AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00130_hinf_reg_300.orf -o00130_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: HI0967 25 H. influenzae predicted coding region HI0967 HI0033 53 conserved hypothetical protein HI0978 40 ribosomal protein L11 methyltransferase (prmA) HI0962 28 isoleucyl-tRNA synthetase (isoleucine--tRNA ligase) (ileRS) 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 HI0285 135 menaquinone-specific isochorismate synthase (menF) #7 HI0329 37 conserved hypothetical protein #8 HI0330 98 opacity associated protein (oapA) #9 HI0331 59 opacity associated protein (oapB) #10 HI0509 46 1,4-dihydroxy-2-naphthoate octaprenyltransferase (menA) #11 HI0531 231 ribosomal protein S21 (rpS21) #12 HI0532 133 DNA primase (dnaG) #13 HI0549 169 dimethyladenosine transferase (ksgA) #14 HI0881 212 octaprenyl-diphosphate synthase (ispB) #15 HI0961 74 hit-related protein #16 HI0963 34 riboflavin kinase / FMN adenylyltransferase (ribF) #17 HI0964 300 virulence factor (mviN) #18 HI0974.1 300 conserved hypothetical protein #19 HI0976 119 conserved hypothetical protein #20 HI1171 41 anthranilate synthase component II (trpG) #21 HI1386 300 H. influenzae predicted coding region HI1386 #22 HI1387 105 anthranilate synthase component I (trpE) Motif number 1 TGAAAATTGACCGCACTTTTTGATTTATTT 1 19 1 CCGCACTTTT 0.998184 -37 GCGAAATTAACCGCGCTTTTTATGTCTAAA 3 26 0 CCGCGCTTTT 0.990432 -99 TGATAGAATTCCGCACCTTTATTGCTAAGT 3 96 1 CCGCACCTTT 0.994778 -29 TTATTTTTCACCGCACTTTTATCTCGGATG 4 19 0 CCGCACTTTT 0.998184 -187 TGAAAAATAACCGCACTTTTTGTAAAAGGG 4 39 1 CCGCACTTTT 0.998184 -167 CGTAAATTAACCGCACTTTTCTCGAAAAAT 6 36 0 CCGCACTTTT 0.998184 -100 AATTTTTTCGCCGCACTTTTGAGCTTCTCA 8 30 1 CCGCACTTTT 0.998184 -69 GGGCGAGTAATCGCCCCTTTTTCTTTTTAA 9 17 1 TCGCCCCTTT 0.893084 -43 CCAAAAACGACCGCACTTTCACACCACGAT 12 99 1 CCGCACTTTC 0.988597 -35 CGGCTATAATCCGCCCGTTTTTCTTAACTT 13 22 0 CCGCCCGTTT 0.972881 -148 CCTATAATAACCGCACTTTTCTTATTAAAT 13 143 1 CCGCACTTTT 0.998184 -27 GTAAAATGCACCGCACTTTTAACTGATAAA 14 184 1 CCGCACTTTT 0.998184 -29 AGCAAATCAATCGCACTTTTTGTTTTACAA 15 20 0 TCGCACTTTT 0.985825 -55 ********** Masking position 8 Map Score: 48.2664 Number of sites scoring better than the average of aligned sites = 654 Number in coding regions = 386 Number in noncoding regions = 268 Number of orfs with sites within 600 bp upstream = 208 Fraction of orfs with sites within 600 bp upstream = 0.0334083 Motif number 2 GAATTTGAAAATTGACCGCACTTTTTGATTTA 1 14 1 ATACCGCACT 0.996883 -42 TAAGCGCGAAATTAACCGCGCTTTTTATGTCT 3 29 0 ATACCGCGCT 0.98523 -96 TGCGGTTATTTTTCACCGCACTTTTATCTCGG 4 22 0 TTACCGCACT 0.988878 -184 TGCGGTGAAAAATAACCGCACTTTTTGTAAAA 4 34 1 AAACCGCACT 0.993143 -172 TTCAGCGTAAATTAACCGCACTTTTCTCGAAA 6 39 0 ATACCGCACT 0.996883 -97 CACATAATTTTTTCGCCGCACTTTTGAGCTTC 8 25 1 TTGCCGCACT 0.948828 -74 CTACGCCAAAAACGACCGCACTTTCACACCAC 12 94 1 AAACCGCACT 0.993143 -40 CAACCCCTATAATAACCGCACTTTTCTTATTA 13 138 1 AAACCGCACT 0.993143 -32 TTCGGGTAAAATGCACCGCACTTTTAACTGAT 14 179 1 ATACCGCACT 0.996883 -34 GACAGAGCAAATCAATCGCACTTTTTGTTTTA 15 23 0 ATATCGCACT 0.965451 -52 ** ******** Masking position 12 Map Score: 27.0887 Number of sites scoring better than the average of aligned sites = 607 Number in coding regions = 378 Number in noncoding regions = 229 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 3 TTTCTTTCCTAAAAATAAAATAAATCAAAAAGT 1 33 0 TTAAAAAAAA 0.965205 -23 TCATTTTTTCTTTCTTAAAGAAAGAATAAATGAAAAGCG 2 13 1 TTAAAGAAAA 0.943985 -39 AACCGCACTTTTTGTAAAAGGGTCAAAAATTTTCGGTAT 4 47 1 TTAAAGTAAA 0.884373 -159 TCCAAGTTGTTTTTTGAAAACCTTAACCAAACTCAAAAA 4 136 0 TTAAAATAAA 0.926389 -70 TGGCTCACTATTTACAAAGAAAATAATCAGCCGTTCTAT 5 89 0 TTAAGAAAAA 0.816273 -212 TCTCTGTTGATTAAGGAAAACGAAAAATATGATAAAACA 5 266 0 TTAAAAAAAA 0.965206 -35 TCTCGAAAAATTTATTAGAAACAAAAGGATTTCACT 6 8 0 TTAGAAAAAA 0.680308 -128 TTGTGGCTAATTAATATAAATAAGAACAAGCATCAGAGG 8 63 1 TTTAAAAAAA 0.804514 -36 GCGCAACATTTTAGGTAATAAATTAAGAAAATCA 11 6 0 TTAATATAAA 0.565892 -226 TAATCTATTTTTAGGGAAAAAGTAAAGGATAGAATGCCA 11 102 0 TTAAAATAAA 0.926416 -130 ACACAGGTGCTTTGGCAAAAATAAAATTTTAAATTGCAA 11 173 1 TTAAAAAAAT 0.873614 -59 GTTTTTAGCTTTCTACGAAAGAAAAAATAATATTGTTCA 13 51 1 TTGAAAAAAA 0.707102 -119 AATAATATTGTTCATGAAAAACTCAATTTGGCATAACCT 13 76 1 TTAAAATAAT 0.758288 -94 CCTAACAATGATTTACAAAGCTAAAACAACCCCTATAAT 13 112 1 ATAAAGAAAA 0.62547 -58 AAGATTTTATTTATAATAAAATAAAAAAATTCCCTTCAT 14 111 1 TTTAAAAAAA 0.804457 -102 TGCGGATTGATTTCAGAAAGTCTGAAAATTCGGGTAAAA 14 151 1 TTAAAGTAAT 0.655867 -62 AAATTTTCCATTGACAAAAGTATAAAAAATCGGCATATT 17 53 0 TTAAAGTAAA 0.884373 -248 CTTATCGGTATTCGTCAAAAAAATAAGGAATATGCATCA 18 17 1 TTAAAAAAAA 0.965206 -284 AATCATCCTTTTTATGAATATGATAAAAATCGAATTTAC 18 137 1 TTAATAAAAA 0.74175 -164 ATACTTTCACTTATAAAAAATTTTAAGGAAGAAAT 18 276 1 TTAAAATAAA 0.92639 -25 AGCGTAGAAATTGCTGAAAGTGAGAAAATTAAATATCAC 19 54 0 TTAAAGAAAT 0.807666 -66 CAAAATATGTTTTGATAAGATTAGAAATAAGATTACGAG 21 41 0 TTAAGAAAAA 0.816273 -260 CAAAATATACTTAATATAAGGCAAAATATGTTTTGATAA 21 62 0 TTTAAGAAAT 0.383866 -239 TAATCAAGGTATTATAAAAATGAAAAGGATCTATACTGA 21 104 1 ATAAAAAAAA 0.733265 -197 TAATCAAAAAGTATAAAAAATAAAAATCAGGCTTGACTT 22 24 1 GTAAAAAAAA 0.69794 -82 TAGTACAAAATTTTCCAAAAGGATAAATAAAT 22 84 1 TTAAAAAAAA 0.965206 -22 ** **** * ** * Masking position 2 Map Score: 29.8852 Number of sites scoring better than the average of aligned sites = 360 Number in coding regions = 241 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 4 AAATCAAAAAGTGCGGTCAATTTTCAAATTCT 1 13 0 GTCGGTCATT 0.913695 -43 GACATAAAAAGCGCGGTTAATTTCGCGCTTAT 3 30 1 GCCGGTTATT 0.904398 -95 TTTACAAAAAGTGCGGTTATTTTTCACCGCAC 4 33 0 GTCGGTTATT 0.97843 -173 TACATAGAACGGCTGATTATTTTCTTTGTAAA 5 86 1 GGTGATTATT 0.909589 -215 TTCGAGAAAAGTGCGGTTAATTTACGCTGAAT 6 40 1 GTCGGTTATT 0.97843 -96 TGGACTCACGGTTTTGTTACTTTAAGCACAAC 12 56 1 GTTTGTTATT 0.799104 -78 TGGTGTGAAAGTGCGGTCGTTTTTGGCGTAGA 12 93 0 GTCGGTCGTT 0.923349 -41 AATAAGAAAAGTGCGGTTATTATAGGGGTTGT 13 137 0 GTCGGTTATA 0.784641 -33 AAAACAAAAAGTGCGATTGATTTGCTCTGTCC 15 24 1 GTCGATTGTT 0.911793 -51 CCGAAAGTAAGTATCGTTATTTTTACAAGCTC 17 115 1 GTTCGTTATT 0.769761 -186 TTCATAAAAAGGATGATTACTTGTTACCTTTT 18 123 0 GGTGATTATT 0.909589 -178 TTGGTTGGTTGGTTGGTTGGTTCATCAGTATA 21 135 0 GGTGGTTGTT 0.982805 -166 TTGGTTGGTTGGTTGGTTGGTTGGTTGGTTGG 21 147 0 GGTGGTTGTT 0.982805 -154 TTGGTTGGTTGGTTGGTTGGTTGGTTGGTTGG 21 159 0 GGTGGTTGTT 0.982805 -142 TTGGTTGGTTGGTTGGTTGGTTGGTTGGTTGG 21 171 0 GGTGGTTGTT 0.982805 -130 TATTTTGGTTGGTTGGTTGGTTGGTTGGTTGG 21 183 0 GGTGGTTGTT 0.982805 -118 TACCGCAACGGTTTTATTATTTTGGTTGGTTG 21 200 0 GTTTATTATT 0.443403 -101 ** ****** ** Masking position 7 Map Score: 26.0268 Number of sites scoring better than the average of aligned sites = 402 Number in coding regions = 266 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 5 TTTTGATTTATTTTATTTTTAGGAAAGAAA 1 36 1 TTTTATTTTT 0.961626 -20 TTTCATTTTTTCTTTCTTAA 2 1 1 TTTCATTTTT 0.973294 -51 TATTAACGCTTTTCATTTATTCTTTCTTTA 2 28 0 TTTCATTTAT 0.880899 -24 GTGACGAACGTATCATTTTTTGAGTTTGGT 4 120 1 TATCATTTTT 0.893955 -86 AGGAGTTAAATTTCATTTTTAAGGGGTCAA 4 185 1 TTTCATTTTT 0.973294 -21 ATCGCTTAAATTTCATTGTTTATTCCTATT 5 149 1 TTTCATTGTT 0.803453 -152 GAAGTTGTTTTATCATATTTTTCGTTTTCC 5 261 1 TATCATATTT 0.529403 -40 TCAAACCATCTCTCATTTTTAGGATATTTC 7 15 0 TCTCATTTTT 0.900991 -23 TGATGCTTGTTCTTATTTATATTAATTAGC 8 68 0 TCTTATTTAT 0.559445 -31 AATCGCCCCTTTTTCTTTTTAAGTTCTTTT 9 25 1 TTTTCTTTTT 0.737587 -35 CAATTTAAAATTTTATTTTTGCCAAAGCAC 11 179 0 TTTTATTTTT 0.961626 -53 TCATGAACAATATTATTTTTTCTTTCGTAG 13 63 0 TATTATTTTT 0.852863 -107 TATGGCAAGATTTTATTTATAATAAAATAA 14 105 1 TTTTATTTAT 0.835678 -108 AAGGGAATTTTTTTATTTTATTATAAATAA 14 117 0 TTTTATTTTA 0.641947 -96 TGTATAGAAATTTTGTTTTTACGCTATATT 17 205 0 TTTTGTTTTT 0.737587 -96 GCATAGAAACTTTCATATTTGGGGAATTAC 18 70 1 TTTCATATTT 0.829454 -231 TATAGATCCTTTTCATTTTTATAATACCTT 21 109 0 TTTCATTTTT 0.973294 -192 ACCGCAACGGTTTTATTATTTTGGTTGGTT 21 201 0 TTTTATTATT 0.654751 -100 CAAGCCTGATTTTTATTTTTTATACTTTTT 22 29 0 TTTTATTTTT 0.961626 -77 ********** Masking position 6 Map Score: 23.1524 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 185 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 6 TTGGTTGGTTGGTTGGTTGGTTCATCAGTA 21 137 0 GGTTGGTTGG 0.998758 -164 TTGGTTGGTTGGTTGGTTGGTTGGTTGGTT 21 149 0 GGTTGGTTGG 0.998758 -152 TTGGTTGGTTGGTTGGTTGGTTGGTTGGTT 21 161 0 GGTTGGTTGG 0.998758 -140 TTGGTTGGTTGGTTGGTTGGTTGGTTGGTT 21 173 0 GGTTGGTTGG 0.998758 -128 TATTTTGGTTGGTTGGTTGGTTGGTTGGTT 21 185 0 GGTTGGTTGG 0.998758 -116 ********** Masking position 4 Map Score: 17.8249 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 7 AGAATTTGAAAATTGACCGCACTTTTTGATTTATTT 1 13 1 AATCACTTTT 0.85444 -43 TTTATGTCTAAATTGAAATTATTTTTA 3 2 0 AATAATTTTT 0.914328 -123 GCGCGGTTAATTTCGCGCTTATTTTTTGCGTGGATT 3 40 1 TTTCATTTTT 0.466878 -85 TGCGGTGAAAAATAACCGCACTTTTTGTAAAAGGGT 4 34 1 AATGCTTTTT 0.449518 -172 TAGCCTCTACAATACCGAAAATTTTTGACCCTTTTA 4 61 0 AATAATTTTT 0.914331 -145 AGTGCGGTTAATTTACGCTGAATTTTCAATATTGAA 6 49 1 ATTCAATTTT 0.837965 -87 GCAGATTGTTAATGACAAAAAATTTTTTTACAAAAT 6 88 0 AATAAATTTT 0.895632 -48 TCTGCGGTAGAATATGGCTAATTTTTT 6 119 1 AATCATTTTT 0.944125 -17 GATCCGATAAAATACACATAATTTTTTCGCCGCACT 8 11 1 AATAATTTTT 0.914314 -88 AACAGGGTAAAATCGCGCAACATTTTAGGTAATAAA 11 23 0 AATCCATTTT 0.809683 -209 ATAGAATGCCAATTCACCTTAATATTTGTGGTTTCA 11 77 0 AATCAATATT 0.382915 -155 TAAAGGACGCAATTCTAATCTATTTTTAGGGAAAAA 11 120 0 AATATATTTT 0.623754 -112 ATTTGCGACCTATTTATATGAATTTTTAAGTGTGGA 14 50 0 TATAAATTTT 0.53884 -163 AAAATCTTGCCATAGGTAGGATTTTTCCGTAGAATT 14 83 0 CATAATTTTT 0.695585 -130 TCAATCCGCAAATGAAGGGAATTTTTTTATTTTATT 14 125 0 AATGATTTTT 0.727136 -88 AGTGCGGTGCATTTTACCCGAATTTTCAGACTTTCT 14 165 0 ATTCAATTTT 0.837965 -48 GGACAGAGCAAATCAATCGCACTTTTTGTTTTACAA 15 20 0 AATCACTTTT 0.854431 -55 ATTGTTGCTTATTTAGTCTAACTTTTAAGGACAGAG 15 48 0 ATTCACTTTT 0.68618 -27 TTTGTCTATCAATCAACAGAAATTTTAGGA 17 5 0 AATAAATTTT 0.895618 -296 AAAGGGCATCAATATGCCGATTTTTTATACTTTTGT 17 43 1 AATCTTTTTT 0.767877 -258 GTCTCACCGAAATCAACACAAATTTTCCATTGACAA 17 75 0 AATAAATTTT 0.89563 -226 TGTGTGGCGGATTTTATCAGTTTTTTTTCACGGAAT 17 172 1 ATTCTTTTTT 0.554078 -129 TTTTTGCCTAATTGTATAGAAATTTTGTTTTTACGC 17 211 0 ATTAAATTTT 0.761702 -90 AGGACTGATGCATATTCCTTATTTTTTTGACGAATA 18 25 0 CATCATTTTT 0.787065 -276 TGTGTTTGCTAATCTTACAACTTTTTTGAATAATTC 18 198 0 AATCCTTTTT 0.841047 -103 ATTTCTTCCTTAAAATTTTTTATAAGTGAA 18 281 0 CTTAATTTTT 0.45979 -20 GTAATTATGCAATAGAAAATATTTTTGG 21 3 0 AATAATTTTT 0.914325 -298 TTTCTAATCTTATCAAAACATATTTTGCCTTATATT 21 53 1 TATATATTTT 0.184158 -248 CCTGATTTTTATTTTTTATACTTTTTGATTAAAAAT 22 19 0 ATTACTTTTT 0.549176 -87 GCACTAGTTTAATAGTACAAAATTTTCCAAAAGGAT 22 72 1 AATCAATTTT 0.93278 -34 *** * ****** Masking position 13 Map Score: 29.2061 Number of sites scoring better than the average of aligned sites = 892 Number in coding regions = 597 Number in noncoding regions = 295 Number of orfs with sites within 600 bp upstream = 243 Fraction of orfs with sites within 600 bp upstream = 0.0390299 Motif number 8 TGGGACTTCAATTCATTTTGCTGAC 5 6 0 ATTCATTTTG 0.747398 -295 TTCATTGTTTATTCCTATTGAAGTGGTTAA 5 160 1 ATTCCTATTG 0.82673 -141 TATGATGGTCTTTTCTTTTGAAAGTTCATA 5 231 1 TTTTCTTTTG 0.840637 -70 AGTGAAATCCTTTTGTTTCTAATAA 6 6 1 AATCCTTTTG 0.955148 -130 ACAAACCGTGAATCCTTTGGACTCACGGTT 12 39 1 AATCCTTTGG 0.785213 -95 GCCGATTTTTTATACTTTTGTCAATGGAAA 17 58 1 TATACTTTTG 0.676133 -243 TGATTACTTGTTACCTTTTGATACGACCAA 18 112 0 TTACCTTTTG 0.82673 -189 GAAATCAGCAAAACCTTTTGAATTATTCAA 18 179 1 AAACCTTTTG 0.82673 -122 CCAAAAATATTTTCTATTGCATAATTACA 21 10 1 TTTTCTATTG 0.541681 -291 GCAACGGTTTTATTATTTTGGTTGGTTGGT 21 198 0 TATTATTTTG 0.422937 -103 GGCTTGACTTATTCCTTTTGCACTAGTTTA 22 53 1 ATTCCTTTTG 0.955148 -53 ATTTATTTATCCTTTTGGAAAATTTTG 22 89 0 TATCCTTTTG 0.955148 -17 ********** Masking position 6 Map Score: 7.45374 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 174 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 9 GCGCTTATTTTTTGCGTGGATTTTGCGCAAGA 3 54 1 TTGCGTGGAT 0.934338 -71 TATTGAAAATTCAGCGTAAATTAACCGCACTT 6 48 0 TCGCGTAAAT 0.721116 -88 ATTGGGTGTCTTAGTGTAGAATACGCGGCTTA 10 13 1 TTGTGTAGAT 0.950622 -34 GCGGTCGTTTTTGGCGTAGATTTTTGTTGTGC 12 81 0 TTGCGTAGAT 0.985556 -53 AGGTAGGATTTTTCCGTAGAATTTGCGACCTA 14 74 0 TTCCGTAGAT 0.942059 -139 AGTCTGAAAATTCGGGTAAAATGCACCGCACT 14 169 1 TTGGGTAAAT 0.821039 -44 TCCTAAAATTTCTGTTGATTGATAGACAAA 17 9 1 TTCTGTTGAT 0.532345 -292 CAATGGAAAATTTGTGTTGATTTCGGTGAGAC 17 79 1 TTGTGTTGAT 0.826894 -222 GGCAAAAATTTTAGGGTAGAGAAGAATATTTT 17 239 1 TTGGGTAGAA 0.880795 -62 AAAAATCGAATTTACGTAGAAATCAGCAAAAC 18 161 1 TTACGTAGAA 0.679423 -140 ATTCTATGTTTTAGCGTAGAAATTGCTGAAAG 19 73 0 TTGCGTAGAA 0.960409 -47 TTTGCGTAAAATGACCTGATTA 20 1 1 TTGCGTAAAT 0.937742 -41 ** ******* * Masking position 10 Map Score: 7.67417 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 101 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 10 ATAAAGGTGCGGAATTCTATCATTGAATACC 3 87 0 GGATTCTATC 0.900461 -38 TTAACTCCTTCGGATTATATCCAAGTTGTTT 4 163 0 CGATTATATC 0.946675 -43 AAAAATTATGTGTATTTTATCGGATC 8 6 0 TGATTTTATC 0.895281 -93 AAGGTGAATTGGCATTCTATCCTTTACTTTT 11 93 1 GGATTCTATC 0.900461 -139 GAAAAACGGGCGGATTATAGCCGTTTTTAGC 13 29 1 CGATTATAGC 0.950578 -141 TGTGTTTTCCTGCTTTTTAGCAGTCCACACT 14 27 1 TGTTTTTAGC 0.696812 -186 AAAAGTGCGGTGCATTTTACCCGAATTTTCA 14 173 0 TGATTTTACC 0.724569 -40 AGAGAATTTCGGCATTATAGCGAGAAG 16 7 0 GGATTATAGC 0.92197 -28 CGATGTGTGGCGGATTTTATCAGTTTTTTTT 17 169 1 CGATTTTATC 0.956279 -132 TTTTTTTTCACGGAATATAGCGTAAAAACAA 17 192 1 CGAATATAGC 0.709631 -109 TACGTAAATTCGATTTTTATCATATTCATAA 18 148 0 CGTTTTTATC 0.844406 -153 ** ******** Masking position 9 Map Score: 5.45869 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 88 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 11 TTGAGTTTGGTTAAGGTTTTCAAAAAACAACT 4 139 1 TTAAGTTTCA 0.667148 -67 CGCCGCACTTTTGAGCTTCTCAATTTTGTGGC 8 38 1 TTGACTTTCA 0.824461 -61 TGATTTTCTTAATTTATTACCTAAAATGTT 11 9 1 TTAATTATAC 0.449461 -223 CATTCTATCCTTTACTTTTTCCCTAAAAATAG 11 105 1 TTTATTTTCC 0.732041 -127 GCGTCCTTTATTAAATTTGTCATTTACACACA 11 146 1 TTAATTTTCA 0.905757 -86 TTATGCCAAATTGAGTTTTTCATGAACAATAT 13 80 0 TTGATTTTCA 0.957485 -90 GCAAAACCTTTTGAATTATTCAAAAAAGTTGT 18 186 1 TTGATTATCA 0.929964 -115 AAGGTGATATTTAATTTTCTCACTTTCAGCAA 19 51 1 TTAATTTTCA 0.905758 -69 TAAGTATATTTTGAGTTAATCAAGGTATTATA 21 88 1 TTGATTATCA 0.929965 -213 ATGGATAAGTTTGATTTTGTACGCTTTTAATA 21 270 0 TTGATTTTAC 0.764416 -31 AAAATCAGGCTTGACTTATTCCTTTTGCACTA 22 46 1 TTGATTATCC 0.925474 -60 **** *** *** Masking position 4 Map Score: 3.42232 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 179 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 12 ACCGCGCTTTTTATGTCTAAATTGAAATTA 3 17 0 TTATGTCTAA 0.903524 -108 TTCCGCACCTTTATTGCTAAGTGAGAACAA 3 104 1 TTATTGCTAA 0.903524 -21 TGAAATCCTTTTGTTTCTAATAAATTTTTC 6 13 1 TTGTTTCTAA 0.903547 -123 CTGCGGTAGAATATGGCTAATTTTTT 6 120 1 ATATGGCTAA 0.726984 -16 CTTCTCAATTTTGTGGCTAATTAATATAAA 8 53 1 TTGTGGCTAA 0.959296 -46 AATTGTTGCTTATTTAGTCTAA 15 63 0 TTGTTGCTTA 0.75519 -12 TTACTTTCGGTTGTGTCTCACCGAAATCAA 17 95 0 TTGTGTCTCA 0.820533 -206 TCTCGTAATCTTATTTCTAATCTTATCAAA 21 40 1 TTATTTCTAA 0.855176 -261 ********** Masking position 10 Map Score: 2.23559 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 83 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 13 ATAGCCTCTACAATACCGAAAATTTTTGACCC 4 66 0 CAATCGAAAA 0.82789 -140 AGGCTATGCTCAATTTCGCAAGAAAAAATGTG 4 91 1 CAATTGCAAG 0.91396 -115 TCCTGCATTACAATTTGGAAAAAGTATTCAAG 5 46 0 CAATTGAAAA 0.939878 -255 ATCAGCCGTTCTATGTAGCAAATCTTCCTGCA 5 71 0 CTATTGCAAA 0.936066 -230 AAAATCTTTTCAATATTGAAAATTCAGCGTAA 6 61 0 CAATTGAAAA 0.939878 -75 ATGAAAAACTCAATTTGGCATAACCTAACAAT 13 89 1 CAATTGCATA 0.936066 -81 AATTTCTATACAATTAGGCAAAAATTTTAGGG 17 223 1 CAATAGCAAA 0.892507 -78 TCAGTCCTTACTATCTGGCATAGAAACTTTCA 18 53 1 CTATTGCATA 0.842763 -248 **** * ***** Masking position 3 Map Score: 2.05736 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 88 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 14 TTAAGGTTTTCAAAAAACAACTTGGATATA 4 149 1 CAAAAAACAA 0.64607 -57 AAATTTAAGCGATAAAGCAATTTCAGAAGC 5 132 0 GATAAAGCAA 0.653326 -169 ACTTCAATAGGAATAAACAATGAAATTTAA 5 154 0 GAATAAACAA 0.684129 -147 CGAAAAATATGATAAAACAACTTCTATGAA 5 255 0 GATAAAACAA 0.922771 -46 TTAACCAGTTGAAACCACAAATATTAAGGT 11 68 1 GAAACCACAA 0.684109 -164 AGGTGCTTTGGCAAAAATAAAATTTTAAAT 11 177 1 GCAAAAATAA 0.732666 -55 TTCTACGAAAGAAAAAATAATATTGTTCAT 13 61 1 GAAAAAATAA 0.702901 -109 GATTTACAAAGCTAAAACAACCCCTATAAT 13 121 1 GCTAAAACAA 0.93262 -49 TAAAAAGCAGGAAAACACAATTAAGCGGAG 14 16 0 GAAAACACAA 0.932114 -197 TTCAATATGGGCTCACACAAACGATGTGTG 17 148 1 GCTCACACAA 0.635669 -153 GGAATATAGCGTAAAAACAAAATTTCTATA 17 203 1 GTAAAAACAA 0.770167 -98 TGTAAGATTAGCAAACACAAGGGACGTATG 18 215 1 GCAAACACAA 0.940848 -86 CAATTTCTACGCTAAAACATAGAATTGCAA 19 80 1 GCTAAAACAT 0.595622 -40 ********** Masking position 9 Map Score: 4.18512 Number of sites scoring better than the average of aligned sites = 455 Number in coding regions = 385 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 15 AAATCAAAAAGTGCGGTCAATTTTCAAATT 1 15 0 GTGCGGTCAA 0.983296 -41 GACATAAAAAGCGCGGTTAATTTCGCGCTT 3 30 1 GCGCGGTTAA 0.93674 -95 CGAGATAAAAGTGCGGTGAAAAATAACCGC 4 23 1 GTGCGGTGAA 0.991199 -183 TTTACAAAAAGTGCGGTTATTTTTCACCGC 4 35 0 GTGCGGTTAT 0.969835 -171 TTCGAGAAAAGTGCGGTTAATTTACGCTGA 6 40 1 GTGCGGTTAA 0.986112 -96 AAGCTCAAAAGTGCGGCGAAAAAATTATGT 8 26 0 GTGCGGCGAA 0.979768 -73 TGGTGTGAAAGTGCGGTCGTTTTTGGCGTA 12 95 0 GTGCGGTCGT 0.928719 -39 AATAAGAAAAGTGCGGTTATTATAGGGGTT 13 139 0 GTGCGGTTAT 0.969835 -31 TCAGTTAAAAGTGCGGTGCATTTTACCCGA 14 180 0 GTGCGGTGCA 0.967652 -33 CACAAACGATGTGTGGCGGATTTTATCAGT 17 163 1 GTGTGGCGGA 0.674063 -138 ********** Masking position 5 Map Score: 17.1199 Number of sites scoring better than the average of aligned sites = 967 Number in coding regions = 589 Number in noncoding regions = 378 Number of orfs with sites within 600 bp upstream = 256 Fraction of orfs with sites within 600 bp upstream = 0.0411179