general stress protein (class III heat-shock) #20 yacB 194 similar to hypothetical proteins #21 yacC 85 similar to hypothetical proteins #22 yacD 46 similar to protein secretion PrsA homolog #23 cysK 75 cysteine synthetase A #24 pabB 166 para-aminobenzoate synthase (subunit A) #25 sigW 300 RNA polymerase ECF-type sigma factor (sigma-W) #26 ybbP 160 alternate gene name: ybbQ; similar to hypothetical proteins #27 yyaF 126 similar to hypothetical proteins #28 yyaE 300 similar to formate dehydrogenase Motif number 1 TAATCAAATGAAATAAAAAACTTTGGTTCGAA 1 54 0 AAATAAAAAT 0.885946 -247 TCTTTAATGAAAATAAAAAAAGTCTGTTCGTG 1 103 0 AAATAAAAAG 0.839409 -198 AGAATAATTAAAATTAAAAATCTTTAATGAAA 1 123 0 AAATAAAAAC 0.969213 -178 CCTAATCAGAATGTCAAAAAGCTCCCGCCCAA 1 269 0 ATGTAAAAAC 0.817768 -32 AAGTGAAAAACTCCTTTCTTGT 2 67 0 AAGTAAAAAT 0.700203 -12 GACGCTCGATATAAGAAAAAGTTTCATGAATA 4 90 1 ATAAAAAAAT 0.669147 -55 CCTCCAAGACAAAATAAAAACTTTTGTATATT 4 118 0 AAAAAAAAAT 0.810107 -27 TGTGGTGCGCAAAACAAAAAGCCCTT 5 5 0 AAAAAAAAAC 0.945325 -157 TCATTCAATGATAAGAAAAAACTTGGACTCAG 5 71 1 ATAAAAAAAC 0.891267 -91 TCATTATGTAAAATAAAAAACCCGCATAGCTC 6 32 0 AAATAAAAAC 0.969213 -179 AAAAAAGGGCAAAACAAAAAGCAGTAAACAAA 7 25 0 AAAAAAAAAC 0.945325 -135 TTTATATCCAAAATAAAAAAACCAGGGAACAG 8 32 0 AAATAAAAAC 0.969213 -116 GGCATAAGGTAAATAAAAAAGTGATCCCGGCT 10 32 0 AAATAAAAAT 0.885946 -162 TTGTCTAAAAATGAAAAAAATCGGCTTCTGCA 15 133 0 ATGAAAAAAC 0.711366 -168 CCAATCATTTACATAAAAAAACTGCCAGCGTC 20 41 0 ACATAAAAAC 0.821183 -154 CCCTTTTCTCAAATTAAAAACCCGCTAAAGAG 22 12 0 AAATAAAAAC 0.969213 -35 GATGCACGAAATATAAAAAAACTCCCGGCGAA 24 30 0 ATATAAAAAC 0.937204 -137 GATTTTTCCGAAAAGAAAAAAGACACCTTTTG 25 98 0 AAAAAAAAAG 0.741651 -203 GATATCGTAGAAATGAAAAAACCGCATCCATG 28 81 1 AAATAAAAAC 0.969213 -220 CTTACCTTCTATATGAAAAAGCATGAGTGTCG 28 267 0 ATATAAAAAC 0.937204 -34 **** ***** * Masking position 6 Map Score: 30.2928 Number of sites scoring better than the average of aligned sites = 578 Number in coding regions = 407 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 2 AAGCTCTTACAAAACCCGCTAGCGTTTTTT 3 12 0 AAAACCCGCT 0.970179 -144 CAGAGGGCGCAAAACCCTCTGAATACATAA 4 18 0 AAAACCCTCT 0.752005 -127 ACTCAGCGAAAAAAGGCGCTTTCTCAAGGC 5 97 1 AAAAGGCGCT 0.918653 -65 CAGTTGAAAACCTGCATAGGAGAGCT 6 7 1 AAAACCTGCA 0.764306 -204 TGTAAAATAAAAAACCCGCATAGCTCTCCT 6 28 0 AAAACCCGCA 0.96671 -183 TTATTTGACAAAAATGGGCTCGTGTTGTAC 6 167 1 AAAATGGGCT 0.833669 -44 TTGGAAACCAAAAAAGGGCAAAACAAAAAG 7 36 0 AAAAAGGGCA 0.893015 -124 AAATATTTTAAAAACGAGCAGGATTTCAGA 10 116 1 AAAACGAGCA 0.835957 -78 CCCGTCTTCATAAACGGGCTATAATTCTTC 14 60 0 TAAACGGGCT 0.81394 -47 AAAAATGAAAAAAATCGGCTTCTGCAAGAG 15 129 0 AAAATCGGCT 0.849036 -172 GGATGATTGTAAAAGCCGCAGCTGAGCCAA 20 69 0 AAAAGCCGCA 0.91877 -126 TTCTTAACCCTAAAAGGGCTGGAATTGATT 21 25 1 TAAAAGGGCT 0.585232 -61 TCTCAAATTAAAAACCCGCTAAAGAGC 22 8 0 AAAACCCGCT 0.970179 -39 TTAATTTGAGAAAAGGGGCTGAAAGCAGGT 22 27 1 AAAAGGGGCT 0.918653 -20 CAGCCCGCAAAAAAAGAGCAAAGCGGCTAA 26 17 0 AAAAAGAGCA 0.621737 -144 TCCTCTATATAAAACCGTCATTGTATGAAC 27 98 0 AAAACCGTCA 0.730214 -29 GTAGAAATGAAAAAACCGCATCCATGCGGA 28 87 1 AAAAACCGCA 0.903534 -214 ********** Masking position 4 Map Score: 17.1477 Number of sites scoring better than the average of aligned sites = 1333 Number in coding regions = 1127 Number in noncoding regions = 206 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 3 AACTTTGGTTCGAAAGTCTTGATTTAAAAG 1 38 0 CGAAAGTCTT 0.747955 -263 GACTTTCGAACCAAAGTTTTTTATTTCATT 1 50 1 CCAAAGTTTT 0.853792 -251 TGATAAACAAAAGGTGTTTCACGTGTA 2 8 1 CAAAAGGTGT 0.971034 -71 TGTCGAAACACAAAAGGTGTTCGACGAATT 2 40 0 CAAAAGGTGT 0.971034 -39 CATGAATATACAAAAGTTTTTATTTTGTCT 4 114 1 CAAAAGTTTT 0.938328 -31 AAGCAGTAAACAAAAGGTTCACTGCCCG 7 9 0 CAAAAGGTTC 0.832441 -151 GGACCGCCGGCAAAAGGCTTATGTCAGCCC 11 41 0 CAAAAGGCTT 0.964368 -152 CATTCTAGCACAAAAGACGTAACCGCGGGA 14 29 0 CAAAAGACGT 0.802628 -78 AGAAACTATTCAAAAGTGGTGATAGAGG 20 177 1 CAAAAGTGGT 0.82399 -18 CACCTTTGATCAAAAGGTGTCTTTTTTCTT 25 88 1 CAAAAGGTGT 0.971034 -213 AGCTTCGTTTCAAAAGGTTTCAATTTTTTT 25 241 0 CAAAAGGTTT 0.966599 -60 ATCATTCAGGCCAAAGTCTTTATCCGCCAA 28 54 0 CCAAAGTCTT 0.845232 -247 ********** Masking position 5 Map Score: 11.9705 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 116 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 4 GTCCTTTGGGCGGGAGCTTTTTGACATTCT 1 264 1 CGGGAGCTTT 0.949822 -37 ACATTCTGATTAGGAGGTTTCAAG 1 287 1 TAGGAGGTTT 0.921061 -14 TTCGACAAGAAAGGAGTTTTTCACTT 2 63 1 AAGGAGTTTT 0.796216 -16 TCCTAAATTCGGAGGTTTATCC 12 9 1 TCGGAGGTTT 0.840159 -14 GACGTAACCGCGGGAGGGTTACGCCTTAAG 14 14 0 CGGGAGGGTT 0.948829 -93 TTTATGAAGACGGGAGTTATGTGACTAAGG 14 76 1 CGGGAGTTAT 0.926279 -31 TATGTGACTAAGGGAGGATTCGCC 14 93 1 AGGGAGGATT 0.812878 -14 TCGTATTCTCCAGGAGGAATGAAT 16 71 1 CAGGAGGAAT 0.592388 -14 CAGCGTCAGCCGGCAGTTTTTTTAGAAAGA 20 18 0 CGGCAGTTTT 0.923311 -177 CGGCTGACGCTGGCAGTTTTTTTATGTAAA 20 36 1 TGGCAGTTTT 0.815614 -159 AGGAAGTGTATAGGAGGTTTAGTA 21 72 1 TAGGAGGTTT 0.921061 -14 CCCGGCGAACCGGGAGTTTTGGCTTTTT 24 9 0 CGGGAGTTTT 0.984005 -158 CCCGGTTCGCCGGGAGTTTTTTTATATTTC 24 25 1 CGGGAGTTTT 0.984005 -142 ********** Masking position 5 Map Score: 10.9779 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 157 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 5 ATCTATGATACCATCTTAGCCTTTAAGATCAAGAATAT 1 173 0 CCCTTCCTTA 0.967238 -128 AATGAAAGGTCCTTCTCTAGCCTATGTAGCGGCAGTCC 5 38 0 CCCTCGCCTA 0.9047 -124 AGCTTTCACCTACTTCTCCATCTAAACATAAGTATG 8 122 0 CCCTTCCATA 0.985479 -26 AAAAGTGATCCCGGCTCTCCCAGAATCACTTTTCTTA 10 10 0 CCCTCCCAGA 0.978746 -184 AGTAGTTCACCACCTTTTCCCTATATAAAAGCATTAG 10 167 0 CCCTTCCCTA 0.990845 -27 CCTCCAATATCCCTTTTATCCATAGAAAAATATATCCT 11 158 0 CCTTTCCATA 0.829625 -35 TCATATATTCCCATCTTCGCCAGAAGAAATTTGATTTA 16 21 0 CCCTTCCAGA 0.982404 -64 TACTAAACCTCCTATACACTTCCTACGCGGTTTCT 21 61 0 CCCTACACTA 0.802893 -25 TGGTTCGAATCCAGCTAGCCCAGTCACAGACACCTTTG 25 58 1 CCCTACCAGA 0.966982 -243 TCACGAATTACCATCTACACCCTGCCAAAAATTTGATA 25 191 1 CCCTACCCTA 0.98269 -110 AATGTGCCAGCCCTCTCAGCCCGCAAAAAAAGAGCAAA 26 25 0 CCCTCCCCGA 0.986566 -136 CGCCGTCTTCTCCTTACCTTCTATATGAAA 28 281 0 CCCTTCCTTT 0.773733 -20 ** *** **** * Masking position 6 Map Score: 10.6672 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 157 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 6 AGACTTTTTTTATTTTCATTAAAGATTTTTAA 1 110 1 TTTTTATTAA 0.487714 -191 TCAATAAAATTATTTTGACAAAATTCTATGAT 6 102 0 TTTTTACAAA 0.95225 -109 AATTTAAATTTTATTTGACAAAAATGGGCTCG 6 157 1 TATTTACAAA 0.88822 -54 AAGTTCCATCTGATTTAACAAAAGATAAAACA 7 78 1 TATTTACAAA 0.88822 -82 AACTATATCCTATTTTTTCAAAAAATATTTTA 10 94 1 TTTTTTCAAA 0.895884 -100 AATTCCACGATTTTTTCTGAAATCCTGCTCGT 10 129 0 TTTTTTGAAA 0.852847 -65 TTTTTAATTCTGATTTTTCAAACTTAGTTGCA 11 72 1 TATTTTCAAA 0.774409 -121 TTCCGGAAATTCTTTTCATAAACGAATATCAA 15 167 1 TTTTTATAAA 0.814934 -134 ATTGTTACCTTCTTTTGACAAAATCCTATCTG 15 227 1 TTTTTACAAA 0.95225 -74 CAGCCGGCAGTTTTTTTAGAAAGAAAGCGAA 20 10 0 TTTTTAGAAA 0.930613 -185 CGCTGGCAGTTTTTTTATGTAAATGATTGGCT 20 43 1 TTTTTTGTAA 0.556125 -152 CTGGTATCGATTTGTTTACAAATGAGCCGCTG 20 103 1 TTGTTACAAA 0.667156 -92 TCTCTACTTTACTTTTTACAAACATTCTACAA 20 148 0 ATTTTACAAA 0.601535 -47 GGGCTGGAATTGATTTATGAAAGAAACCGCGT 21 40 1 TATTTTGAAA 0.698085 -46 AGCGGGTTTTTAATTTGAGAAAAGGGGCTGAA 22 18 1 TATTTAGAAA 0.842774 -29 AGAAATTCACTTTTTTCACTAACAACATTGCT 24 100 1 TTTTTACTAA 0.811519 -67 GTGTCTTTTTTCTTTTCGGAAAAATCATTCCA 25 104 1 TTTTTGGAAA 0.679404 -197 AAGGTTTCAATTTTTTTATAAAATAAGTTTAT 25 226 0 TTTTTATAAA 0.814834 -75 * **** ***** Masking position 6 Map Score: 13.4579 Number of sites scoring better than the average of aligned sites = 710 Number in coding regions = 503 Number in noncoding regions = 207 Number of orfs with sites within 600 bp upstream = 212 Fraction of orfs with sites within 600 bp upstream = 0.0340508 Motif number 7 TATCCTATGAGGAGAAGAAAGCATGTAGAAC 3 68 0 GGAGAGAAAG 0.944491 -88 AGATGGAGAAGTAGGTGAAAGCT 8 135 1 GTAGTGAAAG 0.914021 -13 ATAACAGGTGGGAGATGAGAGGA 15 288 1 GGAGTGAGAG 0.982191 -13 TTTGCTTGGAGGGGTTGAAAGTGTTAGGATA 18 42 1 GGGGTGAAAG 0.989997 -62 TTTGAGAAAAGGGGCTGAAAGCAGGT 22 31 1 GGGGTGAAAG 0.989997 -16 TCTTTTTTTGCGGGCTGAGAGGGCTGGCACA 26 30 1 CGGGTGAGAG 0.927554 -131 TTTATATAGAGGAGATGAAAGA 27 115 1 GGAGTGAAAG 0.987946 -12 **** ****** Masking position 8 Map Score: 8.06727 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 28 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 AGTAGTTCACCACCTTTTCCCTATATAAA 10 175 0 TCCACCTTTC 0.846219 -19 ATTCAGCACCATCCTCTTGTCGTTTTAGTTG 13 64 0 CCCCTCTTGC 0.782408 -21 GGGCGGTGTCTTAACCGCTTGACCAACGGGCCA 15 39 0 TTCCGCTTGC 0.982647 -262 GATTCATATATTCCCATCTTCGCCAGAAGAAAT 16 29 0 TTCATCTTCC 0.658252 -56 AATTCCATTGGCCCCTTTACCAAGCTGTTT 17 69 0 TTCCCCTTTC 0.956036 -20 ACCTGCTTTCAGCCCCTTTTCTCAAATTAAA 22 26 0 TCCCCCTTTC 0.923994 -21 AGTCCGTTGCCTTACCGCTTGGCTATAGCC 25 8 0 CTCCGCTTGC 0.951515 -293 AGCGCGTTAGCCGCTTTGCTCTTTTTTTG 26 7 1 TTCCGCTTTC 0.97685 -154 CAAAAAAGCATTTTCAGCTTGCCAATCCCTTTG 27 12 0 TTCAGCTTGC 0.962451 -115 AAATGCTTTTTTGTCAGCTTGTCTTTTCCAGTG 27 32 1 TTCAGCTTGC 0.962451 -95 GCCAAGACCCTTCACCTCTTTTCCTAAACTGCT 28 26 0 TTCCTCTTTC 0.932566 -275 TGCGTATAATTTTCCAGCTGTTCGCTCCGCATG 28 109 0 TTCAGCTGTC 0.766293 -192 ** ******* * Masking position 9 Map Score: 9.66426 Number of sites scoring better than the average of aligned sites = 417 Number in coding regions = 370 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 9 GTGTAACAATTCGTCGAACACCTTTTGTGT 2 33 1 TCGTCGAACA 0.762703 -46 TATTTCCTCCAAGACAAAATAAAA 4 131 0 TCCTCCAAGA 0.979806 -14 GTGATCCCGGCTCTCCCAGAATCACTTTTC 10 14 0 CTCTCCCAGA 0.701228 -180 AAGGCAGAAACCGTCGAAGATTTCTTTGGT 15 197 1 CCGTCGAAGA 0.893405 -104 CACTTTCAACCCCTCCAAGCAAAGAAGAAG 18 35 0 CCCTCCAAGC 0.88724 -69 TCCTTACCTCCTCCCACAGTAAGCACAA 19 80 0 TCCTCCCACA 0.909814 -18 AGAATAACATTCGTCGCAGACATGGCATAT 24 64 0 TCGTCGCAGA 0.879654 -103 AGTGAATTTCTCTTCCAAGAATAACATTCG 24 81 0 TCTTCCAAGA 0.82875 -86 TTCCTCGTCCTCCAAGATTTCAGTCAT 26 144 0 TCCTCCAAGA 0.979806 -17 AAAGTCTTTATCCGCCAAGACCCTTCACCT 28 42 0 TCCGCCAAGA 0.915908 -259 ********** Masking position 8 Map Score: 5.15549 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 187 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 10 GTAAACAAAAGGTTCACTGCCCG 7 4 0 GGTTCACTGC 0.769023 -156 GGGAACAGCACGTCCCCCGGGTCACATCC 8 10 0 CGTCCCCCGG 0.942219 -138 AATTAAAAAAGGACCGCCGGCAAAAGGCTT 11 51 0 GGACCGCCGG 0.922689 -142 GATCCCCTCCGCCGCTACCATATTT 15 6 1 CCTCCGCCGC 0.962205 -295 AAACTGCCAGCGTCAGCCGGCAGTTTTTTT 20 25 0 CGTCAGCCGG 0.959893 -170 TAAATGATTGGCTCAGCTGCGGCTTTTACA 20 62 1 GCTCAGCTGC 0.669751 -133 CAAAACTCCCGGTTCGCCGGGAGTTTTTTT 24 18 1 GGTTCGCCGG 0.981546 -149 CTAACCTCTGCCTTCACCGGTCTGTATGTA 25 275 0 CCTTCACCGG 0.885508 -26 AGCGCGTTAGCCGCTTTGCTCTTT 26 5 1 CGTTAGCCGC 0.910384 -156 ATTATAAGGAGGTTCACTGGAAAAGACAAG 27 49 0 GGTTCACTGG 0.831043 -78 ********** Masking position 7 Map Score: 4.17691 Number of sites scoring better than the average of aligned sites = 622 Number in coding regions = 579 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 11 TTATATACGACAAAATTCGACACGAACAGA 1 83 1 CAAAATTCGA 0.909184 -218 AGCTCCCGCCCAAAGGACGAGAGCGGCGAT 1 252 0 CAAAGGACGA 0.851159 -49 ATTATTTTGACAAAATTCTATGATTCCTCA 6 96 0 CAAAATTCTA 0.633783 -115 AACTCACCCCCAAAATCCGAATATTTTAAG 9 35 0 CAAAATCCGA 0.96735 -21 CATTCTAGCACAAAAGACGTAACCGCGGGA 14 29 0 CAAAAGACGT 0.857592 -78 GTTTCTCTTGCAGAAGCCGATTTTTTTCAT 15 125 1 CAGAAGCCGA 0.814792 -176 CTTCTTTTGACAAAATCCTATCTGTGCTTT 15 235 1 CAAAATCCTA 0.836648 -66 ATGACGGAGTCAAAGTCCGTTGCCTTACCG 25 24 0 CAAAGTCCGT 0.852256 -277 ACGTAAAACACAAAATACGAAATGACTGAA 26 123 1 CAAAATACGA 0.949184 -38 GCTCTAGGTTCAAAATACGTTCATACAATG 27 80 1 CAAAATACGT 0.894269 -47 ********** Masking position 4 Map Score: 5.82737 Number of sites scoring better than the average of aligned sites = 284 Number in coding regions = 256 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 12 GAAATACACTGAGAAACGGAAGAAAGACTT 3 110 0 GAGAAACGGA 0.799435 -46 AAAGAGCCTTGAGAAAGCGCCTTTTTTCGC 5 102 0 GAGAAAGCGC 0.96522 -60 CTCATCATGAAAGAAAGAGCCTTGAGAAAG 5 115 0 AAGAAAGAGC 0.813576 -47 ATTGGAAACCAAAAAAGGGCAAAACAAAAA 7 37 0 AAAAAAGGGC 0.700954 -123 TCAAGCGGTTAAGACACCGCCCTTTCACGG 15 50 1 AAGACACCGC 0.906865 -251 GCTTCTGCAAGAGAAACCGATTTGTTAGGA 15 112 0 GAGAAACCGA 0.918475 -189 TTTTTTTAGAAAGAAAGCGAA 20 2 0 AAGAAAGCGA 0.916853 -193 TGATTTATGAAAGAAACCGCGTAGGAAGTG 21 50 1 AAGAAACCGC 0.976567 -36 CGTAGAAATGAAAAAACCGCATCCATGCGG 28 86 1 AAAAAACCGC 0.89138 -215 ********** Masking position 6 Map Score: 4.87312 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 383 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 13 TATCCTACTAAAAATCCTTTTAAATCAAGACTT 1 22 1 AAAATCTTAA 0.911546 -279 CGTTGTCAATAAAATTATTTTGACAAAATTCTA 6 106 0 AAAATTTTGA 0.663952 -105 AACTTTCGTTAAAATTATTGGAAACCAAAAAAG 7 50 0 AAAATTTTAA 0.926072 -110 TATTTTTTCAAAAAATATTTTAAAAACGAGCAG 10 104 1 AAAAATTTAA 0.888944 -90 CACTCAATAGAAAATTCTTGCACTTCATGAAGT 11 102 1 AAAATTTTAC 0.798288 -91 TTAGGATATGAATATCTTTAAAATACCTGCTCA 18 65 1 AATATCTTAA 0.523051 -39 AGTACCATAGAAAATCATTCCAATACAAACAAT 19 36 0 AAAATCTTAA 0.911546 -62 TTGACAAAAAATTTTGAAATTGATAGATT 23 7 1 AAAAATTTAA 0.888944 -69 TCTTTTCGGAAAAATCATTCCAACTTCTAACTG 25 114 1 AAAATCTTAA 0.911546 -187 ACATATTTTTAAAATTATTATACAGACTGAACA 25 145 0 AAAATTTTAC 0.798288 -156 TAATAATTTTAAAAATATGTTAAGGTAGTTTAT 25 158 1 AAAAATTGAA 0.716621 -143 ACACCCTGCCAAAAATTTGATAAACTTATTTTA 25 207 1 AAAAATTGAA 0.716621 -94 CTTATTTTATAAAAAAATTGAAACCTTTTGAAA 25 231 1 AAAAAATTAA 0.557881 -70 ****** ** ** Masking position 4 Map Score: 2.80851 Number of sites scoring better than the average of aligned sites = 282 Number in coding regions = 210 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 14 TTCAGGGCGTATGTATATATTCTTGATCTTAAA 1 157 1 ATGTATATCT 0.897353 -144 CAAATCATATATGAATATTATTTATATTTATCC 1 214 0 ATGTATTTTT 0.944185 -87 CCTTATCGTTATGGGTATTGTTTGTAATAGGAC 13 32 1 ATGTATTTTT 0.944185 -53 TGCAGAGCCTATGCTTCTTCTTTGCTTGGAGGG 18 22 1 ATGTCTTTTT 0.838844 -82 TGCTTCCGAGATGGTTATTGTTTGTATTGGAAT 19 20 1 ATGTATTTTT 0.944185 -78 TATTGGTATTATGTATATAATCTATCAATTTCA 23 25 0 ATGTATATCT 0.897353 -51 ATCCATTCCCATGCGTATAATTTTCCAGCTGTT 28 120 0 ATGTATATTT 0.928528 -181 *** **** *** Masking position 1 Map Score: 0.676419 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 45 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 15 GAAAAAATCGTGGAATTGATACACTAATGC 10 144 1 TGGAATTGAT 0.954361 -50 TTATCGTTATGGGTATTGTTTGTAATAGGA 13 34 1 GGGTATTGTT 0.799279 -51 AAGATTTCTTTGGTATTGTTACCTTCTTTT 15 213 1 TGGTATTGTT 0.912091 -88 CAAAGGCAAGTGGAATGGAAACACTTATAC 17 32 1 TGGAATGGAA 0.848971 -57 TTGTTTGTATTGGAATGATTTTCTATGGTA 19 37 1 TGGAATGATT 0.746009 -61 CATCCAATTCTGGTATCGATTTGTTTACAA 20 94 1 TGGTATCGAT 0.791394 -101 TGATCGTGTATGGTATTGTAGAATGTTTGT 20 133 1 TGGTATTGTA 0.720228 -62 CTAAAAGGGCTGGAATTGATTTATGAAAGA 21 34 1 TGGAATTGAT 0.954361 -52 CAAAAAATTTTGAAATTGATAGATTATATA 23 15 1 TGAAATTGAT 0.622308 -61 AGTTAGAAGTTGGAATGATTTTTCCGAAAA 25 116 0 TGGAATGATT 0.746009 -185 TTATACGCATGGGAATGGATATTCGAATTA 28 133 1 GGGAATGGAT 0.896855 -168 ********** Masking position 5 Map Score: 2.93187 Number of sites scoring better than the average of aligned sites = 394 Number in coding regions = 348 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775