AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00630_mthe_reg_100.orf -o00630_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 Input sequences: #1 MTH310 178 conserved protein #2 MTH312 50 ATP-dependent helicase #3 MTH313 79 transcriptional regulator #4 MTH384 249 unknown #5 MTH387 24 conserved protein #6 MTH388 35 unknown #7 MTH393 41 NADH dehydrogenase (ubiquinone), subunit 1 related protein #8 MTH394 55 unknown #9 MTH397 40 formate hydrogenlyase, subunit 7 #10 MTH611 84 prolyl-tRNA synthetase #11 MTH612 50 unknown #12 MTH711 166 transcriptional regulator #13 MTH783 83 hydrogenase expression/formation protein HypA #14 MTH894 179 conserved protein #15 MTH895 51 conserved protein #16 MTH898 22 conserved protein #17 MTH964 103 unknown #18 MTH1063 134 transcriptional regulator related protein #19 MTH1072 67 hydrogenase expression/formation protein HypD #20 MTH1141 300 conserved protein (FlpE) #21 MTH1193 146 transcriptional regulator #22 MTH1202 236 proteasome, beta subunit #23 MTH1203 69 cleavage and polyadenylation specificity factor #24 MTH1204 46 phosphoribosylformylglycinamidine cyclo-ligase #25 MTH1246 30 NADH dehydrogenase I, subunit N #26 MTH1251 147 conserved protein #27 MTH1287 177 transcriptional regulator HypF homolog #28 MTH1396 28 thiamine monphosphate kinase #29 MTH1398 269 conserved protein #30 MTH1522 116 nitrogenase alpha chain (NifD) related protein #31 MTH1547 118 nitrate assimilation protein, narQ #32 MTH1552 139 formate dehydrogenase, alpha subunit homolog #33 MTH1627 220 TATA-binding transcription initiation factor #34 MTH1634 151 transcriptional control factor (enhancer-binding protein) #35 MTH1649 110 hydrogenase expression/formation protein HypC #36 MTH1708 300 carbon monoxide dehydrogenase, alpha subunit #37 MTH1710 21 carbon monoxide dehydrogenase, alpha subunit #38 MTH1722 264 transcriptional regulator Icc related protein #39 MTH1726 117 citrate synthase I #40 MTH1740 86 pyruvate oxidoreductase, gamma subunit #41 MTH1795 72 transcriptional regulator Motif number 1 AGGGTTATAAAAAAATTTATCTATCAATCCTC 1 60 1 AAATTTATCT 0.828948 -119 GTTGCAATGACAACATTTATATATGTTTTCCC 3 43 1 CAATTTATAT 0.944855 -37 CCTTTTTTAAAAAGATTTATAT 4 238 1 AAATTTATAT 0.947312 -12 CGGTAATTAACAATTTTTATATAGATAACTCT 13 25 1 CAATTTATAT 0.944855 -59 TTAGTCTGACAAAATTTTATAATTAGAATTAA 13 58 0 AAATTTATAA 0.926343 -26 TTTTGCACCGGAAGATTTATATGTCATTAACT 18 60 0 GAATTTATAT 0.883747 -75 CAATAAAATCCAATTTTAATCATTTAACCGTT 20 212 0 CAATTAATCA 0.445775 -89 TAAATTTTAGGAACATTTATATATGTAATAC 20 280 1 GAATTTATAT 0.883747 -21 ATCTTCAGATAAACATTTATAAGGGAACATCC 21 37 1 AAATTTATAA 0.926343 -110 AAGAAGTCATCAACTTTTATAAGATAGGGGAT 21 65 0 CAATTTATAA 0.922987 -82 ATTCACTTAAAAAACTTTATAATATAACTTTC 21 107 1 AAATTTATAA 0.926343 -40 AAAAAATCGCAAAGTTTAATAAGGACCTCCTG 22 82 1 AAATTAATAA 0.75795 -155 ATTTATATAGAAAACTTTATATTATCATAAAT 26 84 1 AAATTTATAT 0.947312 -64 TATTTAGGTAATATTTTTATATCTGTAATACT 29 32 0 ATATTTATAT 0.524975 -238 AATATTACCTAAATATTAATAAAGTATTATTA 29 49 1 AAATTAATAA 0.75795 -221 TTTTTATGGTGAAACTTTATCATGATGCACAG 32 45 0 GAATTTATCA 0.589021 -95 TTTTTTACGTCAATATTAATATAGGTGCATTT 33 159 1 CAATTAATAT 0.81011 -62 TGTTTCCCACAAATCTTTATATGTGACGGATC 35 30 1 AAATTTATAT 0.947312 -81 TCACTATATCAAACATTCATATAATATAAAGG 36 16 1 AAATTCATAT 0.668512 -285 ATAATCACTTCAACCTTTATATTATATGAATG 36 29 0 CAATTTATAT 0.944855 -272 CGACAATGCACAAAGTTTATATATAGATTCCA 36 219 1 CAATTTATAT 0.944855 -82 TATATATATTAAAAATTTATAATGATTAACAA 40 46 1 AAATTTATAA 0.926343 -41 *** ******* Masking position 6 Map Score: 26.8552 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 21 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 2 TTTTATAACCCTATGAATGTGAATACTTTAAG 1 40 0 CTGAATGTGA 0.431652 -139 GCTGATCTATCTGGTGGGAAAACATATATA 3 60 0 ATGGTGGGAA 0.81913 -20 CCAGGACATGATGGGGTGGGAAT 4 2 0 AGGGTGGGAA 0.689002 -248 AGAAACCGGTAAGTGGATGTGACTCCATAGGA 4 38 0 ATGGATGTGA 0.933365 -212 TGTGGAATGAAAATGGAAGGGATTTAATCAGA 8 20 1 ATGGAAGGGA 0.949794 -36 ATTGTTAATTACCGGAAGGTGATTTTTC 13 7 0 AGGAAGGTGA 0.842404 -77 TTCAACCTGGAATTTGAGGTGAA 15 39 1 ATTGAGGTGA 0.956883 -13 GTTGCGTGGAATTGTGATGTGATGGTGGGATC 17 14 1 AGTGATGTGA 0.66899 -90 CGTAAAGTTAAACTGGAGGTGAAAAA 17 88 1 ATGGAGGTGA 0.986884 -16 ATGATTAAACACTTGAAGGGGAAGAGGCTGCC 26 31 0 ATGAAGGGGA 0.936539 -117 GCCCATCTCACAGTGGAGGGAATAGTCCAGGG 27 90 1 CTGGAGGGAA 0.877801 -88 TATCAAAAATAGTTGGATGGGAACAG 28 5 0 ATGGATGGGA 0.949794 -24 TAACCACAGACATTTGAGGTGACGTAAT 30 99 1 CTTGAGGTGA 0.892311 -18 TTATGAGTAGAGAGTGAGGTGAAGAGG 32 6 0 AGTGAGGTGA 0.915658 -134 ACTGAAGATAACATGAAGGGGACTGTTAAATT 32 81 1 ATGAAGGGGA 0.936539 -59 AATTTAGAATAGATGGAAGGGAACTTGAGGCT 32 109 1 ATGGAAGGGA 0.949794 -31 TATAATATAAAGGTTGAAGTGATTATTACTAA 36 35 1 ATTGAAGTGA 0.805122 -266 GGTTTCCCTTATATTGTGGTAATATCGCACCC 36 72 1 ATTGTGGTAA 0.497244 -229 CCTTTTTAATAAATGGTGGGGATGTGCCAGAT 36 166 0 ATGGTGGGGA 0.959873 -135 ATTCTTAGTGCAGGGGAAGGGATTCGAACCCT 38 118 0 CGGGAAGGGA 0.775548 -147 GATAAGGTAAAGGTTGAGGTGATAAA 39 5 0 ATTGAGGTGA 0.956883 -113 TAACAATGAGAAATGGAGGTAAACT 40 72 1 ATGGAGGTAA 0.934406 -15 * ********* Masking position 12 Map Score: 25.6577 Number of sites scoring better than the average of aligned sites = 790 Number in coding regions = 715 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 3 ATTTGAAAACCCCCTTCCCGGTATTAAACA 1 107 0 CCCCTTCCCG 0.869045 -72 TCCCCCCATCCAGTATCTGGCCG 2 4 1 CCCCATCCAG 0.851528 -47 ATTCCCACCCCATCATGTCCTGGAGGT 4 8 1 CCCCATCATG 0.839051 -242 TCTGAAGGGTCCCTCTACAGAAGATTTAGT 4 116 0 CCCTCTACAG 0.770733 -134 GTTAACCCTCTAATGGAGTATATTT 10 6 1 CCCTCTAATG 0.753423 -79 ACCAGCAGTTCCCCTTCAAGAGATGGAGAT 12 92 1 CCCCTTCAAG 0.953106 -75 GAAAAATCACCTTCCGGTAATTAACAA 13 8 1 CACCTTCCGG 0.788906 -76 ATTAAGCCCGCCCTTGAAGGAAGAATTCAG 14 66 0 CCCTTGAAGG 0.623295 -114 CAGCACCCTAAGGAGGTATGAT 16 4 1 CACCCTAAGG 0.743823 -19 CCGTTCTTCAACCCCTCAGGAAGCCCCATC 22 45 1 ACCCCTCAGG 0.802784 -192 GCAGCCTCTTCCCCTTCAAGTGTTTAATCA 26 32 1 CCCCTTCAAG 0.953106 -116 ATTTAACAGTCCCCTTCATGTTATCTTCAG 32 82 0 CCCCTTCATG 0.942848 -58 GGACATGGTACCCCCTTCAGCATATGATCT 34 48 1 CCCCCTTCAG 0.723307 -104 GATTCTCTCACCCTCTCCGGATCTTTATAG 34 87 0 CCCTCTCCGG 0.951373 -65 CGCTCGGGCACCCCTGCATGGTAATTGATT 38 46 0 CCCCTGCATG 0.857147 -219 GGGATTCGAACCCTCGAAGGCCTGCGCCAG 38 102 0 CCCTCGAAGG 0.750868 -163 GGTTCGAATCCCCCCTAAGGCTTTTCTACT 38 228 1 CCCCCTAAGG 0.96889 -37 ********** Masking position 10 Map Score: 16.0916 Number of sites scoring better than the average of aligned sites = 926 Number in coding regions = 870 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 4 GTAGAGGGACCCTTCAGATATCAGTAAAAAAAA 4 128 1 CCTCAATATA 0.911029 -122 TGTAGAGAAACCTCCAGATATTAGTAAAAAAGG 4 166 1 CCCCAATATA 0.893731 -84 TAAATCCCCTCTTTTCTGATTAAATCCCT 8 37 0 CCTCTTTCTA 0.925387 -19 TCAATCTCCCATCTCATATGATGTACCGTGA 11 30 0 CCTCTATATA 0.937647 -21 CCTTTGGCCTCCTCCATATATATATGATCGTGA 19 14 1 CCCCAATATT 0.59343 -54 TAAAAAATAATCATCTATTATGAATTATAATTT 20 110 1 TCTCTTTATA 0.618875 -191 AGGGAACATCCCCTATCTTATAAAAGTTGATGA 21 58 1 CCTATTTATA 0.758958 -89 TCAGGAAGCCCCATCTATTATAAAAAAATCGCA 22 60 1 CCTCTTTATA 0.967031 -177 TTAATAAGGACCTCCTGTTATATATTGGTACAG 22 97 1 CCCCTTTATT 0.807001 -140 TCATCGGATCCCCTATTTTATTACGATTTATAT 26 59 1 CCTATTTATA 0.758958 -89 AAACATATATCCATCTTTGATTAACAGTTAAAC 31 74 0 CCTCTTGATA 0.799178 -45 AAGTTCCCTTCCATCTATTCTAAATTTAACAGT 32 102 0 CCTCTTTCTA 0.925387 -38 AGATAAAGATCCGTCACATATAAAGATTTGTGG 35 36 0 CCTCAATATA 0.911029 -75 TGGCACATCCCCACCATTTATTAAAAAGGTCCA 36 169 1 CCCCATTATA 0.942294 -132 AGTTTACCTCCATTTCTCATTGTTAATCA 40 68 0 CCCCATTCTA 0.873483 -19 ** *** **** * Masking position 11 Map Score: 11.5926 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 146 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 5 TTTCAAATAAAACAGAAGAGACTGGTTCCCA 1 129 1 AAAGAAGAGA 0.81059 -50 GTGGAATGAAAATGGAAGGGATTTAATCAGA 8 21 1 AAGGAAGGGA 0.842143 -35 ATTTAATCAGAAAAGAGGGGATTTA 8 41 1 AAAGAGGGGA 0.985175 -15 GGTACATCATATGAGATGGGAGATTGA 11 34 1 ATAGATGGGA 0.782583 -17 GTTCCCCTTCAAGAGATGGAGATTATGAAAG 12 99 1 AAAGATGGAG 0.683586 -68 CAACTTTTATAAGATAGGGGATGTTCCCTTA 21 56 0 AAATAGGGGA 0.950253 -91 ATTTTTTTATAATAGATGGGGCTTCCTGAGG 22 58 0 AAAGATGGGG 0.944675 -179 ACTGCAATTAAAAATAGGAGAAAAA 23 5 0 AAATAGGAGA 0.707333 -65 AAATCGTAATAAAATAGGGGATCCGATGATT 26 57 0 AAATAGGGGA 0.950253 -91 ATTGGTACTAAAGAGAAGGGAGCTATAAA 26 129 1 AAAGAAGGGA 0.971284 -19 TTAAATTTAGAATAGATGGAAGGGAACTTGA 32 106 1 AAAGATGGAA 0.81059 -34 ATACTTAATGAATAGAGGGGGATGAA 33 6 0 AAAGAGGGGG 0.971055 -215 ATATTACCACAATATAAGGGAAACCGAAGAT 36 66 0 AAATAAGGGA 0.906738 -235 ** ******** Masking position 6 Map Score: 12.6298 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 142 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 TGTGAATACTTTAAGTACATGAAAAAACATTAAAT 1 20 0 TTAATCAAAA 0.958049 -159 CTTCCCGGTATTAAACACATTTAAAGATTTCTGAG 1 89 0 TTAACCAAAA 0.769136 -90 GTTTTCGTGATTATATTCACAGAAACCGGTAAGTG 4 55 0 TTATTCAAAA 0.869846 -195 TGATTAGTGTTTATCTCCAGGGAAAAATATATTT 10 61 1 TTATTCAAAA 0.869866 -24 TTATTTTTCATTTATTTCAATAAAATTCAGGTCAG 14 16 1 TTTATCAAAA 0.873801 -164 TTATATGTCATTAACTACAAGTTAAATTTTAACCG 18 41 0 TTAATCATAA 0.878131 -94 TTTAACCGTTTTAAATCCACAATAATCTAAAATTA 20 187 0 TTAATCATAA 0.879981 -114 GTGAACCATTGTAATTACATGAAAATCACAATAAA 20 237 0 GTAATCAAAA 0.769152 -64 TCTTCTAAACTTATATTCACTTAAAAAACTTTATA 21 93 1 TTATTCAAAA 0.869039 -54 TAAACAGGTGTTTACTGCAATTAAAAATAGGAGAA 23 14 0 TTTATCAAAA 0.902706 -56 ACATATAAATTTAAATGCACCTATATTAATATTGA 33 168 0 TTAATCAATA 0.69212 -53 AAATAGGTAATTAAGTACACAAAAATAGTAAATTT 39 50 0 TTAATCAAAA 0.958049 -68 CGCAGAGGAATTTAATTCACAATAA 39 103 1 TTTATCATAA 0.752461 -15 TTTAATCCATCCGAATATTTCACCA 41 1 1 TTTATCAGAA 0.642619 -72 **** * ** *** Masking position 9 Map Score: 9.38365 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 10 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 7 TTGAAAACCCCCTTCCCGGTATTAAACACA 1 105 0 CCTTCCCGGT 0.889321 -74 CAGAATCCTGGCTTCCCGGTGGGAACCAGT 1 149 0 GCTTCCCGGT 0.950105 -30 CTCCATAGGAACCTCCAGGACATGATGGGG 4 18 0 ACCTCCAGGA 0.891153 -232 AGTCACATCCACTTACCGGTTTCTGTGAAT 4 46 1 ACTTACCGGT 0.542248 -204 CTGTAGAGAAACCTCCAGATATTAGTAAAA 4 165 1 ACCTCCAGAT 0.800181 -85 GGCTTCCATGTTCTCATTCAG 6 2 1 GCTTCCATGT 0.72972 -34 GAAAAATCACCTTCCGGTAATTAACAAT 13 9 1 ACCTTCCGGT 0.756836 -75 TTCACCTCAAATTCCAGGTTGAACCTGTT 15 33 0 AATTCCAGGT 0.504957 -19 TTTTTCACCTCCAGTTTAACTTTACG 17 88 0 ACCTCCAGTT 0.941574 -16 TTAAGGGCAGCCTTCCAGTTAGGATCACTG 20 20 0 CCTTCCAGTT 0.702883 -281 TTTAATAAGGACCTCCTGTTATATATTGGT 22 96 1 ACCTCCTGTT 0.6956 -141 TTAAATCACTGCCTCCCTGAGGGAATAATA 29 175 0 GCCTCCCTGA 0.554706 -95 TCAAAGCCTCCAGGTTAAAGAGTCA 31 6 1 GCCTCCAGGT 0.978656 -113 TCCAGGTTCAGCCTCAAGTTCCCTTCCATC 32 120 0 GCCTCAAGTT 0.438435 -20 CTAGATACCTCCCGGTGAAGTTAAAC 33 205 0 ACCTCCCGGT 0.982036 -16 AGTTTACCTCCATTTCTCATTGTTA 40 72 0 ACCTCCATTT 0.714111 -15 ********** Masking position 4 Map Score: 11.3134 Number of sites scoring better than the average of aligned sites = 1041 Number in coding regions = 977 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 8 ATGAAAATCCTTAAAATTTATTACTAAATC 4 94 1 TTAAAATTTA 0.84541 -156 TTGAAATAAATGAAAAATAAATTAA 14 6 0 TGAAAAATAA 0.808438 -174 ACTGACCTTCTGAAAAATTAAGCCCGCCCT 14 82 0 TGAAAAATTA 0.86854 -98 TAACCGAAAGTTAAAAATTAACTGACGGTT 18 17 0 TTAAAAATTA 0.780358 -118 TAACTTTCGGTTAAAATTTAACTTGTAGTT 18 34 1 TTAAAATTTA 0.84541 -101 TGATTATTTTTTAATATTTAACGTGGTTTG 20 93 0 TTAATATTTA 0.711004 -208 TATCACCAAATGAAAATTAAGTATTACAGA 29 13 1 TGAAAATTAA 0.865878 -257 TAATACTTTATTAATATTTAGGTAATATTT 29 48 0 TTAATATTTA 0.711004 -222 AGCTTCTAAATGAATATTAATCAATCCATG 30 21 1 TGAATATTAA 0.725826 -96 ATTCCTCAATTGAAAAATTATTGCGGCCTA 33 85 0 TGAAAAATTA 0.86854 -136 TGATAAACGCTGAATATTAACCGCGTTATT 33 114 1 TGAATATTAA 0.725826 -107 CTAGTTATTATGAATAATAACGCGGTTAAT 33 129 0 TGAATAATAA 0.727325 -92 CTAGAACTATTTAAAATTTACTATTTTTGT 39 37 1 TTAAAATTTA 0.84541 -81 ********** Masking position 6 Map Score: 9.65416 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 16 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 9 TTTAAAGATTTCTGAGGATTGATAGATAAATTT 1 72 0 TCGGATTGAT 0.962812 -107 TTTGTTTTTTTCTGTGGTCTGATATTCAGAAAA 12 28 0 TCGGTCTGAT 0.881695 -139 TATATAACTTTCCATGGTTCGATGAAGTCACTG 14 108 0 TCGGTTCGAT 0.980618 -72 CCAGTTAGGATCACTGGATTGAAGC 20 3 0 TCGGATTGAA 0.931419 -298 ATGATTCATATCCATGGATTGATTAATATTCAT 30 30 0 TCGGATTGAT 0.962812 -87 TGGATATGAATCATGGGATGGATTTGCATCATG 30 49 1 TCGGATGGAT 0.921032 -68 GCGCAGGCCTTCGAGGGTTCGAATCCCTTCCCC 38 105 1 TCGGTTCGAA 0.963689 -160 AAGGCATAGGTCGGGGGTTCGAATCCCCCCTAA 38 213 1 TCGGTTCGAA 0.963689 -52 GTTATTATTATCTACGGTTCCATCTATAAAGTA 41 46 1 TCGGTTCCAT 0.880259 -27 ** ******** Masking position 12 Map Score: 5.68904 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 13 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 10 CTCAGAAATCTTTAAATGTGTTTAATACCG 1 89 1 TTTAAATGTG 0.830923 -90 TCAACCTGGAATTTGAGGTGAA 15 40 1 ATTTGAGGTG 0.866008 -12 TTGCGTGGAATTGTGATGTGATGGTGGGAT 17 15 1 TTGTGATGTG 0.664859 -89 TAAAATTGGATTTTATTGTGATTTTCATGT 20 226 1 TTTTATTGTG 0.64637 -75 TATTATTTTTATTAGAGGTGTATCT 22 222 1 ATTAGAGGTG 0.848001 -15 TTCCCTGTTTTTTAGAAGTGATCTT 23 55 1 TTTAGAAGTG 0.692689 -15 TAAACTATTCTTTAGTGGTGATTTA 24 32 1 TTTAGTGGTG 0.848001 -15 CGCAGCTACTTTTTAATGTGTTATGGGCGT 29 130 0 TTTTAATGTG 0.850597 -140 AACCACAGACATTTGAGGTGACGTAAT 30 100 1 ATTTGAGGTG 0.866008 -17 GATATATGTTTTTAGATGTGAGGTGGTGGG 31 96 1 TTTAGATGTG 0.915663 -23 TCAGTGTCCTTTTTATGGTGAAACTTTATC 32 56 0 TTTTATGGTG 0.745256 -84 CCCACAAATCTTTATATGTGACGGATCTTT 35 35 1 TTTATATGTG 0.548006 -76 TTTCTACTGATTTTAAGGTGTTCTA 38 250 1 TTTTAAGGTG 0.901111 -15 ********** Masking position 2 Map Score: 7.1304 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 66 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 11 ATCCTGGCTTCCCGGTGGGAACCAGTCTCTT 1 144 0 CCCGGTGGGA 0.948606 -35 GAGAATGCTCCCGGTGCGTGCCTGGCACGG 2 31 0 CCCGGTGCGG 0.987171 -20 ATCATACCTCCTTAGGGTGCTG 16 4 0 TCCTTAGGGG 0.748731 -19 TCCGTTGCGTGGAATTGTGAT 17 1 1 TCCGTTGCGG 0.938425 -103 ATATAAATCTTCCGGTGCAAAATGTTTTAAA 18 70 1 TCCGGTGCAA 0.844207 -65 ATGGGGACAGCCCTTTGCAGGGTTAAATGAA 22 143 1 CCCTTTGCAG 0.842899 -94 GAGGCTGAGTTCCTTTGCAAGTCTGTAGACC 27 140 0 TCCTTTGCAG 0.738333 -38 ATCACTGCCTCCCTGAGGGAATAATAAAGAT 29 170 0 CCCTGAGGGA 0.890236 -100 TCTATAAAGATCCGGAGAGGGTGAGAGAATC 34 86 1 TCCGGAGAGG 0.722716 -66 TAATATCGCACCCTGAGCGGAGGGATGACCA 36 91 1 CCCTGAGCGA 0.946166 -210 GTGAACTAAACCCTGTGCGCAGAGGAATTTA 39 86 1 CCCTGTGCGA 0.968734 -32 ********* * Masking position 3 Map Score: 4.92698 Number of sites scoring better than the average of aligned sites = 320 Number in coding regions = 308 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 12 ATTCACATTCATAGGGTTATAAAAAAATTT 1 48 1 ATAGGGTTAT 0.950491 -131 AATACCGGGAAGGGGGTTTTCAAATAAAAC 1 112 1 AGGGGGTTTT 0.914224 -67 ATACTCCATTAGAGGGTTAAC 10 2 0 AGAGGGTTAA 0.844019 -83 CTTAAGAAAAAAAGGGTTTTGTTTTTTTCT 12 48 0 AAAGGGTTTT 0.893086 -119 ATTAGAATTAATAGAGTTATCTATATAAAA 13 39 0 ATAGAGTTAT 0.68196 -45 TATGGTATATAAAGGGTTTTCATTTAACCC 22 162 0 AAAGGGTTTT 0.893086 -75 AGGACTCATGGGGTTATTACGGCAGCC 26 8 1 ATGGGGTTAT 0.91578 -140 ATTAATTTGGAGAGGGTTATTGA 35 98 1 AGAGGGTTAT 0.967943 -13 ********** Masking position 1 Map Score: 3.11397 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 68 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 13 TTTTCTGGACTATGTTGCAGATGCAACAGTT 3 15 1 TATGTTGCAA 0.821851 -65 AAGACATGATGTGGAATGAAAATGG 8 5 1 CATGATGTGA 0.79541 -51 GTTAACATGACATGTTGTAGATTCT 15 5 0 CATGTTGTAA 0.906573 -47 AAATCCATCCCATGATTCATATCCATGGATT 30 43 0 CATGATTCAA 0.856104 -74 TGGCTGGAACCATGATGCAAATCCATCCCAT 30 61 0 CATGATGCAA 0.978862 -56 TGGTTCCAGCCATGTTGCATAACCACAGACA 30 80 1 CATGTTGCAA 0.972633 -37 GAAACTTTATCATGATGCACAGATAAAGGTT 32 36 0 CATGATGCAA 0.978862 -104 ********* * Masking position 2 Map Score: 2.22307 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 15 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 14 CCGGGAAGCCAGGATTCTGGCTTCACAGG 1 160 1 AGATTCTGGC 0.96504 -19 ACCTCTTAATAAAATTATGGCCTTTTTTACT 4 188 0 AAATTATGGC 0.950136 -62 TTATTTCAATAAAATTCAGGTCAGGAGCCAG 14 27 1 AAATTCAGGT 0.665868 -153 GAATTCAGGCAATCTTCTGGCTCCTGACCTG 14 43 0 AACTTCTGGC 0.928303 -137 CCTTGAAGGAAGAATTCAGGCAATCTTCTGG 14 54 0 AGATTCAGGC 0.909955 -126 ATCCAGAGTTAATATTCTGGCAGGAAATTAT 20 136 0 AAATTCTGGC 0.979899 -165 ACAATAATCTAAAATTATGGCCATGCGGCCC 20 173 0 AAATTATGGC 0.950136 -128 CCTCAATTGAAAAATTATTGCGGCCTATCAT 33 81 0 AAATTATTGC 0.680291 -140 ** ******** Masking position 1 Map Score: 2.66229 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 34 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 Motif number 15 GCTGATCTATCTGGTGGGAAAACATATA 3 62 0 ATCTGGTGGG 0.902238 -18 CCAGGACATGATGGGGTGGGAAT 4 4 0 ATGGGGTGGG 0.936055 -246 ATCTTTTTAAAAAAGGTGAGTTAGACCTAA 4 224 0 AAAAGGTGAG 0.807154 -26 GGTACATCATATGAGATGGGAGATTGA 11 34 1 ATGAGATGGG 0.631549 -17 AATTGTGATGTGATGGTGGGATCTGCCCGG 17 23 1 TGATGGTGGG 0.677876 -81 GGGAAAATAAAAAAGGAGGGTAATTA 21 7 0 AAAAGGAGGG 0.682232 -140 ATTAAAAGGAATGAGGTGGGAGTA 22 5 0 ATGAGGTGGG 0.956052 -232 TGAGGAATCTAACAGGTGAGGAATT 25 16 1 AACAGGTGAG 0.737977 -15 TTTAGATGTGAGGTGGTGGGTGT 31 106 1 AGGTGGTGGG 0.955203 -13 AAAGATCCGGAGAGGGTGAGAGAATCAGCA 34 91 1 AGAGGGTGAG 0.772786 -61 CCTTTTTAATAAATGGTGGGGATGTGCCAG 36 168 0 AAATGGTGGG 0.932042 -133 ********** Masking position 5 Map Score: 3.42199 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 191 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604