AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00970_mgen_reg_300.orf -o00970_mgen_300.ace -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -g0.32 -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 = 0.32 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: MG035 28 histidyl-tRNA synthetase MG301 30 glyceraldehyde-3-phosphate dehydrogenase (gap) MG466 25 ribosomal protein L34 (rpL34) Input sequences: #1 MG001 300 DNA polymerase III, subunit beta (dnaN) #2 MG003 84 DNA gyrase subunit B (gyrB) #3 MG014 239 ABC transporter, ATP-binding protein #4 MG015 46 ABC transporter, ATP-binding protein #5 MG017 65 ATP-dependent RNA helicase, putative #6 MG018 188 ATP-dependent RNA helicase, putative #7 MG019 41 heat shock protein (dnaJ) #8 MG109 59 serine/threonine protein kinase, putative #9 MG126 35 tryptophanyl-tRNA synthetase (trpS) #10 MG136 48 lysyl-tRNA synthetase (lysS) #11 MG194 300 phenylalanyl-tRNA synthetase, subunit alpha (pheS) #12 MG254 175 DNA ligase #13 MG267 33 conserved hypothetical protein #14 MG268 150 conserved hypothetical protein #15 MG269 300 conserved hypothetical protein #16 MG283 300 prolyl-tRNA synthetase (proS) #17 MG292 57 alanyl-tRNA synthetase (alaS) #18 MG294 117 conserved hypothetical protein #19 MG296 119 conserved hypothetical protein #20 MG298 202 P115 protein #21 MG304 176 ABC transporter, ATP binding protein #22 MG305 87 heat shock protein 70 (dnaK) #23 MG309 53 lipoprotein, putative #24 MG335.1 58 M. genitalium predicted coding region MG335.1 #25 MG345 43 isoleucyl-tRNA synthetase (ileS) #26 MG364 63 conserved hypothetical protein #27 MG377 46 conserved hypothetical protein #28 MG378 28 arginyl-tRNA synthetase (argS) #29 MG468.1 62 ABC transporter, ATP-binding protein #30 MG469 300 chromosomal replication initiator protein (dnaA) Motif number 1 TCTATTTTAGAGAGTATTAATTATTACTATAA 1 81 1 AATATTAATT 0.82831 -220 CATTTTTGATTAAGTATTAATTTCTGGGTTAT 1 233 0 TATATTAATT 0.858855 -68 ATCAAAAATGAAAATATTAATTAATAAAAGTG 1 255 1 AATATTAATT 0.82831 -46 AATTATTATAACAATTTTAATTTAACCAAAAT 3 173 1 AATTTTAATT 0.897368 -67 TTGTCTTTCAACACTATTAAATTTAT 5 5 0 AATATTAAAT 0.844141 -61 TGAAAGACAAACATTATTAATTTTTGATCAGC 5 27 1 AATATTAATT 0.82831 -39 TTTAATGGGAATGTTTTCAAATCTTCTTAAAT 6 101 0 AGTTTCAAAT 0.600667 -88 ATCATCAAAAACAGTTTTAAAAAGCGCAATTT 6 143 0 AATTTTAAAA 0.886137 -46 TTGTTGAAAATAAGTATCAAATTGAAAAGCTT 8 23 1 TATATCAAAT 0.709045 -37 TCAAATTGAAAAGCTTTTAAATAGGGGTGGG 8 39 1 AGTTTTAAAT 0.808296 -21 AATAAAAGATACGCTTTCAAATAAATTAGGTT 11 21 0 AGTTTCAAAT 0.600667 -280 TCCCACTAAATCGCTTTTAATAAAAAATTACA 11 99 0 TGTTTTAATA 0.789731 -202 ATAGTTTAGTTTGTTATTAAATTAAGCAATTA 11 228 0 TGTATTAAAT 0.745825 -73 GGGTTAAGGTTTATTTTTAATAAAAAACCATC 14 108 0 TATTTTAATA 0.897368 -43 TAAAAGTGAATTTCAATATAACCAAGCT 15 7 1 TATTTCAATA 0.757237 -294 AGTGATGTAGTTAGTTTTAAAAAAATTGCTAA 15 105 1 TATTTTAAAA 0.907542 -196 TGCAGTAATATAGATATTAAATAGTAAATTTC 16 70 1 TGTATTAAAT 0.745825 -231 CAGAAGATTGTGAGTTTTAATACAGATGAGAG 16 135 1 TATTTTAATA 0.897368 -166 TGCTTAATTTTAAATGCAATTTACC 17 43 0 TATTTTAAAT 0.925263 -15 CGTTCTTCACTTACTTTTAAAAAGAAAAATAA 18 36 0 TATTTTAAAA 0.907542 -82 AAACTTTTAAATGATATTGCTT 20 1 1 AATTTTAAAT 0.907542 -202 GCAATTAATGTAATTTTTAAATTAAATAAACT 20 41 1 TATTTTAAAT 0.925263 -162 AATAAACTAGTTACTATTAAAACATAGAAGCT 20 65 1 TATATTAAAA 0.844141 -138 TAGCTCTGACTTATTTTTAAAATTTATAAATA 21 96 1 TATTTTAAAA 0.907542 -81 GTTAAAAACCTCAGTTTTAAATACCCAAAACA 21 145 1 TATTTTAAAT 0.925263 -32 AATAAAAATATAAATTTTAAAATTATTGAAAT 23 19 1 TATTTTAAAA 0.907542 -35 TGCACAGTCAAAAATTTCAATAATTTTAAAAT 23 32 0 AATTTCAATA 0.712073 -22 TAATTTTATAAGACTTTTAAAATGTTTAATTA 24 24 1 AATTTTAAAA 0.886137 -35 TTAAAATGTTTAATTATTAATATATAGCT 24 40 1 TATATTAATA 0.82831 -19 GTAAGTTAGATAAATATTAATAAAATTACTCT 25 16 1 TATATTAATA 0.82831 -28 TTAGGTTATTAATTAGTTTTAGAG 26 3 1 AGTATTAATT 0.674516 -61 AGAAACTTATTAAATTTTAATTCCTATATGCG 27 19 0 TATTTTAATT 0.916861 -28 ACACTATTAGAAAATTTTAATTTTG 29 4 0 AATTTTAATT 0.897368 -59 AAGAGGAACAAAATTTTCAATATCATAATAAT 30 34 1 AATTTCAATA 0.712073 -267 * * ******** Masking position 7 Map Score: 40.9497 Number of sites scoring better than the average of aligned sites = 347 Number in coding regions = 263 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 2 TACTATTATATATAACAGAAATTAATGATATTT 1 48 0 TTAAGAAATT 0.471808 -253 ATTAATACTCTCTAAAATAGATACTATTATATA 1 69 0 TTAATAGATA 0.605444 -232 AATAATAGATATTAAAGAAAATAAAAAAATAGA 1 180 1 ATAAAAAATA 0.862455 -121 AAGAAAATAAAAAAATAGAAATAAATATCATAA 1 194 1 AAAAGAAATA 0.739483 -107 ATACTTAATCAAAAATGAAAATATTAATTAATA 1 248 1 AAAAAAAATA 0.862455 -53 ACAATTTTAATTTAACCAAAATACCCCTCGAAT 3 183 1 TTAAAAAATA 0.834312 -57 ACTTATTGCTTAAAATTAAGATAAATAATTTTC 10 12 1 TAAAAAGATA 0.804675 -37 TGAAAACAAAATTGGAAAATTAT 10 36 0 TAAAAAAATT 0.663664 -13 ACTAAATTGCACAAAAAAAGCTTTTTGACAAAA 11 179 1 AAAAAAGCTT 0.700417 -122 TAATTTAATAACAAACTAAACTATTATTGTTAC 11 236 1 AAAAAAACTA 0.879409 -65 ATATAGCACAATTAATATAACTTC 11 287 1 ATAATAACTT 0.515603 -14 CTTTATAATTGAAATAACTTACTGAA 13 4 1 TTAAGAAATA 0.695073 -30 TGAATTTCAATATAACCAAGCTAACTTGGAATG 15 17 1 TTAAAAGCTA 0.827325 -284 AGCAATTTTTTTAAAACTAACTACATCACTAAA 15 102 0 TAAATAACTA 0.685665 -199 TTTTTAACAAACAAATCTAACTTTTCATTAGCA 15 131 0 AAAATAACTT 0.515603 -170 TAAAGATTGCTAAAACAAAACTAGTAAAGAGGA 15 188 0 TAAAAAACTA 0.854147 -113 TAACATAAACACTAACAAAACTAAAGATTGCTA 15 209 0 ATAAAAACTA 0.879409 -92 AAGCTAATTCTCTAAAGAAGCTAATGATAGCAT 15 275 0 TTAAAAGCTA 0.827325 -26 TCAGTATTGCAGTAATATAGATATTAAATAGTA 16 63 1 ATAATAGATA 0.656455 -238 TATTTCGAAGTTAAATAGAAATTTACTATTTAA 16 86 0 TAAAGAAATT 0.471808 -215 CAAATAAAAGAACTATAGTTATTTT 17 3 1 ATAAGAACTA 0.767508 -55 TTTACCAGTGATAAAAATAACTATAGTTCTTTT 17 16 0 AAAATAACTA 0.730914 -42 ACTTACTTTTAAAAAGAAAAATAATGTTTACTA 18 27 0 AAAAAAAATA 0.862455 -91 TAAATAAACTACTAACCAAAATACTGTAAAAGG 19 24 0 ATAAAAAATA 0.862455 -96 TAATTTTTAAATTAAATAAACTAGTTACTATTA 20 51 1 ATAAAAACTA 0.879409 -152 TAACGCTTCATTTAAAAAAGCTTCTATGTTTTA 20 82 0 TTAAAAGCTT 0.652478 -121 TTAGGTTACTAAAAAATAAGCTAATAACGCTTC 20 106 0 AAAAAAGCTA 0.856451 -97 TTTTAAAATTTATAAATAAGCTTAGTTTGCTAC 21 110 1 TTAAAAGCTT 0.652478 -67 CTCAGTAATTATAAACAAAAATTAGCACTCAAA 22 38 0 AAAAAAAATT 0.710744 -50 GTGGTAATAATAAAAATATAAATTTTAA 23 6 1 ATAAAAAATA 0.862455 -48 TAAAAGTCTTATAAAATTAAATAATCGAATTA 24 10 0 AAAATAAATA 0.700202 -49 CAGATGTAAGTTAGATAAATATTAATA 25 5 1 TTAATAGATA 0.605444 -39 CTAGTTACAATATAATCAAGATAATAATATACT 26 33 0 TTAAAAGATA 0.804675 -31 ACCAAAAAAAGAGAGATATTTTCAAGAG 30 6 1 AAAAGAGATA 0.699004 -295 CTTACAGCAAAAAAATCAAAATTTTCAACAACA 30 71 1 AAAAAAAATT 0.710744 -230 CTCCCCAACCTAAAACAAAAATACCAGGAATAG 30 127 1 TAAAAAAATA 0.834312 -174 * *** ****** Masking position 5 Map Score: 33.8746 Number of sites scoring better than the average of aligned sites = 466 Number in coding regions = 398 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 3 AGCAGTAATAATTACATATGTACA 1 1 1 AAAATAATTA 0.855401 -300 ACATATGTAAAATATCATTAATTTCTGTTATATA 1 39 1 AAATTAATTT 0.834074 -262 TATTTTAGAGAGTATTAATTATTACTATAATTAA 1 83 1 AAAATTATTA 0.670908 -218 TTGTTCATAAAAAGCTTATAATTAAGCATAAATG 1 118 0 AGTATAATTA 0.842912 -183 TAAGAACTAAAATGTCTATAATTTTGTTCATAAA 1 141 0 AGTATAATTT 0.842912 -160 TATTTTCTTTAATATCTATTATTTATTATAAGAA 1 169 0 AATATTATTT 0.770248 -132 AATTTATGGCATAACAAATAATTATAACACATTA 2 26 0 AAAATAATTA 0.855401 -59 TAATTATTATAACAATTTTAATTTAACCAAAATA 3 172 1 AATTTAATTT 0.892083 -68 GAAAGATTTTAAAGAGATTAATTACTTCA 4 28 1 AGATTAATTA 0.734936 -19 TTGAAAGACAAACATTATTAATTTTTGATCAGCT 5 26 1 AAATTAATTT 0.834074 -40 CAAAGGTTTTATGAAGAATTATTTCAAATAGATT 6 67 1 AAAATTATTT 0.670908 -122 AGCAAGAATTATAATTAACACTCTAAG 7 4 1 AATATAATTA 0.906787 -38 TAAAATAACCTTTAATTACCCTATCAAT 9 5 1 AATTTAATTA 0.892083 -31 GCTTAAAATTAAGATAAATAATTTTCCAATTTTG 10 19 1 AAAATAATTT 0.855382 -30 TGTGGAACTAAGCAACTATTATTTAAACACAGCA 11 59 1 AATATTATTT 0.770248 -242 GATTTTACAAAGAAGTTTTAATTTGGAGCAGATA 12 109 0 AATTTAATTT 0.892083 -67 AGTGAGTGTGATGGTTTTTTATTAAAAATAAACC 14 99 1 AGTTTTATTA 0.611096 -52 TGGCAAAAAAAGGGGAAATAATTAAATAA 16 6 0 AGAATAATTA 0.765423 -295 AAAATACTGTAAAAGGTTTAATTTAAAAA 19 6 0 AATTTAATTT 0.892083 -114 TTGTTCTAAAAAGCTTTAATTTGGATGTTGTT 20 181 0 AATTTAATTT 0.892083 -22 AACAAACTTTAATTAGCACTTTTAG 22 2 1 AATTTAATTA 0.892083 -86 TAAGACTTTTAAAATGTTTAATTATTAATATATA 24 32 1 AATTTAATTA 0.892083 -27 AATTAGTTTTAGAGTATATTATTATCTTGATTAT 26 21 1 AGTATTATTA 0.649023 -43 TTTGCATCATTAAATATAATTTAAAGTA 28 9 1 AATATAATTT 0.906787 -20 * * ******** Masking position 9 Map Score: 26.9178 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 174 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 CTTAATTATAAGCTTTTTATGAACAAAATTATAGAC 1 126 1 ATTTTAAAAA 0.960059 -175 TGAATTGAATAAAATTTTGGGAAAAA 1 285 1 ATTTTGAAAA 0.938623 -16 AACAGTACAGAAGCTTTTGCCACAAACTAAATTTAT 2 53 0 ATTTTGACAA 0.659793 -32 TCAACCGTTTACTTTTTTATGAACAAGCACTACAAA 6 35 1 ATTTTAAAAA 0.960059 -154 AAGCACTACAAAGGTTTTATGAAGAATTATTTCAAA 6 59 1 ATTTTAAAAA 0.96006 -130 AGATAGGTGATATTGTTGAAAATAAGTATCAAATT 8 10 1 ATGTTGAAAA 0.584885 -50 TCCCACTAAATCGCTTTTAATAAAAAATTACACGCT 11 95 0 TTTTTAAAAA 0.892086 -206 GCACAAAAAAAGCTTTTTGACAAAAAAATAGTTATT 11 187 1 ATTTTGAAAA 0.938568 -114 GATACCAATCAGGATTTTACAAAGAAGTTTTAATTT 12 119 0 ATTTTAAAAA 0.960059 -57 GGGTTAAGGTTTATTTTTAATAAAAAACCATCACAC 14 104 0 TTTTTAAAAA 0.799806 -47 AAACAAATCTAACTTTTCATTAGCAATTTTTTTAAA 15 120 0 ATTTCAAGAA 0.763441 -181 GAAAAGTTAGATTTGTTTGTTAAAAACCATGGCAAT 15 138 1 AGTTTGAAAA 0.605934 -163 CTGATTTTCTATTTTTTTAGCAAAAATTGGCAAAAA 16 31 0 ATTTTAAAAA 0.959872 -270 GAAAAAATAGTTTTTCTAGTAAACATTATTTT 18 7 1 ATTTTTAGAA 0.650692 -111 CGTTCTTCACTTACTTTTAAAAAGAAAAATAATGTT 18 32 0 TTTTTAAAAA 0.519078 -86 AAAAAGCTTCTATGTTTTAATAGTAACTAGTTTATT 20 65 0 TTTTTAAGAA 0.788051 -138 ATCCAAATTAAAGCTTTTTAGAACAA 20 187 1 ATTTTTAAAA 0.806643 -16 AGCTTATTTATAAATTTTAAAAATAAGTCAGAGCTA 21 96 0 TTTTTAAAAA 0.89061 -81 AAAAAGAGAGATATTTTCAAGAGGAACAAAATTTTC 30 16 1 ATTTCAAGAA 0.762452 -285 AAAAAAATCAAAATTTTCAACAACAATTCACACAAC 30 79 1 ATTTCAAAAA 0.878347 -222 * ***** ** ** Masking position 7 Map Score: 21.576 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 174 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 5 TATAATAATTAGTTAAATACCCTTAGGATTA 3 152 0 AGTTAAATAC 0.791499 -88 TTATAAAAACTGTTAAAATTCGAGGGGTATT 3 202 0 TGTTAAAATC 0.858025 -38 TTCCCATTAAAGATAAGAATCAAATTGCGCT 6 122 1 AGATAAGAAC 0.736477 -67 ACTATTTTTTTGTCAAAAAGCTTTTTTTGTG 11 188 0 TGTCAAAAAC 0.744776 -113 TAGATTTGTTTGTTAAAAACCATGGCAATAA 15 145 1 TGTTAAAAAC 0.944438 -156 TGATGCCCAAAGCTAAAAAGCGGATCTTCTT 16 193 0 AGCTAAAAAC 0.941246 -108 ATTACTCCAGTGATAAAAAGCATAGTAATTA 16 248 0 TGATAAAAAC 0.885018 -53 GTTTTTTGGTAGATAAAAAACAAAAAAGCAG 21 58 0 AGATAAAAAC 0.93687 -119 AATAAGTCAGAGCTAAAAATCTGTTTTTTGG 21 80 0 AGCTAAAAAC 0.941246 -97 GTTTGCTACAAGTTAAAAACCTCAGTTTTAA 21 134 1 AGTTAAAAAC 0.97039 -43 ACTCCAAAGCAGTTAATATCCCAATTTCGAG 30 241 1 AGTTAATATC 0.596849 -60 CAAGAATGATAGTTAAAATTCTCGAAATTGG 30 261 0 AGTTAAAATC 0.920963 -40 ********* * Masking position 6 Map Score: 8.28826 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 85 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 TTGGTTAAATTAAAATTGTTATAATAATTA 3 172 0 TAAAATTGTT 0.560885 -68 TTTTGATTATAAAAACTGTTAAAATTCGAG 3 209 0 AAAAACTGTT 0.799683 -31 TGTAATCATCAAAAACAGTTTTAAAAAGCG 6 149 0 AAAAACAGTT 0.730946 -40 GCTGTGTTTAAATAATAGTTGCTTAGTTCC 11 62 0 AATAATAGTT 0.909938 -239 TTTTTGACAAAAAAATAGTTATTTTTTGTA 11 200 1 AAAAATAGTT 0.909938 -101 ATTAAGTAACAATAATAGTTTAGTTTGTTA 11 244 0 AATAATAGTT 0.909938 -57 GATTTAAATAATTGTTAGAATTTAGA 14 7 1 AATAATTGTT 0.931189 -144 CCAACATATTAAAAAGTGTTTAT 14 138 1 AAAAAGTGTT 0.685267 -13 GGATCTAGTAAATAGTTGTTAAGATCACTA 15 65 0 AATAGTTGTT 0.653274 -236 TTAGTTTTAAAAAAATTGCTAATGAAAAGT 15 115 1 AAAAATTGCT 0.787864 -186 TAACAAAACTAAAGATTGCTAAAACAAAAC 15 200 0 AAAGATTGCT 0.593148 -101 GAAAAAATAGTTTTTCTAGTAA 18 3 1 AAAAATAGTT 0.909938 -115 ATAATTACTGAGTAATTGTTATTGATCTAA 22 59 1 AGTAATTGTT 0.653353 -29 TAGATGACTTAATGATTGTTT 29 52 1 AATGATTGTT 0.853596 -11 TCAATATCATAATAATGGTTTCTTACAGCA 30 50 1 AATAATGGTT 0.756816 -251 CATTGTCAAGAATGATAGTTAAAATTCTCG 30 268 0 AATGATAGTT 0.798282 -33 ********** Masking position 10 Map Score: 9.61308 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 142 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 7 TTCTTTAATATCTATTATTTATTATAAGAA 1 169 0 TCTATTATTT 0.807643 -132 TTATTTCTATTTTTTTATTTTCTTTAATAT 1 188 0 TTTTTTATTT 0.930973 -113 TTGCTTTGTTTTATTTAGCTGATCAA 5 50 0 TGTTTTATTT 0.698369 -16 TGAAAGCGTATCTTTTATTAATGAATGTGG 11 34 1 TCTTTTATTA 0.792851 -267 AAGCGTGTAATTTTTTATTAAAAGCGATTT 11 94 1 TTTTTTATTA 0.863614 -207 GTCATGTTAATCTTTTATTTCTGTTCCCAC 11 125 0 TCTTTTATTT 0.890737 -176 AGTCAGGATTTTTCTTATTTATAGTA 12 160 1 TTTCTTATTT 0.717505 -16 AGTGTGATGGTTTTTTATTAAAAATAAACC 14 103 1 TTTTTTATTA 0.863614 -48 GCAATACTGATTTTCTATTTTTTTAGCAAA 16 43 0 TTTTCTATTT 0.771045 -258 TAAATAGAAATTTACTATTTAATATCTATA 16 78 0 TTTACTATTT 0.634298 -223 TGATCTTGAGTTTATTATTTCGAAGTTAAA 16 104 0 TTTATTATTT 0.874155 -197 TAACTATAGTTCTTTTATTTG 17 2 0 TCTTTTATTT 0.890737 -56 TCCATCCACTTTTATTATTAGATGTATATT 18 75 1 TTTATTATTA 0.765327 -43 TGTGCTGCTCTTTTTTATTTGGAATATGTT 21 24 0 TTTTTTATTT 0.930973 -153 CAACAGCTGCTTTTTTGTTTTTTATCTACC 21 52 1 TTTTTTGTTT 0.63105 -125 AATTTATATTTTTATTATTACCAC 23 5 0 TTTATTATTA 0.765327 -49 ********** Masking position 6 Map Score: 17.3688 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 99 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 8 AATAAAAAAATAGAAATAAATATCATAACC 1 199 1 TAGAAATAAA 0.734925 -102 TATTAATTAATAAAAGTGAATTGAATAAAA 1 269 1 TAAAAGTGAA 0.906062 -32 TATAACACATTAAAAATGAAAGGTTTT 2 8 0 TAAAAATGAA 0.734925 -77 CCATTATTGGTGGAAGTAAATGGACTTGAA 3 63 1 TGGAAGTAAA 0.888079 -177 GGATTATGCTTGGAAGTATAGCTCAGTTGG 3 128 0 TGGAAGTATA 0.738296 -112 GGTTTTTTATTAAAAATAAACCTTAACCCA 14 111 1 TAAAAATAAA 0.667414 -40 TAAAAGTGAATTTCAATATA 15 1 1 TAAAAGTGAA 0.906062 -300 TGGAATGGGTTGAAAGTAAAGTTAGTGATC 15 43 1 TGAAAGTAAA 0.851704 -258 TAAAAGTGGATGGAAGTGAAACGTTCTTCA 18 59 0 TGGAAGTGAA 0.916408 -59 CATCTAATAATAAAAGTGGATGGAAGTGAA 18 69 0 TAAAAGTGGA 0.667942 -49 ATTATACTAGTTGAAGTAAACTAAACTAGG 20 146 0 TTGAAGTAAA 0.603255 -57 GTGGTAATAATAAAAATATAAATTTTAAAA 23 11 1 TAAAAATATA 0.416385 -43 TTGACTTGTATAGAAGTGTACACCTGTATC 30 186 0 TAGAAGTGTA 0.825717 -115 ********** Masking position 5 Map Score: 6.48508 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 103 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 AGCAGTAATAATTACATATGTAC 1 4 1 AGTAATAATT 0.446888 -297 TATATATAACAGAAATTAATGATATTTTAC 1 45 0 AGAAATTAAT 0.632199 -256 TAATTATAGTAATAATTAATACTCTCTAAA 1 86 0 AATAATTAAT 0.422741 -215 TTGATAACCCAGAAATTAATACTTAATCAA 1 230 1 AGAAATTAAT 0.632199 -71 AAATGAAAATATTAATTAATAAAAGTGAAT 1 260 1 ATTAATTAAT 0.386477 -41 TTTATGGCATAACAAATAATTATAACACAT 2 28 0 AACAAATAAT 0.362241 -57 AAATTGTTATAATAATTAGTTAAATACCCT 3 160 0 AATAATTAGT 0.63999 -80 TGAAGTAATTAATCTCTTTAAAA 4 34 0 AGTAATTAAT 0.851501 -13 CTTAATTTTAAGCAATAAGTA 10 2 0 AGCAATAAGT 0.826057 -47 TGTGGAACTAAGCAACTATTATTTAAACAC 11 59 1 AGCAACTATT 0.515712 -242 GTTAGGATCTAGTAAATAGTTGTTAAGATC 15 69 0 AGTAAATAGT 0.84685 -232 CTATTTTTTTAGCAAAAATTGGCAAAAAAA 16 29 0 AGCAAAAATT 0.294901 -272 TAATATAGATATTAAATAGTAAATTTCTAT 16 75 1 ATTAAATAGT 0.440885 -226 TAGTAATTAAAGCAATTAGTACGATTAGAA 16 227 0 AGCAATTAGT 0.947234 -74 TTATCACTGGAGTAATTAGTCGCAACCGTT 16 263 1 AGTAATTAGT 0.92918 -38 CTAGCAAAAAGTAATCTTAACG 16 289 0 AGCAAAAAGT 0.654531 -12 CTTTTCTAAAAGCAATTAATGTAATTTTTA 20 30 1 AGCAATTAAT 0.908191 -173 ATGTTTTAATAGTAACTAGTTTATTTAATT 20 60 0 AGTAACTAGT 0.787939 -143 TTAGGTTATTAATTAGTTTTAGAGTAT 26 8 1 ATTAATTAGT 0.610316 -56 ATTACTCCAAAGCAGTTAATATCCCAATTT 30 238 1 AGCAGTTAAT 0.50028 -63 ********** Masking position 10 Map Score: 8.77694 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 176 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 10 TTACTATAATTAAGCATTTATGCTTAATTA 1 104 1 TAAGCATTTA 0.836378 -197 ATCTTAATTTTAAGCAATAAGTA 10 4 0 TAAGCAATAA 0.900149 -45 AATGTGGAACTAAGCAACTATTATTTAAAC 11 57 1 TAAGCAACTA 0.867385 -244 GTTATTAAATTAAGCAATTACAAAAAATAA 11 218 0 TAAGCAATTA 0.960953 -83 CATAGTAATTAAAGCAATTAGTACGATTAG 16 229 0 AAAGCAATTA 0.960972 -72 TGCTTTTAGAAAAGCAATATCATTTAAAAG 20 14 0 AAAGCAATAT 0.617671 -189 TGCTTTTCTAAAAGCAATTAATGTAATTTT 20 28 1 AAAGCAATTA 0.960972 -175 AAATTACTCCAAAGCAGTTAATATCCCAAT 30 236 1 AAAGCAGTTA 0.883408 -65 ********** Masking position 6 Map Score: 3.8719 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 26 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 11 CATATGTAAAATATCATTAATTTCTGTTAT 1 40 1 ATATCATTAA 0.692002 -261 TGAAAGACAAACATTATTAATTTTTGATCA 5 27 1 ACATTATTAA 0.6132 -39 TTATCACTTGCATCCTTAGAGTGTTAATT 7 23 0 GCATCCTTAG 0.686161 -19 ATAGATCAAAAAATCATTAAGTAACAATAA 11 259 0 AAATCATTAA 0.692002 -42 TAGAACCATCACATCATTAGAGTCGAATCA 14 33 1 ACATCATTAG 0.896386 -118 CAGAAATGGAGCAGCATTAAGACTTGTCAG 14 71 1 GCAGCATTAA 0.835654 -80 ATAGTTGTTAAGATCACTAACTTTACTTTC 15 54 0 AGATCACTAA 0.701674 -247 AAAACTAACTACATCACTAAACTGGTTAGG 15 93 0 ACATCACTAA 0.885347 -208 GATAGCATCAGGATCATTAAAGTCTAAATC 15 253 0 GGATCATTAA 0.891588 -48 TTAGCTTTGGGCATCATTATTCTAATCGTA 16 208 1 GCATCATTAT 0.809756 -93 TTTGCATCATTAAATATAATTTA 28 4 1 GCATCATTAA 0.964286 -25 ********** Masking position 3 Map Score: 1.11016 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 115 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 GCATAATCCTAAGGGTATTTAACTAATTAT 3 149 1 AAGGGTATTT 0.825936 -91 TTAAAATTCGAGGGGTATTTTGGTTAAATT 3 191 0 AGGGGTATTT 0.851413 -49 TTAGAATTGATAGGGTAATTAAAGGTTATT 9 14 0 TAGGGTAATT 0.916019 -22 TTTTTATCACTGGAGTAATTAGTCGCAACC 16 260 1 TGGAGTAATT 0.8702 -41 TTTTGGTGTTTTGGGTATTTAAAACTGAGG 21 153 0 TTGGGTATTT 0.825936 -24 TTTATAATTACTGAGTAATTGTTATTGATC 22 56 1 CTGAGTAATT 0.782286 -32 TAAATCAGAGTAATTTTATTAATAT 25 29 0 CAGAGTAATT 0.8702 -15 ATAGTGTTCTCAGGGTATTTTTTTAGATGA 29 29 1 CAGGGTATTT 0.914465 -34 TTAACTGCTTTGGAGTAATTTCTAACTTTT 30 227 0 TGGAGTAATT 0.8702 -74 ********** Masking position 6 Map Score: 3.23831 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 38 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 13 TAATAATTAGTTAAATACCCTTAGGATTAT 3 151 0 TTAAATACCC 0.736509 -89 TCAAATCTTCTTAAATAATCTATTTGAAAT 6 87 0 TTAAATAATC 0.781639 -102 TAAAATAACCTTTAATTACC 9 1 1 TAAAATAACC 0.874402 -35 GCAAGTTAAAATATACTAAATATTAA 12 7 1 TAAAATATAC 0.736161 -169 GTTTTTTATTAAAAATAAACCTTAACCCAA 14 112 1 AAAAATAAAC 0.550697 -39 TAATGGTGTCTAACATAAACACTAACAAAA 15 222 0 TAACATAAAC 0.644961 -79 GTGGGATAAATTAAATATACATCTAATAAT 18 88 0 TTAAATATAC 0.763726 -30 TTTTTAAATTAAACCTTTTACAGT 19 5 1 TAAATTAAAC 0.569936 -115 TCAGTATTACTTAAATAAACTACTAACCAA 19 38 0 TTAAATAAAC 0.935178 -82 TAAGTAATACTGAAATAAACTGTTTAAGGA 19 55 1 TGAAATAAAC 0.793039 -65 AATTTTTAAATTAAATAAACTAGTTACTAT 20 52 1 TTAAATAAAC 0.935178 -151 CTAGTTGAAGTAAACTAAACTAGGCTAATT 20 140 0 TAAACTAAAC 0.662637 -63 AACCTCAGTTTTAAATACCCAAAACACCAA 21 151 1 TTAAATACCC 0.736509 -26 TCTTATAAAATTAAATAATCGAATTA 24 7 0 TTAAATAATC 0.781639 -52 ********** Masking position 7 Map Score: 6.47526 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 84 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 14 AGCTTTTTATGAACAAAATTATAGACATTT 1 136 1 GAACAAAATT 0.940358 -165 TTTATTATAAGAACTAAAATGTCTATAATT 1 152 0 GAACTAAAAT 0.851353 -149 AAAGTGAATTGAATAAAATTTTGGGAAAAA 1 281 1 GAATAAAATT 0.70837 -20 TTATTTAGCTGATCAAAAATTAATAATGTT 5 36 0 GATCAAAAAT 0.745738 -30 TGAAAACAAAATTGGAAAATTAT 10 36 0 AAACAAAATT 0.796147 -13 GATTTAGTGGGAACAGAAATAAAAGATTAA 11 119 1 GAACAGAAAT 0.898572 -182 TAGTAGATGGGAACAGAAGTTGTATAAAGT 11 153 0 GAACAGAAGT 0.731613 -148 CAGTAATTATAAACAAAAATTAGCACTCAA 22 39 0 AAACAAAAAT 0.851141 -49 ACGCATATAGGAATTAAAATTTAATAAGTT 27 18 1 GAATTAAAAT 0.46875 -29 TTTTCAAGAGGAACAAAATTTTCAATATCA 30 29 1 GAACAAAATT 0.940358 -272 CCCCAACCTAAAACAAAAATACCAGGAATA 30 129 1 AAACAAAAAT 0.851141 -172 ********** Masking position 7 Map Score: 5.94464 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 54 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 15 ********** No masking Map Score: -3.29449e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0