AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02010_mjan_reg_300.orf -o02010_mjan_300.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 MJ0081 300 methyl coenzyme M reductase II, subunit beta (mrtB) #2 MJ0084 261 CODH nickel-insertion accessory protein (cooC) #3 MJ0085 134 iron transport periplasmic binding protein, putative (ceuE) #4 MJ0087 23 hemin permease (hemU) #5 MJ0413 80 nitrate transporter protein (nrtB) homolog (cmpB) #6 MJ0414 108 conserved hypothetical protein #7 MJ0873 132 ferric enterobactin transport ATP-binding protein #8 MJ0876 300 iron(III) dicitrate transport system permease protein #9 MJ1014 164 phosphate transport system permease protein C (pstC) #10 MJ1015 230 periplasmic phosphate-binding protein (pstS) #11 MJ1091 281 cobalamin biosynthesis protein (cbiM) #12 MJ1266 189 high-affinity branched-chain amino acid transport protein (braC) #13 MJ1267 96 high-affinity branched-chain amino acid transport ATP-binding protein (braF) #14 MJ1268 158 high-affinity branched-chain amino acid transport ATP-binding protein (braG) #15 MJ1269 32 high-affinity branched-chain amino acid transport protein (braD) #16 MJ1270 21 high-affinity branched-chain amino acid transport protein (braE) #17 MJ1368 122 sulfate transport system permease protein (cysT) #18 MJ1569 300 cobalamin biosynthesis protein (cbiM) #19 MJ1571 126 cobalt transport protein (cbiQ) Motif number 1 AACTTACGCATTTTTTTGAATCATAAAGAAA 1 82 0 TTTTTTTAAT 0.855613 -219 ATCTTTAAAAAAATTTTGAATTCCTCACAGA 1 132 0 AAATTTTAAT 0.940447 -169 GATTTTAAAGATTTTTTTAATTTTATCATTT 1 160 1 ATTTTTTAAT 0.928019 -141 ATAAAATAGAAAATTTTATATACCTATTACT 1 229 1 AAATTTTTAT 0.901522 -72 CCTATTACTATCATTTTCTATAGCTGTAGTA 1 251 1 TCATTTTTAT 0.816797 -50 TTTTTGGACTTTATTTTTAATTTTAAAATTT 2 38 1 TTATTTTAAT 0.873432 -224 TTTTAATTTTAAAATTTTAATTGGAGGGCAT 2 52 1 AAAATTTAAT 0.900186 -210 AGGTTTTAATTAAATTTAAATCAGACTGAGG 2 234 1 TAAATTTAAT 0.805643 -28 CTTTTTTCTATTTTTTATATAATTTTTATG 3 10 1 ATTTTTTTAT 0.88199 -125 ATATGAACAAAAATTTTTAATATCTAATATA 3 90 0 AAATTTTAAT 0.940447 -45 ACTATCACATTTTTTGAATTATT 4 5 0 ATTTTTTAAT 0.92802 -19 CAAAATTTAAATACCTCATAAT 5 2 1 AAAATTTAAT 0.900186 -79 TAATAATAGTAAAATTTATATTAGATAATCT 7 23 0 AAAATTTTAT 0.839439 -110 ATCTAATTTTTTAATATTTTTTAAA 9 5 1 AATTTTTAAT 0.931321 -160 ATTTTTTAATATTTTTTAAATCCAAATTTAA 9 16 1 ATTTTTTAAT 0.928018 -149 TAAAATTTCTTATCTTTAAATTTGGATTTAA 9 31 0 TATCTTTAAT 0.635206 -134 TAAAGATAAGAAATTTTATATTTGGGAATAA 9 44 1 AAATTTTTAT 0.901522 -121 ATTTGGGAATAATATTTTTATTAAGCAATAT 9 63 1 AATATTTTAT 0.817833 -102 TTTTATAAGTTCTATTTTAATAAGACTTTCG 9 119 0 TCTATTTAAT 0.790429 -46 CCTTTTTTAATCCTTATCTTA 9 154 0 CCTTTTTAAT 0.746768 -11 GAAGTGTTTTACTTTTTATATTGAGTTTTTA 10 22 1 ACTTTTTTAT 0.892815 -209 TTATGAACATTCAATTTTAATAGTTAAAAAC 10 46 0 TCAATTTAAT 0.814548 -185 ATAAAGTTTTCTATTTTGAATTAAAGTTCAT 10 80 0 CTATTTTAAT 0.754987 -151 TCAAAATAGAAAACTTTATATACCTTTATGT 10 92 1 AAACTTTTAT 0.71891 -139 TAGATTTTGTTATTTTTGAATGACACCATAA 10 143 0 TATTTTTAAT 0.861739 -88 AACTTTTTTAATGATTTAAGGT 10 219 0 ACTTTTTAAT 0.934933 -12 AATAACTACTTTTTATATATCTTTATTT 11 8 1 ACTTTTTTAT 0.892815 -274 TTAGTAATAAACTATTTAAATAGTAAGGCAA 11 64 0 ACTATTTAAT 0.891375 -218 TAAATTAAAGACATTTTTAATAATGATTAAT 11 104 0 ACATTTTAAT 0.943608 -178 AAAAATGTCTTTAATTTAAATAAGTAATAAA 11 117 1 TTAATTTAAT 0.797615 -165 TGTTTTTTTCATATTTTTTATTACTTATTTA 11 133 0 ATATTTTTAT 0.896947 -149 AAAATACCGTTAAATTTATATAAGATAAAGA 11 212 1 TAAATTTTAT 0.70614 -70 ATGTGTTAAGTTTTTTTGAATTATATTCAGG 11 252 1 TTTTTTTAAT 0.855613 -30 AATATTATCATTATTTTTAATAACTTCCGTA 12 75 0 TTATTTTAAT 0.873432 -115 TCTATCTCGAAAAATTTAAATATTGCTCATA 12 116 1 AAAATTTAAT 0.900186 -74 TGGCAATTTCATTTTTTATATATGAGCAATA 12 136 0 ATTTTTTTAT 0.88199 -54 TTATTCTTTTAATGGTATCACCT 12 177 0 ATTCTTTAAT 0.7827 -13 AAAATTCCTAAAACTTTAAATAACTCTTTTT 13 11 1 AAACTTTAAT 0.81522 -86 TTAAATAACTCTTTTTTAAATTTTTAAGATA 13 26 1 CTTTTTTAAT 0.72573 -71 TTTATTCTTTAAACTTTTTATCATTTTT 13 79 1 AAACTTTTAT 0.71891 -18 GGTATAATTTTTATAAAACCTAAT 15 4 1 ATAATTTTAT 0.832516 -29 TTTAATAAATTTTTAATGAAAATATTA 17 7 1 AAATTTTAAT 0.940447 -116 TGTTTAACACAAATTTTATATAATTAGGTAA 17 60 1 AAATTTTTAT 0.901522 -63 AACTTATTTTTATTTTTGTTTAA 18 3 1 CTTATTTTAT 0.466957 -298 TATTTTCAGATATTTTTCAATCCAGTGCATG 18 67 1 TATTTTTAAT 0.861739 -234 GATACTAAATATTATTTTAATGGAATTTTTA 18 133 0 ATTATTTAAT 0.880426 -168 CTCAATTTTGTCAATTTTAATTTTATGTAAC 18 163 1 TCAATTTAAT 0.814548 -138 TTATGTAACATTTTTTTATATTAGCTCAAGA 18 185 1 TTTTTTTTAT 0.774533 -116 TTAGCTCAAGACATTTTTAATAAACTTTAAA 18 205 1 ACATTTTAAT 0.943608 -96 TTTTTTTACTTTTTTAATTTCTATATTC 19 8 1 ACTTTTTAAT 0.934933 -119 AAAGATTTTGATAATTTTTATTGAATAATTA 19 80 1 ATAATTTTAT 0.832516 -47 TAATTACATTACAATTTTTATAATTATTCAA 19 100 0 ACAATTTTAT 0.84709 -27 ******* *** Masking position 6 Map Score: 74.263 Number of sites scoring better than the average of aligned sites = 2123 Number in coding regions = 1498 Number in noncoding regions = 625 Number of orfs with sites within 600 bp upstream = 459 Fraction of orfs with sites within 600 bp upstream = 0.0737231 Motif number 2 TAAAAAAATCTTTAAAATCTTTAAAAAAATTTTG 1 145 0 TTTAAATTAA 0.734765 -156 TTTTAAAGATTTTTTTAATTTTATCATTTTAATA 1 162 1 TTTTTATTAT 0.707833 -139 ATTTTATCATTTTAATATTATTATTTTAACATTT 1 179 1 TTTATAATAT 0.82209 -122 TTGGACTTTATTTTTAATTTTAAAATTTTAATTG 2 41 1 TTTTAATTAA 0.737598 -221 ATCAAAAGTTTTAGATAAAATAATATTAATGGAA 2 104 1 TTAATAATAT 0.888915 -158 ACCTAATATCTTATTTAGTATAAATCTTTTTCTA 2 204 0 TTATTAATAA 0.915759 -58 ATATTAGGTTTTAATTAAATTTAAATCAGACTGA 2 229 1 TTATTATTAA 0.758632 -33 TATTGATGTATTTTTAACGATTATTTTTGATAAA 3 43 1 TTTTAAATAT 0.866474 -92 TTAATAAAACTTTAAAAGCATTATGAGGTATTTA 5 18 0 TTTAAAATAT 0.866469 -63 TTTTAAAGTTTTATTAATTTTAAAAGATAACAAA 5 35 1 TTATAATTAA 0.782376 -46 CTTTTATTAAATATCAATATAATTTGT 5 64 0 TTATAAATAA 0.923896 -17 ACATAATTTATTAGAAATAATAATATCATGTTTA 6 31 1 TTAAAAATAT 0.898553 -78 CTCCTAACAATTAATAACAATAATAATAGTAAAA 7 40 0 TTATAAATAT 0.898278 -93 TTATTAAGTATTTCATATCATAAATTATAAAAAA 7 74 1 TTTATAATAA 0.888514 -59 GACCGGGAGTTTTAATATCATCAACGAATGTCCT 8 195 1 TTTATAATAA 0.887971 -106 AAATTTGGATTTAAAAAATATTAAAAAATTAGAT 9 11 0 TTAAAAATAA 0.889251 -154 AAATATAAAATTTCTTATCTTTAAATTTGGATTT 9 33 0 TTTTTATTAA 0.767049 -132 TTATATTGAGTTTTTAACTATTAAAATTGAATGT 10 37 1 TTTTAAATAA 0.898035 -194 ATAGAAAACTTTATATACCTTTATGTATCTTACA 10 97 1 TTAATATTAT 0.768197 -134 ATATTAAGTATTACTAAAAATAAAGATATATAAA 11 22 0 TTATAAATAA 0.923423 -260 AAAGACATTTTTAATAATGATTAATTTTTCTTTT 11 95 0 TTATAAATAA 0.800362 -187 TTTTTATTACTTATTTAAATTAAAGACATTTTTA 11 116 0 TTATTATTAA 0.818842 -166 AAACTTTAATTTTGTTACTATTAATGAGTTATTT 11 164 0 TTTTTAATAA 0.888211 -118 AAAGTTTATTTTATTAATAATAAAATACCGTTAA 11 191 1 TTATAAATAA 0.871189 -91 ACCGTTAAATTTATATAAGATAAAGAGTACTATA 11 217 1 TTAATAATAA 0.916287 -65 ATAATAGTAATTATATAATATCAAAAGCGGGATA 12 14 0 TTAATAATAA 0.916286 -176 CTTTAAAGTATTAGTAATAATAATAGTAATTATA 12 33 0 TTATAAATAT 0.898278 -157 ACGGAAGTTATTAAAAATAATGATAATATTGTTG 12 76 1 TTAAAAATAT 0.89829 -114 AATAACTCTTTTTTAAATTTTTAAGATATGCAAG 13 29 1 TTTAAATTAA 0.756862 -68 AGCGTTTAGATTTTTTACTTTTATCATATTAATC 14 25 0 TTTTTATTAT 0.707833 -134 TTCATTAGGTTTTATAAAAATTATACC 15 4 0 TTTTAAATAT 0.865854 -29 ATTGATGACATTTGATAGTATAATATTTTCATTA 17 24 0 TTTATAATAT 0.854016 -99 TTTAATTACCTTAAAAATGATTAAGATTGATTAG 17 91 1 TTAAAAATAA 0.862769 -32 TAAAAAAATGTTACATAAAATTAAAATTGACAAA 18 169 0 TTAATAATAA 0.916019 -132 CAAGACATTTTTAATAAACTTTAAACAAAAAAGT 18 211 1 TTATAATTAA 0.832869 -90 ACAAAAAAGTTTAAATAGTATTATCAACATTAGA 18 235 1 TTAATAATAT 0.888624 -66 ATTATCAACATTAGATATGATGATAACACAATTA 18 254 1 TTAATAATAT 0.888917 -47 TATCAAAATCTTTAAAATTATTATATTAAAATCA 19 59 0 TTTAAAATAT 0.834059 -68 *** *** ** ** Masking position 7 Map Score: 64.2517 Number of sites scoring better than the average of aligned sites = 945 Number in coding regions = 635 Number in noncoding regions = 310 Number of orfs with sites within 600 bp upstream = 277 Fraction of orfs with sites within 600 bp upstream = 0.0444908 Motif number 3 TAAAATGATAAAATTAAAAAAATCTTTAAAA 1 162 0 AAATTAAAAA 0.954743 -139 AAAAATGTTAAAATAATAATATTAAAATGAT 1 184 0 AAATAAAATA 0.788902 -117 TTTTTAGGATAAAATAGAAAATTTTATATAC 1 221 1 AAAATAAAAA 0.90212 -80 ATAAAACTTAAAATAAGATAATAAAGA 2 7 0 AAATAAATAA 0.794626 -255 AATAAAGTCCAAAAAATAAAACTTAAAATAA 2 22 0 AAAAAAAAAA 0.935307 -240 CCTCCAATTAAAATTTTAAAATTAAAAATAA 2 48 0 AAATTTAAAA 0.71153 -214 AATTATATAAAAAATAGAAAAAAG 3 4 0 AAAATAAAAA 0.90212 -131 ATATTCATAAAAATTATATAAAAAATAGAAA 3 15 0 AAATTAATAA 0.71153 -120 TATCTTTTAAAATTAATAAAACTTTAAAAGC 5 33 0 AATTAAAAAA 0.588521 -48 AATTTATTAGAAATAATAATATCATGTTTAT 6 35 1 AAATAAAATA 0.788902 -74 TTCATATCATAAATTATAAAAAACCTTATTT 7 85 1 AAATTAAAAA 0.954743 -48 AATGATTTTTAAATAAAATAAGGTTTTTTAT 7 100 0 AAATAAATAA 0.794626 -33 ATCTACCTAAAAATAAGAAAAATGGGGATTT 8 278 1 AAATAAAAAA 0.970668 -23 TGGATTTAAAAAATATTAAAAAATTAGAT 9 9 0 AAATATAAAA 0.794626 -156 AACTCAATATAAAAAGTAAAACACTTCTTTG 10 18 0 AAAAAGAAAA 0.497877 -213 ACTTTAATTCAAAATAGAAAACTTTATATAC 10 84 1 AAAATAAAAA 0.90212 -147 TGTCATTCAAAAATAACAAAATCTACTAATG 10 149 1 AAATAAAAAA 0.970668 -82 GTTTATTACTAAAAAAGAAAAATTAATCATT 11 83 1 AAAAAAAAAA 0.935307 -199 TAATTTAAATAAGTAATAAAAAATATGAAAA 11 128 1 AAGTAAAAAA 0.679469 -154 AAAAATATGAAAAAAACAAAATAACTCATTA 11 146 1 AAAAAAAAAA 0.935307 -136 TTTATTTTATTAATAATAAAATACCGTTAAA 11 195 1 TAATAAAAAA 0.716071 -87 GCTCATATATAAAAAATGAAATTGCCATAAC 12 140 1 AAAAAAGAAA 0.472723 -50 CATATCTTAAAAATTTAAAAAAGAGTTATTT 13 28 0 AAATTTAAAA 0.71153 -69 TAAAAAGTTTAAAGAATAAAATTTATAATCT 13 68 0 AAAGAAAAAA 0.8473 -29 AAAAATGATAAAAAGTTTAAAGA 13 84 0 AAATGAAAAA 0.768913 -13 TAATATGATAAAAGTAAAAAATCTAAACGCT 14 28 1 AAAGTAAAAA 0.779606 -131 TGTGAATGCAAAAATAGAAAAGGGAAAATTA 14 88 1 AAAATAAAAA 0.90212 -71 ACTTAAACAAAAATAAAAATAAGTT 18 5 0 AAATAAAATA 0.788902 -296 TCTTGAGCTAATATAAAAAAATGTTACATAA 18 185 0 ATATAAAAAA 0.580639 -116 ATGAATATAGAAATTAAAAAAGTAAAAAAA 19 10 0 AAATTAAAAA 0.954743 -117 ATCACTCCAAAAATAATAGAAGATGAATATA 19 32 0 AAATAAAGAA 0.69415 -95 TTTTATTGAATAATTATAAAAATTGTAATGT 19 95 1 TAATTAAAAA 0.616531 -32 ****** **** Masking position 11 Map Score: 41.8433 Number of sites scoring better than the average of aligned sites = 1383 Number in coding regions = 953 Number in noncoding regions = 430 Number of orfs with sites within 600 bp upstream = 304 Fraction of orfs with sites within 600 bp upstream = 0.0488275 Motif number 4 AATAATATTAAAATGATAAAATTAAAAAAA 1 171 0 AAATGATAAA 0.664389 -130 TTTTTAGGATAAAATAGAAAATTTTATATA 1 221 1 AAAATAGAAA 0.919241 -80 ATAAAACTTAAAATAAGATAATAAAGA 2 8 0 AAATAAGATA 0.771892 -254 AATAAAGTCCAAAAAATAAAACTTAAAATA 2 23 0 AAAAAATAAA 0.79596 -239 TAAAATTTTAAAATTAAAAATAAAGTCCAA 2 41 0 AAATTAAAAA 0.749771 -221 GATTTATACTAAATAAGATATTAGGTTTTA 2 212 1 AAATAAGATA 0.771892 -50 AATTATATAAAAAATAGAAAAAAG 3 5 0 AAAATAGAAA 0.919241 -130 ATATTCATAAAAATTATATAAAAAATAGAA 3 16 0 AAATTATATA 0.587159 -119 AAACTACCGAAAAATATATATTAGATATTA 3 74 1 AAAATATATA 0.518219 -61 TTCATATCATAAATTATAAAAAACCTTATT 7 85 1 AAATTATAAA 0.851014 -48 ATCTACCTAAAAATAAGAAAAATGGGGATT 8 278 1 AAATAAGAAA 0.931462 -23 CCAAATTTAAAGATAAGAAATTTTATATTT 9 37 1 AGATAAGAAA 0.565069 -128 ACTTTAATTCAAAATAGAAAACTTTATATA 10 84 1 AAAATAGAAA 0.919241 -147 TGTCATTCAAAAATAACAAAATCTACTAAT 10 149 1 AAATAACAAA 0.744952 -82 GTTTATTACTAAAAAAGAAAAATTAATCAT 11 83 1 AAAAAAGAAA 0.911335 -199 TCTTTAATTTAAATAAGTAATAAAAAATAT 11 124 1 AAATAAGTAA 0.467119 -158 AAAAATATGAAAAAAACAAAATAACTCATT 11 146 1 AAAAAACAAA 0.688377 -136 AAAAATGATAAAAAGTTTAAAG 13 85 0 AAATGATAAA 0.664389 -12 TGTGAATGCAAAAATAGAAAAGGGAAAATT 14 88 1 AAAATAGAAA 0.919241 -71 TACTTAAACAAAAATAAAAATAAGTT 18 7 0 AAAATAAAAA 0.693826 -294 ATGAATATAGAAATTAAAAAAGTAAAAAAA 19 11 0 AAATTAAAAA 0.749771 -116 ********** Masking position 6 Map Score: 19.4316 Number of sites scoring better than the average of aligned sites = 835 Number in coding regions = 601 Number in noncoding regions = 234 Number of orfs with sites within 600 bp upstream = 221 Fraction of orfs with sites within 600 bp upstream = 0.0354963 Motif number 5 AAAAAAATCTTTAAAATCTTTAAAAAAATTT 1 147 0 TTAAAATTTT 0.619546 -154 TTTTATCATTTTAATATTATTATTTTAACAT 1 180 1 TTAATATATT 0.942366 -121 TATATACCTATTACTATCATTTTCTATAGCT 1 245 1 TTACTATATT 0.888872 -56 GTCTCTTCCATTAATATTATTTTATCTAAAA 2 112 0 TTAATATATT 0.942366 -150 TCAATATTCATAAAAATTATATAAAAAATAG 3 18 0 TAAAAATATA 0.483018 -117 TTGTTATCTTTTAAAATTAATAAAACTTTAA 5 37 0 TTAAAATAAT 0.619546 -44 TTATTAAATATCAATATAATTTGTTATCTTT 5 57 0 TCAATATATT 0.781759 -24 AATATAAATTTTACTATTATTATTGTTATTA 7 32 1 TTACTATATT 0.888872 -101 TTATTTTATTTAAAAATCATTTGAGTGATGC 7 110 1 TAAAAATATT 0.798784 -23 ACCGGGAGTTTTAATATCATCAACGAATGTC 8 196 1 TTAATATATC 0.634212 -105 ATCTAATTTTTTAATATTTTTTAAATCCAAA 9 11 1 TTAATATTTT 0.639304 -154 ATATACAATGTTACAATTATTTAATCCTGCG 9 90 1 TTACAATATT 0.880223 -75 TTTAATTTTGTTACTATTAATGAGTTATTTT 11 163 0 TTACTATAAT 0.464396 -119 TTATCACCCCTGAATATAATTCAAAAAAACT 11 260 0 TGAATATATT 0.660606 -22 TATTATATAATTACTATTATTATTACTAATA 12 28 1 TTACTATATT 0.888872 -162 TCCTTGGTGATTAATATGATAAAAGTAAAAA 14 17 1 TTAATATATA 0.793764 -142 TTAGGTTTTATAAAAATTATACC 15 3 0 TAAAAATATA 0.483018 -30 TAACACAAATTTTATATAATTAGGTAATTTA 17 64 1 TTTATATATT 0.489818 -59 TTAATTACCTTAAAAATGATTAAGATTGATT 17 92 1 TAAAAATATT 0.798783 -31 AAAAATTCCATTAAAATAATATTTAGTATCT 18 134 1 TTAAAATATA 0.779549 -167 ATCAAAATCTTTAAAATTATTATATTAAAAT 19 61 0 TTAAAATATT 0.937588 -66 ATTACAATTTTTATAATTATTCAATAAAAAT 19 93 0 TTATAATATT 0.532029 -34 TCAAAATAATTACATTACAAT 19 116 0 TCAAAATATT 0.766959 -11 ******* *** Masking position 7 Map Score: 19.2298 Number of sites scoring better than the average of aligned sites = 563 Number in coding regions = 418 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 6 GAATTCAAAATTTTTTTAAAGATTTTAAAG 1 140 1 TTTTTTTAAA 0.754639 -161 ATTTTAAAGATTTTTTTAATTTTATCATTT 1 161 1 TTTTTTTAAT 0.803471 -140 ACACCAACCTTTTTGTTAATATATTACTAC 1 276 0 TTTTGTTAAT 0.924205 -25 TATCTAAAACTTTTGATAAAATGTTTGAAT 2 91 0 TTTTGATAAA 0.874123 -171 TATCAAAAGTTTTAGATAAAATAATATTAA 2 103 1 TTTAGATAAA 0.249223 -159 TAACGATTATTTTTGATAAACTACCGAAAA 3 57 1 TTTTGATAAA 0.874123 -78 TATTAAAAATTTTTGTTCATATCATATAGC 3 99 1 TTTTGTTCAT 0.757562 -36 GCTTTTAAAGTTTTATTAATTTTAAAAGAT 5 33 1 TTTTATTAAT 0.723175 -48 CTTTTATTAAATATCAATATA 5 70 0 TTTTATTAAA 0.662792 -11 AAAATAAGGTTTTTTATAATTTATGATATG 7 87 0 TTTTTATAAT 0.755239 -46 AAAAACCTTATTTTATTTAAAAATCATTTG 7 103 1 TTTTATTTAA 0.340157 -30 AAACTCCCGGTCTTGTTAATATGTCTGCAA 8 177 0 TCTTGTTAAT 0.473638 -124 GGGAATAATATTTTTATTAAGCAATATACA 9 67 1 TTTTTATTAA 0.378458 -98 CATTAGTAGATTTTGTTATTTTTGAATGAC 10 150 0 TTTTGTTATT 0.526712 -81 AGTTATTTTGTTTTTTTCATATTTTTTATT 11 142 0 TTTTTTTCAT 0.511656 -140 TAAACTTTAATTTTGTTACTATTAATGAGT 11 169 0 TTTTGTTACT 0.483307 -113 TTAAAGTTTATTTTATTAATAATAAAATAC 11 189 1 TTTTATTAAT 0.723175 -93 ACTATCCCGCTTTTGATATTATATAATTAC 12 12 1 TTTTGATATT 0.456506 -178 TTCTTTAAACTTTTTATCATTTTT 13 83 1 TTTTTATCAT 0.441584 -14 GGTATAATTTTTATAAAACCTAATGAA 15 8 1 TTTTTATAAA 0.698726 -25 ATGTCATCAATTTTGTTTAACACAAATTTT 17 47 1 TTTTGTTTAA 0.70641 -76 TTATTTTTATTTTTGTTTAAGTATAAATCT 18 14 1 TTTTGTTTAA 0.70641 -287 AGTATCTCAATTTTGTCAATTTTAATTTTA 18 158 1 TTTTGTCAAT 0.464348 -143 CTCAAGACATTTTTAATAAACTTTAAACAA 18 209 1 TTTTAATAAA 0.597105 -92 ATTTAAACTTTTTTGTTTAAAGTTTATTAA 18 221 0 TTTTGTTTAA 0.70641 -80 TCATATCTAATGTTGATAATACTATTTAAA 18 244 0 TGTTGATAAT 0.404461 -57 ATTTTAAAGATTTTGATAATTTTTATTGAA 19 75 1 TTTTGATAAT 0.90199 -52 TACATTACAATTTTTATAATTATTCAATAA 19 97 0 TTTTTATAAT 0.755239 -30 ********** Masking position 3 Map Score: 23.9838 Number of sites scoring better than the average of aligned sites = 1211 Number in coding regions = 981 Number in noncoding regions = 230 Number of orfs with sites within 600 bp upstream = 221 Fraction of orfs with sites within 600 bp upstream = 0.0354963 Motif number 7 TAAATAAGATATTAGGTTTTAATTAAATTT 2 221 1 ATTAGGTTTT 0.857131 -41 AAAAATATATATTAGATATTAAAAATTTTT 3 83 1 ATTAGATATT 0.89848 -52 TAAAAGCATTATGAGGTATTTAAATTTTG 5 10 0 ATGAGGTATT 0.819934 -71 TAAAATTTATATTAGATAATCTTTATAGTC 7 15 0 ATTAGATAAT 0.869859 -118 GTTAGGAGTTATTAAGTATTTCATATCATA 7 66 1 ATTAAGTATT 0.89848 -67 CTTTCGCAGGATTAAATAATTGTAACATTG 9 95 0 ATTAAATAAT 0.723027 -70 CTTAGGTAATATTAAGTATTACTAAAAATA 11 34 0 ATTAAGTATT 0.89848 -248 AGTAAGGCAACTTAGGTAATATTAAGTATT 11 44 0 CTTAGGTAAT 0.792745 -238 ATGTGTTCATTAGGTTTTATAAAAATTA 15 15 0 ATTAGGTTTT 0.857131 -18 ATTTTATATAATTAGGTAATTTAATTACCT 17 72 1 ATTAGGTAAT 0.939999 -51 TGATAACACAATTAAATAATACCAAAAGGG 18 274 1 ATTAAATAAT 0.723027 -27 ********** Masking position 4 Map Score: 7.99912 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 112 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 8 AATTTTATCATTTTAATATTATTATTTTAA 1 178 1 TTTTAATATT 0.597005 -123 TTTTAGTAATTTTTAGGATAAAATAGAAAA 1 212 1 TTTTAGGATA 0.757021 -89 CCAACCTTTTTGTTAATATATTACTACAGC 1 273 0 TGTTAATATA 0.52036 -28 CTAATATCTTATTTAGTATAAATCTTTTTC 2 206 0 ATTTAGTATA 0.247772 -56 TTTTTTCTATTTTTTATATAATTTTTATGA 3 12 1 TTTTTATATA 0.744057 -123 GAACAAAAATTTTTAATATCTAATATATAT 3 87 0 TTTTAATATC 0.696186 -48 ATTGTCACCATTTTAGGCTATATGATATGA 3 115 0 TTTTAGGCTA 0.258963 -20 AGACCGGGAGTTTTAATATCATCAACGAAT 8 194 1 TTTTAATATC 0.696186 -107 ATTTTTCTTATTTTTAGGTAGATTATAATT 8 271 0 TTTTTAGGTA 0.624229 -30 ATCTAATTTTTTAATATTTTTTAAATCC 9 9 1 TTTTAATATT 0.597005 -156 TAAATCCAAATTTAAAGATAAGAAATTTTA 9 32 1 TTTAAAGATA 0.417552 -133 TTACAATAGATTGTAAGATACATAAAGGTA 10 112 0 TTGTAAGATA 0.671381 -119 TTTTTTAATGATTTAAGGTATAGATGAACG 10 208 0 ATTTAAGGTA 0.435225 -23 AATAACTACTTTTTATATATCTTTATTTT 11 10 1 TTTTTATATA 0.744057 -272 GCAATTTCATTTTTTATATATGAGCAATAT 12 135 0 TTTTTATATA 0.744057 -55 TTTTTTAAATTTTTAAGATATGCAAGTTCT 13 37 1 TTTTAAGATA 0.927306 -60 TTTAATAAATTTTTAATGAAAATATTATAC 17 11 1 TTTTAATGAA 0.451685 -112 TCTTAATCATTTTTAAGGTAATTAAATTAC 17 87 0 TTTTAAGGTA 0.881553 -36 CATTGTAATATTTTCAGATATTTTTCAATC 18 59 1 TTTTCAGATA 0.561906 -242 TTAATGGAATTTTTAATATAGTATTTGAAA 18 118 0 TTTTAATATA 0.928698 -183 CTAAATATTATTTTAATGGAATTTTTAATA 18 130 0 TTTTAATGGA 0.409119 -171 CTCAAGACATTTTTAATAAACTTTAAACAA 18 209 1 TTTTAATAAA 0.585386 -92 TTTGGAGTGATTTTAATATAATAATTTTAA 19 52 1 TTTTAATATA 0.928698 -75 ATTATAAAAATTGTAATGTAATTATTTTGA 19 107 1 TTGTAATGTA 0.548963 -20 ********** Masking position 4 Map Score: 13.1032 Number of sites scoring better than the average of aligned sites = 1036 Number in coding regions = 769 Number in noncoding regions = 267 Number of orfs with sites within 600 bp upstream = 242 Fraction of orfs with sites within 600 bp upstream = 0.0388693 Motif number 9 GTATAGCCTCTGCGTAAGTTCCATTGTGGGAGT 1 20 0 TCGAAGTTCA 0.906015 -281 TTCAAAAAAATGCGTAAGTTCTATTGAATAGGG 1 93 1 TCGAAGTTTA 0.957983 -208 CAAACATTTTATCAAAAGTTTTAGATAAAATAA 2 94 1 ACAAAGTTTA 0.632 -168 TTCTATTTTTTATATAATTTTTATGAATATTGA 3 16 1 TTAAATTTTA 0.627047 -119 CTCATAATGCTTTTAAAGTTTTATTAATTTTAA 5 25 1 TTTAAGTTTA 0.676892 -56 GTTAAAGTTATTTATAAGTTATACATGAAGCCA 6 67 1 TTAAAGTTTA 0.930015 -42 GCGTTTTAACTGCAACAGTTGTAGCATTTACTG 8 27 1 TCACAGTTTA 0.703074 -274 CATAGATATGTTTGGAAGTTCCACAAATCATTC 8 102 0 TTGAAGTTCA 0.872266 -199 TATTTAATCCTGCGAAAGTCTTATTAAAATAGA 9 107 1 TCGAAGTCTA 0.755702 -58 TCTTATGGCTTTTATAAGTTCTATTTTAATAAG 9 126 0 TTAAAGTTTA 0.930017 -39 AAAGAAGGCGTTCAAAATTTTCATTAGTAGATT 10 168 0 TCAAATTTCA 0.500878 -63 AGCTTTTTGATACGGAAGTTATTAAAAATAATG 12 65 1 TCGAAGTTTT 0.676083 -125 ATTTTTAAGATATGCAAGTTCTAAGATTATAAA 13 45 1 TTGAAGTTTA 0.941694 -52 CATTAGGTTTTATAAAAATTATACC 15 3 0 TTAAAATTTA 0.626602 -30 ATTGAATAATTATAAAAATTGTAATGTAATTAT 19 99 1 TTAAAATTTA 0.626412 -28 * ** ***** ** Masking position 7 Map Score: 6.21029 Number of sites scoring better than the average of aligned sites = 332 Number in coding regions = 244 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 10 ACCTAAGTTTTTATGGCTTCATGTATAACTTA 6 81 0 TTTGGTTCAT 0.844509 -28 CTATTGTAAATTATGGTGTCATTCAAAAATAA 10 133 1 TTTGGGTCAT 0.972305 -98 TTGAATTATATTCAGGGGTGATAAC 11 267 1 TTAGGGTGAT 0.943081 -15 TGCCATAACATTTTGAGGTGATACCATTAAAA 12 162 1 TTTGAGTGAT 0.912214 -28 TTTAACTTATGGGGTGAAAAT 16 7 1 TTTGGGTGAA 0.943088 -15 CTTCTATTATTTTTGGAGTGATTTTAATATAA 19 41 1 TTTGGGTGAT 0.985331 -86 ** *** ***** Masking position 9 Map Score: 0.413673 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 6 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 11 ********** No masking Map Score: -4.85057e-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 12 ********** No masking Map Score: -4.85057e-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: -4.85057e-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