AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00561_hinf_reg_300.orf -o00561_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: HI1137 21 cell division protein (ftsW) Input sequences: #1 HI0123 274 phosphatidylglycerophosphate synthase (pgsA) #2 HI0160 156 phosphatidylserine decarboxylase proenzyme (psd) #3 HI0185 122 alcohol dehydrogenase, class III (adhC) #4 HI0195.1 26 conserved hypothetical transmembrane protein (aefA) #5 HI0197 84 penicillin-insensitive murein endopeptidase (mepA) #6 HI0199 46 lipid A biosynthesis (kdo)2-(lauroyl)-lipid IVA acyltransferase (msbB) #7 HI0211 44 phosphatidylglycerophosphatase B (pgpB) #8 HI0301 300 hemolysin, putative #9 HI0329 37 conserved hypothetical protein #10 HI0330 98 opacity associated protein (oapA) #11 HI0331 59 opacity associated protein (oapB) #12 HI0334 77 GTP pyrophosphokinase (relA) #13 HI0425 146 phosphatidylserine synthase (pssA) #14 HI0604 300 adenylate cyclase (cyaA) #15 HI0605 73 glycerol-3-phosphate dehydrogenase (NAD+) (gpsA) #16 HI0678 165 triosephosphate isomerase (tpiA) #17 HI0685_HI0686 292 HI0685: anaerobic glycerol-3-phosphate dehydrogenase, subunit A (glpA), HI0686: glycerol-3-phosphatase transporter (glpT) #18 HI0687 99 conserved hypothetical protein #19 HI0688 94 H. influenzae predicted coding region HI0688 #20 HI0690 229 glycerol uptake facilitator protein (glpF) #21 HI0734 85 1-acyl-glycerol-3-phosphate acyltransferase (plsC) #22 HI0748 248 glycerol-3-phosphate acyltransferase (plsB) #23 HI0916 107 outer membrane protein, putative #24 HI0920 248 conserved hypothetical protein #25 HI1126.1 181 H. influenzae predicted coding region HI1126.1 #26 HI1129 201 conserved hypothetical protein #27 HI1130 30 conserved hypothetical protein #28 HI1136 122 UDP-N-acetylmuramoylalanine--D-glutamate ligase (murD) #29 HI1139 137 UDP-N-acetylmuramate--alanine ligase (murC) #30 HI1140 71 D-alanine--D-alanine ligase (ddlB) #31 HI1303 147 riboflavin synthase, beta chain (ribH) #32 HI1527 84 lipid A biosynthesis lauroyl acyltransferase (htrB) #33 HI1716 196 undecaprenyl-phosphate alpha-N-acetylglucosaminyltransferase (rfe), putative #34 HI1717 133 H. influenzae predicted coding region HI1717 #35 HI1718 56 H. influenzae predicted coding region HI1718 #36 HI1719 61 uridylyl transferase (glnD) Motif number 1 AGAAAAATTGACCGCACTTTAGCTAAAGAT 1 255 0 ACCGCACTTT 0.99796 -20 ATTAATTTTAACCGCACTTTTGCGCGCTTT 6 16 0 ACCGCACTTT 0.99796 -31 TGTATTTTTAACCGCACTTTAGGTTTAAAC 8 175 1 ACCGCACTTT 0.99796 -126 ATAAAAAATAACCGCACATTGGGTTTAAAC 8 197 0 ACCGCACATT 0.981156 -104 TAATTTTTTCGCCGCACTTTTGAGCTTCTC 10 29 1 GCCGCACTTT 0.993572 -70 GTTAATTTTGGCCGCACTTCCCTACAATGA 17 222 1 GCCGCACTTC 0.979934 -71 CAATTTGCCCACCGCCTTTTTTAAGCTAA 18 10 0 ACCGCCTTTT 0.907097 -90 CTTCATTTCAACCGCACTTCTAAGGAGTGA 20 207 1 ACCGCACTTC 0.993572 -23 TTAAATTTTAACCGCACTTTTGCAGCATTT 24 20 1 ACCGCACTTT 0.99796 -229 CTAAAAAACCACCGCACTTTTTATTTCTCT 24 103 0 ACCGCACTTT 0.99796 -146 GCGAATTTTAACCGCACTTTTAGTTGAGTT 29 91 1 ACCGCACTTT 0.99796 -47 GTCAAAATTGACCGCACTTTTACGCCTATC 33 63 0 ACCGCACTTT 0.99796 -134 GTCAATTTTGACCGCATTTTTTATAAAAAT 33 81 1 ACCGCATTTT 0.984103 -116 ********** Masking position 9 Map Score: 45.9893 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 AGAAAAATTGACCGCACTTTAGCTAAAG 1 257 0 TTACCGCACT 0.99703 -18 GTAATTAATTTTAACCGCACTTTTGCGCGCT 6 18 0 TTACCGCACT 0.99703 -29 TTGTGTATTTTTAACCGCACTTTAGGTTTAA 8 172 1 TTACCGCACT 0.99703 -129 TCAATAAAAAATAACCGCACATTGGGTTTAA 8 199 0 ATACCGCACA 0.919794 -102 ACATAATTTTTTCGCCGCACTTTTGAGCTTC 10 26 1 TTGCCGCACT 0.990658 -73 AATATTGTAAACTAACGCACTAGTCTTTAAT 13 113 1 ACAACGCACT 0.781811 -34 GTTGTTAATTTTGGCCGCACTTCCCTACAAT 17 219 1 TTGCCGCACT 0.990658 -74 ACTCTTCATTTCAACCGCACTTCTAAGGAGT 20 204 1 TCACCGCACT 0.994133 -26 ACCTTAAATTTTAACCGCACTTTTGCAGCAT 24 17 1 TTACCGCACT 0.99703 -232 CAACTAAAAAACCACCGCACTTTTTATTTCT 24 105 0 ACACCGCACT 0.98195 -144 GTTGCGAATTTTAACCGCACTTTTAGTTGAG 29 88 1 TTACCGCACT 0.99703 -50 GCGGTCAAAATTGACCGCACTTTTACGCCTA 33 65 0 TTACCGCACT 0.99703 -132 GCGGTCAATTTTGACCGCATTTTTTATAAAA 33 78 1 TTACCGCATT 0.956726 -119 ** ******** Masking position 9 Map Score: 37.6586 Number of sites scoring better than the average of aligned sites = 1080 Number in coding regions = 679 Number in noncoding regions = 401 Number of orfs with sites within 600 bp upstream = 264 Fraction of orfs with sites within 600 bp upstream = 0.0424028 Motif number 3 GTATTAGGCAATGGAAAAAATAAAGAGAAAACAA 1 95 1 ATGAAATAAA 0.529138 -180 TAAATTATCTCTGATGATAAAAAAAGCCACCTAA 1 212 0 CTATAAAAAA 0.845401 -63 ATTTTTGTTTAAAGGGAATAAAAA 3 1 0 AAGGAAAAAA 0.587822 -122 CCTTTAAACAAAAATGATAAAAAAACACTTGCTT 3 20 1 AAATAAAAAA 0.846245 -103 TTGTCAATGAATTAAGAGGAAAAACA 3 107 1 ATAAAAAAAA 0.938886 -16 GCTCGCCCCTTGATAACAAAAATAACGCGCGC 7 23 0 CTGAAAAAAA 0.846842 -22 CGAAAAGAGGAAAATCAATAAAAAATAACCGCAC 8 210 0 AAATAAAAAA 0.846245 -91 AATTTTGTGGCTAATTAATATAAATAAGAACAAG 10 59 1 CTATAATAAA 0.463232 -40 GAGAAAAGAACTTAAAAAGAAAAAGGGGCGATTA 11 24 0 CTAAAAAAAA 0.922657 -36 ATTTGTGAGCATTATAACGAAAAAAAGCCTTTTT 13 60 1 ATATAAAAAA 0.875658 -87 TCACGTGCTTATTAATAGAAAAAAGGCTTTTTTT 13 79 0 ATAAAAAAAA 0.938886 -68 AATACTTTGCGTTGATAAGAAAAATATCAAGCTA 14 47 1 GTGAAAAAAA 0.715984 -254 CAATTTTTCGAAAAATACTATAAATTTTACCTAT 14 193 0 AAAAAATAAA 0.654563 -108 CTTAGGGAGTATAAATGCAAAAAAATGTGACATA 14 232 0 ATAAGAAAAA 0.487884 -69 GTGTCCCTACCAGAACAACAAAAATTGGCGAACA 14 274 0 CAAAAAAAAA 0.903131 -27 TGCAGAAGATCATAAAATTAAAAAAATTCTCACA 16 78 0 CAAAAAAAAA 0.903131 -88 ATTTAGATGACACATAATTAAAAAGTTGGAGAAA 17 16 0 CAATAAAAAA 0.810381 -277 CGAATCATAAAAGAAAATAAAAAATAAGAAAGTA 17 78 1 AAAAAAAAAA 0.923117 -215 TAAGAAAGTAAAAAAAATCAAAAATGTGAAGTGT 17 102 1 AAAAAAAAAA 0.923117 -191 AATTATTGTGATCAATATCACAAAATCGCTTTCT 17 171 1 ATAAAACAAA 0.522038 -122 CGATTCCCAAAATGTAAGAAAAAATAATATAAAA 17 259 0 AAGTAAAAAA 0.71839 -34 TATTCTTATGATAGTTACAAAAAAGGCGACTAAG 18 40 0 ATGTAAAAAA 0.765483 -60 TAACTATCATAAGAATAATAAAAAGATAAGTATC 18 57 1 AAAAAAAAAA 0.923117 -43 TTTCTATATCGTAGAAACTAAAAATCTACTCTAA 20 54 1 GTGAAAAAAA 0.715984 -176 TTTTTGAGTTCTGATGAAGAAAAAAGTTCAATTT 23 12 0 CTATAAAAAA 0.845401 -96 AATTAATAGGGAGAGAAATAAAAAGTGCGGTGGT 24 92 1 GAAGAAAAAA 0.521375 -157 ATAGAGGTCTCTCAATAATAAAAATA 24 233 1 CTAAAAAAAA 0.922657 -16 ACTGATTTTTATCAAAATAAAAAAGCCGTTTGAA 26 50 0 ATAAAAAAAA 0.938886 -152 AAGTGCTAATATTAGAAATAAAAACGTTGCGAAT 29 63 1 ATAGAAAAAA 0.797447 -75 TTGTCATTGGGAGAAAAGGAAAAATAA 29 121 1 GAAAAAAAAA 0.809551 -17 TCTCTATTTTATTAAAAATATAAAACAACAAAAC 35 14 1 ATAAAATAAA 0.707991 -43 TTTTATTATAAAGAAAAACAAAAAGGGCGTAT 36 9 0 AAAAAAAAAA 0.923117 -53 ** ** * ***** Masking position 10 Map Score: 30.3682 Number of sites scoring better than the average of aligned sites = 751 Number in coding regions = 486 Number in noncoding regions = 265 Number of orfs with sites within 600 bp upstream = 210 Fraction of orfs with sites within 600 bp upstream = 0.0337295 Motif number 4 AAACCATAGTTATTTTTGCCCTATAAGTTAAT 1 27 0 TATTTTTCCT 0.57215 -248 GTTTTCTCTTTATTTTTTCCATTGCCTAATAC 1 95 0 TATTTTTCCT 0.57215 -180 AACGAGCTTTAATTTTATCAATTATTTATAAA 1 172 1 AATTTTACAT 0.754977 -103 TTAGGTGGCTTTTTTTATCATCAGAGATAATT 1 212 1 TTTTTTACAC 0.363337 -63 AAATGTAATTAATTTTAACCGCACTTTTGCGC 6 21 0 AATTTTACCC 0.962921 -26 TGTTGTCTAGAATTTTCCCCTCTCCGTAAAAA 8 140 1 AATTTTCCCC 0.969355 -161 AAAATTGTGTATTTTTAACCGCACTTTAGGTT 8 168 1 ATTTTTACCC 0.889725 -133 AAATATGATAATTTTTCGCCGTCAATAAGACA 8 263 1 ATTTTTCCCT 0.82997 -38 ATACACATAATTTTTTCGCCGCACTTTTGAGC 10 22 1 TTTTTTCCCC 0.744245 -77 AATGCTCACAAATTTTAGCATTTTTTGGCTAA 13 41 0 AATTTTACAT 0.754975 -106 AAATACTATAAATTTTACCTATCAACAATCAA 14 183 0 AATTTTACTT 0.721676 -118 TACTATACCAAAATTTCGCCCCTATTCTTTGC 16 109 0 AAATTTCCCC 0.742732 -57 TAAGCAAGTTAATTTTATCAACTATGGAGAAA 16 139 1 AATTTTACAC 0.861178 -27 AATTTTTTCTCCAACTTTTTAA 17 1 1 AATTTTTCTC 0.646363 -292 TGTGTCATCTAAATTTACCCTTTTGAAACAGT 17 36 1 AAATTTACCT 0.540707 -257 TGATCACAATAATTTTCGCATTCGCTCAAACG 17 153 0 AATTTTCCAT 0.789612 -140 AAATGTTGTTAATTTTGGCCGCACTTCCCTAC 17 215 1 AATTTTGCCC 0.882876 -78 GAATAGAACTATTTTTAGCCCTTTGGTGTTTT 22 167 0 ATTTTTACCT 0.800299 -82 AATAAATTTTCTCTTTGTTATAAGTT 22 233 0 AATTTTCCTT 0.759519 -16 ATGGGTTTAATATTTTCTCTGCCCAATTAAAT 23 62 0 TATTTTCCTC 0.653119 -46 AATCACCTTAAATTTTAACCGCACTTTTGCAG 24 13 1 AATTTTACCC 0.962921 -236 TCTCCCTATTAATTTTTGCCATTTTACGGTAT 24 74 0 AATTTTTCCT 0.818715 -175 ACAAAACACCACTTTTCTCCACTTCTGGCAAG 26 130 0 ACTTTTCCCC 0.751487 -72 AAACGTTGCGAATTTTAACCGCACTTTTAGTT 29 84 1 AATTTTACCC 0.962921 -54 GCCTATCTTTTATTTTACCAGTGGTATCCTAC 33 38 0 TATTTTACAT 0.47709 -159 AAGTGCGGTCAATTTTGACCGCATTTTTTATA 33 74 1 AATTTTGCCC 0.882876 -123 ACGAAGCCCTATTTTTCACTTCAACGCCCGTA 33 110 0 ATTTTTCCTC 0.663926 -87 ******* ** * Masking position 6 Map Score: 25.2755 Number of sites scoring better than the average of aligned sites = 773 Number in coding regions = 568 Number in noncoding regions = 205 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 5 AACTATAACAAAAATTGCTATAATCACGCCTCTTT 2 114 1 AAAATGTATC 0.826847 -43 AATAAAATGTAATTAATTTTAACCGCAC 6 29 0 AAAATTTATT 0.887911 -18 TCTAGACAACAAAATATTCTTATTTTGTTTATATG 8 116 0 AAAATTTTTT 0.902252 -185 CCTCTCCGTAAAAATTGTGTATTTTTAACCGCACT 8 158 1 AAAATGATTT 0.794195 -143 GATTTTTTCTAAAATATGATAATTTTTCGCCGTCA 8 252 1 AAAATTATTT 0.80203 -49 TCCCTGAGTAAAAATGGCTGTTTTTTAGCCAAAAA 13 17 1 AAAATGTTTT 0.935824 -130 CTAATAATAGAAAATATAGATTTTTATATCGGCAG 14 85 1 AAAATTTTTT 0.901779 -216 TCAATATCACAAAATCGCTTTCTTTTACACTCAAA 17 182 1 AAAATGTTTT 0.938502 -111 TTTTACACTCAAAATGTTGTTAATTTTGGCCGCAC 17 204 1 AAAATTTATT 0.887929 -89 AAATAATATAAAAAGTGTAATCATTGTAGGGAAGT 17 237 0 AAAAGGTATT 0.775144 -56 AATCTAAACAAAAATCGTGGAATTTTT 21 3 0 AAAATGATTT 0.912102 -83 CGGATGTGTTAAAATATTTGAGTTTTTGGACGATA 22 132 1 AAAATTATTT 0.866536 -117 CAAAGGGCTAAAAATAGTTCTATTCACAAACTGCT 22 174 1 AAAATGTTTC 0.850781 -75 AGAATACCGTAAAATGGCAAAAATTAATAGGGAGA 24 71 1 AAAATGAATT 0.898312 -178 TCACATTTGTAAAATCTAAAACATCCATTAAAATG 25 48 0 AAAATTAATC 0.674165 -134 AAATCTTATAAAAATCTTTAAATTCAATTTTGATT 25 93 1 AAAATTATTC 0.711835 -89 TTACGCCTTAAAAATTGAACTTATTTTTAGAAAAT 26 176 0 AAAATGTATT 0.926118 -26 ACTAACGTAAAAAAGGTCGCTCTTTCAAAAGTGAA 28 33 0 AAAAGTTTTT 0.718291 -90 TTTTATATCCAAAAGTGCTAATATTAGAAATAAAA 29 51 1 AAAAGGAATT 0.706797 -87 ATTTTTATGGAAAATTTCCTTCATTAAGGTAAACT 31 25 0 AAAATTTATT 0.8879 -123 AAAATCGCGTATATTCAATATTAAT 31 133 0 AAAATGAATT 0.897203 -15 TTTAAAATCTCTCTATTTGAATAACCAA 32 4 1 AAAATTTTTT 0.90436 -81 ***** * * *** Masking position 14 Map Score: 25.1817 Number of sites scoring better than the average of aligned sites = 444 Number in coding regions = 304 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 6 CTAAAGATGGTTTATTCTAAATTATCTCTGATG 1 230 0 TTTATAAATT 0.818215 -45 TTTTATTCCCTTTAAACAAAAATGATAAAAAAA 3 12 1 TTTAAAAAAT 0.818215 -111 AATTATCATATTTTAGAAAAAATCGCAAAACGC 8 243 0 TTTTAAAAAT 0.89125 -58 TTTATAGTATTTTTCGAAAAATTGTGATTTATG 14 203 1 TTTTAAAATT 0.937195 -98 TTTTATGATCTTCTGCAAAGAATAGGGGCGAAA 16 95 1 TTCTAAGAAT 0.425593 -71 TTTTACTTTTCCCAAAAATGATACTTATC 18 81 0 TTTTAAAAAT 0.89125 -19 TCCGTATTCTTTTTTAATAAATTCTCTTCCCTT 20 157 1 TTTTTAAATT 0.891236 -73 ATTCCACGATTTTTGTTTAGATTAGCACATATT 21 15 1 TTTTTAGATT 0.711332 -71 TTAGTTGTTTTTTACAATAAATTTTCAATTTTT 24 129 1 TTTATAAATT 0.818216 -120 TTCTAATCTGTTCTGCAAAAATTGAAAATTTAT 24 145 0 TTCTAAAATT 0.817744 -104 AATTTAAAGATTTTTATAAGATTTGTGACTTGT 25 84 0 TTTTAAGATT 0.817743 -98 CAAACGGCTTTTTTCATAAAATTTTATTGA 26 8 0 TTTTAAAATT 0.937194 -194 GGCTTTTTTATTTTGATAAAAATCAGTTGCTTT 26 57 1 TTTTAAAAAT 0.891236 -145 ATGTAGTACTTTTATCTTAAATTT 27 17 1 TTTATAAATT 0.818216 -14 ACACTATATTTTTATGGAAAATTTCCTTCATTA 31 34 0 TTTAAAAATT 0.89125 -114 AGGGGCGTAGTTTATCGTAAATTTGAGTTGTGG 32 55 0 TTTATAAATT 0.818216 -30 TTGACCGCATTTTTTATAAAAATACGGGCGTTG 33 88 1 TTTTAAAAAT 0.890318 -109 AAAAATATATTTCTAGGTAAATTTGCCTTATGT 33 143 1 TTCTTAAATT 0.711332 -54 TATGTTATCCTTTACAAAAAATTTTAGGGTCAC 33 171 1 TTTAAAAATT 0.89125 -26 ATATCTCTATTTTATTAAAAATATAAAACAAC 35 10 1 TTTTAAAAAT 0.891224 -47 **** ****** Masking position 2 Map Score: 19.7256 Number of sites scoring better than the average of aligned sites = 380 Number in coding regions = 215 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 7 AAGCCACCTAAGGTCGCTTTTTATAAATAATT 1 191 0 AGTCGCTTTT 0.968409 -84 AAGCGACCTTAGGTGGCTTTTTTTATCATCAG 1 204 1 AGTGGCTTTT 0.825511 -71 AGTCAAAGGGAAATCACATTTTTTATTGGATA 2 43 1 AATCACTTTT 0.455858 -114 TGCTATAATCACGCCTCTTTTTTTAACAAGGA 2 129 1 AGCCTCTTTT 0.772271 -28 GCAAGTGTTTTTTTATCATTTTTGTTTAAAGG 3 20 0 TTTATCTTTT 0.328545 -103 GATTTTCCTCTTTTCGCGTTTTGCGATTTTTT 8 228 1 TTTCGCTTTT 0.909713 -73 CATAATTTTTTCGCCGCACTTTTGAGCTTCTC 10 27 1 TGCCGCCTTT 0.826771 -72 GGGCGAGTAATCGCCCCTTTTTCTTTTTAAGT 11 17 1 TGCCCCTTTT 0.719733 -43 TGCTCACAAATTTTAGCATTTTTTGGCTAAAA 13 39 0 TTTAGCTTTT 0.76084 -108 ATTGTGATTTATGTCACATTTTTTTGCATTTA 14 223 1 AGTCACTTTT 0.899881 -78 ATACAGGTAATTGTAGCTTTTTAGCTCAAGAT 16 35 1 TGTAGCTTTT 0.925899 -131 TTTGTGAAACACTTCACATTTTTGATTTTTTT 17 112 0 ATTCACTTTT 0.695902 -181 GCAAATTGCTTAGTCGCCTTTTTTGTAACTAT 18 32 1 TGTCGCTTTT 0.975354 -68 ATAAAAAGATAAGTATCATTTTTGGGAAAAGT 18 74 1 AGTATCTTTT 0.598178 -26 TCTGTGTATTAAGTCACATTTTGTCGCCAAAT 22 81 1 AGTCACTTTT 0.899881 -168 AACCGCACTTTTGCAGCATTTTGACAATAGAA 24 29 1 TGCAGCTTTT 0.899872 -220 ACGGTATTCTATGCCACATTTTCTATTGTCAA 24 49 0 AGCCACTTTT 0.866038 -200 ATTACTTATTTATTAGCATTTTAATGGATGTT 25 32 1 TTTAGCTTTT 0.76084 -150 AACGTAAAAAAGGTCGCTCTTTCAAAAGTGAA 28 33 0 AGTCGCCTTT 0.837133 -90 GGGTTGTGGCGTTTTATAAATAGCC 29 4 1 TGTGGCTTTT 0.859307 -134 CGGTTAAAATTCGCAACGTTTTTATTTCTAAT 29 73 0 TGCAACTTTT 0.724906 -65 CGGTCAATTTTGACCGCATTTTTTATAAAAAT 33 79 1 TACCGCTTTT 0.726255 -118 TTGTTCGCCTTGTTCGCCTTTTAAT 34 4 0 TTTCGCTTTT 0.909713 -130 * ***** **** Masking position 10 Map Score: 20.8952 Number of sites scoring better than the average of aligned sites = 512 Number in coding regions = 430 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 8 TTTCCTTATTTAAATTAACTTATAGGGCAAA 1 14 1 TAAATTACTT 0.686715 -261 ATAAAAAATGTGATTTCCCTTTGACTATCTT 2 38 0 TGATTTCCTT 0.698941 -119 TAGTTAGCGGATAATTTCCTTTATTGAGTTA 2 73 0 ATAATTCCTT 0.684857 -84 ATTCATTGACAAAGTTGCCTTACGTAAGCAA 3 88 0 AAAGTTCCTT 0.763082 -35 CAAAGTATTATAAAATACCTTACTCAATATC 14 25 0 TAAAATCCTT 0.63601 -276 CATAGTTGATAAAATTAACTTGCTTACTATA 16 134 0 AAAATTACTT 0.68671 -32 TCTTTTTTAATAAATTCTCTTCCCTTTACTT 20 164 1 TAAATTTCTT 0.554183 -66 TGTCCTATATAAAATTTCCTTGAAGTATAAC 21 60 0 AAAATTCCTT 0.953317 -26 TTGATAAATATCCTTAATTAAATGA 23 93 0 TAAATACCTT 0.667762 -15 AAAATCACCTTAAATTTTAAC 24 1 1 AAAATCCCTT 0.84573 -248 GATGGAAATATAAATTTCCTTTACTAACGTA 28 59 0 TAAATTCCTT 0.953317 -64 ATTTTTATGGAAAATTTCCTTCATTAAGGTA 31 29 0 AAAATTCCTT 0.953317 -119 TATGAACAATAAAATCGCCTTAAAAATGAGT 31 77 1 AAAATCCCTT 0.845731 -71 ATTTCTAGGTAAATTTGCCTTATGTTATCCT 33 151 1 AAATTTCCTT 0.845939 -46 ATTCAGTTTCTGATTTACCTTGATTAGCTGA 34 105 0 TGATTTCCTT 0.698941 -29 ATGAATTGCCTTTTGTTAGATC 36 50 0 TGAATTCCTT 0.896202 -12 ****** **** Masking position 3 Map Score: 11.6864 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 165 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 9 AGAAAAATTGACCGCACTTTAGCTA 1 260 0 AATTGACCGC 0.929659 -15 CAATAAAGGAAATTATCCGCTAACTAAAAA 2 78 1 AATTATCCGC 0.764581 -79 TTTGATTGTGAATTGATCTCGTAAAAAGAG 8 43 0 AATTGATCTC 0.450135 -258 AAAATATGATAATTTTTCGCCGTCAATAAG 8 262 1 AATTTTTCGC 0.831759 -39 AATACACATAATTTTTTCGCCGCACTTTTG 10 21 1 ATTTTTTCGC 0.609723 -78 CTAAGTGGTAAATTGTTCGCCAATTTTTGT 14 261 1 AATTGTTCGC 0.96978 -40 CAAGTTTATAATTTGTTCGCTCAACTTGCA 26 104 0 ATTTGTTCGC 0.91024 -98 ATGCGGTCAAAATTGACCGCACTTTTACGC 33 68 0 AATTGACCGC 0.929659 -129 GCCTTGTTCGCCTTGTTCGCCTTTTAAT 34 9 0 CCTTGTTCGC 0.949486 -125 GCCTTGTTCGCCTTGTTCGCCTTGTTCGCC 34 27 0 CCTTGTTCGC 0.949486 -107 TCCTCGTTCTCCTTGTCCGCCTTGTTCGCC 34 45 0 CCTTGTCCGC 0.95609 -89 AGTTGGAAAGCATTGTCAGCTAATCAAGGT 34 90 1 CATTGTCAGC 0.686938 -44 ********** Masking position 4 Map Score: 8.09347 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 203 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 10 AAGTTAATTTAAATAAGGAAATAT 1 3 0 AATAGGAAAT 0.70438 -272 TTTTTTTATCATCAGAGATAATTTAGAATAAA 1 221 1 ACAAGATAAT 0.449933 -54 TATCTTCGCAACAACAGGTAATATTCACGCCC 2 12 0 AAAAGGTAAT 0.839371 -145 TGGATAACTCAATAAAGGAAATTATCCGCTAA 2 69 1 ATAAGGAAAT 0.861863 -88 GCAAAACGCGAAAAGAGGAAAATCAATAAAAA 8 220 0 AAAAGGAAAA 0.873819 -81 AAGAACAAGCATCAGAGGCAATCCA 10 84 1 ACAAGGCAAT 0.842758 -15 CTATCCACTAATAATAGAAAATATAGATTTTT 14 78 1 AAAAGAAAAT 0.867966 -223 TAACCTATCAACCACAGGAAAATA 15 3 0 ACAAGGAAAA 0.821169 -71 TTTATCTAGTAAAAGAGGAAATAAGTATAGAT 15 44 0 AAAAGGAAAT 0.965334 -30 TTTGCGAATCATAAAAGAAAATAAAAAATAAG 17 74 1 AAAAGAAAAT 0.867966 -219 CAGCATTTTGACAATAGAAAATGTGGCATAGA 24 42 1 AAAAGAAAAT 0.867966 -207 AACAGATTAGAACAAAGGAATTCATAGCAAGC 24 166 1 ACAAGGAATT 0.612392 -83 TTGAATAGGTATAAAAGCAAAT 25 1 0 AAAAGCAAAT 0.747562 -181 TTTTTACGTTAGTAAAGGAAATTTATATTTCC 28 55 1 ATAAGGAAAT 0.861864 -68 TGTCATTGGGAGAAAAGGAAAAATAA 29 122 1 AAAAGGAAAA 0.873819 -16 CTTCGATCTAACAAAAGGCAATTCAT 36 46 1 AAAAGGCAAT 0.889904 -16 * ** ******* Masking position 6 Map Score: 12.5493 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 116 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 11 CCCTGAGTAAAAATGGCTGTTTTTTAGCCA 13 18 1 AAATGGCTGT 0.906155 -129 ATTAATAGAAAAAAGGCTTTTTTTCGTTAT 13 73 0 AAAAGGCTTT 0.932236 -74 TCAACAATCAAAATGACTTTTTTACCTAAG 14 164 0 AAATGACTTT 0.659417 -137 CAATATCACAAAATCGCTTTCTTTTACACT 17 183 1 AAATCGCTTT 0.76101 -110 TTCTATTCACAAACTGCTTTTTAAACGTCT 22 191 1 AAACTGCTTT 0.819516 -58 TGCCCTAAACAAGCGGCTGTATTCTATTTC 25 139 0 AAGCGGCTGT 0.823315 -43 TAAACAATTCAAACGGCTTTTTTCATAAAA 26 20 0 AAACGGCTTT 0.975934 -182 TTGTTTATTCAAACGGCTTTTTTATTTTGA 26 43 1 AAACGGCTTT 0.975934 -159 TTCAATATTAATAAGGCTTTACCCTATTTT 31 115 0 ATAAGGCTTT 0.684875 -33 ********** Masking position 8 Map Score: 3.14443 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 118 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 12 GTCAGAATTATTTGTTGTTTTCTCTTTATTT 1 112 0 TTTGTGTTTT 0.965592 -163 AAAAGCGACCTTAGGTGGCTTTTTTTATCAT 1 202 1 TTAGTGGCTT 0.630863 -73 ATAAGAATATTTTGTTGTCTAGAATTTTCCC 8 128 1 TTTGTGTCTA 0.784898 -173 TTGATTTGTGTTTGATGTCTTATTGACGGCG 8 279 0 TTTGTGTCTT 0.958587 -22 TTCGCCAATTTTTGTTGTTCTGGTAGGGACA 14 276 1 TTTGTGTTCT 0.867666 -25 ACTTCACATTTTTGATTTTTTTTACTTTCTT 17 103 0 TTTGTTTTTT 0.733412 -190 TTTTTAGCCCTTTGGTGTTTTTATCGTCCAA 22 157 0 TTTGTGTTTT 0.965592 -92 CGGTGGTTTTTTAGTTGTTTTTTACAATAAA 24 119 1 TTAGTGTTTT 0.898662 -130 AAACCTTTGTTTTGTTGTTTTATATTTTTAA 35 25 0 TTTGTGTTTT 0.965592 -32 **** ****** Masking position 6 Map Score: 4.68494 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 50 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 13 CAAAGGGAAATCACATTTTTTATTGGATAA 2 46 1 TCACATTTTT 0.889937 -111 GGTTAAAAATACACAATTTTTACGGAGAGG 8 158 0 ACACAATTTT 0.847158 -143 TCAAACCATCTCTCATTTTTAGGATATTTC 9 15 0 TCTCATTTTT 0.721905 -23 CTTTTGAGCTTCTCAATTTTGTGGCTAATT 10 45 1 TCTCAATTTT 0.833474 -54 GTTATAATGCTCACAAATTTTAGCATTTTT 13 48 0 TCACAAATTT 0.908774 -99 GTGACATAAATCACAATTTTTCGAAAAATA 14 210 0 TCACAATTTT 0.939722 -91 GTGATTTATGTCACATTTTTTTGCATTTAT 14 226 1 TCACATTTTT 0.889937 -75 GTGAAACACTTCACATTTTTGATTTTTTTT 17 111 0 TCACATTTTT 0.889937 -182 GTGAAGTGTTTCACAAATCTTTACACCGTT 17 127 1 TCACAAATCT 0.758874 -166 GTGACTTAATACACAGATTTAAAAAATAAC 22 68 0 ACACAGATTT 0.452804 -181 GTGATACAAGTCACAAATCTTATAAAAATC 25 79 1 TCACAAATCT 0.758874 -103 GGTAAAATCGCCACAATTTTGGTTATTCAA 32 27 0 CCACAATTTT 0.764774 -58 TTTTACCACAACTCAAATTTACGATAAACT 32 50 1 ACTCAAATTT 0.532067 -35 ********** Masking position 5 Map Score: 10.2188 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 79 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 14 TCCTGTACCTAGGGTAGTATACTCTA 5 7 1 ACCTAGGGTA 0.971058 -78 TGAAGAACTAACCTAGAGTATACTACCCTA 5 20 0 ACCTAGAGTA 0.942013 -65 ATAGGACTGAACCTAGGATATACTTACCTA 5 50 1 ACCTAGGATA 0.838465 -35 AAATCCTACCTTGAGAAAAGAACTTAA 11 43 0 ACCTTGAGAA 0.814525 -17 ATCCCTCACAACCGTGGGTAAACATACCCA 20 12 1 ACCGTGGGTA 0.967104 -218 AACCTAGTTAACCGTGGGTATGTTTACCCA 20 26 0 ACCGTGGGTA 0.967104 -204 TTTCTGATTTACCTTGATTAGCTGACAATG 34 100 0 ACCTTGATTA 0.765943 -34 ********** Masking position 1 Map Score: 2.07552 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 25 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 15 TATAAGTTAATTTAAATAAGGAAATAT 1 6 0 TTTAATAGGA 0.849684 -269 GTTCCAACCTTTTTAGTTAGCGGATAATTTCC 2 85 0 TTTTATAGCG 0.781197 -72 ACGCCTCTTTTTTTAACAAGGAAAGATA 2 139 1 TTTTACAGGA 0.82612 -18 TTCCTGTCGCTTTTATTTTGGGTGGATATTGT 12 25 0 TTTTATTGGG 0.883528 -53 AAACAGCCATTTTTACTCAGGGAAACCCT 13 8 0 TTTTATAGGG 0.968327 -139 GTTCAATTGGTTTTATTAAGGGCGTTAGCAAT 19 58 1 TTTTATAGGG 0.968327 -37 ATTCTCTTCCCTTTACTTAGGGAAAACACTCT 20 177 1 CTTTATAGGG 0.921469 -53 TTCAAGGAAATTTTATATAGGACATCCTT 21 67 1 TTTTAAAGGA 0.762222 -19 AAACCCATCATTTAATTAAGGATATTTATCAA 23 86 1 TTTAATAGGA 0.849684 -22 AAATCAGTTGCTTTAATGTGGAATTACTTGCA 26 76 1 CTTTATTGGA 0.68449 -126 CTTTACCCTATTTTATTTAGGACTCATTTTTA 31 97 0 TTTTATAGGA 0.95795 -51 ***** * **** Masking position 5 Map Score: 5.66824 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 27 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234