AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00670_hinf_reg_300.orf -o00670_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 HI0609 300 methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase (folD) #2 HI0622 300 polypeptide deformylase (def) #3 HI0623 92 methionyl-tRNA formyltransferase (fmt) #4 HI0885 191 thiol:disulfide interchange protein (dsbD) #5 HI0886 111 H. influenzae predicted coding region HI0886 #6 HI0887 187 phosphoribosylaminoimidazolecarboxamide formyltransferase (purH) #7 HI0888 95 phosphoribosylamine--glycine ligase (purD) #8 HI0889 123 serine hydroxymethyltransferase (serine methylase) (glyA) #9 HI0899_HI0900 100 HI0899: dihydrofolate reductase (folA), HI0900: glutamate 5-kinase (gamma-glutamyl kinase) (proB) #10 HI0901 80 conserved hypothetical protein #11 HI1428 54 phosphoribosylglycinamide formyltransferase (purN) #12 HI1429 179 phosphoribosylaminoimidazole synthetase (purM) #13 HI1444 300 5,10 methylenetetrahydrofolate reductase (metF) #14 HI1587 300 DNA-binding protein H-NS (hns) #15 HI1588 69 formyltetrahydrofolate deformylase (purU) Motif number 1 TTCTTTCGTATTTTCTTGAAATTTTTATAAAAGAAATCC 1 13 0 TTTTTATTTA 0.631082 -288 AAATCAAAAATTTCATTGACTGAAATAAAAACAAACTTA 1 147 0 TTTTTAGTAA 0.460433 -154 AAAGGGGGATATTTCTTAAAGTGGAATAATTTTGAACAA 1 196 0 ATTTTATAAA 0.888092 -105 ACGAACAATGATTTTTTTACAATGAAAAAGGGGGATATT 1 222 0 ATTTTAAAAA 0.817129 -79 TAGCAAACGCTTTCTTTTTCATCACATAATATCAAGGAT 1 266 1 TTTTTTTAAA 0.949904 -35 GTCCTTCTGTTTTTATTTAACTTAGATAAGTATTTGGTA 2 86 0 TTTTTATAAA 0.963469 -215 TAGACACTTATTTGATTAAATAATGAATAAATTCCCAAA 2 154 0 TTTTTAAATA 0.860755 -147 AGTGTCTAATTTTAATTTTCAATAAGTAAGTAATTTTTC 2 185 1 TTTTTTAGAA 0.855907 -116 TACCTAAAACTATGATTTAGATCACAAAAAGGAAAATCA 4 109 0 TATTTATAAA 0.754755 -83 TTATTTTTTACTTTTGGTAAAAAGTATTTT 5 2 1 TATTTATGAA 0.629443 -110 ATTTTTCAATTTTAATTATTGTTTAACTACCCGTTAAAG 5 36 1 TTTTTTTATA 0.888961 -76 TTGCTTTCCTTTTGTTTAAAGATGAATTAAAACGGCGTC 5 83 0 TTTTTAAATA 0.861137 -29 TTTAGTTGTAGTTTCATAATTTTATCCTT 6 1 1 TTTTTTTAAA 0.950458 -187 ATTAAATATAATTTCTTAAAGTGCGGTAAAAATACGATA 6 82 0 ATTTTATGAA 0.813735 -106 AACGCAAACGTTTGCTTAAATATAGAAAAGATTAAATAT 6 112 0 TTTTTAAAAA 0.933417 -76 TGTATTTTCCTTTCATTAAATAGTTAAAAATAAGCGATG 6 159 0 TTTTTAAAAA 0.93562 -29 GATGAATTAATTTCATTTAAGTGATGAAAATTTAGGAAT 8 24 1 TTTTTATGAA 0.934323 -100 TTAAGTGATTTTTCATTGATTTAGTGATAACGTTAATGC 9 36 0 TTTTTATGTA 0.858168 -65 GCAATCAAAATTTATTTGTACTACTTTAATAGTACAAAT 12 34 0 TTTTTTTTAA 0.748737 -146 TTGCAAGCAATTTCATTTTAATTTTAAAAATGTCATTAA 12 69 1 TTTTTTTAAA 0.949904 -111 ATACAATAGATTTGTTTTTTAGCGCAAAAAAT 13 4 0 TTTTTTGAAA 0.84503 -297 ATTTTTTGTGTATTTTTATAGAAAGATAAATGCGTGTTA 13 48 0 TATTTTAAAA 0.55709 -253 ATTACCGCACTTTCTTTTTCGTTGTAAAATGGGGTAAAT 13 85 1 TTTTTTTAAA 0.950445 -216 TGATCTAAAAATTAGTTATTATTGAACAATAATTATCCA 13 161 1 ATTTTTTAAA 0.852264 -140 ATAATTATCCATTTATTGAATTATTAATAATAATCATAC 13 189 1 ATTTTATATA 0.768068 -112 TTAAAACCTATTTTATTGTACAAATACTATTTTAGAATC 13 258 1 TTTTTTAATA 0.818436 -43 TATTATAAGTATTTTTTCAGAGTGGATAACGAAGAAGAA 14 44 0 ATTTTAGAAA 0.69286 -257 CTGTTGGCATTTTGTTTGTTTTACGGTAATCTCCCCAAT 14 106 0 TTTTTTTGAA 0.913503 -195 TTGTGTTTATTTTCTTTATATTTTTATTAAAGTTTATAA 14 159 0 TTTTTTTATA 0.888959 -142 TGTTTCGACCATTTATTTAATAATAGATATTTACAATAA 14 209 1 ATTTTAAGTA 0.50646 -92 TGTGGGAAAATTTATTTAATAATAGAGAAAATAAAATTT 14 246 0 TTTTTAAAAA 0.936677 -55 *** ** * * * ** Masking position 7 Map Score: 34.1151 Number of sites scoring better than the average of aligned sites = 944 Number in coding regions = 654 Number in noncoding regions = 290 Number of orfs with sites within 600 bp upstream = 218 Fraction of orfs with sites within 600 bp upstream = 0.0350145 Motif number 2 CTTATAATTGACCGCACTTATCGGCGAGTA 1 121 0 ACCGCACTTA 0.945104 -180 TAAGAAATATCCCCCTTTTTCATTGTAAAA 1 217 1 CCCCCTTTTT 0.868308 -84 GCTAAAGCCCACCCTACGTT 3 1 0 ACCCTACGTT 0.852938 -92 GCTTAAGCCCACCGTTTTTTGAAATGATTG 3 34 0 ACCGTTTTTT 0.797482 -59 GCTTAAGCCCACCCTACTTCCTATCAATTA 3 56 1 ACCCTACTTC 0.863285 -37 GTAAAAAATCACCGCACTTTTTTATTGTTA 4 78 0 ACCGCACTTT 0.993316 -114 TCGTATTTTTACCGCACTTTAAGAAATTAT 6 84 1 ACCGCACTTT 0.993316 -104 ATCTAACTATCCCCCTCTTTACAAAAGAGG 7 14 1 CCCCCTCTTT 0.97069 -82 ACCTGCAATTCCCCCTCTTTTGTAAAGAGG 7 27 0 CCCCCTCTTT 0.97069 -69 GTAAAAAATAGCCGTACTTTTTTTAAATTA 7 55 1 GCCGTACTTT 0.899089 -41 ACAAAAAATTACCGCACTTTCTTTTTCGTT 13 78 1 ACCGCACTTT 0.993316 -223 GCAATGATTTACCCCATTTTACAACGAAAA 13 100 0 ACCCCATTTT 0.96223 -201 ACTCAAAACTACCGCACTTTTGTTAGCAAT 13 125 0 ACCGCACTTT 0.993316 -176 ********** Masking position 9 Map Score: 21.2631 Number of sites scoring better than the average of aligned sites = 1810 Number in coding regions = 1252 Number in noncoding regions = 558 Number of orfs with sites within 600 bp upstream = 343 Fraction of orfs with sites within 600 bp upstream = 0.0550916 Motif number 3 GATTTCTTTTATAAAAATTTCAAGAAAATA 1 14 1 ATAAAAATTT 0.931708 -287 ATTTCAGTCAATGAAATTTTTGATTTTTCA 1 160 1 ATGAAATTTT 0.799573 -141 TTCTATCACAAAGAAATTTGAATACCTAAA 4 140 0 AAGAAATTTG 0.655262 -52 AGAATTGAGTATAAAAATATAGATGCTCGA 4 172 0 ATAAAAATAT 0.902055 -20 TTAAACAATAATTAAAATTGAAAAATACTT 5 32 0 ATTAAAATTG 0.854943 -80 AAAAATAAGGATAAAATTATGAAACTACAA 6 16 0 ATAAAATTAT 0.801678 -172 ACCGCACTTTAAGAAATTATATTTAATCTT 6 94 1 AAGAAATTAT 0.645133 -94 CATTTAAGTGATGAAAATTTAGGAATGAAA 8 37 1 ATGAAAATTT 0.900474 -87 TAAAAATTTAATTAAAATTTCATTCCTAAA 8 54 0 ATTAAAATTT 0.89306 -70 CTGTTTATGGATAAAAATTTAATTAAAATT 8 65 0 ATAAAAATTT 0.931708 -59 AATTTTTCCTATAAAAATAGCTCAAGATTG 10 46 0 ATAAAAATAG 0.866682 -35 AAGTAGTACAAATAAATTTTGATTGCAAGC 12 47 1 AATAAATTTT 0.713115 -133 ATCAATTGAAATAAAAATTGGGCAGATTAT 12 149 0 ATAAAAATTG 0.905927 -31 GTATTTGTACAATAAAATAGGTTTTAATAT 13 255 0 AATAAAATAG 0.728694 -46 AACAGATTTTATAAAAATTTTATAAACTTT 14 140 1 ATAAAAATTT 0.931708 -161 ATAAACTTTAATAAAAATATAAAGAAAATA 14 161 1 ATAAAAATAT 0.902055 -140 AAATAAACACAAAAAAATATATCTGTTTCG 14 186 1 AAAAAAATAT 0.861441 -115 TAATAGAGAAAATAAAATTTATTGTAAATA 14 236 0 AATAAAATTT 0.84934 -65 TCTATTATTAAATAAATTTTCCCACATTTA 14 259 1 AATAAATTTT 0.713115 -42 ATGTTTAGATAAAAAAATAGAACCCATAAA 15 37 0 AAAAAAATAG 0.814419 -33 ********** Masking position 8 Map Score: 22.5366 Number of sites scoring better than the average of aligned sites = 701 Number in coding regions = 497 Number in noncoding regions = 204 Number of orfs with sites within 600 bp upstream = 180 Fraction of orfs with sites within 600 bp upstream = 0.028911 Motif number 4 CTCGCCGATAAGTGCGGTCAATTATAAGTTTG 1 123 1 AGTGCGGTAT 0.949167 -178 ACAATGAAAAAGGGGGATATTTCTTAAAGTGG 1 211 0 AGGGGGATTT 0.932841 -90 TGCCGATGGTAGTGTGGGGTTTCCCCATGTGA 2 35 1 AGTGTGGGTT 0.964028 -266 GTAGAATTTTAGTGGGATTATAGCACAGCTAA 2 259 0 AGTGGGATTA 0.840778 -42 AACGTAGGGTGGGCTTTAGCCAGCAAT 3 6 1 AGGGTGGGTT 0.961631 -87 GATAGGAAGTAGGGTGGGCTTAAGCCCACCGT 3 49 0 AGGGTGGGTA 0.899097 -44 ACAATAAAAAAGTGCGGTGATTTTTTACCTGA 4 80 1 AGTGCGGTTT 0.988143 -112 AATTTCTTAAAGTGCGGTAAAAATACGATAAA 6 80 0 AGTGCGGTAA 0.869087 -108 TTTTGTAAAGAGGGGGATAGTTAGATAAA 7 8 0 AGGGGGATTT 0.932841 -88 TCTTTACAAAAGAGGGGGAATTGCAGGTAAAA 7 29 1 AGAGGGGGTT 0.908417 -67 CGAAAAAGAAAGTGCGGTAATTTTTTGTGTAT 13 74 0 AGTGCGGTTT 0.988143 -227 TGCTAACAAAAGTGCGGTAGTTTTGAGTATGT 13 127 1 AGTGCGGTTT 0.988143 -174 ******** ** Masking position 1 Map Score: 14.417 Number of sites scoring better than the average of aligned sites = 771 Number in coding regions = 482 Number in noncoding regions = 289 Number of orfs with sites within 600 bp upstream = 211 Fraction of orfs with sites within 600 bp upstream = 0.0338901 Motif number 5 TCATTGACTGAAATAAAAACAAACTTATAATTGA 1 140 0 AAATAAAAAC 0.69538 -161 AATTTTGAACAATTAAGTTGAAAAATCAAAAATT 1 174 0 AATTAGAAAA 0.919084 -127 ATACTTATCTAAGTTAAATAAAAACAGAAGGACC 2 92 1 AAGTAAAAAA 0.865057 -209 ATGTGACTTCATATGAGTTGAAAAATTACTTACT 2 209 0 ATATAGAAAA 0.607267 -92 ACAAAAAGGAAAATCAGGTAAAAAATCACCGCAC 4 91 0 AAATAGAAAA 0.959958 -101 AGAATTGAGTATAAAAATATAGATGC 4 176 0 AATTAGAAAA 0.919126 -16 GTTAAACAATAATTAAAATTGAAAAATACTTTTT 5 29 0 AATTAAGAAA 0.676876 -83 ATGTGGGCAAAAATAAGGATAAAATTATGAAACT 6 20 0 AAATAGAAAA 0.959958 -168 TAATTTCTTAAAGTGCGGTAAAAATACGATAAAT 6 79 0 AAGTCGAAAA 0.659299 -109 TTTAACTATTTAATGAAAGGAAAATACA 6 170 1 TAATAAAAAA 0.606332 -18 AAAGAGGGGGAATTGCAGGTAAAAAATAGCCGTA 7 37 1 AATTCAAAAA 0.772926 -59 TTATGGATAAAAATTTAATTAAAATTTCATTCCT 8 57 0 AAATTAAAAA 0.643766 -67 CGTTATCACTAAATCAATGAAAAATCACTTAATA 9 43 1 AAATAAAAAA 0.959806 -58 TTATAGGAAAAATTTAAGGTAAAACGATA 10 62 1 AATTAAAAAA 0.918835 -19 TTCCTTATAGAAATCAGCCCAAAAGGGCTGAATT 11 27 0 AAATAGAAAA 0.959958 -28 TTAATAGTACAAATAAGCTCAAGATTTAGGAGAA 12 14 0 AAATAGAAGA 0.706787 -166 GACATTTTTAAAATTAAAATGAAATTGCTTGCAA 12 69 0 AAATAAGAAA 0.815452 -111 AACCTCGATCAATTGAAATAAAAATTGGGCAGAT 12 152 0 AATTAAAAAA 0.918834 -28 AATGCGTGTTAAATAAATACAATAGATTTGTTTT 13 25 0 AAATAAAATA 0.618316 -276 CTTTCTATAAAAATACACAAAAAATTACCGCACT 13 62 1 AAATCAAAAA 0.87775 -239 AATATAAAGAAAATAAACACAAAAAAATATATCT 14 176 1 AAATAAAAAA 0.959806 -125 **** ** **** Masking position 4 Map Score: 24.466 Number of sites scoring better than the average of aligned sites = 415 Number in coding regions = 282 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 6 AAAAACAAACTTATAATTGACCGCACTTATCGG 1 127 0 TATAATTACG 0.75459 -174 AGTTGAAAAATCAAAAATTTCATTGACTGAAAT 1 160 0 TAAAAATTCT 0.854139 -141 TCATATGAGTTGAAAAATTACTTACTTATTGAA 2 202 0 TAAAAATACT 0.9389 -99 GAAAATCAGGTAAAAAATCACCGCACTTTTTTA 4 84 0 TAAAAATACG 0.95219 -108 GGTAAAAATACGATAAATTTCAGGCATAAAAAA 6 64 0 CATAAATTCG 0.760648 -124 AACGTTTGCGTTATAATTCTCATCGCTTATTTT 6 139 1 TATAATTTCT 0.474808 -49 CATTAAATAGTTAAAAATAAGCGATGAGAATTA 6 152 0 TAAAAATAGG 0.807045 -36 GAATTGCAGGTAAAAAATAGCCGTACTTTTTTT 7 46 1 TAAAAATGCG 0.901626 -50 AAACTATCTGCCATAAATTACATAACAGGAGAA 8 97 1 CATAAATACT 0.865979 -27 TTCCAAGTTCTTAAAATTGGCATTAACGTTATC 9 17 1 TAAAATTGCT 0.680497 -84 ACTAAATCAATGAAAAATCACTTAATATCAGGT 9 50 1 TAAAAATACT 0.9389 -51 AAATCCCCCTAAAATTTGCCGTTACTATACC 9 80 0 CAAAATTGCG 0.693677 -21 CAAGATTGTTTCATAAATCAGTGCTTTTATCAA 10 21 0 TATAAATAGG 0.681929 -60 CATTTTAATTTTAAAAATGTCATTAAATGAATT 12 82 1 TAAAAATTCT 0.85414 -98 TAAAAATACACAAAAAATTACCGCACTTTCTTT 13 69 1 CAAAAATACG 0.942138 -232 ATGTGTTGATCTAAAAATTAGTTATTATTGAAC 13 155 1 CAAAAATAGT 0.725842 -146 TTATCCACTCTGAAAAAATACTTATAATAATTG 14 54 1 TAAAAAAACT 0.537663 -247 AATAAACCTCAATAAATAACATTAAATGTGGG 14 279 0 CATAAATACT 0.865993 -22 * ****** ** * Masking position 6 Map Score: 13.7722 Number of sites scoring better than the average of aligned sites = 750 Number in coding regions = 558 Number in noncoding regions = 192 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 7 GCCGATGGTAGTGTGGGGTTTCCCCATGTG 2 36 1 GTGTGGGGTT 0.983137 -265 GTGTCGAAAGATATGGGGTTTTAGCTTTTG 2 128 1 ATATGGGGTT 0.800124 -173 AACGTAGGGTGGGCTTTAGCCAGCAA 3 7 1 GGGTGGGCTT 0.994331 -86 TTTCAAAAAACGGTGGGCTTAAGCCCACCC 3 40 1 CGGTGGGCTT 0.984947 -53 ATAGGAAGTAGGGTGGGCTTAAGCCCACCG 3 50 0 GGGTGGGCTT 0.994331 -43 GCCCACATTTATGTGGGCTTTTTTATGCCT 6 46 1 ATGTGGGCTT 0.980201 -142 ********** Masking position 4 Map Score: 7.45517 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 = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 8 AGCTTTTGGGAATTTATTCATTATTTAATCA 2 150 1 AATTATTCAT 0.975368 -151 TATGACGCCGTTTTAATTCATCTTTAAACAA 5 80 1 TTTTATTCAT 0.781479 -32 ACTTAAATGAAATTAATTCATCATAATGATA 8 15 0 AATTATTCAT 0.975368 -109 TTTAATTAAAATTTCATTCCTAAATTTTCAT 8 47 0 ATTTATTCCT 0.84128 -77 GATATTGTTAAATTAATTCATTTAATGACAT 12 98 0 AATTATTCAT 0.975368 -82 AGTCAATTTCAATTTATTCATTAAAAGTATG 13 223 0 AATTATTCAT 0.975368 -78 AATAAATTGAAATTGACTCATATTAAAACCT 13 236 1 AATTACTCAT 0.924151 -65 **** ****** Masking position 6 Map Score: 5.62169 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 33 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 TTTTTATAAAAGAAATCCTT 1 1 0 AGAAATCCTT 0.743537 -300 TATTTTAACGAACAATGATTTTTTTACAAT 1 238 0 AACAATGATT 0.604086 -63 TCGTTAAAATAGCAAACGCTTTCTTTTTCA 1 257 1 AGCAAACGCT 0.752595 -44 TGAGCTATCCTTGATATTATGT 1 289 0 AGCTATCCTT 0.823605 -12 GGCTTTAGCCAGCAATCATTTCAAAAAACG 3 22 1 AGCAATCATT 0.970781 -71 ATGCTATCAAAGCTATCATTCTATCTGTGC 4 38 1 AGCTATCATT 0.891835 -154 GCTTAAATATAGAAAAGATTAAATATAATT 6 108 0 AGAAAAGATT 0.637568 -80 TCTATATTTAAGCAAACGTTTGCGTTATAA 6 125 1 AGCAAACGTT 0.941722 -63 GGTTGATAAAAGCACTGATTTATGAAACAA 10 19 1 AGCACTGATT 0.784812 -62 TATATCATCAAGCAAACGTTTGCGATATTG 12 122 0 AGCAAACGTT 0.941722 -58 CACTTTTGTTAGCAATGATTTACCCCATTT 13 111 0 AGCAATGATT 0.950893 -190 ********** Masking position 1 Map Score: 5.31595 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 249 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 10 AAAAATTTCAAGAAAATACGAAAGAAGTGGTCGGC 1 26 1 AAAAAAAAGA 0.875895 -275 CTTTTTCATCACATAATATCAAGGATAGCTCA 1 279 1 AATAAAAGGA 0.965381 -22 TCTAAGTTAAATAAAAACAGAAGGACCCCGTGTCG 2 99 1 AAAAAAAGGA 0.976092 -202 CACAGCTAATAAAACATTTATAGGAATGTGACTTC 2 233 0 AAACATAGGA 0.861569 -68 GCATACGCCAAAATAAGTATAAGGATGGAAA 4 7 0 AATAAAAGGA 0.965381 -185 ACTATGATTTAGATCACAAAAAGGAAAATCAGGTA 4 105 0 AATCAAAGGA 0.967961 -87 GCCAATTTTAAGAACTTGGAAAGGATT 9 3 0 AAACTAAGGA 0.861569 -98 ATCAGTGCTTTTATCAACCAAAGGACA 10 3 0 TATCAAAGGA 0.809564 -78 ATAACGAAGAAGAAAAAAGAAAGGAATAGTTGCCG 14 23 0 AAAAAAAGGA 0.976092 -278 ATAAACTTTAATAAAAATATAAAGAAAATAAACAC 14 161 1 AAAAAAAAGA 0.875895 -140 * **** ***** Masking position 12 Map Score: 6.93994 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 25 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 11 CGTTAAAATAGCAAACGCTTTCTTTTTCATCA 1 258 1 GCAACGCTTC 0.551426 -43 GCTTTAGCCAGCAATCATTTCAAAAAACGGTG 3 23 1 GCAACATTTA 0.923397 -70 CTATATTTAAGCAAACGTTTGCGTTATAATTC 6 126 1 GCAACGTTTC 0.499968 -62 AATTTTGATTGCAAGCAATTTCATTTTAATTT 12 61 1 GCAACAATTC 0.90648 -119 TAACAATATCGCAAACGTTTGCTTGATGATAT 12 119 1 GCAACGTTTC 0.499968 -61 ACTTTTGTTAGCAATGATTTACCCCATTTTAC 13 108 0 GCAAGATTTC 0.945459 -193 **** ***** * Masking position 4 Map Score: 2.87171 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 23 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 12 AAACTTATAATTGACCGCACTTATCGGCGA 1 124 0 TTGACCGCAC 0.979423 -177 CAGGTAAAAAATCACCGCACTTTTTTATTG 4 81 0 ATCACCGCAC 0.98555 -111 TTATCGTATTTTTACCGCACTTTAAGAAAT 6 81 1 TTTACCGCAC 0.987827 -107 TACACAAAAAATTACCGCACTTTCTTTTTC 13 75 1 ATTACCGCAC 0.991473 -226 CATACTCAAAACTACCGCACTTTTGTTAGC 13 128 0 ACTACCGCAC 0.981267 -173 ********** Masking position 4 Map Score: 6.00499 Number of sites scoring better than the average of aligned sites = 334 Number in coding regions = 211 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 13 CAACTTAATTGTTCAAAATTATTCCACTTT 1 188 1 GTTCAAAATT 0.913815 -113 AAATATAGATGCTCGAAATTCTATCACAAA 4 158 0 GCTCGAAATT 0.906149 -34 TTAACTACCCGTTAAAGATTAATATGACGC 5 58 1 GTTAAAGATT 0.8611 -54 ACTGTTTATGGATAAAAATTTAATTAAAAT 8 66 0 GATAAAAATT 0.744332 -58 TATAAAAATAGCTCAAGATTGTTTCATAAA 10 37 0 GCTCAAGATT 0.974288 -44 GTACAAATAAGCTCAAGATTTAGGAGAAAA 12 12 0 GCTCAAGATT 0.974288 -168 TATGTGTTGATCTAAAAATTAGTTATTATT 13 154 1 TCTAAAAATT 0.663376 -147 ********** Masking position 6 Map Score: 1.00582 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 113 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 14 GTCCCAAACCAGTTGCGCTACCAAGCTGCG 1 90 1 AGTTGCGCTA 0.956574 -211 TGCGCTACCAAGCTGCGCTACTCGCCGATA 1 103 1 AGCTGCGCTA 0.963769 -198 ATGTTTTATTAGCTGTGCTATAATCCCACT 2 251 1 AGCTGTGCTA 0.964461 -50 CTATCATTCTATCTGTGCAACATTATTGTA 4 50 1 ATCTGTGCAA 0.832263 -142 TCTTGAGCTTATTTGTACTATTAAAGTAGT 12 24 1 ATTTGTACTA 0.839849 -156 ATCAAAATTTATTTGTACTACTTTAATAGT 12 40 0 ATTTGTACTA 0.839849 -140 ATTTTTTGCGCTAAAAAACAAAT 13 4 1 TTTTGCGCTA 0.891616 -297 AATGTTGTGTGCTATGTTTAGATA 15 56 0 TTGTGTGCTA 0.790837 -14 ********** Masking position 10 Map Score: 2.89458 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 42 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 15 ATTCCCAAAAGCTAAAACCCCATATCTTTC 2 133 0 GCTAAAACCC 0.98275 -168 TATTAGCTGTGCTATAATCCCACTAAAATT 2 257 1 GCTATAATCC 0.850183 -44 ATGATTGCTGGCTAAAGCCCACCCTACGTT 3 11 0 GCTAAAGCCC 0.98878 -82 AGTAGGGTGGGCTTAAGCCCACCGTTTTTT 3 44 0 GCTTAAGCCC 0.972126 -49 ********** Masking position 6 Map Score: 0.145997 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 13 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925