AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00620_hinf_reg_100.orf -o00620_hinf_100.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: HI0180 27 formate acetyltransferase (pfl) Input sequences: #1 HI0086 300 cystathionine gamma-synthase (metB) #2 HI0181 300 formate transporter #3 HI0185 122 alcohol dehydrogenase, class III (adhC) #4 HI0318 218 conserved hypothetical protein #5 HI0319 52 conserved hypothetical protein #6 HI0321 93 virulence associated protein B (vapB) #7 HI0323 66 lactoylglutathione lyase (gloA) #8 HI0406 89 acetyl-CoA carboxylase, carboxyl transferase (accA) #9 HI0408 171 ABC transporter, ATP-binding protein (yebM) #10 HI0774 205 acetate CoA-transferase, alpha subunit #11 HI0809 172 phosphoenolpyruvate carboxykinase (pckA) #12 HI0971 152 acetyl-CoA carboxylase, biotin carboxyl carrier protein (accB) #13 HI0972 174 acetyl-CoA carboxylase, biotin carboxylase (accC) #14 HI0986 300 2-isopropylmalate synthase (leuA) #15 HI1203 67 phosphate acetyltransferase (pta) #16 HI1204 214 acetate kinase (ackA) #17 HI1210 206 malate dehydrogenase (mdh) #18 HI1231 113 dihydrolipoamide dehydrogenase (lpdA) #19 HI1232 62 dihydrolipoamide acetyltransferase (aceF) #20 HI1233_HI1234 299 HI1233: pyruvate dehydrogenase, E1 component (aceE), HI1234: methylglyoxal synthase (mgsA) #21 HI1245 197 malate oxidoreductase, putative #22 HI1260 193 acetyl-CoA carboxylase carboxyl transferase subunit beta (accD) #23 HI1272 300 ABC transporter, ATP-binding protein #24 HI1274 51 hydroxyacylglutathione hydrolase, putative #25 HI1573 300 pyruvate kinase, type II (pykA) #26 HI1636 182 phosphoenolpyruvate carboxylase (ppc) #27 HI1649 260 D-lactate dehydrogenase (dld) #28 HI1739.1 211 L-lactate dehydrogenase (lctD) Motif number 1 ATTCCTTGATAAAGTGCGGTCGATTTTTAC 8 50 1 AAAGTGCGGT 0.998409 -40 TTTAAAGGAAAAAGTGCGGTTATGAATAAA 12 96 0 AAAGTGCGGT 0.998409 -57 TTTTCCTTTAAAAGTGCGGTTAAAATTTCA 12 114 1 AAAGTGCGGT 0.998409 -39 CGCAACTTATAAAGTGCGGGTTTAAAATTG 14 235 0 AAAGTGCGGG 0.995424 -66 TCCAAAAGTGCGGTGCGTTTTTCC 14 287 0 AAAGTGCGGT 0.998409 -14 TAGCGTATGATAAGTGCGGTCAATTTTTGA 16 20 0 TAAGTGCGGT 0.986432 -195 AAAGACCGTAAAAGTGCGGTCAATATTTTT 18 74 1 AAAGTGCGGT 0.998409 -40 TTGATGAAAACTGCGGTCAAAAAACAT 19 8 1 AAACTGCGGT 0.98524 -55 TGTTCCTTTTAAAGTGCGGTCATAAAACAC 19 39 0 AAAGTGCGGT 0.998409 -24 TAATTATTTGAAAGTGCGGTAATTTTTTTG 20 106 0 AAAGTGCGGT 0.998409 -194 GATTTTTTAAAAAGTGCGGTCTATTTTTGC 26 16 0 AAAGTGCGGT 0.998409 -167 AAATCCCTAAAAAGTGCGGGTCTTTTTTAG 26 41 1 AAAGTGCGGG 0.995424 -142 ********** Masking position 3 Map Score: 49.7923 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 AATAAATCACAGAAAATGATGGAAAAATGAAATTTT 1 201 1 AAAAATAAAA 0.951462 -100 AGTAGAAATTAGAAAATTACATAAAATTTCATTTTT 1 223 0 AAAAATAAAA 0.951462 -78 TTGGCACAAAGGAAAAAGTGATAAAAGTAGAAATTA 1 248 0 GAAAAAAAAA 0.856536 -53 CCCTTTCATTGCAAAGAAAAGCAAAAATTATTTCAA 2 169 0 GAAAGAAAAA 0.641039 -132 ATTGACATTGAAAAAGTTGATGAAAATTTAATACTT 2 260 0 AAAAGTAAAA 0.854299 -41 TCATTTTTGTTTAAAGGGAATAAAAA 3 1 0 TAAAGGAAAA 0.368511 -122 TTCCCTTTAAACAAAAATGATAAAAAAACACTTGCT 3 17 1 AAAAAAAAAA 0.961126 -106 CAAATCAATCAAAAAAGCAAAGAAAAGTAATAAATA 4 103 1 AAAAAGAAAA 0.897468 -116 AACAAGCGGCATAATATAACAAAAAATCTGATGATA 4 165 0 AAATATAAAA 0.757568 -54 TTGTTATCCTAAAAAGACCGTAAAAATCGACCGCAC 8 63 0 AAAAGAAAAA 0.880886 -27 AAGGATTGTTTAAAACACTATCAAAATAACTTATAC 10 11 1 TAAACAAAAA 0.503263 -195 TAGATTGATATTAAAAATAGCAAAAAGAATTTCGTA 10 72 0 TAAAAAAAAA 0.846407 -134 GCTCTATATCACAATATCACTAAAAAGAGGTAAAGT 11 41 1 AAATATAAAA 0.757568 -132 TAAAGTTCTTAAAAAAATGTTTAAAAATGAGATCTA 11 71 1 AAAAAAAAAA 0.961126 -102 AGTCCGCCCGACAAAAATATTGGAAA 13 1 0 AAAAAAGAAA 0.784685 -174 TATTTTTAATATAAAATGCCAAAAAATAGTTTGACA 14 52 1 AAAAATAAAA 0.951462 -249 TTTTTTATCTAAAAAATACAGGAAAAACGCACCGCA 14 267 1 AAAAATAAAA 0.951462 -34 TTTTATAAATAAAAACTGCCGAAAAATTCGGCAGCT 15 21 0 AAAACTAAAA 0.782792 -47 AAAAACACCTCAAAAATTGACCGCAC 16 1 1 AAAACAAAAA 0.819672 -214 TATTTTTACTAAAAATAGACTTAAAATAGCGTATGA 16 40 0 AAAATAAAAA 0.668589 -175 TTTTACCTCGTAAAAACGTTAAAAATATTGACCGC 18 89 0 GAAAAAAAAA 0.856536 -25 TGACCGCACTTTAAAAGGAACAAAAA 19 47 1 TAAAAGAAAA 0.661127 -16 GTCCTTTTTGAAAAAAATCTGAAAAAACTTTAAAAC 20 17 1 AAAAAAAAAA 0.961126 -283 TTTGTTCGCTAAAATAACCAGTAAAATATTGCATTC 20 64 0 AAATAAAAAA 0.797624 -236 TTTAGCGAACAAAAAAACACAAAAAAATTACCGCAC 20 87 1 AAAAAAAAAA 0.961126 -213 TCTTTATCTCAAAAAATCTTCTAAAATTTACAAGAT 20 183 1 AAAAATAAAA 0.951462 -117 GGTCTGTAAGACAAAAAAATAAAAAAAATGTTCAAT 22 41 1 AAAAAAAAAA 0.961126 -153 TTTCTAGTCAATAAAAAGGTCAAAAA 22 178 1 AAAAAAAAAA 0.961126 -16 TATAACTGGCAAAAAAGTAAACAAAACCAGCTTAAA 25 150 1 AAAAAGAAAA 0.897468 -151 CGCACTTTTTAAAAAATCCCTAAAAAGTGCGGGTCT 26 28 1 AAAAATAAAA 0.951462 -155 AAGAAAAGCTAAAAAATAGCTAAAAAAGACCCGCAC 26 54 0 AAAAATAAAA 0.951462 -129 AGAAATTTTGAAAATAATCAAGAAAAGCTAAAAAAT 26 73 0 AAATAAAAAA 0.797624 -110 GTTGAAACCTTTAAAGATAGAGAAAAATATTATTTA 27 47 0 TAAAGAAAAA 0.622404 -214 TATCAGCAATGCAAAATCCGTTGAAACCTTTAAAGA 27 66 0 GAAAATGAAA 0.410983 -195 AAAATCACCTATAAAATTAGGAAAAATTGTGAATTT 28 41 0 AAAAATAAAA 0.951462 -171 CACTATTTTAACAAATTCAATAAAAATCATAATTAT 28 137 0 AAAATTAAAA 0.615311 -75 CTCTTATTCAATAAAATAGTGAGAAACCTGAGAGGT 28 180 0 AAAAATGAAA 0.742893 -32 ACTATTTTATTGAATAAGAGGTAAAA 28 196 1 TAATAAAAAA 0.467653 -16 * ***** **** Masking position 4 Map Score: 53.421 Number of sites scoring better than the average of aligned sites = 578 Number in coding regions = 396 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 3 TCCGCTATAATTGCGACAGATTTTTGAGCATAATT 4 34 0 TTGCGATTTT 0.898245 -185 CCTTGATAAAGTGCGGTCGATTTTTACGGTCTTTT 8 53 1 GTGCGGTTTT 0.996601 -37 TTTTTCAAATTTGCGATAAAATTCTGTGAATTTCG 12 30 0 TTGCGAATTT 0.643236 -123 TCCTTTAAAAGTGCGGTTAAAATTTCAATCTTTTT 12 117 1 GTGCGGAATT 0.91828 -36 CACATTTTGTGTGCGGCTAAGTTGTGGATAAAAAA 14 181 1 GTGCGGGTTT 0.980519 -120 ACTTTATAAGTTGCGGGTTTTTTATCTAAAAAATA 14 250 1 TTGCGGTTTT 0.987014 -51 TCCAAAAGTGCGGTGCGTTTTTCCTGTATTTT 14 279 0 GTGCGGTTTT 0.996601 -22 CGTATGATAAGTGCGGTCAATTTTTGAGGTGTTTT 16 12 0 GTGCGGTTTT 0.996601 -203 GACCGTAAAAGTGCGGTCAATATTTTTAACGTTTT 18 77 1 GTGCGGTATT 0.982148 -37 TTATTTGAAAGTGCGGTAATTTTTTTGTGTTTTTT 20 98 0 GTGCGGTTTT 0.996601 -202 TCCTATTTTAGTGCTGGTGCTTTCTGGGATTGCAA 23 36 1 GTGCTGTTTT 0.946941 -265 TTAAAAATTCTTGCGGATCCTTTCACTCAATTACC 23 103 1 TTGCGGTTTA 0.882083 -198 TTTTTAAAAAGTGCGGTCTATTTTTGCTAAGT 26 8 0 GTGCGGTTTT 0.996601 -175 TCCCTAAAAAGTGCGGGTCTTTTTTAGCTATTTTT 26 44 1 GTGCGGTTTT 0.996601 -139 ****** *** * Masking position 13 Map Score: 29.7076 Number of sites scoring better than the average of aligned sites = 390 Number in coding regions = 238 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 4 TTTTAAACGGTTAGACAATTTTTTTAAATCTGTAATTGA 1 145 0 TAATTTTTAT 0.846446 -156 TTATTTGAACAAAATGAACTTTTTTTAAACGGTTAGACA 1 167 0 AAACTTTTAA 0.734335 -134 AAATGATGGAAAAATGAAATTTTATGTAATTTTCTAATT 1 214 1 AAAATTTTAA 0.764581 -87 GCGAATATTAATATGGGAATTTTGTCTTTAATTAAACAA 2 107 1 AAAATTTTTT 0.644026 -194 CAAAGTTTGTTGAAATAATTTTTGCTTTTCTTTGCAATG 2 160 1 TAATTTTTTT 0.728867 -141 ACTTGTTAAAAGTATTAAATTTTCATCAACTTTTTCAAT 2 251 1 ATAATTTTAA 0.621269 -50 GCAAGTGTTTTTTTATCATTTTTGTTTAAAGGGAATAAA 3 13 0 TTATTTTTAA 0.708959 -110 TTGTGCCATATCATCAGATTTTTTGTTATATTATGCCGC 4 157 1 TAATTTTTAT 0.846528 -62 ATAATTCTGATTTTTTATTTTACTTATGACA 7 3 1 ATATTTTTTT 0.684136 -64 GTTGGGGAAAATAACGCATTTTTATAGAATTCTCAAGAT 9 119 0 AAATTTTTAA 0.892042 -53 CCCGACACAATGTCGGGATTTTTGCTCTATATCACAATA 11 18 1 TTATTTTTTA 0.542795 -155 AATGTTAAGTAGATCTCATTTTTAAACATTTTTTTAAGA 11 77 0 AAATTTTTAT 0.901173 -96 AATGAGATCTACTTAACATTTTTTTATATTGACATCCAT 11 96 1 ATATTTTTAT 0.816316 -77 ATAATAAGCCACAGTTAAATTTTAATCTTATATATTAGA 11 136 1 AAAATTTTTT 0.644165 -37 GTTGCAAAGATTACCTTAATTTTTTCAAATTTGCGATAA 12 46 0 TAAATTTTAA 0.67058 -107 AGTTTATTCATAACCGCACTTTTTCCTTTAAAAGTGCGG 12 94 1 TAACTTTTTT 0.473518 -59 TTAGTCAGATAGACGTGAATTTTTATGTAGGCTCTTGAA 13 134 0 AAAATTTTTA 0.621271 -41 AAACTGGCTGTCAAACTATTTTTTGGCATTTTATATTAA 14 57 0 TAATTTTTAT 0.846528 -244 AACGTTTTACACAGAGGATTTTTATTTATGTTTCGTATT 14 114 1 AAATTTTTAT 0.901173 -187 TACGCTATTTTAAGTCTATTTTTAGTAAAAATAGTTTAA 16 43 1 TAATTTTTAA 0.833283 -172 TTTAGTAAAAATAGTTTAATTTTTCAAAAAATACGATAA 16 63 1 AAAATTTTAA 0.7709 -152 AATACGATAAAGTTTGTATTTTTTCCTTACCGATGAATT 16 92 1 ATATTTTTTA 0.662464 -123 TATGCAATTCTTATGCAAATTTTGACTATTGAAAAATAA 17 13 0 TAAATTTTAT 0.675166 -194 TCAGTTGATGAAAGTGAATTTTTATGCAATTCTTATGCA 17 35 0 AAATTTTTAA 0.892041 -172 TTTTAAAGTTTTTTCAGATTTTTTTCAAAAAGGACTCAG 20 13 0 TTATTTTTAA 0.708959 -287 CTTGTAAATTTTAGAAGATTTTTTGAGATAAAGATAGTG 20 178 0 TAATTTTTAT 0.846528 -122 CATTAGCTAGACTTTTCATTTTTCAGCAAAAAAGGTAGG 21 43 0 ATATTTTTAA 0.801076 -155 TTACAACTTTATAACAAAATTTTTTTGATGCGAGGCATT 21 78 0 AAAATTTTAT 0.787632 -120 CTCTCCTCTTATTGAACATTTTTTTTATTTTTTTGTCTT 22 48 0 ATATTTTTTT 0.684136 -146 TGCTAGGGATTGTTCCCATTTTTTTATTACTTACTGATA 23 215 1 TTATTTTTTA 0.542795 -86 TAGCAAAAATAGACCGCACTTTTTAAAAAATCCCTAAAA 26 14 1 AAACTTTTAA 0.734359 -169 GCGGGTCTTTTTTAGCTATTTTTTAGCTTTTCTTGATTA 26 56 1 TTATTTTTTT 0.567131 -127 CAAATGCTATTCAGAGAAATTTTGAAAATAATCAAGAAA 26 84 0 TAAATTTTAT 0.691913 -99 GCCAACTGACAAATTTTATTTTTTACTTTTAGGAGTTCC 26 153 1 AAATTTTTTT 0.816315 -30 ATTATTTAACAAACGAAACTTTTACTGAAATACAACCTA 27 16 0 AAACTTTTAA 0.734358 -245 TTCGTTTGTTAAATAATATTTTTCTCTATCTTTAAAGGT 27 38 1 AAATTTTTAT 0.901172 -223 ATATTGATAAATTCACAATTTTTCCTAATTTTATAGGTG 28 33 1 ATATTTTTAT 0.816229 -179 TCCTAATTTTATAGGTGATTTTTCTACTTATATCATTTC 28 55 1 AAATTTTTTT 0.816316 -157 TATCATTTCTATATGTCACTTTTTTAAAATAAATTGTGA 28 85 1 AAACTTTTAA 0.734358 -127 TTCTCAAAATAATTATGATTTTTATTGAATTTGTTAAAA 28 129 1 ATATTTTTAA 0.801076 -83 * * ****** ** Masking position 10 Map Score: 41.5583 Number of sites scoring better than the average of aligned sites = 823 Number in coding regions = 571 Number in noncoding regions = 252 Number of orfs with sites within 600 bp upstream = 217 Fraction of orfs with sites within 600 bp upstream = 0.0348538 Motif number 5 CCTTGATAAAGTGCGGTCGATTTTTACGGT 8 53 1 GTGCGGTCGA 0.978817 -37 AAAGGAAAAAGTGCGGTTATGAATAAACTT 12 93 0 GTGCGGTTAT 0.96705 -60 TCCTTTAAAAGTGCGGTTAAAATTTCAATC 12 117 1 GTGCGGTTAA 0.984806 -36 CACATTTTGTGTGCGGCTAAGTTGTGGATA 14 181 1 GTGCGGCTAA 0.931116 -120 CGTATGATAAGTGCGGTCAATTTTTGAGGT 16 17 0 GTGCGGTCAA 0.994969 -198 GACCGTAAAAGTGCGGTCAATATTTTTAAC 18 77 1 GTGCGGTCAA 0.994969 -37 TTGATGAAAACTGCGGTCAAAAAACATTGT 19 11 1 CTGCGGTCAA 0.962418 -52 TCCTTTTAAAGTGCGGTCATAAAACACAAT 19 36 0 GTGCGGTCAT 0.988956 -27 TTATTTGAAAGTGCGGTAATTTTTTTGTGT 20 103 0 GTGCGGTAAT 0.920732 -197 TTTTTAAAAAGTGCGGTCTATTTTTGCTAA 26 13 0 GTGCGGTCTA 0.968921 -170 ********** Masking position 2 Map Score: 20.5162 Number of sites scoring better than the average of aligned sites = 590 Number in coding regions = 398 Number in noncoding regions = 192 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 6 AAACGGTTAGACAATTTTTTTAAATCTGTAAT 1 148 0 ACATTTTTTA 0.802249 -153 GAACAAAATGAACTTTTTTTAAACGGTTAGAC 1 168 0 AATTTTTTTA 0.691814 -133 CAAAATGCTAAACGTTTTTTAACACGTAAA 1 281 1 AAGTTTTTTA 0.94713 -20 GATATTTTGCAAGGTTTGTTTAATTAAAGACA 2 129 0 AAGTTTGTTA 0.857752 -172 GCAAAATATCAAAGTTTGTTGAAATAATTTTT 2 151 1 AAGTTTGTTA 0.857752 -150 CTCTAAAGCAAGTGTTTTTTTATCATTTTTGT 3 27 0 AGGTTTTTTA 0.827861 -96 AAAGAGTACAAAGGATTTTGAA 4 1 0 AAGATTTTGA 0.67512 -218 TATAATTGCGACAGATTTTTGAGCATAATTAA 4 32 0 ACGATTTTTA 0.874291 -187 GTCGATTTTTACGGTCTTTTTAGGATAACAAA 8 68 1 ACGTCTTTTA 0.627002 -22 AAGGATTGTTTAAAACACTATC 10 1 1 AAGATTGTTA 0.67512 -205 CTCATTTTTAAACATTTTTTTAAGAACTTTAC 11 70 0 AAATTTTTTA 0.782664 -103 AGATCTACTTAACATTTTTTTATATTGACATC 11 100 1 AAATTTTTTA 0.782664 -73 TTTACATCTGACTGTTTTTTTATCCACAACTT 14 199 0 ACGTTTTTTA 0.952789 -102 CATAAAACACAATGTTTTTTGACCGCAGTTTT 19 17 0 AAGTTTTTTA 0.94713 -46 GCTTTGTTTTAAAGTTTTTTCAGATTTTTTTC 20 26 0 AAGTTTTTTA 0.94713 -274 TAAATTTTAGAAGATTTTTTGAGATAAAGATA 20 181 0 AAATTTTTTA 0.782664 -119 AGATTTGTTAAATGTTTGTGAAAAGCAAATAT 20 215 1 AAGTTTGTGA 0.669933 -85 CTTTATAACAAAATTTTTTTGATGCGAGGCAT 21 79 0 AATTTTTTTA 0.691814 -119 GCAGTTCGTCACAATTTTTTGAATAAAAAACA 21 123 1 ACATTTTTTA 0.802249 -75 CTCTTATTGAACATTTTTTTTATTTTTTTGTC 22 50 0 ACTTTTTTTA 0.716622 -144 TACTTGTAAGACCGTTTTTGTACTGCTCCGAT 22 110 0 ACGTTTTTGA 0.87168 -84 TATAATGTGCACCGATTTTTTATCTGGCTAAT 25 223 1 ACGATTTTTA 0.874291 -78 CGCACTTTTTAGGGATTTTTTAAAAAGTGCGG 26 27 0 AGGATTTTTA 0.623688 -156 AAAGGTTTCAACGGATTTTGCATTGCTGATAT 27 71 1 ACGATTTTGA 0.700689 -190 ** ******* * Masking position 7 Map Score: 26.3905 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 173 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 7 TAATTTCTACTTTTATCACTTTTTCCTTTG 1 248 1 TTTTATCACT 0.657727 -53 TGTTTTTCCTCTTAATTCATTG 3 111 0 TTTTTCCTCT 0.721382 -12 TAAATAACCTTTTTATCTCTCTTGGTTTTC 4 67 0 TTTTATCTCT 0.947527 -152 CTTAACGTAATTTAATCTCAACAAGCGGCA 4 190 0 TTTAATCTCA 0.589901 -29 AAGAACGACTCTTTCTCTCTGCCTTTAACA 5 29 1 CTTTCTCTCT 0.881133 -24 ATTTACCCTCTCGTATATACT 6 83 0 TTTACCCTCT 0.767581 -11 ATTCTCAAGATTTTCTCTCTTATGTCGAAT 9 100 0 TTTTCTCTCT 0.90987 -72 TATTCTTTCTTTTAATCTCGTTATTAGGAG 10 180 1 TTTAATCTCG 0.689923 -26 TTTTTAAGAACTTTACCTCTTTTTAGTGAT 11 56 0 CTTTACCTCT 0.931089 -117 CGTATTGTTTCTTTATCTCTCAACCTACTG 14 147 1 CTTTATCTCT 0.929872 -154 TTTTACCTCGTAAAAACGTT 18 104 0 TTTTACCTCG 0.875963 -10 AATTCACTATCTTTATCTCAAAAAATCTTC 20 174 1 CTTTATCTCA 0.766899 -126 TTTTACCTCTTATTCAATAA 28 202 0 TTTTACCTCT 0.948455 -10 ********** Masking position 3 Map Score: 7.34092 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 56 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 8 AATAAATATTCAAAATAAAGGCTTTTTTGT 4 131 1 CAAAATAAAG 0.794386 -88 ATGTCATAAGTAAAATAAAAAATCAGAATT 7 13 0 TAAAATAAAA 0.854175 -54 CCCTAAAATAAAAAAGTTTTCAG 9 4 1 TAAAATAAAA 0.854175 -168 AAAACACTATCAAAATAACTTATACCCGCC 10 22 1 CAAAATAACT 0.64462 -184 ATTTTATATTAAAAATAAACCTACTTACAC 14 39 0 AAAAATAAAC 0.68171 -262 TTTTGATGAATAAAATAAATTCATCGGTAA 16 118 0 TAAAATAAAT 0.854175 -97 TTGACTATTGAAAAATAAAG 17 1 0 AAAAATAAAG 0.797637 -206 AAATACTCCAAAATAAATTTCAGATAAC 22 9 1 CAAAATAAAT 0.851664 -185 TGTAAGACAAAAAAATAAAAAAAATGTTCA 22 45 1 AAAAATAAAA 0.854175 -149 TTAGTGATAGAAAAATAAATTGATTCCACT 24 18 0 AAAAATAAAT 0.854175 -34 TGTAGCGAAGTAAAATAACACCTTTAAAAT 25 256 1 TAAAATAACA 0.649193 -45 CCTAAAAGTAAAAAATAAAATTTGTCAGTT 26 156 0 AAAAATAAAA 0.854175 -27 GTCACTTTTTTAAAATAAATTGTGATCTAG 28 99 1 TAAAATAAAT 0.854175 -113 ********** Masking position 5 Map Score: 7.04586 Number of sites scoring better than the average of aligned sites = 496 Number in coding regions = 312 Number in noncoding regions = 184 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 9 ACGTTTAGCATTTTGGCACAAAGGAAAAAGTGATAAAA 1 258 0 TTTGAAAGAA 0.418258 -43 TGCGACAGATTTTTGAGCATAATTAAAAGAGTACAAAG 4 20 0 TTTATAATAA 0.562842 -199 AGAGTCGTTCTTTTAGAAGAAATTTATAAA 5 3 0 TTTGAAATAA 0.766455 -50 TAGGAATGAATTTTCTTTATAATCTGTAGTCTGAATGC 9 33 0 TTTTTAATGA 0.811959 -139 AATAAGTATCTTATATTTCAAATGGATATGTTTCTTGC 10 136 0 TTTTAAATAA 0.893533 -70 AAATCGAGTATTTTTGGCGAAATTCACAGAATTTTATC 12 13 1 TTTGAAATAA 0.766455 -140 ATTCACAGAATTTTATCGCAAATTTGAAAAAATTAAGG 12 34 1 TTTTAAATGA 0.90109 -119 CTCTAATTGTTTGTATATGAAATACGGACTAAAGTCCG 13 31 0 TTTTAAATGA 0.90109 -144 TTTATTAGTTAAATGTATATTTGATGAAG 14 2 1 TTTAAAATAA 0.731013 -299 TTTTTTGGCATTTTATATTAAAAATAAACCTACTTACA 14 40 0 TTTTAAAAAA 0.542947 -261 ACAGCCAGTTTTTTATTCGTAATATGGAAAACGTTTTA 14 85 1 TTTTTAATGA 0.811994 -216 GTTGCGGGTTTTTTATCTAAAAAATACAGGAAAAACGC 14 259 1 TTTTAAAAAA 0.543096 -42 TCGGCAGTTTTTATTTATAAAATATACATATTAAGGTT 15 35 1 TTTTAAATAA 0.893533 -33 AAGAAAATATTTATCTCAGAAATGTGAACTAGATCATA 17 95 1 TTTTAAATGA 0.90109 -112 GCTGAGTCCTTTTTGAAAAAAATCTGAAAAAACTTTAA 20 12 1 TTTAAAATGA 0.746835 -288 ATCAAAAAAATTTTGTTATAAAGTTGTAAAAGTTTGCA 21 88 1 TTTTAAAGGA 0.666205 -110 ATACGCGCAATTTTCTAGTCAATAAAAAGGTCAAAAA 22 167 1 TTTTCAATAA 0.550362 -27 CAATTTATTTTTCTATCACTAATTAAAAGGACGATT 24 26 1 TTTTTAATAA 0.799144 -26 CACCGATTTTTTATCTGGCTAATATGTAGCGAAGTAAA 25 232 1 TTTTTAATGA 0.811994 -69 TTCAGAGAAATTTTGAAAATAATCAAGAAAAGCTAAAA 26 76 0 TTTATAATAA 0.563008 -107 ** * * **** * * Masking position 4 Map Score: 12.8897 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 115 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 10 GTATTAAATTTTCATCAACTTTTTCAATGT 2 262 1 TTCATCAACT 0.954331 -39 CTACTTACACTTCATCAAATATACATTTAA 14 19 0 TTCATCAAAT 0.945369 -282 ATTTATTTTATTCATCAAAAGGTGTATTCT 16 128 1 TTCATCAAAA 0.930019 -87 AAAATTCACTTTCATCAACTGAAATATGAA 17 52 1 TTCATCAACT 0.954331 -155 ATAGTGAATTTTCATCAAATCATCATATCA 20 154 0 TTCATCAAAT 0.945369 -146 CTTTTCATTTTTCAGCAAAAAAGGTAGGAT 21 41 0 TTCAGCAAAA 0.803497 -157 CTGACGGCTATTAATCAACAAGATTTAATT 23 166 1 TTAATCAACA 0.675497 -135 ********** Masking position 4 Map Score: 3.11729 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 134 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 11 ATTAATATTCGCTCAATTTCATACATTCAGA 2 88 0 GCCAATTTCA 0.907287 -213 AACAAACCTTGCAAAATATCAAAGTTTGTTG 2 141 1 GCAAATATCA 0.628241 -160 CGGGATTTTTGCTCTATATCACAATATCACT 11 31 1 GCCTATATCA 0.784467 -142 ATCTGTTCACGCCAAATTTTATAGGGAGAAC 13 98 1 GCAAATTTTA 0.792096 -77 TATAGGGAGAACAATATTTCAAGAGCCTACA 13 117 1 ACATATTTCA 0.792096 -58 AGATGTAAATACCCAATTTTAAACCCGCACT 14 222 1 ACCAATTTTA 0.815682 -79 CACTTATCATACGCTATTTTAAGTCTATTTT 16 34 1 ACCTATTTTA 0.836781 -181 CCGATGGAATGCAATATTTTACTGGTTATTT 20 58 1 GCATATTTTA 0.815283 -242 TATAATCGACGCAATATTTCAATCCTGTTTC 21 157 1 GCATATTTCA 0.859114 -41 GTCAATAATTACAAAATTTTAAAGGTGTTAT 25 270 0 ACAAATTTTA 0.704174 -31 TATTTCAATCACTCAATATCAGCAATGCAAA 27 87 0 ACCAATATCA 0.662495 -174 AGGTATTATAACACTATTTTAACAAATTCAA 28 153 0 ACCTATTTTA 0.836781 -59 CTCAGGTTTCTCACTATTTTATTGAATAAGA 28 184 1 TCCTATTTTA 0.515585 -28 ** ******** Masking position 6 Map Score: 5.25371 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 138 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 12 ACGACCTTGCCAAGGTCGGGGTCGCGAGTTCG 1 44 0 CAAGTCGGGT 0.990724 -257 CCGACCTTGGCAAGGTCGTGCTCTACCAACTG 1 57 1 CAAGTCGTGT 0.973038 -244 AATCCCGACACAATGTCGGGATTTTTGCTCTA 11 15 1 CAAGTCGGGT 0.990724 -158 TCCCTAGCAACAACATCGGGATCAATTGAATT 23 192 0 CAAATCGGGT 0.942931 -109 ACCACCTTGACATGGTGGGGGTCACTGGTTCG 25 25 0 CATGTGGGGT 0.932303 -276 CCCACCATGTCAAGGTGGTGCTCTAACCAACT 25 38 1 CAAGTGGTGT 0.949654 -263 *** ****** * Masking position 6 Map Score: 2.9324 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 5 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 13 TACAAATACTTCTATAATTGGTGCTATTTTACT 2 211 0 TCATATGGTG 0.966088 -90 TTTTTCAATGTCAATAGTTGGAGTTTGATT 2 281 1 TCATATGGAG 0.95629 -20 TCTTTTAATCTCGTTATTAGGAGGTCTCT 10 187 1 TCTTATGGAG 0.966088 -19 ACCAAAGATTTCATTAATCGGTGGGCTTAAAGC 18 22 0 TCTTATGGTG 0.97375 -92 AAAAAAATGTTCAATAAGAGGAGAGCAAATTAT 22 62 1 TCATAGGGAG 0.870666 -132 TGCAATTGGTTCTTTACTTGGTGCAGGCATTTC 23 66 1 TCTTATGGTG 0.97375 -235 GATATTTTAGGCTTTAATCGGTGTTTTTTTTGG 27 175 0 GCTTATGGTG 0.919446 -86 ** *** * **** Masking position 6 Map Score: 3.13668 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 15 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 14 TCATTGCAAAGAAAAGCAAAAATTATTTCA 2 170 0 GAAAAGCAAA 0.954999 -131 TGAAAGGGGAGGAGAGTAAAATAGCACCAA 2 197 1 GGAGAGTAAA 0.775198 -104 AAATCAATCAAAAAAGCAAAGAAAAGTAAT 4 104 1 AAAAAGCAAA 0.675372 -115 ATGCAAGCAAGAAGATCAAATTACCGTTGT 6 12 0 GAAGATCAAA 0.843259 -82 AAATGTTTGTGAAAAGCAAATATTGCCGTA 20 224 1 GAAAAGCAAA 0.954999 -76 TTCAATAAGAGGAGAGCAAATTATCTTGTT 22 71 1 GGAGAGCAAA 0.972356 -123 TAAAACTTTTGGAAATCAAAAACGGCTCAG 25 189 0 GGAAATCAAA 0.843259 -112 AAATAATCAAGAAAAGCTAAAAAATAGCTA 26 68 0 GAAAAGCTAA 0.769871 -115 AAAATAGGGTGGAGGGCAAATGCTATTCAG 26 109 0 GGAGGGCAAA 0.891521 -74 ********** Masking position 3 Map Score: 3.18649 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 61 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 15 TTGATAAAGTGCGGTCGATTTTTACGGTCT 8 55 1 GCGGTCGATT 0.969437 -35 TATGATAAGTGCGGTCAATTTTTGAGGTGT 16 15 0 GCGGTCAATT 0.981843 -200 CCGTAAAAGTGCGGTCAATATTTTTAACGT 18 79 1 GCGGTCAATA 0.974186 -35 GATGAAAACTGCGGTCAAAAAACATTGTGT 19 13 1 GCGGTCAAAA 0.919809 -50 TTTAAAAAGTGCGGTCTATTTTTGCTAAGT 26 11 0 GCGGTCTATT 0.95536 -172 ********** Masking position 5 Map Score: 2.39836 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 102 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344