AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -inarL_aful_opreg_300.orf -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 AF0140 123 ubiquinone/menaquinone biosynthesis methyltransferase (ubiE) #2 AF0154 139 conserved hypothetical protein #3 AF0155 62 A. fulgidus predicted coding region AF0155 #4 AF0157 99 molybdopterin oxidoreductase, iron-sulfur binding subunit #5 AF0176 58 molybdopterin oxidoreductase, molybdopterin binding subunit #6 AF0177 300 tungsten formylmethanofuran dehydrogenase, subunit E (fwdE) #7 AF0396 154 A. fulgidus predicted coding region AF0396 #8 AF0400 84 NADH oxidase (noxA-3) #9 AF0422 138 uroporphyrin-III C-methyltransferase (cysG-1) #10 AF0499 300 molybdopterin oxidoreductase, iron-sulfur binding subunit #11 AF0681 145 succinate dehydrogenase, flavoprotein subunit A (sdhA) #12 AF0950 177 carbon monoxide dehydrogenase, iron sulfur subunit (cooF) #13 AF1205 53 pantothenate permease (panF-2) #14 AF1208 165 conserved hypothetical protein #15 AF1210 108 conserved hypothetical protein #16 AF1241 81 glutamate-1-semialdehyde aminotransferase (hemL) #17 AF1643 50 conserved hypothetical protein #18 AF1644 35 tungsten formylmethanofuran dehydrogenase, subunit F (fwdF) #19 AF1858 145 NADH oxidase (noxA-5) #20 AF1860 282 A. fulgidus predicted coding region AF1860 #21 AF1868 51 A. fulgidus predicted coding region AF1868 #22 AF1869 78 A. fulgidus predicted coding region AF1869 #23 AF1980 36 heme exporter protein C (helC) #24 AF1984 45 iron-dependent repressor (troR) #25 AF2191 300 A. fulgidus predicted coding region AF2191 #26 AF2371 170 A. fulgidus predicted coding region AF2371 #27 AF2374 159 A. fulgidus predicted coding region AF2374 #28 AF2377 115 conserved hypothetical protein #29 AF2378 47 conserved hypothetical protein #30 AF2383 33 conserved hypothetical protein #31 AF2384 190 molybdopterin oxidoreductase, molybdopterin binding subunit Motif number 1 CCTGGCATCTTTTTACCCAAAAAACATGCAGC 1 57 0 TTTCCCAAAA 0.957617 -67 CCCCAAACACTGTTACCTAACAGTGTTTATAT 2 21 1 TTTCCTAACA 0.92278 -119 AAAGTTTTTGGTTGGCCTAAAATCGGTTTTGA 2 90 0 GTGCCTAAAA 0.918315 -50 AACATCTACCTTTTCCCTAAAATCTTCGAATA 3 20 0 TTTCCTAAAA 0.986958 -43 CAATTTTTCCTAATATTTTAGGGAA 5 4 1 TTTCCTAATA 0.892532 -55 GTCATAAGGTTTTTCCCTAAAATATTAGGAAA 5 16 0 TTTCCTAAAA 0.986958 -43 GCTATTTTCAGCTTACCCAAAAATGTTAAGTT 8 30 0 GTTCCCAAAA 0.970408 -55 AATTCTTATATATTGCCTAAAAAGAGGGGGAC 9 34 0 TTTCCTAAAA 0.986611 -105 TCTGGTTTAAGCTTACCTAAAAATATCTGCAA 9 81 1 GTTCCTAAAA 0.986156 -58 GAACTCTTTTCCAAAATAAAGGTAAG 26 155 0 TTTTCCAAAA 0.807265 -16 AGACTTTTAGGCTTTTCTAAAAAACGGAGGAT 28 42 0 GTTTCTAAAA 0.892228 -74 TAACTTTTCGGATTGCCTAAAAT 29 2 0 GTTCCTAAAA 0.986148 -46 TAGCCAGCAATTTATCCTAAAAATAG 30 5 0 TTACCTAAAA 0.892923 -29 GTTTATAGGTTATTACCTAAAATTGAGAATAC 31 92 0 TTTCCTAAAA 0.985688 -99 * ** ******* Masking position 9 Map Score: 23.5873 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 19 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 2 GCAAAGGAGCGAAAATTTAAAA 1 1 0 GAAATTAAAA 0.915167 -123 GATGGTAAACGAAAGGTATAAATGAATCCTTA 1 88 1 GAAATATAAA 0.784428 -36 GTTAATTTCCAAAACCCTTATATTTTATCAAG 4 31 1 AAAACTTATA 0.828539 -69 TTATCTTAAAGAAAAATTTAAATATCGTCAGT 7 43 0 GAAATTTAAA 0.935911 -112 TCTTTAAGATAAAAACTTAAAACTAATTTGCT 7 63 1 AAAATTAAAA 0.885869 -92 TCTGTACGTCGGAAAATTTATATTGCAATATT 7 119 1 GGAATTTATA 0.805394 -36 AGTACGGCTCGAAAACTTAACATTTTTGGGTA 8 17 1 GAAATTAACA 0.611451 -68 CGCAAATTTCGAAATTCTTATATATTGCCTAA 9 46 0 GAAACTTATA 0.870401 -93 GGGAGTTGTGGGAAGGTTAAAAAACTTCTCGA 9 113 0 GGAATTAAAA 0.767749 -26 ATGTATAGAGGAAAACTTTAAATATAATGGGG 10 94 0 GAAATTTAAA 0.935911 -207 ATAAAAAAGCAAAAGGTTAATATAAGCTAAAT 10 223 1 AAAATTAATA 0.877731 -78 CTTGAATGCAAAAAAATATATATCGAA 12 6 0 AAAATATATA 0.707723 -172 TCTGTTAAAGAAAAGGTAAATACTACAAATAG 14 16 0 AAAATAAATA 0.64142 -150 ATTTAATGGGAAAAAACTTAAATAAAATGA 16 9 0 AAAACTTAAA 0.839352 -73 TCTCAGCAAGAAAACATTTAAAACGAATTGGA 16 49 1 AAAATTTAAA 0.913096 -33 AAATATTCACAAAAGGTTTATAACTGAAAGAT 19 80 1 AAAATTTATA 0.906695 -66 TAAACTTATAAGAATATTAATAAATAAAATCT 19 108 0 AGAATTAATA 0.687473 -38 AAGAATTTTTAAAGCGAGTTTGA 20 2 1 AGAATTTAAA 0.76301 -281 AAGCGAGTTTGAAAAATTTATAGAAATGAATG 20 22 1 GAAATTTATA 0.931063 -261 AGCACATTTCGAAAGCTTAATATTTTCCTTTG 21 23 1 GAAATTAATA 0.908904 -29 ATTGGTAGCAGAAAGATTTATATTAAATGAAG 22 12 0 GAAATTTATA 0.931064 -67 GGAAAAACTTAAAGCCTTGTTCA 23 2 1 GAAACTTAAA 0.87896 -35 TTTAAAATTTAAAAAATAAAAATAAAAAA 28 8 0 AAAATAAAAA 0.659179 -108 CGTTTTTTAGAAAAGCCTAAAAGTCTTGAGGT 28 48 1 AAAACTAAAA 0.794226 -68 CTAATCACTTAAAAGACAAAAAGAAAATTATT 31 43 0 AAAACAAAAA 0.490253 -148 TGGAAATTGCAAAAAGTTTATAGGTTATTACC 31 107 0 AAAATTTATA 0.906695 -84 **** ****** Masking position 4 Map Score: 26.2694 Number of sites scoring better than the average of aligned sites = 342 Number in coding regions = 122 Number in noncoding regions = 220 Number of orfs with sites within 600 bp upstream = 249 Fraction of orfs with sites within 600 bp upstream = 0.0399936 Motif number 3 GCTTATAATGTTAAATATAAACACTGTTAG 2 37 0 TTAAATATAA 0.867981 -103 TACTACTTGATAAAATATAAGGGTTTTGGA 4 38 0 TAAAATATAA 0.8406 -62 AACGCTGTATTTAAATTTAACGGTGTTTTT 6 203 1 TTAAATTTAA 0.491151 -98 TTTTACATGATTAAAAATAATCGAATTAGG 6 229 1 TTAAAAATAA 0.811265 -72 TTAACACCGTTCAAAAATAATTTAAAGCTA 6 263 1 TCAAAAATAA 0.676544 -38 GAGGAAAACTTTAAATATAATGGGGGATAA 10 89 0 TTAAATATAA 0.867981 -212 AGAAGATTAATCAAATATAATAAGTTAAAT 15 77 1 TCAAATATAA 0.921262 -32 GGGAAAAAACTTAAATAAAATGA 16 4 0 TTAAATAAAA 0.800427 -78 TTTCGATAGATTAATTATAATGCTCTAAAT 19 41 0 TTAATTATAA 0.677445 -105 TTTTAGGACGTTAAACATAATCTGGCAGGG 20 145 0 TTAAACATAA 0.790666 -138 ACTTCATTTAATATAAATCTTTCTGC 22 7 1 TTTAATATAA 0.678386 -72 GCAGCGTCCGTTAAATATATATTGCGAGTC 24 21 1 TTAAATATAT 0.68995 -25 GAGGATTGTTTAAAATTTAAAAAATAAAAA 28 18 0 TAAAATTTAA 0.518252 -98 ATTAGTGCAGTCAAATTTAATAATTTTCTT 31 25 1 TCAAATTTAA 0.677873 -166 TGATTAGCAATTAAATATAACTCAGTATTC 31 68 1 TTAAATATAA 0.867981 -123 AAAGTTCTTATTAAATAAAATCAAAAAAAC 31 166 1 TTAAATAAAA 0.800427 -25 ********** Masking position 4 Map Score: 13.2246 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 6 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 4 ACAGTGTTTGGGGTGGTGATGGG 2 1 0 GGGTGGGGGG 0.836232 -139 GAAAGGTTCTGGCAAGAGGAGGTGGAAA 4 82 1 GGCAAGGGGT 0.97715 -18 GAAAGAGACTGGGAAGTTTCGAGGTGAAGAAGG 6 128 0 GGGAAGTGAG 0.810844 -173 ATTGTGTATTGGGAAGAGCTGGGAAAGAGACTG 6 150 0 GGGAAGGGGG 0.969599 -151 TAATAAGCGCTGCAGTCGGGGGTCC 8 70 1 TGCAGTGGGT 0.723836 -15 AAGGGGGAGTTGTGGGAAGGTTAAAA 9 123 0 GGGGAGTGGG 0.902691 -16 ATTACCTGCAGGCAAGCGTAGGTAAATCTGAAA 12 50 1 GGCAAGGGGT 0.97715 -128 TTGCAGGAGGTGGTATTTTGGAGG 13 2 1 TGCAGGGGGT 0.963329 -52 GTATTTTGGAGGCAAGATGGGATATACTGATAC 13 23 1 GGCAAGTGAT 0.8518 -31 AGGCAAATCTTGCAAGGGACGATGTGAGGACTC 20 108 1 TGCAAGGGAT 0.887797 -175 AAATATATATTGCGAGTCTGGAT 24 33 1 TGCGAGCGAT 0.607637 -13 TCTACGACCTTGCAGGACCAGGGCTGGGTGGCA 25 133 1 TGCAGGCGGG 0.909636 -168 GTAAAAAGCATGCGGGGGGCGGGATTCGAACCC 25 189 1 TGCGGGGGGG 0.971984 -112 TTTTCCAAGCGGGGGTTGCCGAGCCAGGAAAAG 25 258 0 GGGGGTGGAG 0.555534 -43 TACATGCATCGGCAGGTTCGGATCAGCGGAG 26 9 0 GGCAGGTGAT 0.878674 -162 GAAGCTTCTCTGCGAGCTCGGGGACACACCATG 27 77 1 TGCGAGTGGG 0.906984 -83 ****** * *** Masking position 11 Map Score: 11.8674 Number of sites scoring better than the average of aligned sites = 1186 Number in coding regions = 1122 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 5 GTTTTTTGGGTAAAAAGATGCCAGGATGGTAAACGAAA 1 64 1 TAAAACCGTG 0.476992 -60 TAGCCTAAATTTAAAAAGTTTTTGGTTGGCCTAAAATC 2 98 0 TTAAATTGTG 0.958245 -42 GGACTCTTAAAAACTCATTAGCTTTAAATTATTTT 6 276 0 TAAAATTGTT 0.719594 -25 AAAGAAAAATTTAAATATCGTCAGTGAGAGGCACAGTA 7 30 0 TTAAATCGAG 0.845973 -125 AGATAAAAACTTAAAACTAATTTGCTTTTTAAGTTTGT 7 69 1 TTAAATTGTT 0.879947 -86 GTGGGAAGGTTAAAAAACTTCTCGATTGCAGATATTTT 9 100 0 TAAAACTGTG 0.699906 -39 TGCCTCTCTTTAAAATTCACTTCGTATGCTTTGTATTG 11 63 0 TAAAATTGTG 0.88932 -83 ATTTGTGTTGTTAAAATTGGTTTGTATTGGTATGTATT 12 101 0 TTAAATTGTT 0.879947 -77 ACGGTAAGGTTTAAATACACTTAGAGTTGAAGCCC 12 153 1 TTAAATTGTT 0.879947 -25 CACACCTCGTTTAAACGAGCTTCGCTTGAACAATTCGA 14 52 0 TTAAATTGTG 0.958245 -114 AAGAAAACATTTAAAACGAATTGGAGAGAGCGAAGC 16 56 1 TTAAATTGAG 0.933535 -26 GCAAGGGTGTTTAAAAGGTTTTAGAGTTGAGCGAATTT 17 23 1 TTAAATTGTT 0.879947 -28 TCTTATAAGTTTAAATATTCATCGAGAGC 19 127 1 TTAAAATGAG 0.724949 -19 AAGAATTTTTAAAGCGAGTTTGAAAAATTTATAGAA 20 9 1 TTAAATTGAA 0.525324 -274 TTTTAGGACGTTAAACATAATCTGGCAGGGACGAGAGT 20 137 0 TTAAATCGAG 0.845973 -146 GCAGCGTCCGTTAAATATATATTGCGAGTCTGGAT 24 21 1 TTAAAATGAG 0.724949 -25 ***** ** * ** Masking position 5 Map Score: 11.8418 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 30 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 6 CTTTTTAAATTTAGGCTATCCTAAACATAACG 2 118 1 TAGGCTACCT 0.749299 -22 GGCAAGGTCATAAGGTTTTTCCCTAAAATATT 5 22 0 TAGGTTTTCC 0.832342 -37 CCTTATAAGCTCAGGCTTCCCCTTCTCAACCT 6 30 1 TAGGCTTCCC 0.982508 -271 GCTTGCTATTTTCAGCTTACCCAAAAATGTTA 8 34 0 TCAGCTTCCC 0.941186 -51 GCTTTCTGGTTTAAGCTTACCTAAAAATATCT 9 77 1 TAAGCTTCCT 0.910388 -62 CCATTATATTTAAAGTTTTCCTCTATACATAA 10 96 1 TAAGTTTCCT 0.648114 -205 TTCCTCCGATTACGGCTTTTCTGTAAACTTCA 10 274 0 TCGGCTTTCT 0.943444 -27 AAAGCAATATTTAGCCTTTTCCGATGTATATT 22 41 0 TAGCCTTTCC 0.808656 -38 GAACAAGGCTTTAAGTTTTTCC 23 1 0 TAAGTTTTCC 0.590816 -36 TCTTAAGCCCTGCGCCTTTTCCTGGCTCGGCA 25 243 1 TCGCCTTTCC 0.805444 -58 TCGTTTACGTTCCGGCTTACCTTTATTTTGGA 26 140 1 TCGGCTTCCT 0.971605 -31 GTGCCGACGATGAAGCTTCTCTGCGAGCTCGG 27 66 1 TAAGCTTTCT 0.832013 -94 ATACTCATCGTAAGGCTTTCGCCTCACTCCTA 27 124 0 TAGGCTTCGC 0.814826 -36 GTCCGGGTTGCCCCATACTCATC 27 147 0 TCGGGTTCCC 0.854042 -13 CTCAAGACTTTTAGGCTTTTCTAAAAAACGGA 28 46 0 TAGGCTTTCT 0.944535 -70 CATATAACTTTTCGGATTGCCTAAAAT 29 6 0 TCGGATTCCT 0.710576 -42 * ****** *** Masking position 7 Map Score: 16.3149 Number of sites scoring better than the average of aligned sites = 376 Number in coding regions = 341 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 7 CTGTTAGGTAACAGTGTTTGGGGTGGTGAT 2 14 0 ACAGTGTTTG 0.947142 -126 CTGTTACCTAACAGTGTTTATATTTAACAT 2 30 1 ACAGTGTTTA 0.948136 -110 CGTTTTTTTTACGGTGTTAATTTCCAAAAC 4 16 1 ACGGTGTTAA 0.952182 -84 CAAGTAGTAAACATTGTTAGCCAGAAAGGT 4 59 1 ACATTGTTAG 0.679054 -41 AAATTTAAATACAGCGTTTGGTTTGAAAAA 6 191 0 ACAGCGTTTG 0.788891 -110 TTTAAATTTAACGGTGTTTTTACATGATTA 6 212 1 ACGGTGTTTT 0.926913 -89 TTATTTTTGAACGGTGTTAAGTTGCCTAAT 6 253 0 ACGGTGTTAA 0.952182 -48 AGCTTCGGCAAGGGTGTTTAAAAGGTTTTA 17 16 1 AGGGTGTTTA 0.790574 -35 ACACGTTGTTAATTTGAAAGCA 22 67 0 ACGTTGTTAA 0.774892 -12 ACAGTGTTTTTTTGATTTTA 31 181 0 ACAGTGTTTT 0.888303 -10 ********** Masking position 7 Map Score: 6.65766 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 69 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 CCAGAAAGGTTCTGGCAAGAGGAGGTGGAAA 4 79 1 TCGGCAAGAG 0.895592 -21 ATAGTGTCTTTTTGGCAAGGTCATAAGGTTT 5 36 0 TTGGCAAGGT 0.85736 -23 ATATTTTTTTGCATTCAAGGGGATTTGTTAA 12 19 1 GCTTCAAGGG 0.877679 -159 TAAATTACCTGCAGGCAAGCGTAGGTAAATC 12 47 1 GCGGCAAGCG 0.969579 -131 ATTTTTCGAATTGTTCAAGCGAAGCTCGTTT 14 47 1 TTTTCAAGCG 0.836116 -119 GCTCAAGCTTCGGCAAGGGTGTTTAAAAG 17 9 1 TTGGCAAGGG 0.972043 -42 ACGAGGCAAATCTTGCAAGGGACGATGTGAG 20 105 1 TCTGCAAGGG 0.980835 -178 CCAGCCCTGGTCCTGCAAGGTCGTAGAGATG 25 129 0 TCTGCAAGGT 0.898444 -172 ATTCTCAAATTTTTCCAAGCGGGGGTTGCCG 25 270 0 TTTCCAAGCG 0.810899 -31 ACACCTTCATGTTTGCAAGCGTGACCTCAAG 28 72 0 GTTGCAAGCG 0.948579 -44 ** ******** Masking position 7 Map Score: 4.93117 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 162 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 9 CCTGAGCTTATAAGGCTGAGAGTGGCAGGATTCC 6 10 0 TGTGAGAGGG 0.982285 -291 ATGAGAGGCGTGAGGTTGAGAAGGGGAAGCCTGAG 6 39 0 TGTGAGAAGG 0.977308 -262 AAGTATAATCTGGTGATGAGTATGGAGATAAGACC 10 56 0 TGTGAGTAGG 0.984388 -245 GTATGCTTTGTATTGATTAGTACGCACGAGAAAAA 11 43 0 TGTTAGTAGC 0.699209 -103 TTAAATGTTTTCTTGCTGAGAATGTTCCCATTTAA 16 35 0 TGTGAGAAGT 0.943925 -47 TTTTGTTGTTGATTGCGTTCCGTTGAAA 19 4 1 TGTGATTGGT 0.734912 -142 CCCACCTCAATCCAGGTGAGACTGTAACAGTCCTC 25 35 1 TGTGAGACGT 0.860252 -266 TGTGTCGCCGTCACTGTGAGTGAGGACTGTTACAG 25 56 0 TTTGAGTGGG 0.876427 -245 TAGAGAGGATTTCCGTTGAGTGAGCTAAAGAAAGA 26 73 1 TGTGAGTGGC 0.971635 -98 GGCGAAAGCCTTACGATGAGTATGGGGCAACCCGG 27 133 1 TGTGAGTAGG 0.984388 -27 * * ****** ** Masking position 7 Map Score: 4.09855 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 249 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 Motif number 10 GAAGGTTCTCGTCGCAGATGAGAGGCGTGAGGTT 6 57 0 GTGCAGTGAG 0.951819 -244 GAGAGGCACAGTAGCAGTGCGGAGGGGATAGG 7 9 0 GTGCAGGGAG 0.994502 -146 TTGCAGGAGGTGGTATTTTGGAGGCAAGATGGG 13 10 1 GTGTATTGAG 0.756023 -44 TGTTTAAAAGGTTTTAGAGTTGAGCGAATTT 17 30 1 GTTTAGGGAG 0.919089 -21 TAAACATAATCTGGCAGGGACGAGAGTCCTCACA 20 130 0 CTGCAGGGAG 0.971892 -153 GTCCTGCAAGGTCGTAGAGATGAGTCAATGTTGT 25 117 0 GTGTAGGGAG 0.988563 -184 AGAGGCAGAGGTGGCAGTGCCGACGATGAAGCTT 27 50 1 GTGCAGGGAC 0.972031 -110 ** **** * *** Masking position 6 Map Score: 2.53946 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 136 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 11 AATGCAATCAAAAATGCATAATGCTTATAA 2 59 0 AAAATGCATA 0.680202 -81 ATCGGTTTTGAAAATGCAATCAAAAATGCA 2 71 0 AAAATGCAAT 0.829231 -69 CTACAAACTTAAAAAGCAAATTAGTTTTAA 7 79 0 AAAAAGCAAA 0.920222 -76 GGTAAGCTGAAAATAGCAAGCCATATAATA 8 45 1 AAATAGCAAG 0.818293 -40 GAATCGAATAAAAAAGCAAAAGGTTAATAT 10 216 1 AAAAAGCAAA 0.920222 -85 TAAATACTACAAATAGAAATT 14 2 0 AAATAGAAAT 0.546037 -164 ATCGAAACAGAAAAAGAAATATTCACAAAA 19 64 1 AAAAAGAAAT 0.75123 -82 TTACTGCAGTAAAAAGCATGCGGGGGGCGG 25 181 1 AAAAAGCATG 0.800783 -120 ATAAACAGCAATTCTCAAATTT 25 289 0 AAACAGCAAT 0.686272 -12 CGATTCCGGAAAAATGAATGGATTTTCGGA 26 113 0 AAAATGAATG 0.40207 -58 CTTAAAAGACAAAAAGAAAATTATTAAATT 31 38 0 AAAAAGAAAA 0.788154 -153 AATAACGTGGAAATTGCAAAAAGTTTATAG 31 116 0 AAATTGCAAA 0.704398 -75 ********** Masking position 3 Map Score: 2.94251 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 112 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 12 TTATAAGGCTGAGAGTGGCAGGATTCC 6 8 0 GAGAGTGGCA 0.91465 -293 CTCGTCGCAGATGAGAGGCGTGAGGTTGAG 6 54 0 ATGAGAGGCG 0.870302 -247 AATATCGTCAGTGAGAGGCACAGTAGCAGT 7 25 0 GTGAGAGGCA 0.96137 -130 ATTGCCTAAAAAGAGGGGGACTTGCAATTA 9 25 0 AAGAGGGGGA 0.815462 -114 CTGCGGACTTAGGAGAGCCAAAATATATCG 10 178 0 AGGAGAGCCA 0.865859 -123 GTGAATTTTAAAGAGAGGCAACAGTTAGTA 11 81 1 AAGAGAGGCA 0.977079 -65 AAACGAATTGGAGAGAGCGAAGC 16 69 1 GAGAGAGCGA 0.889686 -13 TGTAAGGATGAAAAGAGGGAGGGTGGAACA 20 192 1 AAAAGAGGGA 0.765781 -91 CCCCGATCGGGGAAGAGGCAGAGGTGGCAG 27 37 1 GGAAGAGGCA 0.869361 -123 GTCCCCTTAGGAGTGAGGCGAAAGCCTTAC 27 117 1 GAGTGAGGCG 0.804419 -43 ********** Masking position 5 Map Score: 1.83843 Number of sites scoring better than the average of aligned sites = 622 Number in coding regions = 586 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 13 GCAAGGTCATAAGGTTTTTCCCTAAAATAT 5 23 0 AAGGTTTTTC 0.855578 -36 CACAATTTCCATGATTTTTCAAACCAAACG 6 177 1 ATGATTTTTC 0.778569 -124 TGACGATATTTAAATTTTTCTTTAAGATAA 7 45 1 TAAATTTTTC 0.796651 -110 AGAATTGGTGAAGATTTTTCAGATTTACCT 12 69 0 AAGATTTTTC 0.957089 -109 TTTTCTTTAACAGATTTTTCGAATTGTTCA 14 34 1 CAGATTTTTC 0.964202 -132 TGGAGAACGGCAGATTTTTCTCTCTTAAAT 15 11 1 CAGATTTTTC 0.964202 -98 CATTTTATTTAAGTTTTTTCCCATTAAATG 16 12 1 AAGTTTTTTC 0.799883 -70 TTCATTTCTATAAATTTTTCAAACTCGCTT 20 22 0 TAAATTTTTC 0.796651 -261 CAGCAATTCTCAAATTTTTCCAAGCGGGGG 25 276 0 CAAATTTTTC 0.898234 -25 ********** Masking position 5 Map Score: 6.16042 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 64 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 14 CAACTTAGTCAGCAATCAACATCTACCTTTT 3 38 0 ACAATCAACA 0.847383 -25 TTATGAGGTCAAAAATCATCATTTTTCGATA 10 152 1 AAAATCATCA 0.775778 -149 AAAAATCTTCACCAATTCTCAAATACATACC 12 80 1 ACAATTCTCA 0.91347 -98 TTTTAACAACACAAATCCTCATGTATCCTGA 12 123 1 AAAATCCTCA 0.91347 -55 TTCAACGGAACGCAATCAACAACAAAA 19 7 0 CCAATCAACA 0.73075 -139 GTCCTAAAAACTCAATCCTCATTCACTGTAA 20 166 1 CCAATCCTCA 0.963242 -117 GTGAGACTGTAACAGTCCTCACTCACAGTGA 25 50 1 ACAGTCCTCA 0.926068 -251 ATAAACAGCAATTCTCAAATTTTTCCA 25 284 0 ACAATTCTCA 0.91347 -17 TTAAATTTTAAACAATCCTCCGTTTTTTAGA 28 28 1 ACAATCCTCC 0.926068 -88 * ********* Masking position 6 Map Score: 2.13882 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 199 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 15 TCATGGAAATTGTGTATTGGGAAGAGCTGG 6 161 0 TGTGTATTGG 0.846178 -140 CGTCGGAAAATTTATATTGCAATATTGCCA 7 125 1 TTTATATTGC 0.893803 -30 TCGAAATTCTTATATATTGCCTAAAAAGAG 9 40 0 TATATATTGC 0.916382 -99 CATTTTTCGATATATTTTGGCTCTCCTAAG 10 171 1 TATATTTTGG 0.810954 -130 TTAAAATTGGTTTGTATTGGTATGTATTTG 12 99 0 TTTGTATTGG 0.835955 -79 CCTTTTCCGATGTATATTGGTAGCAGAAAG 22 29 0 TGTATATTGG 0.918394 -50 CGGAAAAGGCTAAATATTGCTTTCAAATTA 22 50 1 TAAATATTGC 0.633379 -29 GTCCGTTAAATATATATTGCGAGTCTGGAT 24 26 1 TATATATTGC 0.916382 -20 CCGGCTTACCTTTATTTTGGAAAAGAGTTC 26 151 1 TTTATTTTGG 0.76714 -20 ********** Masking position 5 Map Score: 2.89401 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 4 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925