AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -ipurR_hinf_opreg_100.orf -g0.38 -x5 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 = 0 Input sequences: #1 HI0221 129 inosine-5'-monophosphate dehydrogenase (guaB) #2 HI0222 109 GMP synthase (guaA) #3 HI0329 37 conserved hypothetical protein #4 HI0330 98 opacity associated protein (oapA) #5 HI0331 59 opacity associated protein (oapB) #6 HI0334 77 GTP pyrophosphokinase (relA) #7 HI0336 82 molybdopeterin biosynthesis protein (mog) #8 HI0501 167 high affinity ribose transport protein (rbsD) #9 HI0505 97 ribokinase (rbsK) #10 HI0506 27 rbs repressor (rbsR) #11 HI0638 128 conserved hypothetical protein #12 HI0639 22 adenylosuccinate lyase (purB) #13 HI0752 300 phosphoribosylformylglycinamidine synthase (purL) #14 HI0842 197 H. influenzae predicted coding region HI0842 #15 HI0887 187 phosphoribosylaminoimidazolecarboxamide formyltransferase (purH) #16 HI0888 95 phosphoribosylamine--glycine ligase (purD) #17 HI0889 123 serine hydroxymethyltransferase (serine methylase) (glyA) #18 HI1205 214 conserved hypothetical protein #19 HI1206 86 colicin V production protein (cvpA) #20 HI1401 229 dihydroorotate dehydrogenase (pyrD) #21 HI1429 179 phosphoribosylaminoimidazole synthetase (purM) #22 HI1603 207 conserved hypothetical protein #23 HI1604 24 phosphate permease, putative #24 HI1605 65 conserved hypothetical protein #25 HI1607 62 hemM protein (hemM) #26 HI1615 160 phosphoribosylaminoimidazole carboxylase, catalytic subunit (purE) #27 HI1616 69 phosphoribosylaminoimidazole carboxylase, ATPase subunit (purK) #28 HI1633 128 adenylosuccinate synthetase (purA) #29 HI1635 274 purine nucleotide synthesis repressor (purR) #30 HI1726 124 phosphoribosylaminoimidazole-succinocarboxamide synthase (purC) Motif number 1 TTTGCTGTTTAAAGTGCGGTTGGTTTTTGC 2 37 1 AAAGTGCGGT 0.998502 -73 GAGAAGCTCAAAAGTGCGGCGAAAAAATTA 4 29 0 AAAGTGCGGC 0.995893 -70 CCCTCCAAAAGTGCGGTAAGTTTTTAC 7 8 1 AAAGTGCGGT 0.998502 -75 GGATAAATCAAAAATGCGGTAAAAACTTAC 7 26 0 AAAATGCGGT 0.972407 -57 AAAGGTACTGTAAGTACGGCGAGAAGCATT 14 127 0 TAAGTACGGC 0.773255 -71 ATAATTTCTTAAAGTGCGGTAAAAATACGA 15 84 0 AAAGTGCGGT 0.998502 -104 TAATTTAAAAAAAGTACGGCTATTTTTTAC 16 55 0 AAAGTACGGC 0.957631 -41 TAGCGTATGATAAGTGCGGTCAATTTTTGA 18 186 1 TAAGTGCGGT 0.990157 -29 CCTTACCTTTAAAGTGCGGTGAAAATTGAC 20 169 1 AAAGTGCGGT 0.998502 -61 TTACTGTAAGAAAGTGCGGTCAATTTTCAC 20 187 0 AAAGTGCGGT 0.998502 -43 ATCTCAATAAAAAGTGCGGTTAATTTTAAC 24 14 1 AAAGTGCGGT 0.998502 -52 CATCACAACAAAAGTGCGGTTAAAATTAAC 24 32 0 AAAGTGCGGT 0.998502 -34 CCGCACTTTAAAAGTGCGGTCAGATCTAAA 27 18 0 AAAGTGCGGT 0.998502 -52 CCGCACTTTTAAAGTGCGGTTGTTTTTTTC 27 29 1 AAAGTGCGGT 0.998502 -41 ATTTAAACCTAAAGTGCGGTGAAAAATCAC 28 12 1 AAAGTGCGGT 0.998502 -117 TATAAAAGAAAAAGTGTGGTGATTTTTCAC 28 30 0 AAAGTGTGGT 0.970644 -99 TGTAGAAACAAAACTGCGGTGATAATAAAA 29 18 1 AAACTGCGGT 0.981214 -257 ********** Masking position 5 Map Score: 71.4697 Number of sites scoring better than the average of aligned sites = 1154 Number in coding regions = 731 Number in noncoding regions = 423 Number of orfs with sites within 600 bp upstream = 290 Fraction of orfs with sites within 600 bp upstream = 0.0465789 Motif number 2 TGTTTAAAGTGCGGTTGGTTTTTGCAAAGTTT 2 42 1 GCGGTGTTTT 0.990106 -68 CTCCAAAAGTGCGGTAAGTTTTTACCGCATTT 7 13 1 GCGGTATTTT 0.993173 -70 GTAAATTTGGTCGGAGAATTTTTTATCCTATC 8 35 1 TCGGAATTTT 0.915598 -133 AGTGCGGTGAATTTTTAGGGTGTTT 10 4 1 GCGGTATTTT 0.993173 -24 TTTCATAAACTCGGAAATTTTTATACTTTTAA 13 57 0 TCGGAATTTT 0.915598 -244 TTAATGAAAATCCGTGAGTTTTTCATAACATT 14 90 1 TCCGTATTTT 0.809492 -108 ATAATTCTCATCGCTTATTTTTAACTATTTAA 15 151 1 TCGCTATTTT 0.809492 -37 TAAAAAAAGTACGGCTATTTTTTACCTGCAAT 16 48 0 ACGGCATTTT 0.952013 -48 TATGATAAGTGCGGTCAATTTTTGAGGTGTTT 18 191 1 GCGGTATTTT 0.993173 -24 GTAGAATAGCTCGGTCGTTTTAAACGGCCGTT 19 45 1 TCGGTGTTTA 0.761564 -42 GTCGTTTTAAACGGCCGTTTTTCATTGAGAGA 19 58 1 ACGGCGTTTT 0.931727 -29 TGTATAAAAAACGGCTAGTTTTATTTTTATGG 20 29 0 ACGGCATTTT 0.952013 -201 GTAAGAAAGTGCGGTCAATTTTCACCGCACTT 20 180 0 GCGGTATTTT 0.993173 -50 AATAAAAAGTGCGGTTAATTTTAACCGCACTT 24 19 1 GCGGTATTTT 0.993173 -47 CTTTTAAAGTGCGGTTGTTTTTTTCGTAAATT 27 34 1 GCGGTGTTTT 0.990106 -36 AAGAAAAAGTGTGGTGATTTTTCACCGCACTT 28 23 0 GTGGTATTTT 0.931316 -106 TGCAATGATTATGGTTGTTTTTAGTATGTCTG 29 91 0 ATGGTGTTTT 0.750528 -184 ***** * **** Masking position 9 Map Score: 29.4151 Number of sites scoring better than the average of aligned sites = 628 Number in coding regions = 415 Number in noncoding regions = 213 Number of orfs with sites within 600 bp upstream = 173 Fraction of orfs with sites within 600 bp upstream = 0.0277867 Motif number 3 TGCGGTAAGTTTTTACCGCATTTTTGATTTA 7 22 1 TTTTCCGCAT 0.486057 -61 CGCATTTTTGATTTATCCAATCACGTCAAAA 7 38 1 ATTTTCCAAT 0.49825 -45 ATTTTTCCTTATTTTTATAAA 7 72 0 ATTTTCCTTA 0.886706 -11 TCGGAGAATTTTTTATCCTATCTAGAAATTT 8 45 1 TTTTTCCTAT 0.960928 -123 GACAAATATAATTTGCCCCATAATGTGATAT 9 34 0 ATTTCCCCAT 0.580124 -64 GGCAAATTATATTTGTCCCATTGTGTAGAAA 9 48 1 ATTTTCCCAT 0.784491 -50 TATTTTATCCTGTATTGTTATAT 9 85 0 TTTTTCCTGT 0.769421 -13 AAGCTCATTGTTATGTCCTTAAATTAATTAA 13 30 1 TTATTCCTTA 0.629304 -271 AGAATGGATTTTTTGCCCTTAAGTCTTTATA 14 27 1 TTTTCCCTTA 0.883961 -171 ATTCTCGTCTTTTTATCCTTTCTTTTTTACG 14 169 1 TTTTTCCTTT 0.960928 -29 AGTTTCATAATTTTATCCTTATTTTTGCCCA 15 20 1 TTTTTCCTTA 0.95254 -168 TATGCCTGAAATTTATCGTATTTTTACCGCA 15 69 1 ATTTTCGTAT 0.7191 -119 TGTATTTTCCTTTCATTAAATAG 15 175 0 TATTTCCTTT 0.675353 -13 TTAATTAAATTTTTATCCATAAACAGTTAAA 17 69 1 TTTTTCCATA 0.675124 -55 AAAGTTTGTATTTTTTCCTTACCGATGAATT 18 105 0 TTTTTCCTTA 0.95254 -110 TTTTTCTCCTAAATCTTGAGCT 21 2 1 TTTTTCCTAA 0.95254 -178 TTTTTTACCTTTCAAATTTTCT 22 2 1 TTTTACCTTT 0.718031 -206 ACCTTTCAAATTTTCTCGCTTTTAAAGCGAA 22 17 1 TTTTTCGCTT 0.713606 -191 AGTTTATTTCCTATGTTTTGTTGA 23 11 0 TTATTCCTAT 0.675353 -14 TTTTTCCCCTTAAACATCACAA 24 54 0 TTTTCCCTTA 0.883961 -12 AATTTGACCTATTCTTATAAAA 26 2 1 ATTTACCTAT 0.498246 -159 AAGGATAAAATTTTATCCTAAGCACAATTTT 26 30 0 TTTTTCCTAA 0.95254 -131 TAGGATAAAATTTTATCCTTAAAGTTGCAAT 26 41 1 TTTTTCCTTA 0.95254 -120 GTTGCAATGGTATTTTCCTATAAAAGCCATT 26 64 1 TATTTCCTAT 0.675353 -97 GTGCGGTTGTTTTTTTCGTAAATTTAACGAG 27 42 1 TTTTTCGTAA 0.8427 -28 AATATTTCTCGTTAAATTTACGAA 27 56 0 ATTTTCGTTA 0.676282 -14 AAAGAAGTGATTTTTTCGTATTATTCTTGCT 29 175 0 TTTTTCGTAT 0.867808 -100 ATCCCTAAAAATTTTTCCTATTATAAAGGTT 29 246 0 ATTTTCCTAT 0.905577 -29 ATAATAAACATTTTCCCCCTATACTTCCCCT 30 39 1 TTTTCCCCTA 0.743022 -86 **** ****** Masking position 4 Map Score: 30.7654 Number of sites scoring better than the average of aligned sites = 549 Number in coding regions = 375 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 185 Fraction of orfs with sites within 600 bp upstream = 0.0297141 Motif number 4 TTTTTGTTATCGAAACGTTTCGATAAGACA 8 137 0 CGAAACGTTT 0.937807 -31 TATATTTAACGGAAACGTTTTCCTGATATT 11 104 1 GGAAACGTTT 0.989143 -25 CAATTCTGGAGCAAACATTT 12 13 1 GCAAACATTT 0.966394 -10 CTATATTTAAGCAAACGTTTGCGTTATAAT 15 126 1 GCAAACGTTT 0.996132 -62 TTTACGCAAACGTTTTCTTTTTGGC 19 6 1 GCAAACGTTT 0.996132 -81 TAACAATATCGCAAACGTTTGCTTGATGAT 21 119 1 GCAAACGTTT 0.996132 -61 CATATATCAGGCAAACGTTTGCTAAATGGC 26 89 0 GCAAACGTTT 0.996132 -72 ATCAAATAAAGCAAACGTTTGCTATTTTTT 30 99 0 GCAAACGTTT 0.996132 -26 ********** Masking position 5 Map Score: 20.7295 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 6 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 5 TTATGGCAAATAGTATGAAAATCATAGCATA 1 18 1 TGTATGAAAA 0.931024 -112 GATTTCACTTTATTTTGAAAACGAAATTTTA 1 54 0 TTTTTGAAAA 0.975295 -76 AAATGAGAGATGGTTTGAAAA 3 27 1 TGTTTGAAAA 0.966836 -11 TGAAGTATTTTTGTTTGATAATGTGATATAA 13 108 0 TGTTTGATAA 0.75626 -193 ACAAAATCTTTTTTTTGAAAATAGGGAGTAT 13 248 1 TTTTTGAAAA 0.969527 -53 ATTATGATAATGTTATGAAAAACTCACGGAT 14 99 0 TTTATGAAAA 0.948393 -99 CAATTCCCCCTCTTTTGTAAAGAGGGGGATA 16 21 0 TTTTTGTAAA 0.808629 -75 TCATCTAAGATGGTTTGAAAAATCAGACATA 18 48 1 TGTTTGAAAA 0.966836 -167 CTTTATCGTATTTTTTGAAAAATTAAACTAT 18 132 1 TTTTTGAAAA 0.969527 -83 TCTTACAAATTTTTTTGAAAAATTTTAACTA 22 125 1 TTTTTGAAAA 0.969527 -83 TTTGACCTATTCTTATAAAAATTGTGCTTAG 26 13 1 TTTATAAAAA 0.785077 -148 ATTGCAAATTTTTTATAAAAAGAAGTGATTT 29 193 0 TTTATAAAAA 0.77236 -82 ACGTTTGCTATTTTTTAAAAAGAAATAAAAA 30 84 0 TTTTTAAAAA 0.77025 -41 * ********* Masking position 10 Map Score: 18.542 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 73 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 6 TTTCGTTTTCAAAATAAAGTGAAATCTGTATA 1 59 1 AAAAAAAGGA 0.626847 -71 TTGAAGTTAAAAAATATTGCGACGAGATTATA 1 87 0 AAAAATTGGA 0.827525 -43 CATATTATTTAAAACTTTGCAAAAACCAACCG 2 53 0 AAAATTTGAA 0.940458 -57 GAAATATCCTAAAAATGAGAGATGGTTTGAAA 3 15 1 AAAATGAGGA 0.829105 -23 AATCATTTATAAAAATAAGGAAAAAT 7 67 1 AAAATAAGAA 0.846864 -16 ATCCTATCTAGAAATTTTGTGATCAATATCCC 8 59 1 GAAATTTGGA 0.828529 -109 CCGAGTTTATGAAAGTGTGTAATTTTACGTCT 13 75 1 GAAATGTGAA 0.829105 -226 AAATAAGGATAAAATTATGAAACTACAACTAA 15 12 0 AAAATATGAA 0.846864 -176 TTAAATAGTTAAAAATAAGCGATGAGAATTAT 15 151 0 AAAATAAGGA 0.753615 -37 TTAAGTGATGAAAATTTAGGAATGAAATTTTA 17 40 1 AAAATTAGAA 0.940458 -84 TAATTAATGGAAAATATTGTAAAATTAAGCTC 20 88 0 AAAAATTGAA 0.896638 -142 TTAAAAGCGAGAAAATTTGAAAGGTAAAAAA 22 10 0 GAAATTTGAA 0.897289 -198 AATTTTTCAAAAAAATTTGTAAGAAAAAAGGT 22 117 0 AAAATTTGAA 0.940458 -91 TCAACAAAACATAGGAAATAAACT 23 6 1 AAAAATAGAA 0.896638 -19 TTTTAATTAGAAAATTGAGAAAATAGC 26 144 1 AAAATGAGAA 0.897663 -17 GATTAAAGCCGAAAAAGAGTAAAGTAAACGGC 28 67 1 GAAAAGAGAA 0.727113 -62 TGGTTTGATTAAAAGATTGAAAGTGCAAGCCC 29 51 1 AAAAATTGAA 0.896638 -224 TCTTTTTATAAAAAATTTGCAATAAAGATGAC 29 201 1 AAAATTTGAA 0.940458 -74 TTTATTATTGGAAATTTAGTAAATCCTACGGC 30 15 0 GAAATTAGAA 0.897289 -110 ATTTCTTTTTAAAAAATAGCAAACGTTTGCTT 30 89 1 AAAAATAGAA 0.896638 -36 **** **** ** Masking position 4 Map Score: 25.0498 Number of sites scoring better than the average of aligned sites = 357 Number in coding regions = 254 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 7 TGGATAAATCAAAAATGCGGTAAAAACTTACCGC 7 23 0 AAAAATTAAA 0.947203 -60 AATCATTTATAAAAATAAGGAAAAAT 7 67 1 AAAAATAAAA 0.675114 -16 TGTAGAAAGAAAAAATATAACAATACAGGATAAA 9 71 1 AAAAATCAAT 0.915771 -27 AAAAACACCCTAAAAATTCACCGC 10 14 0 AAAAACTAAA 0.741826 -14 ATTATCAAACAAAAATACTTCAATTGGGTTATCT 13 117 1 AAAAATCAAT 0.915771 -184 ACAACCGCTAAAAAATCAATCAATTACTTTATCT 13 191 0 AAAAATCAAT 0.915771 -110 TTTAAGACTGAAAAATGTTATTAATGAAAATCCG 14 70 1 AAAAATTTAA 0.808541 -128 AAAGTGCGGTAAAAATACGATAAATTTCAGGCAT 15 70 0 AAAAATTAAA 0.947203 -118 GTTTATGGATAAAAATTTAATTAAAATTTCATTC 17 59 0 AAAAATTTAA 0.80854 -65 AGATGGTTTGAAAAATCAGACATAGAATACACCT 18 55 1 AAAAATCATA 0.659798 -160 TAATTTTTCAAAAAATACGATAAAGTTTGTATTT 18 123 0 AAAAATTAAA 0.947203 -92 TATTTTTAGTAAAAATAGTTTAATTTTTCAAAAA 18 143 0 AAAAATTAAT 0.860776 -72 TATTTTTACTAAAAATAGACTTAAAATAGCGTAT 18 160 1 AAAAATTTAA 0.80854 -55 AAAAACACCTCAAAAATTGACCGC 18 201 0 AAAAACCAAA 0.834789 -14 GCTATTCTACAAAAATAAAGCCAAAAAGAAAACG 19 21 0 AAAAATCCAA 0.769874 -66 TAAAAAATCTCTCAATGAAAAACGGC 19 71 0 AAAAATCAAT 0.915771 -16 TTTTAATTTTAAAAATGTCATTAAATGAATTAAT 21 84 1 AAAAATTTAA 0.808541 -96 GAATTAATTTAACAATATCGCAAACGTTTGCTTG 21 110 1 AACAATCAAA 0.733022 -70 CAATTGAAATAAAAATTGGGCAGATTATATCATC 21 143 0 AAAAATCAGA 0.841017 -37 TGTTGATAGTTAAAATTTTTCAAAAAAATTTGTA 22 128 0 TAAAATCAAA 0.639383 -80 AACTATCAACAAAAATCGGGTAATATGCGCACGA 22 151 1 AAAAATTAAT 0.860776 -57 CAATTTTTATAAGAATAGGTCAAATT 26 3 0 AAGAATCAAA 0.733022 -158 TCTCCTCATAAAAAATAACGCAGACATTCTAGCA 29 145 1 AAAAATCAGA 0.841017 -130 AAAAAGAAATAAAAATCCTCTGAAATGTTAGGGG 30 65 0 AAAAATTGAA 0.655458 -60 ****** **** Masking position 5 Map Score: 23.5535 Number of sites scoring better than the average of aligned sites = 393 Number in coding regions = 294 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 8 GTGTAAGCGGTTCATATTATTTAAAACTTTGCA 2 64 0 TTATATATTA 0.855962 -46 TGTTATGTCCTTAAATTAATTAAAAGTATAAAA 13 38 1 TTAATTATTA 0.842399 -263 TGTATTTTCCTTTCATTAAATAGTTAAAA 15 169 0 TTCTTTATTA 0.847274 -19 TTATGATGAATTAATTTCATTTAAGTGATGAAA 17 20 1 TTATTTATTA 0.961535 -104 AGGAACCCTATATTTGATTGAGGTTAATAGA 18 9 1 TAATTTATTA 0.754979 -206 TACCGATGAATTTATTTTATTCATCAAAAGGTG 18 84 0 TTATTTATTA 0.963674 -131 TGCGATATTGTTAAATTAATTCATTTAATGACA 21 99 0 TTAATTATTA 0.855941 -81 TTTTAAGGATTTAGTTTAATTGAGTAAAGTTAC 25 20 0 TTGTTTATTA 0.907946 -43 CACTTTTTCTTTTATATCATTGAGATTAAAGCC 28 44 1 TTATATATTA 0.856325 -85 TAAACGGCTGTTCATTTAACTAATTTAACCGAA 28 91 1 TTATTTACTA 0.815136 -38 TAATAAAAAGTTGGTTTGATTAAAAGATTGAAA 29 40 1 TTGTTTATTA 0.910719 -235 AAACGTTTGCTTTATTTGATTTAAAA 30 109 1 TTATTTATTA 0.963717 -16 ** **** *** * Masking position 9 Map Score: 9.34123 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 107 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 9 TGTGATATAACGAGCTTATTTAGTAGATAG 9 12 0 CGAGCTTATT 0.970021 -86 GACATAACAATGAGCTTATTTTCAGAACCA 13 17 0 TGAGCTTATT 0.964022 -284 TATATTTGATTGAGGTTAATAGAAATCCAT 18 19 1 TGAGGTTAAT 0.942756 -196 ATGATCGTGTAGAGCTTAATTTTACAATAT 20 77 1 AGAGCTTAAT 0.89064 -153 TCCTAAATCTTGAGCTTATTTGTACTATTA 21 17 1 TGAGCTTATT 0.964022 -163 TTCAATTGATCGAGGTTAATC 21 169 1 CGAGGTTAAT 0.952126 -11 CAATAAAAAGTGCGGTTAATTTTAACCGCA 24 18 1 TGCGGTTAAT 0.81393 -48 TTAAAATATGCGAGCTTATTAACTTG 25 47 1 CGAGCTTATT 0.970021 -16 ********** Masking position 8 Map Score: 7.6233 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 20 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 10 ACAGATTTCACTTTATTTTGAAAACGAAAT 1 58 0 CTTTATTTTG 0.595712 -72 TTATAATGCTCTTATTATTGATAGTGTAAG 2 90 0 CTTATTATTG 0.357323 -20 GTAATCGCCCCTTTTTCTTTTTAAGTTCTT 5 23 1 CTTTTTCTTT 0.898728 -37 CTTCCTGTCGCTTTTATTTTGGGTGGATAT 6 28 0 CTTTTATTTT 0.60593 -50 TTAACGGAAACGTTTTCCTGATATTTACTA 11 109 1 CGTTTTCCTG 0.836981 -20 ATTACAAAATCTTTTTTTTGAAAATAGGGA 13 245 1 CTTTTTTTTG 0.916954 -56 TAATTTTATCCTTATTTTTGCCCACATTTA 15 27 1 CTTATTTTTG 0.691435 -161 TTTATGTGGGCTTTTTTATGCCTGAAATTT 15 53 1 CTTTTTTATG 0.485801 -135 CAAACTTTATCGTATTTTTTGAAAAATTAA 18 128 1 CGTATTTTTT 0.544581 -87 TTTACGCAAACGTTTTCTTTTTGGCTTTAT 19 11 1 CGTTTTCTTT 0.894259 -76 TTCTTTTTGGCTTTATTTTTGTAGAATAGC 19 25 1 CTTTATTTTT 0.452089 -62 ATATCGCAAACGTTTGCTTGATGATATAAT 21 124 1 CGTTTGCTTG 0.855193 -56 GAAGATAAACCTTTTTTCTTACAAATTTTT 22 109 1 CTTTTTTCTT 0.677622 -99 ATTAACCGCACTTTTTATTGAGATCAA 24 8 0 CTTTTTATTG 0.732595 -58 AGTAAAGTTACTTTTATTTG 25 1 0 CTTTTATTTG 0.73304 -62 ATTTAGCAAACGTTTGCCTGATATATGTAA 26 92 1 CGTTTGCCTG 0.667519 -69 AATCACCACACTTTTTCTTTTATATCATTG 28 36 1 CTTTTTCTTT 0.898728 -93 AATGAACAGCCGTTTACTTTACTCTTTTTC 28 77 0 CGTTTACTTT 0.677747 -52 AAATAGCAAACGTTTGCTTTATTTGATTTA 30 102 1 CGTTTGCTTT 0.767822 -23 ********** Masking position 3 Map Score: 10.1029 Number of sites scoring better than the average of aligned sites = 596 Number in coding regions = 508 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 11 TATTTTGAAAACGAAATTTTAGGATTTATGC 1 44 0 AGAAATTTTA 0.962069 -86 TCTCATTTTTAGGATATTTCAAAT 3 4 0 AGATATTTCA 0.804335 -34 AAAAACAACTAAGAAATTTCAAATTTGGGAT 8 86 0 AGAAATTTCA 0.927554 -82 CAGAAACTCTAGGCTTTTTTAATGTTCGAGT 11 51 1 AGCTTTTTTA 0.456404 -78 ATCTATTGCTAATAAATTTTAAAACCTTATG 13 164 0 ATAAATTTTA 0.645363 -137 ACCGCACTTTAAGAAATTATATTTAATCTTT 15 94 1 AGAAATTATA 0.729664 -94 CATTTAAGTGATGAAAATTTAGGAATGAAAT 17 37 1 AGAAAATTTA 0.729668 -87 AAATTTAGGAATGAAATTTTAATTAAATTTT 17 51 1 AGAAATTTTA 0.962069 -73 CACTTATCATACGCTATTTTAAGTCTATTTT 18 171 0 AGCTATTTTA 0.804335 -44 TTTTGATTGCAAGCAATTTCATTTTAATTTT 21 63 1 AGCAATTTCA 0.866022 -117 TTACCACACTAGGAAATATTACCCAGTTGCT 22 69 1 AGAAATATTA 0.729668 -139 TAATATGCGCACGAATTTTTAACCCCTTAAT 22 171 1 AGAATTTTTA 0.838198 -37 TGTGCTTAGGATAAAATTTTATCCTTAAAGT 26 35 1 AAAAATTTTA 0.645373 -126 * ********* Masking position 1 Map Score: 4.66787 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 228 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 12 ATTTTTCCTTATTTTTATAAATGATTTTGAC 7 62 0 ATTTTATAAA 0.466973 -21 TTGTTTTTCTATTTTTGTTATCTATATTTGT 8 109 1 ATTTTGTTAT 0.866742 -59 CTAAAAGCTCCTTTTTGTTATCGAAACGTTT 8 147 0 CTTTTGTTAT 0.766546 -21 AATTTTTATACTTTTAATTAATTTAAGGACA 13 43 0 CTTTTATTAA 0.806057 -258 AAACTCACGGATTTTCATTAATAACATTTTT 14 80 0 ATTTTATTAA 0.891691 -118 TAGGAATGAAATTTTAATTAAATTTTTATCC 17 56 1 ATTTTATTAA 0.891691 -68 AAATTAAACTATTTTTACTAAAAATAGACTT 18 151 1 ATTTTACTAA 0.722299 -64 TCATTAATACATTTTAATTATGTATAAAAAA 20 50 0 ATTTTATTAT 0.927955 -180 AAGCAATTTCATTTTAATTTTAAAAATGTCA 21 73 1 ATTTTATTTT 0.578255 -107 TTTTTGAAAAATTTTAACTATCAACAAAAAT 22 136 1 ATTTTACTAT 0.802763 -72 ATCAAACCAACTTTTTATTATCACCGCAGTT 29 29 0 CTTTTATTAT 0.866741 -246 AAAATGAGCGATTTTGGTTATGCAATGATTA 29 112 0 ATTTTGTTAT 0.866742 -163 TAGGGGGAAAATGTTTATTATTGGAAATTTA 30 29 0 ATGTTATTAT 0.670197 -96 ***** ***** Masking position 5 Map Score: 6.06608 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 128 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 13 TAAAAATGAGAGATGGTTTGAAAA 3 24 1 AGATGGTTTG 0.925014 -14 ACCCAATTGAAGTATTTTTGTTTGATAATG 13 116 0 AGTATTTTTG 0.691982 -185 GAAAATAGGGAGTATGTTTGAACATAAATC 13 264 1 AGTATGTTTG 0.945415 -37 CCATCATCTAAGATGGTTTGAAAAATCAGA 18 45 1 AGATGGTTTG 0.925014 -170 GATAATAAAAAGTTGGTTTGATTAAAAGAT 29 38 1 AGTTGGTTTG 0.941393 -237 GGTTGTTTTTAGTATGTCTGTTGTCGTGGG 29 81 0 AGTATGTCTG 0.920978 -194 TATTCTTGCTAGAATGTCTGCGTTATTTTT 29 155 0 AGAATGTCTG 0.899504 -120 ********** Masking position 1 Map Score: 2.02595 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 44 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 14 AATCATAGCATAAATCCTAAAATTTCGTTTT 1 37 1 TAAACCTAAA 0.764605 -93 AAAAATGCGGTAAAAACTTACCGCACTTTTG 7 16 0 TAAAACTTAC 0.737051 -67 AATCAATCCTTAATACCTTAAAA 11 3 1 TCAACCTTAA 0.827995 -126 TAATAAATTTTAAAACCTTATGAACAGCCAG 13 155 0 TAAACCTTAT 0.782469 -146 GGCGTGAGTATAAAGACTTAAGGGCAAAAAA 14 35 0 TAAAACTTAA 0.93015 -163 TTCCTTTCATTAAATAGTTAAAAATAAGCGA 15 161 0 TAAAAGTTAA 0.782315 -27 TGTTTATGGATAAAAATTTAATTAAAATTTC 17 63 0 TAAAATTTAA 0.568494 -61 TTTTTATCCATAAACAGTTAAACTATCTGCC 17 78 1 TAAAAGTTAA 0.782192 -46 CACGAATTTTTAACCCCTTAATTTGGAGTAA 22 180 1 TAACCCTTAA 0.828003 -28 TCAATTAAACTAAATCCTTAAAATATGCGAG 25 30 1 TAAACCTTAA 0.962341 -33 ATATTTAAATCCCTAAAAATTTTTCC 29 259 0 TAAACCCTAA 0.828007 -16 **** ****** Masking position 3 Map Score: 2.0847 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 94 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 15 TTTGAAAACGAAATTTTAGGATTTATGCTAT 1 41 0 AATTTTAGGA 0.950302 -89 AACCATCTCTCATTTTTAGGATATTTCAAAT 3 11 0 CATTTTAGGA 0.782654 -27 AGTGCGGTGAATTTTTAGGGTGTTTTT 10 10 1 AATTTTAGGG 0.951183 -18 TAAAAATGCTATATTTAACGGAAACGTTTTC 11 95 1 ATTTTAACGG 0.402026 -34 TACTTTTAATTAATTTAAGGACATAACAATG 13 35 0 TATTTAAGGA 0.787151 -266 TTAAGTGATGAAAATTTAGGAATGAAATTTT 17 40 1 AAATTTAGGA 0.796145 -84 AAATAAGCTCAAGATTTAGGAGAAAAA 21 7 0 AAATTTAGGA 0.796145 -173 TTTTGTTGTGATGTTTAAGGGGAAAAA 24 49 1 ATTTTAAGGG 0.774533 -17 TAAGCTCGCATATTTTAAGGATTTAGTTTAA 25 34 0 TATTTAAGGA 0.787151 -29 ATACCATTGCAACTTTAAGGATAAAATTTTA 26 46 0 AATTTAAGGA 0.942875 -115 TTTTTTTCGTAAATTTAACGAGAAATATT 27 51 1 AATTTAACGA 0.763612 -19 TAATAGGAAAAATTTTTAGGGATTTAAATAT 29 254 1 AATTTTAGGG 0.951183 -21 AAATCCTCTGAAATGTTAGGGGAAGTATAGG 30 56 0 AATGTTAGGG 0.754494 -69 ** ******** Masking position 8 Map Score: 7.94503 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 73 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714