AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00350_hinf_reg_300.orf -o00350_hinf_300.ace -a/home/amcguire/genomes/ORF_hinf.txt -z/home/amcguire/genomes/hinf.fna -g0.38 -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 Input sequences: #1 HI0185 122 alcohol dehydrogenase, class III (adhC) #2 HI0195.1 26 conserved hypothetical transmembrane protein (aefA) #3 HI0197 84 penicillin-insensitive murein endopeptidase (mepA) #4 HI0199 46 lipid A biosynthesis (kdo)2-(lauroyl)-lipid IVA acyltransferase (msbB) #5 HI0301 300 hemolysin, putative #6 HI0329 37 conserved hypothetical protein #7 HI0330 98 opacity associated protein (oapA) #8 HI0331 59 opacity associated protein (oapB) #9 HI0468 300 ATP phosphoribosyltransferase (hisG) #10 HI0469 92 histidinol dehydrogenase (hisD) #11 HI0470 68 histidinol-phosphate aminotransferase (hisC) #12 HI0549 169 dimethyladenosine transferase (ksgA) #13 HI0916 107 outer membrane protein, putative #14 HI0920 248 conserved hypothetical protein #15 HI0961 74 hit-related protein #16 HI0962 28 isoleucyl-tRNA synthetase (isoleucine--tRNA ligase) (ileRS) #17 HI0963 34 riboflavin kinase / FMN adenylyltransferase (ribF) #18 HI0964 300 virulence factor (mviN) #19 HI0974.1 300 conserved hypothetical protein #20 HI0976 119 conserved hypothetical protein #21 HI0978 40 ribosomal protein L11 methyltransferase (prmA) #22 HI1024 49 hexulose-6-phosphate synthase, putative #23 HI1027 58 L-xylulose kinase (lyx) #24 HI1028 30 conserved hypothetical protein #25 HI1030 71 conserved hypothetical transmembrane protein #26 HI1031 175 conserved hypothetical protein #27 HI1062 85 (3R)-hydroxymyristol (acyl carrier protein) dehydrase (fabZ) #28 HI1064 56 conserved hypothetical protein #29 HI1527 84 lipid A biosynthesis lauroyl acyltransferase (htrB) #30 HI1615 160 phosphoribosylaminoimidazole carboxylase, catalytic subunit (purE) #31 HI1616 69 phosphoribosylaminoimidazole carboxylase, ATPase subunit (purK) #32 HI1617 138 aspartate aminotransferase (aspC) Motif number 1 ATTAATTTTAACCGCACTTTTGCGCGCTTT 4 16 0 ACCGCACTTT 0.998082 -31 TGTATTTTTAACCGCACTTTAGGTTTAAAC 5 175 1 ACCGCACTTT 0.998082 -126 ATAAAAAATAACCGCACATTGGGTTTAAAC 5 197 0 ACCGCACATT 0.9851 -104 TAATTTTTTCGCCGCACTTTTGAGCTTCTC 7 29 1 GCCGCACTTT 0.989898 -70 CCCTATAATAACCGCACTTTTCTTATTAAA 12 142 1 ACCGCACTTT 0.998082 -28 TTAAATTTTAACCGCACTTTTGCAGCATTT 14 20 1 ACCGCACTTT 0.998082 -229 CTAAAAAACCACCGCACTTTTTATTTCTCT 14 103 0 ACCGCACTTT 0.998082 -146 GAGCAAATCAATCGCACTTTTTGTTTTACA 15 21 0 ATCGCACTTT 0.97619 -54 TTTAGATCTGACCGCACTTTTAAAGTGCGG 31 18 1 ACCGCACTTT 0.998082 -52 GAAAAAAACAACCGCACTTTAAAAGTGCGG 31 29 0 ACCGCACTTT 0.998082 -41 GTAAAAAATGACCGCACTTTTTGATGAATA 32 12 1 ACCGCACTTT 0.998082 -127 ********** Masking position 6 Map Score: 48.4259 Number of sites scoring better than the average of aligned sites = 1115 Number in coding regions = 700 Number in noncoding regions = 415 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 2 AATAAGAATATTTTGTTGTCTAGAATTTTCCCCTC 5 127 1 TTTTTTAGAA 0.84068 -174 GCGTTTTGCGATTTTTTCTAAAATATGATAATTTT 5 243 1 ATTTTTAATA 0.869582 -58 AAAAAAGCAATTTTTTTGAAAAAAATTGTGTTTTT 9 26 0 TTTTTTAAAA 0.499065 -275 TTTAAAGTGTATTTTTAAGGCAATATAAGATCTAA 9 65 1 ATTTTAAATA 0.872697 -236 CAATATTATTTTTTCTTTCGTAGAAAGCTAAAAAC 12 51 0 TTTTTTAGAA 0.880483 -119 CAAATTGAGTTTTTCATGAACAATATTATTTTTTC 12 71 0 TTTTATAATA 0.532419 -99 ATAACCGCACTTTTCTTATTAAATAGTACTT 12 149 1 TTTTTTAATA 0.881644 -21 AATTGAACTTTTTTCTTCATCAGAACTCAAAAACA 13 13 1 TTTTTTAGAA 0.658486 -95 AAAATTGAAAATTTATTGTAAAAAACAACTAAAAA 14 126 0 ATTTTTAAAA 0.765149 -123 CTTTGTTCTAATCTGTTCTGCAAAAATTGAAAATT 14 148 0 ATCTTTAAAA 0.682096 -101 TTTTAAAATGTAAAAATTGGAAAAT 16 1 1 TTTTAAAAAA 0.631106 -28 CAAAATATTCTTCTCTACCCTAAAATTTTTGCCTA 18 237 0 TTCTTAAAAA 0.777802 -64 ATATTCCTTATTTTTTTGACGAATACCGATAAGAT 19 15 0 TTTTTTAATA 0.914785 -286 ATTTCTTCCTTAAAATTTTTTATAA 19 286 0 ATTTTTAAAA 0.929795 -15 ACTTTCAGCAATTTCTACGCTAAAACATAGAATTG 20 72 1 ATTTTAAAAA 0.930723 -48 ATACGCAAAATTTTGAAAGGAAAAACAA 21 23 1 TTTTAAAAAA 0.768447 -18 TGGGCTGGATTTTTATTATGTAAAATCCAGCCTAT 23 14 0 TTTTTTAAAA 0.771053 -45 TAAATAAATTATTTATAAATCAATATGTTAAAATA 26 70 0 ATTTTAAATA 0.872211 -106 CCTCTCTTAATTTTATATAGTAAAATTACGTTTCA 26 146 0 TTTTTAAAAA 0.771053 -30 ATTATACGATATTTATAGCTAAAAATAAAACGCAC 27 21 0 ATTTTAAAAA 0.929795 -65 AATAAGCCAATTTTTTAAGCCAGAAGGAAAAAACA 28 11 0 TTTTTAAGAA 0.880483 -46 CCTAAGCACAATTTTTATAAGAATAGGTCAAATT 30 10 0 ATTTTAAATA 0.869582 -151 GCTAAATGGCTTTTATAGGAAAATACCATTGCAAC 30 64 0 TTTTTAAATA 0.912092 -97 ATTTTCTCAATTTTCTAATTAAAAACGTGGCGTAG 30 133 0 TTTTTAAAAA 0.547216 -28 **** ** **** Masking position 4 Map Score: 28.3704 Number of sites scoring better than the average of aligned sites = 536 Number in coding regions = 303 Number in noncoding regions = 233 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 3 AGCAAGTGTTTTTTTATCATTTTTGTTTAAAGG 1 20 0 TTTTTCATTT 0.934755 -103 TGTGCGGTTATTTTTTATTGATTTTCCTCTTTT 5 209 1 TTTTTTTATT 0.782722 -92 CCATCTCTCATTTTTAGGATATTTCAAAT 6 7 0 TTTTTGAATT 0.847341 -31 CCCCTTTTTCTTTTTAAGTTCTTTTCTCAAGGT 8 30 1 TTTTTGTCTT 0.523637 -30 AAAAATTGTGTTTTTAGTACATTTTTACTA 9 8 0 TTTTTTAATT 0.893287 -293 AAAAAATTGCTTTTTTTAATTTTAAAGTGTATT 9 45 1 TTTTTAATTT 0.804619 -256 CTCGGAAGATATTTTATTATCTTCCAAACATAC 9 183 0 ATTTTTACTT 0.755941 -118 AATGTTTTTCCTATTTTAAAGTTGAGA 9 284 0 TTTTTTATTT 0.907844 -17 ATAACCCAGCATTTTGAGATATTGATTATTTAA 10 37 0 ATTTTGAATT 0.816936 -56 AATCCGCCCGTTTTTCTTAACTTTTCCGCCTAA 12 12 0 TTTTTTACTT 0.793908 -158 TCCCTATTAATTTTTGCCATTTTACGGTATTCT 14 71 0 TTTTTCATTT 0.934755 -178 GTGCGGTGGTTTTTTAGTTGTTTTTTACAATAA 14 116 1 TTTTTTTTTT 0.80914 -133 TTTACAATAAATTTTCAATTTTTGCAGAACAGA 14 139 1 ATTTTATTTT 0.587625 -110 TTATTTTCCAATTTTTACATTTTAAAA 16 5 0 ATTTTCATTT 0.920125 -24 AATATGCCGATTTTTTATACTTTTGTCAATGGA 18 53 1 TTTTTTATTT 0.907844 -248 TGTGTGGCGGATTTTATCAGTTTTTTTTCACGG 18 172 1 ATTTTCATTT 0.920125 -129 TACCCTAAAATTTTTGCCTAATTGTATAGAAAT 18 224 0 TTTTTCTATT 0.83972 -77 GTAAATTCGATTTTTATCATATTCATAAAAAGG 19 143 0 TTTTTCAATT 0.924094 -158 TCTTACAACTTTTTTGAATAATTCAAAAGGTTT 19 189 0 TTTTTATATT 0.60095 -112 GTGATATTTAATTTTCTCACTTTCAGCAATTTC 20 54 1 ATTTTCATTT 0.920125 -66 TCCTTTCAAAATTTTGCGTATTTTTACCGCACT 21 11 0 ATTTTGTTTT 0.693274 -30 CAGTAAAATTATTTTAACATATTGATTTATAAA 26 61 1 ATTTTCAATT 0.907301 -115 GAGCTTTCTTATTTTTGTAAATTATGAAACGTA 26 122 1 ATTTTTAATT 0.870329 -54 AATCCGATAGATTTTATTTGTTTATTTTTTGTA 27 53 1 ATTTTTTTTT 0.773176 -33 GCTATTTTCTCAATTTTCTAATTAAA 30 145 0 ATTTTCATTT 0.920119 -16 TGCGGTTGTTTTTTTCGTAAATTTAACGAGAAA 31 43 1 TTTTTTAATT 0.893281 -27 ACGCTTTGATATTTTTAAATATTCATCAAAAAG 32 28 0 ATTTTAAATT 0.737783 -111 ***** ** *** Masking position 5 Map Score: 29.7044 Number of sites scoring better than the average of aligned sites = 772 Number in coding regions = 524 Number in noncoding regions = 248 Number of orfs with sites within 600 bp upstream = 206 Fraction of orfs with sites within 600 bp upstream = 0.0330871 Motif number 4 GCGCAAAAGTGCGGTTAAAATTAATTACATT 4 21 1 GCGGTAAAAT 0.891509 -26 AACCCAATGTGCGGTTATTTTTTATTGATTT 5 202 1 GCGGTATTTT 0.983961 -99 GGTTATTATAGGGGTTGTTTTAGCTTTGTAA 12 124 0 GGGGTGTTTT 0.854941 -46 TAAGAAAAGTGCGGTTATTATAGGGGTTGTT 12 136 0 GCGGTATTAT 0.969529 -34 CTGCAAAAGTGCGGTTAAAATTTAAGGTGAT 14 14 0 GCGGTAAAAT 0.891509 -235 AATAAAAAGTGCGGTGGTTTTTTAGTTGTTT 14 108 1 GCGGTGTTTT 0.980571 -141 AACAAAAAGTGCGATTGATTTGCTCTGTCCT 15 26 1 GCGATGATTT 0.724552 -49 AGTGCGGTAAAAATACGCAAAATT 21 4 1 GCGGTAAAAT 0.891509 -37 TCTTGAGCGGTTATTTTATAGAATAAG 28 40 0 GCGGTATTTT 0.983961 -17 CTTTTAAAGTGCGGTTGTTTTTTTCGTAAAT 31 34 1 GCGGTGTTTT 0.980571 -36 ATCAAAAAGTGCGGTCATTTTTTACA 32 6 0 GCGGTATTTT 0.983961 -133 ATATCAAAGCGTGGTTAATTTTTATAAAATC 32 49 1 GTGGTAATTT 0.778333 -90 ***** ***** Masking position 5 Map Score: 17.6434 Number of sites scoring better than the average of aligned sites = 821 Number in coding regions = 524 Number in noncoding regions = 297 Number of orfs with sites within 600 bp upstream = 214 Fraction of orfs with sites within 600 bp upstream = 0.034372 Motif number 5 TTTTTGTTTAAAGGGAATAAAAA 1 1 0 AAGAATAAAA 0.823008 -122 TTTAAACAAAAATGATAAAAAAACACTTGCTTT 1 22 1 AAGTAAAAAA 0.752057 -101 AAACGCGAAAAGAGGAAAATCAATAAAAAATAA 5 216 0 AGGAAAACAA 0.955282 -85 ATATCTTCCGAGTGTAATAAAAATCAGTGTAAA 9 204 1 AGGAATAAAA 0.834554 -97 AATAAAAATCAGTGTAAAAGCAATAAATACCCC 9 219 1 AGGAAAACAA 0.955282 -82 TTACGGATACAAAGGAAAATAAACA 10 78 1 AAGAAAAAAA 0.952613 -15 GCTTTCTACGAAAGAAAAAATAATATTGTTCAT 12 58 1 AAGAAAATAA 0.718652 -112 AATGATTTACAAAGCTAAAACAACCCCTATAAT 12 118 1 AAGTAAACAA 0.74819 -52 TCTTCATCAGAACTCAAAAACAACGTTCTCTGC 13 26 1 AATAAAACAA 0.647325 -82 ATTAATAGGGAGAGAAATAAAAAGTGCGGTGGT 14 93 1 AGGAATAAAA 0.834554 -156 TTAAATTCATTGTAAAACAAAAAGTGCGATT 15 9 1 ATGAAAAAAA 0.832995 -66 AAATGTAAAAATTGGAAAATAAA 16 16 1 ATGAAAAAAA 0.832999 -13 TCCATTGACAAAAGTATAAAAAATCGGCATATT 18 53 0 AAGATAAAAA 0.61754 -248 CACGGAATATAGCGTAAAAACAAAATTTCTATA 18 200 1 AGGAAAACAA 0.955282 -101 CAAAATTTTGAAAGGAAAAACAA 21 28 1 AAGAAAACAA 0.951673 -13 TCAGTCAATAAATGTAAAATAAATAAATTATTT 26 91 0 AAGAAAAAAA 0.952613 -85 CGATATTTATAGCTAAAAATAAAACGCACTCAA 27 17 0 AGTAAAAAAA 0.670253 -69 ** * **** *** Masking position 9 Map Score: 18.7728 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 203 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 6 AATAAAATGTAATTAATTTTAACCGCACT 4 28 0 AAATAAATTT 0.502384 -19 CTAGACAACAAAATATTCTTATTTTGTTTATATGA 5 115 0 AAATCATTTT 0.94406 -186 AAGTGCGGTTAAAAATACACAATTTTTACGGAGAG 5 159 0 AAAACAATTT 0.70106 -142 AATCAATAAAAAATAACCGCACATTGGGTTTAAAC 5 197 0 AAATCACATT 0.777035 -104 TGACGGCGAAAAATTATCATATTTTAGAAAAAATC 5 252 0 AAATCATTTT 0.836422 -49 GATCCGATAAAATACACATAATTTTTTCGCCGCA 7 10 1 AAATCAATTT 0.891808 -89 TTGATAAATATCCTTAATTAAATGATGGGT 13 88 0 AAATCAATTA 0.610865 -20 AAAATCACCTTAAATTTTAACCGCAC 14 2 1 AAATCAAATT 0.918934 -247 AGAATACCGTAAAATGGCAAAAATTAATAGGGAGA 14 71 1 AAAACAAATT 0.481365 -178 TTTTTACAATAAATTTTCAATTTTTGCAGAACAGA 14 137 1 AAATCTTTTT 0.482974 -112 TATAATGCCGAAATTCTCTTATTTTC 17 19 1 AAATCATTTT 0.836422 -16 TTTTGTCTATCAATCAACAGAAATTTTAGGA 18 7 0 CAATCAAATT 0.668365 -294 TAAAGGGCATCAATATGCCGATTTTTTATACTTTT 18 42 1 CAATCATTTT 0.7727 -259 TGTCTCACCGAAATCAACACAAATTTTCCATTGAC 18 77 0 AAATCAAATT 0.918934 -224 ATTTCTATACAATTAGGCAAAAATTTTAGGGTAGA 18 224 1 AATTCAAATT 0.722189 -77 ATATTTGGGGAATTACACCGAAATTATCTTGGTCG 19 84 1 AATTCAAATT 0.722189 -217 AGTGCGGTAAAAATACGCAAAATTTTGAAAGGAAA 21 11 1 AAATCAATTT 0.891808 -30 ATGTTAAAATAATTTTACTGATTTTGTGATCTAGA 26 46 0 AATTCATTTT 0.767534 -130 CTGGCTTAAAAAATTGGCTTATTCTATAAAATAAC 28 23 1 AAATCATTCT 0.771133 -34 TTGGTTATTCAAATAGAGAGATTTTAAA 29 4 0 AAATGATTTT 0.471577 -81 AGTTGTGGTAAAATCGCCACAATTTTGGTTATTCA 29 28 0 AAATCAATTT 0.944705 -57 AATTTGACCTATTCTTATAAAAATT 30 1 1 AATTCATTCT 0.431144 -160 TGTAAAAAATGACCGCACTTTTTGATGAATA 32 7 1 AAATCACTTT 0.88591 -132 **** * ***** Masking position 2 Map Score: 22.615 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 334 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 7 ATCTCGTAAAAAGAGGGCAAAGATCCTTATCACA 5 24 0 AAGGCAAGAT 0.984815 -277 TGCCCAATTAAATTAGGCAGAGAACGTTGTTTTT 13 41 0 AAGGCAAGAA 0.991973 -67 TGCCTAATTTAATTGGGCAGAGAAAATATTAAAC 13 56 1 AAGGCAAGAA 0.991973 -52 GACAATAGAAAATGTGGCATAGAATACCGTAAAA 14 51 1 AAGGCAAGAA 0.991976 -198 AGAATACCGTAAAATGGCAAAAATTAATAGGGAG 14 71 1 AAGGCAAAAT 0.927381 -178 TGGCAAAAATTAATAGGGAGAGAAATAAAAAGTG 14 85 1 TAGGGAAGAA 0.850224 -164 ATTTCTATACAATTAGGCAAAAATTTTAGGGTAG 18 224 1 AAGGCAAAAT 0.927371 -77 CAGTCCTTACTATCTGGCATAGAAACTTTCATAT 19 54 1 TAGGCAAGAA 0.975043 -247 TCTAATTAAAAACGTGGCGTAGAATAGCACATCT 30 121 0 AAGGCGAGAA 0.966539 -40 ** **** **** Masking position 11 Map Score: 10.7098 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 40 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 CCCTCTCCGTAAAAATTGTGTATTTTTAAC 5 157 1 AAAAATTGTG 0.948769 -144 AGTGCGGCGAAAAAATTATGTGTATTTTAT 7 17 0 AAAAATTATG 0.749501 -82 TAATTAGCCACAAAATTGAGAAGCTCAAAA 7 46 0 CAAAATTGAG 0.880487 -53 TTTTTTTGAAAAAAATTGTGTTTTTAGTAC 9 21 0 AAAAATTGTG 0.948769 -280 AAGATCTAATAACATTTGAGCGAGCATATA 9 91 1 AACATTTGAG 0.724189 -210 AAGTGCGGTTAAAATTTAAGGTGATTTT 14 9 0 AAAATTTAAG 0.576098 -240 TCCTAAAATTTCTGTTGATTGATA 18 5 1 AAAATTTCTG 0.689227 -296 TTGTCAATGGAAAATTTGTGTTGATTTCGG 18 75 1 AAAATTTGTG 0.949837 -226 TCTCTACCCTAAAATTTTTGCCTAATTGTA 18 231 0 AAAATTTTTG 0.724775 -70 TAAAAATACGCAAAATTTTGAAAGGAAAAA 21 18 1 CAAAATTTTG 0.451253 -23 TAAAACGAATCACATTTGTGATAATCAATT 25 43 1 CACATTTGTG 0.732304 -29 TTTGAATAACCAAAATTGTGGCGATTTTAC 29 26 1 CAAAATTGTG 0.690101 -59 TAGTTTATCGTAAATTTGAGTTGTGGTAAA 29 51 0 TAAATTTGAG 0.579181 -34 CTATTCTTATAAAAATTGTGCTTAGGATAA 30 19 1 AAAAATTGTG 0.948769 -142 TTTTTAATTAGAAAATTGAGAAAATAGC 30 143 1 GAAAATTGAG 0.698594 -18 ********** Masking position 4 Map Score: 12.1958 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 151 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 9 TGTTTTTCCTCTTAATTCATTGACAAA 1 106 0 TTCCTTAATT 0.76627 -17 AGACAACAAAATATTCTTATTTTGTTTATATG 5 116 0 ATTCTTATTT 0.897175 -185 TGCGGTTATTTTTTATTGATTTTCCTCTTTTC 5 211 1 TTTTTGATTT 0.631088 -90 CCTCTGATGCTTGTTCTTATTTATATTAATTA 7 70 0 TTTCTTATTT 0.959897 -29 TTTATTGCTTTTACACTGATTTTTATTACACT 9 214 0 TTCCTGATTT 0.814801 -87 AATGTTTTTCCTATTTTAAAGTTGAG 9 285 0 TTTCCTATTT 0.808101 -16 AATCCGCCCGTTTTTCTTAACTTTTCCGCCTA 12 13 0 TTTCTTAACT 0.46957 -157 TTGATAAATATCCTTAATTAAATGATGGG 13 89 0 ATTCTTAATT 0.77145 -19 AATTGTTGCTTATTTAGTCTAACTT 15 60 0 TGTCTTATTT 0.685617 -15 TAATGCCGAAATTCTCTTATTTTC 17 21 1 ATCCTTATTT 0.755444 -14 AATGGAAAATTTGTGTTGATTTCGGTGAGACA 18 80 1 TTTTTGATTT 0.631088 -221 ACCCTAAAATTTTTGCCTAATTGTATAGAAAT 18 224 0 TTTCCTAATT 0.619653 -77 GACTGATGCATATTCCTTATTTTTTTGACGAA 19 27 0 TATCTTATTT 0.595375 -274 ATTCAAAAGGTTTTGCTGATTTCTACGTAAAT 19 170 0 TTTCTGATTT 0.925524 -131 AAATATCACCTTCCTCTCATTTAGAAGAAGGT 20 31 0 TTCCTCATTT 0.649918 -89 CCTTTCAAAATTTTGCGTATTTTTACCGCACT 21 11 0 TTTCGTATTT 0.695881 -30 CGTTTTTCCTTAAATAATATGAGGA 22 35 0 TTTCTTAAAT 0.373941 -15 ATATTCTCCTTAGTTTTTTATGGGC 23 44 0 TTTCTTAGTT 0.740219 -15 GTTAAAATAATTTTACTGATTTTGTGATCTAG 26 47 0 TTTCTGATTT 0.925524 -129 TTTATAAATAATTTATTTATTTTACATTTATT 26 86 1 ATTTTTATTT 0.54568 -90 GATAGATTTTATTTGTTTATTTTTTGTAAGGT 27 58 1 ATTTTTATTT 0.545681 -28 GCTATTTTCTCAATTTTCTAATTAA 30 146 0 ATTCTCAATT 0.425133 -15 AGCTTTTCCTTATGTATGTGTTGTG 32 124 0 TTTCTTATGT 0.695883 -15 ** * ******* Masking position 12 Map Score: 7.98186 Number of sites scoring better than the average of aligned sites = 569 Number in coding regions = 404 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 10 ATATCCTAGGTTCAGTCCTATTGAAGAACTAAC 3 38 0 TCATCTATTG 0.550103 -47 CAATGTGCGGTTATTTTTTATTGATTTTCCTCT 5 206 1 TATTTTATTG 0.692388 -95 GACGGCGAAAAATTATCATATTTTAGAAAAAAT 5 253 0 ATTTCTATTT 0.554316 -48 GATTTGTGTTTGATGTCTTATTGACGGCGAAAA 5 275 0 TATTCTATTG 0.864054 -26 AAATGTTATTAGATCTTATATTGCCTTAAAAAT 9 75 0 AATTTTATTG 0.893283 -226 AAGTGCAGATAAAATTCATATTGTATATGCTCG 9 111 0 AAATCTATTG 0.900077 -190 ACATATTTCGTATTGTTGTATGAAA 11 54 0 AATTCTATTG 0.959412 -15 CTACGAAAGAAAAAATAATATTGTTCATGAAAA 12 63 1 AAATATATTG 0.439957 -107 ATTCTATGCCACATTTTCTATTGTCAAAATGCT 14 43 0 AATTTTATTG 0.893288 -206 AAACTATATCATAAGTTATATTGGCTTGCTATG 14 188 0 AAATTTATTG 0.761336 -61 ATAATGCCGAAATTCTCTTATTTTC 17 20 1 ATTTCTATTT 0.555605 -15 AAATCAACACAAATTTTCCATTGACAAAAGTAT 18 69 0 AATTTCATTG 0.531783 -232 CTGGCATAGAAACTTTCATATTTGGGGAATTAC 19 67 1 ACTTCTATTT 0.737976 -234 TCTTGTGATAATATTTCATATTGTGAA 26 5 0 AATTCTATTG 0.959411 -171 TTATTGACTGAGCTTTCTTATTTTTGTAAATTA 26 113 1 ACTTCTATTT 0.738013 -63 * ** ** ***** Masking position 10 Map Score: 6.00236 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 112 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 11 ATACACAATTTTTACGGAGAGGGGAAAATT 5 150 0 TTTACGGAGA 0.924073 -151 CATCTCTCATTTTTAGGATATTTCAAAT 6 9 0 TTTTAGGATA 0.769654 -29 AAAGTGTATTTTTAAGGCAATATAAGATCT 9 68 1 TTTAAGGCAA 0.808124 -233 TATCATCCATTTTACGGATACAAAGGAAAA 10 67 1 TTTACGGATA 0.909752 -26 CCATCATTTAATTAAGGATATTTATCAA 13 90 1 ATTAAGGATA 0.769655 -18 GCGGTTAAAATTTAAGGTGATTTT 14 5 0 TTTAAGGTGA 0.81713 -244 TAGTCTAACTTTTAAGGACAGAGCAAATCA 15 41 0 TTTAAGGACA 0.922155 -34 TATAAAAAATTTTAAGGAAGAAAT 19 287 1 TTTAAGGAAG 0.791805 -14 CCTCATATTATTTAAGGAAAAACG 22 36 1 TTTAAGGAAA 0.95275 -14 CCATTGCAACTTTAAGGATAAAATTTTATC 30 44 0 TTTAAGGATA 0.963364 -117 TTTTCGTAAATTTAACGAGAAATATT 31 54 1 TTTAACGAGA 0.787618 -16 ********** Masking position 3 Map Score: 5.08106 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 30 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 12 AATCAATATCTCAAAATGCTGGGTTATCAT 10 43 1 TCAAAATGCT 0.957602 -50 TTTTCTATTGTCAAAATGCTGCAAAAGTGC 14 33 0 TCAAAATGCT 0.957602 -216 ATAAAGGGCATCAATATGCCGATTTTTTAT 18 41 1 TCAATATGCC 0.79854 -260 AGTCGTTTACTCAAAATATTCTTCTCTACC 18 253 0 TCAAAATATT 0.59521 -48 CTTGGTCGTATCAAAAGGTAACAAGTAATC 19 111 1 TCAAAAGGTA 0.597301 -190 TTTGAATAATTCAAAAGGTTTTGCTGATTT 19 180 0 TCAAAAGGTT 0.913354 -121 GTATTAATCAATATGCTGTCACCTTCT 20 8 1 TCAATATGCT 0.950016 -112 GTTTTTCCTTTCAAAATTTTGCGTATTTTT 21 19 0 TCAAAATTTT 0.59521 -22 TCAATAGGCTGGATTTTACA 23 1 1 TCAATAGGCT 0.922506 -58 CAGCAATATGTTTCCAGTAAAA 25 3 1 GCAATATGTT 0.727312 -69 TATTTATAAATCAATATGTTAAAATAATTT 26 66 0 TCAATATGTT 0.93405 -110 ********** Masking position 6 Map Score: 7.38517 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 89 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 13 TTCACAATCAAAAATCCATTATTCACAAGT 5 61 1 AAAATCCATT 0.65823 -240 AAAAGCAATAAATACCCCTCGGAAGGCAAT 9 234 1 AATACCCCTC 0.674057 -67 GAGATAAAAGAAAACCCCTCGAAAATTGCC 9 258 0 AAAACCCCTC 0.942116 -43 AAAATGGATGATAACCCAGCATTTTGAGAT 10 50 0 ATAACCCAGC 0.730915 -43 GAGAAAATATTAAACCCATCATTTAATTAA 13 75 1 TAAACCCATC 0.743886 -33 AACGACTTTTAAAATCTAGCATTGTTGTTA 18 276 1 AAAATCTAGC 0.8936 -25 TTTATTATGTAAAATCCAGCCTATTGA 23 8 0 AAAATCCAGC 0.958087 -51 TTACATAATAAAAATCCAGCCCATAAAAAA 23 26 1 AAAATCCAGC 0.958087 -33 ATAAACAAATAAAATCTATCGGATTATACG 27 48 0 AAAATCTATC 0.899803 -38 TTTAAAATCTCTCTATTTGAATA 29 4 1 AAAATCTCTC 0.864757 -81 TAATTTTTATAAAATCTTTCTTGATAAAAT 32 64 1 AAAATCTTTC 0.616761 -75 ********** Masking position 4 Map Score: 4.72773 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 197 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 14 TTGGGCGAGTAATCGCCCCTTTTTCTTTTTA 8 15 1 AACGCCCCTT 0.975166 -45 AACGGCTATAATCCGCCCGTTTTTCTTAACT 12 23 0 ATCGCCCGTT 0.973544 -147 CGTATATTTCATACGTCCCTTGTGTTTGCTA 19 223 0 ATCGTCCCTT 0.961332 -78 CGTATGAAATATACGCCCCTTATACCATTCA 19 239 1 ATCGCCCCTT 0.992346 -62 TTACGATAAACTACGCCCCTAACTTAC 29 68 1 CTCGCCCCTA 0.946716 -17 ** ******** Masking position 10 Map Score: 0.939084 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 7 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 15 CCTTACGTAAGCAAGATAGCAACAGTTTAC 1 72 0 GCAAGATAGC 0.955007 -51 TCCGTAAAATGGATGATAACCCAGCATTTT 10 55 0 GGATGATAAC 0.779704 -38 AAAAACGGGCGGATTATAGCCGTTTTTAGC 12 30 1 GGATTATAGC 0.964915 -140 GAGAATTTCGGCATTATAGCGAGAAG 17 7 0 GCATTATAGC 0.961894 -28 TTTTTTTCACGGAATATAGCGTAAAAACAA 18 193 1 GGAATATAGC 0.962689 -108 TAAAACGCACTCAATATAGC 27 1 0 TCAATATAGC 0.80857 -85 ********** Masking position 6 Map Score: 0.540941 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 14 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049