AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00260_hinf_reg_300.orf -o00260_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 HI0086 300 cystathionine gamma-synthase (metB) #2 HI0087 42 threonine synthase (thrC) #3 HI0089 300 aspartokinase I / homoserine dehydrogenase I (thrA) #4 HI0110 166 seryl-tRNA synthetase (serS) #5 HI0160 156 phosphatidylserine decarboxylase proenzyme (psd) #6 HI0288 34 L-serine deaminase (sdaA) #7 HI0289 222 serine transporter (sdaC) #8 HI0291 74 H. influenzae predicted coding region HI0291 #9 HI0292 76 mercuric ion scavenger protein (merP) #10 HI0425 146 phosphatidylserine synthase (pssA) #11 HI0462 192 ATP-dependent proteinase (lon) #12 HI0463 115 oxygen-independent coproporphyrinogen III oxidase, putative #13 HI0464 132 ribose 5-phosphate isomerase A (rpiA) #14 HI0465 29 D-3-phosphoglycerate dehydrogenase (serA) #15 HI0646 158 aspartate-semialdehyde dehydrogenase (asd) #16 HI0647 277 transport protein, putative #17 HI0648 241 modulator of drug activity B (mdaB) #18 HI0652 62 3-deoxy-d-manno-octulosonic-acid transferase (kdtA) #19 HI0737 247 acetohydroxy acid synthase II, putative #20 HI0738 71 dihydroxyacid dehydratase (ilvD) #21 HI0738.1 79 threonine deaminase (ilvA) #22 HI0885 191 thiol:disulfide interchange protein (dsbD) #23 HI0886 111 H. influenzae predicted coding region HI0886 #24 HI0887 187 phosphoribosylaminoimidazolecarboxamide formyltransferase (purH) #25 HI0888 95 phosphoribosylamine--glycine ligase (purD) #26 HI0889 123 serine hydroxymethyltransferase (serine methylase) (glyA) #27 HI0924 300 glycyl-tRNA synthetase, beta chain (glyS) #28 HI0927 265 glycyl-tRNA synthetase, alpha chain (glyQ) #29 HI1032 175 transcriptional regulator, putative #30 HI1033 149 phosphoserine phosphatase (serB) #31 HI1167 190 phosphoserine aminotransferase (serC) #32 HI1231 113 dihydrolipoamide dehydrogenase (lpdA) #33 HI1232 62 dihydrolipoamide acetyltransferase (aceF) #34 HI1233 299 pyruvate dehydrogenase, E1 component (aceE) #35 HI1367 284 threonyl-tRNA synthetase (thrS) Motif number 1 ATGAAAAATAACCGCACTTTATCCGTAATC 3 132 1 ACCGCACTTT 0.997736 -169 AGAAAAATTGACCGCACTTTGTATTAGAAT 4 52 0 ACCGCACTTT 0.997736 -115 TGCTATAATCACGCCTCTTTTTTTAACAAG 5 129 1 ACGCCTCTTT 0.864075 -28 GCTGAAAATTACCGCACTTTTTATAAAAAA 7 64 1 ACCGCACTTT 0.997736 -159 TTTTGTTTAAAACCCACTTTATAACTCAGA 11 85 1 AACCCACTTT 0.888576 -108 TTTTAAATTAACCACACTTTTTTATTTAAT 15 37 1 ACCACACTTT 0.956253 -122 ACGAAAAATGACCGCACTTTTAAAATAAAA 17 41 0 ACCGCACTTT 0.997736 -201 GTGAATTTTTACCGCTCTTTTGGCTTATTT 19 74 0 ACCGCTCTTT 0.995799 -174 GCCAATTTTCACCGCACTTTTTTTCGTTTT 19 142 1 ACCGCACTTT 0.997736 -106 TTTAACGGTTCCCCTCTTTCATAAGAGGG 21 10 1 TCCCCTCTTT 0.954341 -70 GGAAAAACTAACCGCACTTTATCATCAAAA 21 52 1 ACCGCACTTT 0.997736 -28 GTAAAAAATCACCGCACTTTTTTATTGTTA 22 78 0 ACCGCACTTT 0.997736 -114 TCGTATTTTTACCGCACTTTAAGAAATTAT 24 84 1 ACCGCACTTT 0.997736 -104 ATCTAACTATCCCCCTCTTTACAAAAGAGG 25 14 1 CCCCCTCTTT 0.957561 -82 ACCTGCAATTCCCCCTCTTTTGTAAAGAGG 25 27 0 CCCCCTCTTT 0.957561 -69 AATCTCCCCTACCCCTCTTTGCTAAAGAGG 27 60 1 ACCCCTCTTT 0.992624 -241 ATTCAAGAATTCCCCTCTTTAGCAAAGAGG 27 73 0 TCCCCTCTTT 0.954341 -228 AAAGATCCAATCCCCTCTTTAGCAAAGAGG 27 203 1 TCCCCTCTTT 0.954341 -98 AATCGCCCCTACCCCTCTTTGCTAAAGAGG 27 216 0 ACCCCTCTTT 0.992624 -85 CTGATTTTCAACCGCATTTTTCGCCTTTAT 28 189 1 ACCGCATTTT 0.93602 -77 AAAAATATTGACCGCACTTTTACGGTCTTT 32 74 0 ACCGCACTTT 0.997736 -40 ATGTTTTTTGACCGCAGTTTTCATCAA 33 8 0 ACCGCAGTTT 0.955915 -55 GTGTTTTATGACCGCACTTTAAAAGGAACA 33 39 1 ACCGCACTTT 0.997736 -24 CAAAAAAATTACCGCACTTTCAAATAATTA 34 106 1 ACCGCACTTT 0.997736 -194 GGCTAGAATAACCGCACTTTTAAATACCCA 35 25 0 ACCGCACTTT 0.997736 -260 ATAAAAATTAACCGCACTTTTGCCCTACTT 35 206 0 ACCGCACTTT 0.997736 -79 ********** Masking position 8 Map Score: 92.708 Number of sites scoring better than the average of aligned sites = 1207 Number in coding regions = 764 Number in noncoding regions = 443 Number of orfs with sites within 600 bp upstream = 302 Fraction of orfs with sites within 600 bp upstream = 0.0485063 Motif number 2 TACGGATAAAGTGCGGTTATTTTTCATTGTGTT 3 126 0 GTGCGGTATT 0.998397 -175 CTAATACAAAGTGCGGTCAATTTTTCTTTATTT 4 55 1 GTGCGGTATT 0.998397 -112 TTTATAAAAAGTGCGGTAATTTTCAGCGACAAA 7 58 0 GTGCGGTATT 0.998397 -165 AAATAAAAAAGTGTGGTTAATTTAAAAGAAAAT 15 31 0 GTGTGGTATT 0.970511 -128 TATTTTAAAAGTGCGGTCATTTTTCGTTCGATT 17 44 1 GTGCGGTATT 0.998397 -198 TAAGCCAAAAGAGCGGTAAAAATTCACTAAATT 19 77 1 GAGCGGTAAT 0.949118 -171 ACGAAAAAAAGTGCGGTGAAAATTGGCTTATTT 19 136 0 GTGCGGTAAT 0.995434 -112 TGATGATAAAGTGCGGTTAGTTTTTCCTTTGTT 21 46 0 GTGCGGTATT 0.998397 -34 CAATAAAAAAGTGCGGTGATTTTTTACCTGATT 22 81 1 GTGCGGTATT 0.998397 -111 ATTTCTTAAAGTGCGGTAAAAATACGATAAATT 24 78 0 GTGCGGTAAT 0.995434 -110 TAAAATGACTGTGCCGTAATTTAGCTTTTTTTT 31 32 1 GTGCCGTATA 0.887313 -159 GACCGTAAAAGTGCGGTCAATATTTTTAACGTT 32 77 1 GTGCGGTATT 0.998397 -37 TCCTTTTAAAGTGCGGTCATAAAACACAATGTT 33 33 0 GTGCGGTAAA 0.972369 -30 TTATTTGAAAGTGCGGTAATTTTTTTGTGTTTT 34 100 0 GTGCGGTATT 0.998397 -200 GTATTTAAAAGTGCGGTTATTCTAGCCTTTATT 35 28 1 GTGCGGTATT 0.998397 -257 TAGGGCAAAAGTGCGGTTAATTTTTATAGAATT 35 209 1 GTGCGGTATT 0.998397 -76 ******* * * * Masking position 7 Map Score: 58.0281 Number of sites scoring better than the average of aligned sites = 393 Number in coding regions = 216 Number in noncoding regions = 177 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 3 ATAAAATTTCATTTTTCCATCATTTTCTGTGATTTA 1 203 0 ATTTTATTTT 0.947662 -98 GGAAAAATGAAATTTTATGTAATTTTCTAATTTCTA 1 221 1 AATTTATTTT 0.910318 -80 ATTTAATCCGTTTTTAATCTGATTTCATCTATTTAA 2 17 0 TTTTTATTTC 0.864492 -26 AAAGTGACAAATTTTTCAGAAATTTTCTTAGTCAAT 3 32 0 ATTTTATTTT 0.947662 -269 GAATAGCGGGTTTTTTTATAAATTTAAAAACACAAT 3 258 1 TTTTTATTTA 0.742779 -43 AGTGCGGTCAATTTTTCTTTATTTTTATACGTTGGC 4 64 1 ATTTTTTTTT 0.92528 -103 AGAATTTCCTTACTTTTTTCGTTGAAAT 4 149 0 AATTTTTTTT 0.874089 -18 ATTTTTGTTATAGTTCCAACCTTTTTAGTTAGCGGA 5 93 0 TAGTTTTTTT 0.637395 -64 TCGCCTTTAATTTTTAACGAATTTTGAGAAATTT 6 10 1 ATTTTATTTT 0.947662 -25 AATTGTGATCAAGTTAAAATTTTTTTATAAAAAGTG 7 78 0 AAGTTTTTTT 0.658811 -145 AATGCTCACAAATTTTAGCATTTTTTGGCTAAAAAA 10 37 0 AATTTTTTTT 0.874089 -110 ACTAGTGCGTTAGTTTACAATATTTCACGTGCTTAT 10 101 0 TAGTTATTTC 0.498688 -46 TATTTTGTGAAATTTAATAAAATTTTTCATTATTTT 11 18 1 AATTTATTTT 0.910318 -175 AACTCAGATTTTGTTATAATCTTTTCCTTGAATTCC 11 107 1 TTGTTTTTTC 0.548246 -86 TTAACCACACTTTTTTATTTAATTTCTTTCGCGAAA 15 44 1 TTTTTATTTC 0.864492 -115 ACGAAGATGGATTTTTTGTTTATTTCGTTAAGATTC 16 31 1 ATTTTATTTC 0.875123 -247 TCGGCAAGAAATTTTCTGCCGATTTTTTATTTTAAA 17 17 1 ATTTTATTTT 0.947662 -225 AGTGCGGTCATTTTTCGTTCGATTTCCACCAATTTT 17 53 1 TTTTTATTTC 0.864492 -189 TTTCCACCAATTTTTTACCGAATTTTCAATTCCAGC 17 75 1 TTTTTATTTT 0.942803 -167 TATGCCTTTTTACGTTAATTTTTAAAAGTATA 17 220 0 TTTTTATTTT 0.942803 -22 ATTTTCAATCCTTTTTTTGCTATACT 18 1 1 ATTTTTTTTT 0.92528 -62 TCCCCTAAAAAATTTAGTGAATTTTTACCGCTCTTT 19 84 0 AATTTTTTTT 0.874089 -164 TTCACCGCACTTTTTTTCGTTTTTTTCTCTCCAAGC 19 149 1 TTTTTTTTTT 0.918522 -99 GTGCGGTTAGTTTTTCCTTTGTTTTATCCCCCTCTT 21 33 0 TTTTTTTTTA 0.663861 -47 AGTGCGGTGATTTTTTACCTGATTTTCCTTTTTGTG 22 90 1 TTTTTATTTT 0.942803 -102 TAGTTTCATAATTTTATCCTTATTTTTGCCCACATT 24 19 1 ATTTTATTTT 0.947662 -169 TTATGCCTGAAATTTATCGTATTTTTACCGCACTTT 24 68 1 AATTTTTTTT 0.874089 -120 TCTCATCGCTTATTTTTAACTATTTAATGAAAGGAA 24 156 1 TATTTATTTA 0.618153 -32 TAGGAATGAAATTTTAATTAAATTTTTATCCATAAA 26 56 1 ATTTTATTTT 0.947662 -68 TTTGTTTCTCTTATTTAAAAATTCTGT 27 284 0 TTGTTATTTA 0.445431 -17 TAGTATAGTTTTTTTTGATTAATTTAATAGATTTCG 28 91 0 TTTTTATTTA 0.742779 -175 TAATTTTGAATATTTAGGTAGATTTTAAGTTTTATT 28 128 0 TATTTATTTT 0.902349 -138 ATAAATCAATATGTTAAAATAATTTTACTGATTTTG 29 106 1 ATGTTATTTT 0.834334 -70 AAGTGCAATTAATTTTAGAATATTTTATCTGTTATT 30 25 0 AATTTATTTT 0.910318 -125 ACTGTGCCGTAATTTAGCTTTTTTTTAATCAATCGT 31 39 1 AATTTTTTTT 0.874089 -152 TGTATTTCCTTGCTTTTTATGAAAATAA 31 173 0 TATTTTTTTT 0.863384 -18 GTGCGGTCAATATTTTTAACGTTTTTACGAGGTAAA 32 87 1 TATTTTTTTT 0.863384 -27 GTTTTAAAGTTTTTTCAGATTTTTTTCAAAAAGGAC 34 17 0 TTTTTTTTTT 0.918522 -283 AAGTGCGGTAATTTTTTTGTGTTTTTTTGTTCGCTA 34 89 0 ATTTTTTTTT 0.92528 -211 AATCTTGTAAATTTTAGAAGATTTTTTGAGATAAAG 34 184 0 ATTTTTTTTT 0.92528 -116 TCGCCACGCATTTTTTGCCTAATTTCGCTCGTTCAA 35 154 1 TTTTTATTTC 0.864492 -131 AGTGCGGTTAATTTTTATAGAATTTTAAATGAACAC 35 218 1 ATTTTATTTT 0.947662 -67 ***** ***** Masking position 5 Map Score: 59.027 Number of sites scoring better than the average of aligned sites = 1052 Number in coding regions = 693 Number in noncoding regions = 359 Number of orfs with sites within 600 bp upstream = 266 Fraction of orfs with sites within 600 bp upstream = 0.0427241 Motif number 4 AAGTGCGGTTATTTTTCATTGTGTTTTATCTTGAA 3 116 0 ATTTTCTTTT 0.919901 -185 AGTGCGGTCAATTTTTCTTTATTTTTATACGTTGG 4 64 1 ATTTTCTTTT 0.919901 -103 ATTTCCTTACTTTTTTCGTTGAAATGAAAACAACC 4 139 0 TTTTTCTTAT 0.919901 -28 AAAAAAGGCTTTTTTTCGTTATAATGCTCACAAAT 10 60 0 TTTTTCTTTT 0.967411 -87 ATTTAATAAAATTTTTCATTATTTTAGCCATTATC 11 29 1 ATTTTCTTTT 0.919901 -164 TTTGTTATAATCTTTTCCTTGAATTCCTTTTTCCC 11 116 1 TTTTTCTTAT 0.919901 -77 GTCTCTCTTATAATTTCGTTCCGATAATTTGGGTA 11 163 0 TATTTCTTCT 0.800016 -30 TTCTTTTCCTTATCTTAATAAGTAAA 13 117 0 TTTTTCTTTT 0.967411 -16 GATTAAATTAAATTTTCTTTTAAATTAACCACACT 15 20 1 ATTTTCTTAT 0.816282 -139 GATTTTTTGTTTATTTCGTTAAGATTCGTTCAGAA 16 40 1 TATTTCTTAT 0.829058 -238 ATATTGAAACTCTTTTCATTTTTTTACATAGGATA 19 15 0 TTTTTCTTTT 0.967411 -233 ACTGATGATTAGATTTCATTATATTGAAACTCTTT 19 35 0 AATTTCTTTT 0.829058 -213 TCACCGCACTTTTTTTCGTTTTTTTCTCTCCAAGC 19 150 1 TTTTTCTTTT 0.967411 -98 GTGCGGTTAGTTTTTCCTTTGTTTTATCCCCCTCT 21 34 0 TTTTCCTTTT 0.703341 -46 TTTTTTACCTGATTTTCCTTTTTGTGATCTAAATC 22 100 1 GTTTTCTTTT 0.904516 -92 TTAGGTATTCAAATTTCTTTGTGATAGAATTTCGA 22 141 1 AATTTCTTTT 0.829058 -51 TTGCTTTCCTTTTGTTTAAAGATGAA 23 96 0 TCTTTCTTTT 0.769034 -16 AGTTTCATAATTTTATCCTTATTTTTGCCCACATT 24 20 1 TTTATCTTTT 0.625226 -168 TGTATTTTCCTTTCATTAAATAGTTAA 24 171 0 TTTTTCTTCT 0.904516 -17 TATGATGAATTAATTTCATTTAAGTGATGAAAATT 26 21 1 TATTTCTTAT 0.829058 -103 TAAATTCTTATTTTCTCGTTATCATTTCTGCCAAA 27 244 0 TTTCTCTTTT 0.71203 -57 TGTATTTCCTTGCTTTTTATGAAAAT 31 175 0 GATTTCTTCT 0.560745 -16 AGGTTTTCCTTAATCTGTTTTGAGTG 34 284 0 GTTTTCTTAT 0.785632 -16 CAGAAAAACATTATTTCCTTTTTGTAAAATATGGG 35 83 1 TATTTCTTTT 0.926123 -202 TGTTTTTTCCTTATACAGTGGTCACCC 35 268 0 TTTTTCTTTA 0.615333 -17 * ***** ** * * Masking position 9 Map Score: 27.9771 Number of sites scoring better than the average of aligned sites = 300 Number in coding regions = 209 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 5 GAATAGCGGGTTTTTTTATAAATTTAAAAACACAATATCT 3 258 1 TTTTTTAAAA 0.725083 -43 ATTTCCTTACTTTTTTCGTTGAAATGAAAACAACCTTATT 4 134 0 TTTTCTAAAA 0.52956 -33 GGAAATCACATTTTTTATTGGATAACTCAATAAAGGAAAT 5 51 1 TTTTATATAA 0.596952 -106 TCCTTGTTAGTTGTTTTATTGATGGTTAAACTATAAACCT 9 41 0 TTTTTTATAA 0.919296 -36 AATAAAAGGCTTGTTTTCACAAGCCCTAAAACATTCAA 12 9 0 TTTTTAATAA 0.90948 -107 TAACAAGTTTTCAATTTGGAAAAGTATAAATTAACCTTGT 12 78 0 TCTTTGATAA 0.812932 -38 ATTGTGTTACTTTATTACGAGAGTATTTAATAAACAAGTG 13 75 0 TTTTAGATAA 0.695242 -58 TTTTATTTAATTTCTTTCGCGAAAGATCAATTTTCATTAA 15 56 1 TTTTTGATAA 0.941567 -103 GAAAGAATGGTTATTTTATGCAAAATTCAACCCCAAGCAT 16 114 0 TTTTTTATAA 0.887631 -164 CCTGTTGTTTTTATTTTGGGGATAAGTTCAGCATTGTAGC 19 207 0 TTTTTGATCA 0.594983 -41 GTATGATTAATTTCTTCGTTAATTGATAAAATATTC 20 7 0 TTTTCTATAA 0.826897 -65 TTGCTTTCCTTTTGTTTAAAGATGAATTAAAACGGCGTCA 23 82 0 TTTTTAATAA 0.908458 -30 TGTATTTTCCTTTCATTAAATAGTTAAAAATAAGCGA 24 161 0 TCTTCTATAA 0.563348 -27 CATTTACATTTTAATTTCAATAGAGATTAAATTATCTGCT 27 122 1 TTTTTAATAA 0.907484 -179 CTGAGCTTTCTTATTTTTGTAAATTATGAAACGTAATTTT 29 37 0 TTTTTGATAA 0.941533 -139 TTATGTATGATTACTTTTAATAACATAGAAAGTGCAATTA 30 50 0 TTTTTAAAAA 0.702826 -100 TAATTTAGCTTTTTTTTAATCAATCGTCAAAATTTACCCT 31 48 1 TTTTTAATAA 0.909479 -143 ATCAAAAAAATTCTTTCTATCATTCATAAAATAGAGGGTA 31 82 0 TTTTCAATAA 0.80805 -109 GCATTGATTATCGATTTTTGTAGTGATAAAAAAGACATCA 31 133 1 TCTTTTATAA 0.754569 -58 ATTTTACTGGTTATTTTAGCGAACAAAAAAACACAAAAAA 34 73 1 TTTTTGAAAA 0.790906 -227 TGAGTGAATATTAGTTTAGACAAGGCTAAACACGAATACG 34 250 0 TTTTTGATAA 0.941602 -50 AATATGGGCATTTATTTAACAATACTTCAAGAAAGTGATA 35 110 1 TTTTTAATAA 0.909452 -175 ** *** * * * ** Masking position 6 Map Score: 16.7056 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 156 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 6 GCACAAAGGAAAAAGTGATAAAAGTAGAAATTA 1 248 0 AAATGTAAAA 0.701711 -53 AATCAGATTAAAAACGGATTAAAT 2 29 1 AAAGGTTAAA 0.840101 -14 ATTGCGTATAAAAATAAATGAAA 7 1 0 AAAAATGAAA 0.667082 -222 AAAACAACTAACAAGGAGTAAAA 8 62 1 AAAGATAAAA 0.896962 -13 AAAACAACTAACAAGGAGTAAAA 9 64 1 AAAGATAAAA 0.896962 -13 TTTTTAGCCAAAAAATGCTAAAATTTGTGAGCA 10 38 1 AAATGTAAAA 0.701711 -109 AAATGAAGTGATAATGGCTAAAATAATGAAAAA 11 40 0 AAAGGTAAAA 0.911387 -153 GCTTGTTTTCACAAGCCCTAAAACATTCAA 12 8 0 AAACCTAAAA 0.840303 -108 TATCATCTCTAAAATCAATAAAAGGCTTGTTTT 12 32 0 AAACATAAAA 0.896962 -84 GTATAGCAAAAAAAGGATTGAAAAT 18 3 0 AAAGATGAAA 0.684906 -60 GGGTAGTTAAACAATAATTAAAATTGAAAAATA 23 35 0 AAAAATAAAA 0.889193 -77 GCTTAAATATAGAAAAGATTAAATATAATTTCT 24 105 0 AAAAGTTAAA 0.828862 -83 ATTTTTATCCATAAACAGTTAAACTATCTGCCA 26 77 1 AAACATTAAA 0.816409 -47 ATCTGCTTTCAAAAAACGTTAAAGTAGAACATA 27 155 1 AAAACTTAAA 0.712462 -146 TAACGAGAAAATAAGAATTTAAATCTACAGAAT 27 258 1 AAAAATTAAA 0.803894 -43 CGTATCATATAGAAAGGTTTAAACAATCGAAAT 28 64 1 AAAGGTTAAA 0.840101 -202 CTATACTAAAATAAAACTTAAAATCTACCTAAA 28 119 1 AAAACTAAAA 0.829075 -147 TCTAGATCACAAAATCAGTAAAATTATTTTAAC 29 118 0 AAACATAAAA 0.896962 -58 ATATCATATAATAACAGATAAAATATTCTAAAA 30 16 1 AAAAGTAAAA 0.90459 -134 AACTCCCTTTAAAATAAATAAAATGACTGTGCC 31 14 1 AAAAATAAAA 0.889193 -177 TTTACCTCGTAAAAACGTTAAAAATATTGACCG 32 90 0 AAACGTAAAA 0.911387 -24 AAAAAATCTGAAAAAACTTTAAAACAAAGCCCG 34 28 1 AAAACTTAAA 0.712462 -272 GTTCGCTAAAATAACCAGTAAAATATTGCATTC 34 64 0 AAACATAAAA 0.896962 -236 * ** ** ***** Masking position 9 Map Score: 21.7143 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 212 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 7 ATTTCCTTACTTTTTTCGTTGAAATGAAAACAA 4 141 0 TTTTTCTTAA 0.801095 -26 GCACCGATTTTTTTGTCGCTGAAAATTACCGCA 7 47 1 TTTTTCCTAA 0.975825 -176 TTGTTAGTTGTTTTATTGATGAATGCGATTGGC 8 43 0 TTTTTTATAA 0.746015 -32 AATTTTAGCATTTTTTGGCTAAAAAACAGCCAT 10 30 0 TTTTTGCTAA 0.944978 -117 AAAAAAAGCCTTTTTTCTATTAATAAGCACGTG 10 79 1 TTTTTCATAA 0.916678 -68 GCCAAAATTCTTTTTTGTTTAAAACCCACTTTA 11 73 1 TTTTTGTTAA 0.631619 -120 AAGATGAAATTATCATCTCTAAAATCAATAAAA 12 42 0 TATCTCCTAA 0.494952 -74 TTTTTTTCGTTTTTTTCTCTCCAAGCCCTACCA 19 159 1 TTTTTCCTCA 0.876569 -89 GAATATTTTATCAATTAACGAAGAAATT 20 6 1 TTTTTCATAA 0.916673 -66 ATGTGGGCTTTTTTATGCCTGAAATTTATCGTA 24 56 1 TTTTTGCTAA 0.945013 -132 ATTCCTAAATTTTCATCACTTAAATGAAATTAA 26 30 0 TTTCTCCTAA 0.94097 -94 TTAATTAAAATTTCATTCCTAAATTTTCATCAC 26 44 0 TTTCTTCTAA 0.80975 -80 TTAATTAAATTTTTATCCATAAACAGTTAAACT 26 69 1 TTTTTCATAA 0.916673 -55 TTAGTATAGTTTTTTTTGATTAATTTAATAGAT 28 95 0 TTTTTTATAA 0.746015 -171 TTTTTCCTCTCTTAATTTTATATAG 29 3 1 TTTCTCCTAA 0.940975 -173 TAATTTAGCTTTTTTTTAATCAATCGTCAAAAT 31 48 1 TTTTTTATAA 0.746015 -143 ATGATGTCTTTTTTATCACTACAAAAATCGATA 31 141 0 TTTTTCCTCA 0.876563 -50 TTTGTGTTTTTTTGTTCGCTAAAATAACCAGTA 34 77 0 TTTGTCCTAA 0.819079 -223 TTTTATTCCTTAACTGGGTATTT 35 1 1 TTTTTTCTAA 0.915089 -284 TGACTAAAGGCTTTATCTCTTAAAAATAAAGGC 35 52 0 CTTTTCCTAA 0.786225 -233 GAAATAATGTTTTTCTGACTAAAGGCTTTATCT 35 67 0 TTTTTGCTAA 0.944886 -218 TCGCCACGCATTTTTTGCCTAATTTCGCTCGTT 35 154 1 TTTTTGCTAT 0.513737 -131 **** ** ** ** Masking position 6 Map Score: 20.4071 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 176 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 8 GCATTTTACGGAAATTCAGATAACTGTCAATT 1 119 1 GAAATTCGTA 0.790762 -182 GTAGAAATTAGAAAATTACATAAAATTTCATT 1 226 0 GAAAATTCTA 0.819899 -75 AAATTTTTCAGAAATTTTCTTAGTCAATAAAT 3 28 0 GAAATTTCTA 0.804339 -273 ACAAGCTCGGGAAATTTCGGTATTTCTTTACG 3 75 1 GAAATTTGTA 0.922136 -226 AAATTTCTCAAAATTCGTTAAAAATTAAAG 6 15 0 CAAAATTGTA 0.720991 -20 TACAAATTGACAAATTTAAGTAATTTATGCTT 7 190 1 CAAATTTATA 0.495458 -33 TTTCCAAATTGAAAACTTGTTAATAACACA 12 96 1 GAAAACTGTA 0.581713 -20 TAATTTAAAAGAAAATTTAATTTAATCACTCT 15 15 0 GAAAATTATT 0.528319 -144 CCTTTCTTGCGAAAATTGAGTAGAATCTTGCG 16 172 0 GAAAATTATA 0.846606 -106 AGCTGGAATTGAAAATTCGGTAAAAAATTGGT 17 80 0 GAAAATTGTA 0.929153 -162 TATACTAGCCGAAATTTTTTTAAGTATAACCG 18 31 1 GAAATTTTTA 0.508523 -32 AAATGAAATTCGGTTATACTTAAAAA 18 47 0 GAAATTCGTA 0.790762 -16 AAAGTGCGGTGAAAATTGGCTTATTTTGAATA 19 130 0 GAAAATTGTT 0.726895 -118 CCAATGACTCGAAATTTCGCTACAATGCTGAA 19 189 1 GAAATTTGTA 0.922136 -59 TCACAAAAAGGAAAATCAGGTAAAAAATCACC 22 95 0 GAAAATCGTA 0.807142 -97 CTATCACAAAGAAATTTGAATACCTAAAACTA 22 136 0 GAAATTTATA 0.832884 -56 ATTTAGGAATGAAATTTTAATTAAATTTTTAT 26 53 1 GAAATTTATT 0.502843 -71 CCTAAATATTCAAAATTACTTACTTGATATAT 28 146 1 CAAAATTCTA 0.472849 -120 ATGATTTGATGAAAATTCACTATCTTTATCTC 34 161 1 GAAAATTATA 0.846606 -139 ******* * ** Masking position 11 Map Score: 14.7529 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 127 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 9 TTTCCGTAAAATGCGCACCAATAACAGCGAA 1 102 0 ATGCGCACCA 0.951558 -199 TCGGTGTCGTCATCGCACCGATTTTTTTGTC 7 33 1 CATCGCACCA 0.916465 -190 ATTGGCAGGCCATCCCACCAATCTGAATTGA 8 18 0 CATCCCACCA 0.965715 -57 TTTTCGTTCGATTTCCACCAATTTTTTACCG 17 64 1 ATTTCCACCA 0.676298 -178 GCGTGGGCTTAAGCCCACCCTACATTGGCTA 17 116 0 AAGCCCACCT 0.955002 -126 ACTAGGGTTTATTCCCACCCTACGGGCTGTA 17 152 1 ATTCCCACCT 0.868058 -90 AGGCATAAAAAAGCCCACATAAATGTGGGCA 24 45 0 AAGCCCACAA 0.870795 -143 ATTTCTGCCAAATCGCCCCTACCCCTCTTTG 27 225 0 AATCGCCCCA 0.767373 -76 GGTGGGCTTAAAGCCCACCTACAGA 32 5 0 AAGCCCACCA 0.988444 -109 GGTGGGCTTTAAGCCCACCGATTAATGAAAT 32 17 1 AAGCCCACCA 0.988444 -97 GGATGGGTTTCTGCCCACCAAAGATTTCATT 32 40 0 CTGCCCACCA 0.969313 -74 ********* * Masking position 6 Map Score: 8.6537 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 72 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 10 ATTGACTAAGAAAATTTCTGAAAAATTTGT 3 32 1 AAAATTTCTG 0.822856 -269 ACAAGCTCGGGAAATTTCGGTATTTCTTTA 3 75 1 GAAATTTCGG 0.738416 -226 GTTATCCAATAAAAAATGTGATTTCCCTTT 5 47 0 AAAAAATGTG 0.548463 -110 TTCAGCGACAAAAAAATCGGTGCGATGACG 7 40 0 AAAAAATCGG 0.918414 -183 AAAAAATGCTAAAATTTGTGAGCATTATAA 10 47 1 AAAATTTGTG 0.596057 -100 TAATTTGGGTAAATATTGGGGTAGGGAAAA 11 144 0 AAATATTGGG 0.534442 -49 ATATTTACCCAAATTATCGGAACGAAATTA 11 158 1 AAATTATCGG 0.74841 -35 TAAAAATCGGCAAGAAATTT 17 1 1 TAAAAATCGG 0.460018 -241 AATCGGCAAGAAATTTTCTGCCGATTTTTT 17 15 1 AAATTTTCTG 0.551067 -227 CTTTTAAAATAAAAAATCGGCAGAAAATTT 17 25 0 AAAAAATCGG 0.918414 -217 AAAATTCGGTAAAAAATTGGTGGAAATCGA 17 71 0 AAAAAATTGG 0.406611 -171 AGCTGGAATTGAAAATTCGGTAAAAAATTG 17 82 0 GAAAATTCGG 0.738416 -160 TATACTTAAAAAAATTTCGGCTAGTATAGC 18 29 0 AAAATTTCGG 0.931858 -34 CTCTCCGAGTAAAATTTAGGGTTCGTTTGT 20 45 0 AAAATTTAGG 0.594796 -27 TTAAGTGATGAAAATTTAGGAATGAAATTT 26 40 1 AAAATTTAGG 0.594796 -84 AATAGAGATTAAATTATCTGCTTTCAAAAA 27 140 1 AAATTATCTG 0.502596 -161 TCTCTTATTTAAAAATTCTGTAGATTTAAA 27 275 0 AAAAATTCTG 0.822856 -26 GATAAAGGCGAAAAATGCGGTTGAAAATCA 28 190 0 AAAAATGCGG 0.57895 -76 TCCTTTTTGAAAAAAATCTGAAAAAACTTT 34 18 1 AAAAAATCTG 0.792691 -282 TCCTTTTTGTAAAATATGGGCATTTATTTA 35 98 1 AAAATATGGG 0.781466 -187 ********** Masking position 3 Map Score: 10.9944 Number of sites scoring better than the average of aligned sites = 402 Number in coding regions = 325 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 11 GGTTAGACAATTTTTTTAAATCTGTAATTG 1 146 0 TTTTTTTAAA 0.834996 -155 CAAAATGAACTTTTTTTAAACGGTTAGACA 1 167 0 TTTTTTTAAA 0.834996 -134 AAATTTTATGTAATTTTCTAATTTCTACTT 1 230 1 TAATTTTCTA 0.500598 -71 GAATAGCGGGTTTTTTTATAAATTTAAAAA 3 258 1 TTTTTTTATA 0.759585 -43 AATTTTTCTTTATTTTTATACGTTGGCTTT 4 73 1 TATTTTTATA 0.704971 -94 TCGCCTTTAATTTTTAACGAATTTTGA 6 8 1 TAATTTTTAA 0.692774 -27 TTTCATTTATTTTTATACGCAATCGGT 7 8 1 TATTTTTATA 0.704971 -215 CAAGTTAAAATTTTTTTATAAAAAGTGCGG 7 75 0 TTTTTTTATA 0.759585 -148 TAAACAAGTGTAATTTTTAACAGGCGTTTT 13 55 0 TAATTTTTAA 0.692774 -78 TGCCGATTTTTTATTTTAAAAGTGCGGTCA 17 33 1 TTATTTTAAA 0.821844 -209 CTTTTTACGTTAATTTTTAAAAGTATATTT 17 217 0 TAATTTTTAA 0.692774 -25 CGAGCATCTATATTTTTATACTCAATTCT 22 173 1 TATTTTTATA 0.704971 -19 TTATTTTTTACTTTTGGTAA 23 1 1 TTATTTTTTA 0.650534 -111 TGGTAAAAAGTATTTTTCAATTTTAATTAT 23 25 1 TATTTTTCAA 0.637844 -87 TTCTCATCGCTTATTTTTAACTATTTAATG 24 155 1 TTATTTTTAA 0.748842 -33 ATAGCCGTACTTTTTTTAAATTAGGCATAC 25 62 1 TTTTTTTAAA 0.834996 -34 TTTCCTCTCTTAATTTTATATAGTAAAATT 29 13 1 TAATTTTATA 0.685359 -163 GTCATTTTATTTATTTTAAAGGGAGTTGTT 31 11 0 TTATTTTAAA 0.821844 -180 GTAATTTAGCTTTTTTTTAATCAATCGTCA 31 47 1 TTTTTTTTAA 0.765849 -144 TTTTTTCAGATTTTTTTCAAAAAGGACTCA 34 14 0 TTTTTTTCAA 0.699589 -286 ATTCTAGCCTTTATTTTTAAGAGATAAAGC 35 46 1 TTATTTTTAA 0.748842 -239 ********** Masking position 5 Map Score: 17.4795 Number of sites scoring better than the average of aligned sites = 288 Number in coding regions = 168 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 12 AATGCTAAACGTTTTTTAACACGTAAA 1 284 1 GTTTTTTAAC 0.689713 -17 TTTACACGAAATTTATTGACTAAGAAAATT 3 18 1 ATTTATTGAC 0.808507 -283 GAGATTCTCTATTTATTGGCATAACATAAT 7 130 1 ATTTATTGGC 0.793398 -93 AAATTTTAGCATTTTTTGGCTAAAAAACAG 10 34 0 ATTTTTTGGC 0.90589 -113 AATCTACCAAGTTTTTTGGGCAACCAAGGC 16 73 1 GTTTTTTGGG 0.491283 -205 ATTTCCACCAATTTTTTACCGAATTTTCAA 17 74 1 ATTTTTTACC 0.773593 -168 AACTCTTTTCATTTTTTTACATAGGATAAT 19 13 0 ATTTTTTTAC 0.454708 -235 CTTTTGGCTTATTTATTGACTGATGATTAG 19 58 0 ATTTATTGAC 0.808507 -190 AATTCACTAAATTTTTTAGGGGAAGAACAG 19 97 1 ATTTTTTAGG 0.470565 -151 AAGTGCGGTGATTTTTTACCTGATTTTCCT 22 89 1 ATTTTTTACC 0.773593 -103 AAGTACGGCTATTTTTTACCTGCAATTCCC 25 44 0 ATTTTTTACC 0.773593 -52 ACCTAACTAAATTTATTAACTTTACAAGGA 28 18 0 ATTTATTAAC 0.649904 -248 TTTATTTTACATTTATTGACTGAGCTTTCT 29 66 0 ATTTATTGAC 0.808507 -110 GAGTAATTCAATTTTTTAGCAACTTACAGG 30 124 1 ATTTTTTAGC 0.808879 -26 AAAACACAATGTTTTTTGACCGCAGTTTTC 33 16 0 GTTTTTTGAC 0.834871 -47 AAAACATTGTGTTTTATGACCGCACTTTAA 33 31 1 GTTTTATGAC 0.276737 -32 ATTTTAGAAGATTTTTTGAGATAAAGATAG 34 180 0 ATTTTTTGAG 0.689684 -120 TTCGCCACGCATTTTTTGCCTAATTTCGCT 35 153 1 ATTTTTTGCC 0.88599 -132 ********** Masking position 4 Map Score: 13.5148 Number of sites scoring better than the average of aligned sites = 343 Number in coding regions = 267 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 13 TTTAACGGTTCCCCTCTTTCATAAGA 21 6 1 CGTTCCCCTC 0.970756 -74 TTCCTTTGTTTTATCCCCCTCTTATGAAAGA 21 25 0 TATCCCCCTC 0.924845 -55 TTTATCTAACTATCCCCCTCTTTACAAAAG 25 10 1 CATCCCCCTC 0.987585 -86 AGTAAATCTCCCCTACCCCTCTTTGCTAAAG 27 56 1 CCTACCCCTC 0.977082 -245 ATTTATTCAAGAATTCCCCTCTTTAGCAAAG 27 76 0 GATTCCCCTC 0.94412 -225 CTCCAAAGATCCAATCCCCTCTTTAGCAAAG 27 199 1 CAATCCCCTC 0.938642 -102 GCCAAATCGCCCCTACCCCTCTTTGCTAAAG 27 219 0 CCTACCCCTC 0.977082 -82 * ********* Masking position 10 Map Score: 2.66144 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 3 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 14 ACGGTTAGACAATTTTTTTAAATCTGTAATTGA 1 145 0 AATTTTTAAT 0.520867 -156 ATTTTTAACGAATTTTGAGAAATTT 6 20 1 AATTTTGAAT 0.83202 -15 CGCTCCAACTAAATTTGAGTATTATGTTATGCC 7 147 0 AAATTTGATT 0.782719 -76 TAAATTACTTAAATTTGTCAATTTGTAGAGCAA 7 184 0 AAATTTGATT 0.782721 -39 TAATGCTCACAAATTTTAGCATTTTTTGGCTAA 10 41 0 AAATTTTATT 0.438384 -106 AACTCAATATTTTGTGAAATTTAATAAAAT 11 8 1 TATTTTGAAT 0.520387 -185 AACAAAAAAGAATTTTGGCAAATGAAGTGATAA 11 59 0 AATTTTGAAT 0.833844 -134 ATGTCGGACTTATTTTTATCATT 16 265 1 TATTTTTATT 0.438408 -13 TCCCCTAAAAAATTTAGTGAATTTTTACCGCTC 19 87 0 AATTTAGATT 0.5565 -161 AAAATTGGCTTATTTTGAATATTCCTGTTCTTC 19 118 0 TATTTTGATT 0.782664 -130 AGTATTTTTCAATTTTAATTATTGTTTAACTAC 23 33 1 AATTTTAATT 0.658558 -79 CTTATTTAAAAATTCTGTAGATTTAAATTCTTA 27 269 0 AATTCTGATT 0.650017 -32 TCAAGTAAGTAATTTTGAATATTTAGGTAGATT 28 140 0 AATTTTGATT 0.939038 -126 GAGCTTTCTTATTTTTGTAAATTATGAAACGTA 29 42 0 ATTTTTGATT 0.554474 -134 ATGTTAAAATAATTTTACTGATTTTGTGATCTA 29 116 1 AATTTTAATT 0.659234 -60 ATAGAGGGTAAATTTTGACGATTGATTAAAAAA 31 59 0 AATTTTGATT 0.942892 -132 TGATAGAAAGAATTTTTTTGATTTCAGTAAAAA 31 100 1 AATTTTTATT 0.782892 -91 ACATTTAACAAATCTTGTAAATTTTAGAAGATT 34 197 0 AATCTTGATT 0.639248 -103 ******* *** Masking position 13 Map Score: 8.05668 Number of sites scoring better than the average of aligned sites = 319 Number in coding regions = 251 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 15 CTTTAATCACGAGATGGATT 10 137 1 GAGATGGATT 0.864226 -10 ACCTTGTGTAAAGATGAAATTATCATCTCT 12 55 0 AAGATGAAAT 0.780527 -61 TCTTTCGCGAAAGATCAATTTTCATTAAAA 15 68 1 AAGATCAATT 0.767074 -91 CTTCGTATTGAAGATGGATTTTTTTA 16 7 0 AAGATGGATT 0.953888 -271 CTTCAATACGAAGATGGATTTTTTGTTTAT 16 24 1 AAGATGGATT 0.953888 -254 CTTTTGTTTAAAGATGAATTAAAACGGCGT 23 84 0 AAGATGAATT 0.944843 -28 CCATATCATTATGATGAATTAATTTCATTT 26 12 1 ATGATGAATT 0.780527 -112 ********** Masking position 4 Map Score: 1.39395 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 32 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555