AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02010_mjan_reg_100.orf -o02010_mjan_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: MJ0086 36 unspecified methyltransferase MJ1089 40 cobalt transport protein (cbiQ) MJ1012 30 phosphate specific transport complex component (pstB) Input sequences: #1 MJ0085 134 iron transport periplasmic binding protein, putative (ceuE) #2 MJ0087 23 hemin permease (hemU) #3 MJ0413 80 nitrate transporter protein (nrtB) homolog (cmpB) #4 MJ0414 108 conserved hypothetical protein #5 MJ0873 132 ferric enterobactin transport ATP-binding protein #6 MJ0876 300 iron(III) dicitrate transport system permease protein #7 MJ1014 164 phosphate transport system permease protein C (pstC) #8 MJ1015 230 periplasmic phosphate-binding protein (pstS) #9 MJ1091 281 cobalamin biosynthesis protein (cbiM) #10 MJ1266 189 high-affinity branched-chain amino acid transport protein (braC) #11 MJ1267 96 high-affinity branched-chain amino acid transport ATP-binding protein (braF) #12 MJ1268 158 high-affinity branched-chain amino acid transport ATP-binding protein (braG) #13 MJ1269 32 high-affinity branched-chain amino acid transport protein (braD) #14 MJ1270 21 high-affinity branched-chain amino acid transport protein (braE) #15 MJ1368 122 sulfate transport system permease protein (cysT) #16 MJ1569 300 cobalamin biosynthesis protein (cbiM) #17 MJ1571 126 cobalt transport protein (cbiQ) Motif number 1 TAAAAATTATATAAAAAATAGAAAAAAG 1 9 0 ATAAAAAATA 0.911179 -126 ATCAATATTCATAAAAATTATATAAAAAAT 1 20 0 ATAAAAATTA 0.896532 -115 TATATTAGATATTAAAAATTTTTGTTCATA 1 90 1 ATTAAAAATT 0.942778 -45 ATTATGAGGTATTTAAATTTTG 3 3 0 ATTTAAATTT 0.875531 -78 AGATTATCTAATATAAATTTTACTATTATT 5 23 1 ATATAAATTT 0.84122 -110 ACCTTATTTTATTTAAAAATCATTTGAGTG 5 107 1 ATTTAAAAAT 0.823386 -26 TTTAAAAAATATTAAAAAATTAGAT 7 6 0 ATTAAAAAAT 0.902306 -159 TTAAATTTGGATTTAAAAAATATTAAAAAA 7 17 0 ATTTAAAAAA 0.794219 -148 TTAAATCCAAATTTAAAGATAAGAAATTTT 7 31 1 ATTTAAAGAT 0.739329 -134 TTATTCCCAAATATAAAATTTCTTATCTTT 7 45 0 ATATAAAATT 0.862496 -120 ATATTGCTTAATAAAAATATTATTCCCAAA 7 64 0 ATAAAAATAT 0.854563 -101 CGAAAGTCTTATTAAAATAGAACTTATAAA 7 119 1 ATTAAAATAG 0.891637 -46 TAAGATAAGGATTAAAAAAGG 7 154 1 ATTAAAAAAG 0.906905 -11 AAAACTCAATATAAAAAGTAAAACACTTCT 8 21 0 ATAAAAAGTA 0.86173 -210 GTTTTTAACTATTAAAATTGAATGTTCATA 8 46 1 ATTAAAATTG 0.936215 -185 ACATAAAGGTATATAAAGTTTTCTATTTTG 8 93 0 ATATAAAGTT 0.792128 -138 ACCTTAAATCATTAAAAAAGTT 8 219 1 ATTAAAAAAG 0.906905 -12 ATAAAGATATATAAAAAGTAGTTATT 9 7 0 ATAAAAAGTA 0.86173 -275 TTGCCTTACTATTTAAATAGTTTATTACTA 9 64 1 ATTTAAATAG 0.80617 -218 ATTAATCATTATTAAAAATGTCTTTAATTT 9 104 1 ATTAAAAATG 0.945585 -178 TTTATTACTTATTTAAATTAAAGACATTTT 9 118 0 ATTTAAATTA 0.853267 -164 TAAATAAGTAATAAAAAATATGAAAAAAAC 9 133 1 ATAAAAAATA 0.911179 -149 TCTTTATCTTATATAAATTTAACGGTATTT 9 213 0 ATATAAATTT 0.84122 -69 TACGGAAGTTATTAAAAATAATGATAATAT 10 75 1 ATTAAAAATA 0.931602 -115 TATGAGCAATATTTAAATTTTTCGAGATAG 10 117 0 ATTTAAATTT 0.875531 -73 TTGCTCATATATAAAAAATGAAATTGCCAT 10 138 1 ATAAAAAATG 0.92902 -52 AGGTGATACCATTAAAAGAATAA 10 177 1 ATTAAAAGAA 0.822653 -13 AAAAAGAGTTATTTAAAGTTTTAGGAATTT 11 12 0 ATTTAAAGTT 0.834967 -85 TATCTTAAAAATTTAAAAAAGAGTTATTTA 11 27 0 ATTTAAAAAA 0.794219 -70 AAAAATGATAAAAAGTTTAAAGAATAA 11 80 0 ATAAAAAGTT 0.882887 -17 ATTAGGTTTTATAAAAATTATACC 13 5 0 ATAAAAATTA 0.896532 -28 TAATATTTTCATTAAAAATTTATTAAA 15 8 0 ATTAAAAATT 0.942778 -115 TTACCTAATTATATAAAATTTGTGTTAAAC 15 61 0 ATATAAAATT 0.862496 -62 TTAAACAAAAATAAAAATAAGTT 16 4 0 ATAAAAATAA 0.829279 -297 CAAATACTATATTAAAAATTCCATTAAAAT 16 121 1 ATTAAAAATT 0.942778 -180 TAAAAATTCCATTAAAATAATATTTAGTAT 16 133 1 ATTAAAATAA 0.865759 -168 GTTACATAAAATTAAAATTGACAAAATTGA 16 164 0 ATTAAAATTG 0.936215 -137 TTGAGCTAATATAAAAAAATGTTACATAAA 16 184 0 ATAAAAAAAT 0.874317 -117 TTTAAAGTTTATTAAAAATGTCTTGAGCTA 16 206 0 ATTAAAAATG 0.945585 -95 GAATATAGAAATTAAAAAAGTAAAAAAA 17 9 0 ATTAAAAAAG 0.906905 -118 TAATTATTCAATAAAAATTATCAAAATCTT 17 81 0 ATAAAAATTA 0.896532 -46 TTGAATAATTATAAAAATTGTAATGTAATT 17 100 1 ATAAAAATTG 0.917047 -27 ********** Masking position 5 Map Score: 65.7257 Number of sites scoring better than the average of aligned sites = 2020 Number in coding regions = 1353 Number in noncoding regions = 667 Number of orfs with sites within 600 bp upstream = 495 Fraction of orfs with sites within 600 bp upstream = 0.0795053 Motif number 2 AAATTATATAAAAAATAGAAAAAAG 1 3 0 AAATAGAAAA 0.748965 -132 AAAATACATCAATATTCATAAAAATTATATAAA 1 24 0 ATATCAAAAA 0.8637 -111 AATAATTCAAAAAATGTGATAGT 2 2 1 AAATCAAAAA 0.937271 -22 GTTATCTTTTAAAATTAATAAAACTTTAAAAGC 3 33 0 AAATAAAAAA 0.978981 -48 AATTATATTGATATTTAATAAAAG 3 67 1 AATTAAAAAA 0.831183 -14 ATAATTTATTAGAAATAATAATATCATGTTTAT 4 33 1 AAATAAAATA 0.925743 -76 GGCTTCATGTATAACTTATAAATAACTTTAACT 4 66 0 AAATTAAAAT 0.694346 -43 ACTCCTAACAATTAATAACAATAATAATAGTAA 5 42 0 ATATAAAATA 0.84094 -91 ATTTCATATCATAAATTATAAAAAACCTTATTT 5 83 1 AAATTAAAAA 0.941096 -50 TATGTCTGCAACAACTAAAAATACAGCTCCTAA 6 155 0 AAATAAAATA 0.925743 -146 TAATCTACCTAAAAATAAGAAAAATGGGGATTT 6 276 1 AAATAAAAAA 0.978981 -25 GGATTTAAAAAATATTAAAAAATTAGAT 7 6 0 ATATAAAAAT 0.737269 -159 TTATTAAAATAGAACTTATAAAAGCCATAAGAT 7 127 1 AAATTAAAAA 0.941096 -38 GAATGACACCATAATTTACAATAGATTGTAAGA 8 124 0 AAATTAAATA 0.81048 -107 GGTGTCATTCAAAAATAACAAAATCTACTAATG 8 147 1 AAATAAAAAA 0.978981 -84 AATATTAAGTATTACTAAAAATAAAGATATATA 9 24 0 ATATAAAATA 0.84094 -258 TTTAATTTAAATAAGTAATAAAAAATATGAAAA 9 126 1 AAATAAAAAA 0.978981 -156 ATAACTCATTAATAGTAACAAAATTAAAGTTTA 9 166 1 ATATAAAAAA 0.951812 -116 ACGGTATTTTATTATTAATAAAATAAACTTTAA 9 189 0 ATATAAAAAA 0.951806 -93 ACCCCTGAATATAATTCAAAAAAACTTAACACA 9 253 0 AAATCAAAAA 0.937271 -29 GCTTTAAAGTATTAGTAATAATAATAGTAATTA 10 35 0 ATATAAAATA 0.84094 -155 AATATTGCTCATATATAAAAAATGAAATTGCCA 10 134 1 AATTAAAAAT 0.411429 -56 AAAATTCCTAAAACTTTAAATAA 11 1 1 AAATCCAAAA 0.637867 -96 GCATATCTTAAAAATTTAAAAAAGAGTTATTTA 11 27 0 AAATTAAAAA 0.941096 -70 AAAAATGATAAAAAGTTTAAAGA 11 84 0 AAATGAAAAA 0.886487 -13 TTAATATGATAAAAGTAAAAAATCTAAACGCTG 12 27 1 AAATAAAAAT 0.868814 -132 GGTATAATTTTTATAAAACCTAATGAAC 13 6 1 ATTTTAAAAA 0.41706 -27 ATACTTAAACAAAAATAAAAATAAGTT 16 5 0 AAATAAAATA 0.925743 -296 ACATAAAATTAAAATTGACAAAATTGAGATACT 16 158 0 AAATGAAAAA 0.886487 -143 AACACAATTAAATAATACCAAAAGGGTGAAACT 16 278 1 ATATACAAAA 0.699574 -23 TAGAAATTAAAAAAGTAAAAAAA 17 1 0 AAATAAAAAA 0.978981 -126 AAATCACTCCAAAAATAATAGAAGATGAATATA 17 32 0 AAATAAAGAA 0.730806 -95 TTATTCAATAAAAATTATCAAAATCTTTAAAAT 17 75 0 AAATATAAAA 0.668104 -52 ATTTTTATTGAATAATTATAAAAATTGTAATGT 17 93 1 ATATTAAAAA 0.871391 -34 * ** *** **** Masking position 6 Map Score: 58.8561 Number of sites scoring better than the average of aligned sites = 866 Number in coding regions = 603 Number in noncoding regions = 263 Number of orfs with sites within 600 bp upstream = 241 Fraction of orfs with sites within 600 bp upstream = 0.0387086 Motif number 3 CTTTTTTCTATTTTTTATATAATTT 1 4 1 TTTTATTTTT 0.859953 -131 TGATGTATTTTTAACGATTATTTTTGATAAAC 1 46 1 TTAAATTATT 0.860652 -89 TTAATATCTAATATATATTTTTCGGTAGTTTA 1 73 0 ATATATTTTT 0.71508 -62 ATATTAGATATTAAAAATTTTTGTTCATATCA 1 91 1 TTAAATTTTT 0.8996 -44 CTATCACATTTTTTGAATTATT 2 1 0 TTTTATTATT 0.808887 -23 TAATATAAATTTTACTATTATTATTGTTATTA 5 31 1 TTTAATTATT 0.874735 -102 TTTAAATAAAATAAGGTTTTTTATAATTTATG 5 92 0 ATAATTTTTT 0.773919 -41 ATCTAATTTTTTAATATTTTTTAAATCCAAAT 7 11 1 TTAATTTTTT 0.881059 -154 TAATGATTAATTTTTCTTTTTTAGTAATAAAC 9 83 0 TTTTTTTTTT 0.835425 -199 AAAAGAAAAATTAATCATTATTAAAAATGTCT 9 95 1 TTAAATTATT 0.860652 -187 TGTTTTTTTCATATTTTTTATTACTTATTTAA 9 132 0 ATATTTTATT 0.5885 -150 TAATGAGTTATTTTGTTTTTTTCATATTTTTT 9 145 0 TTTTTTTTTT 0.835425 -137 AGTAACAAAATTAAAGTTTATTTTATTAATAA 9 179 1 TTAATTTATT 0.836223 -103 TATAAATGTGTTAAGTTTTTTTGAATTATATT 9 247 1 TTAATTTTTT 0.881059 -35 ATATTATATAATTACTATTATTATTACTAATA 10 27 1 ATTAATTATT 0.763427 -163 TACTAATACTTTAAAGCTTTTTGATACGGAAG 10 51 1 TTAACTTTTT 0.50126 -139 AACCAACAATATTATCATTATTTTTAATAACT 10 81 0 ATTAATTATT 0.763429 -109 TATGAGCAATATTTAAATTTTTCGAGATAGAT 10 115 0 ATTTATTTTT 0.739423 -75 TGTTATGGCAATTTCATTTTTTATATATGAGC 10 140 0 ATTTTTTTTT 0.701123 -50 AATAACTCTTTTTTAAATTTTTAAGATATGCA 11 29 1 TTTTATTTTT 0.859953 -68 TTCTAAGATTATAAATTTTATTCTTTAAACTT 11 63 1 ATAATTTATT 0.702038 -34 CTTTAAACTTTTTATCATTTTT 11 85 1 TTTAATTTTT 0.910161 -12 ATAACCAGCGTTTAGATTTTTTACTTTTATCA 12 33 0 TTTATTTTTT 0.893336 -126 TAATTTTCCCTTTTCTATTTTTGCATTCACAT 12 87 0 TTTTATTTTT 0.859953 -72 CTAATCAATCTTAATCATTTTTAAGGTAATTA 15 93 0 TTAAATTTTT 0.899603 -30 AACTTATTTTTATTTTTGTTTAAGTAT 16 6 1 ATTTATTTTT 0.739424 -295 ACTTTTTTGTTTAAAGTTTATTAAAAATGTCT 16 213 0 TTAATTTATT 0.836223 -88 ATAATACTATTTAAACTTTTTTGTTTAAAGTT 16 227 0 TTAATTTTTT 0.881059 -74 TTTTTTTACTTTTTTAATTTCTATA 17 4 1 TTTTTTTTTT 0.835425 -123 TATCAAAATCTTTAAAATTATTATATTAAAAT 17 61 0 TTTAATTATT 0.874733 -66 AAAGATTTTGATAATTTTTATTGAATAATTAT 17 80 1 ATAATTTATT 0.702338 -47 CATTACAATTTTTATAATTATTCAATAAAAAT 17 93 0 TTTAATTATT 0.874735 -34 **** ****** Masking position 8 Map Score: 51.9312 Number of sites scoring better than the average of aligned sites = 2114 Number in coding regions = 1401 Number in noncoding regions = 713 Number of orfs with sites within 600 bp upstream = 458 Fraction of orfs with sites within 600 bp upstream = 0.0735625 Motif number 4 TTTTTTCTATTTTTTATATAATTTTTATGAATA 1 12 1 TTTATATATT 0.796471 -123 TTTTTATGAATATTGATGTATTTTTAACGATTA 1 33 1 TATATGTATT 0.850551 -102 CTAATATATATTTTTCGGTAGTTTATCAAAAAT 1 65 0 TTTCGGTATT 0.86028 -70 TTTAAAAGCATTATGAGGTATTTAAATTTTG 3 9 0 TTTAGGTATT 0.976857 -72 TTGTTAGGAGTTATTAAGTATTTCATATCATAA 5 64 1 TTTAAGTATT 0.87947 -69 ATTTTTCTTATTTTTAGGTAGATTATAATTGCT 6 268 0 TTTAGGTAAT 0.8879 -33 TTACAATAGATTGTAAGATACATAAAGGTATAT 8 109 0 TTTAGATAAT 0.694818 -122 GTTGCCTTACTATTTAAATAGTTTATTACTAAA 9 63 1 TATAAATATT 0.467177 -219 TTGTTACTATTAATGAGTTATTTTGTTTTTTTC 9 154 0 TATAGTTATT 0.606547 -128 AAATTTTATATAATTAGGTAATTTAATTACCTT 15 70 1 TATAGGTATT 0.946367 -53 TCTTAATCATTTTTAAGGTAATTAAATTACCTA 15 84 0 TTTAGGTATT 0.976856 -39 CATTGTAATATTTTCAGATATTTTTCAATCCAG 16 59 1 TTTAGATATT 0.923854 -242 CTAAATATTATTTTAATGGAATTTTTAATATAG 16 127 0 TTTATGGATT 0.665096 -174 ATTATAAAAATTGTAATGTAATTATTTTGA 17 107 1 TTTATGTATT 0.93157 -20 ** * ***** ** Masking position 10 Map Score: 11.3014 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 211 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 5 CTTTTTTCTATTTTTTATATAATTTT 1 3 1 TTTCTATTTT 0.583394 -132 ATTGTCACCATTTTAGGCTATATG 1 121 0 ATTCACTTTT 0.971628 -14 ACTATCACATTTTTTGAATTATT 2 10 0 ATTCACTTTT 0.971628 -14 TTTTATCCCACTTCTTTACTACATA 4 2 1 TTTCCCTTCT 0.823755 -107 GATGATATTAAAACTCCCGGTCTTGTTAATATGT 6 183 0 AATCCCTCTT 0.663452 -118 TTAAATCCCCATTTTTCTTATTTTT 6 286 0 TATCCCTTTT 0.821825 -15 AATAATGATTAATTTTTCTTTTTTAGTAATAAAC 9 83 0 ATTTTCTTTT 0.623426 -199 TTATTTTGTTTTTTTCATATTTTTTATTACTTAT 9 136 0 TTTCATTTTT 0.653292 -146 AACTATCCCGCTTTTGATATTATAT 10 2 1 ATTCCCTTTT 0.976537 -188 AACCAACAATATTATCATTATTTTTAATAACTTC 10 79 0 ATTCATTTTT 0.786129 -111 TAAAACTTTAAATAACTCTTTTTTAAATTTTTAA 11 19 1 ATACTCTTTT 0.573413 -78 AACTGTGGTAATTTTCCCTTTTCTATTTTTGCAT 12 93 0 ATTCCCTTCT 0.901168 -66 ATGGTAGTGGAAAATCCACATTTTTAAAAACG 12 137 1 AATCCATTTT 0.580137 -22 AATAATATTTAGTATCTCAATTTTGTCAATTTTA 16 148 1 ATTCTCTTTT 0.946685 -153 ATTTTAATTTTATGTAACATTTTTTTATATTAGC 16 176 1 TTTAACTTTT 0.481294 -125 AGTTTCACCCTTTTGGTATTATTT 16 287 0 ATTCACTTTT 0.971628 -14 TTTTTTTACTTTTTTAATTTCTATA 17 2 1 TTTTACTTTT 0.620663 -125 TTCAATAAAAATTATCAAAATCTTTAAAATTATT 17 71 0 ATTCAATCTT 0.535736 -56 * * **** **** Masking position 11 Map Score: 8.48472 Number of sites scoring better than the average of aligned sites = 858 Number in coding regions = 747 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 6 TATTAGAAATAATAATATCATGTTTATAGT 4 39 1 AATAATATCA 0.911341 -70 CGGGAGTTTTAATATCATCAACGAATGTCC 6 198 1 AATATCATCA 0.899435 -103 ATAGTAATTATATAATATCAAAAGCGGGAT 10 15 0 TATAATATCA 0.697252 -175 TTTAACCAACAATATTATCATTATTTTTAA 10 86 0 AATATTATCA 0.962696 -104 TTATTCTTTTAATGGTATCACCTCAAAATG 10 170 0 AATGGTATCA 0.832222 -20 TTGATAGTATAATATTTTCATTAAAAATTT 15 17 0 AATATTTTCA 0.852552 -106 TATACTATCAAATGTCATCAATTTTGTTTA 15 36 1 AATGTCATCA 0.88035 -87 TGGACATTGTAATATTTTCAGATATTTTTC 16 55 1 AATATTTTCA 0.852552 -246 TATAAGATTCAGTGATATCATGCACTGGAT 16 86 0 AGTGATATCA 0.825402 -215 AAGTTTAAATAGTATTATCAACATTAGATA 16 241 1 AGTATTATCA 0.935179 -60 ATTATTTAATTGTGTTATCATCATATCTAA 16 264 0 TGTGTTATCA 0.726717 -37 TTATTCAATAAAAATTATCAAAATCTTTAA 17 78 0 AAAATTATCA 0.749316 -49 ********** Masking position 10 Map Score: 7.71495 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 128 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 TTTAACGATTATTTTTGATAAACTACCGAA 1 55 1 ATTTTTGATA 0.631822 -80 CGAAAAATATATATTAGATATTAAAAATTT 1 81 1 ATATTAGATA 0.936578 -54 CCATTTTAGGCTATATGATATGAACAAAAA 1 108 0 CTATATGATA 0.810673 -27 AGTAAAATTTATATTAGATAATCTTTATAG 5 17 0 ATATTAGATA 0.936578 -116 GTTTTTTATAATTTATGATATGAAATACTT 5 79 0 ATTTATGATA 0.631822 -54 CTTATAAAAGCCATAAGATAAGGATTAAAA 7 141 1 CCATAAGATA 0.871658 -24 CGTTAAATTTATATAAGATAAAGAGTACTA 9 219 1 ATATAAGATA 0.936578 -63 CCCGCTTTTGATATTATATAATTACTATTA 10 17 1 ATATTATATA 0.514468 -173 ATTTTCACCCCATAAGTTAAA 14 3 0 CCATAAGTTA 0.440296 -19 AAAATTGATGACATTTGATAGTATAATATT 15 31 0 ACATTTGATA 0.863031 -92 TATTTGAAAAATATAAGATTCAGTGATATC 16 97 0 ATATAAGATT 0.631061 -204 AGTATTATCAACATTAGATATGATGATAAC 16 251 1 ACATTAGATA 0.923947 -50 ********** Masking position 4 Map Score: 4.66174 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 184 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 8 ATTCATAAAAATTATATAAAAAATAGAAAA 1 14 0 ATTATATAAA 0.797033 -121 TTTAGGCTATATGATATGAACAAAAATTTT 1 104 0 ATGATATGAA 0.87131 -31 AAGATAACAAATTATATTGATATTTAATAA 3 58 1 ATTATATTGA 0.722679 -23 AACTATAAACATGATATTATTATTTCTAAT 4 40 0 ATGATATTAT 0.543289 -69 TTTATAATTTATGATATGAAATACTTAATA 5 75 0 ATGATATGAA 0.87131 -58 ACATTCGTTGATGATATTAAAACTCCCGGT 6 196 0 ATGATATTAA 0.923826 -105 TAAAGTTCATATTTTATGAACATTCAATTT 8 60 0 ATTTTATGAA 0.63415 -171 ATTAAAGTTTATTTTATTAATAATAAAATA 9 188 1 ATTTTATTAA 0.756146 -94 GTTTTTTTGAATTATATTCAGGGGTGATAA 9 261 1 ATTATATTCA 0.722705 -21 TTTTACTTTTATCATATTAATCACCAAGGA 12 17 0 ATCATATTAA 0.77458 -142 AAATTACCTAATTATATAAAATTTGTGTTA 15 64 0 ATTATATAAA 0.797033 -59 TTTTTCAAATACTATATTAAAAATTCCATT 16 116 1 ACTATATTAA 0.706757 -185 GATACTAAATATTATTTTAATGGAATTTTT 16 134 0 ATTATTTTAA 0.619246 -167 CTTTAAAATTATTATATTAAAATCACTCCA 17 54 0 ATTATATTAA 0.942663 -73 ********** Masking position 1 Map Score: 9.87182 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 143 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 9 TGATATGAACAAAAATTTTTAATATCTAATA 1 92 0 AAAAATTTTA 0.61174 -43 TTTAAAATTAATAAAACTTTAAAAGCATTAT 3 28 0 ATAAACTTTA 0.9071 -53 TATAACTTATAAATAACTTTAACTATAAACA 4 59 0 AAATACTTTA 0.94466 -50 CATAAATTATAAAAAACCTTATTTTATTTAA 5 92 1 AAAAACCTTA 0.790986 -41 AGAAAACTTTATATACCTTTATGTATCTTAC 8 99 1 ATATACTTTA 0.85667 -132 ACTACTTTTTATATATCTTTATTTTTAGTAA 9 15 1 ATATACTTTA 0.85667 -267 TCATTATTAAAAATGTCTTTAATTTAAATAA 9 109 1 AAATGCTTTA 0.809929 -173 TTATTAATAAAATAAACTTTAATTTTGTTAC 9 180 0 AATAACTTTA 0.818265 -102 ATTAATAATAAAATACCGTTAAATTTATATA 9 203 1 AAATACGTTA 0.69845 -79 ATATAATTCAAAAAAACTTAACACATTTATA 9 247 0 AAAAACTTAA 0.71854 -35 CTTCCGTATCAAAAAGCTTTAAAGTATTAGT 10 52 0 AAAAACTTTA 0.965232 -138 AAAATTCCTAAAACTTTAAATAACTCTT 11 8 1 CTAAACTTTA 0.709164 -89 AGTTTATTAAAAATGTCTTGAGCTAATATAA 16 200 0 AAATGCTTGA 0.366425 -101 AGACATTTTTAATAAACTTTAAACAAAAAAG 16 213 1 AATAACTTTA 0.818265 -88 AACTTTAAACAAAAAAGTTTAAATAGTATTA 16 227 1 AAAAAGTTTA 0.700511 -74 TAAAAATTATCAAAATCTTTAAAATTATTAT 17 69 0 CAAAACTTTA 0.874304 -58 ***** ***** Masking position 9 Map Score: 11.7642 Number of sites scoring better than the average of aligned sites = 626 Number in coding regions = 529 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 10 ********** No masking Map Score: 4.16621e-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 11 TTATTAGAAATAATAATATCATGTTTATAG 4 38 1 TAATAATATC 0.69106 -71 CTTATTATTCTCTCTTGCGTTT 6 3 1 TATTATTCTC 0.831193 -298 CCGGGAGTTTTAATATCATCAACGAATGTC 6 197 1 TAATATCATC 0.768267 -104 TTAATAAAAATATTATTCCCAAATATAAAA 7 57 0 TATTATTCCC 0.778069 -108 TAGTAATACTTAATATTACCTAAGTTGCCT 9 40 1 TAATATTACC 0.918823 -242 ATTTAACCAACAATATTATCATTATTTTTA 10 87 0 CAATATTATC 0.768267 -103 ACAACTGTGGTAATTTTCCCTTTTCTATTT 12 99 0 TAATTTTCCC 0.609541 -60 TTTGATAGTATAATATTTTCATTAAAAATT 15 18 0 TAATATTTTC 0.873665 -105 ATGGACATTGTAATATTTTCAGATATTTTT 16 54 1 TAATATTTTC 0.873665 -247 AAAGTTTAAATAGTATTATCAACATTAGAT 16 240 1 TAGTATTATC 0.808514 -61 ********** Masking position 4 Map Score: 1.32486 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 170 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 12 ********** No masking Map Score: 4.16621e-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 13 ********** No masking Map Score: 4.16621e-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 14 ********** No masking Map Score: 4.16621e-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