AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i03010_mthe_reg_100.orf -o03010_mthe_100.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: MTH44 27 ribosomal protein Sa (E.coli S2) MTH1055 21 ribosomal protein S23 (E.coli S12) MTH1680 41 ribosomal protein L10a (E.coli L1) Input sequences: #1 MTH1 170 conserved protein #2 MTH5 22 ribosomal protein L8 (E.coli L2) #3 MTH9 46 ribosomal protein L35 (E.coli L29) #4 MTH21 109 ribosomal protein L19 #5 MTH31 30 ribosomal protein L14 #6 MTH34 236 ribosomal protein S18 (E.coli S13) #7 MTH42 171 DNA-dependent RNA polymerase, subunit K #8 MTH43 51 enolase #9 MTH255 269 ribosomal protein L7a #10 MTH256 49 ribosomal protein S28 #11 MTH261 24 translation initiation factor eIF-2, gamma subunit #12 MTH262 24 conserved protein #13 MTH554 52 conserved protein #14 MTH555 267 magnesium chelatase subunit #15 MTH648 65 ribosomal protein L37 #16 MTH649 300 conserved protein #17 MTH681 55 ribosomal protein L37a #18 MTH684 42 conserved protein #19 MTH686 65 proteasome, alpha subunit #20 MTH689 74 conserved protein #21 MTH690 170 ribosomal protein L15 #22 MTH804 40 chorismate mutase, subunit A #23 MTH805 240 conserved protein (homoserine kinase related) #24 MTH1048 300 DNA-dependent RNA polymerase, subunit H #25 MTH1049 40 DNA-dependent RNA polymerase, subunit B'' #26 MTH1050 22 DNA-dependent RNA polymerase, subunit B' #27 MTH1051 38 DNA-dependent RNA polymerase, subunit A' #28 MTH1058 113 translation elongation factor, EF-1 alpha #29 MTH1059 34 ribosomal protein S20 (E.coli S10) #30 MTH1119 132 ribosomal protein L10 #31 MTH1310 222 ribosomal protein L36a #32 MTH1323 171 ribosomal protein L21 #33 MTH1424 62 conserved protein #34 MTH1425 88 O-sialoglycoprotein endopeptidase #35 MTH1593 205 ribosomal protein S3a #36 MTH1615 34 conserved protein #37 MTH1618 118 conserved protein #38 MTH1677 120 protein translocation complex sec61 gamma subunit related protein #39 MTH1678 26 transcription termination factor NusG #40 MTH1682 52 ribosomal protein Lp1 Motif number 1 AAATAACCAGGAGGATATTCGG 2 8 1 CAGGAGGATA 0.89769 -15 TGCTGAATACAAGGAGGTTTCTTGA 4 95 1 AAGGAGGTTT 0.931518 -15 TTCACTCTTACTGGAGGTTAATGA 6 223 1 CTGGAGGTTA 0.946601 -14 AACTGATTTTAAGGAGGATTAGAAC 15 51 1 AAGGAGGATT 0.844398 -15 GAAAACATGACTGGAGGTAAAAAGGTCTGA 23 15 0 CTGGAGGTAA 0.768866 -226 GTCATGTTTTCAGGAGTTTTTGTTATATCA 23 34 1 CAGGAGTTTT 0.720272 -207 GAGACTTGCCCTGGTGGTGTAGGGGCTATC 24 108 1 CTGGTGGTGT 0.868034 -193 GACTTTTTATCTGGAGGACTGAATT 24 286 1 CTGGAGGACT 0.736561 -15 ACCATCATATATGGAGGTATATT 28 101 1 ATGGAGGTAT 0.672921 -13 CCCTTTTTTACAGGAGGATTTAA 29 22 1 CAGGAGGATT 0.956509 -13 CACAGGATCACAGGAGGATTATTT 30 119 1 CAGGAGGATT 0.956509 -14 AGTGAACCACCAGGTGGTGTCACATACAAA 31 112 1 CAGGTGGTGT 0.890839 -111 AAGGCTTTTTATGGAGGTTAAAGA 32 158 1 ATGGAGGTTA 0.813917 -14 TCAGTATATTCAGGGGGTTTAGTATCGTGT 33 28 0 CAGGGGGTTT 0.896854 -35 AGCAGGGTCACAGGTGGTTAATTAA 34 74 1 CAGGTGGTTA 0.885062 -15 AAATCTTGACATGGTGGTTTGGGGTGCTGT 35 44 0 ATGGTGGTTT 0.79333 -162 GTATTCCATACTGGCGGTGTATGTAACTCT 35 99 1 CTGGCGGTGT 0.747675 -107 AGAGGGGCCTCAGGAGGTTTCATAG 36 20 1 CAGGAGGTTT 0.982184 -15 ********** Masking position 6 Map Score: 23.9765 Number of sites scoring better than the average of aligned sites = 467 Number in coding regions = 413 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 2 ACCAAGCTACCCTACGGTCCC 7 1 0 CCTAGGTCCC 0.907683 -171 AGTTCAAATCTCGGCGGTCCCATCAAATCGA 7 112 1 TCGGGGTCCC 0.935992 -60 AACACGTGCACCGTAGAGCCTCTCCTTCTTC 14 70 0 CCGTGAGCCT 0.840494 -198 CAGGGTCCGCCCTGGGATCCCCCCATCCATG 16 143 0 CCTGGATCCC 0.980747 -158 TACCCCTGTTTCGGAGGCCCCTGTTCTT 20 8 0 TCGGGGCCCC 0.958668 -67 CTCCAGTGACCCTTGAATGGAAG 22 3 1 CCAGGACCCT 0.867623 -38 TAGGGGCTATCATGCGGGCCTGTCGAGCCCG 24 127 1 CATGGGGCCT 0.852887 -174 CAGGGCGTTTCCTGAGGGCCCGTAGCTCAGT 24 180 1 CCTGGGGCCC 0.994429 -121 GGTTCAATTCCCGTCGGGCCCGCTATCTAAT 24 247 1 CCGTGGGCCC 0.962573 -54 AAATAATCCTCCTGTGATCCTGTGAGAATAA 30 112 0 CCTGGATCCT 0.958434 -21 TAATTAACCACCTGTGACCCTGCTCCTTCTG 34 67 0 CCTGGACCCT 0.973385 -22 TATGAAACCTCCTGAGGCCCCTCTGGGATAG 36 13 0 CCTGGGCCCC 0.994429 -22 **** ****** Masking position 9 Map Score: 14.0656 Number of sites scoring better than the average of aligned sites = 630 Number in coding regions = 592 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 3 TCCAAGAAAAACATTAAAATAGAGGTTCTTGGATT 7 142 0 ACAAAAAGGG 0.935877 -30 TAAACTCTAGACTGAAAAATAGTGGTTTATTAGAG 8 12 0 ACAAAAAGGG 0.935944 -40 AGTTTTGCTGCCAATTAAAAAGGGAAGGAATAATG 9 25 0 CCTAAAAGGA 0.838617 -245 AGTAAGACGCCCAGGAAAACAAGGATTAATAGAAA 9 81 0 CCAAAAAAGA 0.90028 -189 AGCCCTGAAACAGAGGACGTGGAGGT 14 2 1 GCGAAAAGGG 0.860966 -266 GAGATAGAACCCGGAGATATAAGGGAAAAAATACG 14 212 1 CCGATAAAGG 0.78998 -56 CTCCTTTTAGCCTTCAAAAAACAGGGAGGCATAAC 18 18 1 CCAAAAACGG 0.964928 -25 CATAAATTATCCATCAATAAAGAGAGGTTAGAAAA 19 41 1 CCAATAAGGA 0.922893 -25 AGAACAGGGGCCTCCGAAACAGGGGTAAAGGGGCT 20 12 1 CCGAAAAGGG 0.982966 -63 GGAACGTATCCCTGAAAAATAGCGGTTTAGGTGCT 21 107 0 CCAAAAAGGG 0.991334 -64 TTAAATCCTCCTGTAAAAAAGGGAAGAGGTGGGT 29 11 0 CCAAAAAGGA 0.976124 -24 AAAAAGTAAGCCTTTAAAATAACTGAACTTTTTTA 31 178 0 CCAAAAAATG 0.747499 -45 ATACTAAACCCCCTGAATATACTGACTGAGGAGGT 33 33 1 CCAATAACGA 0.740409 -30 ATCTTTAACACCGTAAAAACAGCTGGATTTAACAT 35 169 0 CCAAAAAGTG 0.930618 -37 ** **** ** ** Masking position 7 Map Score: 11.0742 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 165 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 4 GGAGGACTGGAAGGGGCATATTTTCCAGT 4 7 1 CGGAAGGGAT 0.974348 -103 AGTTTTTTCGCTGGACTGGAAAATATGCCCCTT 4 21 0 CGGACGGAAA 0.930971 -89 AGGTAAGGCGCAAGACTGGAAATCTTGTGGAGC 6 89 1 CAGACGGAAT 0.858554 -148 TAACCGACGCCGGGACTGGGATTTGAACCCAGG 6 131 0 CGGACGGGTT 0.991926 -106 AGTGAATTCGCGGGACGGGGGTTTGCGAATTCT 6 196 0 CGGACGGGTT 0.991926 -41 GACTTTTCAACTGGAACGGGGATGGTCAGCACC 7 62 1 CGGAAGGGAT 0.974348 -110 CAGTCAAAGACCCGAAAGGGGAAGTACATAAGG 14 101 1 CCGAAGGGAA 0.806998 -167 AGGGCGGACCCTGGAATGGATTTGAAGAGGTAC 16 161 1 CGGAAGGATT 0.959565 -140 CTGTCGAGCCCGCGACTCGGGTTCAATTCCCGG 24 146 1 CCGACCGGTT 0.864228 -155 AGGAAACGCCCTGGCCGGGAATTGAACCCGAGT 24 160 0 CGGCCGGATT 0.924035 -141 AGATAGCGGGCCCGACGGGAATTGAACCCGCGA 24 242 0 CCGACGGATT 0.966282 -59 * **** *** ** Masking position 1 Map Score: 10.2699 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 110 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 5 TAAATCACCTCAGTAACTTTTAG 5 18 0 ATCACCTCAG 0.931849 -13 GGAGGAGCAAAGCTCCACAAGATTTCCAGT 6 103 0 AGCTCCACAA 0.768087 -134 GATATAAAGAAGCTCCTCAAGGTCAGGGGT 14 38 1 AGCTCCTCAA 0.963053 -230 GCACTGCAGTACCTCTTCAAATCCATTCCA 16 172 0 ACCTCTTCAA 0.798477 -129 ATTATCACTCCAGTAAATATGAT 17 43 0 ATCACTCCAG 0.555834 -13 GCTTTATCTTACCTTCTCAGCCCCTTTACC 20 35 0 ACCTTCTCAG 0.755198 -40 CAGATGTAGTAGCACCTAAACCGCTATTTT 21 97 1 AGCACCTAAA 0.693347 -74 CACTCCAGAGAGCACCTCAAGCTCTCAAAC 23 174 0 AGCACCTCAA 0.971694 -67 TAGGCTGCAAAGCACTCCAGAGAGCACCTC 23 186 0 AGCACTCCAG 0.792458 -55 GATGAACCTCCTCAGTCAGTATATT 33 48 0 ACCTCCTCAG 0.963717 -15 ATGACCACACAGCACCCCAAACCACCATGT 35 36 1 AGCACCCCAA 0.945443 -170 CTATGAAACCTCCTGAGGCCCCTCTGG 36 18 0 ACCTCCTGAG 0.721675 -17 CAGTCAGTACACCATCTCAATGTGCAAGAT 37 65 1 ACCATCTCAA 0.769738 -54 ATGATCACCTCAAATTTTATTTT 40 40 0 ATCACCTCAA 0.918371 -13 ********** Masking position 9 Map Score: 10.399 Number of sites scoring better than the average of aligned sites = 770 Number in coding regions = 720 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 6 GGAGGACTGGAAGGGGCATATTTTCCAG 4 9 1 GGAAGGGGCA 0.796091 -101 CTGCCAATTAAAAAGGGAAGGAATAATGGA 9 23 0 AAAAGGGAAG 0.849886 -247 AGGGGTAAGAAGAAGGAGAGGCTCTACGGT 14 62 1 AGAAGGAGAG 0.906451 -206 TCAAAGACCCGAAAGGGGAAGTACATAAGG 14 104 1 GAAAGGGGAA 0.922573 -164 GGGGAAGTACATAAGGAGCAGGTTCCCGAG 14 118 1 ATAAGGAGCA 0.752367 -150 ACCCGGAGATATAAGGGAAAAAATACGTAA 14 220 1 ATAAGGGAAA 0.733094 -48 ATTTAATTGTAAGGGGAAGGGTGGATCA 15 9 1 GTAAGGGGAA 0.875395 -57 TTTGAAGGCTAAAAGGAGAGGAGGA 18 6 0 AAAAGGAGAG 0.931549 -37 TTGAATGGAAGAAAGGGGAATGTAATTT 22 23 1 GAAAGGGGAA 0.922573 -18 GGGAATAACAAAAAGGAGAGAATACC 27 23 1 AAAAGGAGAG 0.931549 -16 CCTCCTGTAAAAAAGGGAAGAGGTGGGT 29 9 0 AAAAGGGAAG 0.849886 -26 ATCTTCAGAGAATAGGAGAGCAATCTAACC 31 28 0 AATAGGAGAG 0.572544 -195 AATAGCCATGATAAGGAAAAATATATATTA 32 50 1 ATAAGGAAAA 0.631203 -122 GTTACACTCCAGAAGGAGCAGGGTCACAGG 34 58 1 AGAAGGAGCA 0.78582 -31 ********** Masking position 4 Map Score: 10.2173 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 247 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 7 TCTGCATTGTGGAAATATTTATAAATAAATCCG 1 133 1 GAAATTTATA 0.950985 -38 TTAATTGGCAGCAAAACTTTATATGTGATGAAG 9 42 1 GAAATTTATA 0.950975 -228 TGCAGTGCAAGAAAACTTATATATTAGTAGAAT 16 194 1 GAAATATATA 0.959845 -107 ATATAGGAATGGAAAAGTATATAAGCAGGTAAC 24 47 1 GAAATATATA 0.959845 -254 AAAAGTCACCGTAAAATTAGATAGCGGGCCCGA 24 260 0 GAAATAGATA 0.848138 -41 CCCCATTAAACTTATATAATTAAAAAGA 28 6 1 TAAATATATA 0.700902 -108 GCCATGATAAGGAAAAATATATATTAATGGAGA 32 54 1 GAAATATATA 0.959845 -118 TGGAAAAGGTTTTTAAATATGGAAA 37 3 1 GAAATTTTTA 0.753357 -116 CCCACTCAAGGAAAACCTTTATAAATCTTGAAG 38 27 1 GAAATTTATA 0.950975 -94 * *** ****** Masking position 8 Map Score: 6.44241 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 6 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 CAGCGGAAAGTTTAAATATGGATACCATACA 1 17 1 TTTAAATATG 0.923109 -154 ATGACATCTATTTAAGTATTGCTGCCGTCGG 6 14 0 TTTAAGTATG 0.673306 -223 AATATGATGTTATAGATATTGTCTGGTCAGT 17 20 0 TATAGATATG 0.814608 -36 TCTACCACTATATAAATATTGCACTTAGATA 23 114 1 TATAAATATG 0.932922 -127 TCACCGTAAAATTAGATAGCGGGCCCGACGG 24 257 0 ATTAGATAGG 0.472058 -44 GGTAACCATTAATAAATATTGTCTTGGACAG 30 63 0 AATAAATATG 0.817022 -70 CATACAAAGGTATAAATAGAGATTTGAGATA 31 134 1 TATAAATAGG 0.910815 -89 TAATGGAGATATTAAATAGAGAACTTATAAG 32 78 1 ATTAAATAGG 0.738918 -94 TATCTCCGGTTATAACTATTGTATCGTTGGA 34 18 0 TATAACTATG 0.704805 -71 TAAGGGAGTATTTAAATCTTGACATGGTGGT 35 56 0 TTTAAATCTG 0.791357 -150 GGAAAAGGTTTTTAAATATGGAAACACAAAG 37 12 1 TTTAAATATG 0.923109 -107 GGAAAACCTTTATAAATCTTGAAGGATAGAT 38 36 1 TATAAATCTG 0.814608 -85 TTTTTAACTATATAAATAGCGGGGATAAACC 38 100 1 TATAAATAGG 0.910815 -21 ********* * Masking position 4 Map Score: 6.46101 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 5 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 9 CTTTGCTCCTCCTGGGTTCAAATCCCAGTCCCGGCGT 6 121 1 CTGGTTCACA 0.839082 -116 ACGCTGGAGACCCGAGTTCAAATCTCGGCGGTCCCAT 7 98 1 CCGGTTCACG 0.990245 -74 CTCTACGGTGCACGTGTTCAGTCAAAGACCCGAAAGG 14 83 1 CCGGTTCAAG 0.974452 -185 TGGCCACATCCCCTGGCTCACCCCTCGGGAACCTGCT 14 134 0 CCTGCTCACG 0.935088 -134 CGGGTTCTATCTCAAGTTCACCCCTGGATGCCGCCGC 14 188 0 CCAGTTCACG 0.97922 -80 GAGCCCGCGACTCGGGTTCAATTCCCGGCCAGGGCGT 24 151 1 CCGGTTCACG 0.990245 -150 ACCAAGTGGTCGCGGGTTCAATTCCCGTCGGGCCCGC 24 233 1 CCGGTTCACG 0.990245 -68 * ** ***** * * Masking position 10 Map Score: 5.07146 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 13 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 10 GGTGTAATTACCGATGGATGGTAGAAAAAC 9 247 1 CCGATGGATG 0.964186 -23 TCAGTTTATACTGCTGTATGA 13 42 1 CTGCTGTATG 0.801103 -11 ATGGCCACATCCCCTGGCTCACCCCTCGGG 14 142 0 CCCCTGGCTC 0.889562 -126 CTCAAGTTCACCCCTGGATGCCGCCGCCCG 14 185 0 CCCCTGGATG 0.977118 -83 ACATGCATCTCTCATGGATGGGGGGATCCC 16 131 1 CTCATGGATG 0.944079 -170 GGGATACGTTCCCATGGATGTGGCGTAAAG 21 130 1 CCCATGGATG 0.956015 -41 AAGATCAACACTGCAGGATCATTTCATCAT 25 16 1 CTGCAGGATC 0.839454 -25 GCATGCCCATTTGCTGGATCTAAAAAATCA 28 65 1 TTGCTGGATC 0.764799 -49 TGCAATGAAACTGATGGATCAACACGGATT 31 67 1 CTGATGGATC 0.944079 -156 ********** Masking position 9 Map Score: 4.38794 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 322 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 11 GGCAAGTAAAACCACAGACCACATCGTATC 1 100 0 ACCACAGACC 0.81421 -71 CTGGGTTCAAATCCCAGTCCCGGCGTCGGT 6 132 1 ATCCCAGTCC 0.958961 -105 GAATTCGCAAACCCCCGTCCCGCGAATTCA 6 197 1 ACCCCCGTCC 0.99031 -40 GGTGCTGACCATCCCCGTTCCAGTTGAAAA 7 65 0 ATCCCCGTTC 0.795925 -107 AACGCTGGAGACCCGAGTTCAAATCTCGGC 7 97 1 ACCCGAGTTC 0.849863 -75 CCTTCTTCTTACCCCTGACCTTGAGGAGCT 14 48 0 ACCCCTGACC 0.920299 -220 GCCCTGGGATCCCCCCATCCATGAGAGATG 16 136 0 CCCCCCATCC 0.826615 -165 CGGGAATTGAACCCGAGTCGCGGGCTCGAC 24 148 0 ACCCGAGTCG 0.810995 -153 CGGGAATTGAACCCGCGACCACTTGGTTAA 24 230 0 ACCCGCGACC 0.959135 -71 ACCACACAGCACCCCAAACCACCATGTCAA 35 39 1 ACCCCAAACC 0.932328 -167 TCCATCACTCATCCCAATCCTAGCCCTTGT 38 70 1 ATCCCAATCC 0.852684 -51 ********** Masking position 3 Map Score: 8.2303 Number of sites scoring better than the average of aligned sites = 247 Number in coding regions = 224 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 12 AAAAGTTACTGAGGTGATTTA 5 20 1 GAGGTGATTT 0.979268 -11 AGTTTATTATGAGGTGTTTTA 8 41 1 GAGGTGTTTT 0.907462 -11 CAATTTAATAAAGGTGATTTA 10 39 1 AAGGTGATTT 0.948622 -11 TTGAGAGCTTGAGGTGCTCTCTGGAGTGCT 23 176 1 GAGGTGCTCT 0.907238 -65 CTGTTTGTCTAAGGTAATTTCCTATATTCT 28 36 0 AAGGTAATTT 0.67339 -78 TTTCACTTACGAGGTGATTAGAT 31 210 1 GAGGTGATTA 0.945332 -13 GTTAAAGATTAAGGTGATATA 35 195 1 AAGGTGATAT 0.819985 -11 AATAAAATTTGAGGTGATCAT 40 42 1 GAGGTGATCA 0.920862 -11 ********** Masking position 2 Map Score: 3.50319 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 84 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 13 GGAGGACTGGAAGGGGCATATTTT 4 5 1 GACTGGAAGG 0.844048 -105 TTTTTCGCTGGACTGGAAAATATGCCCCTT 4 21 0 GACTGGAAAA 0.973297 -89 TAAGGCGCAAGACTGGAAATCTTGTGGAGC 6 92 1 GACTGGAAAT 0.836835 -145 ATAAACTCTAGACTGAAAAATAGTGGTTTA 8 18 0 GACTGAAAAA 0.741733 -34 TATATTAGTAGAATAGAAAAATGAAGTATC 16 213 1 GAATAGAAAA 0.849888 -88 TGAAGTATCTGATTGGAAGATTTTCAGCTC 16 234 1 GATTGGAAGA 0.800592 -67 AAGGTCCGTTTAATGGAAAAATCAAAGGTG 21 16 0 TAATGGAAAA 0.778823 -155 AGTGACCCTTGAATGGAAGAAAGGGGAATG 22 15 1 GAATGGAAGA 0.942109 -26 AAATACTAGAAAAATGTAACTCA 24 4 1 TACTAGAAAA 0.581758 -297 TGTCATATAGGAATGGAAAAGTATATAAGC 24 43 1 GAATGGAAAA 0.958083 -258 TCTCATAACGGAATAGAACATCCACATCTT 37 90 0 GAATAGAACA 0.600603 -29 ********** Masking position 7 Map Score: 4.71242 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 76 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 14 AAAACATTAAAATAGAGGTTCTTGGATTCG 7 140 0 AATAGAGGTT 0.946765 -32 TAGACTGAAAAATAGTGGTTTATTAGAGT 8 10 0 AATAGTGGTT 0.831756 -42 ATTTCAATTTAATAAAGGTGATTTA 10 35 1 AATAAAGGTG 0.652844 -15 CCCCCCATCCATGAGAGATGCATGTGGTGC 16 126 0 ATGAGAGATG 0.765249 -175 TCCATCAATAAAGAGAGGTTAGAAAA 19 50 1 AAGAGAGGTT 0.943286 -16 ATCCCTGAAAAATAGCGGTTTAGGTGCTAC 21 105 0 AATAGCGGTT 0.806007 -66 AGCCGAACAGAATAGAGGTGTAA 21 158 1 AATAGAGGTG 0.959786 -13 CAAAGGTATAAATAGAGATTTGAGATATAC 31 138 1 AATAGAGATT 0.814992 -85 CTATTCCGTTATGAGAGGTTAAACC 37 104 1 ATGAGAGGTT 0.907463 -15 TAGGATTGGGATGAGTGATGGAGTAATCTA 38 62 0 ATGAGTGATG 0.475386 -59 AAAAAATAAAATTTGAGGTGATCAT 40 38 1 ATTTGAGGTG 0.64132 -15 ********** Masking position 1 Map Score: 3.90413 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 113 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 15 TTGCCCAGTCTGCATTGTGGAAATATTTAT 1 125 1 TGCATTGTGG 0.889334 -46 ATGAATGGTCTGCAGTCTGTTCCTTAATCT 16 24 1 TGCAGTCTGT 0.94596 -277 GAATACACTTTGCAGTGTTTGAGAGCTTGA 23 158 1 TGCAGTGTTT 0.941913 -83 GAAATGATCCTGCAGTGTTGATCTTAAAAA 25 11 0 TGCAGTGTTG 0.930436 -30 CAAATGGGCATGCTGTTTGTCTAAGGTAAT 28 48 0 TGCTGTTTGT 0.770982 -66 CTGCATGGGACGCAGTGTTTTATTTTTTCG 32 20 0 CGCAGTGTTT 0.791174 -152 TGGTTTGGGGTGCTGTGTGGTCATGAATAT 35 30 0 TGCTGTGTGG 0.955373 -176 ATATTATAAGTGCTTTGTGTTTCCATATTT 37 25 0 TGCTTTGTGT 0.836352 -94 ATTCTTCTTGTGCAGTCAGTACACCATCTC 37 53 1 TGCAGTCAGT 0.734006 -66 ********** Masking position 6 Map Score: 2.40755 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 101 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493