AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00520_hinf_reg_300.orf -o00520_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 HI0351 172 UDP-glucose 4-epimerase (galE) #2 HI0352 300 conserved hypothetical protein #3 HI0759 176 A/G-specific adenine glycosylase (mutY) #4 HI0812 21 glucosephosphate uridylyltransferase (galU) #5 HI0813 77 carbon storage regulator (csrA) #6 HI0814 187 alanyl-tRNA synthetase (alaS) #7 HI0815 101 universal stress protein A (uspA) #8 HI0817 170 conserved hypothetical protein #9 HI0819 37 galactokinase (galK) #10 HI0820_HI0821 207 HI0820: galactose-1-phosphate uridylyltransferase (galT), HI0821: galactose operon repressor (galR) #11 HI0822 90 galactose ABC transporter, periplasmic-binding protein (mglB) #12 HI0823 65 galactoside ABC transporter, ATP-binding protein (mglA) #13 HI0825 145 H. influenzae predicted coding region HI0825 #14 HI0870.1 300 H. influenzae predicted coding region HI0870.1 #15 HI0873 58 DTDP-glucose 4,6-dehydratase (rffG) #16 HI1354 300 glutaminyl-tRNA synthetase (glnS) #17 HI1355 65 conserved hypothetical protein #18 HI1356 61 4-alpha-glucanotransferase (malQ) #19 HI1358 95 glycogen operon protein (glgX) Motif number 1 AATCAATCAATCAATCAATC 2 1 1 AATCAATCAA 0.994782 -300 TCAATCAATCAATCAATCAATCAATCAATC 2 17 1 AATCAATCAA 0.994782 -284 TCAATCAATCAATCAATCAATCAATCAATC 2 29 1 AATCAATCAA 0.994782 -272 TCAATCAATCAATCAATCAATCAATCAATC 2 41 1 AATCAATCAA 0.994782 -260 TCAATCAATCAATCAATCAATCAATCAATC 2 53 1 AATCAATCAA 0.994782 -248 TCAATCAATCAATCAATCAATCAATCAATC 2 73 1 AATCAATCAA 0.994782 -228 TCAATCAATCAATCAATCAATCAATCAATC 2 85 1 AATCAATCAA 0.994782 -216 TCAATCAATCAATCAATCAATCAATCAATC 2 97 1 AATCAATCAA 0.994782 -204 TCAATCAATCAATCAATCAAAGTCTGTCAT 2 109 1 AATCAATCAA 0.994782 -192 TTAGATATCCTATCAATCAAGGAACGGTTG 5 33 0 TATCAATCAA 0.960355 -45 TTTTAATCAACCAAGTGCGGTCAA 17 5 1 AATCAACCAA 0.972902 -61 ********** Masking position 5 Map Score: 42.045 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 38 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 2 TTGATTGATTGATTGATTGATT 2 2 0 GATTGATGAT 0.997087 -299 TTGATTGATTGATTGATTGATTGATTGATTG 2 18 0 GATTGATGAT 0.997087 -283 TTGATTGATTGATTGATTGATTGATTGATTG 2 30 0 GATTGATGAT 0.997087 -271 TTGATTGATTGATTGATTGATTGATTGATTG 2 42 0 GATTGATGAT 0.997087 -259 TTGATTGATTGATTGATTGATTGATTGATTG 2 54 0 GATTGATGAT 0.997087 -247 TTGATTGATTGATTGATTGATTGATTGATTG 2 70 0 GATTGATGAT 0.997087 -231 TTGATTGATTGATTGATTGATTGATTGATTG 2 82 0 GATTGATGAT 0.997087 -219 TTGATTGATTGATTGATTGATTGATTGATTG 2 94 0 GATTGATGAT 0.997087 -207 GACAGACTTTGATTGATTGATTGATTGATTG 2 106 0 GATTGATGAT 0.997087 -195 AAATGAACCTGATTTATAGATCTTGTAATGA 8 33 0 GATTTATGAT 0.981386 -138 CAAAATATAAGATTTATAGATTATAACAAGG 10 19 0 GATTTATGAT 0.981386 -189 ******* *** Masking position 6 Map Score: 45.1054 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 28 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 3 GTGATTTTCAATAAAATAAAAAACCTGTTGCTA 1 87 0 AAAATAAAAA 0.952735 -86 ATTGCAACGGAAAACATCATAATCTTTAGGTAA 2 185 0 AAAATCAAAT 0.933836 -116 ATAATGATCTTCAAAATAAAATTGATTGCAACG 2 209 0 TAAATAAATT 0.66405 -92 TTTCTTGGCAAGAAAATAAAAAAAGTATTTTTT 2 242 1 AAAATAAAAA 0.952735 -59 AAAACTGTGTACTAGATCACAATTTAAACATTT 7 14 0 ATAATCAAAT 0.839674 -88 TGTAAACCTTTGTAAATAAAAAAGCCATCGCTT 8 118 0 TTAATAAAAA 0.678009 -53 ATTTATGATCAAAATATAAGATTTATAGATTAT 10 26 0 AAAATAAATT 0.875334 -182 ATAAGTATGAACTAAATCATAAAAAATTTTGCT 10 90 1 ATAATCAAAA 0.876969 -118 GATCTTTGTCACAAAATAAGAAAATAAGCAAAA 10 116 0 AAAATAAAAA 0.952735 -92 AATGAAAATGATTACATAAAAAATTATGAATTT 11 28 0 ATAATAAAAA 0.882073 -63 ATAAGATAAGATAAGATAAGATA 14 1 0 AAAATAAATA 0.905269 -300 ATAAGATAAGATAAGATAAGATAAGATAAGATA 14 16 0 AAAATAAATA 0.905269 -285 AGAACAATGAAAAAGATAAGATAAGATAAGATA 14 31 0 AAAATAAATA 0.905269 -270 ATCCCTTATCTTAAAATCAAAAAAGAAAGTAAT 14 90 0 TAAATCAAAA 0.843939 -211 GATAAGAGAGATAAAATCAAAATATCCCTTATC 14 113 0 AAAATCAAAT 0.933836 -188 TACCCACCCGAAAAAATCATAATATACTAAAAT 14 150 0 AAAATCAAAT 0.933836 -151 AGAATATTGGACAAAATAATAATAAACCCTACC 14 227 0 AAAATAAAAT 0.936751 -74 GCCTCCCTCCACTACATCACATTAAAAAGCGGT 16 15 1 ATAATCAATT 0.712883 -286 TTTCTCTCGTTAAAATAAAAAAATATTCGGCT 16 279 0 TAAATAAAAA 0.850179 -22 * ** **** *** Masking position 7 Map Score: 24.5041 Number of sites scoring better than the average of aligned sites = 268 Number in coding regions = 163 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 4 AATAAAATAAAAAACCTGTTGCTAAAAAGTATTGTT 1 75 0 AAACTGGAAA 0.912399 -98 AGTATTGCTCAAAAATTGTAGAACAATTAAAAAATA 2 267 0 AAAATGGCAA 0.917649 -34 AATTATACTGAAAAAATGCAGATAAACAAGCTCTAT 3 107 1 AAAATGGAAA 0.98797 -70 AAAAAGAAAAGTGCGGTTAAAAATGCTGATG 3 156 0 GAAATGGAAA 0.953504 -21 GACGCTATTTGAGAAGTGCGGTTAAAATTTAAGTTA 6 44 0 GAAATGGAAA 0.953504 -144 TTTGATCATAAATAATTTACGATAAATTGAAAGCGG 10 46 1 AAAATTGAAA 0.926643 -162 GTCACAAAATAAGAAAATAAGCAAAATTTTTTATGA 10 106 0 AAAAATGAAA 0.885467 -102 GTTTATTTACAATAATTTAGTATAAATTAATGTAAT 10 152 1 AAAATTTAAA 0.557591 -56 TACATTGATAAAAAACAGGAGTCAAA 10 192 1 AAAAAGGAAA 0.980494 -16 AGATTACAACAAAAATTGATGGGAAA 12 1 0 AAAATGGAAA 0.98797 -65 AATAAAATGAATGAAAAGTGGGCAAATTTGTCCACT 13 26 1 ATAAAGGAAA 0.821476 -120 GAATAGATAAAACAAAAGTGGACAAATTTGCCCACT 13 42 0 AAAAAGGAAA 0.980494 -104 ACTAGATTTAAATAAAAGATTGTAAAAACTTGCCAT 16 186 0 AAAAAGTAAA 0.833754 -115 TTTCTATGGCAAGAACAGGAGATGAACCTTTATTTT 16 223 1 AAAAAGGGAA 0.872122 -78 TTTTAATCAACCAAGTGCGGTCAAAACAAACGTGA 17 10 1 ACAATGGAAA 0.917649 -56 TGATACAAATAAAAAGTGCGGTCAAAATCACGTTTG 17 37 0 AAAATGGAAA 0.98797 -29 ** ** ** * *** Masking position 4 Map Score: 22.4284 Number of sites scoring better than the average of aligned sites = 411 Number in coding regions = 300 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 5 AAAAAGAAAAGTGCGGTTAAAAATGCTGA 3 158 0 AGTGCGGTTA 0.993478 -19 CTATTTGAGAAGTGCGGTTAAAATTTAAGT 6 46 0 AGTGCGGTTA 0.993478 -142 AGCGTCGTGAAGTGCGGTTTTATTTTGGAG 6 74 1 AGTGCGGTTT 0.982315 -114 CGATAAATTGAAAGCGGTTACTTTCATAAG 10 65 1 AAAGCGGTTA 0.927244 -143 ATCACATTAAAAAGCGGTATCGCCGTGAAT 16 30 1 AAAGCGGTAT 0.714355 -271 AAATGCACAAAGTGCGGTAAGTTTTTTGAA 16 122 0 AGTGCGGTAA 0.987905 -179 TAATCAACCAAGTGCGGTCAAAACAAACGT 17 14 1 AGTGCGGTCA 0.992135 -52 ACAAATAAAAAGTGCGGTCAAAATCACGTT 17 39 0 AGTGCGGTCA 0.992135 -27 ********** Masking position 1 Map Score: 15.7288 Number of sites scoring better than the average of aligned sites = 1050 Number in coding regions = 653 Number in noncoding regions = 397 Number of orfs with sites within 600 bp upstream = 270 Fraction of orfs with sites within 600 bp upstream = 0.0433665 Motif number 6 AAAATCACCATTCTTACCACACAAAATAGTGA 1 112 1 TTTACCACAC 0.98272 -61 TATAGGAACTTTCTCCCCACACCGCGTGAGTG 3 40 1 TTTCCCACAC 0.937907 -137 TCATCAGCATTTTTAACCGCACTTTTCTTTTT 3 155 1 TTTACCGCAC 0.995994 -22 ATAACTTAAATTTTAACCGCACTTCTCAAATA 6 43 1 TTTACCGCAC 0.995994 -145 AAACTCCAAAATAAAACCGCACTTCACGACGC 6 75 0 ATAACCGCAC 0.942236 -113 ACATTCAAAAAACTTACCGCACTTTGTGCATT 16 119 1 AATACCGCAC 0.942236 -182 ATCACGTTTGTTTTGACCGCACTTGGTTGATT 17 15 0 TTTACCGCAC 0.995994 -51 ACAAACGTGATTTTGACCGCACTTTTTATTTG 17 36 1 TTTACCGCAC 0.995994 -30 ** * ******* Masking position 11 Map Score: 15.6693 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 303 Number in noncoding regions = 180 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 7 TATTTTATTGAAAATCACCATTCTTACCACACAAAA 1 102 1 AAAATTTTTA 0.852894 -71 TTATTACCTAAAGATTATGATGTTTTCCGTTGCAAT 2 182 1 AAGATTGTTT 0.855388 -119 AATGATCTTCAAAATAAAATTGATTGCAACGGAAAA 2 204 0 AAAATTGTTG 0.872773 -97 TAGAACAATTAAAAAATACTTTTTTTATTTTCTTGC 2 249 0 AAAAATTTTT 0.46938 -52 ATTTTACACGAAAATAGAGCTTGTTTATCTGCATTT 3 120 0 AAAATTTTTT 0.96628 -57 AGTGCGGTTAAAAATGCTGATGATTTTACACGAAAA 3 142 0 AAAATTGTTT 0.977282 -35 AAGTGCGGTTAAAATTTAAGTTATTTCAGATTATTC 6 31 0 AAAATTTTTT 0.968445 -157 TTTAACGCTAGAAATGAACCTGATTTATAGATCTTG 8 39 0 GAAATTGTTT 0.921309 -132 TAAATCATAAAAAATTTTGCTTATTTTCTTATTTTG 10 102 1 AAAATTTTTT 0.968445 -106 CATGGATCACAAATTCATAATTTTTTATGTAATCAT 11 18 1 AAATTTTTTT 0.737109 -73 CAAATTTGCAAAAATGAAAATGATTACATAAAAAAT 11 37 0 AAAATTGTTA 0.891117 -54 AGATAAAATCAAAATATCCCTTATCTTAAAATCAAA 14 102 0 AAAATTTTCT 0.807229 -199 CATTTGATAGGAAATTTTGCTGTTTTTGCCTGCATT 16 57 0 GAAATTGTTT 0.921237 -244 AAGTGCGGTCAAAATCACGTTTGTTTTGACCGCACT 17 24 0 AAAATTTTTT 0.968601 -42 CATTTGCCCAAAAACATCGGTGGTTTATCAGGCGAA 19 43 0 AAAACTGTTT 0.772364 -53 ***** ** *** Masking position 2 Map Score: 12.7677 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 143 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 8 CACCAGCCTCTTAATCTAATTTAATTGGTCAA 8 88 1 TTAATAATTT 0.875913 -83 TTACAAAGGTTTACACTAATTTCAAATTTACT 8 136 1 TTACTAATTT 0.984427 -35 CATAAATAATTTACGATAAATTGAAAGCGGTT 10 52 1 TTACTAAATT 0.958577 -156 CACGGTTTATTTACAATAATTTAGTATAAATT 10 148 1 TTACTAATTT 0.984427 -60 ATGTAAACGATTACATTAATTTATACTAAATT 10 165 0 TTACTAATTT 0.984427 -43 CATAGATTAATTACGATAATTTATTT 11 75 1 TTACTAATTT 0.984427 -16 TGTATGAAAATTACTCTAATGTTAGCTATATA 14 192 1 TTACTAATGT 0.943787 -109 TCTATTTGCATTACCTTAAATTTATTAACCCA 15 35 1 TTACTAAATT 0.958577 -24 **** ****** Masking position 8 Map Score: 11.4181 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 22 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 TGTTGTAGCGAGTGAGATAACCTCTCATAT 1 49 0 AGTGAGATAA 0.729343 -124 CACACAAAATAGTGATATAATTTTTTAGTC 1 129 1 AGTGATATAA 0.790999 -44 TGCAAACTAAGGAGATAAAAG 5 67 1 GGAGATAAAA 0.844063 -11 AATCGTTTACATTGATAAAAAACAGGAGTC 10 185 1 ATTGATAAAA 0.895132 -23 TCAGAATTGAATAGATAAAACAAAAGTGGA 13 56 0 ATAGATAAAA 0.942109 -90 CCATTTTCATAGAGAGAAAAAA 13 134 1 AGAGAGAAAA 0.948665 -12 AGCGGATAAGAGAGATAAAATCAAAATATC 14 120 0 AGAGATAAAA 0.962901 -181 TACATATATAGAGAAAACCTTTATATA 14 284 0 ATAGAGAAAA 0.920561 -17 TCCGAATAGATAAATTGTAGGGGCG 19 6 1 ATAGATAAAT 0.695931 -90 TGCCTACAAAATCGATAAAAAT 19 84 1 ATCGATAAAA 0.833555 -12 ********** Masking position 5 Map Score: 5.87497 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 93 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 10 AAGATTATGATGTTTTCCGTTGCAATCAATTTTA 2 192 1 TGTTTCTTCA 0.946486 -109 ATGTTTAAATTGTGATCTAGTACACAGTTTTTTA 7 16 1 TGTATCGTCA 0.958707 -86 GTAAATAAACCGTGATCTTTGTCACAAAATAAGA 10 128 0 CGTATCTGCA 0.936887 -80 TATAAATTAATGTAATCGTTTACATTGATAAAAA 10 172 1 TGTATCTTCA 0.556098 -36 ATTATGAATTTGTGATCCATGTCACAAA 11 5 0 TGTATCTGCA 0.978335 -86 TAATTTTTTATGTAATCATTTTCATTTTTGCAAA 11 35 1 TGTATCTTCA 0.986836 -56 TCTTATCTTATCTTATCTTTTTCATTGTTCTAGT 14 33 1 TCTATCTTCA 0.942316 -268 AGCCAGTTGTCATCACTTTCAGCTTAGCTAT 18 8 1 TGTATCTTCA 0.988191 -54 *** *** ** ** Masking position 14 Map Score: 9.52729 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 10 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 11 TCTCAATAATTAACAAGGAAATCATT 1 157 1 TAACAAGGAA 0.964096 -16 TTAACAAGAAATTGTTTTTTG 6 2 1 TAACAAGAAA 0.913015 -186 TTATTATGGGTAACAAGGATTCTTTTTA 6 170 1 TAACAAGGAT 0.921146 -18 TTGCTAAAGCTAAAGAGGGAGACTGACTAT 9 12 0 TAAAGAGGGA 0.846544 -26 TTATAGATTATAACAAGGAAAAAGTT 10 7 0 TAACAAGGAA 0.964096 -201 CCAACCTCTTTAAAAAGGGGAAGATCCACT 12 44 0 TAAAAAGGGG 0.780802 -22 TTTTTTATTTTAACGAGAGAAA 16 289 1 TAACGAGAGA 0.904101 -12 CTATAATCCCTAACAAGAGTTATACAGTTG 18 38 1 TAACAAGAGT 0.87868 -24 ********** Masking position 6 Map Score: 3.82348 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 20 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 12 TGCAAAAATAGGGCGACTTAGTTTTTATTT 6 140 1 GGGCGACTTA 0.956491 -48 AAGCTAAAGAGGGAGACTGACTATA 9 6 0 GGGAGACTGA 0.852561 -32 ATTAATCTATGAGCAAATTTGCAAAAATGA 11 56 0 GAGCAAATTT 0.733834 -35 AATGAAAAGTGGGCAAATTTGTCCACTTTT 13 35 1 GGGCAAATTT 0.961073 -111 ATATTCTGGAGGGAAAATTAATACCTTAAA 14 253 1 GGGAAAATTA 0.939328 -48 ACAAATCTAAGGGAAAATAAAGGTTCATCT 16 242 0 GGGAAAATAA 0.792509 -59 TAAATTGTAGGGGCGAATTACATTCGCCTG 19 21 1 GGGCGAATTA 0.974888 -75 CGATGTTTTTGGGCAAATGTAATTTGCCTA 19 60 1 GGGCAAATGT 0.943226 -36 ********** Masking position 6 Map Score: 3.65954 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 148 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 13 TTACCTAAAGATTATGATGTTTTCCGTTGCAAT 2 185 1 ATTATGGTTT 0.893366 -116 GCGTGGCTTCATTTTGAGGTTTTTCT 3 4 0 ATTTTGGTTT 0.971236 -173 GTGCGGTTTTATTTTGGAGTTTTGGCAAAAAGC 6 85 1 ATTTTGGTTT 0.971236 -103 AGTCGCCCTATTTTTGCATATTTTTGAAATTTA 6 125 0 TTTTTGTTTT 0.925838 -63 ATCATAAAAAATTTTGCTTATTTTCTTATTTTG 10 105 1 ATTTTGTTTT 0.954901 -103 ATCATTTTCATTTTTGCAAATTTGCTCATAGAT 11 49 1 TTTTTGATTT 0.754893 -42 GATAAGGGATATTTTGATTTTATCTCTCTTATC 14 113 1 ATTTTGTTAT 0.729021 -188 ATTTTAGTATATTATGATTTTTTCGGGTGGGTA 14 150 1 ATTATGTTTT 0.840091 -151 TTGATAGGAAATTTTGCTGTTTTTGCCTGCATT 16 57 0 ATTTTGGTTT 0.971236 -244 TGCGGTAAGTTTTTTGAATGTTTAGCTTACCAA 16 107 0 TTTTTGTTTT 0.925838 -194 ATTTTTATCGATTTTGTAGGCAAA 19 82 0 TTTTTAGTTT 0.610688 -14 ****** * *** Masking position 5 Map Score: 10.118 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 166 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 14 AAAGTATAGTATTGCTCAAAAATTGTAGAA 2 280 0 ATTGCTCAAA 0.941067 -21 ACAGTTTTTTATTGCTCAAAATGTTAGCAT 7 39 1 ATTGCTCAAA 0.941067 -63 ATCTAATTTAATTGGTCAAGCGATGGCTTT 8 101 1 ATTGGTCAAG 0.834539 -70 ATGAATGAAAAGTGGGCAAATTTGTCCACT 13 32 1 AGTGGGCAAA 0.929301 -114 ATAAAACAAAAGTGGACAAATTTGCCCACT 13 42 0 AGTGGACAAA 0.94091 -104 TTTGCCGATTATTGCATAAATATCCTTAAT 13 86 0 ATTGCATAAA 0.689955 -60 CCTCCAGAATATTGGACAAAATAATAATAA 14 235 0 ATTGGACAAA 0.965247 -66 GCGATGTATAAATGCACAAAGTGCGGTAAG 16 131 0 AATGCACAAA 0.824858 -170 CACCGATGTTTTTGGGCAAATGTAATTTGC 19 57 1 TTTGGGCAAA 0.658435 -39 ********** Masking position 3 Map Score: 5.02415 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 130 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 15 AACCTGTTGCTAAAAAGTATTGTTGTAGCG 1 69 0 TAAAAAGTAT 0.821897 -104 TATTGAGACTAAAAAATTATATCACTATTT 1 135 0 AAAAAATTAT 0.86272 -38 ATCTTTAGGTAATAAACTATAGTCAATTGA 2 167 0 AATAAACTAT 0.744126 -134 CAAGAAAATAAAAAAAGTATTTTTTAATTG 2 250 1 AAAAAAGTAT 0.928468 -51 CAGATTATTCAAAAAACAATTTCTTGTTAA 6 11 0 AAAAAACAAT 0.821897 -177 ATAATAAAAATAAAAACTAAGTCGCCCTAT 6 147 0 TAAAAACTAA 0.508345 -41 TAAAAAGAATCCTTGTTACC 6 178 0 TAAAAAGAAT 0.621309 -10 TTTGAGCAATAAAAAACTGTGTACTAGATC 7 29 0 AAAAAACTGT 0.690232 -73 ATGATTACATAAAAAATTATGAATTTGTGA 11 24 0 AAAAAATTAT 0.86272 -67 AAATAAATTATCGTAATTAAT 11 80 0 AATAAATTAT 0.58473 -11 TCTTAAAATCAAAAAAGAAAGTAATAAGCA 14 85 0 AAAAAAGAAA 0.508345 -216 TCGTTAAAATAAAAAAATATTCGGCTATTC 16 275 0 AAAAAAATAT 0.713239 -26 ********** Masking position 5 Map Score: 2.89634 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 187 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701