AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00340_hinf_reg_300.orf -o00340_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 Purged sequences: HI0962 28 isoleucyl-tRNA synthetase (isoleucine--tRNA ligase) (ileRS) Input sequences: #1 HI0195.1 26 conserved hypothetical transmembrane protein (aefA) #2 HI0197 84 penicillin-insensitive murein endopeptidase (mepA) #3 HI0199 46 lipid A biosynthesis (kdo)2-(lauroyl)-lipid IVA acyltransferase (msbB) #4 HI0301 300 hemolysin, putative #5 HI0329 37 conserved hypothetical protein #6 HI0330 98 opacity associated protein (oapA) #7 HI0331 59 opacity associated protein (oapB) #8 HI0365 225 conserved hypothetical protein #9 HI0366 101 fimbrial biogenesis and twitching motility protein, putative #10 HI0367 71 conserved hypothetical protein #11 HI0468 300 ATP phosphoribosyltransferase (hisG) #12 HI0469 92 histidinol dehydrogenase (hisD) #13 HI0470 68 histidinol-phosphate aminotransferase (hisC) #14 HI0471 111 imidazoleglycerol-phosphate dehydratase / histidinol-phosphatase (hisB) #15 HI0472 65 amidotransferase (hisH) #16 HI0473 35 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (hisA) #17 HI0549 169 dimethyladenosine transferase (ksgA) #18 HI0675 110 aminoacyl-histidine dipeptidase (pepD) #19 HI0821 207 galactose operon repressor (galR) #20 HI0822 90 galactose ABC transporter, periplasmic-binding protein (mglB) #21 HI0823 65 galactoside ABC transporter, ATP-binding protein (mglA) #22 HI0825 145 H. influenzae predicted coding region HI0825 #23 HI0830 37 trp operon repressor (trpR) #24 HI0831 142 monofunctional biosynthetic peptidoglycan transglycosylase #25 HI0916 107 outer membrane protein, putative #26 HI0920 248 conserved hypothetical protein #27 HI0949 300 aminotransferase #28 HI0961 74 hit-related protein #29 HI0963 34 riboflavin kinase / FMN adenylyltransferase (ribF) #30 HI0964 300 virulence factor (mviN) #31 HI0974.1 300 conserved hypothetical protein #32 HI0976 119 conserved hypothetical protein #33 HI0978 40 ribosomal protein L11 methyltransferase (prmA) #34 HI1126.1 181 H. influenzae predicted coding region HI1126.1 #35 HI1129 201 conserved hypothetical protein #36 HI1130 30 conserved hypothetical protein #37 HI1136 122 UDP-N-acetylmuramoylalanine--D-glutamate ligase (murD) #38 HI1137 21 cell division protein (ftsW) #39 HI1139 137 UDP-N-acetylmuramate--alanine ligase (murC) #40 HI1140 71 D-alanine--D-alanine ligase (ddlB) #41 HI1143 83 cell division protein (ftsZ) #42 HI1144 38 UDP-3-0-(3-hydroxymyristoyl) N-acetylglucosamine deacetylase (lpxC) #43 HI1166 87 histidinol-phosphate aminotransferase (hisH) #44 HI1167 190 phosphoserine aminotransferase (serC) #45 HI1527 84 lipid A biosynthesis lauroyl acyltransferase (htrB) Motif number 1 AAAGCGCGCAAAAGTGCGGTTAAAATTAAT 3 16 1 AAAGTGCGGT 0.998265 -31 GTTTAAACCTAAAGTGCGGTTAAAAATACA 4 175 0 AAAGTGCGGT 0.998265 -126 GTTTAAACCCAATGTGCGGTTATTTTTTAT 4 197 1 AATGTGCGGT 0.982651 -104 GAGAAGCTCAAAAGTGCGGCGAAAAAATTA 6 29 0 AAAGTGCGGC 0.994049 -70 TACAGCGGAAAAAGTGCGGTAAAATATCAG 8 34 0 AAAGTGCGGT 0.998265 -192 AGATCGCAAAAAAGTGCGGTAAGATTTTCT 8 84 1 AAAGTGCGGT 0.998265 -142 TTGAAAGAGCGGTTAATTTTTGT 15 4 1 AAAGAGCGGT 0.990825 -62 TTTAATAAGAAAAGTGCGGTTATTATAGGG 17 142 0 AAAGTGCGGT 0.998265 -28 AATAAGTGAGAAAGTGCGGTAAAAATTCGC 24 11 0 AAAGTGCGGT 0.998265 -132 AAATGCTGCAAAAGTGCGGTTAAAATTTAA 26 20 0 AAAGTGCGGT 0.998265 -229 AGAGAAATAAAAAGTGCGGTGGTTTTTTAG 26 103 1 AAAGTGCGGT 0.998265 -146 TGTAAAACAAAAAGTGCGATTGATTTGCTC 28 21 1 AAAGTGCGAT 0.985259 -54 TTCACTTTTGAAAGAGCGACCTTTTTTACG 37 33 1 AAAGAGCGAC 0.78451 -90 AACTCAACTAAAAGTGCGGTTAAAATTCGC 39 91 0 AAAGTGCGGT 0.998265 -47 ********** Masking position 2 Map Score: 54.6774 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 TGTAATTAATTTTAACCGCACTTTTGCGCGCT 3 18 0 TTACCGCACT 0.996934 -29 ATTGTGTATTTTTAACCGCACTTTAGGTTTAA 4 171 1 TTACCGCACT 0.996934 -130 ATCAATAAAAAATAACCGCACATTGGGTTTAA 4 199 0 ATACCGCACA 0.966742 -102 CACATAATTTTTTCGCCGCACTTTTGAGCTTC 6 25 1 TTGCCGCACT 0.977838 -74 TAGGCTGATATTTTACCGCACTTTTTCCGCTG 8 30 1 TTACCGCACT 0.996934 -196 CGATAGAAAATCTTACCGCACTTTTTTGCGAT 8 86 0 TTACCGCACT 0.996934 -140 TGTACAGATTTGTCACCGCATAATCTAGCGGA 8 127 0 TTACCGCATA 0.85832 -99 TACGACAAAAATTAACCGCTCTTTCAA 15 6 0 ATACCGCTCT 0.966742 -60 CAACCCCTATAATAACCGCACTTTTCTTATTA 17 138 1 ATACCGCACT 0.994065 -32 TACTTATGAAAGTAACCGCTTTCAATTTATCG 19 132 1 ATACCGCTTT 0.75729 -76 GCGAATTTTTACCGCACTTTCTCACTTA 24 7 1 TTACCGCACT 0.996934 -136 CACCTTAAATTTTAACCGCACTTTTGCAGCAT 26 16 1 TTACCGCACT 0.996934 -233 ACAACTAAAAAACCACCGCACTTTTTATTTCT 26 105 0 ACACCGCACT 0.95785 -144 TTTTGCGTATTTTTACCGCACT 33 1 0 TTACCGCACT 0.996934 -40 CGTTGCGAATTTTAACCGCACTTTTAGTTGAG 39 87 1 TTACCGCACT 0.996934 -51 * * ******** Masking position 6 Map Score: 43.9676 Number of sites scoring better than the average of aligned sites = 954 Number in coding regions = 586 Number in noncoding regions = 368 Number of orfs with sites within 600 bp upstream = 252 Fraction of orfs with sites within 600 bp upstream = 0.0404754 Motif number 3 AATAAAATGTAATTAATTTTAACCGCAC 3 29 0 AAATTTAATT 0.799757 -18 AAGTGCGGTTAAAAATACACAATTTTTACGGAGA 4 160 0 AAAATAAATT 0.795746 -141 GAAAAGAGGAAAATCAATAAAAAATAACCGCACA 4 209 0 AAATAAAAAA 0.767054 -92 CATATTTTAGAAAAAATCGCAAAACGCGAAAAGA 4 236 0 AAAAAGAAAA 0.731634 -65 GATTTTTTCTAAAATATGATAATTTTTCGCCGTC 4 252 1 AAAAAAAATT 0.788834 -49 ATTTGAAATATCCTAAAAATGAGAGATGG 5 6 1 AAATTTAAAA 0.79987 -32 CTACCTTGAGAAAAGAACTTAAAAAGAAAAAGGG 7 31 0 AAAAATAAAA 0.813003 -29 TCTAGATCGCAAATATTTTCAATTACAGCGGAAA 8 53 0 AAATTTAATT 0.799757 -173 ACTCACAACGAAAAATTCGCAATTAAAAAATGAA 8 166 0 AAAATGAATT 0.739801 -60 AAATTTAATCAAATAATTAGGCGG 10 58 0 AAATTTAAAT 0.854217 -14 TAGTAAAAATGTACTAAAAACACAATTTTT 11 7 1 AAATTTAAAA 0.79987 -294 AGTGTAATAAAAATCAGTGTAAAAGCAATAAATA 11 214 1 AAATAGAAAA 0.706151 -87 GAATTTTGCAAAAATACGACAAAAATTAACCGCT 15 18 0 AAAAAAAAAA 0.788835 -48 TTTAGGCGGAAAAGTTAAGAAAAACGGGCGGAT 17 10 1 AAAATAAAAA 0.795747 -160 AATTTATACTAAATTATTGTAAATAAACCGTGAT 19 49 1 AAATAGAAAT 0.778915 -159 TCTTTGTCACAAAATAAGAAAATAAGCAAAATTT 19 82 1 AAAAAAAATA 0.718154 -126 AGTATGAACTAAATCATAAAAAATTTTGCTTATT 19 102 0 AAATAAAAAT 0.828401 -106 TGATTACATAAAAAATTATGAATTTGTGATCCAT 20 19 0 AAAATTAATT 0.819305 -72 ATCTATGAGCAAATTTGCAAAAATGAAAATGATT 20 48 0 AAATTAAAAT 0.83429 -43 AAATAAATTATCGTAATTAATCTATGAG 20 73 0 AAATAGAATT 0.70615 -18 TAGATAAAACAAAAGTGGACAAATTTGCCCACTT 22 41 0 AAAATAAAAT 0.851006 -105 ATTATTGCATAAATATCCTTAATTCAGAATTGAA 22 75 0 AAATTTAATT 0.799757 -71 AAAAACGGCGAAAAAAAAACAAAAGACAACTCGC 24 71 0 AAAAAAAAAA 0.788835 -72 TCTGATGAAGAAAAAAGTTCAATTTA 25 3 0 AAAAATAATT 0.813002 -105 TTGATAAATATCCTTAATTAAATGATGGG 25 89 0 AAATTTAATT 0.799757 -19 AAAATCACCTTAAATTTTAACCGCA 26 2 1 AAATATAAAT 0.848908 -247 TTTATTGTAAAAAACAACTAAAAAACCACCGCAC 26 116 0 AAAAATAAAA 0.813003 -133 TCTGTTCTGCAAAAATTGAAAATTTATTGTAAAA 26 138 0 AAAATAAATT 0.795746 -111 ATATTGCAAAAAAAATATACAATTGTCCCCGTTT 27 79 1 AAAATAAATT 0.795746 -222 AAAACCTTCTAAAAGAGGTGAAAAAAAATAAGTC 27 269 0 AAAAATAAAA 0.813003 -32 GAAAATAAGAGAATTTCGGCATTAT 29 20 0 AAAAAAAATT 0.788834 -15 TTCCATTGACAAAAGTATAAAAAATCGGCATATT 30 53 0 AAAATAAAAA 0.795747 -248 TGTCTCACCGAAATCAACACAAATTTTCCATTGA 30 78 0 AAATAAAAAT 0.828401 -223 TCCGTGAAAAAAAACTGATAAAATCCGCCACACA 30 172 0 AAAATTAAAT 0.869238 -129 TATTCGTCAAAAAAATAAGGAATATGCATCAGTC 31 25 1 AAAATGAATA 0.659786 -276 AGTGCGGTAAAAATACGCAAAATTTTGAAAGG 33 9 1 AAAATGAAAA 0.739801 -32 CAAATCTTATAAAAATCTTTAAATTCAATTTTGA 34 92 1 AAAATTAAAT 0.869238 -90 ATTCTATTTCAAATTACGTCAAATCAAAATTGAA 34 115 0 AAATATAAAT 0.848908 -67 AAAATAAAGTAAAAGTATTTATAT 34 168 0 AAAAAGAAAA 0.731634 -14 TCAATAAAATTTTATGAAAAAAGCCGTTTG 35 7 1 AAATTTAAAA 0.79987 -195 TATTTTTAGAAAATCTCTAAAAATCTCCACAAAA 35 156 0 AAATTAAAAT 0.83429 -46 GATTTTCTAAAAATAAGTTCAATTTTTAAGGCGT 35 175 1 AAATATAATT 0.792931 -27 TAAGCTGACTAAATATATAAAATATAAATTCCCT 41 37 0 AAATTAAATA 0.70081 -47 TACTACGCCCAAATTTATTTAAAAATACATACTA 43 36 1 AAATTTAAAA 0.79987 -52 AACTCCCTTTAAAATAAATAAAATGACTGTGCCG 44 14 1 AAAAATAAAT 0.864389 -177 GATTGATTAAAAAAAAGCTAAATTACGGCACAGT 44 39 0 AAAAATAATT 0.813002 -152 CTTTTTACTGAAATCAAAAAAATTCTTTCTATCA 44 100 0 AAATAAAATT 0.766922 -91 **** * * **** Masking position 11 Map Score: 48.9049 Number of sites scoring better than the average of aligned sites = 1155 Number in coding regions = 779 Number in noncoding regions = 376 Number of orfs with sites within 600 bp upstream = 277 Fraction of orfs with sites within 600 bp upstream = 0.0444908 Motif number 4 TATTTTTCCCTAATCTAAATGGTAAA 1 5 0 TTTCATAAAG 0.867133 -22 ACATAGATACTTTTCGTCATATAAACAAAATAAGAATA 4 99 1 TTTTATAAAA 0.892615 -202 CCAAATCAAGTATTGGACTTTAAAATTTAGCCTCCATT 10 18 1 TATTTTAAAT 0.695027 -54 AAAAATTGCTTTTTTTAATTTTAAAGTGTATTTTTAAG 11 46 1 TTTTTTAAAG 0.79799 -255 AATGTTTTTCCTATTTTAAAGTTGAGATAAAAG 11 278 0 TTTTTTAAAT 0.817587 -23 CATTTTGAGATATTGATTATTTAAATGGCGAGTCAAAG 12 23 0 TATTATAAAG 0.871523 -70 TTATCATCCATTTTACGGATACAAAGGAAAATAAACA 12 66 1 TTTTATAAAA 0.892626 -27 AGGTTTATCATTTGCTTTATACAAACAGTATAAAACTA 14 51 0 TTTGATAAAG 0.867133 -61 GAAAAAATAATATTGTTCATGAAAAACTCAATTTGGCA 17 71 1 TATTATAAAT 0.884995 -99 ATAGGGGTTGTTTTAGCTTTGTAAATCATTGTTAGGTT 17 110 0 TTTTTTAAAA 0.711116 -60 GACTCCTGTTTTTTATCAATGTAAACGATTACATTAAT 19 14 1 TTTTATAAAA 0.89261 -194 TATCGTAAATTATTTATGATCAAAATATAAGATTTATA 19 159 1 TATTATAAAT 0.885 -49 ATGTAATCATTTTCATTTTTGCAAATTTGCTCATAGAT 20 44 1 TTTCTTAAAT 0.686774 -47 TTTTGCAGCATTTTGACAATAGAAAATGTGGCATAGAA 26 37 1 TTTTATAAAG 0.930264 -212 GTATATTTTTTTTGCAATATGAAAAGTAAATTTAGCTT 27 61 0 TTTGATAAAA 0.802636 -240 TTTTTTATACTTTTGTCAATGGAAAATTTGTGTTGATT 30 63 1 TTTTATAAAT 0.937519 -238 CAGTCCTTACTATCTGGCATAGAAACTTTCATATTTGG 31 54 1 TATCATAAAT 0.790139 -247 TTACAACTTTTTTGAATAATTCAAAAGGTTTTGCTGAT 31 182 0 TTTGATAAAG 0.867133 -119 AAAAATATACTTTCACTTATAAAAAATTTTAAGGAAGA 31 270 1 TTTCATAAAT 0.88102 -31 TTGTTTTTCCTTTCAAAATTTTGCGTATTTT 33 20 0 TTTTTTAAAT 0.817587 -21 TTGTATCACATTTGTAAAATCTAAAACATCCATTAAAA 34 50 0 TTTGATAAAA 0.802621 -132 TTTAAAATTATATCATTGATGGAAATATAAATTTCCTT 37 69 0 TATCATAAAT 0.790139 -54 GTCATAAGTATTTTTTATATCCAAAAGTGCTAATATTA 39 39 1 TTTTATAAAT 0.936536 -99 AAAGTGCTAATATTAGAAATAAAAACGTTGCGAATTTT 39 62 1 TATTATAAAT 0.885011 -76 AAATTCCCTTTATTGTAGATGAAAAATTAAAATAA 41 8 0 TATTATAAAT 0.88453 -76 CCCTCTATTTTATGAATGATAGAAAGAATTTTTTTGAT 44 84 1 TATGATAAAA 0.674035 -107 ATCGCCACAATTTTGGTTATTCAAATAGAGAGATTTTA 45 13 0 TTTTATAAAG 0.93027 -72 **** ** *** * Masking position 10 Map Score: 27.5756 Number of sites scoring better than the average of aligned sites = 443 Number in coding regions = 269 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 5 ACCATTTAGATTAGGGAAAAATA 1 14 1 TAGGAAAAAT 0.856117 -13 ATTTTTACGGAGAGGGGAAAATTCTAGACAAC 4 141 0 AAGGGAAAAT 0.961525 -160 CAAAACGCGAAAAGAGGAAAATCAATAAAAAA 4 219 0 AAGGGAAAAT 0.961525 -82 TGTCTTATTGACGGCGAAAAATTATCATATTT 4 263 0 AGGGAAAAAT 0.936536 -38 ATTTTCAATTACAGCGGAAAAAGTGCGGTAAA 8 41 0 AAGGGAAAAA 0.931341 -185 TCAAAAACTCACAACGAAAAATTCGCAATTAA 8 174 0 AAAGAAAAAT 0.85025 -52 TTTTACGGATACAAAGGAAAATAAACA 12 76 1 AAAGGAAAAT 0.873671 -17 TATAACATACACGGAGAAAAAT 14 100 1 AGGGAAAAAT 0.936536 -12 ACCTCTTTAAAAAGGGGAAGATCCACTTCCCC 21 39 0 AAGGGAAGAT 0.685029 -27 CCATTTTCATAGAGAGAAAAAA 22 134 1 AAGGAAAAAA 0.917603 -12 CACTAGTTTAATAGTGTAAAATGGGAGCATAA 23 14 1 AAGGTAAAAT 0.793818 -24 TTAGTCCTAAATGGTGGAAAAAAAACTGGCAG 24 40 1 AGGGGAAAAA 0.907032 -103 CAAAGCAAAAACGGCGAAAAAAAAACAAAAGA 24 79 0 AGGGAAAAAA 0.889011 -64 GAATAGGTACAAAGCGAAAAATCAGCAACAAA 24 107 0 AAGGAAAAAT 0.953525 -36 ATAAGCGGAAAATGGAATAGGTA 24 130 0 TAGGGAAAAT 0.878751 -13 TTGAGTTCTGATGAAGAAAAAAGTTCAATTTA 25 11 0 AGAGAAAAAA 0.689113 -97 AAAAATTAATAGGGAGAGAAATAAAAAGTGCG 26 89 1 AGGGAGAAAT 0.71218 -160 TATACTTTTGTCAATGGAAAATTTGTGTTGAT 30 68 1 TAAGGAAAAT 0.667291 -233 TTCACGGAATATAGCGTAAAAACAAAATTTCT 30 198 1 AAGGTAAAAA 0.67635 -103 GAAATTGCTGAAAGTGAGAAAATTAAATATCA 32 55 0 AAGGAGAAAA 0.651239 -65 CGCAAAATTTTGAAAGGAAAAACAA 33 26 1 TAAGGAAAAA 0.521215 -15 TCATTGGGAGAAAAGGAAAAATAA 39 124 1 AAAGAAAAAT 0.85025 -14 CCCTTTATTGTAGATGAAAAATTAAAATAA 41 9 0 TGAGAAAAAT 0.542191 -75 * ** ******* Masking position 9 Map Score: 24.7677 Number of sites scoring better than the average of aligned sites = 335 Number in coding regions = 267 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 6 CCAATGTGCGGTTATTTTTTATTGATTTTCC 4 205 1 GTTATTTTTA 0.712439 -96 AAAATATCAGCCTATTTTTTAAGGTGACCAA 8 13 0 CCTATTTTTA 0.575882 -213 TTCGTTGTGAGTTTTTGATAAAAACACCTGC 8 188 1 GTTTTTGATA 0.713186 -38 CAAAAAAATTGCTTTTTTTAATTTTAAAGTG 11 43 1 GCTTTTTTTA 0.922471 -258 CTTTTACACTGATTTTTATTACACTCGGAAG 11 208 0 GATTTTTATA 0.92723 -93 AGCATTTTGAGATATTGATTATTTAAATGGC 12 32 0 GATATTGATA 0.523005 -61 TTTGACTCCTGTTTTTTATCAATGTAAACGA 19 11 1 GTTTTTTATA 0.92723 -197 TTTAATTAAGGATATTTATCAA 25 96 1 GATATTTATA 0.848911 -12 AGAAACGTTTGCTTTTTATTTAGCCGTTTGA 27 22 1 GCTTTTTATT 0.646716 -279 AAGCTGAAACGCTTTTTTTAATAAGTAGCGA 27 184 1 GCTTTTTTTA 0.922471 -117 GATTTTATCAGTTTTTTTTCACGGAATATAG 30 181 1 GTTTTTTTTA 0.848911 -120 AAGTAATCATCCTTTTTATGAATATGATAAA 31 133 1 CCTTTTTATA 0.87474 -168 ACGTAAATTCGATTTTTATCATATTCATAAA 31 147 0 GATTTTTATA 0.92723 -154 TATTCAATTACTTATTTATTAGCATTTTAAT 34 26 1 CTTATTTATA 0.592519 -156 TGAATTTAAAGATTTTTATAAGATTTGTGAC 34 88 0 GATTTTTATA 0.92723 -94 TAAAGCAACTGATTTTTATCAAAATAAAAAA 35 60 0 GATTTTTATA 0.92723 -142 TATGACTGAGGCTATTTATAAAACGCCACAA 39 14 0 GCTATTTATA 0.922471 -124 CCGTAATTTAGCTTTTTTTTAATCAATCGTC 44 45 1 GCTTTTTTTA 0.922471 -146 ATAATGATGTCTTTTTTATCACTACAAAAAT 44 146 0 CTTTTTTATA 0.767315 -45 GTATTTCCTTGCTTTTTATGAAAATAATGAT 44 169 0 GCTTTTTATA 0.964265 -22 ********* * Masking position 6 Map Score: 18.7928 Number of sites scoring better than the average of aligned sites = 282 Number in coding regions = 209 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 7 CGTCATATAAACAAAATAAGAATATTTTGT 4 113 1 ACAAAATAAG 0.947641 -188 ATTCTAGACAACAAAATATTCTTATTTTGT 4 123 0 ACAAAATATT 0.564034 -178 ATACAACAATACGAAATATGT 13 58 1 ACGAAATATG 0.762168 -11 ACAGTATAAAACTAAATAATCTCGAATCGC 14 35 0 ACTAAATAAT 0.817874 -77 TCTACGAAAGAAAAAATAATATTGTTCATG 17 62 1 AAAAAATAAT 0.60208 -108 GAAAATATTGACGAAATAATAGCATAAAAC 18 74 0 ACGAAATAAT 0.78742 -37 GATCTTTGTCACAAAATAAGAAAATAAGCA 19 80 1 ACAAAATAAG 0.947641 -128 ACCATTTAGGACTAAATAAGTGAGAAAGTG 24 25 0 ACTAAATAAG 0.939842 -118 AAGAGGTGAAAAAAAATAAGTCGGGTGCCT 27 261 0 AAAAAATAAG 0.840354 -40 TAAAAGTTAGACTAAATAAGCAACAATT 28 57 1 ACTAAATAAG 0.939842 -18 TGATTGATAGACAAAATAAAGGGCATCAAT 30 26 1 ACAAAATAAA 0.799813 -275 GTATTCGTCAAAAAAATAAGGAATATGCAT 31 24 1 AAAAAATAAG 0.840354 -277 TTAAAATGCTAATAAATAAGTAATTGAATA 34 26 0 AATAAATAAG 0.819618 -156 TTAGTAACTCACGAAATAAG 38 12 1 ACGAAATAAG 0.927987 -10 AGATAAGCTGACTAAATATATAAAATATAA 41 44 0 ACTAAATATA 0.461688 -40 CTCCCTTTAAAATAAATAAAATGACTGTGC 44 16 1 AATAAATAAA 0.500761 -175 ********** Masking position 5 Map Score: 14.0195 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 66 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 8 GAAGAAATACTTAATATGCTTTAATTTGTA 9 59 0 TTAATATGCT 0.733465 -43 AATCAATATCTCAAAATGCTGGGTTATCAT 12 43 1 TCAAAATGCT 0.972342 -50 TTTTCTATTGTCAAAATGCTGCAAAAGTGC 26 33 0 TCAAAATGCT 0.972342 -216 TTCTTACGAGTCAAACGGCTAAATAAAAAG 27 33 0 TCAAACGGCT 0.964437 -268 ATAAAGGGCATCAATATGCCGATTTTTTAT 30 41 1 TCAATATGCC 0.768508 -260 TTTGAATAATTCAAAAGGTTTTGCTGATTT 31 180 0 TCAAAAGGTT 0.768927 -121 GTATTAATCAATATGCTGTCACCTTCT 32 8 1 TCAATATGCT 0.940894 -112 AAAACATCCATTAAAATGCTAATAAATAAG 34 36 0 TTAAAATGCT 0.858705 -146 AATAAACAATTCAAACGGCTTTTTTCATAA 35 22 0 TCAAACGGCT 0.964437 -180 AATTGTTTATTCAAACGGCTTTTTTATTTT 35 41 1 TCAAACGGCT 0.964437 -161 ********** Masking position 4 Map Score: 8.20022 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 40 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 TATTTTTCCCTAATCTAAATGGTAA 1 12 0 ATTTTTCAAC 0.551942 -15 GCGTTTTGCGATTTTTTCTAAAATATGATAATTT 4 243 1 ATTTTTCAAT 0.89827 -58 AATATTTTCAATTACAGCGGAAAAAGTGCGGTAA 8 42 0 ATTACACAAA 0.178801 -184 TTAAGTATTTCTTCCTGCCCAATTAAAAGGAGGA 9 75 1 CTTCCTCAAT 0.490359 -27 GAGGGGTTTTCTTTTATCTCAACTTTAAAATAGG 11 268 1 CTTTTACAAT 0.812997 -33 TTTTTGTCGTATTTTTGCAAAATTCGACCGATTG 15 27 1 ATTTTTCAAT 0.815542 -39 ATAATCCGCCCGTTTTTCTTAACTTTTCCGCCTA 17 13 0 CGTTTTCAAT 0.515169 -157 CCGTTTTTAGCTTTCTACGAAAGAAAAAATAATA 17 49 1 CTTTCTCAAA 0.724625 -121 AATTGCTCCTTTTTACTGAAAATATTGACGAA 18 89 0 CTTTTTCAAA 0.785334 -22 GATTACATTAATTTATACTAAATTATTGTAAATA 19 40 1 ATTTATCAAT 0.63415 -168 AATCATTTTCATTTTTGCAAATTTGCTCATAGAT 20 48 1 ATTTTTCATT 0.396906 -43 TTCCCCTTAGATTACAACAAAAATTGATGGGAAA 21 11 0 ATTACACAAT 0.441369 -55 CATAAATATCCTTAATTCAGAATTGAATAGATAA 22 68 0 CTTAATCAAT 0.341308 -78 GGGTTTGCCGATTATTGCATAAATATCCTTAATT 22 85 0 ATTATTCAAT 0.754215 -61 GCGAATTTTTACCGCACTTTCTCACTTA 24 5 1 ATTTTTCCAT 0.652536 -138 TAAATTTTCAATTTTTGCAGAACAGATTAGAACA 26 146 1 ATTTTTCAAA 0.760474 -103 CTACCCTAAAATTTTTGCCTAATTGTATAGAAAT 30 224 0 ATTTTTCAAT 0.924208 -77 TATTTGGGGAATTACACCGAAATTATCTTGGTCG 31 85 1 ATTACACAAT 0.44191 -216 GGTTTTGCTGATTTCTACGTAAATTCGATTTTTA 31 160 0 ATTTCTCAAT 0.897894 -141 AATTTTGCGTATTTTTACCGCACT 33 1 0 ATTTTTCCAT 0.652536 -40 ATTCAAACGGCTTTTTTCATAAAATTTTATTGA 35 10 0 CTTTTTCAAA 0.785337 -192 TAATGTAGTACTTTTATCTTAAATTT 36 15 1 CTTTTACAAT 0.812942 -16 TTTCTTTCTTCTTAATTGCTATAAATT 37 106 0 CTTTCTCAAT 0.905385 -17 ATAATCAATGCTTTTTACTGAAATCAAAAAAATT 44 110 0 CTTTTTCAAT 0.929767 -81 AATTGTGGCGATTTTACCACAACTCAAATTTACG 45 39 1 ATTTTACAAT 0.800026 -46 ****** * ** * Masking position 3 Map Score: 14.9339 Number of sites scoring better than the average of aligned sites = 436 Number in coding regions = 349 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 10 ATAAGGATCTTTGCCCTCTTTTTACGAGATCAA 4 28 1 TTCCCCTTTT 0.934008 -273 TTTTTATTGATTTTCCTCTTTTCGCGTTTTGCG 4 220 1 TTTCCCTTTC 0.789979 -81 ACATAATTTTTTCGCCGCACTTTTGAGCTTCTC 6 26 1 TTGCCCCTTT 0.801414 -73 TGGGCGAGTAATCGCCCCTTTTTCTTTTTAAGT 7 16 1 ATGCCCTTTT 0.767954 -44 TTTTCCTCCTTTTAATTGGGCAG 9 89 0 TTTCCCTTTT 0.950678 -13 ACTTTAAAATTTAGCCTCCATTTACCGCCTAAT 10 34 1 TTGCCCATTT 0.938248 -38 AAATGCTGGGTTATCATCCATTTTACGGATACA 12 56 1 TTTCACATTT 0.694009 -37 TTTCCCATCAATTTTTGTTGTAAT 21 2 1 TTCCACATTT 0.624827 -64 GGGAAGTGGATCTTCCCCTTTTTAAAGAGGTTG 21 40 1 TCTCCCTTTT 0.68374 -26 GTGGACAAATTTGCCCACTTTTCATTCATTTTA 22 28 0 TTCCCCTTTC 0.734184 -118 GTGGGCAAATTTGTCCACTTTTGTTTTATCTAT 22 43 1 TTTCCCTTTG 0.671472 -103 CCTGTATAATTGCGCCACCATTTTCATAGAGAG 22 117 1 TGGCCCATTT 0.630209 -29 TGCCAGTTTTTTTTCCACCATTTAGGACTAAAT 24 38 0 TTTCCCATTT 0.913688 -105 TTTTGTTTTTTTTTCGCCGTTTTTGCTTTGTTG 24 81 1 TTTCGCTTTT 0.601594 -62 TAACCGCACTTTTGCAGCATTTTGACAATAGAA 26 28 1 TTGCACTTTT 0.855644 -221 TACGGTATTCTATGCCACATTTTCTATTGTCAA 26 49 0 TAGCCCTTTT 0.786865 -200 AAATATACAATTGTCCCCGTTTTGACGTAACCC 27 91 1 TTTCCCTTTT 0.950678 -210 AGGTAACAAGTAATCATCCTTTTTATGAATATG 31 126 1 TATCACTTTT 0.355297 -175 GCGGTTAAAATTCGCAACGTTTTTATTTCTAAT 39 73 0 TTGCACTTTT 0.855644 -65 TCGTCAAAATTTACCCTCTATTTTATGAATGAT 44 71 1 TTCCCCATTT 0.886017 -120 TTGTGGTAAAATCGCCACAATTTTGGTTATTCA 45 28 0 ATGCCCATTT 0.645089 -57 ** *** * **** Masking position 11 Map Score: 20.1002 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 239 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 11 ATCTCGTAAAAAGAGGGCAAAGATCCTTATC 4 27 0 AAGAGGCAAA 0.555485 -274 TCACCTTAAAAAATAGGCTGATATTTTACCG 8 17 1 AAATGGCTGA 0.496765 -209 TCCTCCTTTTAATTGGGCAGGAAGAAATACT 9 78 0 AATTGGCAGG 0.534617 -24 CAATCGGTCGAATTTTGCAAAAATACGACAA 15 30 0 AATTTGCAAA 0.645233 -36 TGAAAAACTCAATTTGGCATAACCTAACAAT 17 90 1 AATTGGCATA 0.832182 -80 CAAAATAAGAAAATAAGCAAAATTTTTTATG 19 91 1 AAATAGCAAA 0.698464 -117 ATCTATGAGCAAATTTGCAAAAATGAAAATG 20 51 0 AAATTGCAAA 0.698464 -40 AATGAATGAAAAGTGGGCAAATTTGTCCACT 22 31 1 AAGTGGCAAA 0.892268 -115 ATTTATGCAATAATCGGCAAACCCTGTATAA 22 95 1 TAATGGCAAA 0.634137 -51 TGCCCAATTAAATTAGGCAGAGAACGTTGTT 25 44 0 AATTGGCAGA 0.911046 -64 TGCCTAATTTAATTGGGCAGAGAAAATATTA 25 56 1 AATTGGCAGA 0.911046 -52 GACAATAGAAAATGTGGCATAGAATACCGTA 26 51 1 AATGGGCATA 0.386076 -198 AGAATACCGTAAAATGGCAAAAATTAATAGG 26 71 1 AAAAGGCAAA 0.765037 -178 CTAGCCCGTCCAATGGGCAAACTAGGGTAAA 27 146 1 CAATGGCAAA 0.719802 -155 AAAGTATAAAAAATCGGCATATTGATGCCCT 30 45 0 AAATGGCATA 0.863305 -256 ATTTCTATACAATTAGGCAAAAATTTTAGGG 30 224 1 AATTGGCAAA 0.944271 -77 ATTTACGTAGAAATCAGCAAAACCTTTTGAA 31 170 1 AAATAGCAAA 0.698464 -131 AGTGCGGTAAAAATACGCAAAATTTTGAAAG 33 11 1 AAATCGCAAA 0.660663 -30 **** ****** Masking position 2 Map Score: 10.1625 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 223 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 12 CATACCCCTATGTTTTCATACAAATTAAAGCATATT 9 41 1 TTTAAAAATT 0.866005 -61 AAAACACAATTTTTTTCAAAAAAATTGCTTTTTTTA 11 27 1 TTTAAAAATT 0.866005 -274 CGCAATTTTTTATTTCTCGATAAATTTAAACTAAGG 18 18 0 TTCCAAAATT 0.84715 -93 AGATCACGGTTTATTTACAATAATTTAGTATAAATT 19 49 0 TTTCAAATTT 0.782 -159 TGATCATAAATAATTTACGATAAATTGAAAGCGGTT 19 145 0 TTTCAAAATT 0.956934 -63 TGCTCATAGATTAATTACGATAATTTATTT 20 71 1 TTTCAAATTT 0.782 -20 TTTTTAGTTGTTTTTTACAATAAATTTTCAATTTTT 26 126 1 TTTCAAAATT 0.956937 -123 TAAGTTATATTGGCTTGCTATGAATTCCTTTGTTCT 26 174 0 TTTCAGAATT 0.896796 -75 ATAAGTCGGGTGCCTTGCGATAAATTTACTGTTTAT 27 240 0 TTTCAAAATT 0.956937 -61 TCGCACTTTTTGTTTTACAATGAATTTAA 28 4 0 TTTCAGAATT 0.896796 -71 ATTTTGTCTATCAATCAACAGAAATTTTAGGA 30 7 0 TTCAAAAATT 0.617413 -294 ATTTCTTCCTTAAAATTTTTTATAAGT 31 284 0 TTTCTAAATT 0.655338 -17 TTCTTTCTTCTTAATTGCTATAAATTTTAAAATTAT 37 96 0 TTTCAAAATT 0.956937 -27 TCTACTACCTTCATTTACTAGGTATTTTCTGAAACT 42 13 0 TTTCAGTATT 0.583804 -26 GGTTAGTATGTATTTTTAAATAAATTTGGGCGTAGT 43 37 0 TTTAAAAATT 0.866003 -51 AGTTGTATTTATAAATATTGATATGGGTT 43 69 0 TTTAAATATT 0.51059 -19 * ** * * ***** Masking position 5 Map Score: 14.6817 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 63 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 13 TTTTATTTCTCGATAAATTTAAACTAAGGT 18 17 0 CGATAAATTT 0.936844 -94 AAATAATTTACGATAAATTGAAAGCGGTTA 19 144 0 CGATAAATTG 0.775537 -64 TTGTTATAATCTATAAATCTTATATTTTGA 19 178 0 CTATAAATCT 0.779772 -30 ATTTCTCTCCCTATTAATTTTTGCCATTTT 26 81 0 CTATTAATTT 0.704633 -168 TTGTTTTTTACAATAAATTTTCAATTTTTG 26 133 1 CAATAAATTT 0.788666 -116 TGAGAGACCTCTATAAATTTGGTGGTAAAC 26 217 0 CTATAAATTT 0.938099 -32 GGGTGCCTTGCGATAAATTTACTGTTTATA 27 239 0 CGATAAATTT 0.936844 -62 ATTGATGGAAATATAAATTTCCTTTACTAA 37 63 0 ATATAAATTT 0.597722 -60 TTCTTAATTGCTATAAATTTTAAAATTATA 37 95 0 CTATAAATTT 0.938099 -28 ********** Masking position 6 Map Score: 4.32542 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 60 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 14 TCCTGTACCTAGGGTAGTATACTCTAGGTT 2 11 1 AGGGTAGTAT 0.753796 -74 CGAAATTATCTTGGTCGTATCAAAAGGTAA 31 102 1 TTGGTCGTAT 0.832545 -199 AGCAAACACAAGGGACGTATGAAATATACG 31 224 1 AGGGACGTAT 0.930487 -77 GAATGGTATAAGGGGCGTATATTTCATACG 31 239 0 AGGGGCGTAT 0.985886 -62 AACATTTCCAATGGGCGTATTTACTACGCC 43 15 1 ATGGGCGTAT 0.971257 -73 TTAAATAAATTTGGGCGTAGTAAATACGCC 43 28 0 TTGGGCGTAG 0.908265 -60 GTAAGTTAGGGGCGTAGTTTATCGTAA 45 68 0 AGGGGCGTAG 0.979169 -17 ********** Masking position 9 Map Score: 2.46179 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 22 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 15 TTTCCCCTCTCCGTAAAAATTGTGTATTTT 4 153 1 CCGTAAAAAT 0.92762 -148 TATTGGTCACCTTAAAAAATAGGCTGATA 8 10 1 CCTTAAAAAA 0.59426 -216 AAGTATTGGACTTTAAAATTTAGCCTCCAT 10 25 1 CTTTAAAATT 0.651157 -47 TAAAAATACACTTTAAAATTAAAAAAAGCA 11 52 0 CTTTAAAATT 0.651157 -249 TCTTATATTGCCTTAAAAATACACTTTAAA 11 65 0 CCTTAAAAAT 0.944779 -236 TTTTATCTCAACTTTAAAATAGGAAAAACA 11 279 1 ACTTTAAAAT 0.192773 -22 TCCTTTGTATCCGTAAAATGGATGATAACC 12 64 0 CCGTAAAATG 0.679563 -29 TGAGAAAGTGCGGTAAAAATTCGC 24 5 0 CGGTAAAAAT 0.680297 -138 AAAATCACCTTAAATTTTAACCGCACT 26 8 1 CCTTAAATTT 0.478756 -241 GCATAGAATACCGTAAAATGGCAAAAATTA 26 67 1 CCGTAAAATG 0.679563 -182 TTTGCTCTGTCCTTAAAAGTTAGACTAAAT 28 44 1 CCTTAAAAGT 0.763096 -31 TTCTTCTCTACCCTAAAATTTTTGCCTAAT 30 235 0 CCCTAAAATT 0.675692 -66 GAGTAAACGACTTTTAAAATCTAGCATTGT 30 271 1 CTTTTAAAAT 0.438546 -30 ATTTCTTCCTTAAAATTTTTTATAAGT 31 284 0 CCTTAAAATT 0.923875 -17 AGTGCGGTAAAAATACGCAAAATT 33 5 1 CGGTAAAAAT 0.680297 -36 TCTAAAACATCCATTAAAATGCTAATAAAT 34 39 0 CCATTAAAAT 0.37384 -143 ATTACGCCTTAAAAATTGAACTTATT 35 186 0 CCTTAAAAAT 0.944779 -16 AACAACTCCCTTTAAAATAAATAAAATG 44 9 1 CCTTTAAAAT 0.836187 -182 ********** Masking position 4 Map Score: 5.85854 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 186 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826