AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00130_mthe_reg_300.orf -o00130_mthe_300.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: MTH147 23 phenylacrylic acid decarboxylase Input sequences: #1 MTH148 47 conserved protein #2 MTH150 75 conserved protein #3 MTH203 300 ATP-dependent RNA helicase, eIF-4A family #4 MTH384 249 unknown #5 MTH387 24 conserved protein #6 MTH388 35 unknown #7 MTH393 41 NADH dehydrogenase (ubiquinone), subunit 1 related protein #8 MTH488 63 unknown #9 MTH491 41 conserved protein #10 MTH492 30 ATP-dependent RNA helicase, eIF-4A family #11 MTH806 240 protease IV #12 MTH807 75 thioredoxin #13 MTH808 34 cobalamin biosynthesis protein D #14 MTH809 138 molybdenum cofactor biosynthesis protein MoaC #15 MTH1246 30 NADH dehydrogenase I, subunit N #16 MTH1251 147 conserved protein #17 MTH1252 143 conserved protein #18 MTH1253 135 unknown #19 MTH1348 139 precorrin-2 methyltransferase #20 MTH1415 175 ATP-dependent RNA helicase, eIF-4A family #21 MTH1418 107 conserved protein #22 MTH1514 125 precorrin-6Y methylase #23 MTH1522 116 nitrogenase alpha chain (NifD) related protein #24 MTH1548 118 NADP-reducing hydrogenase, subunit A #25 MTH1655 78 anthranilate synthase component I #26 MTH1759 70 mannose-1-phosphate guanyltransferase #27 MTH1762 159 DNA mismatch recognition protein MutS #28 MTH1763 28 collagenase #29 MTH1764 154 sensory transduction regulatory protein Motif number 1 GTTAATCTGTTCCAGGAGGTTTCTGTCCTGA 1 17 0 TCCAGGAGGT 0.902827 -31 AAACTGGAAGTTCAGGATTCTGCCAGGCACA 3 213 0 TTCAGGATTT 0.977384 -88 CCCCATCATGTCCTGGAGGTTCCTATGGAGT 4 18 1 TCCTGGAGGT 0.697932 -232 GTAATAAATTTTAAGGATTTTCATAGTCGTT 4 87 0 TTAAGGATTT 0.953287 -163 CATGTTCTCATTCAGGATTATTTACGGGG 6 17 1 TTCAGGATTT 0.977384 -19 GATGTTCACATTAAGGATTCTATC 8 4 0 TTAAGGATTT 0.953287 -60 CATAGAAGTCTTCAGGATGTTCACATTAAGG 8 19 0 TTCAGGATGT 0.970021 -45 GCTGAAAAATTGAAGGATGATGCTGGAGGTA 9 17 1 TGAAGGATGT 0.895198 -25 TCCAGGATTCTATGATCGTTC 11 1 1 TCCAGGATTT 0.969451 -240 TGGTTAAAAATTTAGGATGGTACATGGATGT 11 166 1 TTTAGGATGT 0.848336 -75 CAGTCATGTTTTCAGGAGTTTTTGTTATATC 11 199 0 TTCAGGAGTT 0.944132 -42 CAATTAATTTTTAAGGATTTTTCTG 13 20 1 TTAAGGATTT 0.953287 -15 TGAATTTCTTTGATGGATTCTAAAATACATG 14 57 0 TGATGGATTT 0.739393 -82 TGAATTTCTTTGATGGATTCTAAAATACATG 14 115 0 TGATGGATTT 0.739393 -24 TTTCTGGGATTCCAGGGTTTTGATGCTGTAT 17 84 1 TCCAGGGTTT 0.800972 -60 CACAGAATTATTTAGGATTATTTTAGTGATA 29 133 1 TTTAGGATTT 0.881949 -22 ********* * Masking position 1 Map Score: 23.097 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 133 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 2 TTAATCTGTTCCAGGAGGTTTCTGTCCTGA 1 17 0 CCAGGAGGTT 0.838414 -31 TCGCTGTTGTCTGGGTGGTGTATTCTTTTG 3 49 0 CTGGGTGGTG 0.856223 -252 GTATTCTTTTGTTTGTGGTGTTTTTTGGGG 3 83 0 GTTTGTGGTG 0.73277 -218 CTGGAGTTGTCTGGGTGGTGTATTCTTTTG 3 102 0 CTGGGTGGTG 0.856223 -199 GTGAGGTGTTCCTGGAGTTGTCTGGGTGGT 3 113 0 CCTGGAGTTG 0.823673 -188 GTTTTTTCATCCGTGAGGTGTTCCTGGAGT 3 125 0 CCGTGAGGTG 0.97174 -176 CCCATCATGTCCTGGAGGTTCCTATGGAGT 4 19 1 CCTGGAGGTT 0.979903 -231 TTTACTAATATCTGGAGGTTTCTCTACAGA 4 164 0 TCTGGAGGTT 0.826987 -86 GAAGGATGATGCTGGAGGTATAGT 9 28 1 GCTGGAGGTA 0.907096 -14 GTGTTTGAGAGCTTGAGGTGCTCTCTGGAG 11 60 0 GCTTGAGGTG 0.969398 -181 TGAAAACATGACTGGAGGTAAAAAGGTCTG 11 216 1 ACTGGAGGTA 0.832485 -25 GCGCCAATGACTTTGAGGTTAAATTTCTGG 17 61 1 CTTTGAGGTT 0.907042 -83 CTGTATTCTGACTTGAGGTTAATTGATGCC 17 109 1 ACTTGAGGTT 0.887139 -35 CCGTATACCTGCGGCAGGTGGGACATACAC 18 87 0 GCGGCAGGTG 0.75112 -49 GGCCTTCCTAGTTTGAGGTTTAAGAGATTA 20 80 0 GTTTGAGGTT 0.860789 -96 AACCACAGACATTTGAGGTGACGTAAT 23 100 1 ATTTGAGGTG 0.865871 -17 ATGTTTTTAGATGTGAGGTGGTGGGTGT 24 9 0 ATGTGAGGTG 0.816199 -110 GACTCTTTAACCTGGAGGCTTTGA 24 105 1 CCTGGAGGCT 0.845414 -14 ********** Masking position 7 Map Score: 18.6137 Number of sites scoring better than the average of aligned sites = 1241 Number in coding regions = 1169 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 3 AAAAAATCAGGACAGAAACCTC 1 1 1 AAAATCAGGA 0.847062 -47 TGCTTCTAGTATATATTCATGGAGCCGGTGGC 2 13 0 AATATCATGG 0.903115 -63 GAGAGCAGCCAAAAACACCGGAAACAAAAGAA 3 25 1 AAAAACCGGA 0.577811 -276 CCAACAGTTTAAATACTCCCGGGTACAATAGA 3 154 1 AATATCCCGG 0.749406 -147 GTTTCTGTGAATATAATCACGAAAACGACTAT 4 64 1 AATATCACGA 0.876494 -186 GAATATATAGATGATTACTGGTGA 5 3 1 AATAAGATGA 0.534434 -22 CCCCGTAAATAATCCTGAATGAGAACAT 6 18 0 AATATCCTGA 0.937066 -18 GTGAACGATCATAGAATCCTGGA 11 2 0 AAGATCCTGG 0.844844 -239 CTGATATAACAAAAACTCCTGAAAACATGACT 11 197 1 AAAATCCTGA 0.944217 -44 AATCCATCAAAGAAATTCATGAGTGATGATAA 14 11 1 AAAATCATGA 0.953771 -128 AATCCATCAAAGAAATTCATGAGTGATGATAA 14 69 1 AAAATCATGA 0.953771 -70 AATCCATCAAAGAAATTCATGA 14 127 1 AAAATCATGA 0.953771 -12 ATATTATCATAAATAATCATGTTAATTATTGG 16 102 1 AATATCATGT 0.641088 -46 TAGTGCTGTAATAAAAACATGAGCGTATCAGA 18 28 0 AAAAACATGA 0.861378 -108 TGAACCTTAAATAAATTGATGACCAGATAAAA 20 150 1 AAAATGATGA 0.812478 -26 TCTTTAATGGAGAGATTGCTGAGACCCAGTGA 22 62 1 AAGATGCTGA 0.690054 -64 CCTCCAGGTTAAAGAGTCATGAACTCAAATAT 24 91 0 AAGATCATGA 0.92817 -28 TCCACAAAGTACATATACACGGAGGTACTATT 25 31 0 AATAACACGG 0.523322 -48 * *** ****** Masking position 5 Map Score: 17.577 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 147 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 4 TAAAGTTATTATGTCAGTAAAACTATTAGAAC 2 50 0 ATCAGTAAAA 0.776966 -26 GACCCTTCAGATATCAGTAAAAAAAAGTTTCT 4 135 1 ATCAGTAAAA 0.776966 -115 AAACCTCCAGATATTAGTAAAAAAGGCCATAA 4 173 1 ATTAGTAAAA 0.923086 -77 TAAAAAAGACCTCTTAATAAAATTATGGCCTT 4 195 0 CTTAATAAAA 0.840095 -55 GTTTATGATAATAGAATCATTCCGGT 7 5 1 ATTAATAGAA 0.773168 -37 GTAGAACATTCTATTAATAAAAATGGTTAAAA 11 143 1 CTTAATAAAA 0.840095 -98 TTCATGAGTGATGATAATGAAAGAATTCACCC 14 26 1 ATTAATGAAA 0.892811 -113 TTCATGAGTGATGATAATGAAAGAATTCACCC 14 84 1 ATTAATGAAA 0.892811 -55 TTCTATATAAATCGTAATAAAATAGGGGATCC 16 64 0 ATTAATAAAA 0.947643 -84 ATGATTATTTATGATAATATAAAGTTTTCTAT 16 90 0 ATTAATATAA 0.853176 -58 CAGAAAAATAATGATAATAAAGGCGGGTCTGG 19 56 1 ATTAATAAAG 0.725296 -84 CCACCTATACATGATAGTATAACTATACGATA 21 82 0 ATTAGTATAA 0.793945 -26 GTGCCGGGATATTATAATAAAATGTTGGTATG 22 22 1 ATTAATAAAA 0.947643 -104 TTCTGGTTATTATAATGTAATTGCATATTC 26 9 1 ATTAATGTAA 0.727825 -62 ** ******** Masking position 6 Map Score: 11.0987 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 18 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 5 GGCTTCCATGTTCTCATTCAGG 6 3 1 CTTCCATGTT 0.726434 -33 TTATATCAGACATCCATGTACCATCCTAAA 11 176 0 CATCCATGTA 0.943961 -65 TTTTTACCTCCAGTCATGTTTTCAGGAGTT 11 210 0 CAGTCATGTT 0.94185 -31 TCATTATCATCACTCATGAATTTCTTTGAT 14 16 0 CACTCATGAA 0.879882 -123 TGAAAGAATTCACCCATGTATTTTAGAATC 14 43 1 CACCCATGTA 0.984063 -96 TCATTATCATCACTCATGAATTTCTTTGAT 14 74 0 CACTCATGAA 0.879882 -65 TGAAAGAATTCACCCATGTATTTTAGAATC 14 101 1 CACCCATGTA 0.984063 -38 TGAGTCGCTGCAGCGATGTTGCTCACCAGT 17 24 1 CAGCGATGTT 0.830925 -120 CATTCTGATACGCTCATGTTTTTATTACAG 18 25 1 CGCTCATGTT 0.860274 -111 ATCATGGTTCCAGCCATGTTGCATAACCAC 23 76 1 CAGCCATGTT 0.974328 -41 ********** Masking position 6 Map Score: 8.97517 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 154 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 6 TGTCTGGGTGGTGTATTCTTTTGTTTCCGG 3 42 0 GTGTATTCTT 0.977489 -259 TGTCTGGGTGGTGTATTCTTTTGTTTGTGG 3 95 0 GTGTATTCTT 0.977489 -206 ATGAATTATGGTTTAATCTTATTTAA 10 7 0 GTTTAATCTT 0.818147 -24 ACACTGCAAAGTGTATTCATCAATTAAATA 11 86 1 GTGTATTCAT 0.93186 -155 AAATACATGGGTGAATTCTTTCATTATCAT 14 36 0 GTGAATTCTT 0.972172 -103 AAATACATGGGTGAATTCTTTCATTATCAT 14 94 0 GTGAATTCTT 0.972172 -45 CCCTTCAAGTGTTTAATCATCGGATCCCCT 16 43 1 GTTTAATCAT 0.587064 -105 AAATAATCATGTTAATTATTGGTACTAAAG 16 112 1 GTTAATTATT 0.69469 -36 GACCTTCGATGTGAATTATTGCACCTAATA 27 36 1 GTGAATTATT 0.874029 -124 ********** Masking position 5 Map Score: 8.48435 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 33 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 7 GAGGTTTCTGTCCTGATTTTTT 1 3 0 TCCTGATTTT 0.567991 -45 AGTAGCTGTGTACTGATTTTTAATTATCTG 3 185 1 TACTGATTTT 0.664747 -116 AACTGGAAGTTCAGGATTCTGCCAGGCACA 3 213 0 TCAGGATTCT 0.955607 -88 TAATAAATTTTAAGGATTTTCATAGTCGTT 4 87 0 TAAGGATTTT 0.945835 -163 ATGTTCTCATTCAGGATTATTTACGGGG 6 18 1 TCAGGATTAT 0.706213 -18 ATTAACACCGGAATGATTCTATTATCATAA 7 13 0 GAATGATTCT 0.748188 -29 ATGTTCACATTAAGGATTCTATC 8 4 0 TAAGGATTCT 0.970117 -60 TCCAGGATTCTATGATCGTTC 11 2 1 CCAGGATTCT 0.80213 -239 AATTAATTTTTAAGGATTTTTCTG 13 21 1 TAAGGATTTT 0.945835 -14 GAATTTCTTTGATGGATTCTAAAATACATG 14 57 0 GATGGATTCT 0.86716 -82 GAATTTCTTTGATGGATTCTAAAATACATG 14 115 0 GATGGATTCT 0.86716 -24 GCCGCAGGTATACGGATTTTTCCGGAAGTG 18 102 1 TACGGATTTT 0.916226 -34 ACCGAACTAATAAGTATTTTTTTCCAGCGA 26 39 0 TAAGTATTTT 0.515258 -32 CCTGGATATATATGGATTCAGAGTGCGTGT 27 124 0 TATGGATTCA 0.559994 -36 ********** Masking position 6 Map Score: 8.26838 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 119 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 8 TCGCCACCGGCTCCATGAATATATACTAG 2 7 1 CCCTCCATAA 0.952702 -69 ACAACAGCGACCAGCCCCAAAAAACACCACAAA 3 69 1 CCCCCCAAAA 0.975536 -232 ATTCCCACCCCATCATGTCCTGGAGG 4 4 1 CCCCCCATAT 0.975536 -246 CTCATCACCATTAACACCGGAATG 7 28 0 TCCACCATAA 0.895789 -14 TACGGCAGCCTCTTCCCCTTCAAGTGTTTAATC 16 28 1 TCCCCCTTAA 0.912641 -120 TTATATAGTTCCACCCCCTTAAATAGGTCC 19 8 0 CCCCCCTTAA 0.960754 -132 TGAACACGCATCATCCCCAATAAACCCCCATTT 20 36 1 TCCCCCAAAA 0.944498 -140 AAGAGAGTGTCCCATACCAACATTTTATTATAA 22 33 0 CCTACCAAAT 0.538164 -93 AAAATTACCCCTATTCCATCAAATCAGCACGG 22 104 0 CCTTCCATAA 0.850375 -22 ATGATGCAAATCCATCCCATGATTCATATCCAT 23 48 0 TCTCCCATAT 0.827632 -69 ** ****** ** Masking position 12 Map Score: 5.9499 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 202 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 9 CTCATCACCATTAACACCGGAA 7 30 0 TCATCACCAT 0.792913 -12 ATAATTATCTTCTTCCCCTTTTTAGATAAAT 12 32 0 TCTTCCCCTT 0.980259 -44 TTCTTAACCTCCGTGAGAGTAA 12 64 0 TCTTAACCTC 0.80983 -12 AATTCCTCACCTGTTAGATTCCTC 15 17 0 TCCTCACCTT 0.897864 -14 TACGGCAGCCTCTTCCCCTTCAAGTGTTTAA 16 28 1 TCTTCCCCTC 0.987463 -120 TGAACACGCATCATCCCCAATAAACCCCCAT 20 36 1 TCATCCCCAT 0.887741 -140 AGTAAAAAAATCTTCCCCTACCGAGGATCGT 29 32 1 TCTTCCCCTC 0.987463 -123 CGGGAAAAGATCTTCTCCTCCGCTGGAGGAC 29 81 1 TCTTCTCCTC 0.937859 -74 ********* * Masking position 4 Map Score: 5.36265 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 155 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 CTGGTCGCTGTTGTCTGGGTGGTGTATTCT 3 53 0 TTGTCTGGGT 0.952612 -248 GTTCCTGGAGTTGTCTGGGTGGTGTATTCT 3 106 0 TTGTCTGGGT 0.952612 -195 TCCTGAAGACTTCTATGGAACAGAAATGAG 8 33 1 TTCTATGGAA 0.6175 -31 TCTATGATCGTTCACTGAATAGATTATTAG 11 19 1 TTCACTGAAT 0.750919 -222 GGTTAAATTTCTCTGAGTCGCTGCAGCG 17 9 1 TTCTCTGAGT 0.899214 -135 CTGGTCATCCTTCTCTGGAAATATCCAGAC 19 82 0 TTCTCTGGAA 0.94957 -58 GAGGCAGATATTCACTGGGTCTCAGCAATC 22 75 0 TTCACTGGGT 0.94314 -51 TATTTAAATCTTGTCTGTATAATA 25 5 0 TTGTCTGTAT 0.674479 -74 TAATTGCATATTCGCTGGAAAAAAATACTT 26 28 1 TTCGCTGGAA 0.853275 -43 AACTATAAATTTCCCTGGATATATATGGAT 27 137 0 TTCCCTGGAT 0.927466 -23 ********** Masking position 6 Map Score: 4.93339 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 158 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 11 AGTATTTAAACTGTTGGTTTTTTCATCCGTGAGGT 3 136 0 CTGTGGTTCA 0.992845 -165 TTACTAATATCTGGAGGTTTCTCTACAGAAACTTT 4 158 0 CTGAGGTTTA 0.739406 -92 ATGAATTTCTTTGATGGATTCTAAAATACATGGGT 14 54 0 TTGTGGTTAA 0.878926 -85 ATGAATTTCTTTGATGGATTCTAAAATACATGGGT 14 112 0 TTGTGGTTAA 0.878926 -27 AATTCCTCACCTGTTAGATTCCTCATTTTA 15 6 0 CTGTAGTTCA 0.964695 -25 TGTAGACATGATGATGGTCTGGTCATCCTTCTCTG 19 95 0 ATGTGGCTCA 0.80789 -45 AAGGTCGCTGCTGATGGGTATGGCAGTTATA 27 7 0 CTGTGGTACA 0.956284 -153 TTTACTCTTCCTGATAGATTAACCATC 29 3 0 CTGTAGTTCA 0.964687 -152 TTCCCGGCTCCTGATGGATTAACCACGATCCTCGG 29 52 0 CTGTGGTTCA 0.992845 -103 *** *** ** ** Masking position 2 Map Score: 4.23942 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 141 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 12 ACCCGGGAGTATTTAAACTGTTGGTTTTTTC 3 147 0 ATTAAACTGT 0.652528 -154 TGTATTCATCAATTAAATAGTATCTAAGTGC 11 97 1 ATTAAATAGT 0.94873 -144 TAAGTGCAATATTTATATAGTGGTAGAACAT 11 121 1 ATTATATAGT 0.920225 -120 TTTTATTACGATTTATATAGAAAACTTTATA 16 74 1 ATTATATAGA 0.808539 -74 CACTCTCTAAACTTATATAGTTCCACCCCCT 19 22 0 ATTATATAGT 0.920183 -118 TTAGAGAAAAATTTAAATATTGGGTTTTTAT 21 47 1 ATTAAATATT 0.673896 -61 TTTGATTAACAGTTAAACAGATCTTTTGTCC 24 48 1 ATTAAACAGA 0.793229 -71 TACAGACAAGATTTAAATAGTACCTCCGTGT 25 16 1 ATTAAATAGT 0.948732 -63 * ********* Masking position 5 Map Score: 1.87194 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 5 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 13 CCAGCCCCAAAAAACACCACAAACAAAAGAATACA 3 79 1 AACCCCAAAA 0.747207 -222 TACACCACCCAGACAACTCCAGGAACACCTCACGG 3 110 1 AAACTCAGGA 0.805902 -191 GTAAGTGGATGTGACTCCATAGGAACCTCCAGGAC 4 27 0 GGCCCTAGGA 0.505264 -223 CTTCTGTAGAGGGACCCTTCAGATATCAGTAAAAA 4 123 1 GGCCTCAGAA 0.924633 -127 ATATCTGGAGGTTTCTCTACAGAAACTTTTTTTTA 4 152 0 GTCCTCAGAA 0.888035 -98 ATTAGGCTGCAAAGCACTCCAGAGAGCACCTCAAG 11 44 1 AACCTCAGAA 0.981613 -197 CTGGTGAGCAACATCGCTGCAGCGACTCAGAGAAA 17 18 0 AACCTCAGCA 0.909533 -126 TTATAAACCTCCGCAGGCATCAATTAACC 17 125 0 AACCCCAGGA 0.960804 -19 TGTTTTTATTACAGCACTATAGATATTAATATGGG 18 41 1 AACCTTAGAA 0.906357 -95 ATAAGTTTAGAGAGTGCCACAGAAAAATAATGATA 19 37 1 AATCCCAGAA 0.91467 -103 AACACCTTTAATAACTCTGTAGACATGATGATGGT 19 112 0 AACCTTAGAA 0.906357 -28 CAGCCATGTTGCATAACCACAGACATTTGAGGTGA 23 86 1 GAACCCAGAA 0.832224 -31 TTACTCCCAGATTTTACTTCAGAAAGAGTGGGGAT 27 65 0 ATTCTCAGAA 0.725314 -95 ACATAACTTTATAATGCTTCAGACACAGAATTATT 29 110 1 AATCTCAGAA 0.921785 -45 * * * ** **** * Masking position 11 Map Score: 7.1063 Number of sites scoring better than the average of aligned sites = 423 Number in coding regions = 380 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 14 ATACAGCACCGCTCGAGAGCA 3 2 1 TACAGCACCG 0.970759 -299 GACAACAGCGACCAGCCCCAAAAAACACCA 3 68 1 ACCAGCCCCA 0.876283 -233 CCTTCAATTTTTCAGCCCCGGA 9 3 0 TTCAGCCCCG 0.967562 -39 ACTATACCTCCAGCATCATCCTTCAATT 9 24 0 TCCAGCATCA 0.88867 -18 CAAGTCAGAATACAGCATCAAAACCCTGGA 17 94 0 TACAGCATCA 0.794444 -50 ATGTTTTTATTACAGCACTATAGATATTAA 18 40 1 TACAGCACTA 0.847042 -96 TCTGGAAATATCCAGACCCGCCTTTATTAT 19 69 0 TCCAGACCCG 0.896417 -71 TAACCTGATTTTCAGCACTGAAAGGAACCT 20 121 1 TTCAGCACTG 0.883631 -55 GCATCATGGTTCCAGCCATGTTGCATAACC 23 74 1 TCCAGCCATG 0.789593 -43 ********** Masking position 4 Map Score: 2.99978 Number of sites scoring better than the average of aligned sites = 295 Number in coding regions = 271 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 15 CGCATAAAGTTATTATGTCAGTA 2 63 0 ATAAAGTTAT 0.929838 -13 AGACCTCTTAATAAAATTATGGCCTTTTTT 4 191 0 ATAAAATTAT 0.835635 -59 CGTGAGAGTAATATAATTATCTTCTTCCCC 12 45 0 ATATAATTAT 0.692386 -31 TTATGATAATATAAAGTTTTCTATATAAAT 16 84 0 ATAAAGTTTT 0.801222 -64 GTGGCACTCTCTAAACTTATATAGTTCCAC 19 27 0 CTAAACTTAT 0.776414 -113 AAATTTTTCTCTAAAGTTATAATTCATGGT 21 31 0 CTAAAGTTAT 0.937281 -77 ATACTTTATCGTATAGTTATACTATCATGT 21 76 1 GTATAGTTAT 0.751721 -32 CTGAAGCATTATAAAGTTATGTCCTCCAGC 29 102 0 ATAAAGTTAT 0.929838 -53 ********** Masking position 5 Map Score: 1.36142 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 3 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617