AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -icrp_mthe_opreg_300.orf -g0.495 -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 = 0.495 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MTH101 231 unknown #2 MTH243 231 conserved protein #3 MTH248 195 conserved protein #4 MTH249 64 conserved protein #5 MTH250 23 tRNA intron endonuclease #6 MTH251 54 tryptophanyl-tRNA synthetase #7 MTH252 22 conserved protein #8 MTH253 75 threonine synthase #9 MTH478 49 sulfate transport system permease protein #10 MTH479 136 conserved protein #11 MTH480 91 unknown #12 MTH631 143 UDP-glucose 4-epimerase #13 MTH644 145 conserved protein #14 MTH645 24 collagenase #15 MTH648 65 ribosomal protein L37 #16 MTH649 300 conserved protein #17 MTH700 110 conserved protein #18 MTH702 27 acetyl-CoA synthetase related protein #19 MTH816 43 sporulation protein IVFB related protein #20 MTH817 56 conserved protein #21 MTH853 22 conserved protein #22 MTH855_MTH856 172 MTH855: inosine-5'-monophosphate dehydrogenase related protein VIII, MTH856: zinc metalloproteinase #23 MTH922 67 unknown #24 MTH923 21 unknown #25 MTH925 32 conserved protein #26 MTH927 139 ferredoxin #27 MTH928 300 cobalamin biosynthesis protein N #28 MTH978 95 NADP-dependent glyceraldehyde-3-phosphate dehydrogenase #29 MTH980 74 conserved protein #30 MTH981 21 aminopeptidase P #31 MTH982 104 unknown #32 MTH1142 300 H(2)-dependent N5,N10-methylenetetrahydromethanopterin dehydrogenase #33 MTH1143 104 biotin synthetase (BioB) #34 MTH1145 78 conserved protein #35 MTH1147 38 conserved protein #36 MTH1338 81 peptidyl-prolyl cis-trans isomerase B #37 MTH1444 64 acetolactate synthase, large subunit #38 MTH1591 30 phosphonopyruvate decarboxylase #39 MTH1592 21 conserved protein #40 MTH1593 205 ribosomal protein S3a #41 MTH1594 72 conserved protein #42 MTH1598 300 conserved protein #43 MTH1850 105 fumarate reductase Motif number 1 GGATATATGTACCTGCAGGTACTTCACATTT 1 25 1 ACCTGCAGTA 0.525843 -207 GGTAGAACTGCCCTGCCCTTAGAAGGGTACA 1 199 0 CCCTGCCCTA 0.955496 -33 GAATCATGGGCCATCCCCTGGGCACAGCCTC 2 20 0 CCATCCCCGG 0.865546 -212 GTCACACTCTCCCCTGGATTATAGGTA 2 215 0 CTCTCCCCGG 0.820307 -17 AAACCAGCACCCCTCCAGCGGAATATTCCCC 3 101 0 CCCTCCAGGG 0.982973 -95 CAAACCCTGACCCTCCAGGGGAAATCCTTCA 3 164 0 CCCTCCAGGG 0.982971 -32 ACCTCCCGTGAGTGCTGGTTG 5 13 0 ACCTCCCGGA 0.892 -11 ATAACAGTCCCCCTCCACATACTGACCTGGA 13 84 0 CCCTCCACTA 0.941338 -62 GTTGATCCACCCTTCCCCTTACAATTAAAT 15 10 0 CCTTCCCCTA 0.918621 -56 AGCTGAGGACCCCCGCAGTTATAATGGATAT 26 46 0 CCCCGCAGTA 0.735329 -94 AGGGCTTTAACCTTGCCGTTATATTTATAAA 27 70 1 CCTTGCCGTA 0.899204 -231 AGAGACGTAGCCCTGCTCTGGATTATAGATT 28 45 0 CCCTGCTCGG 0.873347 -51 TTAAGGGCAGCCTTCCAGTTAGGATCACTGG 32 11 1 CCTTCCAGTA 0.869582 -290 AGGTCAACCTCCTCCCCCTGGAGGAGGCCAG 41 24 0 CCTCCCCCGG 0.8511 -49 AACTGGGAGGCCCTCCCGAAATGGAGGTCAA 41 48 0 CCCTCCCGAA 0.902525 -25 GTTCTCATGGCCCTCCTGTGGGGCGTTATCA 42 12 0 CCCTCCTGGG 0.954821 -289 GTCTCGGGCACCTTGCCGTTGTGGTGGATGT 42 68 0 CCTTGCCGTG 0.934926 -233 GGTCTCCCTCCCGGTGTGCAGCAGGT 42 285 0 CCCTCCCGTG 0.990652 -16 ******** ** Masking position 6 Map Score: 19.6111 Number of sites scoring better than the average of aligned sites = 1132 Number in coding regions = 1072 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 2 TCCCGGGCATCACGGGACCCGGGGCCCCTCA 3 54 0 CACGGACCCG 0.894286 -142 TCCCTGGAAAACCAGCACCCCTCCAGCGGAA 3 109 0 ACCAGACCCC 0.886456 -87 CCTCCATTAACTCAGAACACCTATATCGACA 10 107 0 CTCAGACACC 0.94151 -30 TACCCACAAAAACAGGCCACCAAACCTTATT 12 78 1 AACAGCCACC 0.722815 -66 TTTTAAAAATAACAGTCCCCCTCCACATACT 13 92 0 AACAGCCCCC 0.923275 -54 AGGGTCCGCCCTGGGATCCCCCCATCCATGA 16 142 0 CTGGGTCCCC 0.811009 -159 TACTACCACACAGGGGACACCGCCTGG 18 11 1 CAGGGACACC 0.905855 -17 ATGATTTATTCATAGCACCCCATATAATAGA 19 21 1 CATAGACCCC 0.952469 -23 ATTTTGAGTTCACAGAACCACTGCATGTGAA 22 88 0 CACAGACCAC 0.884037 -85 CTGAAAGTAATTCAGCACACCTTTCAGGAGC 23 36 0 TTCAGACACC 0.780386 -32 TACATGGCAGCTGAGGACCCCCGCAGTTATA 26 54 0 CTGAGACCCC 0.968298 -86 CAGATTTCATCATGGCACCCCATGTTCTATA 31 44 1 CATGGACCCC 0.937513 -61 TCAACATTAATACAGGTCCCCATATAAATTT 36 22 0 TACAGTCCCC 0.856621 -60 TCAAATGGATCGGGACCCCTC 39 9 1 ATCGGACCCC 0.941129 -13 TTCATGACCACACAGCACCCCAAACCACCAT 40 33 1 CACAGACCCC 0.993114 -173 ACATACCGGATAGAGAACCCCCCTCAATAAC 42 218 1 TAGAGACCCC 0.929035 -83 ***** ***** Masking position 5 Map Score: 16.4444 Number of sites scoring better than the average of aligned sites = 553 Number in coding regions = 525 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 3 AAAAATTTTAATTAATAATCATTATAAATTGAAGT 1 69 1 ATAAATTTAT 0.969845 -163 TTCTCATGGTACTTACAATATTTATTTACCATCAG 2 157 1 ATAAATTTAT 0.969854 -75 TGATAAGGTGAATCAGAAACTTTATTCTTACCGGT 8 48 1 ATAAAATTAT 0.91961 -28 GACATTTATCATTAATAATCATTATTAATTTTTCC 17 65 1 ATAAATTTAT 0.969845 -46 GGTTCTGTGAACTCAAAATATTTAAATGAACATCC 22 100 1 ATAAATTTAA 0.91961 -73 GGACCCCCGCAGTTATAATGGATATCCTCACGTAT 26 36 0 ATAAATATAT 0.878182 -104 TGATTGATCGATTCAGAATTTTTCTGAAACGTTTA 27 34 1 ATAAATTTCT 0.846695 -267 AACTCAAGAAATTAAAAATTTTTATAAATATAACG 27 86 0 ATAAATTTAT 0.969359 -215 ATATGAAAATAATCATAATTATTAAGATATTAATA 32 71 0 ATAAATTTAA 0.91961 -230 ATAATTTTCAAATCAAAAAACTTATAAGGAGAATT 32 204 0 ATAAAATTAT 0.91961 -97 TTGAACCTAAACTGATAATAAATATTTATGTTGAG 36 49 1 ATAAATATAT 0.878183 -33 TATCAGTTAAAATCACAAACCTTAATATGTGTTGA 43 33 1 ATAAAATTAA 0.802646 -73 * * * *** **** Masking position 8 Map Score: 9.35376 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 3 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 4 AAATTTTTCTGTTCATGTGGCAAATGTGAAGTACC 1 42 0 GTTCTGGGAT 0.993065 -190 AGAGTGTTGAGTTCCTGAGGAATATTATACCTTGA 3 22 1 GTTCTGGGAT 0.993065 -174 GGCCTTCCGTGTTCCTGGGGAATATTCCGCTGGAG 3 85 1 GTTCTGGGAT 0.993065 -111 ATTATTAATTTTTCCTGACGCTGATGAGGTGTAAT 17 85 1 TTTCTGCGAT 0.902575 -26 ACAGTACTGTTTTCATGAGGTCCATTAAGAAAGAT 26 87 1 TTTCTGGGAT 0.982448 -53 AAATTTTTAATTTCTTGAGTTACATACATCGGTAA 27 100 1 TTTCTGGTAT 0.927551 -201 TTTCCCTTAAGTTCATGCGTTCCATGTAC 35 5 0 GTTCTGGTAT 0.970373 -34 CCACTACCATGTTCATGTGGAGATTATTTAAGAAA 42 147 1 GTTCTGGGTT 0.962494 -154 **** ** ** ** Masking position 6 Map Score: 8.87016 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 20 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 ATGACGGCTTAAGCAACAGAAATGACTTAA 6 21 1 AAGCAACAGA 0.884402 -34 CCATTCATAAAATGAACAGGG 16 2 0 AATGAACAGG 0.788836 -299 AAAGCAGATTAAGGAACAGACTGCAGACCA 16 29 0 AAGGAACAGA 0.913785 -272 AAATCTAACTAACGAGCTGAAAATCTTCCA 16 247 0 AACGAGCTGA 0.87052 -54 GCTATCCATAAATGAACTGATTACTGGTAT 22 137 0 AATGAACTGA 0.927973 -36 TGAATCGATCAATCAACTGAAGAGGCCATT 27 19 0 AATCAACTGA 0.902912 -282 TTTCAATCCCAAGCAGCTGAAACTGGTGTT 33 82 1 AAGCAGCTGA 0.944714 -23 ATATAACAGGAAACAGCTGATCAAAA 34 63 1 AAACAGCTGA 0.892166 -16 AACTTAAGGGAAAGAGCAGAAA 35 27 1 AAAGAGCAGA 0.856004 -12 AACACCGTAAAAACAGCTGGATTTAACATA 40 168 0 AAACAGCTGG 0.822231 -38 AAGGAACTGGGAGGCCCTCC 41 63 0 AAGGAACTGG 0.919514 -10 AAAACTTCAGAATGAACTGAATTTTAATTG 43 72 0 AATGAACTGA 0.927973 -34 ********** Masking position 5 Map Score: 9.43622 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 89 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 ATGTGTTTTTCCAGTTATCAGTTTATCACCCCGGCA 2 58 1 CATATAGTTT 0.666327 -174 GTTTCTGATTCACCTTATCAATATGTACCTGAATTA 8 32 0 CCTATAATTT 0.962249 -44 ATCTCTCTCCCCAATAATGTATTTTTTCACTGAACA 11 48 0 CATATTATTT 0.758024 -44 AACATCACCTCAGATTAATATATGAAATCAGAC 12 8 1 CTAATAATTT 0.788522 -136 CTCTTCACCCATCTTTAATATGTGGACCATCAC 13 123 0 CCTTTAATTT 0.877687 -23 ACTTTACGTGCACCACATGCATCTCTCATGGATGGG 16 117 1 CCAATCATTT 0.834102 -184 AATAAAGTTTCTCATCTTAAATGTTTAAGTTCCACA 17 20 0 CCTTTAATTT 0.877687 -91 ATCATTAATAATCATTATTAATTTTTCCTGACGCTG 17 72 1 ACTATAATTT 0.529436 -39 TTTCAATTTTTTTATTTTTCAGGAAATAC 26 4 1 CATTTTATTT 0.468618 -136 TTCCACAGGTCCATATATAAATCTTTCTTAATGGAC 26 106 0 CAAATAATTT 0.876264 -34 TATGCAATAACGCGTGATGAATGTATTAAATTTTCA 27 165 1 CCTATAATTT 0.962249 -136 TTATTTAAGACTTTTTATTAATTTTTTTATTACATA 27 235 0 CTTATAATTT 0.835383 -66 ATCATGGCACCCCATGTTCTATATATAAGGAGGTAT 31 52 1 CCTTTTATTT 0.699124 -53 GCCACAGATCCGTGATATTAATATCTTAATAATTAT 32 56 1 CTAATAATTT 0.788522 -245 TGAATAAATTCTCCTTATAAGTTTTTTGATTTGAAA 32 198 1 CCTATAGTTT 0.840297 -103 TGAAAATTATCAAAAAATATATTTATATTGGAAACC 32 229 1 CAAATTATTT 0.697106 -72 TAATACAGGTCCCCATATAAATTTTTGGTGATATC 36 10 0 CCAATAATTT 0.949305 -72 TTAACCACCTCAACATAAATATTTATTATCAGTT 36 58 0 CCAATAATTT 0.94931 -24 AACATAAATTCAAAAAATTCATATTTAACTGGTTAA 40 138 0 CAAATCATTT 0.656145 -68 * * * ** *** * * Masking position 8 Map Score: 12.4901 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 48 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 7 ACAGTGGATATATGTACCTGCAGGTACTTC 1 20 1 TATGTACCTG 0.961521 -212 ACCTTATCAATATGTACCTGAATTAACCAG 8 27 0 TATGTACCTG 0.961521 -49 GATATGTATATATGTCCATGTCGATATAGG 10 89 1 TATGTCCATG 0.609991 -48 CACCAAACCTTATTTACATGTTAACAGAAA 12 95 1 TATTTACATG 0.840522 -49 AGCCGGATTATATTTAAATCTAACTAACGA 16 262 0 TATTTAAATC 0.566999 -39 GAACTCAAAATATTTAAATGAACATCCATA 22 108 1 TATTTAAATG 0.741326 -65 AAGATTTATATATGGACCTGTGGAATATAC 26 117 1 TATGGACCTG 0.896736 -23 ATTACCGATGTATGTAACTCAAGAAATTAA 27 106 0 TATGTAACTC 0.860008 -195 AAGGAGAATTTATTCACCTGTGGCAATTTC 32 184 0 TATTCACCTG 0.717397 -117 TCATACTGTTTATGGACCTGTTTTTCTCTG 34 30 0 TATGGACCTG 0.896736 -49 GATAAGGGAGTATTTAAATCTTGACATGGT 40 59 0 TATTTAAATC 0.566999 -147 ACTGGCGGTGTATGTAACTCTAAATCATGG 40 108 1 TATGTAACTC 0.860008 -98 AAAAAATTCATATTTAACTGGTTAACCATG 40 133 0 TATTTAACTG 0.87877 -73 ********** Masking position 2 Map Score: 9.13732 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 208 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 CATCTACATTAATATCAGTTTCTAAATGTTAC 1 142 0 AAATCAGTTC 0.938158 -90 TAGATCACCTTCGGTAGAACTG 1 220 0 TAATCACTTC 0.858079 -12 CATGAGAAAAAAAATCAGATTCTATACTGACC 2 133 0 AAATCAGTTC 0.938158 -99 AGTTCCCTGGAAAACCAGCACCCCTCCAGCGG 3 111 0 AAACCAGACC 0.792822 -85 TTTTTCACTGAACATCAGATTCATGGACAAAC 11 30 0 AAATCAGTTC 0.938158 -62 GGTTTCTGAAAAACCCACCTTCAATGTTCCAG 13 17 1 AACCCACTTC 0.901143 -129 TTATACCACATCCGGTGCTATCC 22 160 0 TAACCACTCC 0.881901 -13 TTTAAACCAGGATCTGATACC 24 3 1 TAACCAGATC 0.760128 -19 CTCAACACCACATTCCAGTGTAACA 29 60 0 AAACCACTTC 0.966503 -15 TTTAACACCAGTTTCAGCTGCTTGG 33 90 0 AAACCAGTTC 0.971027 -15 AACAGCAGAGAAAAACAGGTCCATAAACAGTA 34 25 1 AAAACAGTCC 0.676613 -54 GATTAACCCACCTTCCTAGATTTAT 38 16 0 TACCCACTTC 0.808429 -15 GTTTATGATCAATATCACCTGCTGCACACCGG 42 269 1 AAATCACTGC 0.73145 -32 ** ***** *** Masking position 7 Map Score: 8.45908 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 77 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 9 TTATCACCATTCCATATATCTCTCTCCCCA 11 71 0 TCCATATATC 0.860475 -21 ATGGTCTGATTTCATATATTAATCTGAGGT 12 17 0 TTCATATATT 0.666663 -127 ACAGTCCCCCTCCACATACTGACCTGGAAA 13 82 0 TCCACATACT 0.859757 -64 AAAGTGATGGTCCACATATTAAAGATGGGT 13 120 1 TCCACATATT 0.835434 -26 ATGTTTAAGTTCCACATAATTAAAT 17 6 0 TCCACATAAT 0.895944 -105 TTCATAGCACCCCATATAATAGAAC 19 29 1 CCCATATAAT 0.855305 -15 TAAATGAACATCCATATACCAGTAATCAGT 22 122 1 TCCATATACC 0.881621 -51 ATTCCACAGGTCCATATATAAATCTTTCTT 26 113 0 TCCATATATA 0.732416 -27 GTATTAAATTTTCATATAATTATTACTTAA 27 187 1 TTCATATAAT 0.772296 -114 TATGATTATTTTCATATAATATTATATGGA 32 89 1 TTCATATAAT 0.772296 -212 CCATCCATTATCCATATAATATTATATGAA 32 99 0 TCCATATAAT 0.949264 -202 AACAGTATGAACCATATAACAGGAAACAGC 34 50 1 ACCATATAAC 0.547824 -29 AATACAGGTCCCCATATAAATTTTTGGTGA 36 15 0 CCCATATAAA 0.594592 -67 CCGAGACGTCTCCATATACTGTTTGATTTC 42 92 1 TCCATATACT 0.930176 -209 ********** Masking position 6 Map Score: 10.1935 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 59 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 10 ACGGGACCCGGGGCCCCTCAAGGTATAATATTC 3 41 0 GGCCCCTAAG 0.901384 -155 CTGGGGTGTCAGCGCCCTGAAGGATTTCCCCTG 3 147 1 ACGCCCTAAG 0.866218 -49 ATCCATGGAAGACCCCTTTAACAGATGCAGCCA 4 22 1 GCCCCTTAAA 0.719774 -43 AGAACATGGGATCGTCCTGAAAGATAAAGAAGG 10 39 0 ACGTCCTAAG 0.801799 -98 CCTTTTTTCTGGCCTCCTAAACATCATCTTTCC 13 54 1 GCCTCCTAAA 0.960575 -92 AAAAATAACAGTCCCCCTCCACATACTGACCTG 13 86 0 GCCCCCTCAA 0.942818 -60 GTTCTAATCCTCCTTAAAATCAGTTAATC 15 47 0 ACCTCCTAAA 0.945233 -19 AATCATAAGCACCCACCTACAGAATTAATAAGA 22 35 0 ACCACCTCAA 0.792872 -138 TGCACTGGAAACGCTCCTGAAAGGTGTGCTGAA 23 24 1 AGCTCCTAAG 0.801799 -44 TTTCTTAATGGACCTCATGAAAACAGTACTGTT 26 86 0 GCCTCATAAA 0.738892 -54 AGGCCCCATCAAAGAACAGCAGAG 34 2 1 GCCCCATAAG 0.864753 -77 TTAACCACCTCAACATAAATATTTA 36 67 0 ACCACCTAAA 0.900533 -15 GGATAGCACTGGCCTCCTCCAGGGGGAGGAGGT 41 16 1 GCCTCCTCAG 0.93566 -57 ATGACCTCACATCCACCACAACGGCAAGGTGCC 42 60 1 ACCACCAAAG 0.539173 -241 CGGATAGAGAACCCCCCTCAATAACTCAGTGTA 42 224 1 ACCCCCTAAA 0.965065 -77 * ****** ** * Masking position 11 Map Score: 10.3494 Number of sites scoring better than the average of aligned sites = 782 Number in coding regions = 736 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 11 GTCATCACCACAGTGGATATAT 1 3 1 CATCACCACA 0.984289 -229 ACATTTGCCACATGAACAGAAAAATTTTAA 1 50 1 CATGAACAGA 0.723034 -182 AACATCACCTCAGATTAATATA 12 3 1 CATCACCTCA 0.964606 -141 CTCAACACCACATTCCAGTGTA 29 63 0 CAACACCACA 0.928603 -12 TCATCACCAGAGGACAGAGAG 30 11 0 CATCACCAGA 0.963551 -11 TGTTCATATTCATGACCACACAGCACCCCA 40 25 1 CATGACCACA 0.979464 -181 GATGATTAAACATGACCTCACATCCACCAC 42 49 1 CATGACCTCA 0.954021 -252 ********** Masking position 5 Map Score: 6.48702 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 59 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 12 CGTGATGCCCGGGAGGCCTTCCGTGTTCCT 3 71 1 GGGAGGCCTT 0.987843 -125 AGGTCTTTGTGGTCTGCCTTTGCATAGCTT 12 49 0 GGTCTGCCTT 0.92283 -95 TGTTTTTGTGGGTAGGTCTTTGTGGTCTGC 12 62 0 GGTAGGTCTT 0.836155 -82 TCCATTCCAGGGTCCGCCCTGGGATCCCCC 16 151 0 GGTCCGCCCT 0.922639 -150 TTAAGGGCAGCCTTCCAGTTAGGA 32 5 1 GGGCAGCCTT 0.977554 -296 ATCCTCCTTTGGGAAGCCTTTACCATCCAT 32 121 0 GGGAAGCCTT 0.97302 -180 AAGGAACTGGGAGGCCCTCCCGAAATGG 41 55 0 GGGAGGCCCT 0.982035 -18 ********** Masking position 10 Map Score: 3.91087 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 162 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 13 AAACTGATAACTGGAAAAACACATGTAACC 2 52 0 CTGGAAAAAC 0.926542 -180 ATAGAGTTCCCTGGAAAACCAGCACCCCTC 3 117 0 CTGGAAAACC 0.973909 -79 AACCCGGTTTCTGAAAAACCCACCTTCAAT 13 12 1 CTGAAAAACC 0.924436 -134 TGAGTCAATGATGGTAAAGCAGATTAAGGA 16 44 0 ATGGTAAAGC 0.745904 -257 AACTCGAGCGATGAAAAACCGAATGGATAT 20 23 1 ATGAAAAACC 0.70666 -34 GTTCACTGCACTGGAAACGCTCCTGAAAGG 23 18 1 CTGGAAACGC 0.959086 -50 CTGGAAACACCCCGTAAAGG 28 86 0 CTGGAAACAC 0.91231 -10 TCATATTTAACTGGTTAACCATGATTTAGA 40 126 0 CTGGTTAACC 0.755308 -80 CTGATAACGCCCCACAGGAG 42 1 1 CTGATAACGC 0.801194 -300 ********** Masking position 7 Map Score: 2.83938 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 190 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 14 CGGGACCCGGGGCCCCTCAAGGTATAATAT 3 43 0 GGCCCCTCAA 0.870431 -153 GAACACGGAAGGCCTCCCGGGCATCACGGG 3 69 0 GGCCTCCCGG 0.967627 -127 CCTTTTTTCTGGCCTCCTAAACATCATCTT 13 54 1 GGCCTCCTAA 0.974843 -92 GGCACTAAATGGCCTCTTCAGTTGATTGAT 27 12 1 GGCCTCTTCA 0.89758 -289 GGATGGTAAAGGCTTCCCAAAGGAGGATAA 32 123 1 GGCTTCCCAA 0.912135 -178 GGATAGCACTGGCCTCCTCCAGGGGGAGGA 41 16 1 GGCCTCCTCC 0.935367 -57 ATTTCGGGAGGGCCTCCCAGTTCCTT 41 57 1 GGCCTCCCAG 0.985152 -16 ********** Masking position 6 Map Score: 1.73498 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 214 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 15 CTTTAATCAGTACTTGTGTATGGC 4 51 0 AATCAGTACT 0.753253 -14 TCACCTTATCAATATGTACCTGAATTAACC 8 29 0 AATATGTACC 0.683865 -47 AAAATCAGTTAATCTGTAAAGTTGATCCAC 15 31 0 AATCTGTAAA 0.682 -35 TTAGAGCAAGAATATGTAATAAAAAAATTA 27 223 1 AATATGTAAT 0.853017 -78 TATAATTTTGAATCTATAATCCAGAGCAGG 28 35 1 AATCTATAAT 0.701619 -61 GCCATGATGAAATCTGTACTGAACCAGGCA 31 30 0 AATCTGTACT 0.955937 -75 GAAACCGATTAATCTGTACTACTAATAATA 32 259 1 AATCTGTACT 0.955937 -42 TTTCCTATAAAATATATACTTTCAAATAA 37 10 0 AATATATACT 0.614385 -55 TTTTATAGGAAATATGTCATTAATAATAAT 37 28 1 AATATGTCAT 0.713991 -37 CTTGAACGGAATCTGTCATTATTATTAAT 37 46 0 AATCTGTCAT 0.854009 -19 ********** Masking position 7 Map Score: 1.6874 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 38 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172