AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00720_mjan_reg_100.orf -o00720_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 MJ0087 23 hemin permease (hemU) MJ0266 27 pyruvate ferredoxin oxidoreductase, subunit beta (porB) MJ1425 25 malate dehydrogenase MJ0267 21 pyruvate ferredoxin oxidoreductase, subunit alpha (porA) Input sequences: #1 MJ0033 254 succinate dehydrogenase, flavoprotein subunit (sdhA) #2 MJ0085 134 iron transport periplasmic binding protein, putative (ceuE) #3 MJ0090 80 collagenase (prtC) #4 MJ0091 95 Na+/Ca+ exchanger protein, putative #5 MJ0210 86 succinyl-CoA synthetase, beta subunit #6 MJ0269 283 pyruvate ferredoxin oxidoreductase, subunit gamma (porG) #7 MJ0276 119 2-ketoglutarate ferredoxin oxidoreductase, subunit alpha (korA) #8 MJ0537 276 2-ketoglutarate ferredoxin oxidoreductase, subunit beta (korB) #9 MJ0542 127 phosphoenolpyruvate synthase #10 MJ0617 108 tartrate dehydratse, subunit beta (ttdB) #11 MJ0720 194 3-isopropylmalate dehydrogenase 1 (leuB1) #12 MJ1246 300 succinyl-CoA synthetase, alpha subunit (sucD) #13 MJ1296 38 biotin synthetase (bioB) #14 MJ1424 202 tRNA intron endonuclease (endA) #15 MJ1596 226 3-isopropylmalate dehydrogenase 2 (leuB2) Motif number 1 AAAATAGTAATATTTTTAATAAGGCACTGGTA 1 110 0 TATTTTAAAA 0.878056 -145 TATACTATGCCAATTTTTTCATTTAGGATTAT 1 159 1 CATTTTTTAT 0.745059 -96 CATTTAGGATTATTTTTTTCATCAAAGCTATT 1 178 1 TATTTTTTAT 0.891949 -77 TTTGATTTATAAGTTTTAAATATCTGATGAGG 1 209 1 AATTTTAATA 0.644697 -46 CTTTTTTCTATTTTTTATATAATTTTTATG 2 9 1 TATTTTTAAT 0.924834 -126 TTTTTTATATAATTTTTATGAATATTGATGTA 2 21 1 AATTTTATAA 0.812488 -114 TATGAACAAAAATTTTTAATATCTAATATATA 2 88 0 AATTTTAAAT 0.936786 -47 TGGTTATTGCTATTTTATACTTCAAATATAAT 3 36 1 TATTTATATT 0.660298 -45 ACTTCAAATATAATTTAAAATTTAAAAAAATT 3 54 1 TATTTAAATT 0.509583 -27 AATTTTGCTTAAGTTTAAATATTATTGCAGAA 4 32 1 AATTTAAAAT 0.87403 -64 TTCAAAAACAAACTTTAATTAATTTAGTAGGG 4 68 1 AATTTAATAA 0.701979 -28 TTTATCACCAAATTTTTTATATGATAATTTTA 5 23 1 AATTTTTAAT 0.91687 -64 TTTTATATGATAATTTTAAAATTTTGCATTAA 5 37 1 TATTTTAAAT 0.943022 -50 CCATGTAAATTAATTTTATTTTTTCTTATGCC 6 168 1 TATTTTATTT 0.767686 -116 AAATCTCCAAAACTTTATATATTACTTTTAAT 6 223 1 AATTTATAAT 0.857 -61 CTTTATATATTACTTTTAATAATTGTTAATGA 6 235 1 TATTTTAAAA 0.878056 -49 CCCATGCTTCTATTTTTTTAAATTGTTATTTT 7 20 1 TATTTTTTAA 0.78211 -100 CCTTCTAAGCTACTTTTATATAATATAACCTT 7 88 0 TATTTTATTA 0.589666 -32 AGTTAAGCCCTATTTTAATCAAACGAACTCAT 8 202 0 TATTTAATAA 0.724393 -75 CACCTCAAATAATTTTTAATTTATAATGGATA 8 250 0 AATTTTAATT 0.800908 -27 AACTTTTTTTAATTTTTTATAACATTTTCACT 9 17 1 AATTTTTAAA 0.827465 -111 ATAACTCTACTATTTTATTTATAATATTATCA 9 53 1 TATTTATTAT 0.817845 -75 ATTTTAAAATAAATTTAAATATTTGAATGATA 9 80 0 AATTTAAAAT 0.87403 -48 AAAAGGTCTAAATTTTTATGTAAGAGATTTTA 10 21 1 AATTTTATTA 0.562927 -88 TATTTATAATTAGTTTTAAAATCTCTTACATA 10 37 0 TATTTTAAAT 0.943022 -72 ATCAAAACCATAATTTATTTATAATTAGTTTT 10 52 0 TATTTATTAT 0.817845 -57 GTTTTATTTTTAATTTTAAAATCATTTTGGTG 11 16 0 TATTTTAAAT 0.943022 -179 CTTCCCTTAAAAGTTTTATTTTTAATTTTAAA 11 28 0 AATTTTATTT 0.747563 -167 TTTTGTTGAGTATTTTAATCATTTTTGATATG 11 94 1 TATTTAATAT 0.858025 -101 TATGTGAAAGTATTTTTATTAATATTGCTATA 11 151 1 TATTTTATAA 0.82858 -44 GCACCCCCACCATTTTTTAAATAACTTAAATC 12 26 0 CATTTTTAAT 0.813292 -275 AGAACTTTCACAATTTATATATTTATAAGGCA 12 225 0 CATTTATAAT 0.703192 -76 TATCCCCTTTTACTTTTTATATGTGTCGTTGT 12 257 0 TATTTTTAAT 0.924834 -44 TTAAACCGTAAAATTTATATATCCCCTTTTAC 12 276 0 AATTTATAAT 0.857 -25 AATAAACATTAACTTTTAAAATTTA 13 4 0 AATTTTAAAT 0.936786 -35 TAGAACTTCGCAGTTTTTATATTAAAAAGGTA 14 86 0 CATTTTTAAT 0.813292 -117 TATCCACAATAAATTTTAAGATTTTATAAATA 14 175 1 AATTTTAAAT 0.936786 -28 GAAGACAGTATAGTTTAAAGATATTTTTAAGT 15 69 0 TATTTAAAAT 0.893007 -158 AAATTAATTAAAGTTTATTAATAAATATTTGA 15 102 1 AATTTATTAT 0.800986 -125 CAGCACCAAAAACTTTTTTATATAGTGTCTTT 15 202 0 AATTTTTTTA 0.488955 -25 ** ****** ** Masking position 6 Map Score: 50.2498 Number of sites scoring better than the average of aligned sites = 1997 Number in coding regions = 1342 Number in noncoding regions = 655 Number of orfs with sites within 600 bp upstream = 452 Fraction of orfs with sites within 600 bp upstream = 0.0725988 Motif number 2 TTTTTATCACCAAAAATAGGATACCC 1 239 0 TCACCAAAAA 0.980576 -16 CGGTAGTTTATCAAAAATAATCGTTAAAAA 2 53 0 TCAAAAATAA 0.87525 -82 ATTTTATACTTCAAATATAATTTAAAATTT 3 47 1 TCAAATATAA 0.694366 -34 CAGAATATATTCAAAAACAAACTTTAATTA 4 59 1 TCAAAAACAA 0.873047 -37 CCTATCACCTTAAATGATAAATTT 5 73 0 TCACCTTAAA 0.790845 -14 TGACAGTAATTCAACAATAAAGCTGTTTAA 6 36 1 TCAACAATAA 0.941028 -248 AGTGTCATTCTCAAAAATAAATACAACATC 6 114 1 TCAAAAATAA 0.87525 -170 ACACTCACCTTAAACTGTCATTAT 6 270 0 TCACCTTAAA 0.790845 -14 CTTTTCACCAAAAAGGTCTAAATT 10 5 1 TCACCAAAAA 0.980576 -104 TTAATCACCAAAATGATTTTAAAA 11 5 1 TCACCAAAAT 0.883947 -190 ATTAAAATACTCAACAAAAAACAACACAAA 11 83 0 TCAACAAAAA 0.965491 -112 ATGGTTTAAGTCACCAACAAAACATTTTTA 11 123 1 TCACCAACAA 0.965779 -72 AAAAATACTTTCACATAAAAATGTTTTGTT 11 138 0 TCACATAAAA 0.87786 -57 ACTTATCACCAAAAAGATTAATTAT 11 180 0 TCACCAAAAA 0.980576 -15 TATACTGTCTTCAAAATTAATTAAAGTTTA 15 89 1 TCAAAATTAA 0.618734 -138 ATAGTGTCTTTCAAAAACATTTTGAAGTAA 15 183 0 TCAAAAACAT 0.509228 -44 AGACAGCACCAAAAACTTTTTTATA 15 212 0 GCACCAAAAA 0.857336 -15 ********** Masking position 3 Map Score: 20.9992 Number of sites scoring better than the average of aligned sites = 462 Number in coding regions = 343 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 3 TAATATCTAATATATATTTTTCGGTAGTTT 2 74 0 TATATATTTT 0.721266 -61 TTAAATGATAAATTTCTTTTTAATGCAAAA 5 58 0 AATTTCTTTT 0.889236 -29 AATGATGTTGTATTTATTTTTGAGAATGAC 6 117 0 TATTTATTTT 0.968034 -167 ATGTAAATTAATTTTATTTTTTCTTATGCC 6 170 1 ATTTTATTTT 0.637249 -114 AAACTTTATATATTACTTTTAATAATTGTT 6 232 1 TATTACTTTT 0.656611 -52 CAAATATTTAAATTTATTTTAAAATAAAAG 9 87 1 AATTTATTTT 0.953457 -41 TCAAAACCATAATTTATTTATAATTAGTTT 10 53 0 AATTTATTTA 0.637155 -56 GCATTATAAGTATTTATATTTTGTGTTGTT 11 64 1 TATTTATATT 0.829836 -131 AAATCTTTCTGATTTATTTT 12 1 0 GATTTATTTT 0.863336 -300 AGTTAATGTTTATTTATTGTATATAGG 13 22 1 TATTTATTGT 0.943891 -17 AACCATATGTTATTTATTTTATTATCCACA 14 153 1 TATTTATTTT 0.968034 -50 AAAATCTTAAAATTTATTGTGGATAATAAA 14 170 0 AATTTATTGT 0.919364 -33 TTATTGTTTCTATTTCTATTAAACGTTAAT 15 24 0 TATTTCTATT 0.656604 -203 TAATACGGTATATTTATTGTTTCTATTTCT 15 37 0 TATTTATTGT 0.943891 -190 AATAAACTTTAATTAATTTTGAAGACAGTA 15 91 0 AATTAATTTT 0.768206 -136 GGCATTTAAATATTTATTGTCAAATATTTA 15 123 0 TATTTATTGT 0.943891 -104 ********** Masking position 7 Map Score: 15.1913 Number of sites scoring better than the average of aligned sites = 439 Number in coding regions = 332 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 4 ATCCGTTTTGATGAACCTTTTACTAAAAGGT 1 41 1 ATAACCTTTT 0.980907 -214 TTTCCTTCACATGAACCTTTTAGTAAAAGGT 1 55 0 ATAACCTTTT 0.980907 -200 TTAAAAAGAAATTTATCATTTAAGGTGATAG 5 65 1 ATTATCATTT 0.599072 -22 CTAAGTTTTGATCAACCTTTTCTAAAAGGTT 8 102 1 ATAACCTTTT 0.980907 -175 AGGTTACTCGAACAACCTTTTAGAAAAGGTT 8 115 0 AAAACCTTTT 0.920061 -162 AGGTTGTTCGAGTAACCTTTTACTAAAAGGT 8 128 1 AGAACCTTTT 0.906328 -149 TTATGAAACTTTTTTTAATTTTT 9 3 1 ATAAACTTTT 0.910046 -125 AGGGGATTATATATAGCTTTTATTTTAAAAT 9 102 0 ATTAGCTTTT 0.73181 -26 AAAATTAAAAATAAAACTTTTAAGGGAAGTA 11 31 1 ATAAACTTTT 0.909943 -164 TATTGCTATAATTAATCTTTTTGGTGATAAG 11 173 1 ATAATCTTTT 0.935469 -22 TCATTATTCAATAAATCATTTATTCCTGCGA 14 37 0 ATAATCATTT 0.823118 -166 TTAGGCATCTAAATACCTTTTTAATATAAAA 14 73 1 AATACCTTTT 0.786881 -130 GTTAAATAACATAAACCATATGTTATTTATT 14 140 1 ATAACCATAT 0.637008 -63 ** ******** Masking position 5 Map Score: 14.2804 Number of sites scoring better than the average of aligned sites = 342 Number in coding regions = 229 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 5 TTCACATGAACCTTTTAGTAAAAGGTTCATC 1 50 0 CCTTTTAGAA 0.964328 -205 CTCGGTAATGCCTCTTAGCATAG 8 3 0 CCTCTTAGAT 0.924116 -274 ATAGCTTCGCCCTATTGGGATACCTATTTAA 8 71 1 CCTATTGGAT 0.976071 -206 ACTCGAACAACCTTTTAGAAAAGGTTGATCA 8 110 0 CCTTTTAGAA 0.964328 -167 TTGCTCCCAACCTTTTAGTAAAAGGTTACTC 8 137 0 CCTTTTAGAA 0.964328 -140 GGTCCAGCGCCCTATAGGCAACTGGAGTCCC 12 96 1 CCTATAGGAA 0.945555 -205 GAATAAATCTACTATTGGAATGACGATACCC 12 180 1 ACTATTGGAT 0.799952 -121 ATGACGATACCCTTTAGGCATCAAAGTGCCT 12 199 1 CCTTTAGGAT 0.971692 -102 AATAATGATGCCTTTAGGCATCTAAATACCT 14 60 1 CCTTTAGGAT 0.971692 -143 ******** ** Masking position 5 Map Score: 7.99194 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 74 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 6 GCCTCGCTACGCTCGGCAGTGCCTC 1 4 0 GCTGGCGTGC 0.977827 -251 GCCGAGCGTAGCGAGGCAGTGCATCCGTTTTG 1 19 1 GCGGGCGTGC 0.995227 -236 ACCTCGCTACGCTCGGTAATGCCTCTTAGCAT 8 13 0 GCTGGTATGC 0.979126 -264 ACCGAGCGTAGCGAGGTAATGCATCTGTTTTG 8 28 1 GCGGGTATGC 0.991831 -249 TCCCAATAGGGCGAAGCTATGGTGCGTTGATC 8 59 0 GCGAGCATGG 0.971852 -218 CAATGTTTGAGCTTAGCCATGCGGTAGTTATG 8 165 1 GCTAGCATGC 0.777329 -112 AAACTTTTAAGGGAAGTAATGCATTATAAGTA 11 44 1 GGGAGTATGC 0.887273 -151 CTACATTGATGCGGGGGTGTGGTGTAGCCAGG 12 137 0 GCGGGGGTGG 0.961158 -164 *** *** **** Masking position 10 Map Score: 7.55594 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 7 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 AAATAGTAATATTTTTAATAAGGCACTGGT 1 111 0 ATTTTTAATA 0.860723 -144 AGCTATTTTGATTTATAAGTTTTAAATATC 1 203 1 ATTTATAAGT 0.711166 -52 ATATTGATGTATTTTTAACGATTATTTTTG 2 42 1 ATTTTTAACG 0.766852 -93 ATGAACAAAAATTTTTAATATCTAATATAT 2 89 0 ATTTTTAATA 0.860723 -46 TGATAAATTTCTTTTTAATGCAAAATTTTA 5 53 0 CTTTTTAATG 0.708426 -34 TTTATATATTACTTTTAATAATTGTTAATG 6 236 1 ACTTTTAATA 0.707294 -48 ACTTTTAATAATTGTTAATGATTGATAATG 6 246 1 ATTGTTAATG 0.827117 -38 ATTGTTAATGATTGATAATGACAGTTTAAG 6 256 1 ATTGATAATG 0.789755 -28 ATAATTTTTAATTTATAATGGATACCCCAA 8 244 0 ATTTATAATG 0.937304 -33 CTACTATTTTATTTATAATATTATCATTCA 9 59 1 ATTTATAATA 0.829077 -69 ACCATAATTTATTTATAATTAGTTTTAAAA 10 48 0 ATTTATAATT 0.826578 -61 TAAAAGTTTTATTTTTAATTTTAAAATCAT 11 23 0 ATTTTTAATT 0.860673 -172 TAAAAATAAAACTTTTAAGGGAAGTAATGC 11 36 1 ACTTTTAAGG 0.816878 -159 AAATATAAATACTTATAATGCATTACTTCC 11 55 0 ACTTATAATG 0.847444 -140 CAATTTATATATTTATAAGGCACTTTGATG 12 217 0 ATTTATAAGG 0.895065 -84 GTTTAAAGATATTTTTAAGTATTAATACGG 15 59 0 ATTTTTAAGT 0.78805 -168 ********** Masking position 6 Map Score: 14.9152 Number of sites scoring better than the average of aligned sites = 534 Number in coding regions = 376 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 8 CAGTGCATCCGTTTTGATGAACCTTTTACT 1 35 1 GTTTTGATGA 0.980857 -220 AATCAAAATAGCTTTGATGAAAAAAATAAT 1 186 0 GCTTTGATGA 0.958474 -69 TAATGCATCTGTTTTGATCAACGCACCATA 8 44 1 GTTTTGATCA 0.980857 -233 ATTTAACTAAGTTTTGATCAACCTTTTCTA 8 96 1 GTTTTGATCA 0.980857 -181 ATAAATTATGGTTTTGATTATAGAGTAAGC 10 66 1 GTTTTGATTA 0.949456 -43 ********** Masking position 5 Map Score: 4.46599 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 15 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 9 TTATTAAAAATATTACTATTTTCTTGTTCTT 1 120 1 TATTCTATTT 0.916237 -135 ACTATTTTCTTGTTCTTTTTTTATTTATACT 1 134 1 TGTTTTTTTT 0.860776 -121 CTTTTTTCTATTTTTTATATAAT 2 3 1 TTTTCTATTT 0.86576 -132 TCATATTGGTTATTGCTATTTTATACTTCAA 3 30 1 TATTCTATTT 0.916237 -51 TTAAATGATAAATTTCTTTTTAATGCAAAAT 5 57 0 AATTCTTTTT 0.748888 -30 ACACTATAGCAGTTCCTTTTTTAACTCCTTC 6 88 0 AGTTCTTTTT 0.845 -196 AATGATGTTGTATTTATTTTTGAGAATGACA 6 116 0 TATTATTTTT 0.697903 -168 TGTAAATTAATTTTATTTTTTCTTATGCCTA 6 171 1 TTTTTTTTTT 0.666017 -113 AATTAGCCCATGCTTCTATTTTTTTAAATTG 7 14 1 TGCTCTATTT 0.804973 -106 TATTTTTTTAAATTGTTATTTTCTTCTCTAT 7 30 1 AATTTTATTT 0.630736 -90 TATAACCTTGTGTTAATATTTAACGACTATA 7 66 0 TGTTATATTT 0.851798 -54 GGCTTAACTCTATCTCTATTTGGGGTATCCA 8 225 1 TATCCTATTT 0.537017 -52 ATGAAACTTTTTTTAATTTTTTATAACATTT 9 13 1 TTTTATTTTT 0.576647 -115 GATTATATATAGCTTTTATTTTAAAATAAAT 9 98 0 AGCTTTATTT 0.391925 -30 GCATTATAAGTATTTATATTTTGTGTTGTTT 11 64 1 TATTATATTT 0.758699 -131 TTATATTTTGTGTTGTTTTTTGTTGAGTATT 11 77 1 TGTTTTTTTT 0.860776 -118 ATATATCCCCTTTTACTTTTTATATGTGTCG 12 261 0 TTTTCTTTTT 0.825743 -40 AGTTATTATTTATAAAATCTT 14 192 0 AGTTTTATTT 0.75742 -11 GTATATTTATTGTTTCTATTTCTATTAAACG 15 29 0 TGTTCTATTT 0.952371 -198 **** ****** Masking position 7 Map Score: 15.1898 Number of sites scoring better than the average of aligned sites = 838 Number in coding regions = 613 Number in noncoding regions = 225 Number of orfs with sites within 600 bp upstream = 212 Fraction of orfs with sites within 600 bp upstream = 0.0340508 Motif number 10 GATACCCTCATCAGATATTTAAAACTTATA 1 216 0 TCAGATATTT 0.817125 -39 TTATCCCTACTAAATTAATTAAAGTTTGTT 4 74 0 TAAATTAATT 0.76567 -22 AAATTTTTTATATGATAATTTTAAAATTTT 5 32 1 TATGATAATT 0.641626 -55 GTAATCCATGTAAATTAATTTTATTTTTTC 6 163 1 TAAATTAATT 0.76567 -121 TTCTTATGCCTAAACTATTTTCGTTAATTG 6 190 1 TAAACTATTT 0.743302 -94 TTTACCACCTCAAATAATTTTTAATTTAT 8 258 0 TCAAATAATT 0.736974 -19 TTGTAATAACTCTACTATTTTATTTATAAT 9 48 1 TCTACTATTT 0.653432 -80 ATATTATCATTCAAATATTTAAATTTATTT 9 76 1 TCAAATATTT 0.814296 -52 CAGAAAGATTTAAGTTATTTAAAAAATGGT 12 20 1 TAAGTTATTT 0.838987 -281 TGCGAAGTTCTATATTAATTCATTCATTAA 14 106 1 TATATTAATT 0.676154 -97 ACATATGGTTTATGTTATTTAACAAAATTA 14 133 0 TATGTTATTT 0.76903 -70 ACATAAACCATATGTTATTTATTTTATTAT 14 148 1 TATGTTATTT 0.76903 -55 ATATTTATTGTCAAATATTTATTAATAAAC 15 114 0 TCAAATATTT 0.814296 -113 ********** Masking position 7 Map Score: 5.63487 Number of sites scoring better than the average of aligned sites = 746 Number in coding regions = 583 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 11 AGGCACTGCCGAGCGTAGCGAGGCAGTGCAT 1 12 1 GAGCGTAGCA 0.994755 -243 GAAGGAAATAGAGCATAGGAAAGAATTAGGA 1 78 1 GAGCATAGGA 0.932928 -177 AGGCATTACCGAGCGTAGCGAGGTAATGCAT 8 21 1 GAGCGTAGCA 0.994755 -256 TATCCCAATAGGGCGAAGCTATGGTGCGTTG 8 62 0 GGGCGAAGCA 0.958008 -215 AGCAATGTTTGAGCTTAGCCATGCGGTAGTT 8 163 1 GAGCTTAGCA 0.966341 -114 ********* * Masking position 7 Map Score: 2.41562 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 4 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 12 TTAATTTAGTAGGGATAAGA 4 86 1 AGGGATAAGA 0.89384 -10 AAAATAGTTTAGGCATAAGAAAAAATAAAA 6 181 0 AGGCATAAGA 0.952276 -103 GAATCTTCACAGGAATAAATCTACTATTGG 12 168 1 AGGAATAAAT 0.834502 -133 GATACCCTTTAGGCATCAAAGTGCCTTATA 12 204 1 AGGCATCAAA 0.971861 -97 GAACTTTCGCAGGAATAAATGATTTATTGA 14 31 1 AGGAATAAAT 0.834502 -172 AGATGCCTAAAGGCATCATTATTCAATAAA 14 53 0 AGGCATCATT 0.789975 -150 TGATGCCTTTAGGCATCTAAATACCTTTTT 14 65 1 AGGCATCTAA 0.916068 -138 CGTTAATAAGAGGGATAAAA 15 1 0 AGGGATAAAA 0.936983 -226 TTCCAAAGGAAGGCATTTAAATATTTATTG 15 134 0 AGGCATTTAA 0.733125 -93 ********** Masking position 5 Map Score: 2.40484 Number of sites scoring better than the average of aligned sites = 284 Number in coding regions = 250 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 13 AATATTCATAAAAATTATATAAAAAATAGA 2 17 0 AAAATTATAT 0.524411 -118 TCTTTCTCTAAAAATGATGTTGTATTTATT 6 129 0 AAAATGATGT 0.895473 -155 CTATTTTTTTAAATTGTTATTTTCTTCTCT 7 29 1 AAATTGTTAT 0.4789 -91 AACCTTTTCTAAAAGGTTGTTCGAGTAACC 8 115 1 AAAAGGTTGT 0.617258 -162 TTATAAATTAAAAATTATTTGAGGTGGTAA 8 256 1 AAAATTATTT 0.705575 -21 ATTACAAGTGAAAATGTTATAAAAAATTAA 9 25 0 AAAATGTTAT 0.887901 -103 TTAATCACCAAAATGATTTTAAAATTAAA 11 10 1 AAAATGATTT 0.944962 -185 AACCATATCAAAAATGATTAAAATACTCAA 11 99 0 AAAATGATTA 0.669941 -96 CTTTCACATAAAAATGTTTTGTTGGTGACT 11 131 0 AAAATGTTTT 0.936923 -64 TTCGCAGGAATAAATGATTTATTGAATAAT 14 36 1 TAAATGATTT 0.669941 -167 TGGTTACTTCAAAATGTTTTTGAAAGACAC 15 180 1 AAAATGTTTT 0.936923 -47 ACACTATATAAAAAAGTTTTTGGTGCTGTC 15 206 1 AAAAAGTTTT 0.647305 -21 ********** Masking position 3 Map Score: 6.08085 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 186 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 14 TATTGTTGAATTACTGTCATAAATCTTAAT 6 25 0 TTACTGTCAT 0.794956 -259 AGGAACTGCTATAGTGTCATTCTCAAAAAT 6 102 1 ATAGTGTCAT 0.960828 -182 CACTCACCTTAAACTGTCATTATCAATCAT 6 263 0 AAACTGTCAT 0.934819 -21 AAAATTAAAAAAAGTTTCATAA 9 3 0 AAAGTTTCAT 0.709592 -125 TTTAGGCATCAAAGTGCCTTATAAATATAT 12 211 1 AAAGTGCCTT 0.816558 -90 TCTTTAAACTATACTGTCTTCAAAATTAAT 15 80 1 ATACTGTCTT 0.934819 -147 ACTTTTTTATATAGTGTCTTTCAAAAACAT 15 193 0 ATAGTGTCTT 0.949591 -34 ********** Masking position 3 Map Score: 1.27755 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 51 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 15 ATTTTTAATATCTAATATATATTTTTCGGT 2 79 0 TCTAATATAT 0.832593 -56 CATTTTAGGCTATATGATATGAACAAAAAT 2 107 0 TATATGATAT 0.783928 -28 TTTTAAATTTTAAATTATATTTGAAGTATA 3 51 0 TAAATTATAT 0.610013 -30 AATCAAATCGGCTATTATATTGAAGGAGTT 6 67 1 GCTATTATAT 0.786197 -217 TATTTTCTTCTCTATTATATTATAGTCGTT 7 46 1 TCTATTATAT 0.940257 -74 AACACAAGGTTATATTATATAAAAGTAGCT 7 83 1 TATATTATAT 0.908445 -37 TACTATTTTATTTATAATATTATCATTCAA 9 60 1 TTTATAATAT 0.652772 -68 TAGAGTAAGCTATAAAATATCAGGAGGGAT 10 86 1 TATAAAATAT 0.661539 -23 CTGCGAAAGTTCTATAATATTGAGGTGAAT 14 13 0 TCTATAATAT 0.907498 -190 ********** Masking position 4 Map Score: 0.829482 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 176 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454