AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ityrR_ecoli_bsub_300.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 aroP 300 aromatic amino acid transport protein #2 aroL 182 shikimate kinase II #3 yaiA 49 orf, hypothetical protein #4 aroM 257 protein of aro operon, regulated by aroR #5 aroG 300 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (DAHP synthetase, phenylalanine repressible) #6 ycjX 155 putative EC 2.1 enzymes #7 tyrR 147 transcriptional regulation of aroF, aroG, tyrA and aromatic amino acid transport #8 tyrP 190 tyrosine-specific transport system #9 aroF 170 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (DAHP synthetase, tyrosine repressible) #10 mtr 153 tryptophan-specific transport protein #11 deaD 128 inducible ATP-independent RNA helicase #12 yhbM 108 putative control proteins #13 pnp 177 polynucleotide phosphorylase; cytidylate kinase activity #14 rpsO 148 30S ribosomal subunit protein S15 #15 rbfA 163 ribosome-binding factor A #16 infB 24 protein chain initiation factor IF-2 #17 nusA 27 transcription pausing; L factor #18 yhbC 300 orf, hypothetical protein #19 dnaB 82 replicative DNA helicase; part of primosome #20 alr 52 alanine racemase 1 #21 tyrB 252 tyrosine aminotransferase, tyrosine repressible #22 ydgF 171 similar to amino acid ABC transporter (permease) #23 dinB 168 nuclease inhibitor #24 gabP 300 gamma-aminobutyrate (GABA) permease #25 yqiR 152 similar to transcriptional regulator (sigma-L-dependent) #26 aapA 300 amino acid permease #27 ytnA 135 similar to proline permease #28 asnB 149 asparagine synthetase #29 metK 300 S-adenosylmethionine synthetase #30 gerAA 300 gerAA #31 yvbW 300 similar to amino acid permease #32 rocR 240 transcriptional regulator (NtrC/NifA family) Motif number 1 CCGCATCAGACTGCTCGGAAGGGA 4 2 1 CGCACAACGC 0.772232 -256 GCAGCCGTTATGCCTTAACCTGCGCCGCAGATA 8 135 1 TGCCTACCGC 0.98278 -56 CGAACAACAACGCCCTCACCCGTTAAGGTGATG 11 48 0 CGCCTCCCGT 0.804821 -81 GGTTGCCATTTGCCCTCCGCTGCGGCGGGGGGC 12 11 1 TGCCTCGCGC 0.858033 -98 TCCAGTGAATTGCTGCCGTCAGCTTGAAAAAAG 13 48 0 TGCTCCTCGC 0.791885 -130 GCAGCGTAAACGCCTTATCCCGCATGGAACCCT 15 18 0 CGCCTACCGC 0.986285 -146 AAGGCGTTTACGCTGCATCCGGCATGGATTGCC 15 35 1 CGCTCACCGC 0.985316 -129 GCTACCAGGCTGCTCCACCCCGCGCCTGAAACG 18 25 0 TGCTCACCGC 0.981568 -276 TTCTGGAAAGTGCTCCAGACCGCAGTTGCGGTT 18 182 1 TGCTCAACGC 0.860824 -119 AAGGCATTCACGCCGCATCCGGCACAGACAATC 21 27 0 CGCCCACCGC 0.99475 -226 GCGGCGTGAATGCCTTATCCGGCCAATAAAATC 21 44 1 TGCCTACCGC 0.98278 -209 ATCGATTTGATCCCCCTGCCGGCCTCAATCATA 26 41 1 TCCCCTCCGC 0.765566 -260 ATAGGGCCTGTCCCTCCGCCAGCTCGGGA 29 7 0 TCCCCCCCGC 0.961797 -294 GATTTGCTTCCTCCTGCACAAGGCCTC 29 284 0 TGCTCCCCGC 0.982984 -17 CAGGCTGCGTCGCACCACCCCGCAGCTCTCTGT 31 48 0 CGCACACCGC 0.966878 -253 CAAAAAAGCCCGCCGTCTCCTACCTAATCTAAT 31 246 0 CGCCTCCCAC 0.804821 -55 **** ** ** ** Masking position 10 Map Score: 21.3886 Number of sites scoring better than the average of aligned sites = 2131 Number in coding regions = 1738 Number in noncoding regions = 393 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 2 CATAGTGTAAAACCCCGTTTACACATTCTG 5 218 1 AACCCCGTTT 0.925679 -83 TAATATATACAGCCCCGATTTTTACCATCG 10 43 1 AGCCCCGATT 0.9728 -111 ACAGAAAAAAAGCCCCGATGGTAAAAATCG 10 58 0 AGCCCCGATG 0.918694 -96 GGGCCACTCAGGCCCCCTTTTCTGAAACTC 13 18 0 GGCCCCCTTT 0.764602 -160 GGGCCTGAGTGGCCCCTTTTTTCAAGCTGA 13 33 1 GGCCCCTTTT 0.939668 -145 AGGGGCTGTTAGCCCCTTTTTAAAATTAAT 15 123 0 AGCCCCTTTT 0.983056 -41 AGGGGCTAACAGCCCCTTTTTTGTCAGGAG 15 136 1 AGCCCCTTTT 0.983056 -28 AGTTATATAAAGCCCCGATTTATCGGGGTT 18 224 1 AGCCCCGATT 0.9728 -77 GATAACAAAAAACCCCGATAAATCGGGGCT 18 234 0 AACCCCGATA 0.632952 -67 ACTGGGCTTTAGGCCCTTTTTTTATGTCTT 18 277 1 AGGCCCTTTT 0.905952 -24 CCATTTAGGGAGCCGCTTTT 22 1 0 AGCCGCTTTT 0.905951 -171 CCCTAAATGGAGCCGCTTTTTTCGGGAAAT 22 21 1 AGCCGCTTTT 0.905951 -151 CTTCAGAAAACCCCTTTATCTTTTCATT 25 9 1 AACCCCTTTA 0.736657 -144 GTCATCATTGAACCCCTATTTATAGACGCT 28 106 0 AACCCCTATT 0.902749 -44 GCGGAGGGACAGGCCCTATGAAGCCCAGCA 29 21 1 AGGCCCTATG 0.673484 -280 ********** Masking position 9 Map Score: 19.1305 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 133 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 3 GTTCATAGTGTAAAACCCCGTTTACACATT 5 215 1 TAAAACCCCG 0.887917 -86 CCTCCTCAAAAAAAGCCTAGCGTAGCGATT 8 15 1 AAAAGCCTAG 0.694497 -176 AAATAATATATACAGCCCCGATTTTTACCA 10 40 1 TACAGCCCCG 0.951879 -114 AAGACAGAAAAAAAGCCCCGATGGTAAAAA 10 61 0 AAAAGCCCCG 0.986401 -93 CTGCCCGGTTAAAAGCCCCCCGCCGCAGCG 12 28 0 AAAAGCCCCC 0.965815 -81 TCTATGTGGGTAAAGCCTCTCATTAGCCGC 13 128 0 TAAAGCCTCT 0.577964 -50 AAAAGGGGCTAACAGCCCCTTTTTTGTCAG 15 133 1 AACAGCCCCT 0.798446 -31 GGATGAGGTGAAAAGCCCGCG 17 17 1 AAAAGCCCGC 0.883104 -11 TTCAGTTATATAAAGCCCCGATTTATCGGG 18 221 1 TAAAGCCCCG 0.98428 -80 TCAGATAACAAAAAACCCCGATAAATCGGG 18 237 0 AAAAACCCCG 0.901743 -64 AAAAAGGGCCTAAAGCCCAGTTATTCTGTA 18 268 0 TAAAGCCCAG 0.939428 -33 ACAGGCCCTATGAAGCCCAGCAACCGGTTT 29 29 1 TGAAGCCCAG 0.709824 -272 TCAAAAACAAAAAAGCCCGCCGTCTCCTAC 31 256 0 AAAAGCCCGC 0.883104 -45 ********** Masking position 4 Map Score: 12.9826 Number of sites scoring better than the average of aligned sites = 382 Number in coding regions = 312 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 4 ACCATGCATAAAGCGGGTGCATTCGCTGCCG 1 135 1 AAGCGGGTCA 0.918031 -166 AATGCGGCGAAAGCCGGTGTCATGAGAATAG 2 138 0 AAGCCGGTTC 0.880894 -45 AAGTCTTCATAAGCGGCAATCGCTACGCTAG 8 31 0 AAGCGGCATC 0.974144 -160 ACGCGACGTTAAGCGGCAGTATTCTACTCGT 14 40 0 AAGCGGCATA 0.937388 -109 TAAGGCGTTTACGCTGCATCCGGCATGGATT 15 34 1 ACGCTGCACC 0.770134 -130 TAAGGCATTCACGCCGCATCCGGCACAGACA 21 30 0 ACGCCGCACC 0.838251 -223 AAAAGCGGCTCCCTAAATGGAGC 22 3 1 AAGCGGCTCC 0.97801 -169 TTCCCGAAAAAAGCGGCTCCATTTAGGGAGC 22 18 0 AAGCGGCTCA 0.946448 -154 AATTTGAAATAAGCTGGTATATTTTCTTACA 24 194 1 AAGCTGGTTA 0.655171 -107 CTTAACCAGTAAGCGGCTATAAAA 28 4 0 AAGCGGCTTA 0.945486 -146 CTTACTGGTTAAGCGGCTTTCCCTTTTTTAT 28 22 1 AAGCGGCTTC 0.977602 -128 TTCAAGATATACGCGGGAATCCTTTGAATAT 30 41 1 ACGCGGGATC 0.923387 -260 TACAGGTCAAAAGCAGGATTCTTCATGAAGA 31 164 1 AAGCAGGATC 0.700649 -137 ******** ** Masking position 1 Map Score: 10.8464 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 415 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 5 GAGTGCCACTACAAGGGATCTGCGTCACATT 4 39 1 ACAAGGGTCT 0.755859 -219 GCAGGTGAATATAAGGCATTGGTTTAAGATT 5 50 1 ATAAGGCTTG 0.813426 -251 CCGGTTGCTAACAAGGCGTCCTGCCCGGTTA 12 47 0 ACAAGGCTCC 0.979531 -62 TCCATGCGGGATAAGGCGTTTACGCTGCATC 15 23 1 ATAAGGCTTT 0.881392 -141 TATTGGCCGGATAAGGCATTCACGCCGCATC 21 41 0 ATAAGGCTTC 0.950036 -212 CAGACAACAAGGCTTTCGAGTAGTCGA 27 7 1 ACAAGGCTTC 0.983033 -129 AAGGATAACAACAAGGCTTTCGACTACTCGA 27 26 0 ACAAGGCTTC 0.983033 -110 TATCATATATACAAGGTCTTTCGGGAGGCCT 29 260 1 ACAAGGTTTT 0.716913 -41 TTCCTCCTGCACAAGGCCTCCCGAAAGACCT 29 273 0 ACAAGGCTCC 0.979531 -28 ******* *** Masking position 4 Map Score: 6.67173 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 55 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 6 ATTTATTATTTACACTTCATTCTTGAATATTTATTGGTA 2 16 1 TCCTTCTATA 0.642906 -167 GAGGGCTTCTCTCCAGTGAAAAATAGTGCGACTGC 10 129 0 TCCTCCTATA 0.917477 -25 TATCTTCCCCTCCTCATTATAGTTTACCC 23 1 1 TTTTCCTTTA 0.674431 -168 TGTCAATTAGTTTATTCCTCTAAACTATATATGTCAACA 23 59 1 TTTTCCTATA 0.916926 -110 TGACAAAATATTTTTTCCGCTGGACAATAAAGGAAATGA 25 34 0 TTTTCCTATA 0.908908 -119 TGTTACCACGTTTTCTTCTCTTGACAAAATATTTTTTCC 25 55 0 TTCTTCTAAA 0.673307 -98 TTTTATTTTCCTCCAGTAATAAAAAGATGAGTAAA 26 276 0 TTCTCCTAAA 0.946403 -25 GCTTCTTCTCCCCTAGAAAAAAATATCATTAT 27 114 0 TTCTCCTAAA 0.946558 -22 TTTGTCCTGCCGTACTCCTTTGATGTATAAGAGACATCA 30 84 1 CTCTCCTATA 0.773253 -217 TGCCACTTCGTATCCTCCGCTTTCATAAAAAAACTTACT 30 188 1 TTCTCCTAAA 0.94667 -113 GTAGAGGTTATCTTTTCCTGTTAAAAAAATGATATACTG 30 245 0 TTTTCCTAAA 0.893405 -56 GAATATTCAATCTATTCCGTTCCGTCTTACCACTCCCGG 31 99 0 TTTTCCTTTA 0.674431 -202 CATGTTATCCTGCTTTCCCTTTATATAAATGCAAGTTCT 32 41 1 TCTTCCTAAA 0.847519 -200 CTTTTGCATATCCTCTCCGTTTTTTTATAAAATAGAAGC 32 178 1 TCCTCCTATA 0.939399 -63 * * **** * *** Masking position 19 Map Score: 7.24507 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 41 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 GTAGCAGCAGACGTGCACGGCATAATGTAA 4 144 0 ACGTGCACGG 0.758763 -114 GGTGCTTCACACTTGCCCGGTAATTAACGA 4 212 1 ACTTGCCCGG 0.982879 -46 ATTGATTATCAACTGCCCGTGTTGTCATCG 6 66 0 AACTGCCCGT 0.945629 -90 CTTTACGCCGAAGTGCCCGTTTTTCCGTCT 7 37 1 AAGTGCCCGT 0.916253 -111 TAACAAGGCGTCCTGCCCGGTTAAAAGCCC 12 40 0 TCCTGCCCGG 0.9648 -69 TGTTTTAACCACCTGCCCGTAAACCTGGAG 21 224 1 ACCTGCCCGT 0.977436 -29 TCTTCTTTGAACTCGCCCGGGAGTGGTAAG 31 83 1 ACTCGCCCGG 0.947418 -218 ********** Masking position 5 Map Score: 3.17223 Number of sites scoring better than the average of aligned sites = 259 Number in coding regions = 236 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 8 ACGCTAGGCTTTTTTTGAGGAGGGACG 8 3 0 TTTTGGAGGA 0.981523 -188 GTCGCACTATTTTTCACTGGAGAGAAGCCCTC 10 132 1 TTTTGGAGGA 0.981519 -22 ACAGCCCCTTTTTTGTCAGGAGAATTTATT 15 144 1 TTTTGGAGAT 0.900617 -20 CAATAAACAATTTTCAATGGAGGAACACATAAA 22 149 1 TTTTGGAGAA 0.98471 -23 TTTGATGGGATTTTTGGCGGAGCAAATAAATTGGA 24 37 0 TTTTGGAGAA 0.984707 -264 AATGATTGCATTTTAAAAGGAGGTAACTT 24 282 1 TTTTGGAGTA 0.930414 -19 ACTCATCTTTTTATTACTGGAGGAAAATAAAA 26 279 1 TTATGGAGAA 0.900597 -22 TAATGATATTTTTTTCTAGGGGAGAAGAAGC 27 115 1 TTTTGGGGGA 0.917186 -21 TAAAAAAACCTTTTCCATCGAGGAAAGGGTTTGGT 29 158 0 TTTTCGAGAA 0.892923 -143 TGTGTTAGAGTATTTCATGGAGTAAGTTTTTTTAT 30 212 0 TATTGGAGAA 0.900598 -89 **** **** ** Masking position 4 Map Score: 5.44905 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 19 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 CTTCTTTGATGTAAACAAATTAATACAACAAACGGAA 1 214 1 GAAAATTACA 0.848683 -87 AGAATGAAGTGTAAATAATAAATTACAT 2 2 0 GAAATATACA 0.925259 -181 AATTTCGATTGTAAAGAAAAAATTCCACTTAAAGTGA 2 78 0 GAAAAATCCA 0.745123 -105 TACATATGGTGTAAATATAAATGTACAATAAAAAGCA 8 82 0 GAAAAATACA 0.915895 -109 CCTTACCTCTGTATAGATAAATTTACACTCCCT 9 7 0 GAAAAATACA 0.915895 -164 TCCATATTTCGTACATTTTTATTTACACAGGCAATTT 9 59 0 GAATTTTACA 0.766563 -112 AACACATAAAGTAAAGTTTTCAATCCATATTTCGTAC 9 82 0 GAATTTTCCA 0.468526 -89 AATCGGGGCTGTATATATTATTTTACAGATTGTGTTC 10 26 0 GAAATATACA 0.925259 -128 TAGTTTAGAGGAATAAACTAATTGACATTGAACATAA 23 49 0 GAAATAGACA 0.810979 -120 ATCACACAGCGAATAAAAAACGAAACATTTTTTCCAC 24 125 1 GAAAAAAACA 0.777588 -176 CGCTGAAAGCGCAAACAAAACACTACAAATTTGAAAT 24 167 1 GAAAAATACA 0.915895 -134 AAATAGGTGTGCAAATTTTTTCATACAAAGGGGTATC 25 123 1 GAATTTTACA 0.766563 -30 GAGTAAAACAGGAAAGTCATTTGGACAATCTGACAGG 26 115 0 GAATATGACA 0.500281 -186 TCACTCAGTTGAACATAATAAATAACAGAGAAACCGG 29 52 0 GAAATAAACA 0.798972 -249 CCTTGTCCTCGAAAATTGTAGAAAACACACGAATTCT 32 91 0 GAATTAAACA 0.671805 -150 * * * * ** **** Masking position 5 Map Score: 5.83859 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 39 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 10 CCCGTGAAATAAGGAAGAACG 3 39 1 AGGAAGAACG 0.829535 -11 GTAATTAACGACGAAAGAAAAGTAAGGTGGA 4 231 1 AGAAAGAAAA 0.788938 -27 CATTGACACAAAGACGGAAAAACGGGCACTT 7 47 0 AGACGGAAAA 0.854819 -101 GGCGCAGGTTAAGGCATAACGGCTGCTTCGT 8 130 0 AGGCATAACG 0.629042 -61 AAAGATCGTCAGGACAGAAGAAAGC 8 176 1 AGACAGAAGA 0.687284 -15 CTCAGCGAGGATGACGTAACGATAACACATA 9 111 0 AGACGTAACG 0.749442 -60 ACGAGTACAAAAGACAGAAAAAAAGCCCCGA 10 70 0 AGACAGAAAA 0.857361 -84 AGTATATAGAATGAAAGGACGCCGATCTCTA 14 115 0 AGAAAGGACG 0.686323 -34 AAACTGTAGCAGGAAGGAACAGC 16 12 1 AGAAGGAACA 0.919773 -13 CCCCAAGACATAAAAAAAGGGCCTA 18 286 0 AGACATAAAA 0.565696 -15 TTATAAGAGCATGAAAGAACATCAACTTATT 21 87 0 AGAAAGAACA 0.921282 -166 ACAATTTTCAATGGAGGAACACATAAA 22 155 1 AGGAGGAACA 0.864257 -17 GTGACGAAGGAACACTTTTTCTCT 24 4 1 AGAAGGAACA 0.919773 -297 TGGCATATTTATGAAATAAAAAAACCTTTTC 29 178 0 AGAAATAAAA 0.447522 -123 TCAAAGGAGTACGGCAGGACAAATCCAAAAT 30 76 0 AGGCAGGACA 0.722968 -225 CGGGAGTGGTAAGACGGAACGGAATAGATTG 31 100 1 AGACGGAACG 0.932445 -201 * ********* Masking position 9 Map Score: 6.68744 Number of sites scoring better than the average of aligned sites = 375 Number in coding regions = 336 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 11 GAATAATGGTATGCGGCAGCGAATGCACCC 1 149 0 ATGCGGCAGC 0.79381 -152 TATGAAAAATGTGACGCAGATCCCTTGTAG 4 47 0 GTGACGCAGA 0.828887 -211 ATGACAAAAAGCGTAGCAGCAGACGTGCAC 4 156 0 GCGTAGCAGC 0.867316 -102 CCGGGCAAGTGTGAAGCACCACTGCTGACA 4 202 0 GTGAAGCACC 0.528237 -56 AGGTTATGAAACGCAGCAGAGAATCTTGAA 5 87 1 ACGCAGCAGA 0.900503 -214 CGTCGGTTTGACGAAGCAGCCGTTATGCCT 8 120 1 ACGAAGCAGC 0.943035 -71 GCCTTAACCTGCGCCGCAGATATCACTCAT 8 146 1 GCGCCGCAGA 0.95865 -45 TAAAAGCCCCCCGCCGCAGCGGAGGGCAAA 12 19 0 CCGCCGCAGC 0.939416 -90 CAGGCGCGGGGTGGAGCAGCCTGGTAGCTC 18 30 1 GTGGAGCAGC 0.793809 -271 ACTTTATCATATGAAGCAGACCCTGACGAT 19 27 0 ATGAAGCAGA 0.654089 -56 TAAGGCATTCACGCCGCATCCGGCACAGAC 21 31 0 ACGCCGCATC 0.78336 -222 GCGTCGCACCACCCCGCAGCTCTCTGTTCT 31 45 0 ACCCCGCAGC 0.831069 -256 GCGGGGTGGTGCGACGCAGCCTGATTCTTC 31 58 1 GCGACGCAGC 0.976884 -243 ********** Masking position 8 Map Score: 6.39107 Number of sites scoring better than the average of aligned sites = 2162 Number in coding regions = 2060 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 12 GCATTCGCTGCCGCATACCATTATTCTTGATCTGA 1 153 1 CGCATCTTAT 0.871112 -148 CTTGATCTGACGGAAGTCTTTTTGTAACAATTCAA 1 178 1 CGAAGCTTTT 0.81755 -123 TGAAGCACCACTGCTGACACTTACTTGTGCTACAA 4 186 0 CGCTGCTTAT 0.76764 -72 CAGCGCAGGACTGAATGCTTTTTATTGTACATTTA 8 67 1 CGAATCTTTT 0.869436 -124 AATCCGGCCCCCGCAACCACTTTCCCTTAGAGTCC 18 92 1 CGCAACTTTC 0.838147 -209 CGATCTTCGCCTTCTTCCGGTTTATTGTGTTTTAA 21 197 1 CTCTTCTTTT 0.75275 -56 AAATTCTTTTCATCAATCCTTTTTTAGTAAAAAAG 22 67 1 CTCAACTTTT 0.807366 -105 TTTATTGAGTCAGCAATCTATTTTTAATGATTATT 22 121 0 CGCAACTTTT 0.967913 -51 CCCGATACCCCTTTGTATGAAAAAAT 25 137 0 CGATACTTTT 0.828684 -16 ACTGGTTAAGCGGCTTTCCCTTTTTTATCGTTGTA 28 25 1 CGCTTCTTTT 0.956355 -125 CTATGAAGCCCAGCAACCGGTTTCTCTGTTATTTA 29 36 1 CGCAACTTTT 0.967913 -265 ACATGTTATCCTGCTTTCCCTTTATATAAATGCAA 32 40 1 CGCTTCTTTT 0.956355 -201 * **** * *** * Masking position 11 Map Score: 3.68186 Number of sites scoring better than the average of aligned sites = 403 Number in coding regions = 372 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 13 GCAATGCGGCGAAAGCCGGTGTCATGAGAA 2 141 0 GAAAGCCGGT 0.753376 -42 GAACGTTAAGTATAGGCGCTCGAAAA 3 7 0 TATAGGCGCT 0.766711 -43 AAGGGATTCTGAGTGCCACTACAAGGGATC 4 29 1 GAGTGCCACT 0.588708 -229 CTAGCGTAGCGATTGCCGCTTATGAAGACT 8 31 1 GATTGCCGCT 0.931351 -160 TCTATGTGGGTAAAGCCTCTCATTAGCCGC 13 128 0 TAAAGCCTCT 0.630036 -50 ACGAGTAGAATACTGCCGCTTAACGTCGCG 14 40 1 TACTGCCGCT 0.819956 -109 GCTCCATTTAGGGAGCCGCTTTT 22 4 0 GGGAGCCGCT 0.940427 -168 GCTCCCTAAATGGAGCCGCTTTTTTCGGGA 22 18 1 TGGAGCCGCT 0.921651 -154 TTTTATAGCCGCTTACTGGTTAA 28 4 1 TATAGCCGCT 0.962094 -146 ATAAAAAAGGGAAAGCCGCTTAACCAGTAA 28 23 0 GAAAGCCGCT 0.963178 -127 AACCCCTATTTATAGACGCTGTGAATAGTA 28 96 0 TATAGACGCT 0.689195 -54 ********** Masking position 10 Map Score: 1.92081 Number of sites scoring better than the average of aligned sites = 605 Number in coding regions = 568 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 14 ATATCTTTACGCCGAAGTGCCCGTTTTTCC 7 33 1 GCCGAAGTGC 0.734089 -115 TTTCTTCTGTCCTGACGATCTTTATGAGTG 8 169 0 CCTGACGATC 0.882228 -22 CGTCATCCTCGCTGAGGATCAACTATCGCA 9 126 1 GCTGAGGATC 0.703445 -45 TCATCGCTGAACAGCGAACACAATC 10 6 1 GCTGAACAGC 0.871451 -148 TTCCCACTCCCGAAGACCACGGTTGAAT 12 91 0 CCCGAAGACC 0.895273 -18 ATCAGGTCAACGTGAACAGCCCTTCCACCT 15 90 1 CGTGAACAGC 0.746003 -74 GGGTTATGAGCCCGACGAGCTACCAGGCTG 18 46 0 CCCGACGAGC 0.941284 -255 GGGCTCATAACCCGAAGATCGTCGGTTCAA 18 63 1 CCCGAAGATC 0.958982 -238 GCCGTTCGCTCCTGAACATCCACTCGATCT 21 173 1 CCTGAACATC 0.885443 -80 ACCGGAAGAAGGCGAAGATCGAGTGGATGT 21 188 0 GGCGAAGATC 0.764526 -65 CGTGATTCTACCTGAATAGCAGAGTAAAAC 26 143 0 CCTGAATAGC 0.756241 -158 ********** Masking position 5 Map Score: 1.5112 Number of sites scoring better than the average of aligned sites = 597 Number in coding regions = 560 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 15 TACAAAAAGACTTCCGTCAGATCAAGAATA 1 174 0 CTTCCGTCAG 0.966 -127 TGGTTTAAGATTTCAGCCAGGTTATGAAAC 5 69 1 TTTCAGCCAG 0.790712 -232 CAATCTATATCTTCCGTCAGAATGTGTAAA 5 235 0 CTTCCGTCAG 0.966 -66 TTATGAAGACTTTGCGCCAGCGCAGGACTG 8 50 1 TTTGCGCCAG 0.847674 -141 CAGTGAATTGCTGCCGTCAGCTTGAAAAAA 13 49 0 CTGCCGTCAG 0.846735 -129 GTGTCCTCCAGAACGTATCGT 19 2 1 TGTCCTCCAG 0.764202 -81 GACAAACGTACATCCGCCAGAGGCACGACC 21 119 0 CATCCGCCAG 0.947628 -134 TTTTATTTTCCTCCAGTAATAAAAAG 26 285 0 TTTCCTCCAG 0.924252 -16 AGGGCCTGTCCCTCCGCCAGCTCGGGA 29 8 0 CCTCCGCCAG 0.964134 -293 GATTTGCTTCCTCCTGCACAAGGCCT 29 285 0 CTTCCTCCTG 0.800908 -16 ********** Masking position 8 Map Score: 5.80451 Number of sites scoring better than the average of aligned sites = 1343 Number in coding regions = 1307 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097