AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iargR_ecoli_bsub_100.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 carA 300 carbamoyl-phosphate synthetase, glutamine (small) subunit #2 argF 300 ornithine carbamoyltransferase 2, chain F #3 argA 141 N-acetylglutamate synthase; amino acid acetyltransferase #4 argG 300 argininosuccinate synthetase #5 argR 300 repressor of arg regulon; cer-mediated site specific recombination #6 argD 85 acetylornithine delta-aminotransferase #7 pabA 31 p-aminobenzoate synthetase, component II #8 yhfG 104 orf, hypothetical protein #9 argE_argC 153 argE: acetylornithine deacetylase, argC: N-acetyl-gamma-glutamylphosphate reductase #10 argH 60 argininosuccinate lyase #11 argI 161 ornithine carbamoyltransferase 1 #12 argC 206 N-acetylglutamate gamma-semialdehyde dehydrogenase #13 carA 70 carbamoyl-phosphate transferase-arginine (subunit A) #14 pyrB 145 aspartate carbamoyltransferase #15 yodT 300 similar to adenosylmethionine-8-amino-7-oxononanoate aminotransferase #16 ahrC 134 transcriptional regulator #17 argG 169 argininosuccinate synthase #18 rocD 240 ornithine aminotransferase Motif number 1 TCACTTTATTTGCATATTAATTCACAATGATGA 1 255 0 TGATATTATC 0.978347 -46 ACATATAAAGTGAATTTTAATTCAATAAGTGGC 2 258 1 TGATTTTATC 0.992311 -43 TCGAAATTAGTGTATTTTTATTCTGTTTTTTCG 3 96 0 TGATTTTATC 0.992311 -46 GAAAGTGAACTGGATATTCATTCACATGATTAG 4 95 0 TGATATTATC 0.978347 -206 CCGCTCTCACTGAATTTTTATGCAAAATAAATG 4 235 0 TGATTTTATC 0.992311 -66 TGCATACAGATGAATTTTTATGCAAACAGTCAG 5 242 0 TGATTTTATC 0.992311 -59 TGCCATTTAGTGATTTTTTATGCATATTTTGTG 6 19 1 TGTTTTTATC 0.954195 -67 TCAACGTTAGTGTATTTTTATTCATAAATACTG 9 91 1 TGATTTTATC 0.992311 -63 AAATACTGCATGAATATTGATACTATCATGACC 9 116 1 TGATATTATC 0.978347 -38 GACTTGCAAATGAATAATCATCCATATAAATTG 11 100 1 TGATAATATC 0.794492 -62 CCATATAAATTGAATTTTAATTCATTGAGGCGT 11 121 1 TGATTTTATC 0.992311 -41 GCGGTCAGCCTGTTTTTTTATGCGGCTGAAATG 12 12 1 TGTTTTTATC 0.954195 -195 TACGATTGAATTAATTTTTATTCATGTTATAAT 12 145 1 TTATTTTATC 0.927932 -62 ATTATAAAAATGAATTTTTATGCCTTTATATCG 13 19 0 TGATTTTATC 0.992311 -52 ACATACAAAATGTATTTTTATTAAATATAATTT 17 103 1 TGATTTTATA 0.872141 -67 TTAAATATAATTTATTTTTATACAAAATAGAAA 17 123 1 TTATTTTATC 0.927932 -47 ** ***** ** * Masking position 8 Map Score: 43.247 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 27 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 2 AAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTT 1 14 1 CTTTCCTTTT 0.990973 -287 CAAGCCTCGCCATGTTCTCCGCCATTTTAGAAGCATAA 2 34 1 CTGTCCATTT 0.829936 -267 ACACGGACGGGTTTGCCTCCACCTTTGTAAGAAAGAAT 2 190 1 GTTTCCTTTT 0.974429 -111 ATCCACGCCACATTTTGTCAACGTTTATTGCTAATCAT 4 65 1 CTTTCCTTTT 0.990973 -236 AATGAGTTTTCATTTAATCATCTTTTATCGGAGACAGG 4 201 0 CTTTCCTTTT 0.990973 -100 TCTTTCATAACATTATTTCAGCCTTCTTCAGGGCTGAC 5 209 1 CTTTCCTTCT 0.974389 -92 ACACCACTGACATTGCCTCCACCTTTGTGACAAAGATT 11 53 1 CTTTCCTTTT 0.990973 -109 ATCCATACATGCTGTTTTCATCCTTTCTTATCACGATA 15 40 0 GTGTCCTTTT 0.936 -261 CCTATTATTCCGGTACATCTGCTTTTTTTTCTTTTAAC 16 14 0 CGTTCCTTTT 0.949611 -121 CGCTATTATTCCTTTTTTCTGCATTCATGTACAATGTG 16 53 1 CTTTCCTTCT 0.974389 -82 CTATTTCCAAGCTTATCTGTTCTTTTATGTTATATGAT 16 97 0 GTTTGCTTTT 0.802074 -38 AATTCTTTTGCATATCCTCTCCGTTTTTTTATAAAATA 18 50 0 CTATCCTTTT 0.939198 -191 * ** ** * *** * Masking position 8 Map Score: 16.4164 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 35 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 3 GAGAATATTCACTCACTTTATTTGCATATTAATTCACA 1 262 0 ACATTTTGTA 0.984536 -39 TTGAATTAAAATTCACTTTATATGTGTAATTATTCATT 2 245 0 ACATTTTGTA 0.984536 -56 TTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGT 4 222 1 ACATATTGTA 0.88998 -79 GTGATTTTTTATGCATATTTTGTGGTTATAATTTCACA 6 28 1 ACATTTTGTA 0.984536 -58 ATCAATATTCATGCAGTATTTATGAATAAAAATACACT 9 99 0 ACAATTTGTA 0.940464 -55 ATGAATTAAAATTCAATTTATATGGATGATTATTCATT 11 108 0 ACATTTTGTG 0.960683 -54 GAAAGGATGAAAACAGCATGTATGGATACTCTGGGTAC 15 51 1 ACAATTTGTA 0.940464 -250 CTTATTAGGAAGGCTCTTTTTATGTGAAAAAGTTTTTG 15 207 1 ACTTTTTGAA 0.667456 -94 AAACCCCTTTTACCATATTGTATGAGTGTCCAAATGGC 15 261 0 TCATTTTGTG 0.756374 -40 TTTAATAAAAATACATTTTGTATGTATACACTTTAACA 17 90 0 ACATTTTGTA 0.984536 -80 CTTTATATAAATGCAAGTTCTGTGCCAAATCAAGAATT 18 165 0 ACATTTTGAA 0.940464 -76 * ** ** * ** ** Masking position 11 Map Score: 11.2678 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 17 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 4 TGAAATAAAAACGAGCAGAAAAAAGTGGAC 1 30 0 ACGAGCAGAA 0.790703 -271 CGTTCGCCATGCGAGGATAAA 2 290 1 GCGAGGATAA 0.679411 -11 GCGCTTAAGGGAGAGCAGGAGAAGGCAAAA 4 141 0 GAGAGCAGGA 0.967714 -160 AAAATTCAGTGAGAGCGGAAATCCAGGCTC 4 250 1 GAGAGCGGAA 0.958391 -51 AATGTTATGAAAGAGCGGGATTTTATCAAA 5 193 0 AAGAGCGGGA 0.931896 -108 GTTACGCCGGGAGAGCAGAAGCGCGGGCAA 8 32 0 GAGAGCAGAA 0.955021 -73 CACAAAGACCAAGAGGGTGAACTTGTT 12 190 1 AAGAGGGTGA 0.763606 -17 AAGGGTTATGAAGAGAAGGAAGCTTCAATG 14 42 1 AAGAGAAGGA 0.584816 -104 AAGTTGAAAAGAGAGGGGAAAGAAC 14 131 1 GAGAGGGGAA 0.958391 -15 ATCGTGATAAGAAAGGATGAAAACAGCATG 15 41 1 GAAAGGATGA 0.625523 -260 TAAAAGAAAAAAAAGCAGATGTACCGGAAT 16 16 1 AAAAGCAGAT 0.36191 -119 AAACACGGTTGAGAGGGGATTTTTATC 17 153 1 GAGAGGGGAT 0.860982 -17 TAAAAAAACGGAGAGGATATGCAAAAGAAT 18 57 1 GAGAGGATAT 0.574062 -184 TATATAAAGGGAAAGCAGGATAACATGTTG 18 194 1 GAAAGCAGGA 0.876174 -47 GAAACAGAAAACAAGGGGGAATTCAAAT 18 223 1 ACAAGGGGGA 0.577303 -18 ********** Masking position 4 Map Score: 10.5929 Number of sites scoring better than the average of aligned sites = 873 Number in coding regions = 734 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 5 ATGGGCGCTAAAAGTCAACTTAATGGCGGGA 1 163 0 AAAGTCACTT 0.762311 -138 TATTGAATTAAAATTCACTTTATATGTGTAA 2 254 0 AAATTCATTT 0.904816 -47 TAAACGGTAAACATTCTTTTTATATTCACGG 3 15 1 ACATTCTTTT 0.671822 -127 CACGGCATGCAAATTCTGCTTAAAAGTAAAT 5 135 0 AAATTCTCTT 0.872464 -166 GTTTGCATAAAAATTCATCTGTATGCACAAT 5 248 1 AAATTCACTG 0.940594 -53 TAAACGTAAAACATTCACCTTACGGCTGGTG 9 47 1 ACATTCACTT 0.869609 -107 CAATGAATTAAAATTCAATTTATATGGATGA 11 117 0 AAATTCATTT 0.783941 -45 AAAGGCATAAAAATTCATTTTTATAATTAAT 13 25 1 AAATTCATTT 0.936634 -46 GCTGCGGGACAAATACATTTGTGTTAATTGT 15 102 1 AAATACATTG 0.753809 -199 AATACTATGAAACTTCACCTGAAATTTAGGT 17 18 1 AACTTCACTG 0.731059 -152 TATTTAATAAAAATACATTTTGTATGTATAC 17 99 0 AAATACATTT 0.786287 -71 AGCAAGTGCAAAATTCTTTTGCATATCCTCT 18 68 0 AAATTCTTTG 0.829315 -173 ******* *** Masking position 1 Map Score: 7.28195 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 57 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 6 AAACGAGCAGAAAAAAGTGGACCAAATGGT 1 22 0 AAAAAAGTGG 0.81118 -279 ATTCTTTCTTACAAAGGTGGAGGCAAACCC 2 198 0 ACAAAGGTGG 0.958936 -103 AATTTTAATTCAATAAGTGGCGTTCGCCAT 2 270 1 CAATAAGTGG 0.753647 -31 ATAATCATGCAAAGAGGTGTGCC 3 129 1 AAAGAGGTGT 0.819968 -13 TAAACGTTGACAAAATGTGGCGTGGATCAC 4 62 0 CAAAATGTGG 0.849438 -239 CGCAACATTCCAACAGGTGGTGACAATATA 5 63 1 CAACAGGTGG 0.974158 -238 ACTATCATGACCAGAGGTGTGTCAACA 9 137 1 CCAGAGGTGT 0.919275 -17 AATCTTTGTCACAAAGGTGGAGGCAATGTC 11 61 0 ACAAAGGTGG 0.958936 -101 GAGGCGTTAGCCACAGGAGGGATCT 11 147 1 CCACAGGAGG 0.862002 -15 AATTATTCATCAAGAGGTGGGCTGTTAG 13 53 1 CAAGAGGTGG 0.984008 -18 ********** Masking position 5 Map Score: 6.35039 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 180 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 7 TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACA 1 98 1 TTTTTAATGC 0.954475 -203 TCACTCACTTTATTTGCATATTAATTCACAATGATGA 1 255 0 TATTTAATTC 0.555529 -46 CGAACGCCACTTATTGAATTAAAATTCACTTTATATG 2 259 0 TTATTAATTC 0.771623 -42 CGAGAGCGACTTTTTTATCAGTAATGCCGTGAATATA 3 35 0 TTTTTAATGC 0.954475 -107 TTTAGTGTGTTTTTTGTAAAATAATGCGCTTAAGGGA 4 159 0 TTTTTAATGC 0.954475 -142 AAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCG 4 230 1 ATTTTAATTC 0.687887 -71 TACAGATGAATTTTTATGCAAACAGTCAGCCCTGAAG 5 234 0 TTTTTCAGTC 0.713944 -67 TAGTGTATTTTTATTCATAAATACTGCATGAATATTG 9 98 1 TTATTACTGC 0.638185 -56 CTGTTTCCTTATTTTGAAATTCAATGCCGGAAAGCTG 10 30 0 ATTTTAATGC 0.759809 -31 ATATGGATGATTATTCATTTGCAAGTCTAAAGCATAA 11 90 0 TTATTAAGTC 0.829046 -72 CGTGCTGATTTTTTTTGAGCGGAATTCCCATTGAACA 12 76 1 TTTTTAATTC 0.935927 -131 TTTTTTTTCGATATAAAGGCATAAAAATTC 13 4 1 TTTTTAAGGC 0.967838 -67 CTTTCCCCTCTCTTTTCAACTTAAGGCTGAAAAAAAA 14 116 0 TCTTTAAGGC 0.792368 -30 TATACGACATTTTATGCGGGCCAAGTCCCAA 15 5 0 TTTATAAGTC 0.627415 -296 TGTGAAAAAGTTTTTGCGGGGAACGTCATGCCGCCAT 15 229 1 TTTTTACGTC 0.884065 -72 ACATCTGCTTTTTTTTCTTTTAACGTC 16 1 0 TTTTTACGTC 0.884065 -134 TTAGGTGAAGTTTTTTTTATAAAAGGCTTGAAAAAAC 17 43 1 TTTTTAAGGC 0.967838 -127 ***** ***** Masking position 5 Map Score: 14.4808 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 79 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 8 TTTTGTCGCTTAATGCCTGTAAAACATGCAT 1 109 1 TAATGCCTGA 0.94615 -192 AAAGTCAACTTAATGGCGGGATTTTTTATAT 1 153 0 TAATGGCGGA 0.97634 -148 AATTTCTGGCAAACGGCGGCATTCTGGAGAT 1 194 0 AAACGGCGGA 0.877958 -107 TATGCTTCTAAAATGGCGGAGAACATGGCGA 2 40 0 AAATGGCGGG 0.779419 -261 TTTTTATCAGTAATGCCGTGAATATAAAAAG 3 30 0 TAATGCCGTA 0.914419 -112 TGGATCACTATAATGCCTGCAGATTTTACGT 4 39 0 TAATGCCTGA 0.946273 -262 CAAATCCGGGTTACGCCGGGAGAGCAGAAGC 8 40 0 TTACGCCGGA 0.913477 -65 TTTTGAAATTCAATGCCGGAAAGCTGCGCCT 10 25 0 CAATGCCGGA 0.949605 -36 AAATGAATTTTTATGCCTTTATATCGAAAAA 13 14 0 TTATGCCTTA 0.51691 -57 ATGAGTGTCCAAATGGCGGCATGACGTTCCC 15 247 0 AAATGGCGGA 0.9494 -54 TAGCGCCCTATTATTCCGGTACATCTGCTTT 16 27 0 TTATTCCGGA 0.690551 -108 ********* * Masking position 3 Map Score: 6.36488 Number of sites scoring better than the average of aligned sites = 966 Number in coding regions = 896 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 9 CAACTTAATGGCGGGATTTTTTATATTATT 1 149 0 GCGGGATTTT 0.957311 -152 CTGCTGGGATTTGGTGTACCGA 4 3 1 GCTGGGATTT 0.909193 -298 TGATGATGAGCCTGGATTTCCGCTCTCACT 4 257 0 CCTGGATTTC 0.699599 -44 TTATGAAAGAGCGGGATTTTATCAAATTTC 5 189 0 GCGGGATTTT 0.957311 -112 CCTTACGGCTGGTGGGTTTTATTACGCTCA 9 64 1 GGTGGGTTTT 0.827124 -90 CTGGAGTCGTGCTGATTTTTTTTGAGCGGA 12 69 1 GCTGATTTTT 0.734682 -138 CTATCTTAGACCGGGGTTTTTTTTCAGCCT 14 100 1 CCGGGGTTTT 0.84715 -46 TTTGCTAGATGCTGAAATTTCAAAAGAGCC 15 174 1 GCTGAAATTT 0.864227 -127 TGAAACTTCACCTGAAATTTAGGTGAAGTT 17 25 1 CCTGAAATTT 0.688423 -145 ACGGTTGAGAGGGGATTTTTATC 17 157 1 GGGGATTTTT 0.526837 -13 TTTTGCACTTGCTGAAATTTTCGCTCGAAA 18 86 1 GCTGAAATTT 0.864227 -155 CAGAAAACAAGGGGGAATTCAAAT 18 227 1 GGGGGAATTC 0.662125 -14 ********** Masking position 8 Map Score: 5.25961 Number of sites scoring better than the average of aligned sites = 1356 Number in coding regions = 1146 Number in noncoding regions = 210 Number of orfs with sites within 600 bp upstream = 183 Fraction of orfs with sites within 600 bp upstream = 0.0293929 Motif number 10 AGAACATGGCGAGGCTTGCTGCCTTACTTC 2 22 0 GAGGCTTGCT 0.960497 -279 CGGTACAAAAGAACCGCGCTATT 7 4 0 GAACCGCGCT 0.910706 -28 TTTTGTGCTGGAGTCGTGCTGATTTTTTTT 12 62 1 GAGTCGTGCT 0.857112 -145 GGGCAGCATTGAAGCTTCCTTCTCTTCATA 14 48 0 GAAGCTTCCT 0.939258 -98 AATTTCAAAAGAGCCTTCCTTATTAGGAAG 15 189 1 GAGCCTTCCT 0.983898 -112 CACATAAAAAGAGCCTTCCTAATAAGGAAG 15 203 0 GAGCCTTCCT 0.983898 -98 TGTATGAACCTCCCTCAATTATTTT 18 6 1 GAACCTCCCT 0.952171 -235 ********** Masking position 2 Map Score: 4.68795 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 29 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 11 AACAGAATAAAAATACACTAATTTCGAATAA 3 102 1 AAAACACTAA 0.979803 -40 ATTTTACAAAAAACACACTAAACTCTTCCTG 4 174 1 AAAACACTAA 0.979803 -127 ATATGCATAAAAAATCACTAAATGGCAATCA 6 15 0 AAATCACTAA 0.936488 -71 TTATGAATAAAAATACACTAACGTTGAGCGT 9 87 0 AAAACACTAA 0.979803 -67 AAATTGTAGAAAACACACGAATTCTTGATTT 18 146 1 AAAACACGAA 0.956244 -95 *** ******* Masking position 7 Map Score: 3.23894 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 3 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 12 AGAATGATTGGCCTTCTTTATGATTTTAAG 2 74 0 GCCTTCTTTA 0.954405 -227 CATTATTTCAGCCTTCTTCAGGGCTGACTG 5 219 1 GCCTTCTTCA 0.970041 -82 TTGATGCCTCCCTGAACGTGTCCAT 8 90 0 GCCTCCCTGA 0.977358 -15 TTTCAAAAGAGCCTTCCTTATTAGGAAGGC 15 191 1 GCCTTCCTTA 0.984114 -110 CATAAAAAGAGCCTTCCTAATAAGGAAGGC 15 201 0 GCCTTCCTAA 0.972323 -100 TGTATGAACCTCCCTCAATTATTTTCT 18 8 1 ACCTCCCTCA 0.924753 -233 ********** Masking position 4 Map Score: 2.98653 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 46 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 13 CAATCTTCTTGCTGCGCAAGCGTTTTCCAGAAC 1 62 1 GCGCGCGCGT 0.925525 -239 ATATTATTTTGTGGCTCATGCATGTTTTACAGG 1 124 0 GTGCTCGCAT 0.977282 -177 AATTCAATAAGTGGCGTTCGCCATGCGAGGATA 2 276 1 GTGCGTGCCA 0.951859 -25 TGATAAAAAAGTCGCTCTCGCATAAAATTTACA 3 52 1 GTGCTCGCAT 0.977282 -90 GTAATTAACAGTCGCTTATGCATTAGCGCAACA 5 37 1 GTGCTTGCAT 0.93377 -264 TTTGCATGCCGTGACGCAGGCATGTTTCTCAAT 5 153 1 GTACGCGCAT 0.92789 -148 TGATTTCTCGCGCGGGCAATCTTGCCCGC 8 7 1 CTGCGCGCAA 0.93932 -98 CGGGAGAGCAGAAGCGCGGGCAAGATTGCCCGC 8 22 0 GAGCGCGCAA 0.975001 -83 TTAATTCATTGAGGCGTTAGCCACAGGAGGGAT 11 137 1 GAGCGTGCCA 0.878617 -25 ** **** **** Masking position 5 Map Score: 2.86135 Number of sites scoring better than the average of aligned sites = 1072 Number in coding regions = 977 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 14 CCCGTCCGTGTGTGAAAATAATCGTATCTG 2 171 0 TGTGAAAATA 0.947494 -130 AAGAAAGAATTGTGAAATGGGGTTGCAAAT 2 218 1 TGTGAAATGG 0.788021 -83 TCACTTTATATGTGTAATTATTCATTTGCA 2 241 0 TGTGTAATTA 0.697792 -60 TCCAACAGGTGGTGACAATATACCCTACCG 5 71 1 GGTGACAATA 0.77667 -230 CATAAACAAATGTGAAATTATAACCACAAA 6 46 0 TGTGAAATTA 0.93609 -40 GTCAGTGGTGTGTGACAATAAGAGTATCGG 11 34 0 TGTGACAATA 0.937046 -128 CCTCCACCTTTGTGACAAAGATTTATGCTT 11 68 1 TGTGACAAAG 0.818002 -94 TCTTGGTCTTTGTGAAATTATTTAACATTA 12 174 0 TGTGAAATTA 0.93609 -33 GCTCTTTTTATGTGAAAAAGTTTTTGCGGG 15 219 1 TGTGAAAAAG 0.844938 -82 ********** Masking position 7 Map Score: 2.73588 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 64 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 15 AATGGGGTTGCAAATGAATAATTACACATA 2 233 1 CAAATGAATA 0.907016 -68 TTACACATATAAAGTGAATTTTAATTCAAT 2 254 1 AAAGTGAATT 0.895623 -47 TCAACAAATGAAAGTGAACTGGATATTCAT 4 107 0 AAAGTGAACT 0.697294 -194 ATTGTGCATACAGATGAATTTTTATGCAAA 5 249 0 CAGATGAATT 0.713521 -52 CAGACATAAGAAGGTGAATAGCCCCG 9 7 0 AAGGTGAATA 0.738998 -147 TTTAGACTTGCAAATGAATAATCATCCATA 11 96 1 CAAATGAATA 0.907016 -66 TCATCCATATAAATTGAATTTTAATTCATT 11 117 1 AAATTGAATT 0.621822 -45 AGAAAATTTATAAATGAATAAAAATATTAA 12 112 1 TAAATGAATA 0.65147 -95 TTAACATTATAACATGAATAAAAATTAATT 12 153 0 AACATGAATA 0.698819 -54 ATTAATTATAAAAATGAATTTTTATGCCTT 13 26 0 AAAATGAATT 0.928267 -45 ACAATTAACACAAATGTATTTGTCCCGCAG 15 103 0 CAAATGTATT 0.697632 -198 AATAATTAATAAAATGAACAAGACAACAAT 15 128 0 AAAATGAACA 0.797949 -173 GAATGCAGAAAAAAGGAATAATAGCGCCCT 16 49 0 AAAAGGAATA 0.666219 -86 CGTACTTGTTAAAGTGTATACATACAAAAT 17 84 1 AAAGTGTATA 0.723975 -86 GTATACATACAAAATGTATTTTTATTAAAT 17 99 1 AAAATGTATT 0.776765 -71 ********** Masking position 8 Map Score: 5.96235 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 146 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675