AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00240_mgen_reg_300.orf -o00240_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: MG030 33 uracil phosphoribosyltransferase (upp) MG034 28 thymidine kinase (tdk) 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 MG022 29 DNA-directed RNA polymerase, subunit delta (rpoE) #9 MG031 264 DNA polymerase III, subunit alpha (polC-1) #10 MG077 233 oligopeptide ABC transporter, permease protein (oppB) #11 MG081 55 ribosomal protein L11 (rpl11) #12 MG087 28 ribosomal protein S12 (rpS12) #13 MG090 51 ribosomal protein S6 (rpS6) #14 MG094 49 replicative DNA helicase (dnaB) #15 MG096 182 conserved hypothetical protein #16 MG097 56 uracil DNA glycosylase (ung) #17 MG098 99 Glu-tRNA amidotransferase subunit gatC-related protein #18 MG140 300 conserved hypothetical protein #19 MG142 258 translation initiation factor 2 (infB) #20 MG144 24 conserved hypothetical protein #21 MG148 38 conserved hypothetical protein #22 MG149 75 lipoprotein, putative #23 MG149.1 90 conserved hypothetical protein #24 MG150 89 ribosomal protein S10 (rpS10) #25 MG227 300 thymidylate synthase (thyA) #26 MG261 300 DNA polymerase III, subunit alpha (polC-2) #27 MG332 300 conserved hypothetical protein #28 MG341 89 DNA-directed RNA polymerase, subunit beta (rpoB) #29 MG342 78 conserved hypothetical protein #30 MG345 43 isoleucyl-tRNA synthetase (ileS) #31 MG382 300 uridine kinase (udk) #32 MG422 37 conserved hypothetical protein #33 MG424 188 ribosomal protein S15 (rps15) Motif number 1 TGTCTATAATTTTGTTCATAAAAAGCTTATAA 1 131 0 TTTTTATAAA 0.850529 -170 TAATATTTTCATTTTTGATTAAGTATTAATTT 1 242 0 ATTTTATTAA 0.909482 -59 TCAATTCACTTTTATTAATTAATATTTTCATT 1 261 0 TTTTTATTAA 0.552406 -40 AATTAGCTGTTTTGATTATAAAAACTGTTAAA 3 216 0 TTTATATAAA 0.658425 -24 CTTTGTAGTGCTTGTTCATAAAAAAGTAAACG 6 40 0 CTTTTATAAA 0.698421 -149 ATTTGAAATAATTCTTCATAAAACCTTTGTAG 6 64 0 ATTTTATAAA 0.92889 -125 TTTTTTTTTTTTTTTTTACGAAAAAGTGGCTA 9 182 1 TTTTTACGAA 0.633553 -83 ACTAAAAATAATTATTGATAAATTTCGATCTT 9 216 1 ATTTTATAAA 0.926435 -49 TTATTTTGATTTTTTTAATAAACGCTT 9 248 1 TTTTTATAAA 0.60613 -17 ATTAGTATCATTTTTTTATAAAATAATCAAGA 10 23 1 TTTTTATAAA 0.94863 -211 ATACTTAATAAAAATATAACTT 13 1 1 ATATTATAAA 0.602702 -51 AATTTAAACTTTTCTTTTCAAAACTGAATGGC 15 19 0 TTTTTTCAAA 0.643061 -164 TAATGGTAAAATTATTCATTAAACTTTCCTTG 15 50 1 ATTTTATTAA 0.909212 -133 TTGACACTTGTTTATTGATTAGAAAAACAACA 17 29 1 TTTTTATTAG 0.705038 -71 CCTTGTAAAATTATTTAACTAAGTGATTATTA 17 62 1 TTATTACTAA 0.523313 -38 GGCGATATTTGATTATAAAGGGAAGTTTT 18 282 0 TTTATATAAA 0.658425 -19 ATAACAAGACTTTGTTTATTAACAAGAAAACA 19 19 1 TTTTTATTAA 0.935523 -240 AACTAATTAATTAGTTAACTAATA 21 25 1 TTATTACTAA 0.4122 -14 ATTAGGTGTCTTTCTTTACTAAAAAT 22 60 1 TTTTTACTAA 0.921842 -16 CTTACACTGTTTTTTTATTTAATTGAGAAAAT 23 63 1 TTTTTTTTAA 0.6889 -28 CCGTAGTCAATTTATTAACTAACTAGTGAACT 24 60 1 TTTTTACTAA 0.540593 -30 TTTATTTTGTTTTTTTAATAAACATTTTAACA 25 236 0 TTTTTATAAA 0.60613 -65 GAACAATCTAATTCTTTATTAGAATTTAAACG 26 19 1 ATTTTATTAG 0.550588 -282 TGACACTAAAATTCTTTACAAAGATAAAAACA 27 214 1 ATTTTACAAA 0.886692 -87 CTTCTATTAAATTGTTTTTAAATACTTTTTAT 29 36 1 ATTTTTTAAA 0.60437 -43 GCTTTAAGGATTTTTTAATAAATTTCTTTTAT 31 41 0 TTTTTATAAA 0.60613 -260 AAATTGACTATTTTTTTAAAAATAGTTAAGAA 31 103 0 TTTTTAAAAA 0.593212 -198 ACTTAAATTTATTTTTAACTAAGGTTTTTGTG 31 142 0 ATTTTACTAA 0.855937 -159 TTAAAAGTTGATTTTTAATAAATTAATTAACA 31 223 1 ATTTTATAAA 0.91455 -78 TTTATCTTATTTTGTTAATTAATTTATTAAAA 31 235 0 TTTTTATTAA 0.586517 -66 ATCGAGAGAATTTATTAATAAAAATAAAAACT 33 65 1 TTTTTATAAA 0.499301 -124 *** ** ***** Masking position 6 Map Score: 36.1147 Number of sites scoring better than the average of aligned sites = 299 Number in coding regions = 246 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 2 CTATTATATATAACAGAAATTAATGATATTTTACAT 1 43 0 TAAAAATAAA 0.89757 -258 TAATAGATATTAAAGAAAATAAAAAAATAGAAATAA 1 182 1 TAAAAAAAAA 0.871592 -119 TACTTAATCAAAAATGAAAATATTAATTAATAAAAG 1 249 1 AAAAAATATA 0.83486 -52 TTTGATCAGCTAAATAAAACAAAGCAA 5 49 1 TAAAAAAAAA 0.871592 -17 TTTTCGTAAAAAAAAAAAAAAAAAAAGCAGTTTTTG 9 170 0 AAAAAAAAAA 0.946076 -95 AAAGTGGCTAAAACTAAAAATAATTATTGATAAATT 9 204 1 AAAAAATAAA 0.957717 -61 TTTATTAAAAAAATCAAAATAAAAGATCGAAATTTA 9 234 0 AAAAAAAAAA 0.946076 -31 ATTTTATAAAAAAATGATACTAATAACGATTACTAG 10 11 0 AAAATATAAA 0.570808 -223 CTGGTTACCTGAAACAAAAGTAACCAGCTTCTAAAT 10 145 0 GAAAAATAAA 0.729459 -89 TTACTAAATAGAAATAAAAAAAGAACCTGTT 10 213 0 AAAAAAAAAA 0.946076 -21 ACAGTATTGAAAACTACAACTAACAAGGAAAGTTTA 15 69 0 AAACAATAAA 0.88912 -114 ATGAAATTAAAAAAGACAATTAAATAACATATTTTA 15 150 0 AAACAATAAA 0.88912 -33 CTAAAGTGCAATTAAGTAATAATCACTT 17 82 0 AAACAATAAA 0.88912 -18 TCACTACTAATAATTTAAATTAAGCACTCATACTAA 18 214 1 TAAAAATAAA 0.897569 -87 TTATTTAGAAAAATTCAAAATAAGCAAATTATAATT 22 27 1 AAAAAATAAA 0.957717 -49 CAATATTTTCTCAATTAAATAAAAAAACAGTGTAAG 23 63 0 TCAAAAAAAA 0.532301 -28 TGTTTATTAAAAAAACAAAATAAAAAGCGGTTTTAT 25 244 1 AAAAAATAAA 0.957717 -57 ACATATGGCAAAAGATAAAAAAAATAAGGTTGATGG 26 73 1 AAAAAAAAAA 0.946076 -228 CTTAAATTTTAAATAAAAAGTATTTAAAAACAATTT 29 44 0 AAAAAATATA 0.83486 -35 CAATAAAAATTAATTTAAATAAAAGAAATTTATTAA 31 23 1 TAAAAAAAAA 0.871582 -278 GAATCAATAGAAAAGGAAATTATTGATATTTGTGCT 31 70 0 AAAAAATATA 0.83486 -231 TAAATAGTTAAAAACTCAATAATAAACGCTTTAAAA 31 263 1 AAACAAAATA 0.580955 -38 TTAAATCTATACATCTAAACAAATTAACAAAGCCAT 33 18 0 ACAAAAAAAA 0.74631 -171 *** *** *** * Masking position 9 Map Score: 25.9647 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 178 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 3 GTATTTAACTAATTATTATAACAATTTTAATTTAACCAAA 3 163 1 AATAATTTAA 0.864652 -77 TGTAAAACCAAGTTCTTGAAAGATTTTAAAGAGATTAAT 4 10 1 AATTATTTAA 0.926275 -37 GATCAAAAATTAATAATGTTTGTCTTTCAACACTATTAAA 5 16 0 TATATTTTAA 0.731751 -50 TTTCAAATCTTCTTAAATAATCTATTTGAAATAATTCTTC 6 79 0 TCTATTTTAA 0.444453 -110 CAGAATAAACAACTATTTGAAGTTTTTAAATTCACACTTT 9 39 1 AATAATTTAA 0.864652 -226 ACACTTTGAAAAACTTGTGTAACATTTAAAACTGTTAGTA 9 72 1 AACTATTTAA 0.826652 -193 CTTTATCACTAAATTTATGTTTGGTTTCAAATGAAGTTGG 10 70 1 AATTTTTTAA 0.947694 -164 ATTAGCTCCCACATTTTTGGAAAATTTTAAA 11 2 0 ACTTATTTAA 0.786541 -54 TTTAATGAATAATTTTACCATTAATTTAAACTTTTCTTTT 15 33 0 AATTTTTTAA 0.947694 -150 ATACTGTTTGTATTTCGAAGTTCATTTTAAAAAATTCGTA 15 98 1 TATTTTTTAA 0.842889 -85 TAAAATATGTTATTTAATTGTCTTTTTTAATTTCATAAAT 15 150 1 TATTTTTTAA 0.842889 -33 AACAAGTGTCAACTACAGCTTTGTTTTTAA 17 1 0 AATATTTTAA 0.902081 -99 ATTTTACAAGACGTAAAAGTTCTCTTTTAACAAAATGTTT 19 46 0 ACTATTTTAA 0.729864 -213 CATTACAACTAACCTTAAGGTGTTTTTCAACTACAGCTTT 19 181 0 AACTTTTTAA 0.873047 -78 GGAACAGAGCAATCAGTTGATCTATTTGAACGTACAAAAC 26 107 1 AACATTTTAA 0.777613 -194 GAAGATACACAAGTTTTAAATGAAGTTGAACTTGATGATA 26 149 1 AATTTGTTAA 0.795044 -152 GTTCTTTTCTAAGCTCTGTTATCTTTTTAATATCATCAAG 26 179 0 AACTATTTAA 0.826652 -122 CTTAGAAAAGAACTTGAACATACTTTTGAACCACAAACAA 26 206 1 AATTTTTTAA 0.947694 -95 CTATTTCTTTAATTTCACGCTTAATTTGCATTCTTGTTTG 26 239 0 AATTTTTTCA 0.572113 -62 CATGTCTTTGTAGCTAATAAAACCTTTCAAGACAAATATG 27 11 1 TACTATTTAA 0.585414 -290 CAGGTGTTACACATTTTGAGAGTGTTTTAATTGATGACAC 27 180 1 ACTTATTTAA 0.786541 -121 AAAGTTGACCAAGTTGCTAATAATTTTTAATCTTAC 27 275 1 AATTTTTTAA 0.947694 -26 AAATTAACACTTAAATTTTAAATAAAAAGTA 29 58 0 AATATTTTAA 0.902081 -21 GTGACTAAATAAATTGACTATTTTTTTAAAAATAGTTAAG 31 105 0 AATTTTTTAA 0.947694 -196 TAAAACACTTAATTTAAAAGAAAGTTTAAATAATATGTTC 31 186 0 AATTATTTAA 0.926275 -115 TTAATTAACAAAATAAGATAAATAGTTAAAAACTCAATAA 31 245 1 AATAAGTTAA 0.577655 -56 TAATTAATAAACACGTTGAATTATAACAAA 33 169 0 TATTAGTTAA 0.443362 -20 ** ** * *** ** Masking position 16 Map Score: 25.9 Number of sites scoring better than the average of aligned sites = 404 Number in coding regions = 350 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 4 GCATTTATGCTTAATTATAAGCTTTTTATGAACAAA 1 117 1 TTTTAATTTT 0.576368 -184 TTTATTTTCTTTAATATCTATTATTTATTATAAGAA 1 169 0 TTTCTAATTT 0.867108 -132 GGTTATGATATTTATTTCTATTTTTTTATTTTCTTT 1 193 0 TTTCTATTTT 0.960422 -108 CAATTCACTTTTATTAATTAATATTTTCATTTTTGA 1 256 0 TTTTTAATTT 0.656729 -45 TTTTTCCCAAAATTTTATTCAATTCA 1 285 0 TTTCAATTTT 0.8227 -16 AAAGCGCAATTTGATTCTTATCTTTAATGGGAATGT 6 119 0 TTTTTATTTA 0.796238 -70 GCACATGATCTTTATCACTAAATTTATGTTTGGTTT 10 61 1 TTTCTATTTA 0.930203 -173 AATGGTAAAATTATTCATTAAACTTTCCTTGTTAGT 15 51 1 TTTTTACTTT 0.798034 -132 AATTTCAAGTTGGTTGTCTAATTTTACAAGACGTAA 19 70 0 TGTCTATTTA 0.572656 -189 TTTGAGGTGTTTTTTATCTAGCTTTAAACCAAAAAC 19 148 0 TTTCTATTTA 0.930203 -111 CTAAATTAAGTTAATAACTATCTTTTTTAG 23 5 0 TTTCTATTTT 0.960422 -86 GTGGGTGTTTATACCTAACTTTTCACCTGACAT 25 8 1 TTTCTATTTT 0.960422 -293 AACAATCTAATTCTTTATTAGAATTTAAACGATTTC 26 20 1 TTTTTAATTT 0.656729 -281 TATGTTCAAGTTCTTTTCTAAGCTCTGTTATCTTTT 26 192 0 TTTCTACTCT 0.575372 -109 TTCTAAGGGATTACTTACTAATCTTAAGGTAGTTGT 27 64 1 TTTCTACTTA 0.88097 -237 GTTGACCAAGTTGCTAATAATTTTTAATCTTAC 27 278 1 TTTTAATTTA 0.427663 -23 TATTAAATTGTTTTTAAATACTTTTTATTTAAAATT 29 40 1 TTTATATTTT 0.596309 -39 TTTCTATTGATTCTTAACTATTTTTAAAAAAATAGT 31 93 1 TTTCTATTTA 0.930203 -208 CTTAAATTTATTTTTAACTAAGGTTTTTGTGACTAA 31 137 0 TTTCTAGTTT 0.792848 -164 CTTTCAAATTTTAATTGCTAATCTTTAAGGTAC 32 8 0 TTTCTACTTT 0.930921 -30 ** * *** **** Masking position 5 Map Score: 12.5546 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 124 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 5 TGTTATGCCATAAATTTAGTTTGTGGCAAA 2 44 1 TAAATTTAGT 0.932035 -41 ATAAATTTAATAGTGTTGAAA 5 2 1 TAAATTTAAT 0.604958 -64 AAACCAAACATAAATTTAGTGATAAAGATC 10 67 0 TAAATTTAGT 0.932035 -167 AAATTAATGGTAAAATTATTCATTAAACTT 15 46 1 TAAAATTATT 0.630584 -137 AAATAAACTTTAAATTTATCTAGGTAAAAG 16 37 0 TAAATTTATC 0.725304 -20 AACAACCTTGTAAAATTATTTAACTAAGTG 17 57 1 TAAAATTATT 0.630584 -43 ACTAATAATTTAAATTAAGCACTCATACTA 18 219 1 TAAATTAAGC 0.66007 -82 TAGTTAATTCTAAATTAAGTTAATAACTAT 23 20 0 TAAATTAAGT 0.898616 -71 AAATCCGTAGTCAATTTATTAACTAACTAG 24 56 1 TCAATTTATT 0.574802 -34 ACACAAGTTTTAAATGAAGTTGAACTTGAT 26 155 1 TAAATGAAGT 0.5292 -146 TAAATCAGAGTAATTTTATTAATATTTATC 30 24 0 TAATTTTATT 0.477016 -20 TTCTTTTATTTAAATTAATTTTTATTGCAT 31 20 0 TAAATTAATT 0.886231 -281 GATTTTTTAATAAATTTCTTTTATTTAAAT 31 35 0 TAAATTTCTT 0.574802 -266 TTTTTGTGACTAAATAAATTGACTATTTTT 31 120 0 TAAATAAATT 0.5403 -181 AATTGCAACTTAAATTTATTTTTAACTAAG 31 151 0 TAAATTTATT 0.923385 -150 AACTTTCTTTTAAATTAAGTGTTTTAAAAG 31 200 1 TAAATTAAGT 0.898616 -101 TGATTTTTAATAAATTAATTAACAAAATAA 31 231 1 TAAATTAATT 0.886231 -70 TTACTTATAATAAATATAGTTTTTATTTTT 33 84 0 TAAATATAGT 0.674173 -105 ********** Masking position 1 Map Score: 9.83881 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 94 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 AACACATTAAAAATGAAAGGTTTT 2 1 0 AAAAAGTTTT 0.966454 -84 AAAATTAGCTGTTTTGATTATAAAA 3 225 0 AAAAGGTTTT 0.947495 -15 TGTTCATAAAAAAGTAAACGGTTGAAGTTTGATG 6 26 0 AAAAAGGTTG 0.752589 -163 TTCTGCTAAATCAATGGTTTTGTAATCATCA 6 168 0 AAAAAGTTTT 0.955894 -21 AAAAAAAAAAAAAAAAGCAGTTTTTGCTATTTTA 9 162 0 AAAAGGTTTT 0.948264 -103 TGAGAACCTGAAAAAAACAGGTTCTTTTTTTATT 10 198 1 AAAAAGGTTC 0.75252 -36 ATGTGGGAGCTAATTAAGCGTTTGTACCACAGCA 11 28 1 TAAAAGTTTG 0.675308 -28 TTCAGTTTTGAAAAGAAAAGTTTAAATTAATGGT 15 23 1 AAAAAGTTTA 0.754042 -160 AAGGAACAACAAAGGAAAAGGTTTGACTAACACC 18 15 0 AAAAAGGTTT 0.912886 -286 GTGAATCTTCAAAGTAACTGTTTCTATAAAAATA 18 184 0 AAAAAGTTTC 0.893102 -117 AGTTCTCTTTTAACAAAATGTTTTCTTGTTAATA 19 35 0 TAAAAGTTTT 0.877259 -224 AAAAACAAAATAAAAAGCGGTTTTATACAATGTA 25 254 1 TAAAGGTTTT 0.830989 -47 ATAGAACGCAAAATGAAACGTTCTAGTCGCTAAT 26 275 1 AAAAAGTTCT 0.774263 -26 TACTAATCTTAAGGTAGTTGTTTTAGCGTCACAA 27 79 1 AAGAGGTTTT 0.702237 -222 CTTAAATTTTAAATAAAAAGTATTTAAAAACAAT 29 46 0 AAAAAGTATT 0.698269 -33 ACTTTCTTTTAAATTAAGTGTTTTAAAAGTTGAT 31 201 1 AAAAAGTTTT 0.96629 -100 CTAACCTTGGCAATGAGCCGTTTTCTAATTTTGT 33 140 1 CAAAGGTTTT 0.742992 -49 *** ** ***** Masking position 6 Map Score: 11.4476 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 159 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 7 CTATTTTAGAGAGTATTAATTATTACTATAA 1 82 1 GAGATTAATT 0.79208 -219 ATTTTTGATTAAGTATTAATTTCTGGGTTAT 1 233 0 AAGATTAATT 0.881048 -68 TCAAAAATGAAAATATTAATTAATAAAAGTG 1 256 1 AAAATTAATT 0.664346 -45 ATTAATTAATAAAAGTGAATTGAATAAAATT 1 270 1 AAAGTGAATT 0.549086 -31 TGCATCCTTAGAGTGTTAATTATAATTCTTG 7 13 0 GAGGTTAATT 0.909401 -29 TTGAAAGATTAAAGGTTAATTAGATACAGAA 9 13 1 AAAGTTAATT 0.839166 -252 AAGTTTTTCAAAGTGTGAATTTAAAAACTTC 9 57 0 AAGGTGAATT 0.820178 -208 AAGCGTTTATTAAAAAAATCA 9 254 0 AAGGTTTATT 0.945781 -11 TTATTTAACTAAGTGATTATTACTTAATTGC 17 72 1 AAGGATTATT 0.583493 -28 GTGACTGTTAAAATGTTTATTAAAAAAACAA 25 231 1 AAAGTTTATT 0.82323 -70 TTTGTCTTGAAAGGTTTTATTAGCTACAAAG 27 16 0 AAGTTTTATT 0.578849 -285 TTTAAAATTTAAGTGTTAATTT 29 67 1 AAGGTTAATT 0.951318 -12 TTCATGCAATAAAAATTAATTTAAATAAAAG 31 17 1 AAAATTAATT 0.664358 -284 AAATATTTTAAAGCGTTTATTATTGAGTTTT 31 273 0 AAGGTTTATT 0.945781 -28 AAAATATCGAGAGAATTTATTAATAAAAATA 33 60 1 GAGATTTATT 0.772746 -129 AAGTAAGTAGGAGAATTTATTACTTCTAACC 33 115 1 GAGATTTATT 0.772746 -74 TTATAATTCAACGTGTTTATTAATTA 33 173 1 ACGGTTTATT 0.674959 -16 *** ******* Masking position 9 Map Score: 12.3496 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 8 ACCCTCAACCTCCTGAGTGCAA 3 1 1 ACCTCACCTC 0.952103 -239 ATGGACTTGAACCATCGACCTCACCCTTATCA 3 82 1 ACATCACCTC 0.972302 -158 TGATTAGAAAAACAACAACCTTGTAAAATTAT 17 44 1 ACAACACCTT 0.979006 -56 TTGGCTGGGGAGCCACCACCTTGAGTGACTTT 25 152 0 ACCACACCTT 0.963513 -149 CAGCCAAAAAAACAACCACCTATCCTGCTTTA 25 177 1 ACAACACCTA 0.934098 -124 ATTGCTCTGTTCCATCAACCTTATTTTTTTTA 26 88 0 TCATCACCTT 0.838954 -213 GTGACGCTAAAACAACTACCTTAAGATTAGTA 27 79 0 ACAACACCTT 0.979006 -222 GTGCAAACAGATCAACTACCTCTTGCTTGTTT 27 241 0 ACAACACCTC 0.982552 -60 * **** ***** Masking position 8 Map Score: 7.63039 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 12 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 9 AAACCTTTCATTTTTAATGTGTTATAATTATT 2 12 1 TTTTATGTGT 0.914751 -73 ACCCCTCGAATTTTAACAGTTTTTATAATCAA 3 205 1 TTTTAAGTTT 0.894912 -35 ATAAATTTAATAGTGTTGAAAGACAA 5 5 1 ATTTAAGTGT 0.789781 -61 AAATTGCGCTTTTTAAAACTGTTTTTGATGAT 6 143 1 TTTTAACTGT 0.788346 -46 TTACACAAGTTTTTCAAAGTGTGAATTTAAAA 9 62 0 TTTTAAGTGT 0.914751 -203 CTTGTGTAACATTTAAAACTGTTAGTAAGAAC 9 85 1 ATTTAACTGT 0.56599 -180 CGATCTTTTATTTTGATTTTTTTAATAAACGC 9 241 1 TTTTATTTTT 0.652764 -24 AGGGGTTATTATTTGAGTGTTTTTGGTTTAAA 19 130 1 ATTTATGTTT 0.748844 -129 AATTTGCTTATTTTGAATTTTTCTAAATAAGC 22 25 0 TTTTATTTTT 0.652764 -51 ATAAAACCGCTTTTTATTTTGTTTTTTTAATA 25 248 0 TTTTATTTGT 0.703154 -53 GTTCAACTTCATTTAAAACTTGTGTATCTTCA 26 148 0 ATTTAACTTG 0.288109 -153 GTGTTACACATTTTGAGAGTGTTTTAATTGAT 27 183 1 TTTTAAGTGT 0.914751 -118 TGTTAGTGGCTTTTTAATGTTTTGATCCGCTT 28 56 1 TTTTATGTTT 0.894912 -34 ATAGCTATTTTTTTCAATGTTG 29 1 0 TTTTATGTTG 0.769055 -78 AAATTAAGTGTTTTAAAAGTTGATTTTTAATA 31 211 1 TTTTAAGTTG 0.769055 -90 ATTATTGAGTTTTTAACTATTTATCTTATTTT 31 254 0 TTTTATATTT 0.426607 -47 **** * ***** Masking position 6 Map Score: 5.36067 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 121 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 TTCCAAGCATAATCCTAAGGGTATTTAACT 3 143 1 AATCCTAAGG 0.881281 -97 CCAGCTTCTAAATCTAAAGCATGATTACAA 10 128 0 AATCTAAAGC 0.92793 -106 AGAGTTAAGCAATCTAAAGGGATTAATATA 18 250 0 AATCTAAAGG 0.973256 -51 TCTTAATCAAAATCTCAAGGGCAGGGGTTA 19 108 1 AATCTCAAGG 0.942509 -151 CATTACAACTAACCTTAAGGTGTTTTTCAA 19 191 0 AACCTTAAGG 0.89583 -68 TATCAACTAAAAACTAAAGCGTTATGATTG 24 21 0 AAACTAAAGC 0.727744 -69 ATTACTTACTAATCTTAAGGTAGTTGTTTT 27 73 1 AATCTTAAGG 0.965456 -228 TCATGTTAGTAATTTAAAGGGCTTGTTTGG 27 145 1 AATTTAAAGG 0.80252 -156 ********** Masking position 7 Map Score: 2.14175 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 29 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 11 AATGGGGATGTAGCTCAACTGATAGAGCAC 3 38 0 TAGCTCAACT 0.78253 -202 CTTGGAAGTATAGCTCAGTTGGTTAGAGCA 3 120 0 TAGCTCAGTT 0.915432 -120 TTATTAATTTTTGATCAGCTAAATAAAACA 5 40 1 TTGATCAGCT 0.948609 -26 TAAGAAATTTTTGATCAGTTACTTTTACCT 16 16 1 TTGATCAGTT 0.932225 -41 GATTTTGATTAAGATCAATTTCAAGTTGGT 19 92 0 AAGATCAATT 0.533154 -167 GATCAACTGATTGCTCTGTTCCATCAACCT 26 99 0 TTGCTCTGTT 0.853471 -202 TACGTTCAAATAGATCAACTGATTGCTCTG 26 111 0 TAGATCAACT 0.793715 -190 GTTCTTTTCTAAGCTCTGTTATCTTTTTAA 26 189 0 AAGCTCTGTT 0.661287 -112 AATTACTAACATGATCAGCTCAAGGGTATC 27 129 0 ATGATCAGCT 0.880273 -172 CAAGAGGTAGTTGATCTGTTTGCACACAAA 27 248 1 TTGATCTGTT 0.861653 -53 TTTTAATGTTTTGATCCGCTTTTCACCCCA 28 67 1 TTGATCCGCT 0.830586 -23 ********** Masking position 5 Map Score: 2.48579 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 96 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 12 ATGAACTTCGAAATACAAACAGTATTGAAA 15 93 0 AAATACAAAC 0.786482 -90 GCCATTGAATAGTTAAAAACCTGATTTATT 18 158 1 AGTTAAAAAC 0.836376 -143 TGCAACTAATAACAAGACTTTGT 19 4 1 AACTAATAAC 0.862968 -255 AAAAACACTCAAATAATAACCCCTGCCCTT 19 124 0 AAATAATAAC 0.762207 -135 TCTAGCTTTAAACCAAAAACACTCAAATAA 19 138 0 AACCAAAAAC 0.832644 -121 TTCTAAATTAAGTTAATAACTATCTTTTTT 23 13 0 AGTTAATAAC 0.765602 -78 TTGGTGTATCAACTAAAAACTAAAGCGTTA 24 27 0 AACTAAAAAC 0.907881 -63 CATACTTTTGAACCACAAACAAGAATGCAA 26 224 1 AACCACAAAC 0.785101 -77 AAGCCCTTTAAATTACTAACATGATCAGCT 27 139 0 AATTACTAAC 0.70182 -162 TTCTTTACAAAGATAAAAACAAGCAAGAGG 27 225 1 AGATAAAAAC 0.836376 -76 AACATTAAAAAGCCACTAACAGCGTTATAA 28 47 0 AGCCACTAAC 0.704038 -43 TAAGATAAATAGTTAAAAACTCAATAATAA 31 258 1 AGTTAAAAAC 0.836376 -43 TTATTAATAAAAATAAAAACTATATTTATT 33 76 1 AAATAAAAAC 0.833784 -113 ********** Masking position 5 Map Score: 6.71315 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 177 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 13 ATTTAGTTTGTGGCAAAAGCTTCTGTACTGT 2 57 1 TGGCAAAAGT 0.966724 -28 TAGTCTAAAATAGCAAAAACTGCTTTTTTTT 9 157 1 TAGCAAAAAT 0.870383 -108 TACGAAAAAGTGGCTAAAACTAAAAATAATT 9 198 1 TGGCTAAAAT 0.949448 -67 CAAAACTGAATGGCTAAAATTG 15 2 0 TGGCTAAAAT 0.949448 -181 AATTAATTAGTTGCAAAAAGTTTAGA 21 6 0 TTGCAAAAAT 0.870383 -33 AAATCACATATGGCAAAAGATAAAAAAAATA 26 68 1 TGGCAAAAGT 0.966724 -233 ********* * Masking position 6 Map Score: 0.285193 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 9 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 14 ********** No masking Map Score: 5.3315e-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 Motif number 15 ********** No masking Map Score: 5.3315e-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