AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i020_ecoli_bsub_300.orf -o020_ecoli_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 pdhR 300 transcriptional regulator for pyruvate dehydrogenase complex #2 aceE 160 pyruvate dehydrogenase (decarboxylase component) #3 lpdA 300 lipoamide dehydrogenase (NADH); component of 2-oxodehydrogenase and pyruvate complexes; L-protein of glycine cleavage complex #4 sdhC 300 succinate dehydrogenase, cytochrome b556 #5 yfjN 300 similar to hypothetical proteins #6 yfjM 195 yfjM #7 yfjL 29 alternate gene name: yztA #8 acoA 231 acetoin dehydrogenase E1 component (TPP-dependent alpha subunit) #9 pdhA 300 pyruvate dehydrogenase (E1 alpha subunit) #10 pdhC 114 pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit) #11 odhB 29 2-oxoglutarate dehydrogenase complex (dihydrolipoamide transsuccinylase, E2 subunit) #12 odhA 227 2-oxoglutarate dehydrogenase (E1 subunit) #13 yojN 63 similar to nitric-oxide reductase #14 yojM 92 similar to superoxide dismutase #15 yojL 300 similar to cell wall-binding protein #16 bfmBAA 73 branched-chain alpha-keto acid dehydrogenase E1 (2-oxoisovalerate dehydrogenase alpha subunit) #17 yqiS 124 similar to phosphate butyryltransferase #18 yqiR 152 similar to transcriptional regulator (sigma-L-dependent) Motif number 1 CGTTTAGTTGCCGCGCTTTTATATGCGCTT 2 52 0 CCGCGCTTTT 0.801663 -109 AAACGTAGAACCTGTCTTATTGAGCTTTCC 2 77 1 CCTGTCTTAT 0.870578 -84 TTCTTAGTGGCCTTGCTTTTGAACTTTTTG 5 87 0 CCTTGCTTTT 0.961402 -214 TGTAAAAATCCCTTTATTTTGTTAGCCTTT 6 30 0 CCTTTATTTT 0.93217 -166 CTAAAATAAACCTGGATTTTCGGTAAATCC 6 70 1 CCTGGATTTT 0.895816 -126 TTTTACTCAGCCTGTCTTTTCTCTAATTTA 6 120 1 CCTGTCTTTT 0.970532 -76 ACTAAATATACCATTATTTTCTTACAATAA 6 147 0 CCATTATTTT 0.787019 -49 GTTCCCACTCTTTTCCTCATATGT 7 16 0 CCACTCTTTT 0.844795 -14 CGGGTGATATCCGGTCTTTTTTTTGCATGC 8 54 1 CCGGTCTTTT 0.905301 -178 AAGAAGTGTGCCAGTCTTTTGAGCCCGTAA 8 170 0 CCAGTCTTTT 0.898536 -62 GTCACCTCTTCCTTTCTTTTAAACAGTCAT 9 276 0 CCTTTCTTTT 0.973125 -25 GAACGTTTTCCCTCTATTATATATCTGTTT 10 38 1 CCTCTATTAT 0.61077 -77 TTTGATTCTACCTTGATTGTTCACAAAATA 12 85 0 CCTTGATTGT 0.85106 -143 ACTGTCTCCCCCTTGTTTTTTCTAACAGTG 14 73 0 CCTTGTTTTT 0.662459 -20 AGTTTCTCCTCCTTTCTTGTCTATTTTTCT 15 22 0 CCTTTCTTGT 0.956307 -279 CTGTTACCACCTTTCTTGTTTCGACTCCG 17 106 0 CCTTTCTTGT 0.956307 -19 CTTTTCATTTCCTTTATTGTCCAGCGGAAA 18 30 1 CCTTTATTGT 0.892551 -123 ********** Masking position 7 Map Score: 22.4161 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 155 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 2 GGAAAGGAGTTTTTTAACGATTATTAAACTATAAAAAT 1 80 0 TTTTATTTAA 0.859574 -221 GGTGAATACTTTGTTACTTTAGCGTCACAGACATGAAA 1 227 1 TTTTAGGTAC 0.681832 -74 TGTATTGAGGTTATTAGCGAATAGACAAATCGGTTGCC 3 35 1 TTTTATGAAA 0.560496 -266 TTGCCGTTTGTTGTTTAAAAATTGTTAACAATTTTGTA 3 68 1 TTTTTTGTAA 0.945777 -233 TGTAGGTTAATTGTAATGATTTTGTGAACAGCCTATAC 4 44 1 TTTAATGTAA 0.791014 -257 AACAGGGCAATTATTTTGCGTTGGTAATATGGAGAACT 5 12 1 TTTTTTGTAT 0.543318 -289 TCTACCCTATTTTTTATATTCTGGTTAACTGGCGCTGA 5 126 0 TTTTATGTAA 0.954418 -175 AAAGCATTTCTTATCAATCTATAGTAAATTTTGAAGAT 5 181 0 TTTCATGTAA 0.688381 -120 GCATGGTCAGTTTTTAATTTGGGATAAAGGTTCAGCCG 5 242 1 TTTTAGATAA 0.640405 -59 TCCCTTTATTTTGTTAGCCTTTTTTGAATCAAGCACTG 6 14 0 TTTTATTTAA 0.859833 -182 AAATATACCATTATTTTCTTACAATAAATTAGAGAAAA 6 136 0 TTTTTCATAA 0.386301 -60 ATCCGGTCTTTTTTTTGCATGCTGTAAAACGAGACAAA 8 62 1 TTTTTCGTAA 0.803592 -170 TTGACGGTTCTTCTTTATTTGGTGTAAACTAATCCATG 9 63 1 TTTTTGGTAA 0.906274 -238 TTGAACTGTATTATTTCGAAGTTGTAAAAAACTAATAC 9 113 0 TTTTTTGTAA 0.945901 -188 TTTCCCTCTATTATATATCTGTTTTCAATGCTTACGAT 10 44 1 TTTATTTTAA 0.481286 -71 TTGGCGTTTGTTTTTTCGAATGATTAAATTTTTTGTTT 12 29 1 TTTTTGTTAA 0.739683 -199 AATGATTAAATTTTTTGTTTTTTATAAAGGTTTTTTAC 12 47 1 TTTTTTATAA 0.729063 -181 TTATAAAGGTTTTTTACTATTTTGTGAACAATCAAGGT 12 68 1 TTTTATGTAA 0.954265 -160 GGAAGCGTTTTTATTACATAATTTTGACACAGCGTTCG 12 140 1 TTTTATTTAC 0.531843 -88 CGTTCGAAAGTTATTTCAAGATAGTGAATCAATCACTT 12 172 1 TTTTTTGTAA 0.945925 -56 CCCTTGTTTTTTCTAACAGTGTGGTCAATCATTGTCTG 14 56 0 TTTAATGTAA 0.791016 -37 AAAACCATCATTTTTACCCTCGCTTAAATAGTTCCTTA 15 69 1 TTTTAGTTAA 0.772498 -232 ** *** * ** ** Masking position 4 Map Score: 14.9296 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 124 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 3 GATATCATATAAAGGGGGAGAGGAAA 6 180 1 AAAGGGGGAG 0.986774 -16 GATCATTGTCAAAGGCCGGGTGATATCCGG 8 38 1 AAAGGCCGGG 0.920074 -194 TGTTTAAAAGAAAGGAAGAGGTGACTTAGT 9 281 1 AAAGGAAGAG 0.914473 -20 TTAGAAAAAACAAGGGGGAGACAGT 14 78 1 CAAGGGGGAG 0.958259 -15 AATAGACAAGAAAGGAGGAGAAACTGCTTC 15 27 1 AAAGGAGGAG 0.985738 -274 TTAAAAGCATAAAGGAGGGGCTTGA 16 59 1 AAAGGAGGGG 0.978951 -15 TTGCATAATAAAAGGCGGAGTCGAAACAAG 17 91 1 AAAGGCGGAG 0.986774 -34 ********** Masking position 3 Map Score: 8.92232 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 23 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 4 GATTTCAATCAAAACCTGTATGGACATAAGG 1 198 1 AAACCTGTAT 0.691098 -103 TAATAACCTCAATACATTCATGAGATTACCA 3 20 0 AAACATTCAT 0.849626 -281 ACAAAAATCAAATCCTTTCATTATGGGATAC 5 279 0 AACCTTTCAT 0.931869 -22 ATTGTGTAAAAATCCCTTTATTTTGTTAGCC 6 33 0 AACCCTTTAT 0.963466 -163 ATGTAAAGCGAATACATTTATTGAAAATCAG 9 20 1 AAACATTTAT 0.847206 -281 CAGTTTGCCAAAACCTTTTATGTAGGATAGT 9 162 0 AACCTTTTAT 0.930664 -139 TTAGACGTGCATTCCTTTTATACATACAAAC 9 246 0 ATCCTTTTAT 0.588207 -55 TAATAGAGGGAAAACGTTCATCTTCCCTCTC 10 26 0 AAACGTTCAT 0.768199 -89 AAAATAGTAAAAAACCTTTATAAAAAACAAA 12 60 0 AAACCTTTAT 0.934143 -168 GTATGACAAAAAGCCTTTTATAGGCTTTTTT 14 17 1 AACCTTTTAT 0.930664 -76 TCATCAATAGAAAACCATCATTTTTACCCTC 15 59 1 AAACCATCAT 0.60602 -242 GCAGATGGCAAAGCCATTCATTTTTAAAAGC 16 36 1 AACCATTCAT 0.913074 -38 CTTCAGAAAACCCCTTTATCTTTTCATTT 18 9 1 AACCCTTTAT 0.963466 -144 ** ******** Masking position 10 Map Score: 11.0378 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 132 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 5 ATTGAACTCTCGCCGGAAAGCTCAATAAGACAGGTT 2 85 0 CGCCGACTAT 0.879438 -76 ACCTTGCTGCACCCAGAAATCCATAGGGTATGTGAA 3 150 0 ACCCGACCAG 0.976221 -151 AGGTAGCAAGCGCCAGAATCCCCAGGAGCTTACATA 3 182 1 CGCCGACCGG 0.970086 -119 CCTATACTGCCGCCAGGTCTCCGGAACACCCTGCAA 4 75 1 CGCCGTCCAA 0.972268 -226 TCTCCGGAACACCCTGCAATCCCGAGCCACCCAGCG 4 92 1 ACCCGACCAG 0.976181 -209 CTGTCTGACCCGCAAGCAGACCGGAGGAAGGAAATC 4 193 1 CGCAGACCAG 0.963067 -108 TTAACCTCTGTGCCCGTAGTCCCCAGGGAATAATAA 4 253 1 TGCCGACCAG 0.95094 -48 CGAAGGTCAGCGCCAGTTAACCAGAATATAAAAAAT 5 120 1 CGCCGTCCAA 0.972346 -181 TTTAGCCGATCCCCAGTTTGCCAAAACCTTTTATGT 9 170 0 CCCCGTCCAA 0.967213 -131 ACTAAAAAAGCCCCTGTATGCTCAATACAAAAGGGC 13 21 0 CCCCGACTAT 0.859478 -43 GTGCTGTCATACCAGGTATACCGAAACATTCGTGCA 17 34 0 ACCAGACCAA 0.762636 -91 **** * * ** ** Masking position 11 Map Score: 8.03031 Number of sites scoring better than the average of aligned sites = 489 Number in coding regions = 455 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 6 GAACCGATTCACTTACCAATTTTGTGATTTTT 1 41 0 ACTTCCAATT 0.616513 -260 ACTGTGCACATTTTAACAACTTGACATATATA 1 161 0 TTTTACAATT 0.874405 -140 AGTCAATTGGTCTTACCAATTTCATGTCTGTG 1 252 0 TCTTCCAATT 0.895476 -49 TTTACAAAATTGTTAACAATTTTTAAACAACA 3 76 0 TGTTACAATT 0.949874 -225 ATCCGTCGGTATTTTACAAAATTGTTAACAAT 3 88 0 ATTTACAAAT 0.496467 -213 CAGTATAGGCTGTTCACAAAATCATTACAATT 4 52 0 TGTTACAAAT 0.935018 -249 AATAAAGGGATTTTTACACAATTCTTGACTAA 6 42 1 TTTTACACAT 0.708687 -154 TTGTATTAGTTTTTTACAACTTCGAAATAATA 9 111 1 TTTTACAATT 0.874405 -190 CTACCTTGATTGTTCACAAAATAGTAAAAAAC 12 76 0 TGTTACAAAT 0.935018 -152 ATTTTACCACTGTTTGCAATTTGATTCTACCT 12 102 0 TGTTGCAATT 0.81575 -126 GCTAGTATTTTGTTTCCAAAAATGGCACACAA 15 243 0 TGTTCCAAAA 0.590637 -58 CTGTTACCACCTTTCTTGTTTCG 17 112 0 TGTTCCACTT 0.898848 -13 CGTTTTCTTCTCTTGACAAAATATTTTTTCCG 18 54 0 TCTTACAAAT 0.864571 -99 CACAACCCTATGTTACCACGTTTTCTTCTCTT 18 72 0 TGTTCCACTT 0.898848 -81 **** **** ** Masking position 8 Map Score: 6.86675 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 108 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 7 TTTACGTAGGAAAGGAGTTTTTTAACGATT 1 96 0 AAAGGAGTTT 0.793186 -205 TTTTTGGATAAAAAGGATTCCAACCTAAAT 5 63 0 AAAAGGATTC 0.774825 -238 ATCCCATAATGAAAGGATTTGATTTTTGTT 5 281 1 GAAAGGATTT 0.774825 -20 CTAACAAAATAAAGGGATTTTTACACAATT 6 35 1 AAAGGGATTT 0.94968 -161 TATCCTACATAAAAGGTTTTGGCAAACTGG 9 164 1 AAAAGGTTTT 0.851208 -137 AAAAGCCTATAAAAGGCTTTTTGTCATACT 14 16 0 AAAAGGCTTT 0.893067 -77 CAAATGTTTGAAAAGGGTTTAACTTGCTGA 15 194 1 AAAAGGGTTT 0.968018 -107 ATGAAAAGATAAAGGGGTTTTCTGAAG 18 8 0 AAAGGGGTTT 0.974868 -145 TTTTTCATACAAAGGGGTATCGGG 18 139 1 AAAGGGGTAT 0.860608 -14 ********** Masking position 3 Map Score: 4.88625 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 103 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 8 TCTTAAGCCACTTGCCGAAGTCAATTGGTC 1 272 0 CTTGCCGAAG 0.923033 -29 CTATGGATTTCTGGGTGCAGCAAGGTAGCA 3 160 1 CTGGGTGCAG 0.927629 -141 CGTCGTCTTTCAGGCCGCAGCGGCGTTAGC 3 245 0 CAGGCCGCAG 0.974958 -56 TTCCGGAGACCTGGCGGCAGTATAGGCTGT 4 71 0 CTGGCGGCAG 0.947096 -230 GTTTTCGCATCTGGAAGCAGTGTTTTGCAT 4 140 1 CTGGAAGCAG 0.875947 -161 TTTTCAAACATTTGGCGCAGCATTTTCAGC 15 178 0 TTTGGCGCAG 0.864152 -123 AGAAGCTGCGCTTGCCGCAGATGGCAAAGC 16 20 1 CTTGCCGCAG 0.986904 -54 ********** Masking position 9 Map Score: 3.62307 Number of sites scoring better than the average of aligned sites = 626 Number in coding regions = 606 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 9 TGATTTTTCTGGTAAAAATTATC 2 4 1 TTTTTCTGGT 0.95442 -157 GCTTTTTTCTGGTAATCTCATGA 3 4 1 TTTTTCTGGT 0.95442 -297 CTACATATAGTTTGTCGGGTTTTATCCTGA 4 19 0 TTTGTCGGGT 0.957732 -282 AACTGATTCATTTGTCTCGTTTTACAGCAT 8 80 0 TTTGTCTCGT 0.970051 -152 GTTTGAGACGTGTGTCTCGTTTTGTCTCAA 8 109 0 TGTGTCTCGT 0.922137 -123 GTGGTCAATCATTGTCTGGTATAAACAAAA 14 44 0 ATTGTCTGGT 0.938605 -49 ********** Masking position 5 Map Score: 2.47242 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 50 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 10 ATAAGACAGGTTCTACGTTTAGTTGCCGCGCTTTTA 2 61 0 TCACGTGTTC 0.966426 -100 GGTCGTTCTATCCGTCGGTATTTTACAAAATTGTTA 3 93 0 TCTCGTTTTC 0.980707 -208 AACGACACGTTACAACGCTGGGTGGCTCGGGATTGC 4 107 0 TCACGTGTGC 0.972033 -194 AGGAAATAAATACGTCGATCATTGTCAAAGGCCGGG 8 22 1 TCTCGTTTGC 0.983949 -210 GTCAATCGTTTTCATCGCTGATTTTCAATAAATGTA 9 32 0 TCTCGTTTTC 0.980707 -269 CCCTTAATCCTATGCTTTTTGGCGTTTGTTTTT 12 8 1 TCATGTTTGC 0.933512 -220 AATTTGATTCTACCTTGATTGTTCACAAAATAGTAA 12 81 0 TCTTGTTTCC 0.839681 -147 TAAAAACGCTTCCAACGATATTTTACCACTGTTTGC 12 117 0 TCACGTTTTC 0.980706 -111 * * *** * *** * Masking position 9 Map Score: 3.2118 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 105 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 11 CCGACGGATAGAACGACCCGGTGGTGGTTAG 3 111 1 GAACGACCCG 0.968232 -190 GGCGTGAAGCTAACGCCGCTGCGGCCTGAAA 3 237 1 TAACGCCGCG 0.820452 -64 GCTGCGGCCTGAAAGACGACGGGTATGACCG 3 254 1 GAAAGACGAG 0.924357 -47 GCAGTTATAGAAAGGACGCTGTCTGACCCGC 4 175 1 AAAGGACGCG 0.948119 -126 AGGCCACTAAGAAAGACGAAGGTCAGCGCCA 5 104 1 GAAAGACGAG 0.924357 -197 CTGCGTACAAAAAAGACCCGGATTTACCGAA 6 88 0 AAAAGACCCG 0.907237 -108 TGTTTAAAAGAAAGGAAGAGGTGACTTAGT 9 281 1 AAAGGAAGAG 0.503814 -20 AGTATACTAAAAAAGCCCCTGTATGCTCAAT 13 31 0 AAAAGCCCCG 0.807888 -33 TTCTATTGATGAACGAAGCAGTTTCTCCTCC 15 40 0 GAACGAAGCG 0.931163 -261 TTTAAAGGTCGAACGATGCTGAAAATGCTGC 15 161 1 GAACGATGCG 0.884675 -140 ********* * Masking position 3 Map Score: 3.22571 Number of sites scoring better than the average of aligned sites = 866 Number in coding regions = 804 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 12 TGTTGTAAATCAAGCGCATATAAAAGCGCG 2 41 1 CAAGCGCATA 0.83951 -120 TTTTAAACAACAAACGGCAACCGATTTGTC 3 58 0 CAAACGGCAA 0.912635 -243 AGCAAGGTAGCAAGCGCCAGAATCCCCAGG 3 178 1 CAAGCGCCAG 0.963211 -123 CTCCATATTACCAACGCAAAATAATTGCCC 5 16 0 CCAACGCAAA 0.94804 -285 AAGACGAAGGTCAGCGCCAGTTAACCAGAA 5 116 1 TCAGCGCCAG 0.855855 -185 TTCGAAAAAACAAACGCCAAAAAGCATAGG 12 19 0 CAAACGCCAA 0.967238 -209 TTTGCAGAATAAACGCAAACATCTGCACG 17 10 1 TAAACGCAAA 0.809798 -115 CCTTTATTGTCCAGCGGAAAAAATATTTTG 18 40 1 CCAGCGGAAA 0.911024 -113 ********** Masking position 3 Map Score: 1.86218 Number of sites scoring better than the average of aligned sites = 1350 Number in coding regions = 1310 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 13 AGTCTACATTTGTGCATAGTTACAACTTTGA 1 125 1 TGTGCAAGTT 0.923705 -176 ATCATGAAACTGTGCACATTTTAACAACTTG 1 170 0 TGTGCAATTT 0.970684 -131 AAAAACATATCGTGCTTATGTAAAATGTTAG 15 115 1 CGTGCTATGT 0.848815 -186 CCGAAACATTCGTGCAGATGTTTGCGTTTAT 17 19 0 CGTGCAATGT 0.957908 -106 AACATAGGGTTGTGCAAATTATTGCAACGGA 18 90 1 TGTGCAATTA 0.890934 -63 AATAAATAGGTGTGCAAATTTTTTCATACAA 18 120 1 TGTGCAATTT 0.970684 -33 ****** **** Masking position 8 Map Score: 0.349109 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 28 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 14 ACGACCCGGTGGTGGTTAGGGTATTACTTC 3 123 1 GGTGGTTAGG 0.944686 -178 AGTAAGTGACTGGGGTGAGGGCGTGAAGCT 3 218 1 TGGGGTGAGG 0.888608 -83 GGGATTGCAGGGTGTTCCGGAGACCTGGCG 4 85 0 GGTGTTCCGG 0.812548 -216 TACAACGCTGGGTGGCTCGGGATTGCAGGG 4 103 0 GGTGGCTCGG 0.953897 -198 ATCATATAAAGGGGGAGAGGAAA 6 183 1 GGGGGAGAGG 0.966934 -13 TTTGGCAAACTGGGGATCGGCTAAAATATA 9 181 1 TGGGGATCGG 0.952093 -120 TTCATACAAAGGGGTATCGGG 18 142 1 GGGGTATCGG 0.952093 -11 ********** Masking position 4 Map Score: 0.347168 Number of sites scoring better than the average of aligned sites = 325 Number in coding regions = 301 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 15 GCTCAATAAGACAGGTTCTACGTTTAGTTGC 2 71 0 ACAGTTCTAC 0.868387 -90 AACTGACCATGCTTCTTTTACACTTATCGCA 5 223 0 GCTTTTTTAC 0.766724 -78 TTTTTTGTACGCAGCTTTTACTCAGCCTGTC 6 105 1 GCAGTTTTAC 0.96713 -91 AGATGAGAAGACTGATTTTACGGGCTCAAAA 8 153 1 ACTGTTTTAC 0.870668 -79 CGTTTTCATCGCTGATTTTCAATAAATGTAT 9 31 0 GCTGTTTTCA 0.798755 -270 GATGAACGAAGCAGTTTCTCCTCCTTTCTTG 15 33 0 GCAGTTCTCC 0.97169 -268 CAAAATACTAGCTGTTTTTGCAAAAAAACAG 15 263 1 GCTGTTTTGC 0.929852 -38 TGCGGCAAGCGCAGCTTCTCCAATTGCT 16 8 0 GCAGTTCTCC 0.97169 -66 **** ****** Masking position 6 Map Score: 1.12326 Number of sites scoring better than the average of aligned sites = 790 Number in coding regions = 750 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899