AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i03010_mgen_reg_100.orf -o03010_mgen_100.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: MG087 28 ribosomal protein S12 (rpS12) MG466 25 ribosomal protein L34 (rpL34) MG362 22 ribosomal protein L7/L12 (rpl7) MG311 22 ribosomal protein S4 Input sequences: #1 MG070 110 ribosomal protein S2 (rpS2) #2 MG077 233 oligopeptide ABC transporter, permease protein (oppB) #3 MG081 55 ribosomal protein L11 (rpl11) #4 MG090 51 ribosomal protein S6 (rpS6) #5 MG142 258 translation initiation factor 2 (infB) #6 MG144 24 conserved hypothetical protein #7 MG148 38 conserved hypothetical protein #8 MG149 75 lipoprotein, putative #9 MG149.1 90 conserved hypothetical protein #10 MG150 89 ribosomal protein S10 (rpS10) #11 MG194 300 phenylalanyl-tRNA synthetase, subunit alpha (pheS) #12 MG196 58 translation initiation factor 3 (infC) #13 MG227 300 thymidylate synthase (thyA) #14 MG232 92 ribosomal protein L21 (rpL21) #15 MG256 166 conserved hypothetical protein #16 MG257 45 ribosomal protein L31 (rpL31) #17 MG312 59 cytadherence accessory protein (hmw1) #18 MG313 44 conserved hypothetical protein #19 MG314 23 conserved hypothetical protein #20 MG316 40 conserved hypothetical protein #21 MG319 103 conserved hypothetical protein #22 MG328 38 conserved hypothetical protein #23 MG332 300 conserved hypothetical protein #24 MG361 119 ribosomal protein L10 (rpl10) #25 MG363.1 63 ribosomal protein S20 (rpsT) #26 MG418 37 ribosomal protein L13 (rpL13) #27 MG422 37 conserved hypothetical protein #28 MG424_MG425 188 MG424: ribosomal protein S15 (rps15), MG425: ATP-dependent RNA helicase (deaD) #29 MG426 22 ribosomal protein L28 (rpL28) #30 MG446 300 ribosomal protein S16 (rps16) #31 MG468.1 62 ABC transporter, ATP-binding protein #32 MG469 300 chromosomal replication initiator protein (dnaA) Motif number 1 GGTTTTTAGCTTGTTTATAACAATATTATTGCAGT 1 58 1 TTTTTTAAAA 0.813268 -53 TGTTCTTGATTATTTTATAAAAAAATGATACTAAT 2 23 0 TATTTTAAAA 0.853204 -211 ATACTTAATAAAAATATAACTTTACT 4 2 1 TATTATAAAA 0.930341 -50 AAATGTTTTCTTGTTAATAAACAAAGTCTTGTTAT 5 19 0 TTTTATAAAA 0.859652 -240 TGCAACTAATTAATTAGTTAACTAATA 7 22 1 TATTATTATA 0.930372 -17 GGTTTAATTTGTTAGCTTATTTAGAAAAA 8 5 1 TATTTTTATA 0.904784 -71 ATTTTTAGTAAAGAAAGACACCTAAT 8 60 0 TTTTATAAAA 0.859652 -16 CTAAAAAAGATAGTTATTAACTTAATTTAGAATTA 9 11 1 TATTATAATA 0.904784 -80 ACTGTTTTTTTATTTAATTGAGAAAATATTGGG 9 68 1 TATTATTGAA 0.890601 -23 AACGCTTTAGTTTTTAGTTGATACACCAAAATCCG 10 28 1 TTTTATTGAA 0.788661 -62 TCTAGTTCACTAGTTAGTTAATAAATTGACTACGG 10 60 0 TATTATTAAA 0.949468 -30 CAAAAGCGTGTAATTTTTTATTAAAAGCGATTTAG 11 91 1 TATTTTTAAA 0.930369 -210 AAAAAATAACTATTTTTTTGTCAAAAAGCTTTTTT 11 192 0 TATTTTTGAA 0.852711 -109 AATAATAGTTTAGTTTGTTATTAAATTAAGCAATT 11 229 0 TATTTTTAAA 0.930372 -72 AGTTACCAACTATTTTGTTAGTAAAACTTAATACA 12 33 1 TATTTTTAAA 0.930372 -26 CTTATTTTTTGACAAAGACCAATAAA 16 30 0 TTTTTTTGAA 0.726308 -16 GCTGTTTTATTAATAGATTTATTTTGAACTT 20 20 0 TTTTATAGTA 0.653651 -21 ATGGTTTATGTAATTAATTAAATTAACTATAGAGC 21 22 0 TATTATTATA 0.929132 -82 GATAATATACTTATTTATCTAATATTCCAACA 22 8 1 TATTATTATA 0.930372 -31 TCTAAGGGATTACTTACTAATCTTAAGGTAGTTGT 23 65 1 TATTATAATA 0.904784 -236 AAGTTGCTAATAATTTTTAATCTTAC 23 285 1 TATTTTAATA 0.871089 -16 GTTATGTTATTATTTACTTGCAATAAAACCAAAGA 24 20 1 TATTATTGAA 0.890601 -100 ACTCTAAAACTAATTAATAACCTAA 25 49 1 TATTATAATA 0.904784 -15 TCGAGAGAATTTATTAATAAAAATAAAAACTATAT 28 66 1 TTTTATAAAA 0.858506 -123 TCCTACTTACTTATTACTTATAATAAATATAGTTT 28 92 0 TTTTATTAAA 0.895974 -97 GCAAACTCATTATTTTTTTAGATAAATAAGTTCTT 30 108 0 TATTTTTATA 0.904344 -193 TTTATTCGTCTAGTTAATAAATTTAATCATCCAAT 30 173 0 TATTATAATA 0.904784 -128 GACCAATGATTTTTTTCTTAATAAAGCGGCTAATT 30 264 0 TTTTTTTAAA 0.859641 -37 GTTCTCAGGGTATTTTTTTAGATGACTTAATGATT 31 34 1 TATTTTTATA 0.90477 -29 ** *** *** * * Masking position 8 Map Score: 40.6308 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 142 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 2 GGTTTTGTGGTTTTTAGCTTGTTTATAACAATATT 1 50 1 TTTTACTTTA 0.958255 -61 GCACATGATCTTTATCACTAAATTTATGTTTGGTT 2 61 1 TTTTCCTTTT 0.611744 -173 ACAGGTTCTTTTTTTATTTCTATTTAGTAA 2 214 1 TTTTATTTTT 0.886988 -20 TTTGAGGTGTTTTTTATCTAGCTTTAAACCAAAAA 5 149 0 TTTTACTTTT 0.955259 -110 AAGACACCTAATTATAATTTGCTTATTTTGAATTT 8 37 0 ATTTATTTTA 0.714173 -39 AAAAAGATAGTTATTAACTTAATTTAGAATTAACT 9 14 1 TTATACTTTT 0.744022 -77 TTACACTGTTTTTTTATTTAATTGAGAAAATATTG 9 64 1 TTTTATTTGA 0.622173 -27 ATAGTTATTTTTTGTAATTGCTTAATTTAATAACA 11 214 1 TTTTATTTAA 0.771105 -87 GTGGGTGTTTATACCTAACTTTTCACCTGACA 13 8 1 TTTTACTTTT 0.955259 -293 ATAAAACCGCTTTTTATTTTGTTTTTTTAATAAAC 13 245 0 TTTTATTTTT 0.886988 -56 ATTCTAACAAATTCTAACTGCTTTAATAG 14 5 0 ATTTACTTTA 0.871748 -88 AACCGTTGCCTTTCTAATTTATATATTAGGGATTA 14 60 0 TTTTATTATA 0.667414 -33 AATTGCTAGGTTTTTATCTAGTTTTAGGGGGTGTA 15 70 1 TTTTACTTTT 0.955259 -97 TACTCTGTGAATTTTAACTTTATTTAGTTAAGCAA 21 57 0 ATTTACTTTT 0.863428 -47 CATGTCTTTGTAGCTAATAAAACCTTTCAAG 23 7 1 TTTTACTAAA 0.685655 -294 CTCTTGCTTGTTTTTATCTTTGTAAAGAATTTTAG 23 219 0 TTTTACTTAA 0.901618 -82 AAATAACGAGTTTTTAACTTTAATAAAGTTATCGA 24 55 1 TTTTACTATA 0.845283 -65 TTAGAGTATATTATTATCTTGATTATATTGTAACT 25 21 0 TTATACTTTA 0.757606 -43 TTAGGTTATTAATTAGTTTTAGAGTATATT 25 44 0 TTATATTTTT 0.516593 -20 ACAAAACCGCATTCTATTTTAATATTA 26 3 0 ATTTATTTAT 0.481277 -35 AGAATGCGGTTTTGTATCTAAATAT 26 23 1 TTTTACTTAT 0.895003 -15 ATAAATATAGTTTTTATTTTTATTAATAAATTCTC 28 70 0 TTTTATTTTA 0.894049 -119 AATGAGCCGTTTTCTAATTTTGTTATAATTCAACG 28 151 1 TTTTATTTTA 0.894048 -38 AGTTCTTATCTTTATATCTAACAAAGTCTTAATTA 30 80 0 TTTTACTAAA 0.685655 -221 AAAGCGGCTAATTATAACTTTTTAAAGTTCTATTT 30 242 0 ATTTACTTAA 0.730698 -59 TTTGGAGTAATTTCTAACTTTTTGTCATACTCTTT 32 214 0 TTTTACTTGT 0.806449 -87 AATTTCGAGAATTTTAACTATCATTCTTGACAATG 32 263 1 ATTTACTATT 0.600755 -38 *** ** ** *** Masking position 9 Map Score: 26.0866 Number of sites scoring better than the average of aligned sites = 326 Number in coding regions = 279 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 3 TTATTTTATAAAAAAATGATACTAATAACG 2 19 0 AAAAAATGAT 0.750056 -215 ACCATTTCCAAAAAACTGAGAACCTGAAAA 2 182 1 AAAAACTGAG 0.453168 -52 TGAGAACCTGAAAAAAACAGGTTCTTTTTT 2 198 1 AAAAAAACAG 0.933874 -36 AAATAGAAATAAAAAAAGAACCTGTTTTTT 2 209 0 AAAAAAAGAA 0.816969 -25 AACTTTTTGGAAAAACTCATTGAGTAAAGT 4 29 0 AAAAACTCAT 0.666307 -23 GTTTATTAACAAGAAAACATTTTGTTAAAA 5 32 1 AAGAAAACAT 0.646059 -227 AAGCTAGATAAAAAACACCTCAAAGCTGTA 5 160 1 AAAAACACCT 0.797024 -99 GCTGTAGTTGAAAAACACCTTAAGGTTAGT 5 184 1 AAAAACACCT 0.797024 -75 TCAATTAAATAAAAAAACAGTGTAAGTGTA 9 59 0 AAAAAAACAG 0.933874 -32 CACATTCATTAATAAAAGATACGCTTTCAA 11 33 0 AATAAAAGAT 0.716338 -268 TGGGAACAGAAATAAAAGATTAACATGACT 11 126 1 AATAAAAGAT 0.716338 -175 TAAATTGCACAAAAAAAGCTTTTTGACAAA 11 181 1 AAAAAAAGCT 0.855101 -120 TATATAGATCAAAAAATCATTAAGTAACAA 11 262 0 AAAAAATCAT 0.855745 -39 CTCCCCAGCCAAAAAAACAACCACCTATCC 13 172 1 AAAAAAACAA 0.898204 -129 AATGTTTATTAAAAAAACAAAATAAAAAGC 13 242 1 AAAAAAACAA 0.898204 -59 AAAAAACAAAATAAAAAGCGGTTTTATACA 13 253 1 ATAAAAAGCG 0.429234 -48 CTAAAACTAGATAAAAACCTAGCAATTTAA 15 67 0 ATAAAAACCT 0.644381 -100 TAAATCTATTAATAAAACAGC 20 30 1 AATAAAACAG 0.803753 -11 CTTTGTAGCTAATAAAACCTTTCAAGACAA 23 16 1 AATAAAACCT 0.771853 -285 CTTTACAAAGATAAAAACAAGCAAGAGGTA 23 227 1 ATAAAAACAA 0.578154 -74 ATTTACTTGCAATAAAACCAAAGAAAATAA 24 31 1 AATAAAACCA 0.634258 -89 TTTATTAAGAAAAAAATCATTGGTCAAAAT 30 274 1 AAAAAATCAT 0.855745 -27 ACCAAAAAAAGAGAGATATTTTC 32 4 1 AAAAAAAGAG 0.877213 -297 TCTTACAGCAAAAAAATCAAAATTTTCAAC 32 70 1 AAAAAATCAA 0.752524 -231 ********** Masking position 5 Map Score: 17.5177 Number of sites scoring better than the average of aligned sites = 548 Number in coding regions = 491 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 4 ATTTTTTTATAAAATAATCAAGAACATCAGCAC 2 32 1 AAAATATCAA 0.939011 -202 TTTAAAATTTTCCAAAAATGTGGGAG 3 4 1 AAAATTTCAA 0.967631 -52 TGCTTATTTTGAATTTTTCTAAATAAGCTAACA 8 20 0 GAATTTTCAA 0.686873 -56 TGATGACACTAAAATTCTTTACAAAGATAAAAA 23 211 1 AAAATTTTAA 0.762402 -90 TTCTAGTTACAATATAATCAAGATAATAATATA 25 17 1 AATATATCAA 0.865524 -47 TCAAGATAATAATATACTCTAAAACTAATTAAT 25 34 1 AATATATCAA 0.865524 -30 AAATTCTCTCGATATTTTCGATATTTAAATCTA 28 45 0 GATATTTCAA 0.840859 -144 TAAACAACAGAAAATAATTAAGACTTTGTTAGA 30 66 1 AAAATATTAA 0.623016 -235 CAAAATTAAAATTTTCTAATAGTGTTCTCA 31 8 1 AAAATTTCAT 0.732378 -55 AAAAAAGAGAGATATTTTCAAGAGGAACAAAAT 32 15 1 GATATTTCAA 0.840859 -286 CAAGAGGAACAAAATTTTCAATATCATAATAAT 32 33 1 AAAATTTCAA 0.967631 -268 CAAAAAAATCAAAATTTTCAACAACAATTCACA 32 78 1 AAAATTTCAA 0.967631 -223 AAAAAGTTAGAAATTACTCCAAAGCAGTTAATA 32 226 1 AAATTATCAA 0.727675 -75 AATGATAGTTAAAATTCTCGAAATTGGGATATT 32 255 0 AAAATTTCAA 0.967631 -46 ATTCTTCTATAACATTGTCAAGAATGATAGTTA 32 277 0 AACATTTCAA 0.849161 -24 ****** ** * * Masking position 11 Map Score: 13.0399 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 74 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 TCAATAAAACTCGATAATAACTAAAA 1 3 1 AATAAACTTA 0.397253 -108 ACTAAAAGCCATAAAACCTTGGTTTTGTGGTTTT 1 30 1 ATAAACCTTT 0.743062 -81 CAGGATTTATAATCCAACTTCATTTGAAACCAAA 2 89 0 AATCAACTTT 0.525383 -145 TAGAAATAAAAAAAGAACCTGTTTTTTTCAGGTT 2 202 0 AAAAAACCTT 0.475426 -32 ACTTAATAAAAATATAACTTTACTCAATGAGTTT 4 13 1 AATAAACTCT 0.732678 -39 GCTTTGCATCATTACAACTAACCTTAAGGTGTTT 5 196 0 ATTAAACTCT 0.77319 -63 CTAAATTAAGTTAATAACTATCTTTTTTAG 9 7 0 TTAAAACTTT 0.755065 -84 GCAATTACAAAAAATAACTATTTTTTTGTCAAAA 11 201 0 AAAAAACTTT 0.911474 -100 GTGGGTGTTTATACCTAACTTTTCACCTGAC 13 8 1 TTTAACCTTT 0.323093 -293 TATACATTGTATAAAACCGCTTTTTATTTTGTTT 13 256 0 ATAAACCGTT 0.316556 -45 ATTCTAACAAATTCTAACTGCTTTAATAG 14 6 0 ATTCAACTTT 0.579259 -87 AATTACTTGTTTTAAAACTATCTTAATCCCTAAT 14 37 1 TTTAAACTTT 0.681293 -56 CCAATTTATGATAAAAACTTAGTTAAATTGCTAG 15 45 1 ATAAAACTTT 0.928326 -122 TAAACTGGCATAAATAACTTTTCTTG 17 44 1 TAAAAACTCT 0.484745 -16 AGCTTCAATCTAAAAAACTGTTTTGAAACTTT 18 23 1 TAAAAACTTT 0.712468 -22 TAAAAAGTTCAAAATAAATCTATTAATAAAACAG 20 16 1 AAAAAAATTT 0.2413 -25 TACTCTGTGAATTTTAACTTTATTTAGTTAAGCA 21 58 0 ATTTAACTTT 0.470911 -46 ATTAGTCAAAAATAAAACTACTCTGTGAATTTTA 21 76 0 AATAAACTCT 0.732691 -28 TTGTGACGCTAAAACAACTACCTTAAGATTAGTA 23 79 0 AAAAAACTTT 0.912389 -222 TTGCAAGTAAATAATAACATAACTTGATAAAT 24 9 0 ATAAAACACT 0.337315 -111 AAAACCAAAGAAAATAACGAGTTTTTAACTTTAA 24 44 1 AAAAAACGTT 0.625175 -76 ATTAATAAAAATAAAAACTATATTTATTATAAGT 28 78 1 ATAAAACTTT 0.928317 -111 AACACGTTGAATTATAACAAAATTAGAAAACGGC 28 156 0 ATTAAACATT 0.481852 -33 AGATATAAAGATAAGAACTTATTTATCTAAAAAA 30 96 1 ATAAAACTTT 0.928325 -205 AAAGCGGCTAATTATAACTTTTTAAAGTTCTATT 30 243 0 ATTAAACTTA 0.450465 -58 GTTCCTCTTGAAAATATCTCTCTTTTTTTGGT 32 9 0 AAAAATCTTT 0.36916 -292 CGAAATTGGGATATTAACTGCTTTGGAGTAATTT 32 236 0 ATATAACTTT 0.562083 -65 **** **** ** Masking position 6 Map Score: 12.5757 Number of sites scoring better than the average of aligned sites = 417 Number in coding regions = 367 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 TGATGTTCTTGATTATTTTATAAAAAAATG 2 31 0 GATTATTTTA 0.691215 -203 CACATTTTTGGAAAATTTTAAA 3 3 0 GAAAATTTTA 0.882945 -53 ATTTAATTGAGAAAATATTGGG 9 79 1 GAAAATATTG 0.828013 -12 TTAAGTGAATATATTAATATTTATTG 16 7 1 GAATATATTA 0.882945 -39 GTGCTATTGCGAATATTGTAGTTA 24 106 1 GAATATTGTA 0.587281 -14 TTATTATCTTGATTATATTGTAACTAGAAC 25 16 0 GATTATATTG 0.586591 -48 ATTAGTTTTAGAGTATATTATTATCTTGAT 25 33 0 GAGTATATTA 0.749282 -31 AATATCGAGAGAATTTATTAATAAAAATAA 28 62 1 GAATTTATTA 0.613995 -127 GTAAGTAGGAGAATTTATTACTTCTAACCT 28 117 1 GAATTTATTA 0.613995 -72 AACACTATTAGAAAATTTTAATTTTG 31 7 0 GAAAATTTTA 0.882945 -56 TTATGATATTGAAAATTTTGTTCCTCTTGA 32 32 0 GAAAATTTTG 0.848035 -269 AATTGTTGTTGAAAATTTTGATTTTTTTGC 32 77 0 GAAAATTTTG 0.848035 -224 TCCCAATTTCGAGAATTTTAACTATCATTC 32 259 1 GAGAATTTTA 0.749282 -42 ********** Masking position 2 Map Score: 6.21528 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 37 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 TCAATAAAACTCGATAATAACTAAA 1 5 1 TAAAACCGAT 0.631714 -106 ATGATTACAATAAAGCAGGATTTATAATCCA 2 107 0 TAAAGCGGAT 0.959849 -127 CTTCTAAATCTAAAGCATGATTACAATAAAG 2 123 0 TAAAGCTGAT 0.960613 -111 GTTTTTGGTTTAAAGCTAGATAAAAAACACC 5 148 1 TAAAGCAGAT 0.857488 -111 CTAATTGTTGTAAGGCGGTAATCATTGCAGT 5 232 0 TAAGGCGTAA 0.605142 -27 AACTAAAAACTAAAGCGTTATGATTGTAGCA 10 16 0 TAAAGCTTAT 0.887216 -74 TGGAGTTTGGTAAAGCAGGATAGGTGGTTGT 13 188 0 TAAAGCGGAT 0.959849 -113 GCCAGTTTAGTCAAGCTTGATTATAAAACTT 17 22 0 TCAAGCTGAT 0.821205 -38 TTTTTTAGATTGAAGCTTGAATGTGAATT 18 9 0 TGAAGCTGAA 0.620198 -36 AGCTTTCTAAAGCTCTATAGTTAATTTA 21 8 1 TAAAGCCTAT 0.885197 -96 CATATTATTTTAAGGCGTTAAACTTGTTTTC 30 34 0 TAAGGCTTAA 0.609915 -267 AATCATCCAATAAGGCCCGATTTTCATTTTG 30 153 0 TAAGGCCGAT 0.930384 -148 ****** **** Masking position 3 Map Score: 6.0186 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 36 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 8 AAAGAAAGACACCTAATTATAATTTGCTTA 8 47 0 ACCTAATTAT 0.629333 -29 AAAAGCGTGTAATTTTTTATTAAAAGCGAT 11 92 1 AATTTTTTAT 0.353261 -209 TATTATTGTTACTTAATGATTTTTTGATCT 11 257 1 ACTTAATGAT 0.89525 -44 AATTACTTATTACTATCAAG 12 1 1 AATTACTTAT 0.794016 -58 ACCTTGAGTGACTTTATTATCAGAAGAATT 13 137 0 ACTTTATTAT 0.773053 -164 AGGGAAGGCCAATTTATGATAAAAACTTAG 15 37 1 AATTTATGAT 0.469716 -130 CCTCTCTAAAATTACTTATCAAA 19 10 1 AATTACTTAT 0.794016 -14 GATAATATACTTATTTATCTAATATTCC 22 9 1 ACTTATTTAT 0.840516 -30 CTAAGGGATTACTTACTAATCTTAAGGTAG 23 66 1 ACTTACTAAT 0.604993 -235 AAATTCTCCTACTTACTTATTACTTATAAT 28 103 0 ACTTACTTAT 0.915859 -86 TTGTTTTCAGAATTAATGATGAAATAGTTG 30 12 0 AATTAATGAT 0.751655 -289 TCTAACAAAGTCTTAATTATTTTCTGTTGT 30 69 0 TCTTAATTAT 0.533918 -232 AAAGATAAGAACTTATTTATCTAAAAAAAT 30 102 1 ACTTATTTAT 0.840516 -199 TTTTTAGATGACTTAATGATTGTTT 31 48 1 ACTTAATGAT 0.89525 -15 ********** Masking position 9 Map Score: 6.64036 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 61 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 CGATAATAACTAAAAGCCATAAAACCTTGGTTTT 1 22 1 TAAACTAAAA 0.791536 -89 ATAAACAAGCTAAAAACCACAAAACCAAGGTTTT 1 42 0 TAAACCAAAA 0.911745 -69 TGGTACTGGTTACCTGAAACAAAAGTAACCAGCT 2 152 0 TACCACAAAA 0.71853 -82 AGGTAACCAGTACCATTTCCAAAAAACTGAGAAC 2 171 1 TACCTCAAAA 0.831136 -63 TTTAAAATTTTCCAAAAATGTGGGAGC 3 4 1 AAAATCAAAA 0.739101 -52 TGTCTAATTTTACAAGACGTAAAAGTTCTCTTTT 5 58 0 TACACTAAAA 0.804751 -201 AACTATTATTTAAACACAGCAAAAGCGTGTAATT 11 72 1 TAAAACAAAA 0.769165 -229 TCCCATCTACTAAATTGCACAAAAAAAGCTTTTT 11 171 1 TAAACCAAAA 0.911745 -130 GTTTATTAAAAAAACAAAATAAAAAGCGGTTTTA 13 245 1 AAAAATAAAA 0.35066 -56 AGACAGGTTATACATTGTATAAAACCGCTTTTTA 13 264 0 TACATTAAAA 0.719353 -37 ATACAATGTATAACCTGTCTAAAAGACAATTTC 13 278 1 TAACTTAAAA 0.624978 -23 ACCACTAAACTACACCCCCTAAAACTAGATAAAA 15 81 0 TACACTAAAA 0.804751 -86 GTGGTAGAACAACAGTCTCCAAAACTGTCTGTGT 15 110 1 AACATCAAAA 0.75461 -57 TTTGTTAAAAAGTTCAAAATAAATCTATT 20 6 1 TAAATCAAAA 0.865312 -35 TCAAAATGTGTAACACCTGCAAAACCAAACAAGC 23 165 0 TAACTCAAAA 0.819306 -136 TCATCAATTAAAACACTCTCAAAATGTGTAACAC 23 183 0 AAACCCAAAA 0.762753 -118 TAACAATTTATAAAATACTTGT 29 2 1 AACATTAAAA 0.53057 -21 AATAATATGCTAAACAACAGAAAATAATTAAGAC 30 56 1 TAAACGAAAA 0.502117 -245 ATTCCTCCCCAACCTAAAACAAAAATACCAGGAA 32 123 1 AACCACAAAA 0.529555 -178 GAATGATAGTTAAAATTCTCGAAATTGGGATATT 32 255 0 TAAACCGAAA 0.509501 -46 **** * ***** Masking position 12 Map Score: 11.7421 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 203 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 10 CTCAAATAATAACCCCTGCCCTTGAGATTT 5 117 0 AACCCCTGCC 0.965019 -142 AAGGTGGTGGCTCCCCAGCCAAAAAAACAA 13 162 1 CTCCCCAGCC 0.990959 -139 CGATTCCTTCCACCCCCGCCATTTACAG 15 149 1 CACCCCCGCC 0.989262 -18 CAATTCACACAACCACAGCCTATTCCTCCC 32 102 1 AACCACAGCC 0.930347 -199 CAGCCTATTCCTCCCCAACCTAAAACAAAA 32 117 1 CTCCCCAACC 0.954551 -184 ********** Masking position 6 Map Score: 1.30158 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 2 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 11 TTGTTAATAAACAAAGTCTTGTTATTAGTTGCA 5 8 0 AAAAGCTTAT 0.957074 -251 TTTTTAGTAAAGAAAGACACCTAATTATAATTTGCT 8 49 0 AAAAGCTAAT 0.966442 -27 CAGAAGTTGTATAAAGTCATGTTAATCTTTTATTTC 11 134 0 AAAAGCTTAT 0.956936 -167 TTATTTTTTGACAAAGACCAATAAATATTAATATAT 16 19 0 AAAAGCTAAT 0.966734 -27 TGCAAAACCAAACAAGCCCTTTAAATTACTAACATG 23 146 0 ACAAGCTAAT 0.951352 -155 ATTTATCAAGTTATGTTATTATTTACTTGC 24 5 1 ACAAGTTTAT 0.660674 -115 AAACAAATTAACAAAGCCATTTAACTT 28 2 0 AAAAGCTAAT 0.966728 -187 * **** * *** * Masking position 5 Map Score: 1.09518 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 9 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 12 TTTTTGCAACTAATTAATTAGTTAACTAATA 7 18 1 TAATTATGTT 0.823529 -21 CAAAATCTAGTTCACTAGTTAGTTAATAAA 10 70 0 TAGTTATGTT 0.964279 -20 GTTTAAATAATAGTTGCTTAGTTCCACATTCAT 11 54 0 TAGTTCTGTT 0.920682 -247 GATGCCATTATTGTTACCTTGTTTGCGATACCC 13 57 0 TTGTTCTGTT 0.887997 -244 GATAAAAACTTAGTTAAATTGCTAGGTTTTTAT 15 54 1 TAGTTATGCT 0.849165 -113 TTAGGGGGTGTAGTTTAGTGGTAGAACAACAGT 15 93 1 TAGTTATGTA 0.791599 -74 TTTGTTAAAAAGTTCAAAATAAAT 20 2 1 TTGTTAAGTT 0.744031 -39 AAGCAAGAGGTAGTTGATCTGTTTGCACACAAA 23 245 1 TAGTTACGTT 0.863149 -56 TTAGGTTATTAATTAGTTTTAGAGTATA 25 46 0 TTATTATGTT 0.761195 -18 TTAAATGGCTTTGTTAATTTGTTTAGATGTATA 28 14 1 TTGTTATGTT 0.948556 -175 ***** * * *** Masking position 5 Map Score: 2.75843 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 60 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 13 ********** No masking Map Score: 8.83505e-13 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 14 ********** No masking Map Score: 8.83505e-13 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 TCACTAAATTTATGTTTGGTTTCAAATGAAG 2 75 1 TATTTTGGTT 0.585474 -159 TTTTTGGAAATGGTACTGGTTACCTGAAACA 2 165 0 TGGACTGGTT 0.558675 -69 AGAACCTGTTTTTTTCAGGTTCTCAGTTTTT 2 192 0 TTTTCAGGTT 0.702973 -42 AACAAAGTCTTGTTATTAGTTGCA 5 4 0 TGTATTAGTT 0.800283 -255 ATTATTTGAGTGTTTTTGGTTTAAAGCTAGA 5 137 1 TGTTTTGGTT 0.941746 -122 AAGTGTACACTGTCATTAGTTAATTCTAAAT 9 35 0 TGTATTAGTT 0.800283 -56 ATAACGCTTTAGTTTTTAGTTGATACACCAA 10 26 1 AGTTTTAGTT 0.577031 -64 TTGTATTAAGTTTTACTAACAA 12 47 0 TGTTTAAGTT 0.850278 -12 TTGCTAGGTTTTTATCTAGTTTTAGGGGGTG 15 72 1 TTTTCTAGTT 0.851302 -95 GAATTTTAACTTTATTTAGTTAAGCAAATGG 21 53 0 TTTTTTAGTT 0.840701 -51 ATTTATCAAGTTATGTTATTAT 24 2 1 TTTTCAAGTT 0.685702 -118 AACTCGTTATTTTCTTTGGTTTTATTGCAAG 24 36 0 TTTTTTGGTT 0.851302 -84 ATATGGTTCTAGTTACAATATAAT 25 4 1 TGGTCTAGTT 0.812731 -60 CTGGTATTTTTGTTTTAGGTTGGGGAGGAAT 32 123 0 TGTTTAGGTT 0.860347 -178 AGTGTACACCTGTATCTAGTTTTTCTTGGCG 32 171 0 TGTTCTAGTT 0.941746 -130 *** ******* Masking position 10 Map Score: 9.51755 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 169 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234