AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00272_ecoli_reg_300.orf -o00272_ecoli_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 cysS 173 cysteine tRNA synthetase #2 aspC 184 aspartate aminotransferase #3 ompF 300 outer membrane protein 1a (Ia;b;F) #4 pabB 73 p-aminobenzoate synthetase, component I #5 sdaA 183 L-serine deaminase #6 cysZ 229 required for sulfate transport #7 cysK 184 cysteine synthase A, O-acetylserine sulfhydrolase A #8 yfeK 104 orf, hypothetical protein #9 b2420 32 orf, hypothetical protein #10 cysM 23 cysteine synthase B, O-acetylserine sulfhydrolase B #11 BIME116 74 BIME #12 cysW 300 sulfate transport system permease W protein #13 cysH 21 3'-phosphoadenosine 5'-phosphosulfate reductase #14 cysJ 300 sulfite reductase (NADPH), flavoprotein beta subunit #15 sdaC 300 probable serine transporter #16 sdaB 57 L-serine dehydratase (deaminase), L-SD2 #17 metC 103 cystathionine beta-lyase (beta-cystathionase) #18 yhaP 119 putative L-serine dehydratase #19 yhaQ 65 putative L-serine dehydratase #20 tdcE 33 probable formate acetyltransferase 3 #21 tdcC 21 anaerobically inducible L-threonine, L-serine permease #22 tdcB 98 threonine dehydratase, catabolic #23 tdcA 188 transcriptional activator of tdc operon #24 cysE 79 serine acetyltransferase #25 secB 62 protein export; molecular chaperone; may bind to signel sequence #26 grxC 141 glutaredoxin 3 #27 yibN 244 orf, hypothetical protein #28 metB 276 cystathionine gamma-synthase Motif number 1 GGACCAAAGTCCTGTTTTTTCGGCATTTAA 2 26 0 CCTGTTTTTT 0.97027 -159 GGACTTTGGTCCTGTTTTTTTTATACCTTC 2 44 1 CCTGTTTTTT 0.97027 -141 GAAAACGCAGGCTGTTTTTGCAAGACGTGA 2 84 0 GCTGTTTTTG 0.974273 -101 TAGTTAAATCGCGGTTTTTGATTAGTTTAA 5 64 1 GCGGTTTTTG 0.919268 -120 CGTGCTTTTTGCTGTTTTTTCGAACATATC 6 132 1 GCTGTTTTTT 0.975453 -98 CGAAACTTTACCTGATTCTGGCAGTCAAAT 8 53 1 CCTGATTCTG 0.662773 -52 ATTACCTTATCCTTGTTTTGTGATAGCCGA 8 82 0 CCTTGTTTTG 0.486287 -23 GTACTCTACGGCGGTTTTATCG 14 3 0 GCGGTTTTAT 0.75947 -298 TACCGGAAAGGCTGTTTTTTCGCATTATCT 14 30 1 GCTGTTTTTT 0.975453 -271 GCGCAAAATCGCTGATTTATCTTAATGATT 14 74 1 GCTGATTTAT 0.772751 -227 AATCGACTAACCTGTTTTAGCAATAGTCTT 14 154 0 CCTGTTTTAG 0.891525 -147 AGTAAGCAAAGCTGTTTCTGCGCCCTGTCA 14 266 0 GCTGTTTCTG 0.880814 -35 GTCGGGATTCCTGTTTTTATACGTCTGGA 17 85 0 CCTGTTTTTA 0.77644 -19 TCTGTCGGCGGCGGGTTTATTGTCGAAGAA 18 25 1 GCGGGTTTAT 0.552513 -95 CAGCATAAACCCTGATTTTTGTCAAAAAAA 23 11 0 CCTGATTTTT 0.913556 -178 CAGGGTTTATGCTGATTTTTATACTTTAAC 23 27 1 GCTGATTTTT 0.927892 -162 AAATTAGCTCCTGTTTTTTTACCCTGAAA 26 123 0 CCTGTTTTTT 0.97027 -19 CCAGATTTACGCTTTTTTTTCGTCGCGCCC 27 120 1 GCTTTTTTTT 0.755683 -125 TAACGCGCTGGCTGTATTTGCCGCACCGCG 27 169 1 GCTGTATTTG 0.719819 -76 ATACTCCTTTCCTGGTTTTTTTAATCACTA 27 204 1 CCTGGTTTTT 0.927337 -41 ********** Masking position 7 Map Score: 27.5507 Number of sites scoring better than the average of aligned sites = 790 Number in coding regions = 633 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 2 GAAGGGAAGTCCGCTATCAGGGTAACGGGAGATTTACA 2 134 0 CCGCGGAACG 0.927172 -51 CTGACTCTACTGGCTATGTGCCGGGTAGCATGAAATAA 4 41 0 TGGCGCGGTG 0.810575 -33 AGAGGGAACGCGGCGACTGGCTTAACTATTCACATGAA 5 94 0 CGGCGCAACA 0.977641 -90 CGTATTTTACCGGGTAATTGCGCAATGGACAGTTAGGA 6 160 0 CGGGGCAATG 0.971283 -70 GTCAGCCAGATGGCGTGCAGCATGTCCGGATCGGCCAG 12 53 0 TGGCGCGTCG 0.823188 -248 TTTACCGGTACGGCAATCAGCGCGATCATCACCGTCAG 12 86 0 CGGCGCGATA 0.972935 -215 ACCTGGTGTTCGGCATTCTGCTGGCCTGGCTGGTGACG 12 123 1 CGGCGCGCCG 0.97743 -178 CGGCAACCACCGGCGATACGGCAAACGGAATGTCCAGT 12 199 0 CGGCGGAACG 0.949951 -102 ACGGCCCGCTCGGCGGTTGGCTCGACGAGCATAACCTG 12 267 1 CGGCGCGACA 0.983041 -34 AATCTGTCTATCGGCGATGGCTTAATCATTTACCGCCG 15 196 0 TCGGGCAATA 0.661438 -105 CAGTTCAGCCCGGGAAGGTGCCTGACCGTAAAAATGAA 15 233 0 CGGGGCGACG 0.986248 -68 CGGGCTGAACTGGCTAAAAGCTGAATTATTTGCATTCC 15 259 1 TGGCGCAATA 0.888272 -42 AATAAACCCGCCGCCGACAGAGTAATAGGTTTTAC 18 8 0 CCGCGAAATG 0.743722 -112 AAGAACACTTCGGCCTGTCGCACGATGTCGAAACGTCC 18 53 1 CGGCGCGATT 0.881833 -67 GTAACCGTAACCGACACCTGCAAGACAGACAGGTGGAT 22 38 0 CCGAGCGACG 0.882568 -61 CCGCTATGACCCGGCCCGCGCAGAACGGGCCGGTCATT 24 30 1 CCGGGCAACG 0.761531 -50 TAACAATAAGTCGCTGGGGGCCTAATTGCAGCTAACGG 26 38 0 TCGCGCAATG 0.947964 -104 TTCATGTTGCAGGGCGGCAGCAAAATGGAGTGTCCCCA 26 84 0 AGGGGCAATG 0.673085 -58 AAATATACGACCGCTCGCGGCAAGCCGATGCCAGATTT 27 90 1 CCGCGCGCCA 0.893727 -155 TTTTTTTTCGTCGCGCCCCGCAAAATTGCATTCCAGTT 27 132 1 TCGCGCAATG 0.947964 -113 **** ** *** * Masking position 10 Map Score: 20.6891 Number of sites scoring better than the average of aligned sites = 2797 Number in coding regions = 2667 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 3 GAGTAAATGTTTGCCGTGGTGGCAAGGTGTTA 6 28 0 TTGCCGGTGG 0.90815 -202 TTACAGAATCTGGCCGATCCGGACATGCTGCA 12 44 1 TGGCCGCCGG 0.968187 -257 ATCGCGCTGATTGCCGTACCGGTAAACCTGGT 12 98 1 TTGCCGCCGG 0.990217 -203 TCAGCAGTAACTGGCGTCCAGGGAAGTTAAAG 12 163 0 CTGGCGCAGG 0.84377 -138 GACATTCCGTTTGCCGTATCGCCGGTGGTTGC 12 203 1 TTGCCGTCGC 0.826627 -98 TCGCCGGTGGTTGCCGGTCTGGTGTATTTGCT 12 221 1 TTGCCGCTGG 0.972859 -80 TTCTACGGCTCTAACGGCCCGCTCGGCGGTTG 12 254 1 CTAACGCCGC 0.884601 -47 CATCTGACTTCTTCCGGGGCGCGCAA 15 5 0 CTTCCGGCGC 0.819895 -296 AGATTTCATTTTTACGGTCAGGCACCTTCCCG 15 229 1 TTTACGCAGG 0.777938 -72 AACGACCTTACGACCGTCCCGCTCACGAGGCT 19 11 0 CGACCGCCGC 0.879006 -55 ACCCTCGGATTGCCGTTCAGTGAAGTGGAGC 19 45 0 TTGCCGCAGT 0.903873 -21 GATGAGATAATGACCGGCCCGTTCTGCGCGGG 24 44 0 TGACCGCCGT 0.718294 -36 CTAATTGCAGCTAACGGCCTGCATCATGAAAG 26 23 0 CTAACGCTGC 0.730797 -119 CTCCATTTTGCTGCCGCCCTGCAACATGAAAT 26 92 1 CTGCCGCTGC 0.957528 -50 GGAATGCAATTTTGCGGGGCGCGACGAAAAAA 27 134 0 TTTGCGGCGC 0.536783 -111 TGCATTCCAGTTAACGCGCTGGCTGTATTTGC 27 158 1 TTAACGCTGG 0.811891 -87 CTGGCTGTATTTGCCGCACCGCGCAGGTATAC 27 176 1 TTGCCGCCGC 0.989035 -69 TCTCAATTTATTGACGAAGAGGATTAAGTATC 28 13 0 TTGACGGAGG 0.788478 -264 ACTATGCGGGTTTACGGTCAGTACCCACATCA 28 59 0 TTTACGCAGT 0.436096 -218 CCCGCATAGTTTACCGTACAGGCGTTACCGTG 28 81 1 TTACCGCAGG 0.941746 -196 ****** **** Masking position 6 Map Score: 19.5253 Number of sites scoring better than the average of aligned sites = 3270 Number in coding regions = 3161 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 4 AATCAAACGGAACAGGATGCAAAA 1 3 0 AACAGGATAA 0.896283 -171 GTATAAAAAAAACAGGACCAAAGTCCTGTTTT 2 38 0 AACAGGACAA 0.927578 -147 CCATTATGGTTACAGAAGGGAAGTCCGCTATC 2 154 0 TACAGAAGAA 0.941973 -31 CCAACAATTTAGCAGGAGTTAACA 4 3 0 AGCAGGAGAA 0.946511 -71 CATATCTATATACAGAAGGGAAATAATGACAT 7 84 0 TACAGAAGAA 0.941973 -101 GGAAGGCATTTACAGGAGGTAAC 9 20 1 TACAGGAGAA 0.976487 -13 GCGCCCATAAAACAGAAGAGAAGGTAAGGTTA 14 234 0 AACAGAAGAA 0.963021 -67 AGGGTAAAAAAACAGGAGCTAATTT 26 127 1 AACAGGAGAA 0.985212 -15 ******** ** Masking position 7 Map Score: 6.26627 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 48 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 5 TGCGCAATTACCCGGTAAAATACGCAGAATT 6 174 1 CCCGGTAAAT 0.89028 -56 TTGACCAATCCCAGGAAAATTCTGCGTATTT 6 191 0 CCAGGAAAAT 0.970029 -39 TAACTGGCGTCCAGGGAAGTTAAAGCGCGTC 12 157 0 CCAGGGAAGT 0.984125 -144 GCCAGTTCAGCCCGGGAAGGTGCCTGACCGT 15 242 0 CCCGGGAAGT 0.980819 -59 TTGCATTCCTCCAGGAGAAATAG 15 288 1 CCAGGAGAAT 0.883203 -13 CCCCAGGGAACCTTTGTTACCGC 24 3 1 CCAGGGAACT 0.977043 -77 TTCGTCGCGCCCCGCAAAATTGCATTCCAGT 27 138 1 CCCGCAAAAT 0.795036 -107 ATTAAAAAAACCAGGAAAGGAGTATACCTGC 27 198 0 CCAGGAAAGA 0.86036 -47 CCGACAAAGCCCAGGGAACTTCATCAC 28 260 1 CCAGGGAACT 0.977043 -17 ********* * Masking position 8 Map Score: 5.31768 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 132 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 ATTGATGAGAGTTTGGTGTCTTTATGTGTCTG 3 200 0 GTTGGTGCTT 0.756998 -101 TGACGGCAGTGGCAGGTGTCATAAAAAAAACC 3 263 1 GCAGGTGCAT 0.924106 -38 CAGTCACCTTGTCAGGAGTATTATC 5 169 1 GCAGGAGATT 0.675154 -15 TTCAGCAAGGGGCTGATGCCGGTTTTACAGAA 12 20 1 GCTGATGCGG 0.891742 -281 ATCACCGTCAGCCAGATGGCGTGCAGCATGTC 12 65 0 GCAGATGCGT 0.940011 -236 CTGCTGGCCTGGCTGGTGACGCGCTTTAACTT 12 140 1 GCTGGTGCGC 0.921573 -161 GTGGTTGCCGGTCTGGTGTATTTGCTGTTCTA 12 227 1 GCTGGTGATT 0.925815 -74 CCCGGAAGAAGTCAGATGTCGTTTAATGGGCA 15 19 1 GCAGATGCGT 0.940011 -282 GTTCAGCCCGGGAAGGTGCCTGACCGTAAAAA 15 237 0 GAAGGTGCTG 0.800424 -64 CTGCAAGACAGACAGGTGGATTATTTATGTTT 22 27 0 GCAGGTGATT 0.951292 -72 CTGTCTGTCTTGCAGGTGTCGGTTACGGTTAC 22 44 1 TCAGGTGCGG 0.822881 -55 TTATCACGCCGACAGGTGCATTACACGATGTC 28 112 0 GCAGGTGATT 0.951292 -165 ACAATGTTTACTCTGGTGCCTGACATTTCACC 28 230 1 CCTGGTGCTG 0.791593 -47 * ****** *** Masking position 5 Map Score: 6.43817 Number of sites scoring better than the average of aligned sites = 1041 Number in coding regions = 979 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 7 GTAAGAGGGAACGCGGCGACTGGCTTAACT 5 105 0 ACGCGGCGAC 0.886787 -79 GGATCGCGGGAAGCGCCTCCGGGCGTTTAA 11 26 0 AAGCGCCTCC 0.866555 -49 TCGTCGAGCCAACCGCCGAGCGGGCCGTTA 12 265 0 AACCGCCGAG 0.878881 -36 TTGCGCGCCCCGGAAGAAGTCA 15 3 1 GCGCGCCCCG 0.975015 -298 CGCCGCCCGAAAGCGGCGCGAAAGGAC 16 8 0 AAGCGGCGCG 0.976731 -50 AAAACGGAGGAAGCGCCGCCCGAAAGCGGC 16 21 0 AAGCGCCGCC 0.976731 -37 TCGACAATAAACCCGCCGCCGACAGAGTAA 18 21 0 ACCCGCCGCC 0.978407 -99 TACCGCTATGACCCGGCCCGCGCAGAACGG 24 28 1 ACCCGGCCCG 0.97339 -52 ATGAGATAATGACCGGCCCGTTCTGCGCGG 24 45 0 GACCGGCCCG 0.918117 -35 TTTTTTTTCGTCGCGCCCCGCAAAATTGCA 27 132 1 TCGCGCCCCG 0.934672 -113 ********** Masking position 4 Map Score: 9.34101 Number of sites scoring better than the average of aligned sites = 1368 Number in coding regions = 1296 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 8 TCGGATCATCACGCAATGTATGCTGATTCGCGC 1 92 1 ACCAGTATGC 0.915827 -82 CCTGTTTCACACAAACGGTTTACAAAATAACCG 7 19 0 ACAAGTTTAC 0.848864 -166 AGAATGCCGAACACCAGGTTTACCGGTACGGCA 12 109 0 ACCCGTTTAC 0.930332 -192 AGATTCCTCACTGTTTGCCTT 13 4 0 CCCAGTTTGC 0.984419 -18 CGTCTTTAATCCACACCGTTTGCCCCGTTAACC 14 206 1 CCCAGTTTGC 0.983821 -95 GACCGTAAACCCGCATAGTTTACCGTACAGGCG 28 72 1 CCCAGTTTAC 0.981276 -205 ACGTCCATTAACACAATGTTTACTCTGGTGCCT 28 218 1 ACCAGTTTAC 0.977477 -59 ** ** ****** Masking position 9 Map Score: 3.17361 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 45 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 9 ATAGTTGGAATTTTGTAAATCTCCCGTTAC 2 121 1 TTTTGTAAAT 0.644528 -64 AGATTAAAATTGCTGTAAATATCATCACGT 3 31 1 TGCTGTAAAT 0.942477 -270 GTTCACAAAGTTCCTTAAATTTTACTTTTG 3 81 1 TTCCTTAAAT 0.629037 -220 TCATCAATAGTTCCGTAAATTTTTATTGAC 3 224 1 TTCCGTAAAT 0.955596 -77 CGTCAATAAGTTCTGTCAATAAAAATTTAC 3 238 0 TTCTGTCAAT 0.935119 -63 CACCTGCCACTGCCGTCAATAAGTTCTGTC 3 251 0 TGCCGTCAAT 0.905634 -50 ATTATTTCCCTTCTGTATATAGATATGCTA 7 89 1 TTCTGTATAT 0.745152 -96 GTTACCTCCTGTAAATGCCTTCCCAA 9 17 0 TCCTGTAAAT 0.859394 -16 ATCGGCCAGATTCTGTAAAACCGGCATCAG 12 32 0 TTCTGTAAAA 0.74515 -269 CAACGCTTTACTCTGTAAATCAAAAGTAAA 15 72 0 CTCTGTAAAT 0.812509 -229 ATACACTTCATGCCGTCAATGAGGTAATTA 23 157 1 TGCCGTCAAT 0.905634 -32 ********** Masking position 9 Map Score: 4.76529 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 171 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 10 TGTTTTGTAGATGTAAAGATAAGTATAG 5 7 0 ATGTAAGTAA 0.903462 -177 ATCTTTGTGCTGTGAAAGTTAATAGTGCACTT 6 91 0 TGTGAAGTAA 0.443398 -139 TAGGTTGAGTGAATGTTAAACGCCCGGAG 11 8 1 AGTGAAGTAA 0.780483 -67 GATCCGGGCTTTTTAATGGCAAGGTTTGTAAC 11 51 1 TTTTAAGCAA 0.677084 -24 ACAGAAGAGAAGGTAAGGTTAACGGGGCAAAC 14 223 0 AGGTAAGTAA 0.839538 -78 GTAAAAGAGAATTTAAGGGCAATATTTGCCCA 15 45 0 ATTTAAGCAA 0.903463 -256 ACTTGTTGATATTTAAAGGTATTTAATTGTAA 23 55 1 ATTTAAGTAT 0.568532 -134 TCTGGAAAGTATTGAAAGTTAATTTGTGAGTG 23 96 1 ATTGAAGTAA 0.864127 -93 ATACTGCGCAATGTAATGCCAACGTTCACACG 25 11 0 ATGTAAGCAA 0.884512 -52 ATTGCGCAGTATTTAAGGACAACACTTAAGGG 25 31 1 ATTTAAGCAA 0.903462 -32 GCAACATGAAATTTCAGGGTAAAAAAACAGGA 26 112 1 ATTTCAGTAA 0.79768 -30 GCATTACACGATGTCACGGTAACGCCTGTACG 28 95 0 ATGTCAGTAA 0.764342 -182 ****** * *** Masking position 6 Map Score: 1.63156 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 72 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 11 AGTCCTGTTTTTTCGGCATTTAACAAAGAG 2 19 0 TTTCGGCATT 0.694327 -166 TATGGAAATATGACGGTGTTCACAAAGTTC 3 64 1 TGACGGTGTT 0.888121 -237 CAGAACTTATTGACGGCAGTGGCAGGTGTC 3 253 1 TGACGGCAGT 0.954456 -48 GCCATCTGGCTGACGGTGATGATCGCGCTG 12 77 1 TGACGGTGAT 0.706985 -224 TTCCGGTACTCTACGGCGGTTTTATCG 14 8 0 CTACGGCGGT 0.830406 -293 CCTCAAATTATTACGGCGGTAAATGATTAA 15 183 1 TTACGGCGGT 0.954456 -118 CCTATTACTCTGTCGGCGGCGGGTTTATTG 18 17 1 TGTCGGCGGC 0.911668 -103 ATTACCTCATTGACGGCATGAAGTGTATCA 23 155 0 TGACGGCATG 0.8821 -34 GTAATGCACCTGTCGGCGTGATAATGCATA 28 120 1 TGTCGGCGTG 0.922928 -157 ********** Masking position 4 Map Score: 1.30207 Number of sites scoring better than the average of aligned sites = 1437 Number in coding regions = 1375 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 12 TGTATGCTGATTCGCGCGGGAAATATGGGT 1 108 1 TTCGCGCGGG 0.844863 -66 CCGCATATTCTCTGAGCGGGTATGCTACCT 7 130 1 TCTGAGCGGG 0.980281 -55 CGAGCCAACCGCCGAGCGGGCCGTTAGAGC 12 261 0 GCCGAGCGGG 0.874031 -40 AGCCTCGTGAGCGGGACGGTCGTAA 19 6 1 CGTGAGCGGG 0.977795 -60 ACCGGCCCGTTCTGCGCGGGCCGGGTCATA 24 34 0 TCTGCGCGGG 0.882239 -46 ATCGGCTTGCCGCGAGCGGTCGTATATTTT 27 89 0 CGCGAGCGGT 0.937109 -156 AAGGAGTATACCTGCGCGGTGCGGCAAATA 27 183 0 CCTGCGCGGT 0.822474 -62 ********** Masking position 6 Map Score: 5.69645 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 274 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 13 ACAGCAATTTTAATCTATTTATATGATTTC 3 17 0 TAATCTATTT 0.908753 -284 AAGCACGATTTCATCTATCTTTGTGCTGTG 6 109 0 TCATCTATCT 0.863589 -121 TTAGGTTGGTTAATCTATTTTGTTGTTAAA 14 126 1 TAATCTATTT 0.908753 -175 AGCGTTGGGATAATCTATCTTCCAAGTAGA 15 95 1 TAATCTATCT 0.953648 -206 TCAAATACAATAATCTACTTGGAAGATAGA 15 108 0 TAATCTACTT 0.870187 -193 GAAAAATAATCTCTCTACAATACTTC 20 18 0 TAATCTCTCT 0.863589 -16 TAAACATAAATAATCCACCTGTCTGTCTTG 22 26 1 TAATCCACCT 0.809888 -73 ********** Masking position 3 Map Score: 1.18756 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 4 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 14 GTGAATGTTAAACGCCCGGAGGCGCTTCCC 11 19 1 AACGCCCGGA 0.981946 -56 TTGCCATTAAAAAGCCCGGATCGCGGGAAG 11 43 0 AAAGCCCGGA 0.876044 -32 CCTGTTTTTATACGTCTGGATGTCTAAACT 17 75 0 TACGTCTGGA 0.956497 -29 ACGATGTCGAAACGTCCGTACCTTACGATT 18 74 1 AACGTCCGTA 0.924156 -46 TTTTAATCACTACGTCGGGAGTTGTTACCC 27 222 1 TACGTCGGGA 0.928172 -23 ATGTCACGGTAACGCCTGTACGGTAAACTA 28 87 0 AACGCCTGTA 0.904242 -190 TGGACGTCAATACATCTGGACATCTAAACT 28 195 0 TACATCTGGA 0.740778 -82 ********** Masking position 2 Map Score: 0.588029 Number of sites scoring better than the average of aligned sites = 344 Number in coding regions = 319 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 15 GGTGGTGTTATAGCATAACCGCACGATCGG 1 66 1 TAGCATAACC 0.922992 -108 CGCACGATCGGATCATCACGCAATGTATGC 1 85 1 GATCATCACG 0.921556 -89 TTGCTGTAAATATCATCACGTCTCTATGGA 3 40 1 TATCATCACG 0.82118 -261 CTGTTTTTTCGAACATATCCTAACTGTCCA 6 143 1 GAACATATCC 0.738581 -87 ATACAACAGGTAGCATACCCGCTCAGAGAA 7 137 0 TAGCATACCC 0.786689 -48 CAATCAGCGCGATCATCACCGTCAGCCAGA 12 81 0 GATCATCACC 0.950261 -220 TTGGCTCGACGAGCATAACCTGCAAATT 12 283 1 GAGCATAACC 0.96841 -18 TTGCTTACTGGAACATAACGACGC 14 287 1 GAACATAACG 0.893215 -14 ********** Masking position 5 Map Score: 0.445059 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 259 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234