AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00300_hinf_reg_300.orf -o00300_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: HI0102 27 succinyl-diaminopimelate desuccinylase (dapE) Input sequences: #1 HI0089 300 aspartokinase I / homoserine dehydrogenase I (thrA) #2 HI0103 78 conserved hypothetical protein #3 HI0104 216 heat shock protein (htpG) #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 HI0255 100 dihydrodipicolinate synthetase (dapA) #8 HI0301 300 hemolysin, putative #9 HI0646 158 aspartate-semialdehyde dehydrogenase (asd) #10 HI0647 277 transport protein, putative #11 HI0648 241 modulator of drug activity B (mdaB) #12 HI0652 62 3-deoxy-d-manno-octulosonic-acid transferase (kdtA) #13 HI0727 260 diaminopimelate decarboxylase (lysA) #14 HI0749 248 lexA repressor (lexA) #15 HI0750 143 diaminopimelate epimerase (dapF) #16 HI0836 181 lysyl-tRNA synthetase analog (genX) #17 HI0916 107 outer membrane protein, putative #18 HI0920 248 conserved hypothetical protein #19 HI0949 300 aminotransferase #20 HI1126.1 181 H. influenzae predicted coding region HI1126.1 #21 HI1129 201 conserved hypothetical protein #22 HI1130 30 conserved hypothetical protein #23 HI1166 87 histidinol-phosphate aminotransferase (hisH) #24 HI1167 190 phosphoserine aminotransferase (serC) #25 HI1211 300 lysyl-tRNA synthetase (lysU) #26 HI1303 147 riboflavin synthase, beta chain (ribH) #27 HI1527 84 lipid A biosynthesis lauroyl acyltransferase (htrB) #28 HI1634 274 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase (dapD) Motif number 1 GCGTAAAGAAATACCGAAATTTCCCGAGCTTG 1 76 0 AACCGAATTT 0.917018 -225 CAATGAAAAATAACCGCACTTTATCCGTAATC 1 130 1 TACCGCATTT 0.996533 -171 CAAGGAATTTAAACCGCACTTTAAATGAAATA 3 109 0 AACCGCATTT 0.982071 -108 TTGTGTTTTTTTACCGCACTTTTCCTCTTAAA 3 138 1 TACCGCATTT 0.996534 -79 TAATTAATTTTAACCGCACTTTTGCGCGCTTT 6 16 0 TACCGCATTT 0.996533 -31 TGTGTATTTTTAACCGCACTTTAGGTTTAAAC 8 173 1 TACCGCATTT 0.996533 -128 CAATAAAAAATAACCGCACATTGGGTTTAAAC 8 197 0 TACCGCAATT 0.948831 -104 TCTTTTAAATTAACCACACTTTTTTATTTAAT 9 35 1 TACCACATTT 0.977866 -124 GAACGAAAAATGACCGCACTTTTAAAATAAAA 11 41 0 TACCGCATTT 0.996534 -201 CACCAATTTTTTACCGAATTTTCAATTCCAGC 11 79 1 TACCGAATTT 0.982991 -163 TTTGCTATACTAGCCGAAATTTTTTTAAGTAT 12 26 1 TGCCGAATTT 0.967746 -37 TTTTTAAGTATAACCGAATTTCATTT 12 47 1 TACCGAATTC 0.846736 -16 GCTTTATAATTTGCCGCATTTTATCAGATTTA 13 25 0 TGCCGCATTT 0.993345 -236 TCACATTTTGTCGCCAAATTTTCTAAATTAGT 14 144 0 TGCCAAATTT 0.821772 -105 CCGTAAATTTTTACCGCACTTTATTCATTCCT 15 21 0 TACCGCATTT 0.996534 -123 TACGGTATTTTTACCGCACTTTGCTTATACTA 15 48 1 TACCGCATTT 0.996534 -96 CCTTAAATTTTAACCGCACTTTTGCAGCATTT 18 18 1 TACCGCATTT 0.996533 -231 ACGGTATTCTATGCCACATTTTCTATTGTCAA 18 49 0 AGCCACATTT 0.814333 -200 AACTAAAAAACCACCGCACTTTTTATTTCTCT 18 103 0 CACCGCATTT 0.969921 -146 TGTGGTAAAATCGCCACAATTTTGGTTATTCA 27 28 0 TGCCACATTT 0.958224 -57 CTTTTTATTATCACCGCAGTTTTGTTTCTACA 28 246 1 TACCGCATTT 0.996532 -29 * ****** *** Masking position 11 Map Score: 60.9947 Number of sites scoring better than the average of aligned sites = 1155 Number in coding regions = 732 Number in noncoding regions = 423 Number of orfs with sites within 600 bp upstream = 289 Fraction of orfs with sites within 600 bp upstream = 0.0464182 Motif number 2 TTACGGATAAAGTGCGGTTATTTTTCATTGT 1 129 0 AGTGCGGTAT 0.996456 -172 TTTCATTTAAAGTGCGGTTTAAATTCCTTGT 3 111 1 AGTGCGGTTA 0.980757 -106 TAAGAGGAAAAGTGCGGTAAAAAAACACAAG 3 137 0 AGTGCGGTAA 0.997732 -80 AGCGCGCAAAAGTGCGGTTAAAATTAATTAC 6 18 1 AGTGCGGTAA 0.997733 -29 TTAAACCTAAAGTGCGGTTAAAAATACACAA 8 172 0 AGTGCGGTAA 0.997733 -129 TTAAACCCAATGTGCGGTTATTTTTTATTGA 8 199 1 TGTGCGGTAT 0.96766 -102 TAAATAAAAAAGTGTGGTTAATTTAAAAGAA 9 34 0 AGTGTGGTAA 0.966647 -125 TTATTTTAAAAGTGCGGTCATTTTTCGTTCG 11 43 1 AGTGCGGTAT 0.996456 -199 GAATGAATAAAGTGCGGTAAAAATTTACGGT 15 23 1 AGTGCGGTAA 0.997732 -121 GTATAAGCAAAGTGCGGTAAAAATACCGTAA 15 47 0 AGTGCGGTAA 0.997732 -97 ATGCTGCAAAAGTGCGGTTAAAATTTAAGGT 18 17 0 AGTGCGGTAA 0.997733 -232 AGAAATAAAAAGTGCGGTGGTTTTTTAGTTG 18 105 1 AGTGCGGTGT 0.979703 -144 TAGAAACAAAACTGCGGTGATAATAAAAAGT 28 245 0 ACTGCGGTAT 0.964848 -30 ******** ** Masking position 8 Map Score: 40.2886 Number of sites scoring better than the average of aligned sites = 842 Number in coding regions = 496 Number in noncoding regions = 346 Number of orfs with sites within 600 bp upstream = 239 Fraction of orfs with sites within 600 bp upstream = 0.0383874 Motif number 3 CTTAGTCAATAAATTTCGTGTAAACTAACCG 1 8 0 AAATTTTAAA 0.879831 -293 TTGACTAAGAAAATTTCTGAAAAATTTGTCACTT 1 33 1 AAATTTAAAA 0.957165 -268 TTGTGTTTTTAAATTTATAAAAAAACCCGCTATT 1 259 0 AAATTTAAAA 0.957165 -42 GAAAAGAGGAAAATCAATAAAAAATAACCGCACA 8 209 0 AAATCAAAAA 0.656934 -92 AAAATTATCATATTTTAGAAAAAATCGCAAAACG 8 244 0 TATTTTAAAA 0.750675 -57 GATTAAATTAAATTTTCTTTTAAATTAACCACAC 9 20 1 AATTTTTAAA 0.818924 -139 TTCGCGAAAGAAATTAAATAAAAAAGTGTGGTTA 9 45 0 AAATTAAAAA 0.784563 -114 GCGAAAGATCAATTTTCATTAAAAATACTTGATT 9 74 1 AATTTTAAAA 0.932445 -85 CTTGGGGTTGAATTTTGCATAAAATAACCATTCT 10 117 1 AATTTTAAAA 0.932445 -161 TTAAAATAAAAAATCGGCAGAAAATTTCTTGCCG 11 18 0 AAATCGAAAA 0.853859 -224 AAATTGGTGGAAATCGAACGAAAAATGACCGCAC 11 54 0 AAATCGAAAA 0.853859 -188 TGGAATTGAAAATTCGGTAAAAAATTGGTGGAAA 11 75 0 AATTCGAAAA 0.783032 -167 ATACTTTTAAAAATTAACGTAAAAAGGCATA 11 221 1 AAATTAAAAA 0.784563 -21 AGGTTCTTTATATTTTCCTGAAAAAGATCAAGCT 13 175 1 TATTTTAAAA 0.750906 -86 CAAAAATTGAAAATTTATTGTAAAAAACAACTAA 18 129 0 AAATTTTAAA 0.879831 -120 GACCTCTATAAATTTGGTGGTAAACTATATCATA 18 208 0 AATTTGTAAA 0.692204 -41 TACAAGTCACAAATCTTATAAAAATCTTTAAATT 20 83 1 AAATCTAAAA 0.921567 -99 CGTCAAATCAAAATTGAATTTAAAGATTTTTATA 20 99 0 AAATTGTAAA 0.78452 -83 TCAATAAAATTTTATGAAAAAAGCCGTTTG 21 7 1 AAATTTAAAA 0.957165 -195 ACGGCTTTTTTATTTTGATAAAAATCAGTTGCTT 21 55 1 TATTTTAAAA 0.750887 -147 AAATCTCTAAAAATCTCCACAAAACACCACTTTT 21 146 0 AAATCTAAAA 0.921567 -56 AAATTTAAGATAAAAGTACTACAT 22 17 0 AAATTTTAAA 0.879831 -14 TACTACGCCCAAATTTATTTAAAAATACATACTA 23 36 1 AAATTTAAAA 0.957165 -52 AAGACATCATTATTTTCATAAAAAGCAAGGAAAT 24 164 1 TATTTTAAAA 0.750887 -27 AATTTCTTATTAATTTATAAAAAAGGTAAACAAT 25 277 1 TAATTTAAAA 0.829955 -24 TAATGAAGGAAATTTTCCATAAAAATATAGTGTT 26 34 1 AATTTTAAAA 0.932445 -114 ATGAACAATAAAATCGCCTTAAAAATGAGTCCTA 26 78 1 AAATCGAAAA 0.853859 -70 ACCACAACTCAAATTTACGATAAACTACGCCCCT 27 54 1 AAATTTTAAA 0.879831 -31 CTTTATTGCAAATTTTTTATAAAAAGAAGTGATT 28 68 1 AATTTTAAAA 0.932445 -207 ****** **** Masking position 4 Map Score: 38.2358 Number of sites scoring better than the average of aligned sites = 439 Number in coding regions = 278 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 4 TGTCAAACAGAAAGTGACAAATTTTTCAGAAATTT 1 43 0 AAAAAATTTT 0.887138 -258 TTATAAATTTAAAAACACAATATCTAGGAGAACCA 1 273 1 AAAAATATCT 0.502344 -28 ACTTTAAATGAAATAAAAAATTTCTTATCCCCCTT 3 89 0 AAAAATTTCT 0.796534 -128 TGCGGTAAAAAAACACAAGGAATTTAAACCGCACT 3 121 0 AAAAGAATTT 0.680822 -96 AATAAAATGTAATTAATTTTAACCGCACTT 6 27 0 AATAAATTTT 0.761792 -20 AAACTCCTTTAATGAAAAAAAATTTGCAAATTAAC 7 14 1 AATAAAATTT 0.452615 -87 AAAAATTTGCAAATTAACGTTATTTTAGCGACTAT 7 31 1 AAAATTATTT 0.556605 -70 TCATATAAACAAAATAAGAATATTTTGTTGTCTAG 8 115 1 AAAAATATTT 0.730912 -186 GTGCGGTTAAAAATACACAATTTTTACGGAGAGGG 8 157 0 AAAAATTTTT 0.896936 -144 TTTTTTCTAAAATATGATAATTTTTCGCCGTCAAT 8 254 1 AATAATTTTT 0.826644 -47 AGCGTTAGAAAATCAAGTATTTTTAATGAAAATT 9 84 0 AAAAATTTTT 0.904831 -75 AAAGACTTGGAAAGGTAAAGATTTTAAGCTAAGTG 10 213 1 AAAAGATTTT 0.892361 -65 AACTTATAACAAAGAGAAAATTTATT 14 2 0 AAAAATTTAT 0.710655 -247 GCAGTTTGTGAATAGAACTATTTTTAGCCCTTTGG 14 62 1 AATAATTTTT 0.826132 -187 TATCGTCCAAAAACTCAAATATTTTAACACATCCG 14 103 1 AAAATATTTT 0.767898 -146 AGTGCGGTAAAAATTTACGGTATTTTTACCGCACT 15 33 1 AAAAGTATTT 0.74821 -111 TCCTTTGTATAAATTCAAGATTTTTGCATTATAAA 15 112 0 AAAAATTTTT 0.904638 -32 CTCTCAACTCAATCTTAGCTTTTTTGAGGTAGATC 16 142 0 AATATTTTTT 0.668194 -40 TAAATTGAACTTTTTTCTTCATCAGA 17 2 1 AAAATTTTTT 0.831492 -106 TGTTCTGCAAAAATTGAAAATTTATTGTAAAAAAC 18 135 0 AAAAATTTAT 0.710653 -114 GGCTAAATAAAAAGCAAACGTTTCTAATAAGAACA 19 12 0 AAAAGTTTCT 0.805109 -289 AAACGGGGACAATTGTATATTTTTTTTGCAATATG 19 78 0 AATATTTTTT 0.668196 -223 GCCTTGCGATAAATTTACTGTTTATAAAACAGACA 19 230 0 AAAAGTTTAT 0.709154 -71 ATCAAAATTGAATTTAAAGATTTTTATAAGATTTG 20 92 0 AATAATTTTT 0.826598 -90 AAAATAAAGTAAAAGTATTTATATGCCCTA 20 162 0 AAAAGTATTT 0.760997 -20 ATTCCACATTAAAGCAACTGATTTTTATCAAAATA 21 65 0 AAAAGATTTT 0.891674 -137 ACGCCTTAAAAATTGAACTTATTTTTAGAAAATCT 21 174 0 AATATATTTT 0.574796 -28 TTTTTACTGAAATCAAAAAAATTCTTTCTATCATT 24 98 0 AATAAATTCT 0.517231 -93 GATTTCAGTAAAAAGCATTGATTATCGATTTTTGT 24 119 1 AAAAGATTAT 0.633981 -72 GTAAACAAAGAAAATAAAAATTTCTTATTAATTTA 25 259 1 AAAAATTTCT 0.796409 -42 TTGGTTATTCAAATAGAGAGATTTTAAA 27 4 0 AAAAGATTTT 0.891952 -81 AAACCTTTATAATAGGAAAAATTTTTAGGGATTTA 28 16 0 AATAAATTTT 0.762035 -259 ATTTTTTATAAAAAGAAGTGATTTTTTCGTATTAT 28 79 1 AAAAGATTTT 0.83669 -196 TGAGGAGAACAAAATGAGCGATTTTGGTTATGCAA 28 143 1 AAAAGATTTT 0.891276 -132 TCTTTTAATCAAACCAACTTTTTATTATCACCGCA 28 229 1 AAAATTTTAT 0.509127 -46 *** * ****** Masking position 7 Map Score: 34.8538 Number of sites scoring better than the average of aligned sites = 712 Number in coding regions = 461 Number in noncoding regions = 251 Number of orfs with sites within 600 bp upstream = 185 Fraction of orfs with sites within 600 bp upstream = 0.0297141 Motif number 5 TGAGGATTTTTCTTTTTTAGGTGAAAT 2 62 1 TCTTTTTTAG 0.595231 -17 TTGAAATCTTTCTTTTTATTCTTATATCTG 3 176 1 TCTTTTTATT 0.750072 -41 ATCTTTGCCCTCTTTTTACGAGATCAATTC 8 34 1 TCTTTTTACG 0.546382 -267 AATGTGCGGTTATTTTTTATTGATTTTCCT 8 207 1 TATTTTTTAT 0.689525 -94 CGCGTTTTGCGATTTTTTCTAAAATATGAT 8 242 1 GATTTTTTCT 0.789076 -59 AAAATCAAGTATTTTTAATGAAAATTGAT 9 81 0 TATTTTTAAT 0.649982 -78 ATTGAAGATGGATTTTTTTA 10 1 0 GATTTTTTTA 0.748701 -277 TACGAAGATGGATTTTTTGTTTATTTCGTT 10 30 1 GATTTTTTGT 0.75826 -248 ATTTTCTGCCGATTTTTTATTTTAAAAGTG 11 27 1 GATTTTTTAT 0.792489 -215 TTCACAAACTGCTTTTTAAACGTCTATAAG 14 44 0 GCTTTTTAAA 0.738502 -205 TTGCAACTGTTATTTTTTAAATCTGTGTAT 14 180 0 TATTTTTTAA 0.592015 -69 TTAGGGGATTTATTTTTACTTTCTATTGAT 16 22 0 TATTTTTACT 0.645273 -160 CTCAATCTTAGCTTTTTTGAGGTAGATCAC 16 140 0 GCTTTTTTGA 0.735032 -42 TATTTTTATTATTGAGAGAC 18 239 0 TATTTTTATT 0.689173 -10 AGAAACGTTTGCTTTTTATTTAGCCGTTTG 19 22 1 GCTTTTTATT 0.837683 -279 GACAATTGTATATTTTTTTTGCAATATGAA 19 76 0 TATTTTTTTT 0.726154 -225 AAGCGTTTCAGCTTTTTTGTTTTTACCCTA 19 168 0 GCTTTTTTGT 0.809367 -133 AAGCTGAAACGCTTTTTTTAATAAGTAGCG 19 184 1 GCTTTTTTTA 0.801299 -117 GCACCCGACTTATTTTTTTTCACCTCTTTT 19 263 1 TATTTTTTTT 0.726154 -38 TGAATTTAAAGATTTTTATAAGATTTGTGA 20 89 0 GATTTTTATA 0.713564 -93 AATTCAAACGGCTTTTTTCATAAAATTTTA 21 15 0 GCTTTTTTCA 0.767903 -187 TATTCAAACGGCTTTTTTATTTTGATAAAA 21 48 1 GCTTTTTTAT 0.837907 -154 GTTTTGTGGAGATTTTTAGAGATTTTCTAA 21 155 1 GATTTTTAGA 0.631493 -47 AAATTGAACTTATTTTTAGAAAATCTCTAA 21 170 0 TATTTTTAGA 0.499132 -32 GGTTAGTATGTATTTTTAAATAAATTTGGG 23 43 0 TATTTTTAAA 0.54819 -45 CCGTAATTTAGCTTTTTTTTAATCAATCGT 24 45 1 GCTTTTTTTT 0.86057 -146 GATAATCAATGCTTTTTACTGAAATCAAAA 24 115 0 GCTTTTTACT 0.808944 -76 AATAATGATGTCTTTTTTATCACTACAAAA 24 148 0 TCTTTTTTAT 0.75038 -43 GTATTTCCTTGCTTTTTATGAAAATAATGA 24 170 0 GCTTTTTATG 0.716281 -21 ACCAACACTATATTTTTATGGAAAATTTCC 26 41 0 TATTTTTATG 0.520302 -107 AAAAATCACTTCTTTTTATAAAAAATTTGC 28 75 0 TCTTTTTATA 0.662263 -200 AAAAAGAAGTGATTTTTTCGTATTATTCTT 28 88 1 GATTTTTTCG 0.646654 -187 ATGTCTGCGTTATTTTTTATGAGGAGAACA 28 124 1 TATTTTTTAT 0.689525 -151 ********** Masking position 5 Map Score: 23.5007 Number of sites scoring better than the average of aligned sites = 950 Number in coding regions = 685 Number in noncoding regions = 265 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 6 TGTGATAAGGATCTTTGCCCTCTTTTTACGAGAT 8 24 1 ATTTTGCCTT 0.908421 -277 CGGCAGAAAATTTCTTGCCGATTTTTA 11 4 0 TTCTTGCCTT 0.884528 -238 CGGCAAGAAATTTTCTGCCGATTTTTTATTTTAA 11 18 1 TTTCTGCCTT 0.978457 -224 TTTCCACCAATTTTTTACCGAATTTTCAATTCCA 11 75 1 TTTTTACCTT 0.86004 -167 AAAAGTATATTTGTCTGCCACGTTATTTCTAGAC 11 195 0 TTTCTGCCTT 0.978457 -47 AAAGGCTTTATAATTTGCCGCATTTTATCAGATT 13 27 0 TATTTGCCTT 0.837883 -234 GTTGTGTGCCTGTTTTAGTTATTTT 13 246 0 TTTGTGCCTT 0.928056 -15 CTAGAGTTCTTTATTTGCCATGATTTTTGCTGCT 15 77 1 TTTTTGCCAT 0.837883 -67 AAAAACAACGTTCTCTGCCTAATTTAATTGGGCA 17 41 1 TTTCTGCCTT 0.978457 -67 GTTTAATATTTTCTCTGCCCAATTAAATTAGGCA 17 56 0 TTTCTGCCTT 0.978457 -52 TTTTACGGTATTCTATGCCACATTTTCTATTGTC 18 51 0 TTTATGCCTT 0.896945 -198 CTCCCTATTAATTTTTGCCATTTTACGGTATTCT 18 71 0 ATTTTGCCTT 0.90842 -178 ATTGTTTACCTTTTTTATAAATTAA 25 286 0 TTTTTACCTT 0.86004 -15 ** ****** ** Masking position 6 Map Score: 16.5331 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 92 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 7 TGAAGTAGCATAAGGGTTAAAATCCTCAGTCT 2 22 1 TAAGGTAAAA 0.594746 -57 ATTTCACCTAAAAAAGAAAAATCCTCAATC 2 59 0 TAAAAGAAAA 0.718787 -20 CAAGAGGAATTTAAGAGGAAAAGTGCGGTAAA 3 147 0 TTAGAGAAAA 0.529855 -70 CGTCACAGATATAAGAATAAAAAGAAAGATTT 3 179 0 ATAGATAAAA 0.691828 -38 TTAGCGACTATAACAAGTGAAACCAAATAATA 7 55 1 TAAAATGAAA 0.67812 -46 AAACCAAATAATAAAATTAAAAACCGACGGAG 7 74 1 ATAAATAAAA 0.55903 -27 TATTTTGTTTATATGACGAAAAGTATCTATGT 8 99 0 ATAGAGAAAA 0.732223 -202 GCAAAACGCGAAAAGAGGAAAATCAATAAAAA 8 220 0 AAAGAGAAAA 0.916543 -81 TATAGCAAAAAAAGGATTGAAAAT 12 3 0 AAAGATGAAA 0.900516 -60 AGTGAGAAAGAAAAAATGAAAAAATTACTATT 13 92 1 AAAAAGAAAA 0.861144 -169 ATCATTCCCAAAATAACTAAAACAGGCACACA 13 237 1 AAAAATAAAA 0.835837 -24 TAAAAACACCAAAGGGCTAAAAATAGTTCTAT 14 73 0 AAAGGTAAAA 0.780741 -176 GAATTTATACAAAGGATGGAAAA 15 131 1 AAAGAGGAAA 0.916844 -13 NTTTTATGTCTAAAGATGGAAANGTATCGGAT 16 105 1 TAAGAGGAAA 0.819632 -77 TTATTGTAAAAAACAACTAAAAAACCACCGCA 18 117 0 AAAAATAAAA 0.835837 -132 GGTAAAAACAAAAAAGCTGAAACGCTTTTTTT 19 171 1 AAAAGTGAAA 0.668738 -130 AAACCTTCTAAAAGAGGTGAAAAAAAATAAGT 19 270 0 AAAAGTGAAA 0.668738 -31 ACTCCCTTTAAAATAAATAAAATGACTGTGCC 24 15 1 AAAAATAAAA 0.835837 -176 CTCCTAAAGTAAACAAAGAAAATAAAAATTTC 25 251 1 AAAAAGAAAA 0.861144 -50 TAGTTTACCTTAATGAAGGAAATTTTCCATAA 26 24 1 TAAGAGGAAA 0.819632 -124 TGGTTTGATTAAAAGATTGAAAGTGCAAGCCC 28 213 0 AAAGATGAAA 0.900516 -62 *** ** ***** Masking position 3 Map Score: 16.053 Number of sites scoring better than the average of aligned sites = 594 Number in coding regions = 431 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 163 Fraction of orfs with sites within 600 bp upstream = 0.0261805 Motif number 8 TAATCGTGCTAATGATTACGGATAAAGTGCGGT 1 142 0 AATGTTAGGT 0.811573 -159 AAAAATACACAATTTTTACGGAGAGGGGAAAAT 8 151 0 AATTTTAGGG 0.915937 -150 AAATGGCAAAAATTAATAGGGAGAGAAATAAAA 18 82 1 AATTATAGGG 0.861391 -167 TATTTATTAGCATTTTAATGGATGTTTTAGATT 20 38 1 CATTTAAGGT 0.75199 -144 TTGAATAAACAATTCAAACGGCTTTTTTCATAA 21 22 0 AATTAAAGGT 0.779637 -180 TTGAATTGTTTATTCAAACGGCTTTTTTATTTT 21 38 1 TATTAAAGGT 0.719887 -164 AAATAAGTTCAATTTTTAAGGCGTAAT 21 185 1 AATTTTAGGG 0.915937 -17 TATTTATAAATATTGATATGGGTTAGTATGTAT 23 60 0 TATTATAGGT 0.860095 -28 ACCAACACTATATTTTTATGGAAAATTTCCTTC 26 38 0 TATTTTAGGA 0.602648 -110 ATTTAGGACTCATTTTTAAGGCGATTTTATTGT 26 82 0 CATTTTAGGG 0.841921 -66 GTATATTCAATATTAATAAGGCTTTACCCTATT 26 117 0 TATTATAGGT 0.860095 -31 TAATAGGAAAAATTTTTAGGGATTTAAATAT 28 9 0 AATTTTAGGT 0.936863 -266 AAATTTTTCCTATTATAAAGGTTTGTTGAGAAT 28 27 1 TATTTAAGGT 0.818378 -248 TTGGTTATGCAATGATTATGGTTGTTTTTAGTA 28 166 1 AATGTTAGGT 0.811572 -109 **** *** ** * Masking position 8 Map Score: 6.55273 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 85 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 AAGATACAGAAAACCCGCGATTCAACTGAATAGC 1 231 1 AAACCCTTCA 0.96727 -70 ATTTATAAAAAAACCCGCTATTCAGTTGAATCGC 1 247 0 AAACCCTTCA 0.96727 -54 ATAAGGGTTAAAATCCTCAGTCTGATTAGATTGA 2 31 1 AAACCCTCTG 0.843554 -48 TAAAAAAGAAAAATCCTCAATCTAATCAGACTGA 2 47 0 AAACCCTCTA 0.921364 -32 TCACAATCAAAAATCCATTATTCACAAGTTATCC 8 62 1 AAACCTTTCA 0.92153 -239 TAAAAAAATCCATCTTCAATACGAAGATG 10 6 1 AAACCTTCAA 0.823197 -272 GCGTGGGCTTAAGCCCACCCTACATTGGCTACAT 11 113 0 AAGCCCTACA 0.758476 -129 GGCAAATTATAAAGCCTTTCTCAAGCTTGTGAAA 13 42 1 AAACCTTCAA 0.823197 -219 ACTTATCGGTAAATCCGCCTTTCACAAGCTTGAG 13 61 0 AAACCCTTCA 0.96727 -200 AGAAAATATTAAACCCATCATTTAATTAAGGATA 17 76 1 AAACCTTTTA 0.74418 -32 ACCCTACATCAAAACCTGTTTCCAACCTAGCCCG 19 120 1 AAACCGTCCA 0.872982 -181 ACTGGCGTAGAAAACCGTAATACGCAAGCCGTAT 25 74 1 AAACCTTACG 0.664256 -227 AAATTTCTACAAGCCCGCTTTTAAACTCGCTTCA 25 133 0 AAGCCCTTAA 0.679988 -168 TATATTATCGAAAGCCCCCTTCCGTACGTTCGCG 25 197 0 AAACCCTCCG 0.956078 -104 *** ** * **** Masking position 2 Map Score: 8.68038 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 76 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 10 TTTTGAAGTTTGATGTGATAAGGATCT 8 8 1 GTTTGATGTG 0.939078 -293 AATAAGAATATTTTGTTGTCTAGAATTTTC 8 127 1 TTTTGTTGTC 0.777735 -174 ATTGATTTGTGTTTGATGTCTTATTGACGG 8 281 0 GTTTGATGTC 0.92148 -20 TGTTTCCTTAGTTTGTTGTGCTTGAATAGC 9 136 0 GTTTGTTGTG 0.972553 -23 AGATTATTGAGTTTGTTGAGCTTGATCTTT 13 197 0 GTTTGTTGAG 0.939078 -64 TATTATAAAGGTTTGTTGAGAATTTAGTCA 28 37 1 GTTTGTTGAG 0.939078 -238 TTTTTAGTATGTCTGTTGTCGTGGGGCTTG 28 190 1 GTCTGTTGTC 0.89248 -85 ********** Masking position 4 Map Score: 3.58844 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 25 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 11 AATTGGTTCTCCTAGATATTGTGT 1 287 0 TTGGTTTCTA 0.940902 -14 ATACTCTAGGTTAGTTCTTCAATAGGACTGAA 5 29 1 TTAGTTTCAA 0.77522 -56 TTAAAAATACTTGATTTTSCTAACGCTATCTT 9 92 1 TTGATTTCTA 0.711341 -67 TTTGTAAGCCTTGGTTGCCCAAAAAACTTGGT 10 78 0 TTGGTTCCAA 0.879118 -200 TTACCGCACTTTGCTTATACTAGAGTTCTTTA 15 58 1 TTGCTTTCTA 0.784735 -86 CAATTGTATATTTTTTTTGCAATATGAAAAGT 19 72 0 TTTTTTTCAA 0.574123 -229 GCCGTTTGAATTGTTTATTCAAACGGCTTTTT 21 33 1 TTGTTTTCAA 0.927187 -169 CGCCACAATTTTGGTTATTCAAATAGAGAGAT 27 17 0 TTGGTTTCAA 0.96712 -68 ATGAGCGATTTTGGTTATGCAATGATTATGGT 28 156 1 TTGGTTTCAA 0.964634 -119 CACCGCAGTTTTGTTTCTACAAAGTGCG 28 257 1 TTGTTTTCAA 0.931824 -18 ****** * *** Masking position 6 Map Score: 4.56088 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 125 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 12 AATTAACGTTATTTTAGCGACTATAACAAGTGAAA 7 42 1 ATTAGCATTA 0.957941 -59 CGAATTTTCAATTCCAGCTAATGTAGCCAATGTAG 11 93 1 ATTAGCATTA 0.957941 -149 ACTTAAAAAAATTTCGGCTAGTATAGCAAAAAAAG 12 21 0 ATTGGCATTA 0.973206 -42 TACGCCACATCCTGTAGCGAATATACAAGCTGAAC 13 138 0 CCTAGCATTA 0.753326 -123 CTCCCTATTAATTTTTGCCATTTTACGGTATTCTA 18 70 0 ATTTGCATTA 0.848919 -179 CTTTTCTCCACTTCTGGCAAGTTTATAATTTGTTC 21 116 0 CTTGGCATTA 0.962771 -86 AGATCGATTTATTGAAGCGAGTTTAAAAGCGGGCT 25 121 1 ATTAGCATTA 0.957941 -180 TTAAGGTAAACTATCGGCAATTTTAT 26 2 0 CTAGGCATTA 0.766677 -146 AGGACTCATTTTTAAGGCGATTTTATTGTTCATAA 26 76 0 TTTGGCATTA 0.866827 -72 AATAACCAAAATTGTGGCGATTTTACCACAACTCA 27 30 1 ATTGGCATTA 0.973206 -55 TAACGCAGACATTCTAGCAAGAATAATACGAAAAA 28 101 0 ATTAGCAATA 0.743192 -174 *** *** * * ** Masking position 10 Map Score: 6.6648 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 36 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 13 TCCTGTACCTAGGGTAGTATACTCTA 5 7 1 ACCTAGGGTA 0.984259 -78 TGAAGAACTAACCTAGAGTATACTACCCTA 5 20 0 ACCTAGAGTA 0.890236 -65 ATAGGACTGAACCTAGGATATACTTACCTA 5 50 1 ACCTAGGATA 0.890238 -35 CCACGCGTTTAACTAGGGTTTATTCCCACC 11 141 1 AACTAGGGTT 0.862705 -101 CCAATGGGCAAACTAGGGTAAAAACAAAAA 19 155 1 AACTAGGGTA 0.968024 -146 TAAAACAGACACATAGGGCATTTGACTCGC 19 211 0 ACATAGGGCA 0.839964 -90 GTCCTAAATAAAATAGGGTAAAGCCTTATT 26 106 1 AAATAGGGTA 0.891996 -42 ********** Masking position 5 Map Score: 2.41827 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 17 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 14 TTCATTTGAGATGAAGTAGC 2 1 1 TTCATTTGAG 0.808313 -78 ATTGATTTGTGTTTGATGTCT 8 290 0 TTGATTTGTG 0.940767 -11 TTACTTTCTATTGATTGGAGGATATC 16 7 0 TTGATTGGAG 0.871258 -175 AAAGCTAAGATTGAGTTGAGAGTAGCTCTC 16 155 1 TTGAGTTGAG 0.961497 -27 AACGTTGTTTTTGAGTTCTGATGAAGAAAA 17 23 0 TTGAGTTCTG 0.846338 -85 AAATTCAATTTTGATTTGACGTAATTTGAA 20 112 1 TTGATTTGAC 0.808318 -70 AAGAATTTTTTTGATTTCAGTAAAAAGCAT 24 107 1 TTGATTTCAG 0.900128 -84 TATCGTAAATTTGAGTTGTGGTAAAATCGC 27 46 0 TTGAGTTGTG 0.939642 -39 ********** Masking position 4 Map Score: 1.86016 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 70 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 15 GATAAAACACAATGAAAAATAACCGCACTT 1 121 1 AATGAAAAAT 0.774105 -180 CCGCACTTTAAATGAAATAAAAAATTTCTT 3 98 0 AATGAAATAA 0.688654 -119 AAACTCCTTTAATGAAAAAAAATTTGCAAA 7 14 1 AATGAAAAAA 0.927244 -87 AACGAATCTTAACGAAATAAACAAAAAATC 10 40 0 AACGAAATAA 0.757425 -238 AATGATAAAAATAAGTCCGA 10 268 0 AATGATAAAA 0.538466 -10 GTGGAAATCGAACGAAAAATGACCGCACTT 11 52 0 AACGAAAAAT 0.828697 -190 TTTAAAAATTAACGTAAAAAGGCATA 11 226 1 AACGTAAAAA 0.656897 -16 AGAAAGAAAAAATGAAAAAATTACTATTAA 13 96 1 AATGAAAAAA 0.927244 -165 GATACCAAGGAATGAATAAAGTGCGGTAAA 15 14 1 AATGAATAAA 0.538466 -130 TGCTCTTTATAATGCAAAAATCTTGAATTT 15 107 1 AATGCAAAAA 0.787202 -37 ATTAATTTGTAACGAAAAATGGCACAATGC 16 70 0 AACGAAAAAT 0.828697 -112 TCTTCATCAGAACTCAAAAACAACGTTCTC 17 26 1 AACTCAAAAA 0.359199 -82 TGTAAAAAACAACTAAAAAACCACCGCACT 18 115 0 AACTAAAAAA 0.658838 -134 AATAAAATTTTATGAAAAAAGCCGTTTGAA 21 13 1 TATGAAAAAA 0.688654 -189 GCAAGAATAATACGAAAAAATCACTTCTTT 28 90 0 TACGAAAAAA 0.757425 -185 ********** Masking position 2 Map Score: 7.40417 Number of sites scoring better than the average of aligned sites = 463 Number in coding regions = 371 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829