AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00380_hinf_reg_300.orf -o00380_hinf_300.ace -a/home/amcguire/genomes/ORF_hinf.txt -z/home/amcguire/genomes/hinf.fna -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: HI1664 27 conserved hypothetical protein Input sequences: #1 HI0121 300 conserved hypothetical protein #2 HI0329 37 conserved hypothetical protein #3 HI0330 98 opacity associated protein (oapA) #4 HI0331 59 opacity associated protein (oapB) #5 HI0549 169 dimethyladenosine transferase (ksgA) #6 HI0637 128 tryptophanyl-tRNA synthetase (trpS) #7 HI0774 205 acetate CoA-transferase, alpha subunit #8 HI0928 265 catalase (hktE) #9 HI0961 74 hit-related protein #10 HI0962 28 isoleucyl-tRNA synthetase (isoleucine--tRNA ligase) (ileRS) #11 HI0963 34 riboflavin kinase / FMN adenylyltransferase (ribF) #12 HI0964 300 virulence factor (mviN) #13 HI0974.1 300 conserved hypothetical protein #14 HI0976 119 conserved hypothetical protein #15 HI0978 40 ribosomal protein L11 methyltransferase (prmA) #16 HI1062 85 (3R)-hydroxymyristol (acyl carrier protein) dehydrase (fabZ) #17 HI1064 56 conserved hypothetical protein #18 HI1662 157 2-oxoglutarate dehydrogenase E1 component (sucA) #19 HI1665 53 H. influenzae predicted coding region HI1665 #20 HI1667 73 conserved hypothetical protein #21 HI1668 21 tail specific protease (prc) #22 HI1669 38 conserved hypothetical protein #23 HI1670 183 H. influenzae predicted coding region HI1670 Motif number 1 GAGAAGCTCAAAAGTGCGGCGAAAAAATTA 3 29 0 AAAGTGCGGC 0.989974 -70 TTTAATAAGAAAAGTGCGGTTATTATAGGG 5 142 0 AAAGTGCGGT 0.997639 -28 ATAAAGGCGAAAAATGCGGTTGAAAATCAG 8 68 1 AAAATGCGGT 0.976433 -198 TGTAAAACAAAAAGTGCGATTGATTTGCTC 9 21 1 AAAGTGCGAT 0.988126 -54 TCTCTTAAACAAAGTGCGGTTATTTTTACT 18 22 0 AAAGTGCGGT 0.997639 -136 TTTAAGAGATGAAGTGCGGTTTTTTATTGT 18 43 1 GAAGTGCGGT 0.99117 -115 TTTCTCAAACAAAGTGCGGTCAAAACCATT 20 17 0 AAAGTGCGGT 0.997639 -57 AGAAAAGCAACAAGTGCGGTGATTTTAATA 20 42 1 CAAGTGCGGT 0.99117 -32 AATTTTGTAAAAAGTGCGATAAACTAGGCA 23 129 1 AAAGTGCGAT 0.988126 -55 ********** Masking position 5 Map Score: 26.9654 Number of sites scoring better than the average of aligned sites = 1115 Number in coding regions = 700 Number in noncoding regions = 415 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 2 AACGGCTGATTATTTTCTTTGTAAATAGTGAGCCAT 1 93 1 TTTCTTTAAT 0.921273 -208 TTCGCCGCACTTTTGAGCTTCTCAATTTTGTGGCTA 3 36 1 TTTGCTTAAT 0.731985 -63 TGATGCTTGTTCTTATTTATATTAATTAGCCACAAA 3 62 0 TTTTTTTAAT 0.971769 -37 ATAGGGGTTGTTTTAGCTTTGTAAATCATTGTTAGG 5 112 0 TTTCTTTAAT 0.921249 -58 AAGAAAGATGTATTTCTTTTACGAAATTCTTTTTGC 7 53 1 TTTTTTCAAA 0.77584 -153 ACGAAATTCTTTTTGCTATTTTTAATATCAATCTAG 7 73 1 TTTTATTAAT 0.838546 -133 TATTTGTTGATATTCTTTCTTTTAATCTCGTTATTA 7 170 1 TTTTTTTAAT 0.971769 -36 GTATAGTTTTTTTTGATTAATTTAATAGATTTCGAT 8 162 1 TTTTTATAAT 0.700133 -104 TATTTTCCAATTTTTACATTTTAAAA 10 1 0 TTTCATTAAA 0.638403 -28 TGATGCCCTTTATTTTGTCTATCAATCAACAGAAAT 12 18 0 TTTGTTTAAT 0.889304 -283 TGCCGATTTTTTATACTTTTGTCAATGGAAAATTTG 12 57 1 TATTTTTAAT 0.812831 -244 ACCGAAATTATCTTGGTCGTATCAAAAGGTAACAAG 13 100 1 TTTTCTTAAA 0.921273 -201 TTGTTTTTCCTTTCAAAATTTTGCGTA 15 24 0 TTTTCTTAAA 0.921273 -17 AGATTTTATTTGTTTATTTTTTGTAAGGTATCAAC 16 61 1 TTTTTTTTAA 0.700171 -25 GTGCGGTTATTTTTACTTGTATTAAAAT 18 3 0 TTTTTTTAAA 0.971531 -155 GAAGTGCGGTTTTTTATTGTTTGAAATCTAAAGAGT 18 53 1 TTTTTTTAAA 0.971765 -105 TCACCGCACTTGTTGCTTTTCTCAAACAAAGTGCGG 20 28 0 TTTTTTTAAA 0.971769 -46 AGTCTTGGCGTTATTTTTGTGTGAAATTTATTCAGC 23 75 1 TATTTTTAAA 0.81283 -109 CGGGATCCGTTGTTAATTTTGTAAAAAGTGCGATAA 23 115 1 TTTTTTTAAA 0.971664 -69 ACTAGGCAAATCTTTATTTTATTAATGCCTCAAGGA 23 151 1 TTTTTTTAAT 0.971769 -33 * ** ** * * *** Masking position 4 Map Score: 22.5542 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 86 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 3 ACTTGAATACTTTTTCCAAATTGTAATGCAGG 1 45 1 TTTTCAAATT 0.966755 -256 ATAGAAGTTGTTTTATCATATTTTTCGTTTTC 1 258 1 TTTTCATATT 0.949484 -43 CATCTCTCATTTTTAGGATATTTCAAAT 2 7 0 TTTTGATATT 0.90542 -31 CTTCTCAATTTTGTGGCTAATTAATATAAATA 3 53 1 TTGTCTAATT 0.860225 -46 CATTGTTAGGTTATGCCAAATTGAGTTTTTCA 5 90 0 TTATCAAATT 0.894856 -80 GTGTGAACAGTTTTAAGGTATTAAGGATTGAT 6 106 1 TTTTGGTATT 0.735361 -23 GATGTATTTCTTTTACGAAATTCTTTTTGCTA 7 59 1 TTTTGAAATT 0.936754 -147 AATTGTTGCTTATTTAGTCTAACT 9 61 0 TTGTCTTATT 0.799106 -14 ACCCTAAAATTTTTGCCTAATTGTATAGAAAT 12 224 0 TTTTCTAATT 0.910569 -77 TAAATTCGATTTTTATCATATTCATAAAAAGG 13 143 0 TTTTCATATT 0.949484 -158 CTTACAACTTTTTTGAATAATTCAAAAGGTTT 13 189 0 TTTTATAATT 0.669648 -112 ATACTTTCACTTATAAAAAATTTTAAGGAAGA 13 276 1 TTATAAAATT 0.62886 -25 ATCTATCGGATTATACGATATTTATAGCTAAA 16 33 0 TTATGATATT 0.736958 -53 TTATCGGAAATTGTTACAAATTTGTGATCTAG 18 94 0 TTGTCAAATT 0.946172 -64 TGCGGTTGATTTTTCACAAATTTCTGTTGGTT 22 12 1 TTTTCAAATT 0.966756 -27 TCTATCGTTGTTTTAACGTATTTGTGAAGTCT 23 48 1 TTTTCGTATT 0.845099 -136 GGCGTTATTTTTGTGTGAAATTTATTCAGCAT 23 81 1 TTGTGAAATT 0.899526 -103 TTATCGCACTTTTTACAAAATTAACAACGGAT 23 119 0 TTTTAAAATT 0.852716 -65 **** ****** Masking position 4 Map Score: 19.2556 Number of sites scoring better than the average of aligned sites = 348 Number in coding regions = 272 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 4 ACATAGAACGGCTGATTATTTTCTTTGTAAA 1 87 1 GCTGATATTT 0.619658 -214 GGTTATTATAGGGGTTGTTTTAGCTTTGTAA 5 124 0 GGGGTTTTTT 0.914557 -46 TAAGAAAAGTGCGGTTATTATAGGGGTTGTT 5 136 0 GCGGTTTTAT 0.944972 -34 TGAATTTCTTGCGTATCATATAGAAAGGTTT 8 203 0 GCGTATATAT 0.399226 -63 AACAAAAAGTGCGATTGATTTGCTCTGTCCT 9 26 1 GCGATTATTT 0.905153 -49 GCATATTGATGCCCTTTATTTTGTCTATCAA 12 29 0 GCCCTTATTT 0.72194 -272 GCATCAATATGCCGATTTTTTATACTTTTGT 12 48 1 GCCGATTTTT 0.936922 -253 ACGATGTGTGGCGGATTTTATCAGTTTTTTT 12 168 1 GCGGATTTAT 0.881059 -133 TATATTGAGTGCGTTTTATTTTTAGCTATAA 16 13 1 GCGTTTATTT 0.869454 -73 TATAGAATAAGCCAATTTTTTAAGCCAGAAG 17 20 0 GCCAATTTTT 0.729207 -37 TCTTGAGCGGTTATTTTATAGAATAAG 17 40 0 GCGGTTTTTT 0.98671 -17 TAAACAAAGTGCGGTTATTTTTACTTGTATT 18 16 0 GCGGTTTTTT 0.98671 -142 GAGATGAAGTGCGGTTTTTTATTGTTTGAAA 18 48 1 GCGGTTTTTA 0.856385 -110 TAAAGGAAAAGCCATTGATTTTCGTATTGCG 19 30 1 GCCATTATTT 0.815711 -24 AGCAACAAGTGCGGTGATTTTAATAAAGGTT 20 47 1 GCGGTGTTTT 0.898353 -27 GTGCGGTTGATTTTTCACAAATT 22 3 1 GCGGTTATTT 0.981357 -36 GTGAAGTCTTGGCGTTATTTTTGTGTGAAAT 23 71 1 GGCGTTTTTT 0.832341 -113 ****** **** Masking position 9 Map Score: 19.4162 Number of sites scoring better than the average of aligned sites = 882 Number in coding regions = 616 Number in noncoding regions = 266 Number of orfs with sites within 600 bp upstream = 193 Fraction of orfs with sites within 600 bp upstream = 0.030999 Motif number 5 GTAATTTTGAATATTTAGGTAGATTTTAAGTTTTA 8 122 1 AATTTTAGTT 0.975261 -144 TTAATTTAATAGATTTCGATTGTTTAAACCTTTCT 8 178 1 AATTTTTGTT 0.984434 -88 TAAAGTTAATAAATTTAGTTAGGTTGAAATGAATT 8 228 0 AATTTTAGTT 0.975259 -38 TCCTAAAATTTCTGTTGATTGATAGACAAA 12 6 1 AATTTTTGTT 0.984434 -295 TGTCAATGGAAAATTTGTGTTGATTTCGGTGAGAC 12 76 1 AATTTTTGTT 0.984434 -225 ATAATCCGATAGATTTTATTTGTTTATTTTTTGTA 16 51 1 AATTTTTGTT 0.984434 -35 GATTTTTCACAAATTTCTGTTGGTTCTGTT 22 19 1 AATTTTTGTT 0.984434 -20 AATAAAATAAAGATTTGCCTAGTTTATCGCACTTT 23 139 0 AATTTTAGTT 0.975259 -45 * **** *** ** Masking position 3 Map Score: 13.7584 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 35 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 ATGATGGTCTTTTCTTTTGAAAGTTCATAG 1 232 1 TTTCTTTTGA 0.940746 -69 TGTATTTCTCTGTTGATTAAGGAAAA 1 285 0 TCTCTGTTGA 0.811521 -16 ATCGCCCCTTTTTCTTTTTAAGTTCTTTTC 4 26 1 TTTCTTTTTA 0.639368 -34 CAGGAAAACGTTTCCGTTAAATATAGCATT 6 21 1 TTTCCGTTAA 0.941984 -108 GAAAGATGTATTTCTTTTACGAAATTCTTT 7 55 1 TTTCTTTTAC 0.694226 -151 GTTGATATTCTTTCTTTTAATCTCGTTATT 7 175 1 TTTCTTTTAA 0.877846 -31 TCCTAAAATTTCTGTTGATTGATAGACA 12 9 1 TTTCTGTTGA 0.96723 -292 CAACACAAATTTTCCATTGACAAAAGTATA 12 68 0 TTTCCATTGA 0.800233 -233 CAATGGAAAATTTGTGTTGATTTCGGTGAG 12 79 1 TTTGTGTTGA 0.726996 -222 TTGTTTTTCCTTTCAAAATTTTGCG 15 26 0 TTTCCTTTCA 0.761536 -15 TTTGTAACAATTTCCGATAAGAGGCTTATT 18 106 1 TTTCCGATAA 0.615104 -52 AAGAGGCTTATTTCCGTTGCAATCCTATGT 18 124 1 TTTCCGTTGC 0.918917 -34 ATCAATGGCTTTTCCTTTAATGTGATAACT 19 19 0 TTTCCTTTAA 0.897266 -35 TTTTCACAAATTTCTGTTGGTTCTGTT 22 22 1 TTTCTGTTGG 0.835174 -17 ********** Masking position 3 Map Score: 9.75855 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 228 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 7 GTCAGCAAAATGAATTGAAGTC 1 2 1 TCAGAAAATG 0.963562 -299 CTCTGTTGATTAAGGAAAACGAAAAATATGA 1 273 0 TAAGAAAACG 0.974255 -28 GCGGAAAAGTTAAGAAAAACGGGCGGATTAT 5 16 1 TAAGAAAACG 0.974255 -154 TACTATTTAATAAGAAAAGTGCGGTTATTAT 5 146 0 TAAGAAAGTG 0.723624 -24 TAGTAAATATCAGGAAAACGTTTCCGTTAA 6 10 1 TCAGAAAACG 0.986297 -119 TATACCCGCCTAAGAAAGATGTATTTCTTTT 7 42 1 TAAGAAGATG 0.764618 -164 CAATATGGGCTCACACAAACGATGTGTGGCG 12 150 1 TCACCAAACG 0.763595 -151 GTCAAAAAAATAAGGAATATGCATCAGTCCT 13 30 1 TAAGAATATG 0.794442 -271 TACGTAGAAATCAGCAAAACCTTTTGAATTA 13 173 1 TCAGAAAACC 0.893677 -128 CGCCAAGACTTCACAAATACGTTAAAACAAC 23 54 0 TCACAATACG 0.826624 -130 TGAAATTTATTCAGCATAACGGGATCCGTTG 23 96 1 TCAGATAACG 0.901431 -88 **** ****** Masking position 3 Map Score: 6.42001 Number of sites scoring better than the average of aligned sites = 290 Number in coding regions = 256 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 8 TCTGAAATTGCTTTATCGCTTAAATTTCATT 1 135 1 CTTTATGCTT 0.858015 -166 AAATTTCATTGTTTATTCCTATTGAAGTGGT 1 156 1 GTTTATCCTA 0.576569 -145 TTTCGCCGCACTTTTGAGCTTCTCAATTTTG 3 35 1 CTTTTGGCTT 0.516399 -64 GATTATAGCCGTTTTTAGCTTTCTACGAAAG 5 41 1 GTTTTTGCTT 0.857823 -129 TATAGGGGTTGTTTTAGCTTTGTAAATCATT 5 118 0 GTTTTACTTT 0.487371 -52 AATCAATCCTTAATACCTTAAAACTGTTC 6 110 0 CTTAATCCTT 0.8593 -19 AATCTAGTTCCTTTATTGCCTATCAAGGATC 7 102 1 CTTTATGCCT 0.450523 -104 TGGTATTATACTTGAATCCGTAAAAGGGATA 8 40 1 CTTGAACCGT 0.524433 -226 CATTTTTCGCCTTTATCCCTTTTACGGATTC 8 53 0 CTTTATCCTT 0.950058 -213 GATTTCGATTGTTTAAACCTTTCTATATGAT 8 189 1 GTTTAACCTT 0.855818 -77 AGGATGATTACTTGTTACCTTTTGATACGAC 13 115 0 CTTGTTCCTT 0.933914 -186 TTGTTTTTCCTTTCAAAATTTTG 15 28 0 GTTTTTCTTT 0.730852 -13 GTTGATACCTTACAAAAAATA 16 75 0 GTTGATCCTT 0.918309 -11 TGTTTTTTCCTTCTGGCTTAAA 17 2 1 GTTTTTCCTT 0.949983 -55 CGATAAGAGGCTTATTTCCGTTGCAATCCTA 18 120 1 CTTATTCCGT 0.630791 -38 AATCACCGCACTTGTTGCTTTTCTCAAACAA 20 35 0 CTTGTTCTTT 0.668916 -39 AGTTATATCCTTGAGGCATTAA 23 172 0 GTTATACCTT 0.681016 -12 ****** **** Masking position 3 Map Score: 6.04713 Number of sites scoring better than the average of aligned sites = 414 Number in coding regions = 325 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 9 ATTTTTAACCTAGCTTTTGAACTCGAACATT 6 48 1 TACTTTTGAA 0.883106 -81 ATAAGTATCTTATATTTCAAATGGATATGTT 7 142 0 TAATTTCAAA 0.754988 -64 AATATTTAGGTAGATTTTAAGTTTTATTTTA 8 131 1 TAATTTTAAG 0.881327 -135 ATTAATTTAATAGATTTCGATTGTTTAAACC 8 177 1 TAATTTCGAT 0.547348 -89 TTATTTAGTCTAACTTTTAAGGACAGAGCAA 9 45 0 TACTTTTAAG 0.84504 -30 TTCCAATTTTTACATTTTAAAA 10 2 0 TAATTTTAAA 0.879344 -27 GGTAGAGAAGAATATTTTGAGTAAACGACTT 12 253 1 AAATTTTGAG 0.843739 -48 ACAACAATGCTAGATTTTAAAAGTCGTTTAC 12 273 0 TAATTTTAAA 0.879344 -28 GATTACTTGTTACCTTTTGATACGACCAAGA 13 110 0 TACTTTTGAT 0.677425 -191 AAATCAGCAAAACCTTTTGAATTATTCAAAA 13 180 1 AACTTTTGAA 0.795541 -121 AGTGAAAGTATATTTTTTGAATGGTATAAGG 13 256 0 TATTTTTGAA 0.718529 -45 TCACTTATAAAAAATTTTAAGGAAGAAAT 13 282 1 AAATTTTAAG 0.792742 -19 AAAAATACGCAAAATTTTGAAAGGAAAAACA 15 19 1 AAATTTTGAA 0.841241 -22 AGAATAAGCCAATTTTTTAAGCCAGAAGGAA 17 17 0 AATTTTTAAG 0.486927 -40 TCAAACTCTTTAGATTTCAAACAATAAAAAA 18 62 0 TAATTTCAAA 0.754988 -96 ** ******** Masking position 2 Map Score: 8.14291 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 183 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 10 TGGCTCACTATTTACAAAGAAAATAATCAG 1 98 0 TTTACAAAGA 0.975775 -203 CTAACAATGATTTACAAAGCTAAAACAACC 5 113 1 TTTACAAAGC 0.936425 -57 AAAATCAGGCTTTATAAAGATATATCAAGT 8 90 1 TTTATAAAGA 0.931516 -176 ATTTATTAACTTTACAAGGAGTCTACA 8 249 1 TTTACAAGGA 0.947772 -17 CACTTTTTGTTTTACAATGAATTTAA 9 7 0 TTTACAATGA 0.924493 -68 ACGTTTTTGATTTATAAAGAAAGACCACAA 23 13 0 TTTATAAAGA 0.931516 -171 ********** Masking position 6 Map Score: 3.90283 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 9 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 11 ATTTGAAATATCCTAAAAATGAGAGATGG 2 9 1 TACCTAAAAA 0.488318 -29 TTATTTTTTCTTTCGTAGAAAGCTAAAAACG 5 50 0 TTCGTAGAAA 0.920943 -120 GCAAAAAGAATTTCGTAAAAGAAATACATCT 7 58 0 TTCGTAAAAG 0.881679 -148 TTATACTTGAATCCGTAAAAGGGATAAAGGC 8 45 1 ATCGTAAAAG 0.867639 -221 TTTTAAAATGTAAAAATTGGAAAATA 10 6 1 AATGTAAAAA 0.607626 -23 TTACGCTATATTCCGTGAAAAAAAACTGATA 12 186 0 TTCGTGAAAA 0.89763 -115 TCACGGAATATAGCGTAAAAACAAAATTTCT 12 199 1 TACGTAAAAA 0.913629 -102 TCTTATCGGTATTCGTCAAAAAAATAAGGAA 13 16 1 ATCGTCAAAA 0.80726 -285 TTTTTATCATATTCATAAAAAGGATGATTAC 13 135 0 ATCATAAAAA 0.597805 -166 AAAATCGAATTTACGTAGAAATCAGCAAAAC 13 162 1 TTCGTAGAAA 0.921473 -139 TTCTATGTTTTAGCGTAGAAATTGCTGAAAG 14 73 0 TACGTAGAAA 0.817266 -47 CCTATGTATAATGCGTAAAAA 18 147 1 ATCGTAAAAA 0.960657 -11 ACCAACAGAAATTTGTGAAAAATCAACCGCA 22 12 0 ATTGTGAAAA 0.562122 -27 GACTTCACAAATACGTTAAAACAACGATAGA 23 48 0 ATCGTTAAAA 0.738782 -136 CCGTTGTTAATTTTGTAAAAAGTGCGATAAA 23 121 1 TTTGTAAAAA 0.821862 -63 ** ******** Masking position 9 Map Score: 9.39607 Number of sites scoring better than the average of aligned sites = 392 Number in coding regions = 328 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 12 ACTTCTATGAACTTTCAAAAGAAAAGACCA 1 236 0 ACTTTCAAAA 0.961063 -65 TGTTTAAAACACTATCAAAATAACTTATAC 7 17 1 ACTATCAAAA 0.900357 -189 TGAGTAAACGACTTTTAAAATCTAGCATTG 12 270 1 ACTTTTAAAA 0.84952 -31 TTATCTTGGTCGTATCAAAAGGTAACAAGT 13 107 1 CGTATCAAAA 0.703448 -194 GCCCCTTATACCATTCAAAAAATATACTTT 13 253 1 CCATTCAAAA 0.875248 -48 ATATACTTTCACTTATAAAAAATTTTAAGG 13 274 1 ACTTATAAAA 0.673915 -27 TTGTTTTTCCTTTCAAAATTTTGCGTAT 15 23 0 CCTTTCAAAA 0.975093 -18 GTTGATACCTTACAAAAAATAAACAAA 16 69 0 CCTTACAAAA 0.934777 -17 ********** Masking position 7 Map Score: 2.79459 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 152 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 13 TTTTCAAACCATCTCTCATTT 2 27 0 TTTCAAACCA 0.792911 -11 TTTGATAGTGTTTTAAACAATCCTT 7 6 0 TTTTAAACAA 0.843032 -200 CTATTTTTAATATCAATCTAGTTCCTTTAT 7 88 1 TATCAATCTA 0.638276 -118 TTATTTTGTCTATCAATCAACAGAAATTTT 12 15 0 TATCAATCAA 0.917988 -286 GTATTAATCAATATGCTGTCA 14 2 1 TATTAATCAA 0.785799 -118 GCACTTCATCTCTTAAACAAAGTGCGGTTA 18 30 0 TCTTAAACAA 0.816603 -128 ACTCTTTAGATTTCAAACAATAAAAAACCG 18 59 0 TTTCAAACAA 0.942487 -99 TTGTTGCTTTTCTCAAACAAAGTGCGGTCA 20 25 0 TCTCAAACAA 0.931441 -49 GGTCTTTCTTTATAAATCAAAAACGTGCCA 23 17 1 TATAAATCAA 0.592151 -167 GCTGAATAAATTTCACACAAAAATAACGCC 23 81 0 TTTCACACAA 0.773632 -103 ********** Masking position 5 Map Score: 2.76874 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 85 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 14 CTTAAAAAGAAAAAGGGGCGATTACTCGCC 4 18 0 AAAAGGGGCG 0.984428 -42 AAAGTTAAGAAAAACGGGCGGATTATAGCC 5 21 1 AAAACGGGCG 0.95932 -149 ATTGTAAAACAAAAAGTGCGATTGATTTGC 9 19 1 AAAAAGTGCG 0.970438 -56 GATAGACAAAATAAAGGGCATCAATATGCC 12 31 1 ATAAAGGGCA 0.772145 -270 ATTAGCAAACACAAGGGACGTATGAAATAT 13 221 1 ACAAGGGACG 0.882131 -80 TTTGAATGGTATAAGGGGCGTATATTTCAT 13 242 0 ATAAGGGGCG 0.971332 -59 CATCTCTTAAACAAAGTGCGGTTATTTTTA 18 24 0 ACAAAGTGCG 0.975395 -134 CTTTTCTCAAACAAAGTGCGGTCAAAACCA 20 19 0 ACAAAGTGCG 0.975395 -55 TTAATTTTGTAAAAAGTGCGATAAACTAGG 23 127 1 AAAAAGTGCG 0.970438 -57 ********** Masking position 4 Map Score: 13.2863 Number of sites scoring better than the average of aligned sites = 452 Number in coding regions = 301 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 15 CGATAAAGCAATTTCAGAAGCACAATGGCTC 1 122 0 ATTCAGAAGC 0.960462 -179 TTATTTAACCACTTCAATAGGAATAAACAAT 1 163 0 ATTCAATAGG 0.887372 -138 GTTAAATAATAGTTCAGTGGCGTTAATTATA 1 185 1 ATTCAGTGGC 0.813076 -116 TTAGCCACAAAATTGAGAAGCTCAAAAGTGC 3 42 0 ATTGAGAAGC 0.800908 -57 TTAATGTTCGAGTTCAAAAGCTAGGTTAAAA 6 50 0 ATTCAAAAGC 0.952669 -79 AGTATCTTATATTTCAAATGGATATGTTTCT 7 139 0 ATTCAAATGG 0.838092 -67 AAATTTATTAACTTTACAAGGAGTCTACA 8 247 1 ATTTACAAGG 0.697612 -19 TTTTTTGAATAATTCAAAAGGTTTTGCTGAT 13 182 0 ATTCAAAAGG 0.961437 -119 GAATTGCAACAATTCACAGGGATACATCA 14 101 1 ATTCACAGGG 0.921292 -19 * ********* Masking position 6 Map Score: 1.10581 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 100 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925