AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00970_hpyl_reg_300.orf -o00970_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: HP1141 23 methionyl-tRNA formyltransferase (fmt) HP1253 31 tryptophanyl-tRNA synthetase (trpS) Input sequences: #1 HP0122 186 H. pylori predicted coding region HP0122 #2 HP0123 39 threonyl-tRNA synthetase (thrS) #3 HP0181 257 H. pylori predicted coding region HP0181 #4 HP0243 205 neutrophil activating protein (napA) (bacterioferritin) #5 HP0246 188 flagellar basal-body P-ring protein (flgI) #6 HP0320 71 conserved hypothetical secreted protein #7 HP0322 141 poly E-rich protein #8 HP0403 80 phenylalanyl-tRNA synthetase, alpha subunit (pheS) #9 HP0417 168 methionyl-tRNA synthetase (metS) #10 HP0476 117 glutamyl-tRNA synthetase (gltX) #11 HP0616 77 chemotaxis protein (cheV) #12 HP0617 34 aspartyl-tRNA synthetase (aspS) #13 HP0640 62 poly(A) polymerase (papS) #14 HP0643 164 glutamyl-tRNA synthetase (gltX) #15 HP0774 23 tyrosyl-tRNA synthetase (tyrS) #16 HP0777 107 uridine 5'-monophosphate (UMP) kinase (pyrH) #17 HP0778 127 H. pylori predicted coding region HP0778 #18 HP0885 167 virulence factor mviN protein (mviN) #19 HP0961 131 glycerol-3-phosphate dehydrogenase (NAD(P)+) #20 HP0966 220 conserved hypothetical protein #21 HP0967 285 virulence associated protein D (vapD) #22 HP0971 49 H. pylori predicted coding region HP0971 #23 HP0972 111 glycyl-tRNA synthetase, beta subunit (glyS) #24 HP1142 39 H. pylori predicted coding region HP1142 #25 HP1143 243 H. pylori predicted coding region HP1143 #26 HP1153 130 valyl-tRNA synthetase (valS) #27 HP1190 61 histidyl-tRNA synthetase (hisS) #28 HP1241 119 alanyl-tRNA synthetase (alaS) #29 HP1254 116 biotin synthesis protein (bioC) #30 HP1422 24 isoleucyl-tRNA synthetase (ileS) #31 HP1423 101 conserved hypothetical protein #32 HP1483 26 gerC2 protein (gerC2) #33 HP1490 103 hemolysin #34 HP1491 138 phosphate permease #35 HP1550 62 protein-export membrane protein (secD) #36 HP1551 47 conserved hypothetical secreted protein #37 HP1552 23 Na+/H+ antiporter (nhaA) #38 HP1553 248 helicase Motif number 1 TATCATTGTTATATTTTTGTTTTAAGAAACTTAATGATC 1 27 0 ATTTTTAAAA 0.708011 -160 TTTTGAAACCTTGAGATTGTTTTAGTGTATTATAGCTAT 3 18 1 TTTTTTAGTA 0.920931 -240 TTAGTGTATTATAGCTATATTTTAATTTAAGAATTTTAG 3 39 1 ATTTTTAATA 0.88511 -219 AGAATTTTAGATTGATTTTTTTAAGGGTAGTTTTTTTTA 3 68 1 ATTTTAAGTA 0.935363 -190 AGAGTGTGAATTGGCATGATTTAAGAGTAATGGGTGTTT 3 140 1 TTTTTAAGTA 0.918272 -118 ATTTAATATTATTTAATCTTTTTAAAATTTTGTTTTATA 4 46 0 ATTTTTAATT 0.790913 -160 AGTCCTTTTTTTAAAATTGTTTTAGGCTTTTATTTTCAT 4 173 0 TTTTTTAGTT 0.851099 -33 ATAAACTTTAAATCAAAGATTTTAATTTTAGCCTTTTAT 5 56 0 AATTTTAATT 0.796798 -133 ATAAGCCTTTTATAAAAACTTTAAACCTAATTGAGCGTA 5 120 0 TATTTAAATA 0.856829 -69 ATTCCCTAAATTCTAATTATTTTAGCATAAGCCTTTTAT 5 146 0 TTTTTTAGTA 0.920931 -43 TTTGTTTGAATTATAGCTTTTTTAAAAAATAATTGATAG 6 14 0 TTTTTTAAAA 0.6531 -58 TATCCATTTTATCGCTTTTTTTAAATCTTTTATTATAAT 7 72 0 ATTTTAAATT 0.784903 -70 ATTTGATAAGAAACGCTTCTTTAAGCCTATCCATTTTAT 7 99 0 AATTTAAGTA 0.937504 -43 GCTTTTTTGCTCCCTTTTAAGGTTTTTCTTTTATT 8 7 1 TTTTTAAGTT 0.846484 -74 TAAAGTTGTATTATAGCTTTTTAAAAATAAAATATAAGG 8 45 1 TTTTTAAATA 0.852361 -36 GAGCGTTAATTATAATGAATTTTAAGCTAAAAACACCCC 9 44 1 TATTTTAATA 0.861181 -125 CTCTTAATTTTAACATGCTTTTAAAAATTTAGAGAATAG 9 106 0 TATTTAAATT 0.745999 -63 ATTAAGAGATTTAAACAAATTTAAGGTAACACGATTATA 9 137 1 TTTTTAAGAA 0.779471 -32 ACAATAAGAGTATTTTATTTTTAAGGTTAGAACA 10 94 1 TATTTAAGTA 0.92093 -24 GTTTGTAAAAACCTTTTAAACTAAATTAGGGTAG 11 6 1 TATTTAAAAA 0.6531 -72 ATTTAATTTTTGTTTTAATTTAAAGGGATAAA 12 4 1 TATTTTAATA 0.861184 -31 TCTTTGTGTTATTATATCTTTTTAGAATTTTTAAGGAAT 13 15 0 ATTTTTAGTT 0.880408 -48 CAAACATGAATAGGCATCATTTAAGAGATTAGCACTTGG 14 59 0 TATTTAAGAT 0.642615 -106 AAAAACCCTTTATTTAAAAATAGTTTTTGATT 14 143 0 AATTTAAATA 0.885003 -22 AAAAACACCCTTTCTGAATTTTAAGCCTACATTCTCAGC 16 17 0 TTTTTAAGTA 0.918272 -91 TTCTCATTAATTAATAAAATTTTAATAAAACTTGTGATT 16 73 0 TTTTTTAAAA 0.653061 -35 AAATTCTTATATTATACCATTTAAGGATTAAAAA 18 6 0 ATTTTAAGTT 0.876569 -162 TGTTGGTTAAAAATATTTTTTTTAGCATACTGGTTGTAT 18 92 0 AATTTTAGTA 0.939578 -76 TATACATATTAAATAATATTTTAAAATTAAAAAGCG 19 8 0 AATTTAAATA 0.885162 -124 TTTTGAATGTAAGGGCTATTTTAAACTTATTATTGTAAA 19 67 1 AATTTAAATA 0.885162 -65 GAGAGAGAGAAAGCGAATTTTTAAGAATAATCATCATTA 20 53 0 AATTTAAGTA 0.937504 -168 TTTTTGCGTCTTATTTAGATTTTAGTTTTTAATTTTAAA 20 186 1 TTTTTTAGTT 0.851032 -35 ACGCCGCTTCTTCGCTGCTTTTAAGCCAAAAAGAGCAGG 21 52 1 TTTTTAAGAA 0.779472 -234 TTTAGAAGCGAACTGATTTTTTAAAGCTTTTGCTAGAGG 21 149 0 AATTTAAATT 0.790913 -137 CCTAAAAAACAAAATCACTTTTAAGACTAAATCATGTTA 23 70 0 AATTTAAGTA 0.937504 -42 GTTGTCCCAAAAGCACAAGTTTTAGAGAACCATACG 25 8 0 AATTTTAGAA 0.830273 -236 AAAATTATACAACAAAGCATTTAAATTAAAAAGGATAGT 26 14 0 AATTTAAAAA 0.708011 -117 TTTTTTAAGGAACGCTCTATTTTAGGATAATA 26 109 1 AATTTTAGTA 0.939576 -22 CAATAGCCCTTTTTTAAAGATTTTAAGCTAAA 27 4 1 TATTTAAATT 0.745999 -58 TAAAGATTTTAAGCTAAAATTTTAGCATACAAATACAAG 27 25 1 AATTTTAGTA 0.939488 -37 TCTCCTTTAATTTTGGATGTTTAAAGTATAATAAACTAT 28 16 1 TTTTTAAAAT 0.471261 -104 AAAGTATAATAAACTATCTTTTTAAAAAAATAACTTAAA 28 38 1 AATTTTAAAA 0.715389 -82 TAAGGCTATTTTATAGCTCTTTTAAGTTATTTTTTTAAA 28 58 0 TTTTTTAATA 0.856829 -62 TTGTTGTTTTATCGCGTATTTTAAGGCTATTTTATAGCT 28 79 0 ATTTTAAGTA 0.935363 -41 AAGCGTGATTTTTTCTAAATTTTAGGCATTTAAGGAATC 29 12 0 TTTTTTAGAT 0.626696 -105 GCTTGAAATTAAAACTAAATTTTAGTGTATTCTTAGCAA 29 66 0 AATTTTAGTA 0.910377 -51 TATCCATAACTTATAAGGGTTTTAGTTTTAGCATGTTAG 31 43 0 TTTTTTAGTT 0.851099 -59 AATATATAAAATCTCAGAATTTTAACATAAAAGATTAAG 33 42 0 ATTTTTAATA 0.885162 -62 TTTTATATTTATCGTTAGGTTTTAGGTTTAAAGTT 33 79 1 ATTTTTAGTT 0.880407 -25 TTTTTAAAACTCTCTTTAAAATTTTACTTTAAGA 34 6 1 AATTTAAATT 0.790913 -133 ATTTGAGATTAAAACATCTTTTAAGGAAATTAA 36 25 1 AATTTAAGAA 0.825145 -23 AATTAAAAATTTTAAGGTTGTCT 37 1 1 AATTTTAATT 0.796797 -23 ATAGCAAAAGATTAAGGTTTTTTAGCTTAAGTAAAAAAG 38 171 1 ATTTTTAGTA 0.937504 -78 TAGCTTAAGTAAAAAAGGCTTTTAGGTTATAATAAAGAC 38 193 1 AATTTTAGTA 0.939578 -56 AATAAAGACAAAATTAGAATTTTAGGATAGATCTCA 38 223 1 AATTTTAGTA 0.939577 -26 ** ****** ** Masking position 10 Map Score: 77.0039 Number of sites scoring better than the average of aligned sites = 1029 Number in coding regions = 780 Number in noncoding regions = 249 Number of orfs with sites within 600 bp upstream = 219 Fraction of orfs with sites within 600 bp upstream = 0.0351751 Motif number 2 TTCTTTTTGGTTTATGATTTTATTGTATAATGGGC 1 127 1 TTATTTTTTG 0.936812 -60 TTGAGATTGTTTTAGTGTATTATAGCTATATTTTA 3 28 1 TTATATTTAG 0.804614 -230 ATTGATTTTTTTAAGGGTAGTTTTTTTTAAGTTGT 3 78 1 TTATAGTTTT 0.643049 -180 ATTTAATCTTTTTAAAATTTTGTTTTATAGTAAAA 4 40 0 TTATTTTTTT 0.952141 -166 CCCATTCAATTTAATATTATTTAATCTTTTTAAAA 4 58 0 TTATATTAAT 0.489874 -148 AAAAATTTTTTTGATCTTATTTTTGTCAAATATTG 4 99 0 TTATATTTTG 0.91023 -107 TTAAAATTGTTTTAGGCTTTTATTTTCATAAAAAC 4 167 0 TTATTTTTTT 0.952141 -39 AGATTTTAATTTTAGCCTTTTATTAGCTTTTTATA 5 44 0 TTATTTTTTA 0.901901 -145 TTAAACCTAATTGAGCGTATTTTTATGCTATACTC 5 104 0 TTATATTTTA 0.862784 -85 TCAATTAGGTTTAAAGTTTTTATAAAAGGCTTATG 5 125 1 TTATTTTTAA 0.788722 -64 ATTCCCTAAATTCTAATTATTTTAGCATAAGCCTT 5 150 0 TTTTATTTAG 0.567859 -39 TTTGTTTGAATTATAGCTTTTTTAAAAAATAATTG 6 18 0 TTTTTTTTAA 0.543686 -54 ATCGCTTTTTTTAAATCTTTTATTATAATCAAAAA 7 66 0 TTATTTTTTA 0.901901 -76 TTGCTCCCTTTTAAGGTTTTTCTTTTATTAAAGTT 8 17 1 TTATTTTTTT 0.952141 -64 TAGTGTATGATTGAGATTATTTTTGATTAGGATCA 10 14 0 TTATATTTTG 0.91023 -104 TAAAAATGGTTTCACTTTTTTCTATTAAAATTAGT 10 45 0 TTATTTTTAT 0.889867 -73 ATTTAATTTTTGTTTTAATTTAAAGGG 12 3 1 TTATTGTTTA 0.548996 -32 ATTATATCTTTTTAGAATTTTTAAGGAATTTTG 13 9 0 TTATTTTAAG 0.511334 -54 AACCCTTTATTTAAAAATAGTTTTTGATTATACCT 14 137 0 TTATAGTTTT 0.643048 -28 TTACCTAATTTTCAGTGTTTTTTTGTTAGCATATT 18 54 0 TTATTTTTTG 0.936812 -114 AAGCTGTTGGTTAAAAATATTTTTTTTAGCATACT 18 100 0 TTATATTTTT 0.931535 -68 GCTTTTTAATTTTAAAATATTATTTAATATGTATA 19 12 1 TTATATTTTT 0.931536 -120 AAGGGCTATTTTAAACTTATTATTGTAAAATGGTG 19 77 1 TTATATTTTG 0.91023 -55 TTGCGTCTTATTTAGATTTTAGTTTTTAATTTTAA 20 189 1 TTATTTATTT 0.532727 -32 AAAAGGCTTTGATGATTTTTTTTATGTGGAATG 21 9 1 TTATTTTTTT 0.952141 -277 ATACGCTAAATTCAAGCTTTTTTTAAGCGAGGAAG 21 106 1 TTATTTTTTA 0.901901 -180 TTATCTCAATTTCTTCATTTTTTTTATTTATAATG 25 64 1 TTTTTTTTTT 0.863914 -180 TTTTTGCCTTTTTTATTTTTTGTTGTTTGTATTTA 25 120 1 TTTTTTTTTG 0.825506 -124 TAAGATTTGATTTTTTATATTTTATAATAGAATGA 25 209 0 TTTTATTTAT 0.638117 -35 GCCTTTTGCTTTTACGCTTTTAATTGTTGCGTATT 26 58 0 TTATTTTATT 0.775649 -73 TTATAGCTCTTTTAAGTTATTTTTTTAAAAAGATA 28 52 0 TTATATTTTT 0.931536 -68 ATCGCGTATTTTAAGGCTATTTTATAGCTCTTTTA 28 73 0 TTATATTTAT 0.846767 -47 AAAACTAAATTTTAGTGTATTCTTAGCAAATTTTA 29 60 0 TTATATTTTA 0.862784 -57 GCGTTTATTTTACCCTATTCTTTAAGTTTTTAT 31 79 0 TTATATTTTT 0.931536 -23 GACTTTTCTTTTTTCATGGCTTGTCT 32 9 0 TTTTTTTATG 0.451192 -18 TTCTGAGATTTTATATATTTTATATTTATCGTTAG 33 62 1 TTTTTTTTAT 0.720535 -42 AAAACTCTCTTTAAAATTTTACTTTAAGATACCAT 34 16 1 TTATTTATTT 0.532727 -123 TAACGCTCGTTTAATCGTTTTTATTGGCGCGCTTC 35 18 1 TTATTTTATT 0.775649 -45 AGACAACCTTAAAATTTTTAATT 37 1 0 TTATTTTATT 0.775649 -23 GCTCATTTGATTCTTAATTTTCTTAAGAACACCTA 38 51 1 TTTTTTTTTA 0.745786 -198 TCGTAGGGTTTTGTCGTTTTTCTATCATTTTAATA 38 134 0 TTTTTTTTAT 0.720535 -115 AATTCTAATTTTGTCTTTATTATAACCTAAAAGCC 38 209 0 TTTTATTTAA 0.448998 -40 ** * **** *** Masking position 8 Map Score: 49.9987 Number of sites scoring better than the average of aligned sites = 1028 Number in coding regions = 778 Number in noncoding regions = 250 Number of orfs with sites within 600 bp upstream = 192 Fraction of orfs with sites within 600 bp upstream = 0.0308384 Motif number 3 ATTAAGTTTCTTAAAACAAAAATATAACAA 1 31 1 TTAAAACAAA 0.78536 -156 ACAAACTAGCTAAAACTAAAGCTCTATCAT 1 68 0 TAAAACTAAA 0.879465 -119 CAATAAAATCATAAACCAAAAAGAATACAC 1 122 0 ATAAACCAAA 0.802013 -65 TCTAAAATTCTTAAATTAAAATATAGCTAT 3 49 0 TTAAATTAAA 0.811208 -209 TCATAGCGTCTTAAAACAAACACCCATTAC 3 166 0 TTAAAACAAA 0.78536 -92 ATTCAAACCCTAAACCCAAACCTTTCTCTC 3 217 0 TAAACCCAAA 0.787951 -41 GAGTTTTACTATAAAACAAAATTTTAAAAA 4 37 1 ATAAAACAAA 0.682926 -169 AATAAAAGGCTAAAATTAAAATCTTTGATT 5 55 1 TAAAATTAAA 0.795059 -134 CTTATAAACTTTAAATCAAAGATTTTAATT 5 68 0 TTAAATCAAA 0.785358 -121 TATAGCTTTTTAAAAATAAAATATAAGGAT 8 56 1 TAAAAATAAA 0.795061 -25 ATAATGAATTTTAAGCTAAAAACACCCCAC 9 55 1 TTAAGCTAAA 0.828725 -114 GTTCTAACCTTAAAAATAAAATACTCTTAT 10 97 0 TAAAAATAAA 0.795061 -21 TAAAAACCTTTTAAACTAAATTAGGGTAGT 11 16 1 TTAAACTAAA 0.88988 -62 AAATTAAAACAAAAATTAAAT 12 2 0 AAAAATTAAA 0.695461 -33 TTTTATCCCTTTAAATTAAAACAAAAATTA 12 14 0 TTAAATTAAA 0.811208 -21 AAAAGATATAATAACACAAAGAAATTTTAA 13 32 1 ATAACACAAA 0.563328 -31 AAATCCCGTAAAAAGCCAAAAATCCTAGAG 18 147 0 AAAAGCCAAA 0.686259 -21 AATAATATTTTAAAATTAAAAAGCG 19 6 0 TAAAATTAAA 0.795059 -126 TATGGGGGTGAAAAGATAAAGCGGCTGACT 20 101 0 AAAAGATAAA 0.577667 -120 CAATCCTTTAAAATTAAAAACTAAAATC 20 203 0 TAAAATTAAA 0.795059 -18 TTCGCTGCTTTTAAGCCAAAAAGAGCAGGT 21 62 1 TTAAGCCAAA 0.804753 -224 AAAACATGCTATAACACAAACCAATAAAGG 21 259 1 ATAACACAAA 0.563328 -27 GTATTAAGAAATAAACTAAACTGAGTGTAA 23 25 1 ATAAACTAAA 0.826513 -87 AATTCTCCCTAAAAAACAAAATCACTTTTA 23 86 0 AAAAAACAAA 0.660065 -26 TACAAACAACAAAAAATAAAAAAGGCAAAA 25 121 0 AAAAAATAAA 0.695461 -123 TAAAACCTGCTTAAGTTAAATTGATCTCAT 25 183 1 TTAAGTTAAA 0.72009 -61 ATAAAATATAAAAAATCAAATCTTAAAGGA 25 219 1 AAAAATCAAA 0.660065 -25 AACAAAGCATTTAAATTAAAAAGGATAGTC 26 13 0 TTAAATTAAA 0.811208 -118 TTTAAAGATTTTAAGCTAAAATTTTAGCAT 27 23 1 TTAAGCTAAA 0.828725 -39 TTTTAAAAAAATAACTTAAAAGAGCTATAA 28 57 1 ATAACTTAAA 0.602734 -63 CGCTTGAAATTAAAACTAAATTTTAGTGTA 29 76 0 TAAAACTAAA 0.879465 -41 GCTAACATGCTAAAACTAAAACCCTTATAA 31 42 1 TAAAACTAAA 0.879465 -60 GTTATGGATAAAAACTTAAAGAATAGGGTA 31 72 1 AAAACTTAAA 0.577667 -30 TCTCAGAATTTTAACATAAAAGATTAAGCC 33 40 0 TTAACATAAA 0.720471 -64 AACTTTAAACCTAAAACCTAACGAT 33 89 0 TAAACCTAAA 0.813787 -15 CCTTTTTTACTTAAGCTAAAAAACCTTAAT 38 181 0 TTAAGCTAAA 0.828725 -68 TGTCTTTATTATAACCTAAAAGCCTTTTTT 38 203 0 ATAACCTAAA 0.740495 -46 TAGGTTATAATAAAGACAAAATTAGAATTT 38 215 1 TAAAGACAAA 0.663949 -34 ********** Masking position 4 Map Score: 45.5078 Number of sites scoring better than the average of aligned sites = 852 Number in coding regions = 636 Number in noncoding regions = 216 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 4 TAGATTGATTTTTTTAAGGGTAGTTTTTTTTAA 3 75 1 TTTTTAAGTG 0.907061 -183 AGGGTAGTTTTTTTTAAGTTGTGTTATTATTTT 3 91 1 TTTTTAAGGG 0.889245 -167 GTAAAACTCATTTTTAAGGGGGATAGTTATCCA 4 13 0 TTTTTAAGGA 0.808414 -193 GCGATCAAGGTTTTTATGAAAATAAAAGCCTAA 4 158 1 TTTTTATGAT 0.809118 -48 ATTGAGCGTATTTTTATGCTATACTCAAAAATC 5 97 0 TTTTTATGAA 0.883695 -92 AGGTTTAAAGTTTTTATAAAAGGCTTATGCTAA 5 131 1 TTTTTATAAG 0.491348 -58 TGGTTGGTTGTTTTTATCATAGAGTGTAATTTA 7 27 0 TTTTTATCAA 0.720524 -115 AGTGAAACCATTTTTAAGCCATTTTTGAATACA 10 64 1 TTTTTAAGAT 0.863112 -54 GAGTATTTTATTTTTAAGGTTAGAACA 10 101 1 TTTTTAAGTG 0.907061 -17 CTTTTTAGAATTTTTAAGGAATTTTG 13 4 0 TTTTTAAGAT 0.863112 -59 AACGCCAAGCTTTTTATGGTTGGTTATCAAAAA 14 24 0 TTTTTATGTG 0.867752 -141 GGTAGTTCTGTTTTTATCAAACATGAATAGGCA 14 82 0 TTTTTATCAA 0.720516 -83 TCAAAAACTATTTTTAAATAAAGGGTTTTT 14 145 1 TTTTTAAAAG 0.589626 -20 AGAAAGGGTGTTTTTAAGCAAGATTAGGTTACA 16 41 1 TTTTTAAGAA 0.918709 -67 AAAAAAAATATTTTTAACCAACAGCTTAGGGAT 18 108 1 TTTTTAACAA 0.793163 -60 AGAAAGCGAATTTTTAAGAATAATCATCATTAC 20 52 0 TTTTTAAGTA 0.83684 -169 TAGTTTTTAATTTTAAAGGATTG 20 208 1 TTTTAAAGTG 0.615207 -13 TTGATGATTTTTTTTATGTGGAATGCTATAAAT 21 19 1 TTTTTATGGA 0.739371 -267 ATTCAAGCTTTTTTTAAGCGAGGAAGTCGCTTT 21 115 1 TTTTTAAGAG 0.955564 -171 TATAATGTAGTTTTTATGCGAAGGGTATTTTTT 25 92 1 TTTTTATGAG 0.935307 -152 ATCCAACCATTTTTTAAGGAACGCTCTATTTTA 26 100 1 TTTTTAAGAG 0.955564 -31 GCCACCACTCTTTTTAAGGAATTTGT 31 4 0 TTTTTAAGAT 0.863112 -98 ATTCTTTAAGTTTTTATCCATAACTTATAAGGG 31 63 0 TTTTTATCTA 0.539188 -39 AAGGCTTGATTTTTAAAGTTAGGCTTAATCTTT 33 19 1 TTTTAAAGAG 0.778896 -85 TAAAGTAAAATTTTAAAGAGAGTTTTAAAAA 34 9 0 TTTTAAAGAT 0.508092 -130 TAATGAGCCATTTTTATCAAACAACGCTTTTTA 34 52 1 TTTTTATCAA 0.720516 -87 CAAACAACGCTTTTTAAGAGTGGCTCAAGGGCT 34 69 1 TTTTTAAGTG 0.907061 -70 TAGAACAAGGTTTTTATGACGAT 34 126 1 TTTTTATGGT 0.612812 -13 AACTTTTTAACGCTCGTTTAATCGTT 35 4 1 TTTTTAACTG 0.768067 -59 TTAAAAGATGTTTTAATCTCAAATTATAGCATT 36 16 0 TTTTAATCAA 0.296931 -32 ******** * * Masking position 6 Map Score: 35.4429 Number of sites scoring better than the average of aligned sites = 644 Number in coding regions = 493 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 5 ATTTTTGAATAGAAAGGGTGGTT 1 174 1 AGAAAGGGTG 0.891005 -13 GATATATGAGAGAAAGGTTTGGGTTTAGGG 3 210 1 AGAAAGGTTT 0.575199 -48 ACAATTTTAAAAAAAGGACTTTTG 4 192 1 AAAAAGGACT 0.690567 -14 TTAGGGAATAAGAAAGGGTTTGA 5 176 1 AGAAAGGGTT 0.96243 -13 CAAAAAATTGAAAAAGAGTTCAAGGAATAG 9 15 0 AAAAAGAGTT 0.908945 -154 AAAATGGCTTAAAAATGGTTTCACTTTTTT 10 59 0 AAAAATGGTT 0.924801 -59 TATTGTATTCAAAAATGGCTTAAAAATGGT 10 70 0 AAAAATGGCT 0.845953 -48 CCCTTTATTTAAAAATAGTTTTTGATTATA 14 140 0 AAAAATAGTT 0.695999 -25 CTATTTTTAAATAAAGGGTTTTT 14 152 1 ATAAAGGGTT 0.830762 -13 CTTAAAATTCAGAAAGGGTGTTTTTAAGCA 16 31 1 AGAAAGGGTG 0.891005 -77 AACTAAAAGTAAAAAGAGTTTTGTTATCAT 17 60 0 AAAAAGAGTT 0.908945 -68 ATGCGATACAAAAAAGGATTTTAA 17 114 1 AAAAAGGATT 0.833276 -14 AAAATCCCCAAAAAAGGGTTTATATGGGTT 20 149 0 AAAAAGGGTT 0.981692 -72 GCGTTCCTTAAAAAATGGTTGGATTTGGAA 26 94 0 AAAAATGGTT 0.924801 -37 AAAATCTTTAAAAAAGGGCTATTG 27 5 0 AAAAAGGGCT 0.95991 -57 CAAATTCCTTAAAAAGAGTGGTGGCTGAAT 31 12 1 AAAAAGAGTG 0.76108 -90 GTTGTTTGATAAAAATGGCTCATTATATGG 34 47 0 AAAAATGGCT 0.845953 -92 AGCCACTCTTAAAAAGCGTTGTTTGATAAA 34 64 0 AAAAAGCGTT 0.818078 -75 AGCTTAAGTAAAAAAGGCTTTTAGGTTATA 38 194 1 AAAAAGGCTT 0.807723 -55 ********** Masking position 5 Map Score: 25.9131 Number of sites scoring better than the average of aligned sites = 776 Number in coding regions = 639 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 6 AAAACTCCCTTAAAATGATC 1 1 1 AAAACTCCCT 0.638559 -186 CTTTCTATTCAAAAATACCTAACTAACCGC 1 160 0 AAAAATACCT 0.818431 -27 CAACTTAAAAAAAACTACCCTTAAAAAAAT 3 82 0 AAAACTACCC 0.965144 -176 GCGTCTTAAAACAAACACCCATTACTCTTA 3 161 0 ACAAACACCC 0.797018 -97 AGTATAGCATAAAAATACGCTCAATTAGGT 5 105 1 AAAAATACGC 0.820317 -84 AATTCAAACAAAAACCAACCAATAAGATTA 6 41 1 AAAACCAACC 0.901107 -31 ACTCTATGATAAAAACAACCAACCAAGTGG 7 35 1 AAAAACAACC 0.917399 -107 ATTTTAAGCTAAAAACACCCCACAAATAAG 9 62 1 AAAAACACCC 0.972228 -107 TAAATGCTATAATACTACCCTAATTTAGTT 11 29 0 AATACTACCC 0.676953 -49 AATCTTGCTTAAAAACACCCTTTCTGAATT 16 36 0 AAAAACACCC 0.972228 -72 ATTAGGTAATAAATACAACCAGTATGCTAA 18 80 1 AAATACAACC 0.611349 -88 CATTGATTGTAAAACTCACCATTTTACAAT 19 98 0 AAAACTCACC 0.807574 -34 AAAATCCCCAAAAAATCCCCAAAAAAGGGT 20 160 0 AAAAATCCCC 0.941601 -61 AATAAGACGCAAAAATCCCCAAAAAATCCC 20 171 0 AAAAATCCCC 0.941601 -50 AAAAAAGGCAAAAAATACCCTTCGCATAAA 25 104 0 AAAAATACCC 0.971223 -140 ATAATTTTGAAAAAATACGCAACAATTAAA 26 45 1 AAAAATACGC 0.820317 -86 AAGGCGTTCCAAATCCAACCATTTTTTAAG 26 88 1 AAATCCAACC 0.563421 -43 ATCTTTTTAAAAAAATAACTTAAAAGAGCT 28 53 1 AAAAATAACT 0.58849 -67 ********** Masking position 1 Map Score: 20.5521 Number of sites scoring better than the average of aligned sites = 926 Number in coding regions = 824 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 7 TTTCTATTCAAAAATACCTAACTAACCGCC 1 159 0 AAAATACCTA 0.66055 -28 TCAAATATTGATAAACCCCATTCAATTTAA 4 79 0 ATAAACCCCA 0.686313 -127 ATTATTTTTTAAAAAAGCTATAATTCAAAC 6 20 1 AAAAAAGCTA 0.59021 -52 TTAATAAAAGAAAAACCTTAAAAGGGAGCA 8 18 0 AAAAACCTTA 0.798949 -63 TTTAAGCTAAAAACACCCCACAAATAAGCA 9 64 1 AAACACCCCA 0.907649 -105 AAAAACCCTTTATTTAAAAA 14 155 0 AAAAACCCTT 0.865518 -10 TCTTGCTTAAAAACACCCTTTCTGAATTTT 16 34 0 AAACACCCTT 0.686318 -74 CCTAGAGCATAAAATCCCTAAGCTGTTGGT 18 124 0 AAAATCCCTA 0.947723 -44 GTAAAAAGCCAAAAATCCTAGAGCATAAAA 18 140 0 AAAAATCCTA 0.874832 -28 AAATCCCCAAAAAATCCCCAAAAAAGGGTT 20 159 0 AAAATCCCCA 0.920215 -62 ATAAGACGCAAAAATCCCCAAAAAATCCCC 20 170 0 AAAATCCCCA 0.920215 -51 TTCTAAGTAAAAACATGCTATAACACAAAC 21 250 1 AAACATGCTA 0.412314 -36 ACCCCCAAACAAAAACGCCAGACTTTGCGT 22 20 0 AAAAACGCCA 0.895141 -30 GTTTGTATTTAAAATCCCTATTTTACTGAA 25 144 1 AAAATCCCTA 0.947723 -100 AGAAAACCCTACCCCTAAAAG 35 52 0 GAAAACCCTA 0.843981 -11 CTAAAAATGCTATAATTTGAGA 36 3 1 AAAAATGCTA 0.673605 -45 AGAAAAACGACAAAACCCTACGATTATAGC 38 146 1 CAAAACCCTA 0.843981 -103 ACTTAAGCTAAAAAACCTTAATCTTTTGCT 38 173 0 AAAAACCTTA 0.798949 -76 ********** Masking position 3 Map Score: 13.4236 Number of sites scoring better than the average of aligned sites = 1469 Number in coding regions = 1313 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 8 ATTTTAAGGTTTGAAGAAAGGAAAC 2 4 1 TTAGGTTGAA 0.875976 -36 ATTTTCAAATTTCAAGTCTAAAGAGTGTGAAT 3 119 1 TTAAGTTAAA 0.89961 -139 ATTGGCATGATTTAAGAGTAATGGGTGTTTGT 3 149 1 TTAAGATAAT 0.785598 -109 AGGTTTGGGTTTAGGGTTTGAATTATATTGAT 3 224 1 TTGGGTTGAA 0.706092 -34 TCAAATTAAATTGAGGTATGAATCTCCC 5 7 0 TTAGGTTGAA 0.876034 -182 AATACGCTCAATTAGGTTTAAAGTTTTTATAA 5 118 1 ATAGGTTAAA 0.527517 -71 ACCAATAAGATTAAGGAGTAAAGT 6 58 1 TTAGGATAAA 0.936677 -14 ACAAAGAAATTTTAAGAGTAAAAAGC 13 47 1 TTAAGATAAA 0.901719 -16 TTAAGTATTCTTTAGGTATAATCAAAAACTAT 14 124 1 TTAGGTTAAT 0.855097 -41 TAAGCCCTAATTAAGGAATGAAC 15 11 1 TTAGGATGAA 0.876034 -13 ATTATACCATTTAAGGATTAAAAA 18 3 0 TTAGGATAAA 0.936614 -165 AAAGCGAATTTTTAAGAATAATCATCATTACA 20 51 0 TTAAGATAAT 0.785598 -170 AACCCATGCGTTTGAGAATAAAACAATTTCAT 21 191 0 TTGAGATAAA 0.757424 -95 TGAGTGTAAATTCAAGTATAATTCTAACATGA 23 46 1 TTAAGTTAAT 0.785601 -66 CAAAATCACTTTTAAGACTAAATCATGTTAGA 23 68 0 TTAAGATAAA 0.897225 -44 TTTTGGATGTTTAAAGTATAATAAACTATCTT 28 26 1 TTAAGTTAAT 0.785604 -94 ATCGTTAGGTTTTAGGTTTAAAGTT 33 89 1 TTAGGTTAAA 0.933707 -15 AATGCTATAATTTGAGATTAAAACATCTTTTA 36 16 1 TTGAGATAAA 0.757384 -32 ** **** **** Masking position 9 Map Score: 22.1058 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 178 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 9 TTTAATATTATTTAATCTTTTTAAAATTTTG 4 53 0 TTTATCTTTT 0.795556 -153 AAAAAATTTTTTTGATCTTATTTTTGTCAAA 4 104 0 TTTGTCTTAT 0.780331 -102 TTAAAATTGTTTTAGGCTTTTATTTTCATAA 4 171 0 TTTAGCTTTT 0.641672 -35 ACTTTACTCCTTAATCTTATTGGTTGGTTT 6 52 0 CTTATCTTAT 0.924483 -20 TAGTCAGCCGCTTTATCTTTTCACCCCCATA 20 100 1 CTTTTCTTTT 0.887102 -121 CGCCCGCTCACCTGCTCTTTTTGGCTTAAAA 21 70 0 CCTGTCTTTT 0.833647 -216 TTCTCTAAAACTTGTGCTTTTGGGACAACTT 25 18 1 CTTGGCTTTT 0.940509 -226 TTTGGAACGCCTTTTGCTTTTACGCTTTTAA 26 70 0 CTTTGCTTTT 0.783361 -61 AAAAATCACGCTTGATCTTATCTAAAATTTG 29 38 1 CTTGTCTTAT 0.951442 -79 TGATTAATCCTTAGTCTTTTGTCT 30 5 0 CTTATCTTTT 0.955484 -20 TAAAGTTAGGCTTAATCTTTTATGTTAAAAT 33 32 1 CTTATCTTTT 0.955484 -72 TCATAAAAACCTTGTTCTAATAGTGGTCTTA 34 114 0 CTTGTCTAAT 0.658525 -25 CTGTCTTTGCCTTGTTCCTATTAAAATGATA 38 116 1 CTTGTCCTAT 0.740814 -133 GCTAAAAAACCTTAATCTTTTGCTATAATCG 38 166 0 CTTATCTTTT 0.955484 -83 **** ****** Masking position 3 Map Score: 10.594 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 255 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 10 TAAGTTTCTTAAAACAAAAATATAACAATG 1 33 1 AAAACAAAAA 0.775452 -154 ATAAAATCATAAACCAAAAAGAATACACCC 1 120 0 AAACCAAAAA 0.755128 -67 AACCGCCCATTATACAATAAAATCATAAAC 1 136 0 TATACAATAA 0.402834 -51 ATAGCGTCTTAAAACAAACACCCATTACTC 3 164 0 AAAACAAACA 0.755128 -94 ATTCAAACAAAAACCAACCAATAAGATTAA 6 42 1 AAACCAACCA 0.905482 -30 CTCTATGATAAAAACAACCAACCAAGTGGA 7 36 1 AAAACAACCA 0.914736 -106 GCCATTTTTGAATACAATAAGAGTATTTTA 10 81 1 AATACAATAA 0.658317 -37 CCTTTAAATTAAAACAAAAATTAAAT 12 7 0 AAAACAAAAA 0.775452 -28 AGCTTTTTGATAACCAACCATAAAAAGCTT 14 21 1 TAACCAACCA 0.770334 -144 TTAGGTAATAAATACAACCAGTATGCTAAA 18 81 1 AATACAACCA 0.856845 -87 GCTATAACACAAACCAATAAAGGAGTTAAA 21 266 1 AAACCAATAA 0.755128 -20 ATTTTAAATACAAACAACAAAAAATAAAAA 25 129 0 CAAACAACAA 0.654566 -115 AAGCAGGTTTTATCCAATAAGTTCAGTAAA 25 165 0 TATCCAATAA 0.375926 -79 TTTTCAAAATTATACAACAAAGCATTTAAA 26 28 0 TATACAACAA 0.701208 -103 AGGCGTTCCAAATCCAACCATTTTTTAAGG 26 89 1 AATCCAACCA 0.84239 -42 AATACGCGATAAAACAACAAAAAGGAATAC 28 98 1 AAAACAACAA 0.92316 -22 AAATGATAGAAAAACGACAAAACCCTACGA 38 139 1 AAAACGACAA 0.588509 -110 ********** Masking position 7 Map Score: 11.5678 Number of sites scoring better than the average of aligned sites = 436 Number in coding regions = 357 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 11 AATGATCATTTTAAGGGAGTTTT 1 3 0 TTAGGGAGTT 0.863053 -184 AAACTCATTTTTAAGGGGGATAGTTATCCAA 4 12 0 TTAGGGGGAT 0.659281 -194 ATAATTAGAATTTAGGGAATAAGAAAGGGTT 5 165 1 TTAGGGAATA 0.9371 -24 TGAAAAAGAGTTCAAGGAATAGACAG 9 6 0 TTAAGGAATA 0.938305 -163 CTTTTAAAAATTTAGAGAATAGAGGTTGCAT 9 97 0 TTAGAGAATA 0.440553 -72 TTGATAGGGCTTTAGGGGAAAATAG 11 63 1 TTAGGGGAAA 0.820604 -15 TTGTTTTAATTTAAAGGGATAAAAC 12 20 1 TTAAGGGATA 0.856057 -15 TTTTAGAATTTTTAAGGAATTTTG 13 4 0 TTAAGGAATT 0.886788 -59 TATTATACCATTTAAGGATTAAAAA 18 5 0 TTAAGGATTA 0.658987 -163 GATTTTGTTTTTTAGGGAGAATTGAGATT 23 93 1 TTAGGGAGAA 0.905728 -19 AAATCAAATCTTAAAGGAAAATC 25 231 1 TTAAGGAAAA 0.922729 -13 ACATCCAAAATTAAAGGAGAAAACC 28 5 0 TTAAGGAGAA 0.907475 -115 ATTTTAGGCATTTAAGGAATCA 29 2 0 TTAAGGAATC 0.741208 -115 CACCACTCTTTTTAAGGAATTTGT 31 4 0 TTAAGGAATT 0.886788 -98 TAAAACATCTTTTAAGGAAATTAA 36 34 1 TTAAGGAAAT 0.860146 -14 CCAAAATAACTTTAAGGAGAATTCTC 38 6 0 TTAAGGAGAA 0.907475 -243 ** ******** Masking position 4 Map Score: 14.5532 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 197 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 12 CTAACCGCCCATTATACAATAAAATCATAAA 1 137 0 ATTATAAATA 0.468366 -50 TTAGTTAGGTATTTTTGAATAGAAAGGGTGG 1 164 1 ATTTTTAATA 0.885388 -23 TAGACTTGAAATTTGAAAATAATAACACAAC 3 108 0 ATTTGAAATA 0.84521 -150 ACCCCATTCAATTTAATATTATTTAATCTTT 4 64 0 ATTTAAATTA 0.283724 -142 GTTTATCAATATTTGACAAAAATAAGATCAA 4 93 1 ATTTGAAAAA 0.62908 -113 GATCAAAAAAATTTTTTATTAACTCTTTTGG 4 118 1 ATTTTTATTA 0.745186 -88 GCCTAAAACAATTTTAAAAAAAGGACTTTTG 4 185 1 ATTTTAAAAA 0.840693 -21 AATTCTAATTATTTTAGCATAAGCCTTTTAT 5 146 0 ATTTTACATA 0.806099 -43 CCTATCAATTATTTTTTAAAAAAGCTATAAT 6 13 1 ATTTTTAAAA 0.705857 -59 AATGATCCTTATTTTAAATTACACTCTATGA 7 13 1 ATTTTAATTA 0.865656 -129 AACCAAGTGGATTTTTGATTATAATAAAAGA 7 55 1 ATTTTTATTA 0.745186 -87 CTTATATTTTATTTTTAAAAAGCTATAATAC 8 52 0 ATTTTTAAAA 0.705372 -29 GATTGAGATTATTTTTGATTAGGATCAACC 10 10 0 ATTTTTATTA 0.745186 -108 TTTTTAAGCCATTTTTGAATACAATAAGAGT 10 74 1 ATTTTTAATA 0.885388 -44 ATCAAAAACTATTTTTAAATAAAGGGTTTTT 14 144 1 ATTTTTAATA 0.885381 -21 TAATATAAGAATTTGAAAAAAGAAATATGCT 18 31 1 ATTTGAAAAA 0.628938 -137 CGCTTTTTAATTTTAAAATATTATTTAATA 19 10 1 ATTTTAAATA 0.944506 -122 TACAATAATAAGTTTAAAATAGCCCTTACAT 19 73 0 AGTTTAAATA 0.566299 -59 AAAACTCACCATTTTACAATAATAAGTTTAA 19 87 0 ATTTTAAATA 0.944509 -45 GATTTTTTATATTTTATAATAGAATGAGATC 25 205 0 ATTTTAAATA 0.94451 -39 GGAACGCTCTATTTTAGGATAATA 26 117 1 ATTTTAGATA 0.740533 -14 TTAAGCTAAAATTTTAGCATACAAATACAAG 27 33 1 ATTTTACATA 0.806099 -29 TTCTTAGCAAATTTTAGATAAGATCAAGCGT 29 45 0 ATTTTAATAA 0.66688 -72 AAATCTCAGAATTTTAACATAAAAGATTAAG 33 42 0 ATTTTACATA 0.806099 -62 AAATGCTATAATTTGAGATTAAAACATCTTT 36 15 1 ATTTGAATTA 0.673962 -33 CAAAATTAGAATTTTAGGATAGATCTCA 38 231 1 ATTTTAGATA 0.740533 -18 ****** **** Masking position 3 Map Score: 28.3872 Number of sites scoring better than the average of aligned sites = 408 Number in coding regions = 296 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 13 TTTGTATTACTAAGCTTTTTAATAAGAGGG 1 93 1 TAAGCTTTTT 0.951883 -94 GGATAGCGATCAAGGTTTTTATGAAAATAA 4 153 1 CAAGGTTTTT 0.889325 -53 TAAAATTGTTTTAGGCTTTTATTTTCATAA 4 171 0 TTAGGCTTTT 0.78112 -35 TAGCCTTTTATTAGCTTTTTATAAAGTTTC 5 37 0 TTAGCTTTTT 0.910236 -152 GATTTTAATTTTAGCCTTTTATTAGCTTTT 5 48 0 TTAGCCTTTT 0.865796 -141 TTAAAGTTTATAAGATTTTTGAGTATAGCA 5 84 1 TAAGATTTTT 0.586679 -105 TATTTTAGCATAAGCCTTTTATAAAAACTT 5 138 0 TAAGCCTTTT 0.926393 -51 TGTTTGAATTATAGCTTTTTTAAAAAATAA 6 21 0 ATAGCTTTTT 0.852586 -51 TGCTCCCTTTTAAGGTTTTTCTTTTATTAA 8 18 1 TAAGGTTTTT 0.916269 -63 AAGTTGTATTATAGCTTTTTAAAAATAAAA 8 47 1 ATAGCTTTTT 0.852586 -34 ATTTAGTTTAAAAGGTTTTTACAAAC 11 7 0 AAAGGTTTTT 0.861828 -71 AAACGCTGTTAGCTTTTTGATAACCAAC 14 9 1 TTAGCTTTTT 0.910236 -156 TGGCTAACGCCAAGCTTTTTATGGTTGGTT 14 32 0 CAAGCTTTTT 0.935593 -133 AAAAATCATCAAAGCCTTTT 21 1 0 AAAGCCTTTT 0.877703 -285 ACGCTAAATTCAAGCTTTTTTTAAGCGAGG 21 108 1 CAAGCTTTTT 0.935593 -178 ACTATTAGAACAAGGTTTTTATGACGAT 34 121 1 CAAGGTTTTT 0.889325 -18 AGCAAAAGATTAAGGTTTTTTAGCTTAAGT 38 173 1 TAAGGTTTTT 0.916269 -76 TTATAACCTAAAAGCCTTTTTTACTTAAGC 38 195 0 AAAGCCTTTT 0.877703 -54 ********** Masking position 7 Map Score: 31.1057 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 358 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 14 TACTAAGCTTTTTAATAAGAGGGTGTATTC 1 100 1 TTTAATAAGA 0.872511 -87 AAAACAAAATTTTAAAAAGATTAAATAATA 4 49 1 TTTAAAAAGA 0.67412 -157 CACCAAAAGAGTTAATAAAAAATTTTTTTG 4 121 0 GTTAATAAAA 0.630941 -85 AGGCTTTTATTTTCATAAAAACCTTGATCG 4 159 0 TTTCATAAAA 0.661818 -47 CTAAAACAATTTTAAAAAAAGGACTTTTG 4 187 1 TTTAAAAAAA 0.81206 -19 GGTTTAAAGTTTTTATAAAAGGCTTATGCT 5 132 1 TTTTATAAAA 0.414271 -57 GATTTTTGATTATAATAAAAGATTTAAAAA 7 64 1 TATAATAAAA 0.670297 -78 TAATAAAAGATTTAAAAAAAGCGATAAAAT 7 76 1 TTTAAAAAAA 0.81206 -66 GGACTCCTTATTTGATAAGAAACGCTTCTT 7 117 0 TTTGATAAGA 0.728357 -25 ATAATACAACTTTAATAAAAGAAAAACCTT 8 29 0 TTTAATAAAA 0.913627 -52 ATACACTAATTTTAATAGAAAAAAGTGAAA 10 41 1 TTTAATAGAA 0.829814 -77 CCTATTCATGTTTGATAAAAACAGAACTAC 14 84 1 TTTGATAAAA 0.829657 -81 TTAATAAAATTTTAATAAAACTTGTGATTG 16 72 0 TTTAATAAAA 0.913627 -36 CTTCTCATTAATTAATAAAATTTTAATAAA 16 83 0 ATTAATAAAA 0.535691 -25 TTTTATATTTTATAATAGAATGAGATCAAT 25 202 0 TATAATAGAA 0.409061 -42 AAACTATCTTTTTAAAAAAATAACTTAAAA 28 48 1 TTTAAAAAAA 0.81206 -72 AAAAGCGTTGTTTGATAAAAATGGCTCATT 34 53 0 TTTGATAAAA 0.829657 -86 TTTCTATCATTTTAATAGGAACAAGGCAAA 38 121 0 TTTAATAGGA 0.700139 -128 ********** Masking position 3 Map Score: 15.241 Number of sites scoring better than the average of aligned sites = 420 Number in coding regions = 320 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 15 TAAAAAAAGCGATAAAATGGATAGGCTTAA 7 88 1 GATAAAATGG 0.53563 -54 CCCTAATTTAGTTTAAAAGGTTTTTACAAA 11 12 0 GTTTAAAAGG 0.57785 -66 CCCTATCAAAGATTAAATGCTATAATACTA 11 42 0 GATTAAATGC 0.775599 -36 TAACGCCAAGCTTTTTATGGTTGGTTATCA 14 28 0 CTTTTTATGG 0.747614 -137 TTTTTAATCCTTAAATGGTATAATATAA 18 9 1 CCTTAAATGG 0.648981 -159 ACAGCTTAGGGATTTTATGCTCTAGGATTT 18 128 1 GATTTTATGC 0.628475 -40 TAATGAGAGCCATTAAATGGTGCTAGGAGT 20 20 1 CATTAAATGG 0.835889 -201 ATGGGTATGGGTTTATATGGGGGTGAAAAG 20 116 0 GTTTATATGG 0.942129 -105 GTTTATATGGGTTTATATGGGTATGGGTTT 20 132 0 GTTTATATGG 0.942129 -89 CCAAAAAAGGGTTTATATGGGTTTATATGG 20 142 0 GTTTATATGG 0.942129 -79 TTATAATGTAGTTTTTATGCGAAGGGTATT 25 91 1 GTTTTTATGC 0.66779 -153 AAAAATGGCTCATTATATGGTATCTTAAAG 34 37 0 CATTATATGG 0.875111 -102 ********** Masking position 7 Map Score: 3.88464 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 196 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344