AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00071_ecoli_reg_300.orf -o00071_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 adhC 34 alcohol dehydrogenase class III; formaldehyde dehydrogenase, glutathione-dependent #2 yaiN 166 putative alpha helix chain #3 adhE 300 CoA-linked acetaldehyde dehydrogenase and iron-dependent alcohol dehydrogenase; pyruvate-formate-lyase deactivase #4 ycjL 121 probable amidotransferase subunit #5 ycjC 26 orf, hypothetical protein #6 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #7 ydbO 284 orf, hypothetical protein #8 fadD 204 acyl-CoA synthetase, long-chain-fatty-acid--CoA ligase #9 b1806 39 putative outer membrane protein #10 yeaZ 57 orf, hypothetical protein #11 b1808 83 putative enzyme #12 atoS 214 sensor protein AtoS for response regulator AtoC #13 atoD 195 acetyl-CoA:acetoacetyl-CoA transferase alpha subunit #14 atoB 30 acetyl-CoA acetyltransferase #15 hcaA1 135 large terminal subunit of phenylpropionate dioxygenase #16 aas 300 2-acyl-glycerophospho-ethanolamine acyltransferase; acyl-acyl-carrier protein synthetase #17 yqeF 251 putative acyltransferase #18 yiaY 189 putative oxidoreductase #19 selA 97 selenocysteine synthase: L-seryl-tRNA (Ser) selenium transferase #20 yibF 227 putative S-transferase #21 fadB 189 4-enzyme protein: 3-hydroxyacyl-CoA dehydrogenase; 3-hydroxybutyryl-CoA epimerase; delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase; enoyl-CoA hydratase Motif number 1 CGGAAAACAAAGAGGAAAGGGGGGGGGGCTAATCG 2 50 0 AAAAGGGGGG 0.98846 -117 CCAGTGTTATATACTATAGGGGGGTATGCATTGAC 2 113 1 AAATGGGGGT 0.950643 -54 GCAATATACTATAGGGGGGTATTCTATATG 2 147 0 AAATGGGGGT 0.950643 -20 AAAAAGTTTAACATTATCAGGAGAGCATT 3 282 1 AAATGGAGAG 0.774751 -19 AACGGCATGTATATCATTTGGGGTTGCGATGACGA 8 154 1 AAATGGGGTT 0.847009 -51 GTATGCCCTGAGAAAAAAAGGAGTCGCACC 9 20 1 AAAAGGAGTC 0.817527 -20 ATCCCTGTTCAAATCAACAGGGGGTAGT 11 66 1 AAAAGGGGGT 0.978756 -18 CAGTCAGGCAATAGCAAGGGGAGTGCCAGAATGAG 13 138 0 AAAAGGAGTG 0.964375 -58 CGTTTTTTCGATAACAAGGGGAAGGTG 15 3 0 AAAAGGAAGG 0.851469 -133 TCCTTATGGCACAAAAATAGAAGGTCAATACATCT 15 90 1 AAAAGAAGGT 0.854722 -46 TGATTCAGTAAAAGCGAATGGAGGGAGATTACACG 16 259 0 AAGAGGAGGG 0.932146 -42 TTACTGAATCAGAGCAAAGGGAGTTGGA 16 283 1 AAAAGGAGTT 0.935735 -18 TCTACAAATTAAACAAAATGGAGGGCAATTTACCA 17 26 1 AAAAGGAGGG 0.989493 -226 ACTTAAGGTCAAAAAAACAGAAGGGTAAAAA 21 7 0 AAAAGAAGGG 0.916233 -183 * * ** ****** Masking position 3 Map Score: 14.1824 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 57 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 2 AATCGGCAGGGAAGGCCGCCCCGGATAGCGGG 2 23 0 GAACCGCCCC 0.962491 -144 CTTCCCTGCCGATTAGCCCCCCCCCCTTTCCT 2 41 1 GATGCCCCCC 0.905734 -126 ATATGTCAATGCATACCCCCCTATAGTATATA 2 120 0 GCACCCCCCT 0.970432 -47 TTGACATATAGAATACCCCCCTATAGTATATT 2 143 1 GAACCCCCCT 0.947241 -24 CCGGGTAAGCGCAATGCGCCCGGCAATCTATA 6 28 1 GCAGCGCCCG 0.939545 -247 GGATTCGCTCACTTGCCGCCTTGATGCAACTT 6 73 0 ACTCCGCCTT 0.614726 -202 ACTTCATCCTTCAAGCCGCCTCTGCCTTGGCT 6 146 0 TCACCGCCTC 0.594291 -129 AAATAAACGGGCATACGGCCCGGGGATCTCTG 6 199 1 GCACGGCCCG 0.855725 -76 GGCCCGGGGATCTCTGCGCCCTGACGTTCACA 6 215 1 TCTGCGCCCT 0.859753 -60 AGTATGGTATGATGCGCGCCTTTTTATTGATC 10 21 1 GATGCGCCTT 0.90073 -37 TTCAACTGGCGAAAGCGCCCTCATCCTGACAT 11 33 1 GAACGCCCTC 0.455751 -51 CTGAGGCGGAGCTTCGCCCCTTTGAAATACCT 12 48 0 GCTGCCCCTT 0.88511 -167 AAGTATGGGAGATTAACGCCCTATCTACCCCT 17 72 1 GATACGCCCT 0.924313 -180 TCCTCAGTAAGCTGCCCGCCCTTTTTTACACT 18 154 1 GCTCCGCCCT 0.989026 -36 CCGTGGTTATGTTAAACGCCCTTCTCCGTGTG 19 49 1 GTTACGCCCT 0.686376 -49 AAACCTGGCTGATCAAGGCCCTCTCACACGGA 19 73 0 GATAGGCCCT 0.747063 -25 *** ******* Masking position 9 Map Score: 10.3824 Number of sites scoring better than the average of aligned sites = 1887 Number in coding regions = 1751 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 3 AATCTATTACCATATTGAGGAAGAGCGAGAG 1 14 1 CAATTGAAGC 0.986205 -21 GCAAAGCTGACACCTTTCAGCATCGCTTTTCGCCAT 3 32 0 CACTTGCAGC 0.977385 -269 TGATCCAAATCAAATTTTTGCAAAGCTGACACCTTT 3 51 0 CAATTGCAGC 0.992931 -250 CCACTACAGTTTAAGGAAATGCAAAT 5 7 1 CATTTGAAGC 0.963196 -20 AACTGCGGAAAACATTAATGCACTGATAAATAATGA 7 116 1 AAATTGCAGA 0.730558 -169 GCGCACTGTGCAAATTTCTGCATAGCAAGTTTTGGT 13 12 0 CAATTGCAGC 0.992931 -184 GCACAGTGCGCAATTTTCTGCATAGCCGCTCATTCT 13 37 1 CATTTGCAGC 0.980923 -159 GTTACTGTTACAGATTGATGACCGGCAAAAAAAACC 16 12 0 CAATTGACGC 0.943512 -289 ATGCAAACAAAAGATTAAAGAAATGCCGATCTGATC 21 92 0 AAATTGAAGC 0.933674 -98 ** *** *** ** Masking position 6 Map Score: 7.47936 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 131 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 CTATCCGGGGCGGCCTTCCCTGCCGATTAGCCCC 2 27 1 CGGTTCCCCC 0.971624 -140 CTTTCAGCATCGCTTTTCGCCATTATAGCTAACA 3 21 0 CGCTTCGCTT 0.940049 -280 GATTGCCGGGCGCATTGCGCTTACCCGGCTTACA 6 22 0 CGCTGCGCAC 0.948993 -253 GTAAGCTCATCGGGATTCGCTCACTTGCCGCCTT 6 83 0 CGGTTCGCAC 0.984683 -192 TCTGCCTTGGCTGCGTTCGCTCCCCCGAATCACT 6 124 0 CTGTTCGCCC 0.978905 -151 TGAACTGTGACGGATTTCGCACCCTATTTTTATA 7 154 0 CGGTTCGCCC 0.995775 -131 TAAATAGTGACGCGCTTCGCAACCTTTTCGTTGG 8 82 1 CGCTTCGCCC 0.996586 -123 TTATTCGGTACGCTCTTCGTACCCTGTCTCTTGC 16 159 1 CGCTTCGTCC 0.966235 -142 TGTAATCTCCCTCCATTCGCTTTTACTGAATCAG 16 261 1 CTCTTCGCTT 0.75536 -40 *** ***** ** Masking position 6 Map Score: 8.32483 Number of sites scoring better than the average of aligned sites = 486 Number in coding regions = 470 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 5 ATAAAATTTATCCGGTGAATGTGGTCGGAAA 2 79 0 TCGGTGAATG 0.961301 -88 TTTAACATTATCAGGAGAGCATT 3 288 1 TCGGAGAGCA 0.839193 -13 ATGAGCTTACTCAGGTAAGTGATTCGGGGGA 6 107 1 TCGGTAAGTG 0.897379 -168 GGTAAGTGATTCGGGGGAGCGAACGCAGCCA 6 120 1 TCGGGGAGCG 0.908894 -155 ATGTGAAACATCTGGAGAGTAGCG 7 4 0 TCGGAGAGTA 0.90324 -281 TTTGTTACGGAGTATGGTATGATGCG 10 6 1 TAGGAGTATG 0.75223 -52 AAGCTCCGCCTCAGGTGACCGATGGAGTGTG 12 66 1 TCGGTGACCG 0.903332 -149 TTCTCTCTTCTCTGGAATATGATACACCGCC 12 131 1 TCGGAATATG 0.828287 -84 ACTAGTCTTGTCCGGTATATGACGATTATCA 12 184 0 TCGGTATATG 0.739858 -31 TGGGGATTTATAAGGAGAATGAGCGGCTATG 13 57 0 TAGGAGAATG 0.854092 -139 TTTTACACTTTCAGGAGTGTGTT 18 177 1 TCGGAGTGTG 0.972103 -13 CCTTGCGGATTCAGGAGACTGAC 21 177 1 TCGGAGACTG 0.965929 -13 ** ******** Masking position 1 Map Score: 7.60309 Number of sites scoring better than the average of aligned sites = 696 Number in coding regions = 624 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 6 AAATCGCGAATCATAAAAAGCAAAGGATCTTTTAACGAAA 7 52 1 TAAAACAATT 0.93989 -233 ACACAATAGTTAAGTAAAATCACAAATTTTGTATGTTTGA 7 185 0 TAAAACACTT 0.985583 -100 GGGGTTGCGATGACGACGAACACGCATTTTAGAGGTGAAG 8 173 1 TAAGACACTT 0.947801 -32 CAGGGTTGTACGAAAAGAAGCAAGGTATTTCAAAGGGGCG 12 26 1 CAAAACAATT 0.805942 -189 ATTTCCTTTGTGATAAAAATCACTTTTTTTAAACAATTAA 17 169 1 TAAAACACTT 0.985583 -83 TCTTATGAATTTAAAAAAAGCACATTGTTTAATGAATACA 18 52 1 TAAAACACTT 0.985582 -138 AAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACA 18 77 0 TAAAACACTT 0.985582 -113 AGAAGGGCGTTTAACATAACCACGGATTGTAACGTGAGAT 19 34 0 TAAAACACTT 0.985583 -64 * * * ** *** * * Masking position 9 Map Score: 5.44783 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 11 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 7 CTCTCGCTCTTCCTCAATATGGTA 1 21 0 TCGCTCTTCT 0.966875 -14 CAAATCATCACCGCACTGACTATACTCTCGT 3 230 1 CCGCACTGCT 0.934737 -71 TTAATGTTTTCCGCAGTTGCTATACAGATCG 7 103 0 CCGCAGTTCT 0.978969 -182 AGCGGACCAGCCGCTGTTTCTTTTTCTTTAA 8 21 0 CCGCTGTTCT 0.990741 -184 AGCGGCTGGTCCGCTGTTTCTGCATTCTTAC 8 37 1 CCGCTGTTCT 0.990741 -168 TTCTGCATAGCCGCTCATTCTCCTTATAAAT 13 52 1 CCGCTCATCT 0.956922 -144 CTCCCTCCATTCGCTTTTACTGAATCAGAGC 16 267 1 TCGCTTTTCT 0.880192 -34 ******** ** Masking position 11 Map Score: 6.02619 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 121 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 8 CTTTCCTCTTTGTTTTCCGACCACATTCACCGGATAAATTT 2 66 1 TTTACATTAC 0.97393 -101 TGGGTTTTCATTTTTGCAAACTCAATTTAACATTTGACAAA 4 19 0 TTTACATTAC 0.97393 -103 ATCCTTTGCTTTTTATGATTCGCGATTTAACTATTAGCAAC 7 39 0 TTTTCATTAC 0.978735 -246 CGCACCCTATTTTTATAAATCATTATTTATCAGTGCATTAA 7 130 0 TTTTCATTAC 0.978735 -155 AGAATGAGATTATTGGATTTAGTTATTTAACTAATTGAATA 13 105 0 TTTTAATTAC 0.81858 -91 GGTCAATACATCTTATCTTTCAGGATTAAAAAAT 15 112 1 TTTTCATTAA 0.837013 -24 TGCGCAGGTTTTTTTTCGCACCTAATTTACTGTCGCTCGCG 16 208 1 TTTACATTAT 0.80664 -93 TGTATTAATTTATTTTAAAACTTAATTAATCATTTCC 18 7 0 TTTACATTAC 0.973929 -183 TGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAG 18 97 0 TTTTCATTAC 0.978606 -93 * ** ** *** * * Masking position 15 Map Score: 5.4325 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 49 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 9 CTCACTTCTGGGTACTGATTACGTGATCCA 3 80 0 GGTACTGATT 0.841778 -221 TAGTCAGTGCGGTGATGATTTGCTTAACCT 3 222 0 GGTGATGATT 0.945713 -79 TCGTATTCGAGCAGATGATTTACTAAAAAA 3 257 1 GCAGATGATT 0.743688 -44 GCTTACTCAGGTAAGTGATTCGGGGGAGCG 6 111 1 GTAAGTGATT 0.742254 -164 CAGAGGTTAAGGTGATGATTTCTCGGCGGT 12 156 0 GGTGATGATT 0.945713 -59 CCATAAGGATGTTGCTGGTTGGTTGCTAAT 15 69 0 GTTGCTGGTT 0.780091 -67 AGATCCCAGAGGTATTGATTGGTGAGATTA 16 132 1 GGTATTGATT 0.661076 -169 TGTTTAATTTGTAGATGATACGTTCAGATA 17 11 0 GTAGATGATA 0.522036 -241 CTATTGGTGGGTTAGTGGTTGCAAACCTTA 17 104 1 GTTAGTGGTT 0.689086 -148 CAGTGCAATAGTAAATGATTGTTAATTACA 17 215 0 GTAAATGATT 0.854894 -37 GGAAATGATTAATTAAGTTT 18 1 1 GGAAATGATT 0.88772 -189 GGCAGAAAATGTTGATGGTTTGTTACTTCC 20 154 0 GTTGATGGTT 0.878893 -74 ********** Masking position 6 Map Score: 4.52399 Number of sites scoring better than the average of aligned sites = 723 Number in coding regions = 674 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 10 AAACAAAGAGGAAAGGGGGGGGGGCTAATC 2 51 0 GAAAGGGGGG 0.969871 -116 TGATAGACGTGAAACAGGAGTCATA 6 260 1 GAAACAGGAG 0.880381 -15 GATCTGTATAGCAACTGCGGAAAACATTAA 7 104 1 GCAACTGCGG 0.874065 -181 TAAAGAAAAAGAAACAGCGGCTGGTCCGCT 8 22 1 GAAACAGCGG 0.961408 -183 TAAGAATGCAGAAACAGCGGACCAGCCGCT 8 37 0 GAAACAGCGG 0.961408 -168 CCTGTTCAAATCAACAGGGGGTAGT 11 69 1 TCAACAGGGG 0.776965 -15 TTTATAAGGAGAATGAGCGGCTATGCAGAA 13 52 0 GAATGAGCGG 0.759925 -144 TCAGGCAATAGCAAGGGGAGTGCCAGAATG 13 140 0 GCAAGGGGAG 0.914534 -56 AACGGTGTATGCAAGAGGGATAAAAA 13 180 1 GCAAGAGGGA 0.758555 -16 CTGAATCAGAGCAAAGGGAGTTGGA 16 286 1 GCAAAGGGAG 0.62341 -15 GAAAGTGTAAAAAAGGGCGGGCAGCTTACT 18 159 0 AAAAGGGCGG 0.702207 -31 ********** Masking position 3 Map Score: 5.0055 Number of sites scoring better than the average of aligned sites = 945 Number in coding regions = 859 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 11 GAGGAAAGGGGGGGGGGCTAATCGGCAGGGA 2 43 0 GGGGGGCTAA 0.810968 -124 CCGGTGAATGTGGTCGGAAAACAAAGAGGAA 2 68 0 TGGCGGAAAA 0.914271 -99 ATAAGGAGAATGAGCGGCTATGCAGAAAATT 13 48 0 TGACGGCTAT 0.869852 -148 TAATTGAATATGAAGGGATAAATTGGATGGG 13 84 0 TGAGGGATAA 0.92252 -112 TACAGATTGATGACCGGCAAAAAAAACCT 16 9 0 TGACGGCAAA 0.940111 -292 CGCAAAGGAATGAAGGGAAATGCAACGAGGT 16 61 0 TGAGGGAAAT 0.928809 -240 TAAAAGCGAATGGAGGGAGATTACACGAGAT 16 255 0 TGGGGGAGAT 0.904867 -46 TTAAACAAAATGGAGGGCAATTTACCATAAA 17 34 1 TGGGGGCAAT 0.957521 -218 ATTTGTCTGCTGACAGGCGAAACCCTACAGA 20 35 1 TGAAGGCGAA 0.726678 -193 TATGGCCTGGTGATGGGAAAAAGGGCAGAAA 20 176 0 TGAGGGAAAA 0.950251 -52 *** ******* Masking position 10 Map Score: 3.24911 Number of sites scoring better than the average of aligned sites = 573 Number in coding regions = 515 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 12 GTGGTCGGAAAACAAAGAGGAAAGGGGGGGG 2 59 0 AACAAGAGGA 0.852232 -108 AAAAATATTGAACATAAAGGTCATTTAAAGC 4 72 1 AACAAAAGGT 0.965098 -50 AACTATTAGCAACAGAAATGTGAAACATCTG 7 21 0 AACAAAATGT 0.707271 -264 CGAATCATAAAAAGCAAAGGATCTTTTAACG 7 58 1 AAAGAAAGGA 0.723578 -227 GAAAACTGGAATCGTAAAGGTGATGAC 7 268 1 ATCGAAAGGT 0.892803 -17 ATAATTACCCAACGAAAAGGTTGCGAAGCGC 8 93 0 AACGAAAGGT 0.967702 -112 CCAGCGAGAAAACGCAAAGGAATGAAGGGAA 16 73 0 AACGAAAGGA 0.967702 -228 CTACAAATTAAACAAAATGGAGGGCAATTTA 17 27 1 AACAAATGGA 0.813417 -225 AGTGATTTTTATCACAAAGGAAATATGCCTG 17 162 0 ATCAAAAGGA 0.884891 -90 AGGTCAAAAAAACAGAAGGGTAAAAA 21 6 0 AACAAAGGGT 0.865976 -184 **** ****** Masking position 6 Map Score: 5.65023 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 81 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 13 ATAATATTAACTCATCATACCAGCTTGATAAT 8 119 0 CTCATCTCCA 0.967409 -86 TAAAAAGGCGCGCATCATACCATACTCCGTAA 10 15 0 CGCATCTCCA 0.979024 -43 CGAAAGCGCCCTCATCCTGACATAATCCCTGT 11 42 1 CTCATCTACA 0.915842 -42 ATCCAATAATCTCATTCTGGCACTCCCCTTGC 13 128 1 CTCATTTGCA 0.901229 -68 TTAACTATTTCACATATTAGCAACCAACCAGC 15 54 1 CACATATGCA 0.864274 -82 ACAATTTACACACCTCGTTGCATTTCCCTTCA 16 50 1 CACCTCTGCA 0.928768 -251 AAAAAACCTGCGCATCCGCGCAGGTTGGTGCA 16 190 0 CGCATCGGCA 0.967083 -111 CTTAAGTCTCCGCATCTTAGCACATCGTTCAT 21 35 1 CGCATCTGCA 0.99104 -155 ****** * *** Masking position 12 Map Score: 3.02829 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 102 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 14 TAAGCAAGATTACTCACTTCTGGGTACTGA 3 92 0 TACTCACTTC 0.950502 -209 ACATTCTTTATATACACTTCATCCTTCAAG 6 163 0 TATACACTTC 0.875715 -112 TTCTTCACCTCTAAAATGCGT 8 194 0 TCTTCACCTC 0.625976 -11 CGCTACCTTAACCACACTCCATCGGTCACC 12 79 0 ACCACACTCC 0.879767 -136 ACCGACAATTTACACACCTCGTTGCATTTC 16 46 1 TACACACCTC 0.945783 -255 AACACACTCCTGAAAGTGTA 18 180 0 AACACACTCC 0.915782 -10 TCTGATGGATATCTCACTTCAGGCTTTCTT 20 71 0 ATCTCACTTC 0.747032 -157 TAACACAAAATACACACTTCGACTCATCTG 21 133 1 TACACACTTC 0.968559 -57 ********** Masking position 6 Map Score: 1.23465 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 105 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 15 CTCTCGCTCTTCCTCAATAT 1 25 0 CTCTCGCTCT 0.947593 -10 CAAAAGCTTACTCGCGCTCACACTCACTGT 3 184 0 CTCGCGCTCA 0.966007 -117 CCCTGAAAGCCTCGCGCTAC 12 1 0 CTCGCGCTAC 0.954419 -214 TTTACTGTCGCTCGCGTTCTTTATCTCGTG 16 233 1 CTCGCGTTCT 0.951364 -68 CCTGACCCATCTCACGTTACAATCCGTGGT 19 26 1 CTCACGTTAC 0.785827 -72 CTCGGCAGAAATCACGCTCTGGATGAACGA 21 59 0 ATCACGCTCT 0.925665 -131 TGCCGATCTGATCACGCTCGGCAGAAATCA 21 75 0 ATCACGCTCG 0.879459 -115 ********** Masking position 8 Map Score: 0.748556 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 224 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234