AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00310_hinf_reg_300.orf -o00310_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 HI0033 53 conserved hypothetical protein Input sequences: #1 HI0028 55 conserved hypothetical protein #2 HI0030 51 lipoprotein, putative #3 HI0034 124 conserved hypothetical protein #4 HI0035 205 conserved hypothetical protein #5 HI0121 300 conserved hypothetical protein #6 HI0151 109 hflK protein (hflK) #7 HI0152 300 H. influenzae predicted coding region HI0152 #8 HI0195.1 26 conserved hypothetical transmembrane protein (aefA) #9 HI0197 84 penicillin-insensitive murein endopeptidase (mepA) #10 HI0199 46 lipid A biosynthesis (kdo)2-(lauroyl)-lipid IVA acyltransferase (msbB) #11 HI0301 300 hemolysin, putative #12 HI0415 300 hydroxyethylthiazole kinase #13 HI0419 168 protease, putative #14 HI0587 99 peptidase E (pepE) #15 HI0774 205 acetate CoA-transferase, alpha subunit #16 HI0885 191 thiol:disulfide interchange protein (dsbD) #17 HI0886 111 H. influenzae predicted coding region HI0886 #18 HI0887 187 phosphoribosylaminoimidazolecarboxamide formyltransferase (purH) #19 HI0888 95 phosphoribosylamine--glycine ligase (purD) #20 HI0889 123 serine hydroxymethyltransferase (serine methylase) (glyA) #21 HI0916 107 outer membrane protein, putative #22 HI0920 248 conserved hypothetical protein #23 HI1024 49 hexulose-6-phosphate synthase, putative #24 HI1027 58 L-xylulose kinase (lyx) #25 HI1028 30 conserved hypothetical protein #26 HI1030 71 conserved hypothetical transmembrane protein #27 HI1031 175 conserved hypothetical protein #28 HI1527 84 lipid A biosynthesis lauroyl acyltransferase (htrB) #29 HI1541 97 protease IV (sppA) #30 HI1661 102 2-oxoglutarate dehydrogenase E2 component, dihydrolipoamide succinyltransferase(sucB) #31 HI1662 157 2-oxoglutarate dehydrogenase E1 component (sucA) #32 HI1665 53 H. influenzae predicted coding region HI1665 #33 HI1667 73 conserved hypothetical protein #34 HI1668 21 tail specific protease (prc) #35 HI1669 38 conserved hypothetical protein #36 HI1670 183 H. influenzae predicted coding region HI1670 #37 HI1682 197 protease, putative (sohB) Motif number 1 AATAAATCAAAAAGTGCGGTCAATTTTCAA 1 18 0 AAAGTGCGGT 0.998673 -38 TTAGACATAAAAAGCGCGGTTAATTTCGCG 3 27 1 AAAGCGCGGT 0.988289 -98 ATCCGAGATAAAAGTGCGGTGAAAAATAAC 4 20 1 AAAGTGCGGT 0.998673 -186 CCTTTTACAAAAAGTGCGGTTATTTTTCAC 4 38 0 AAAGTGCGGT 0.998673 -168 AAAGCGCGCAAAAGTGCGGTTAAAATTAAT 10 16 1 AAAGTGCGGT 0.998673 -31 GTTTAAACCTAAAGTGCGGTTAAAAATACA 11 175 0 AAAGTGCGGT 0.998673 -126 GTTTAAACCCAATGTGCGGTTATTTTTTAT 11 197 1 AATGTGCGGT 0.982745 -104 CTTGTAAAGGAAAGTGCGGTTAAATTCTTA 13 67 0 AAAGTGCGGT 0.998673 -102 TAACAATAAAAAAGTGCGGTGATTTTTTAC 16 78 1 AAAGTGCGGT 0.998673 -114 ATAATTTCTTAAAGTGCGGTAAAAATACGA 18 84 0 AAAGTGCGGT 0.998673 -104 AAATGCTGCAAAAGTGCGGTTAAAATTTAA 22 20 0 AAAGTGCGGT 0.998673 -229 AGAGAAATAAAAAGTGCGGTGGTTTTTTAG 22 103 1 AAAGTGCGGT 0.998673 -146 CTTATAAGTAAAAGTGCGGTGGATTATAGC 29 21 1 AAAGTGCGGT 0.998673 -77 TCTCTTAAACAAAGTGCGGTTATTTTTACT 31 22 0 AAAGTGCGGT 0.998673 -136 TTTAAGAGATGAAGTGCGGTTTTTTATTGT 31 43 1 GAAGTGCGGT 0.988961 -115 TTTCTCAAACAAAGTGCGGTCAAAACCATT 33 17 0 AAAGTGCGGT 0.998673 -57 AGAAAAGCAACAAGTGCGGTGATTTTAATA 33 42 1 CAAGTGCGGT 0.988961 -32 AATTTTGTAAAAAGTGCGATAAACTAGGCA 36 129 1 AAAGTGCGAT 0.972338 -55 ********** Masking position 10 Map Score: 88.8744 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 AAATAAATCAAAAAGTGCGGTCAATTTTCA 1 19 0 AAAAGTGCGG 0.998306 -37 TTTAGACATAAAAAGCGCGGTTAATTTCGC 3 26 1 AAAAGCGCGG 0.983408 -99 ACTTAGCAATAAAGGTGCGGAATTCTATCA 3 96 0 AAAGGTGCGG 0.984254 -29 CATCCGAGATAAAAGTGCGGTGAAAAATAA 4 19 1 AAAAGTGCGG 0.998306 -187 CCCTTTTACAAAAAGTGCGGTTATTTTTCA 4 39 0 AAAAGTGCGG 0.998306 -167 GAAAGCGCGCAAAAGTGCGGTTAAAATTAA 10 15 1 AAAAGTGCGG 0.998306 -32 GGTTTAAACCTAAAGTGCGGTTAAAAATAC 11 176 0 TAAAGTGCGG 0.993225 -125 GGTTTAAACCCAATGTGCGGTTATTTTTTA 11 196 1 CAATGTGCGG 0.942831 -105 GCTTGTAAAGGAAAGTGCGGTTAAATTCTT 13 68 0 GAAAGTGCGG 0.988504 -101 GTAACAATAAAAAAGTGCGGTGATTTTTTA 16 77 1 AAAAGTGCGG 0.998306 -115 TATAATTTCTTAAAGTGCGGTAAAAATACG 18 85 0 TAAAGTGCGG 0.993225 -103 CTAATTTAAAAAAAGTACGGCTATTTTTTA 19 56 0 AAAAGTACGG 0.961035 -40 AAAATGCTGCAAAAGTGCGGTTAAAATTTA 22 21 0 AAAAGTGCGG 0.998306 -228 GAGAGAAATAAAAAGTGCGGTGGTTTTTTA 22 102 1 AAAAGTGCGG 0.998306 -147 CCTTATAAGTAAAAGTGCGGTGGATTATAG 29 20 1 AAAAGTGCGG 0.998306 -78 ATCTCTTAAACAAAGTGCGGTTATTTTTAC 31 23 0 CAAAGTGCGG 0.995681 -135 GTTTAAGAGATGAAGTGCGGTTTTTTATTG 31 42 1 TGAAGTGCGG 0.939559 -116 TTTTCTCAAACAAAGTGCGGTCAAAACCAT 33 18 0 CAAAGTGCGG 0.995681 -56 GAGAAAAGCAACAAGTGCGGTGATTTTAAT 33 41 1 ACAAGTGCGG 0.984254 -33 TAATTTTGTAAAAAGTGCGATAAACTAGGC 36 128 1 AAAAGTGCGA 0.961035 -56 ********** Masking position 3 Map Score: 75.3082 Number of sites scoring better than the average of aligned sites = 1045 Number in coding regions = 637 Number in noncoding regions = 408 Number of orfs with sites within 600 bp upstream = 276 Fraction of orfs with sites within 600 bp upstream = 0.0443302 Motif number 3 TGACCGCACTTTTTGATTTATTTTATTTTTAGGAAAGA 1 26 1 TTTTTATTTT 0.885223 -30 TTTCATTTTTTCTTTCTTAAAGAAAGAATAAAT 2 6 1 TTTTCTCTTA 0.748933 -46 AAAATATTAACGCTTTTCATTTATTCTTTCTT 2 30 0 TATTCTTTTT 0.797413 -22 TACCGAAAATTTTTGACCCTTTTACAAAAAGTGCGGTT 4 47 0 TTTTCTTTTA 0.935509 -159 ATAGAAGTTGTTTTATCATATTTTTCGTTTTCCTTAAT 5 258 1 TTTTCATTTT 0.956899 -43 GTTAAAATAATATTTACCAATTTTTGTTGTACCCGTTA 7 130 0 TATTCATTTT 0.797413 -171 TGCGGTTATTTTTTATTGATTTTCCTCTTTTCGCGTTT 11 211 1 TTTTTTTTTT 0.885223 -90 GCGGTCAAATTTTTCCCTCATTTTGCAAATAATGAGAA 12 26 0 TTTTCATTTA 0.935509 -275 ATCCTGTTTATTTTCCCAATTTTCTACATTTTATTACA 12 212 1 TTTTCTTTTA 0.935509 -89 TAGCGGGCATTTTTGTTTATTTTATATTCAACACAAGG 12 272 1 TTTTTTTTTT 0.885223 -29 AATATTCTCTTTTGTCTGATTTCAGGTCAGGGACTTA 13 142 0 TTTTCATTTT 0.956899 -27 TACGAAATTCTTTTTGCTATTTTTAATATCAATCTAGT 15 72 1 TTTTCTTTTA 0.935509 -134 TATTTGTTGATATTCTTTCTTTTAATCTCGTTATTAGG 15 170 1 TATTTTTTTT 0.577593 -36 TGCGGTGATTTTTTACCTGATTTTCCTTTTTGTGATCT 16 92 1 TTTTCATTTT 0.956899 -100 TGGTAAAAAGTATTTTTCAATTTTAATTATTGTTTAAC 17 25 1 TATTTATTTT 0.577593 -87 TTTATCGTATTTTTACCGCACTTTAAGAAATTATATTT 18 80 1 TTTTCACTTA 0.748933 -108 CATCGCTTATTTTTAACTATTTAATGAAAGGAAAATAC 18 159 1 TTTTCTTTAA 0.72003 -29 ATAGCCGTACTTTTTTTAAATTAGGCATACGCAAGGAC 19 62 1 TTTTTATTAT 0.577593 -34 TCCCTATTAATTTTTGCCATTTTACGGTATTCTATGCC 22 66 0 TTTTCTTTTT 0.956899 -183 TGCGGTGGTTTTTTAGTTGTTTTTTACAATAAATTTTC 22 117 1 TTTTTTTTTA 0.834416 -132 GTTAAAATAATTTTACTGATTTTGTGATCTAGATCCTA 27 41 0 TTTTTTTTTT 0.885223 -135 AGCTTTCTTATTTTTGTAAATTATGAAACGTAATTTTA 27 123 1 TTTTTATTAA 0.471855 -53 TTTTTCCTCTCTTAATTTTATATAGTAA 27 158 0 TTTTCTCTTT 0.820321 -18 TTATTTTTCCTTTTCTTCTTTTTTACTATATCTTAATT 30 74 0 TTTTTTTTTA 0.834416 -29 TTTTTACGCATTATACATAGGATTGCAA 31 140 0 TTTTCATTAT 0.797413 -18 TGCGGTTGATTTTTCACAAATTTCTGTTGGTTCTGTT 35 12 1 TTTTCATTTT 0.956899 -27 TCTATCGTTGTTTTAACGTATTTGTGAAGTCTTGGCGT 36 48 1 TTTTCATTTA 0.935509 -136 TTTATTTTCATTTTGGCTAATTTGGCATAGCATAAGCG 37 40 0 TTTTCATTTT 0.956899 -158 **** * **** * Masking position 12 Map Score: 34.6228 Number of sites scoring better than the average of aligned sites = 602 Number in coding regions = 445 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 4 AATTTCGCGCTTATTTTTTGCGTGGATTTTGCG 3 48 1 TTTTTTTGCT 0.946068 -77 GTTCGTCACATTTTTTCTTGCGAAATTGAGCAT 4 96 0 TTTTTTTGCA 0.96409 -110 GACGAACGTATCATTTTTTGAGTTTGGTTAAGG 4 122 1 TCTTTTTGAT 0.552564 -84 TATATCCAAGTTGTTTTTTGAAAACCTTAACCA 4 146 0 TTTTTTTGAA 0.932964 -60 TTAAATTTCATTGTTTATTCCTATTGAAGTGGT 5 154 1 TTTTTTTCCA 0.569104 -147 TATGATGGTCTTTTCTTTTGAAAGTTCATAGAA 5 231 1 TTTCTTTGAA 0.834868 -70 TGTATTTCTCTGTTGATTAAGGAAAACG 5 283 0 TTTCTTTGAT 0.767622 -18 AAATCAAGGATTTTTTATTGCCTAAAAAGCCTT 6 30 1 TTTTTTTGCT 0.946068 -80 TACGTCAAAGTTTACTGTTGCAATATCTGACGG 7 99 0 TTACTTTGCA 0.633586 -202 ATTGGGGTTGTTGTTGCTTGCTTGGTCGGTGTT 7 192 1 TTTTGTTGCT 0.712352 -109 GAATAATGGATTTTTGATTGTGAATTGATCTCG 11 52 0 TTTTGTTGTA 0.545971 -249 TGTGCGGTTATTTTTTATTGATTTTCCTCTTTT 11 209 1 TTTTTTTGAT 0.900924 -92 TGACCGCTTGTTTTTTCTTGAAAAGAAGCGTAA 12 57 1 TTTTTTTGAA 0.932964 -244 AATATTCTCTTTTGTCTGATTTCAGGT 13 152 0 TTTCTTTGTT 0.669064 -17 CTGATACGGTTTATTTTTTGATATTCGTCAAAC 14 20 1 TTTTTTTGAA 0.932964 -80 ACAATTATAATTTTTCGTTGAAAATTAACCTTT 14 51 1 TTTTCTTGAA 0.516353 -49 TCAATCTAGTTCCTTTATTGCCTATCAAGGATC 15 100 1 TCTTTTTGCT 0.704347 -106 TCAAATGGATATGTTTCTTGCGATGATCCTTGA 15 124 0 ATTTTTTGCA 0.562904 -82 TATAAGATACTTATTTGTTGATATTCTTTCTTT 15 159 1 TTTTTTTGAA 0.932964 -47 ATCACCGCACTTTTTTATTGTTACAATAATGTT 16 68 0 TTTTTTTGTA 0.894933 -124 TTATTTTTTACTTTTGGTAAAAA 17 1 1 TTTTTTTACT 0.59533 -111 TTTTTCAATTTTAATTATTGTTTAACTACCCGT 17 37 1 TTATTTTGTT 0.496652 -75 CTATGCCACATTTTCTATTGTCAAAATGCTGCA 22 40 0 TTTCTTTGTA 0.755756 -209 TCTCTCCCTATTAATTTTTGCCATTTTACGGTA 22 75 0 TTATTTTGCA 0.826387 -174 GGTTTTTTAGTTGTTTTTTACAATAAATTTTCA 22 123 1 TTTTTTTACA 0.692459 -126 TATTTTTATTATTGAGAGACCTCTATA 22 232 0 TTATTTTGAA 0.711603 -17 TTTCCTTTTCTTCTTTTTTACTATATCTTAATT 30 74 0 TTTTTTTACA 0.692459 -29 TGAAGTGCGGTTTTTTATTGTTTGAAATCTAAA 31 52 1 TTTTTTTGTT 0.847685 -106 ** *** **** * Masking position 8 Map Score: 25.6001 Number of sites scoring better than the average of aligned sites = 478 Number in coding regions = 358 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 5 AAAAGTGCGGTCAATTTTCAAATTCTTT 1 9 0 TCAATTTTCA 0.646777 -47 AAAAGTGCGGTTATTTTTCACCGCACTTTT 4 29 0 TTATTTTTCA 0.813236 -177 TCCGAAGGAGTTAAATTTCATTTTTAAGGG 4 180 1 TTAAATTTCA 0.938667 -26 GCTTTATCGCTTAAATTTCATTGTTTATTC 5 144 1 TTAAATTTCA 0.938667 -157 CAATGTGCGGTTATTTTTTATTGATTTTCC 11 206 1 TTATTTTTTA 0.525709 -95 TATTAAGCGGTTAAATTTTATATAAAATTC 13 34 1 TTAAATTTTA 0.73519 -135 TTAGAAAAGGTTAATTTTCAACGAAAAATT 14 59 0 TTAATTTTCA 0.926161 -41 AATAAGTATCTTATATTTCAAATGGATATG 15 144 0 TTATATTTCA 0.851753 -62 TTATTTTTTACTTTTGGTAA 17 1 1 TTATTTTTTA 0.525709 -111 TAAAAATACGATAAATTTCAGGCATAAAAA 18 65 0 ATAAATTTCA 0.750009 -123 ATTTCATTCCTAAATTTTCATCACTTAAAT 20 38 0 TAAATTTTCA 0.872096 -86 AAAATTTAATTAAAATTTCATTCCTAAATT 20 52 0 TAAAATTTCA 0.827704 -72 AAATTTTAATTAAATTTTTATCCATAAACA 20 64 1 TAAATTTTTA 0.617303 -60 AAAATCACCTTAAATTTTAACCGCACTTT 22 10 1 TTAAATTTTA 0.73519 -239 TTTTTTACAATAAATTTTCAATTTTTGCAG 22 136 1 TAAATTTTCA 0.872096 -113 TTTCTTGTGATAATATTTCATATTGTGAA 27 10 0 TAATATTTCA 0.754986 -166 TTCAAACTCTTTAGATTTCAAACAATAAAA 31 64 0 TTAGATTTCA 0.677915 -94 GTTATGCTGAATAAATTTCACACAAAAATA 36 86 0 ATAAATTTCA 0.750009 -98 ATTTATAACAAAAAATTTTAAATTAATTCT 37 83 0 AAAAATTTTA 0.286896 -115 TTTAATGGATTAAATTTTCACGACACTGGT 37 161 0 TAAATTTTCA 0.872096 -37 ATTTAATCCATTAAATATCAACGGGAGTAA 37 176 1 TTAAATATCA 0.516218 -22 ********** Masking position 6 Map Score: 18.1242 Number of sites scoring better than the average of aligned sites = 324 Number in coding regions = 232 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 6 TTTCTTTCCTAAAAATAAAATAAATCAAAAAGTG 1 32 0 AAAAAATAAA 0.943373 -24 TTTCTTTAAGAAAGAAAAAATGAAA 2 2 0 AAAAAATGAA 0.664785 -50 TTTCTTTCTTAAAGAAAGAATAAATGAAAAGCGT 2 19 1 AAAAAATAAA 0.943373 -33 AAGGAAAACGAAAAATATGATAAAACAACTTCTA 5 259 0 AAAAGATAAA 0.959857 -42 GAAAAGAGGAAAATCAATAAAAAATAACCGCACA 11 209 0 AAAAAAAAAA 0.572294 -92 AATTGGGAAAATAAACAGGATAAAATCGTGATAG 12 199 0 ATAAGATAAA 0.657594 -102 TCCTTGTGTTGAATATAAAATAAACAAAAATGCC 12 277 0 GAAAAATAAA 0.678735 -24 AATGTGGGCAAAAATAAGGATAAAATTATGAAAC 18 21 0 AAAAGATAAA 0.959857 -167 AAAGTGCGGTAAAAATACGATAAATTTCAGGCAT 18 70 0 AAAAGATAAA 0.959857 -118 CTCAGTCAATAAATGTAAAATAAATAAATTATTT 27 91 0 AAAAAATAAA 0.943373 -85 ACCACAACTCAAATTTACGATAAACTACGCCCCT 28 54 1 AAAAGATAAA 0.959857 -31 CTTTTACTTATAAGGGATAATAAA 29 1 0 TAAAAATAAA 0.587706 -97 TTTACAGAGGAAAGCAAAGATAAAAACCTTTATT 30 25 0 AAAAGATAAA 0.959857 -78 AAAAAGAAGAAAAGGAAAAATAAA 30 89 1 AAAAAATAAA 0.943373 -14 CAAATACGTTAAAACAACGATAGAATGGCACGTT 36 38 0 AAAAGATAGA 0.740018 -146 TAATTTTGTAAAAAGTGCGATAAACTAGGCAAAT 36 128 1 AAAGGATAAA 0.740018 -56 CAAATTAGCCAAAATGAAAATAAAAAGTAAGAAT 37 54 1 AAAAAATAAA 0.943373 -144 *** * ****** Masking position 10 Map Score: 21.981 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 93 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 7 ACCGAAAATTTTTGACCCTTTTACAAAAAGT 4 53 0 TTTGACCTTT 0.807661 -153 ATTGACCCCTTAAAAATGAAA 4 195 0 ATTGACCCTT 0.839878 -11 TGAACTATTATTTAACCACTTCAATAGGAAT 5 170 0 TTTAACCCTT 0.891426 -131 TATTTTTCCCTAATCTAAATGGTA 8 13 0 TTTTCCCAAT 0.611092 -14 TAACCGCACTTTTGCGCGCTTTCCGAA 10 7 0 TTTGCGCCTT 0.885269 -40 GATAAGGATCTTTGCCCTCTTTTTACGAGAT 11 27 1 TTTGCCCCTT 0.988443 -274 ATGAGAAGAATTTGACCGCTTA 12 2 0 TTTGACCCTT 0.981581 -299 GCGGTCAAATTTTTCCCTCATTTTGCAAATA 12 33 0 TTTTCCCCAT 0.887546 -268 GAGGGAAAAATTTGACCGCTTGTTTTTTCTT 12 45 1 TTTGACCCTT 0.981581 -256 ATCCTGTTTATTTTCCCAATTTTCTACATTT 12 212 1 TTTTCCCATT 0.78986 -89 TTATATAAAATTTAACCGCTTAATAGGTTGT 13 28 0 TTTAACCCTT 0.891426 -141 TATCCTTATTTTTGCCCACATTTATGTGGGC 18 33 1 TTTGCCCCAT 0.972791 -155 TAATATTTTCTCTGCCCAATTAAATTAGGCA 21 56 0 TCTGCCCATT 0.712956 -52 ACTAAATGGTTTTGACCGCACTTTGTTTGAG 33 13 1 TTTGACCCAC 0.764699 -61 ******* *** Masking position 3 Map Score: 10.4285 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 168 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 8 AACCGCGCTTTTTATGTCTAAATTGAAATTATT 3 15 0 TTTTTTAAAT 0.936267 -110 GGCTGATTATTTTCTTTGTAAATAGTGAGCCAT 5 96 1 TTTTTTAAAT 0.936267 -205 AAGGATTTAGTTTGTGTGTAAATTAGCGAATCA 7 241 0 TTTTTTAAAT 0.936267 -60 TTAACCGCACTTTAGGTTTAAACCCAATGTGCG 11 182 1 TTTGTTAAAC 0.756752 -119 ATTTTCCTTTTTGTGATCTAAATCATAGTTTTA 16 111 1 TTGGTTAAAT 0.721805 -81 GCCGTTTTAATTCATCTTTAAACAAAAGGAAAG 17 86 1 TTCTTTAAAC 0.790767 -26 TAATTAAAATTTCATTCCTAAATTTTCATCACT 20 43 0 TTCTCTAAAT 0.790767 -81 TAATTAAATTTTTATCCATAAACAGTTAAACTA 20 70 1 TTTTCTAAAC 0.756752 -54 CGTTTTTCCTTAAATAATATGAGGA 23 35 0 TTTTCTAAAT 0.87114 -15 TTTTAACATATTGATTTATAAATAATTTATTTA 27 72 1 TTGTTTAAAT 0.849355 -104 TGAGCTTTCTTATTTTTGTAAATTATGAAACGT 27 121 1 TATTTTAAAT 0.591146 -55 TATCTTTGCTTTCCTCTGTAAATAGGGGAGCCA 30 37 1 TTCTTTAAAT 0.891453 -66 GCTTGTGGTCTTTCTTTATAAATCAAAAACGTG 36 11 1 TTTTTTAAAT 0.936267 -173 ATTTAAAATTTTTTGTTATAAATAGCACAAACA 37 90 1 TTTGTTAAAT 0.87114 -108 *** * * ***** Masking position 10 Map Score: 7.90954 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 170 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 9 ATCAAGGATTTTTTATTGCCTAAAAAGCCTT 6 32 1 TTTTTTGCCT 0.741196 -78 AATAAGAATATTTTGTTGTCTAGAATTTTCC 11 127 1 TTTTTTGTCT 0.658973 -174 ATCCTTATACTTATTTTGGCGTATGCTATCA 16 16 1 TTATTTGGCG 0.949283 -176 TTGCCCACATTTATGTGGGCTTTTTTATGCC 18 44 1 TTATTGGGCT 0.949283 -144 ATATCATAAGTTATATTGGCTTGCTATGAAT 22 185 0 TTATTTGGCT 0.977543 -64 CTCCTTAGTTTTTTATGGGCTGGATTTTTAT 24 33 0 TTTTTGGGCT 0.894462 -26 ATAAAGGTTTTTATCTTTGCTTTCCTCTGTA 30 26 1 TTATTTTGCT 0.791801 -77 TATATCTTAATTATCTTGGCTCCCCTATTTA 30 55 0 TTATTTGGCT 0.977543 -48 CTTTTTATTTTCATTTTGGCTAATTTGGCAT 37 50 0 TCATTTGGCT 0.900775 -148 CAATGTTTTATTATGTTGGCGATCTACACAC 37 127 1 TTATTTGGCG 0.949283 -71 **** ****** Masking position 6 Map Score: 7.43879 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 96 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 10 TCAAAAAAATCCTTATATAAAATC 6 5 1 AAAAATCCTT 0.965977 -105 TTAGGCAATAAAAAATCCTTGATTTTATAT 6 25 0 AAAAATCCTT 0.965977 -85 TTTATTGCCTAAAAAGCCTTGTATTTTCAT 6 43 1 AAAAAGCCTT 0.916086 -67 AAAAGAGGGCAAAGATCCTTATCACATCAA 11 20 0 AAAGATCCTT 0.866285 -281 ATTCACAATCAAAAATCCATTATTCACAAG 11 60 1 AAAAATCCAT 0.918896 -241 TAGTGTTTTAAACAATCCTT 15 1 0 AACAATCCTT 0.842634 -205 ATCGCAAGAAACATATCCATTTGAAATATA 15 133 1 ACATATCCAT 0.547261 -73 ATTAAAATTGAAAAATACTTTTTACCAAAA 17 22 0 AAAAATACTT 0.691428 -90 TTGATAAATATCCTTAATTAAATGA 21 93 0 AAATATCCTT 0.887493 -15 TTTACATAATAAAAATCCAGCCCATAAAAA 24 25 1 AAAAATCCAG 0.680887 -34 CTAGCGTATCACAAAGCCTTGTCAAAAACT 29 53 0 ACAAAGCCTT 0.807321 -45 ********** Masking position 5 Map Score: 5.76673 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 142 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 11 TGATAAAACAACTTCTATGAACTTTCAAAAGAAA 5 242 0 ACTTATAATT 0.962976 -59 TAAATGGGGCACGTCTATGAAAATACAAGGCTTT 6 55 0 ACTTATAAAT 0.931737 -55 AAATAGCCGTACTTTTTTTAAATTAGGCATACGC 19 60 1 ACTTTTAATT 0.80354 -36 AATTTTCATCACTTAAATGAAATTAATTCATCAT 20 22 0 ACTAATAATT 0.804041 -102 TTATTGAGAGACCTCTATAAATTTGGTGGTAAAC 22 217 0 ACTTATAATT 0.962161 -32 ACAAATTACCTTTAAAAAATTTGTGCTAGCG 29 77 0 ACTTAAAATT 0.800747 -21 AAAGATAAAAACCTTTATTAAATTAACCGCACT 30 10 0 ACTTATAATT 0.959027 -93 GGTTATTTTTACTTGTATTAAAAT 31 1 0 ACTTATAAAT 0.931638 -157 TTCCTAAACCTTTATTAAAATCACCGCACTT 33 53 0 ACTTATAAAT 0.927917 -21 ** * *** ** ** Masking position 10 Map Score: 5.25085 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 15 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 12 TTTCTTTCCTAAAAATAAAA 1 46 0 TTTCTTTCCT 0.842176 -10 CCATTCAAAGGTGCTTTTATATTAAAAGGA 7 269 0 GTGCTTTTAT 0.827987 -32 CCTTTGAATGGTGCTTTTATTTT 7 288 1 GTGCTTTTAT 0.827987 -13 TTGCTTTCCTTTTGTTTAAA 17 102 0 TTGCTTTCCT 0.971826 -10 TGTATTTTCCTTTCATTAAATAGTTA 18 172 0 TTCCTTTCAT 0.850509 -16 GTTTTTATCTTTGCTTTCCTCTGTAAATAG 30 32 1 TTGCTTTCCT 0.971826 -71 TTTATTTTTCCTTTTCTTCTTTTTTAC 30 86 0 TTCCTTTTCT 0.901732 -17 ACCGCACTTGTTGCTTTTCTCAAACAAAGT 33 32 0 TTGCTTTTCT 0.956037 -42 ********** Masking position 5 Map Score: 3.64486 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 30 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 13 AATACCGAAAATTTTTGACCCTTTTACAAAAAGTG 4 52 0 ATTTTCTTTT 0.787917 -154 ATTTAGCTAAACTCTTAACAATTTTTTGACAA 6 88 1 ATCTTCTTTT 0.869003 -22 TTCCTGCGCCAATCTTAGTTGGTTTAATGCCTGCA 7 34 1 ATCTTTGTTT 0.645401 -267 ACAACAAAATATTCTTATTTTGTTTATATGACGAA 11 111 0 ATCTTTGTTT 0.645408 -190 AAGCGGTCAAATTCTTCTCATTATTTGCAAAATGA 12 12 1 ATCTTCTATT 0.923546 -289 AATAGCGGGCATTTTTGTTTATTTTATATTCAACA 12 270 1 ATTTTTTTTT 0.737001 -31 GTGCGGTTAAATTCTTAGTGGAATTTTATATAAAA 13 49 0 ATCTTTAATT 0.678192 -120 CTTTTACGAAATTCTTTTTGCTATTTTTAATATCA 15 68 1 ATCTTTTATT 0.901106 -138 ATTTGTTGATATTCTTTCTTTTAATCTCGTTATTA 15 171 1 ATCTTTTAAT 0.382012 -35 AAGTGCGGTGATTTTTTACCTGATTTTCCTTTTTG 16 89 1 ATTTTCGATT 0.711011 -103 GTAGTTTCATAATTTTATCCTTATTTTTGCCCACA 18 18 1 ATTTTCTATT 0.871201 -170 AATTATATTTAATCTTTTCTATATTTAAGCAAACG 18 108 1 ATCTTCTATT 0.923524 -80 TTAGGAATGAAATTTTAATTAAATTTTTATCCATA 20 55 1 ATTTTTAATT 0.532055 -69 TCTCCCTATTAATTTTTGCCATTTTACGGTATTCT 22 71 0 ATTTTCTTTT 0.787917 -178 ATGTTAAAATAATTTTACTGATTTTGTGATCTAGA 27 46 0 ATTTTTTTTT 0.736995 -130 AAGTGCGGTTATTTTTACTTGTATTAAAAT 31 6 0 ATTTTTTATT 0.83613 -152 GTATTTGTGAAGTCTTGGCGTTATTTTTGTGTGAA 36 65 1 ATCTTCTATT 0.923547 -119 AGTTTATCGCACTTTTTACAAAATTAACAACGGAT 36 119 0 ATTTTCAATT 0.609771 -65 AAACTAGGCAAATCTTTATTTTATTAATGCCTCAA 36 149 1 ATCTTTTATT 0.901106 -35 AAACATTGTGATTGTTTGTGCTATTTATAACAAAA 37 100 0 ATGTTTTATT 0.515526 -98 * **** * **** Masking position 6 Map Score: 16.2429 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 196 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 14 AATCCACGCAAAAAATAAGCGCGAAATTAA 3 46 0 AAAAATAAGC 0.836648 -79 CCTCTTGCGCAAAATCCACGCAAAAAATAA 3 58 0 AAAATCCACG 0.665882 -67 AAGTGCGGTGAAAAATAACCGCACTTTTTG 4 31 1 AAAAATAACC 0.91011 -175 AAGGTTTTCAAAAAACAACTTGGATATAAT 4 151 1 AAAAACAACT 0.679398 -55 ATCCTTATATAAAATCAAGGATTTTTTATT 6 19 1 AAAATCAAGG 0.696879 -91 ACGTCTATGAAAATACAAGGCTTTTTAGGC 6 49 0 AAATACAAGG 0.458171 -61 CCAAGCAAGCAACAACAACCCCAATTAAAC 7 187 0 AACAACAACC 0.654429 -114 AAAATCAATAAAAAATAACCGCACATTGGG 11 204 0 AAAAATAACC 0.91011 -97 CTTTTCAAGAAAAAACAAGCGGTCAAATTT 12 52 0 AAAAACAAGC 0.920009 -249 TTGAGGAATTAAATACAACCTATTAAGCGG 13 14 1 AAATACAACC 0.779322 -155 ATTTTATATAAAATTTAACCGCTTAATAGG 13 32 0 AAATTTAACC 0.399081 -137 TTTTTCGTTGAAAATTAACCTTTTCTAAGC 14 61 1 AAAATTAACC 0.810449 -39 AAATCAGGTAAAAAATCACCGCACTTTTTT 16 85 0 AAAAATCACC 0.816173 -107 AAATGTGGGCAAAAATAAGGATAAAATTAT 18 26 0 AAAAATAAGG 0.707971 -162 TTAAATAGTTAAAAATAAGCGATGAGAATT 18 153 0 AAAAATAAGC 0.836648 -35 ATCAGAACTCAAAAACAACGTTCTCTGCCT 21 31 1 AAAAACAACG 0.914979 -77 AAAACAACTAAAAAACCACCGCACTTTTTA 22 110 0 AAAAACCACC 0.908844 -139 ATTTATTGTAAAAAACAACTAAAAAACCAC 22 121 0 AAAAACAACT 0.679398 -128 TTTATTATGTAAAATCCAGCCTATTGA 24 8 0 AAAATCCAGC 0.680503 -51 TTACATAATAAAAATCCAGCCCATAAAAAA 24 26 1 AAAATCCAGC 0.680503 -33 TAATACAAGTAAAAATAACCGCACTTTGTT 31 15 1 AAAAATAACC 0.91011 -143 AAATTTGTGAAAAATCAACCGCAC 35 5 0 AAAATCAACC 0.905672 -34 ACAAATACGTTAAAACAACGATAGAATGGC 36 43 0 TAAAACAACG 0.37687 -141 AATTTCACACAAAAATAACGCCAAGACTTC 36 73 0 AAAAATAACG 0.82736 -111 ********** Masking position 8 Map Score: 30.0405 Number of sites scoring better than the average of aligned sites = 636 Number in coding regions = 475 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 15 ACCTTAACCAAACTCAAAAAATGATACGTT 4 126 0 AACTCAAAAA 0.658611 -80 TTTTATATTCAACACAAGGA 12 291 1 AACACAAGGA 0.925918 -10 ATCAAGGATCATCGCAAGAAACATATCCAT 15 123 1 ATCGCAAGAA 0.721126 -83 TATGATTTAGATCACAAAAAGGAAAATCAG 16 108 0 ATCACAAAAA 0.891859 -84 TCGAAATTCTATCACAAAGAAATTTGAATA 16 146 0 ATCACAAAGA 0.917133 -46 TTCATCTTTAAACAAAAGGAAAGCAA 17 96 1 AACAAAAGGA 0.496172 -16 TCTTCATCAGAACTCAAAAACAACGTTCTC 21 26 1 AACTCAAAAA 0.658611 -82 AGACTTTCTTAACACAAGGAGACTTTT 25 14 1 AACACAAGGA 0.925918 -17 ATGAAATATTATCACAAGAAAATAGGATCT 27 19 1 ATCACAAGAA 0.917133 -157 TAGGATCTAGATCACAAAATCAGTAAAATT 27 41 1 ATCACAAAAT 0.537133 -135 GTGCTAGCGTATCACAAAGCCTTGTCAAAA 29 56 0 ATCACAAAGC 0.697712 -42 ********** Masking position 6 Map Score: 2.48812 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 87 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974