AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00220_hinf_reg_300.orf -o00220_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 HI0307 65 pyrroline-5-carboxylate reductase (proC) #2 HI0540 75 urease, beta subunit (ureB) #3 HI0541 162 urease, gamma subunit (ureA) #4 HI0591 250 ornithine decarboxylase (speF) #5 HI0592 300 H. influenzae predicted coding region HI0592 #6 HI0596 300 ornithine carbamoyltransferase (arcB) #7 HI0811 134 argininosuccinate lyase (argH) #8 HI0812 21 glucosephosphate uridylyltransferase (galU) #9 HI0813 77 carbon storage regulator (csrA) #10 HI0814 187 alanyl-tRNA synthetase (alaS) #11 HI0815 101 universal stress protein A (uspA) #12 HI0817 170 conserved hypothetical protein #13 HI0819 37 galactokinase (galK) #14 HI0820 207 galactose-1-phosphate uridylyltransferase (galT) #15 HI0900 100 glutamate 5-kinase (gamma-glutamyl kinase) (proB) #16 HI1240 97 conserved hypothetical transmembrane protein #17 HI1723 135 conserved hypothetical protein #18 HI1726 124 phosphoribosylaminoimidazole-succinocarboxamide synthase (purC) #19 HI1727 155 argininosuccinate synthetase (argG) Motif number 1 TGTAAGCCCCTTGAAAGAAAAAAAATCCTCCTTA 3 53 0 TTAAAAAAAA 0.952346 -110 TTACAAAAAATTCTGACAAAATATTTTTCCTATT 3 82 1 TTTAAAATAT 0.878892 -81 AGTCAGCGAATTTTACGTAAAAAATCTAAAATAG 3 111 0 TTTCAAAAAA 0.922427 -52 ATATATTTATTTTAAATTAAATAAGATCAAGTTA 4 104 0 TTAAAAATAA 0.948948 -147 TACTTTAGTTTTTATAATAAAAAACTAGATCGTG 4 141 1 TTAAAAAAAA 0.952312 -110 AATAGATTTATTTAGAATAAAATAACACGATCTA 4 166 0 TTAAAAAATA 0.756341 -85 TGGTTTAAGATTTATATAAAATAGCTTTATTTCT 5 96 1 TTAAAAATAG 0.663418 -205 CAATTTTAAATTTTACATAAAAAATACAAAACCA 5 168 0 TTTCAAAAAA 0.922427 -133 AAGATCACATTTTTTAAAAAATATTATTGACATG 5 211 1 TTTAAAATAT 0.87886 -90 CACATTCCTCTTCATCAAAAATAAACTAAAACAT 6 31 1 TTACAAATAA 0.927864 -270 GTAGATGAATTTAAACGAAAATATGTTTTAGTTT 6 53 0 TTACAAATAT 0.853755 -248 ATATTCTATATTAATAATAAAACAAAAATGGACA 7 51 0 TTAAAAAACA 0.82996 -84 GAATATTGCTTTATGAATAAATATGCACAATAAT 7 79 1 TTTAAAATAT 0.878891 -56 TTATTTCAGATTATTCAAAAAACAATTTCTTGTT 10 13 0 TTTCAAAACA 0.743932 -175 GCCATTATTTATAATAAAAATGTCATTACAA 12 8 1 TTAAAAAAAT 0.900694 -163 GTGTAAACCTTTGTAAATAAAAAAGCCATCGCTT 12 118 0 TTTAAAAAAA 0.945028 -53 ATCTTATATTTTGATCATAAATAATTTACGATAA 14 37 1 TTACAAATAA 0.927864 -171 ACCGTGATCTTTGTCACAAAATAAGAAAATAAGC 14 120 0 TTTAAAATAA 0.941141 -88 ATTACATTAATTTATACTAAATTATTGTAAATAA 14 154 0 TTAAAAATTA 0.742744 -54 GGCATTAACGTTATCACTAAATCAATGAAAAATC 15 53 0 TTTAAAATCA 0.796142 -48 TAATGCGCCATTATGCTAAAAATTCATTAAATTT 16 31 1 TTTCAAAATT 0.456121 -67 TATAGCACGATTTCTAGGAAAAAACTGGATTGCA 17 46 1 TTCAAAAAAA 0.73054 -90 TTGCTATTTTTTAAAAAGAAATAAAAATCCTCTG 18 77 0 TTAAAAATAA 0.948948 -48 TTTTAAATCAAATAAAGCAAACGTT 18 110 0 TTAAAAATAA 0.948948 -15 TTATTTAGCTTTGTGCATAAAAAATCCTAATTT 19 10 0 TTTCAAAAAA 0.922459 -146 GTTTTGTGCATTAAAAGCAAAAATCTTTATTTAG 19 36 0 TTAAAAAAAT 0.900695 -120 TAATCGATTTTTGTGAATAAAAATTCTATAGAGT 19 98 0 TTTAAAAAAT 0.886393 -58 ** * * ****** Masking position 9 Map Score: 34.3994 Number of sites scoring better than the average of aligned sites = 532 Number in coding regions = 322 Number in noncoding regions = 210 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 2 ATAGGGTAGAATGTGCGGTATTATAGCCCA 1 29 1 ATGTGCGGTA 0.950061 -37 AATAATTTGTAAGTGCGGTTTCTATATAAG 3 27 1 AAGTGCGGTT 0.995576 -136 GAATATACCCAAGAGAGGTTACTTTAGATA 5 263 1 AAGAGAGGTT 0.959719 -38 GTTGCATTATAAGAGAGGTAAAATGAAATT 6 205 0 AAGAGAGGTA 0.925919 -96 GCTATTTGAGAAGTGCGGTTAAAATTTAAG 10 47 0 AAGTGCGGTT 0.995576 -141 TAGCGTCGTGAAGTGCGGTTTTATTTTGGA 10 73 1 AAGTGCGGTT 0.995576 -115 TCATGTACCTAAGTGCGGTTAAAATTGGTT 16 78 0 AAGTGCGGTT 0.995576 -20 TTTTTCAAAAAAGTGAGATAAAA 17 4 0 AAGTGAGATA 0.794977 -132 CAAAGAGGAAAAGTGCGGTTATACTCTATA 19 76 1 AAGTGCGGTT 0.995576 -80 ********** Masking position 9 Map Score: 21.2313 Number of sites scoring better than the average of aligned sites = 1510 Number in coding regions = 1021 Number in noncoding regions = 489 Number of orfs with sites within 600 bp upstream = 318 Fraction of orfs with sites within 600 bp upstream = 0.0510761 Motif number 3 CGTTTTTCCTACTTTTATGGGCTA 1 52 0 TTTTCCTATT 0.939124 -14 GATTAATTTCCTTCTTAATAATTTGT 3 6 1 ATTTCCTTTT 0.902548 -157 GACAAAATATTTTTCCTATTTTAGATTTTTT 3 96 1 TTTTCCTATT 0.939124 -67 GCATACGGTTTTCTGCTTGTTCAAATGCAAT 5 35 0 TTCTGCTTTT 0.820405 -266 ATGAAATTTGTTGTCGTTTTTCAACTGGTAA 6 182 0 TTGTCGTTTT 0.73095 -119 ATCTTTCATTTTGTCCATTTTATTTGTATTA 7 18 0 TTGTCCATTT 0.923907 -117 ATGAAAGATTTTGTCCATTTTTGTTTTATTA 7 40 1 TTGTCCATTT 0.923907 -95 TATTCTATTATTGTGCATATTTATTCATAAA 7 88 0 TTGTGCATTT 0.849204 -47 AATTTTTCCTTTTTGTTTTAATTA 7 121 0 TTTTCCTTTT 0.982869 -14 GTCGCCCTATTTTTGCATATTTTTGAAATTT 10 126 0 TTTTGCATTT 0.90307 -62 AACTTTTTCCTTGTTATAATCTATA 14 5 1 TTTTCCTTTT 0.982869 -203 TCATAAAAAATTTTGCTTATTTTCTTATTTT 14 106 1 TTTTGCTTTT 0.963781 -102 AACTATTTCCTACTTTCCTAAAATT 17 121 0 ATTTCCTATT 0.71349 -15 AAATAAAGATTTTTGCTTTTAATGCACAAAA 19 38 1 TTTTGCTTTA 0.694831 -118 ATAACCGCACTTTTCCTCTTTGTCTAGTGTT 19 67 0 TTTTCCTCTT 0.900488 -89 ATATTTTCCTTACTAATAATTAGA 19 142 0 TTTTCCTTCT 0.879167 -14 ******** ** Masking position 4 Map Score: 17.929 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 260 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 4 ATTTTCATTCCTTAATTTATTATACGAAAGTCA 3 140 0 TTTTATTTAT 0.95831 -23 TAACTTGATCTTATTTAATTTAAAATAAATATATTC 4 104 1 TTTTATTTAT 0.95831 -147 AAATATATTCTTACTTTAGTTTTTATAATAAAAAAC 4 130 1 TTTTAGTTAT 0.8084 -121 AATAACGCAATAGATTTATTTAGAATAAAATAACAC 4 172 0 TATTATTTAT 0.782904 -79 ATCTATTGCGTTATTAAAATTAATAATGCTGGGTAA 4 193 1 TTTAAATTAA 0.453662 -58 AATAAACTCCTTTATTTATTTTTGACGTAAAGTTAC 4 225 0 TTTTATTTAC 0.769861 -26 TTATATAAAATAGCTTTATTTCTAATTCTAAAAATT 5 107 1 TATTATTTAT 0.782911 -194 GTCAAAAACAATTTTAAATTTTACATAAAAAATACA 5 174 0 ATTAATTTAT 0.557652 -127 AAAATATGTTTTAGTTTATTTTTGATGAAGAGGAAT 6 34 0 TTTTATTTAT 0.970817 -267 TTATTGTTATTTGTTTGATTTCTAATAGTAGATGAA 6 78 0 TTTTATTTAT 0.970791 -223 GTTAGATTATTTTATTAAATTCTAATAATACTAAAA 6 117 1 TTTTAATTAT 0.940654 -184 TTGTCCATTTTTGTTTTATTATTAATATAGAATATT 7 50 1 TTTTATTAAT 0.661418 -85 CGGTTAAAATTTAAGTTATTTCAGATTATTCAAAAA 10 26 0 TTGTATTTAT 0.847965 -162 AAAAAGCCTTTTTATAAATTTCAAAAATATGCAAAA 10 111 1 TTTAATTTAA 0.548996 -77 TAAAAATGTTTAAATTGTGATCTAGTACACA 11 6 1 ATTTAATTAT 0.632575 -96 ATAAAAAATTTTGCTTATTTTCTTATTTTGTGACAA 14 108 1 TTTTTTTTAT 0.660724 -100 ATACCTGATATTAAGTGATTTTTCATTGATTTAGTG 15 37 1 TTGTATTTAT 0.847988 -64 CCTTTCCAAGTTCTTAAAATTGGCATTAACGTTATC 15 72 0 TTTAAATTAT 0.852574 -29 ATGCTAAAAATTCATTAAATTTTAAAGTAAAATGAA 16 43 1 TTTTAATTAA 0.731319 -55 ATTTCCTACTTTCCTAAAATTTCAATCCCGCCATTA 17 106 0 TTTAAATTAT 0.852574 -30 GCCGTAGGATTTACTAAATTTCCAATAATAAACATT 18 15 1 TTTAATTTAT 0.891465 -110 TAGCAAACGTTTGCTTTATTTGATTTAAAA 18 105 1 TTTTATTTTT 0.661423 -20 AAATCGATTATTTATTCAATTCTAATTATTAGTAAG 19 122 1 TTTTAATTAT 0.940775 -34 ** ** **** ** Masking position 10 Map Score: 24.1435 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 196 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 5 TAGCCCACAAAATAAAAATATCAATGGTGG 2 26 1 AATAAAAATA 0.878633 -50 CCCTTGAAAGAAAAAAAATCCTCCTTATAT 3 50 0 AAAAAAAATC 0.724048 -113 TGTTCTAGGCAATACAAAAATATCCAGAAA 4 52 0 AATACAAAAA 0.905234 -199 TAGTTTTTATAATAAAAAACTAGATCGTGT 4 146 1 AATAAAAAAC 0.936423 -105 ATTTATTTAGAATAAAATAACACGATCTAG 4 165 0 AATAAAATAA 0.681217 -86 ATACAAAACCAAAACAAAAAAATAATAAAG 5 149 0 AAAACAAAAA 0.745563 -152 TTACATAAAAAATACAAAACCAAAACAAAA 5 160 0 AATACAAAAC 0.918606 -141 CCTCTTCATCAAAAATAAACTAAAACATAT 6 37 1 AAAAATAAAC 0.449579 -264 ATTAGAATTTAATAAAATAATCTAACTCTT 6 113 0 AATAAAATAA 0.681217 -188 AAATTCTAATAATACTAAAAATCTCGCAAT 6 133 1 AATACTAAAA 0.633272 -168 AAAATCTCGCAATAAAATTCTACATACTGG 6 150 1 AATAAAATTC 0.594511 -151 ATAGCACTAATACAAATAAAATGGACAA 7 9 1 AATACAAATA 0.847261 -126 TATTAATAATAAAACAAAAATGGACAAAAT 7 47 0 AAAACAAAAA 0.745563 -88 ATAATTAATTAAAACAAAAAGGAAAAATT 7 116 1 AAAACAAAAA 0.745563 -19 TGTTACCCATAATAAAAATAAAAACTAAGT 10 155 0 AATAAAAATA 0.878633 -33 CATTTTGAGCAATAAAAAACTGTGTACTAG 11 32 0 AATAAAAAAC 0.936423 -70 CATTATTTATAATAAAAATGTCATTACAAG 12 13 1 AATAAAAATG 0.695786 -158 AACCTTTGTAAATAAAAAAGCCATCGCTTG 12 117 0 AATAAAAAAG 0.797511 -54 TTTGTCACAAAATAAGAAAATAAGCAAAAT 14 115 0 AATAAGAAAA 0.569326 -93 CTAAATTTCCAATAATAAACATTTTCCCCC 18 28 1 AATAATAAAC 0.726974 -97 TTTAAAAAGAAATAAAAATCCTCTGAAATG 18 72 0 AATAAAAATC 0.895325 -53 GATTTTTGTGAATAAAAATTCTATAGAGTA 19 97 0 AATAAAAATT 0.456085 -59 ********** Masking position 4 Map Score: 22.3133 Number of sites scoring better than the average of aligned sites = 528 Number in coding regions = 309 Number in noncoding regions = 219 Number of orfs with sites within 600 bp upstream = 187 Fraction of orfs with sites within 600 bp upstream = 0.0300353 Motif number 6 CCGTAGGGTGGGCTTTAGCCCACAAA 2 4 1 TAGTGGCTTT 0.83498 -72 TTGTTCCTTGTAGGGTGGGCTTTAGCCCACCAT 2 49 0 TAGTGGCTTT 0.83498 -27 TTACCGCTTTAATTGTGTGCATACGGTTTTCTG 5 51 0 AAGTGGCATA 0.921514 -250 ATTTTTTAAAAAATGTGATCTTAGTCAAAAACA 5 200 0 AAGTGTCTTA 0.776684 -101 AATAACAATAAAGAGTTAGATTATTTTATTAAA 6 103 1 AAGTTGATTA 0.525639 -198 TCAATCAAGGAACGGTTGGCATTCCACCAACCA 9 18 0 AAGTTGCATT 0.951418 -60 TTATTGCTCAAAATGTTAGCATTGGAGCCAGTT 11 47 1 AAGTTGCATT 0.951406 -55 TTAATTGGTCAAGCGATGGCTTTTTTATTTACA 12 108 1 AAGATGCTTT 0.758998 -63 GATAAATTGAAAGCGGTTACTTTCATAAGTATG 14 66 1 AAGGTACTTT 0.520812 -142 TAAATCATAAAAAATTTTGCTTATTTTCTTATT 14 102 1 AATTTGCTTA 0.661473 -106 ATTGTAAATAAACCGTGATCTTTGTCACAAAAT 14 132 0 AAGTGTCTTT 0.85036 -76 AAATTAATGTAATCGTTTACATTGATAAAAAAC 14 175 1 AAGTTACATT 0.712459 -33 AAATTTAATGAATTTTTAGCATAATGGCGCATT 16 32 0 AATTTGCATA 0.544598 -66 GTGCGGTTAAAATTGGTTTCATTTTACTTTAAA 16 63 0 AAGGTTCATT 0.488006 -35 AAAAAATAGCAAACGTTTGCTTTATTTGATTTA 18 99 1 AAGTTGCTTT 0.969694 -26 GACAAAGAGGAAAAGTGCGGTTATACTCTATAG 19 74 1 AAGTGGGTTA 0.616682 -82 ** *** ***** Masking position 2 Map Score: 5.53201 Number of sites scoring better than the average of aligned sites = 497 Number in coding regions = 411 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 7 TTTCCTACTTTTATGGGCTATAATACCGCA 1 42 0 TTATGGGCTA 0.906376 -24 CCGTAGGGTGGGCTTTAGCCCACAA 2 6 1 GGGTGGGCTT 0.988473 -70 TATTTTTATTTTGTGGGCTAAAGCCCACCC 2 16 0 TTGTGGGCTA 0.980589 -60 AAAATATCAATGGTGGGCTAAAGCCCACCC 2 40 1 TGGTGGGCTA 0.99129 -36 GTTCCTTGTAGGGTGGGCTTTAGCCCACCA 2 50 0 GGGTGGGCTT 0.988473 -26 ********** Masking position 4 Map Score: 4.27806 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 12 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 GGTTTCTATATAAGGAGGATTTTTTTTCTTTCA 3 43 1 TAAGGATTTT 0.949647 -120 ATATTTTTCCTATTTTAGATTTTTTACGTAAAA 3 102 1 TATAGATTTT 0.823701 -61 GTCAAAAATAAATAAAGGAGTTTATT 4 235 1 AATGGAGTTT 0.867293 -16 CTTTAGATAGAAAGAGGGATTTTTCCT 5 284 1 AAAGGATTTT 0.949616 -17 GTAATGCCAGTATGTAGAATTTTATTGCGAGAT 6 153 0 TATGAATTTT 0.575078 -148 AAATGGACAAAATGAAAGATTTTGTCCATTTTT 7 29 1 AATAGATTTT 0.823701 -106 AGTGCGGTTTTATTTTGGAGTTTTGGCAAAAAG 10 84 1 TATGGAGTTT 0.867318 -104 TTGAAATTTATAAAAAGGCTTTTTGCCAAAACT 10 102 0 TAAGGCTTTT 0.764015 -86 TTATTATGGGTAACAAGGATTCTTTTTA 10 170 1 TAAGGATTCT 0.76404 -18 AAATTAGGATTTTTTATGCACAA 19 1 1 AAAGGATTTT 0.948327 -155 GCACAAAGCTAAATAAAGATTTTTGCTTTTAAT 19 28 1 AAAAGATTTT 0.823696 -128 GAATTGAATAAATAATCGATTTTTGTGAATAAA 19 111 0 AATCGATTTT 0.731981 -45 *** ******* Masking position 2 Map Score: 4.34475 Number of sites scoring better than the average of aligned sites = 243 Number in coding regions = 183 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 9 TTCTTAATAATTTGTAAGTGCGGTTTCTATATA 3 22 1 TTAAGTGCGG 0.992415 -141 ACGACGCTATTTGAGAAGTGCGGTTAAAATTTA 10 49 0 TGAAGTGCGG 0.99297 -139 TCAAATAGCGTCGTGAAGTGCGGTTTTATTTTG 10 68 1 TGAAGTGCGG 0.992969 -120 TCATGTACCTAAGTGCGGTTAAAATTGG 16 80 0 TTAAGTGCGG 0.992415 -18 AAAGGGTTATTAGATAATGGCGGGATTGAAATT 17 92 1 TTAATGGCGG 0.880965 -44 CTAGACAAAGAGGAAAAGTGCGGTTATACTCTA 19 71 1 AAAAGTGCGG 0.927403 -85 * ********* Masking position 7 Map Score: 4.05167 Number of sites scoring better than the average of aligned sites = 404 Number in coding regions = 261 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 10 AAATTCTGACAAAATATTTTTCCTATTTTAG 3 89 1 AAAAATTTTT 0.56768 -74 TTAATTTCATAAAACATTTCTTACCTGTTCT 4 76 0 AAAAATTTCT 0.839714 -175 CTAAAGTAAGAATATATTTATTTTAAATTAA 4 118 0 AATAATTTAT 0.858713 -133 TTAATAACGCAATAGATTTATTTAGAATAAA 4 179 0 AATAATTTAT 0.858713 -72 ATTTATATAAAATAGCTTTATTTCTAATTCT 5 105 1 AATACTTTAT 0.906462 -196 CTAAAAATTTAATAACTTTATTATTTTTTTG 5 134 1 AATACTTTAT 0.905966 -167 AAAAATGGACAAAATCTTTCATTTTGTCCAT 7 31 0 AAAACTTTCA 0.699063 -104 TAAAAATGTTTAAATTGTGATCT 11 3 1 AAAAGTTTAA 0.61013 -99 AATAGATTTCCTGAGTAAATT 12 160 0 AATAATTTCC 0.620753 -11 ACTTTTTTGAAAAAACTTTACGAGATTATAG 17 20 1 AAAACTTTAC 0.851092 -116 GTATAGGGGGAAAATGTTTATTATTGGAAAT 18 32 0 AAAAGTTTAT 0.848047 -93 ATTAAAAGCAAAAATCTTTATTTAGCTTTGT 19 30 0 AAAACTTTAT 0.929756 -126 **** ****** Masking position 4 Map Score: 3.77266 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 220 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 11 AATTTTACGTAAAAAATCTAAAATAGGAAA 3 107 0 AAAAAATCTA 0.772643 -56 AATATCCAGAAATTAATCTATGGAGACTCT 4 34 0 AATTAATCTA 0.954297 -217 TTTTATTCTAAATAAATCTATTGCGTTATT 4 178 1 AATAAATCTA 0.823893 -73 TCTTCATCAAAAATAAACTAAAACATATTT 6 39 1 AAATAAACTA 0.637263 -262 TTTTCGTTTAAATTCATCTACTATTAGAAA 6 66 1 AATTCATCTA 0.781876 -235 GAATTTAATAAAATAATCTAACTCTTTATT 6 109 0 AAATAATCTA 0.938148 -192 TGTTTTAATTAATTATTCTATTATTGTGCA 7 102 0 AATTATTCTA 0.838211 -33 GTAAATTTGAAATTAGTGTAAACCTTTGTA 12 137 0 AATTAGTGTA 0.629095 -34 TTTTGATCATAAATAATTTACGATAAATTG 14 45 1 AAATAATTTA 0.597901 -163 ATTTATACTAAATTATTGTAAATAAACCGT 14 149 0 AATTATTGTA 0.668649 -59 ATTTAGTATAAATTAATGTAATCGTTTACA 14 166 1 AATTAATGTA 0.890506 -42 AGAATTGAATAAATAATCGATTTTTGTGAA 19 115 0 AAATAATCGA 0.722516 -41 ********** Masking position 2 Map Score: 4.8144 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 115 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 12 CCGTAGGGTGGGCTTTAGCCCACAAAATA 2 10 1 GGGCTTTAGC 0.985356 -66 CTTGTAGGGTGGGCTTTAGCCCACCATTGA 2 46 0 GGGCTTTAGC 0.985356 -30 TTCTACATACTGGCATTACCAGTTGAAAAA 6 167 1 TGGCATTACC 0.941952 -134 TCTCCCTCTTTAGCTTTAGCAAAGAGGG 13 20 1 TAGCTTTAGC 0.922748 -18 TTCTTAAAATTGGCATTAACGTTATCACTA 15 68 0 TGGCATTAAC 0.916312 -33 ********** Masking position 6 Map Score: 1.09324 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 32 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 13 GTAAGAAATGTTTTATGAAATTAACTTGAT 4 83 1 TTTTATGAAA 0.354834 -168 ACCGCTTTAATTGTGTGCATACGGTTTTCT 5 52 0 TTGTGTGCAT 0.774291 -249 AAATCTTTCATTTTGTCCATTTTATTTGTA 7 21 0 TTTTGTCCAT 0.857655 -114 AAATGAAAGATTTTGTCCATTTTTGTTTTA 7 38 1 TTTTGTCCAT 0.857655 -97 TAGAATATTGCTTTATGAATAAATATGCAC 7 77 1 CTTTATGAAT 0.718661 -58 ATTATTCTATTATTGTGCATATTTATTCAT 7 91 0 TATTGTGCAT 0.814405 -44 CAAGAAATTGTTTTTTGAATAATCTGAAAT 10 15 1 TTTTTTGAAT 0.647447 -173 CAAAAAGCCTTTTTATAAATTTCAAAAATA 10 110 1 TTTTATAAAT 0.63209 -78 TAGTGTAAACCTTTGTAAATAAAAAAGCCA 12 124 0 CTTTGTAAAT 0.739067 -47 TATACTAAATTATTGTAAATAAACCGTGAT 14 146 0 TATTGTAAAT 0.537621 -62 TACTTTAAAATTTAATGAATTTTTAGCATA 16 42 0 TTTAATGAAT 0.511865 -56 TTATTGGAAATTTAGTAAATCCTACGGCTT 18 13 0 TTTAGTAAAT 0.537619 -112 CTTTATTTAGCTTTGTGCATAAAAAATCCT 19 16 0 CTTTGTGCAT 0.914458 -140 TTGTCTAGTGTTTTGTGCATTAAAAGCAAA 19 49 0 TTTTGTGCAT 0.961953 -107 AATAATCGATTTTTGTGAATAAAAATTCTA 19 104 0 TTTTGTGAAT 0.958858 -52 ********** Masking position 9 Map Score: 8.21165 Number of sites scoring better than the average of aligned sites = 616 Number in coding regions = 531 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 14 ATATTCTTACTTTAGTTTTTATAATAAAAA 4 134 1 TTTAGTTTTT 0.73798 -117 AATAACACGATCTAGTTTTTTATTATAAAA 4 150 0 TCTAGTTTTT 0.955974 -101 AATAATCTCCTTGTGTTTTGACTATACA 6 283 0 CCTTGTGTTT 0.778269 -18 ATTATCATATCCATTGTTTAA 8 3 0 TCCATTGTTT 0.804201 -19 TTTGACTCCTGTTTTTTATCAATGTA 14 192 0 TCCTGTTTTT 0.919401 -16 TCAAGTGCAATCCAGTTTTTTCCTAGAAAT 17 55 0 TCCAGTTTTT 0.963265 -81 TTCCTCTTTGTCTAGTGTTTTGTGCATTAA 19 56 0 TCTAGTGTTT 0.963265 -100 ********** Masking position 6 Map Score: 0.580644 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 98 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 15 TATTTTATTCTAAATAAATCTATTGCGTTA 4 176 1 TAAATAAATC 0.679074 -75 AAAGCTATTTTATATAAATCTTAAACCAAA 5 94 0 TATATAAATC 0.895543 -207 TATTAGATATCCTATCAATCAAGGAACGGT 9 35 0 CCTATCAATC 0.884985 -43 CATTACAAGATCTATAAATCAGGTTCATTT 12 34 1 TCTATAAATC 0.962095 -137 CTTGTTATAATCTATAAATCTTATATTTTG 14 20 1 TCTATAAATC 0.962095 -188 CCAGTTTTTTCCTAGAAATCGTGCTATAAT 17 44 0 CCTAGAAATC 0.884985 -92 ********** Masking position 4 Map Score: 0.264431 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 5 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555