AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -inarP_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 AF0950 177 carbon monoxide dehydrogenase, iron sulfur subunit (cooF) #11 AF1241 81 glutamate-1-semialdehyde aminotransferase (hemL) #12 AF1643 50 conserved hypothetical protein #13 AF1644 35 tungsten formylmethanofuran dehydrogenase, subunit F (fwdF) #14 AF1858 145 NADH oxidase (noxA-5) #15 AF1860 282 A. fulgidus predicted coding region AF1860 #16 AF1868 51 A. fulgidus predicted coding region AF1868 #17 AF1869 78 A. fulgidus predicted coding region AF1869 #18 AF1980 36 heme exporter protein C (helC) #19 AF1984 45 iron-dependent repressor (troR) #20 AF2191 300 A. fulgidus predicted coding region AF2191 #21 AF2371 170 A. fulgidus predicted coding region AF2371 #22 AF2374 159 A. fulgidus predicted coding region AF2374 #23 AF2377 115 conserved hypothetical protein #24 AF2378 47 conserved hypothetical protein #25 AF2383 33 conserved hypothetical protein #26 AF2384 190 molybdopterin oxidoreductase, molybdopterin binding subunit Motif number 1 GCTGCATGTTTTTTGGGTAAAAAGATGCCAGG 1 57 1 TTTTGGGAAA 0.956125 -67 ATATAAACACTGTTAGGTAACAGTGTTTGGGG 2 21 0 TGTTAGGAAA 0.914818 -119 TCAAAACCGATTTTAGGCCAACCAAAAACTTT 2 90 1 TTTTAGGCAC 0.909404 -50 TATTCGAAGATTTTAGGGAAAAGGTAGATGTT 3 20 1 TTTTAGGAAA 0.985516 -43 TTCCCTAAAATATTAGGAAAAATTG 5 4 0 TATTAGGAAA 0.881255 -55 TTTCCTAATATTTTAGGGAAAAACCTTATGAC 5 16 1 TTTTAGGAAA 0.985516 -43 AACTTAACATTTTTGGGTAAGCTGAAAATAGC 8 30 1 TTTTGGGAAC 0.966977 -55 GTCCCCCTCTTTTTAGGCAATATATAAGAATT 9 34 1 TTTTAGGAAA 0.985206 -105 TTGCAGATATTTTTAGGTAAGCTTAAACCAGA 9 81 0 TTTTAGGAAC 0.984523 -58 CTTACCTTTATTTTGGAAAAGAGTTC 21 155 1 TTTTGGAAAA 0.789023 -16 ATCCTCCGTTTTTTAGAAAAGCCTAAAAGTCT 23 42 1 TTTTAGAAAC 0.880839 -74 ATTTTAGGCAATCCGAAAAGTTA 24 2 1 TTTTAGGAAC 0.984516 -46 CTATTTTTAGGATAAATTGCTGGCTA 25 5 1 TTTTAGGTAA 0.8816 -29 GTATTCTCAATTTTAGGTAATAACCTATAAAC 26 92 1 TTTTAGGAAA 0.984383 -99 ******* ** * Masking position 10 Map Score: 26.7196 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 TTTTAAATTTTCGCTCCTTTG 1 2 1 TTTAAATTTT 0.960913 -122 CCAAAAACTTTTTAAATTTAGGCTATCCTA 2 111 1 TTTAAATTTA 0.881013 -29 AAACGCTGTATTTAAATTTAACGGTGTTTT 6 202 1 TTTAAATTTA 0.881013 -99 ACTCATTAGCTTTAAATTATTTTTGAACGG 6 269 0 TTTAAATTAT 0.650406 -32 ACTGACGATATTTAAATTTTTCTTTAAGAT 7 43 1 TTTAAATTTT 0.960913 -112 GCAAATTAGTTTTAAGTTTTTATCTTAAAG 7 64 0 TTTAAGTTTT 0.921534 -91 AATATTGCAATATAAATTTTCCGACGTACA 7 121 0 TATAAATTTT 0.907473 -34 CGCTTTCTGGTTTAAGCTTACCTAAAAATA 9 76 1 TTTAAGCTTA 0.692348 -63 TCTAAGTGTATTTAAACCTTACCGTCAGGA 10 148 0 TTTAAACCTT 0.850491 -30 TCATTTTATTTAAGTTTTTTCCCATTAA 11 9 1 TTTAAGTTTT 0.921534 -73 TCCAATTCGTTTTAAATGTTTTCTTGCTGA 11 51 0 TTTAAATGTT 0.769347 -31 ATCTTTCAGTTATAAACCTTTTGTGAATAT 14 82 0 TATAAACCTT 0.694138 -64 TCGATGAATATTTAAACTTATAAGAATATT 14 122 0 TTTAAACTTA 0.824889 -24 CATTCATTTCTATAAATTTTTCAAACTCGC 15 24 0 TATAAATTTT 0.907473 -259 CTTCATTTAATATAAATCTTTCTGCTACCA 17 12 1 TATAAATCTT 0.781045 -67 TGAACAAGGCTTTAAGTTTTTCC 18 4 0 TTTAAGTTTT 0.921534 -33 ATTTTTATTTTTTAAATTTTAAACAATCCT 23 17 1 TTTAAATTTT 0.960913 -99 GGTAATAACCTATAAACTTTTTGCAATTTC 26 107 1 TATAAACTTT 0.861872 -84 ********** Masking position 3 Map Score: 23.1542 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 35 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 3 GGCATCTTTTTACCCAAAAAACATGCAGCC 1 56 0 TACCCAAAAA 0.915178 -68 GTTTTTGGTTGGCCTAAAATCGGTTTTGAA 2 89 0 GGCCTAAAAT 0.928721 -51 ATCTACCTTTTCCCTAAAATCTTCGAATAT 3 19 0 TCCCTAAAAT 0.954134 -44 ATAAGGTTTTTCCCTAAAATATTAGGAAAA 5 15 0 TCCCTAAAAT 0.954134 -44 ATTTTCAGCTTACCCAAAAATGTTAAGTTT 8 29 0 TACCCAAAAA 0.915178 -56 TCTTATATATTGCCTAAAAAGAGGGGGACT 9 33 0 TGCCTAAAAA 0.968053 -106 GGTTTAAGCTTACCTAAAAATATCTGCAAT 9 84 1 TACCTAAAAA 0.961675 -55 TATGTTTAACGTCCTAAAAACTCAATCCTC 15 156 1 GTCCTAAAAA 0.766322 -127 CTTTTCGGATTGCCTAAAAT 24 1 0 TGCCTAAAAT 0.968053 -47 TATAGGTTATTACCTAAAATTGAGAATACT 26 91 0 TACCTAAAAT 0.961675 -100 ********** Masking position 6 Map Score: 11.6158 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 13 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 AAGGTTCTGGCAAGAGGAGGTGGAAA 4 84 1 CAAGAGGAGG 0.983663 -16 GCACAGTAGCAGTGCGGAGGGGATAGG 7 8 0 AGTGCGGAGG 0.903625 -147 TATTGCCTAAAAAGAGGGGGACTTGCAATT 9 26 0 AAAGAGGGGG 0.983663 -113 TACCTGCAGGCAAGCGTAGGTAAATCTGAA 10 52 1 CAAGCGTAGG 0.893475 -126 GTAAGGATGAAAAGAGGGAGGGTGGAACAG 15 193 1 AAAGAGGGAG 0.840268 -90 ACTACGAGAGAATGAGGAGGTTGAGGT 15 266 1 AATGAGGAGG 0.961781 -17 CAGTAAAAAGCATGCGGGGGGCGGGATTCG 20 187 1 CATGCGGGGG 0.979204 -114 CAAATTTTTCCAAGCGGGGGTTGCCGAGCC 20 266 0 CAAGCGGGGG 0.990478 -35 GCTTTTCTAAAAAACGGAGGATTGTTTAAA 23 34 0 AAAACGGAGG 0.885623 -82 GTTCCGAGTTACAGAGGAGGA 23 105 1 ACAGAGGAGG 0.928494 -11 ********** Masking position 6 Map Score: 11.3527 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 262 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 ATCACCACCCCAAACACTGTTACCTAACAG 2 14 1 CAAACACTGT 0.871845 -126 ATGTTAAATATAAACACTGTTAGGTAACAG 2 30 0 TAAACACTGT 0.966796 -110 GTTTTGGAAATTAACACCGTAAAAAAAACG 4 16 0 TTAACACCGT 0.969294 -84 TATCAAGTAGTAAACATTGTTAGCCAGAAA 4 56 1 TAAACATTGT 0.85149 -44 TAATCATGTAAAAACACCGTTAAATTTAAA 6 212 0 AAAACACCGT 0.956579 -89 ATTAGGCAACTTAACACCGTTCAAAAATAA 6 253 1 TTAACACCGT 0.969294 -48 AAGAAAAATTTAAATATCGTCAGTGAGAGG 7 37 0 TAAATATCGT 0.706246 -118 TAAAACCTTTTAAACACCCTTGCCGAAGCT 12 16 0 TAAACACCCT 0.902488 -35 TGCTTTCAAATTAACAACGTGT 17 67 1 TTAACAACGT 0.861419 -12 GATGAAATTATAAATAACGTGGAAATTGCA 26 128 0 TAAATAACGT 0.706246 -63 TAAAATCAAAAAAACACTGT 26 181 1 AAAACACTGT 0.890037 -10 ********** Masking position 6 Map Score: 8.60353 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 97 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 AGCAAAGGAGCGAAAATTTAAAA 1 4 0 CGAAAATTTA 0.59651 -120 GGATGGTAAACGAAAGGTATAAATGAATCC 1 87 1 CGAAAGGTAT 0.618576 -37 TTAGGCCAACCAAAAACTTTTTAAATTTAG 2 102 1 CAAAAACTTT 0.820584 -38 TCATCTGCGACGAGAACCTTCCACTGCGTG 6 70 1 CGAGAACCTT 0.827776 -231 AAGTACGGCTCGAAAACTTAACATTTTTGG 8 16 1 CGAAAACTTA 0.92977 -69 TATCTGCAATCGAGAAGTTTTTTAACCTTC 9 104 1 CGAGAAGTTT 0.825322 -35 TCGCTCAACTCTAAAACCTTTTAAACACCC 12 27 0 CTAAAACCTT 0.570661 -24 GAAATATTCACAAAAGGTTTATAACTGAAA 14 79 1 CAAAAGGTTT 0.77086 -67 AAATGAATGCCGAAAGCCTATCCACAATCG 15 45 1 CGAAAGCCTA 0.908307 -238 GAGCACATTTCGAAAGCTTAATATTTTCCT 16 22 1 CGAAAGCTTA 0.930989 -30 AGGAGTGAGGCGAAAGCCTTACGATGAGTA 22 125 1 CGAAAGCCTT 0.939404 -35 TTAGGCAATCCGAAAAGTTATATGCTTTAA 24 14 1 CGAAAAGTTA 0.90527 -34 GTGGAAATTGCAAAAAGTTTATAGGTTATT 26 110 0 CAAAAAGTTT 0.767519 -81 ********** Masking position 5 Map Score: 7.15025 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 253 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 7 TTCCACCTCCTCTTGCCAGAACCTTTCTGG 4 79 0 TCTTGCCAGA 0.757027 -21 AACCTTATGACCTTGCCAAAAAGACACTAT 5 37 1 CCTTGCCAAA 0.978966 -22 TTTTAAACACCCTTGCCGAAGCTTGAGC 12 9 0 CCTTGCCGAA 0.975184 -42 TCACATCGTCCCTTGCAAGATTTGCCTCGT 15 105 0 CCTTGCAAGA 0.774344 -178 GGACTCTCGTCCCTGCCAGATTATGTTTAA 15 135 1 CCCTGCCAGA 0.966937 -148 ATCTCTACGACCTTGCAGGACCAGGGCTGG 20 130 1 CCTTGCAGGA 0.873305 -171 ********** Masking position 4 Map Score: 5.65373 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 52 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 CCCATCACCACCCCAAACACTGTTACCT 2 1 1 CCCACCCAAC 0.948077 -139 GGAATCCTGCCACTCTCAGCCTTATAAGCTCAGGCTT 6 10 1 CCCTCCTAAA 0.898916 -291 CTCAGGCTTCCCCTTCTCAACCTCACGCCTCTCATCTG 6 39 1 CCCTCCTAGC 0.99467 -262 GCGACGAGAACCTTCCACTGCGTGAAGGGAGCAATCCT 6 76 1 CCCACCTAGG 0.940475 -225 CTGACCTTATCCTTCTTCACCTCGAAACTTCCCAGTCT 6 118 1 CCTTCCCAAC 0.919062 -183 CAGTCTCTTTCCCAGCTCTTCCCAATACACAATTTCCA 6 150 1 CCCTCCCAAC 0.985004 -151 CTGTAACAGTCCTCACTCACAGTGACGGCGACACATCA 20 56 1 CCCTCATAGG 0.907627 -245 TGGTGTGTCCCCGAGCTCGCAGAGAAGCTTCATCGTCG 22 70 0 CCCTCAAAGC 0.870081 -90 CCGGGTTGCCCCATACTCATCGTAAGGCTTTCGCCTCA 22 130 0 CCCTCCTAGC 0.99467 -30 AACCCTACTTCGCCTTAAAGCATATAACTTT 24 27 0 CCTTCCTAGC 0.969933 -21 ** *** * * * ** Masking position 15 Map Score: 7.99229 Number of sites scoring better than the average of aligned sites = 334 Number in coding regions = 317 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 CCCATCACCACCCCAAACACTGT 2 1 1 CCCACACCCC 0.985187 -139 CTCAGGCTTCCCCTTCTCAACCTCACGCCTCTC 6 39 1 CCCTCTCCCT 0.985864 -262 CAGTCTCTTTCCCAGCTCTTCCCAATACACAAT 6 150 1 CCCACTCCCC 0.995838 -151 TTTTAACCTTCCCACAACTCCCCCTT 9 123 1 CCCAAACCCC 0.93832 -16 GACGAGAGTCCTCACATCGTCCCTTGCAAGATT 15 113 0 CTCAATCCCC 0.939177 -170 TCCACCCTCCCTCTTTTCATCCTTACAGTGAAT 15 186 0 CTCTTTCCCT 0.818215 -97 CCCATCATTACTCTGTTCCACCCTCCCTCTTTT 15 202 0 CTCTTTCCCC 0.913398 -81 GCTTTAATTTCCCACCTCAATCCAGGTGAGACT 20 25 1 CCCACTCTCC 0.954346 -276 CGTCGGCACTGCCACCTCTGCCTCTTCCCCGAT 22 42 0 GCCACTCCCT 0.929685 -118 AACCCTACTTCGCCTTAAAGCATAT 24 33 0 CCCTCTTCCT 0.859022 -15 **** *** *** Masking position 3 Map Score: 8.02622 Number of sites scoring better than the average of aligned sites = 607 Number in coding regions = 577 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 10 TGCTTATAATGTTAAATATAAACACTGTTAG 2 37 0 GTTAAAATAA 0.911507 -103 TTACTACTTGATAAAATATAAGGGTTTTGGA 4 38 0 ATAAAAATAA 0.562195 -62 TAAAAACACCGTTAAATTTAAATACAGCGTT 6 203 0 GTTAAATTAA 0.485314 -98 TTTTTACATGATTAAAAATAATCGAATTAGG 6 228 1 ATTAAAATAA 0.933455 -73 AAGTTTTTATCTTAAAGAAAAATTTAAATAT 7 50 0 CTTAAAAAAA 0.672304 -105 TGGGAAAAAACTTAAATAAAATGA 11 4 0 CTTAAAAAAA 0.672302 -78 GTTTCGATAGATTAATTATAATGCTCTAAAT 14 41 0 ATTAATATAA 0.56219 -105 TAAGAATATTAATAAATAAAATCTTTCAGTT 14 101 0 AATAAAAAAA 0.481258 -45 TTTTTAGGACGTTAAACATAATCTGGCAGGG 15 145 0 GTTAAAATAA 0.911507 -138 ACTTCATTTAATATAAATCTTTCTGC 17 6 1 ATTTAAATAA 0.56219 -73 TGCAGCGTCCGTTAAATATATATTGCGAGTC 19 20 1 GTTAAAATAT 0.485311 -26 AAATTTAAAAAATAAAAATAAAAAA 23 5 0 AATAAAATAA 0.708838 -111 GTGATTAGCAATTAAATATAACTCAGTATTC 26 67 1 ATTAAAATAA 0.933454 -124 TGCTGATGAAATTATAAATAACGTGGAAATT 26 131 0 ATTATAATAA 0.562197 -60 CAAAGTTCTTATTAAATAAAATCAAAAAAAC 26 165 1 ATTAAAAAAA 0.842399 -26 ****** **** Masking position 10 Map Score: 7.12754 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 27 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 11 CTGGCAAGAGGAGGTGGAAA 4 90 1 GAGGTGGAAA 0.760207 -10 CTGAGCTTATAAGGCTGAGAGTGGCAGGAT 6 14 0 AAGGCTGAGA 0.922967 -287 TGAGAGGCGTGAGGTTGAGAAGGGGAAGCC 6 43 0 GAGGTTGAGA 0.884268 -258 GGGAAGTTTCGAGGTGAAGAAGGATAAGGT 6 121 0 GAGGTGAAGA 0.884268 -180 TCGTCAGTGAGAGGCACAGTAGCAGTGCGG 7 21 0 GAGGCACAGT 0.629771 -134 GAGTTGTGGGAAGGTTAAAAAACTTCTCGA 9 113 0 AAGGTTAAAA 0.435394 -26 AAGGGGGAGTTGTGGGAAGG 9 129 0 AAGGGGGAGT 0.655555 -10 AAAGGGTTAAAAGGCTAAGAATAAAGGTGT 13 12 1 AAGGCTAAGA 0.882156 -24 AGAGAATGAGGAGGTTGAGGT 15 272 1 GAGGTTGAGG 0.892218 -11 TACATCGGAAAAGGCTAAATATTGCTTTCA 17 45 1 AAGGCTAAAT 0.569986 -34 GAGCCAGGAAAAGGCGCAGGGCTTAAGACC 20 241 0 AAGGCGCAGG 0.880248 -60 GATCGGGGAAGAGGCAGAGGTGGCAGTGCC 22 41 1 GAGGCAGAGG 0.884073 -119 CCTTAGGAGTGAGGCGAAAGCCTTACGATG 22 121 1 GAGGCGAAAG 0.843757 -39 TATATGCTTTAAGGCGAAGTAGGGTT 24 32 1 AAGGCGAAGT 0.891113 -16 ********** Masking position 8 Map Score: 5.94242 Number of sites scoring better than the average of aligned sites = 2326 Number in coding regions = 2229 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 12 CTAAAATCTTCGAATATGAAAAAAA 3 3 0 CGATGAAAAA 0.97115 -60 ATTAATCTATCGAAACAGAAAAAGAAATATTCA 14 56 1 CGAAGAAAAA 0.910963 -90 ATTTTTAAAGCGAGTTTGAAAAATTTATAGAAA 15 15 1 CGATGAAAAA 0.97115 -268 GACCAAGCGTGTATGAACAAGGCTTTAAGT 18 17 0 CGTTGAACAA 0.824641 -20 CGGGGGTTGCCGAGCCAGGAAAAGGCGCAGGGC 20 249 0 CGACGGAAAA 0.971182 -52 GGAACGTAAACGATTCCGGAAAAATGAATGGAT 21 120 0 CGATGGAAAA 0.97599 -51 GCCTCTTCCCCGATCGGGGACAATAATAGTAGT 22 23 0 CGACGGACAA 0.957766 -137 *** * ****** Masking position 10 Map Score: 2.25112 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 36 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 13 GGTTTTGAAAATGCAATCAAAAATGCATAA 2 68 0 ATGCAATCAA 0.787576 -72 CCAACTTAGTCAGCAATCAACATCTACCTT 3 40 0 CAGCAATCAA 0.811137 -23 ATAATAAGCGCTGCAGTCGGGGGTCC 8 69 1 CTGCAGTCGG 0.971428 -16 CTAAAAATATCTGCAATCGAGAAGTTTTTT 9 97 1 CTGCAATCGA 0.959168 -42 GTTAAATTACCTGCAGGCAAGCGTAGGTAA 10 45 1 CTGCAGGCAA 0.97105 -133 GCCTCGTATAGTGCAGGCGGTCTGAAGTTT 15 82 0 GTGCAGGCGG 0.890401 -201 GAGACTCTTACTGCAGTAAAAAGCATGCGG 20 174 1 CTGCAGTAAA 0.872557 -127 TAAAGGATTAGTGCAGTCAAATTTAATAAT 26 19 1 GTGCAGTCAA 0.962784 -172 ********** Masking position 5 Map Score: 2.08777 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 140 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 14 GCGTGAAGGGAGCAATCCTGTAGCTGACCT 6 95 1 AGCAATCCTG 0.754089 -206 TCCTGTAATTGCAAGTCCCCCTCTTTTTAG 9 20 1 GCAAGTCCCC 0.811569 -119 TAACCTTCCCACAACTCCCCCTT 9 126 1 ACAACTCCCC 0.788879 -13 AGGTAATTTAACAAATCCCCTTGAATGCAA 10 27 0 ACAAATCCCC 0.941152 -151 AAAAATCTTCACCAATTCTCAAATACATAC 10 80 1 ACCAATTCTC 0.833635 -98 TTTTAACAACACAAATCCTCATGTATCCTG 10 123 1 ACAAATCCTC 0.944754 -55 GTGAGACTGTAACAGTCCTCACTCACAGTG 20 50 1 AACAGTCCTC 0.792323 -251 TTCCTGGCTCGGCAACCCCCGCTTGGAAAA 20 261 1 GGCAACCCCC 0.743347 -40 ATAAACAGCAATTCTCAAATTTTTCC 20 285 0 AGCAATTCTC 0.801793 -16 CTCACTCAACGGAAATCCTCTCTAACTGAC 21 67 0 GGAAATCCTC 0.896331 -104 TTAAATTTTAAACAATCCTCCGTTTTTTAG 23 28 1 AACAATCCTC 0.898712 -88 ********** Masking position 4 Map Score: 2.66605 Number of sites scoring better than the average of aligned sites = 481 Number in coding regions = 450 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 15 GTTGAGAAGGGGAAGCCTGAGCTTATAAGG 6 30 0 GGAAGCCTGA 0.877125 -271 GAATTTTTCTGTACGTCGGAAAATTTATAT 7 112 1 GTACGTCGGA 0.906709 -43 GGACCCCCGACTGCAGCGCT 8 75 0 GGACCCCCGA 0.903392 -10 AACGGACGCTGCAACACGGAGC 19 3 0 GCAACACGGA 0.920722 -43 CAAAATAAAGGTAAGCCGGAACGTAAACGA 21 140 0 GTAAGCCGGA 0.97714 -31 TGAGTATGGGGCAACCCGGAC 22 149 1 GCAACCCGGA 0.983768 -11 TCCTCCTCTGTAACTCGGAACGCACACCT 23 97 0 GTAACTCGGA 0.949928 -19 ********** Masking position 3 Map Score: 1.05573 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 67 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555