AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00230_hinf_reg_300.orf -o00230_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: HI0206 22 5'-nucleotidase, putative HI0221.1 109 H. influenzae predicted coding region HI0221.1 HI0540 75 urease, beta subunit (ureB) HI0798.1 28 ribosomal protein L36 (rpL36) Input sequences: #1 HI0011 105 DNA polymerase III, psi subunit (holD) #2 HI0075 280 anaerobic ribonucleoside-triphosphate reductase (nrdD) #3 HI0137 60 DNA polymerase III, epsilon subunit (dnaQ) #4 HI0205 292 H. influenzae predicted coding region HI0205 #5 HI0221 129 inosine-5'-monophosphate dehydrogenase (guaB) #6 HI0222 109 GMP synthase (guaA) #7 HI0229 298 polynucleotide phosphorylase (pnp) #8 HI0329 37 conserved hypothetical protein #9 HI0330 98 opacity associated protein (oapA) #10 HI0331 59 opacity associated protein (oapB) #11 HI0334 77 GTP pyrophosphokinase (relA) #12 HI0349 84 adenylate kinase (adk) #13 HI0350 141 permease, putative #14 HI0351 172 UDP-glucose 4-epimerase (galE) #15 HI0352 300 conserved hypothetical protein #16 HI0457 69 conserved hypothetical protein #17 HI0458 70 stationary phase survival protein SurA, putative #18 HI0459 131 pyrimidine operon regulatory protein (pyrR) #19 HI0514 241 DNA-directed RNA polymerase, beta' chain (rpoC) #20 HI0515 300 DNA-directed RNA polymerase, beta chain (rpoB) #21 HI0518 83 purine-nucleoside phosphorylase (deoD) #22 HI0519 98 transport protein, putative #23 HI0521 212 conserved hypothetical protein #24 HI0541 162 urease, gamma subunit (ureA) #25 HI0551 118 diadenosine-tetraphosphatase (apaH) #26 HI0583 93 2',3'-cyclic-nucleotide 2'-phosphodiesterase (cpdB) #27 HI0584 71 hydrolase #28 HI0586 66 H. influenzae predicted coding region HI0586 #29 HI0587 99 peptidase E (pepE) #30 HI0604 300 adenylate cyclase (cyaA) #31 HI0638 128 conserved hypothetical protein #32 HI0639 22 adenylosuccinate lyase (purB) #33 HI0674 110 xanthine-guanine phosphoribosyltransferase (gptA) #34 HI0692 283 xanthine-guanine phosphoribosyltransferase (gptB) #35 HI0698 150 conserved hypothetical protein #36 HI0699 79 peptidyl-prolyl cis-trans isomerase, FkbP-type (slyD) #37 HI0700 108 conserved hypothetical protein #38 HI0739 300 DNA polymerase III, alpha subunit (dnaE) #39 HI0752 300 phosphoribosylformylglycinamidine synthase (purL) #40 HI0787 300 H. influenzae predicted coding region HI0787 #41 HI0788 280 ribosomal protein L14 (rpL14) #42 HI0792 36 ribosomal protein S8 (rpS8) #43 HI0799 139 ribosomal protein S13 (rpS13) #44 HI0801 27 ribosomal protein S4 (rpS4) #45 HI0802 31 DNA-directed RNA polymerase, alpha chain (rpoA) #46 HI0856 148 DNA polymerase I (polA) #47 HI0876 300 nucleoside diphosphate kinase (ndk) #48 HI0885 191 thiol:disulfide interchange protein (dsbD) #49 HI0886 111 H. influenzae predicted coding region HI0886 #50 HI0887 187 phosphoribosylaminoimidazolecarboxamide formyltransferase (purH) #51 HI0888 95 phosphoribosylamine--glycine ligase (purD) #52 HI0921 248 leucyl-tRNA synthetase (leuS) #53 HI0922 49 rare lipoprotein B, putative #54 HI0993 191 chromosomal replication initiator protein (dnaA) #55 HI0994 27 transferrin-binding protein 1 precursor (tbp1) #56 HI0995 97 transferrin-binding protein 2 precursor (tbp2) #57 HI1152 88 pmbA protein (pmbA) #58 HI1153 210 hypoxanthine phosphoribosyltransferase (hpt) #59 HI1205 214 conserved hypothetical protein #60 HI1206 86 colicin V production protein (cvpA) #61 HI1230 147 adenine phosphoribosyltransferase (apt) #62 HI1231 113 dihydrolipoamide dehydrogenase (lpdA) #63 HI1232 62 dihydrolipoamide acetyltransferase (aceF) #64 HI1233 299 pyruvate dehydrogenase, E1 component (aceE) #65 HI1397 234 DNA polymerase III, chi subunit (holC) #66 HI1428 54 phosphoribosylglycinamide formyltransferase (purN) #67 HI1429 179 phosphoribosylaminoimidazole synthetase (purM) #68 HI1573 300 pyruvate kinase, type II (pykA) #69 HI1603 207 conserved hypothetical protein #70 HI1604 24 phosphate permease, putative #71 HI1605 65 conserved hypothetical protein #72 HI1607 62 hemM protein (hemM) #73 HI1615 160 phosphoribosylaminoimidazole carboxylase, catalytic subunit (purE) #74 HI1616 69 phosphoribosylaminoimidazole carboxylase, ATPase subunit (purK) #75 HI1632 300 H. influenzae predicted coding region HI1632 #76 HI1633 128 adenylosuccinate synthetase (purA) #77 HI1655 71 antigen #78 HI1658 56 hemolysin, putative #79 HI1659 179 ribonucleoside-diphosphate reductase, alpha chain (nrdA) #80 HI1660 141 ribonucleoside diphosphate reductase, beta chain (nrdB) #81 HI1723 135 conserved hypothetical protein #82 HI1726 124 phosphoribosylaminoimidazole-succinocarboxamide synthase (purC) #83 HI1741 260 guanosine-3',5'-bis(diphosphate) 3'- pyrophosphohydrolase (spoT) #84 HI1742 62 DNA-directed RNA polymerase, omega chain (rpoZ) #85 HI1743 249 guanylate kinase (gmk) Motif number 1 TTGCTGTTTAAAGTGCGGTTGGTTTTTGCAA 6 38 1 AAGTGCGGTG 0.990028 -72 TAAACGCCCAAAGTGCGGTCATTTTTTCGAA 7 208 1 AAGTGCGGTA 0.998107 -91 AGAAGCTCAAAAGTGCGGCGAAAAAATTATG 9 27 0 AAGTGCGGCA 0.960314 -72 AAGTGCGGTAAAAATTATAAA 12 1 1 AAGTGCGGTA 0.998107 -84 TGATAAAGCATAGTGCGGTCAAATTTTTTAT 12 27 0 TAGTGCGGTA 0.943571 -58 AAAGTGCGGTTAATTTTAGTTG 13 130 0 AAGTGCGGTA 0.998107 -12 GAAATCGCCGAAGTGCGGTCAAAATTCTCCG 19 173 1 AAGTGCGGTA 0.998107 -69 TAAAGGTTTAAAGTGCGGTTAAAAATTTCGG 19 201 0 AAGTGCGGTA 0.998107 -41 GTAAGGTTCAGAGTGCGGTCATTTTAACGGT 20 222 1 GAGTGCGGTA 0.961215 -79 ATCAATTAAAAAGTGCGGTAAAAAATGACCG 21 20 1 AAGTGCGGTA 0.998107 -64 AAAATGAATAAAGTGCGGTCATTTTTTACCG 21 35 0 AAGTGCGGTA 0.998107 -49 CGTTTACAAAAAGTGCGGTGAAAATTCGCCG 22 12 1 AAGTGCGGTA 0.998107 -87 AATAATTTGTAAGTGCGGTTTCTATATAAGG 24 27 1 AAGTGCGGTT 0.97962 -136 TTATTTATAAAAGAGCGGTCAAAA 25 105 1 AAGAGCGGTA 0.943571 -14 CACTTAAATAAAGTGCGGTCAATTTTTTACT 27 15 0 AAGTGCGGTA 0.998107 -57 CACTTTATTTAAGTGCGGTCTGTTTTTATAG 27 31 1 AAGTGCGGTT 0.97962 -41 TTCATTGCCAAAGTGCGGTAAATTTTTGAGC 35 19 0 AAGTGCGGTA 0.998107 -132 TTTGGCAATGAAGTGCGGTATTTTTTATGAA 35 38 1 AAGTGCGGTT 0.97962 -113 ACAAGAACAAAAGTGCGGTTATTTTAGTGGA 37 74 0 AAGTGCGGTA 0.998107 -35 AAAATCCTTAAAGTGCGGTTAAATTTTGCCG 38 278 0 AAGTGCGGTA 0.998107 -23 ATAATTCCAAAAGTGCGGTAAATTTTAACTG 41 103 1 AAGTGCGGTA 0.998107 -178 AACAATAAAAAAGTGCGGTGATTTTTTACCT 48 79 1 AAGTGCGGTA 0.998107 -113 TAATTTCTTAAAGTGCGGTAAAAATACGATA 50 82 0 AAGTGCGGTA 0.998107 -106 GAGAAATAAAAAGTGCGGTGGTTTTTTAGTT 52 135 0 AAGTGCGGTG 0.990028 -114 AATGCTGCAAAAGTGCGGTTAAAATTTAAGG 52 221 1 AAGTGCGGTA 0.998107 -28 TAATAGAGAAAAGTGCGGTAAAAATTGTCGG 54 149 0 AAGTGCGGTA 0.998107 -43 AGCGTATGATAAGTGCGGTCAATTTTTGAGG 59 187 1 AAGTGCGGTA 0.998107 -28 TAATGCTCAAAAGTGCGGTAAAAAAAGAAAC 61 124 0 AAGTGCGGTA 0.998107 -24 AAGACCGTAAAAGTGCGGTCAATATTTTTAA 62 75 1 AAGTGCGGTA 0.998107 -39 TTGATGAAAACTGCGGTCAAAAAACATTG 63 9 1 AACTGCGGTA 0.937 -54 GTTCCTTTTAAAGTGCGGTCATAAAACACAA 63 37 0 AAGTGCGGTA 0.998107 -26 AATTATTTGAAAGTGCGGTAATTTTTTTGTG 64 104 0 AAGTGCGGTA 0.998107 -196 TAGATCATAAAAGCGCGGTGGATTTTCAGAC 65 115 1 AAGCGCGGTG 0.823512 -120 TCTCAATAAAAAGTGCGGTTAATTTTAACCG 71 15 1 AAGTGCGGTA 0.998107 -51 ATCACAACAAAAGTGCGGTTAAAATTAACCG 71 30 0 AAGTGCGGTA 0.998107 -36 CGCACTTTAAAAGTGCGGTCAGATCTAAAGA 74 16 0 AAGTGCGGTA 0.998107 -54 CGCACTTTTAAAGTGCGGTTGTTTTTTTCGT 74 30 1 AAGTGCGGTG 0.990028 -40 TTTAAACCTAAAGTGCGGTGAAAAATCACCA 76 13 1 AAGTGCGGTA 0.998107 -116 ATAAAAGAAAAAGTGTGGTGATTTTTCACCG 76 28 0 AAGTGTGGTA 0.909378 -101 TCCTTCAAAGTGCGGTGAAAAATTCAAC 79 8 1 AAGTGCGGTA 0.998107 -172 AAATAAGAAAAAGTGCGGTAAAAATTTGTTG 79 35 0 AAGTGCGGTA 0.998107 -145 TCTTTTAAAAGTGCGGTAAAAAATAAAGG 83 9 1 AAGTGCGGTA 0.998107 -252 AAATCATCAAAAGTGCGGTGATTTTTTACGG 85 174 0 AAGTGCGGTA 0.998107 -76 ********* * Masking position 2 Map Score: 210.373 Number of sites scoring better than the average of aligned sites = 961 Number in coding regions = 606 Number in noncoding regions = 355 Number of orfs with sites within 600 bp upstream = 247 Fraction of orfs with sites within 600 bp upstream = 0.0396723 Motif number 2 GCTGTTTAAAGTGCGGTTGGTTTTTGCAAAGTTT 6 40 1 GTGCGGTGTT 0.989709 -70 AACGCCCAAAGTGCGGTCATTTTTTCGAAAGATT 7 210 1 GTGCGGTATT 0.99766 -89 AAGTGCGGTAAAAATTATAAAAAATT 12 3 1 GTGCGGTATT 0.99766 -82 ATAAAGCATAGTGCGGTCAAATTTTTTATAATTT 12 22 0 GTGCGGTATT 0.99766 -63 AAAGTGCGGTTAATTTTAGTTGTATTT 13 125 0 GTGCGGTATT 0.99766 -17 AATCGCCGAAGTGCGGTCAAAATTCTCCGAAATT 19 175 1 GTGCGGTATT 0.99766 -67 AAGGTTTAAAGTGCGGTTAAAAATTTCGGAGAAT 19 196 0 GTGCGGTAAT 0.98886 -46 AAGGTTCAGAGTGCGGTCATTTTAACGGTCATTC 20 224 1 GTGCGGTATA 0.988497 -77 AATGAATAAAGTGCGGTCATTTTTTACCGCACTT 21 30 0 GTGCGGTATT 0.99766 -54 TTTACAAAAAGTGCGGTGAAAATTCGCCGACTTT 22 14 1 GTGCGGTATT 0.99766 -85 TAATTTGTAAGTGCGGTTTCTATATAAGGAGGAT 24 29 1 GTGCGGTTTA 0.903699 -134 CTTAAATAAAGTGCGGTCAATTTTTTACTATTT 27 10 0 GTGCGGTATT 0.99766 -62 CTTTATTTAAGTGCGGTCTGTTTTTATAGCCTTT 27 33 1 GTGCGGTTTT 0.978976 -39 CATTGCCAAAGTGCGGTAAATTTTTGAGCTGTTT 35 14 0 GTGCGGTATT 0.99766 -137 TGGCAATGAAGTGCGGTATTTTTTATGAAAAAAC 35 40 1 GTGCGGTTTT 0.978976 -111 AAGAACAAAAGTGCGGTTATTTTAGTGGATAAAT 37 69 0 GTGCGGTATA 0.988497 -40 AATCCTTAAAGTGCGGTTAAATTTTGCCGTAAAT 38 273 0 GTGCGGTATT 0.99766 -28 AATTCCAAAAGTGCGGTAAATTTTAACTGGATTA 41 105 1 GTGCGGTATT 0.99766 -176 CAATAAAAAAGTGCGGTGATTTTTTACCTGATTT 48 81 1 GTGCGGTATT 0.99766 -111 ATTTCTTAAAGTGCGGTAAAAATACGATAAATTT 50 77 0 GTGCGGTATA 0.988497 -111 GAAATAAAAAGTGCGGTGGTTTTTTAGTTGTTTT 52 130 0 GTGCGGTGTT 0.989709 -119 TGCTGCAAAAGTGCGGTTAAAATTTAAGGTGATT 52 223 1 GTGCGGTATT 0.99766 -26 ATAGAGAAAAGTGCGGTAAAAATTGTCGGAGATT 54 144 0 GTGCGGTATT 0.99766 -48 CGTATGATAAGTGCGGTCAATTTTTGAGGTGTTT 59 189 1 GTGCGGTATT 0.99766 -26 ATGCTCAAAAGTGCGGTAAAAAAAGAAACGTTTT 61 119 0 GTGCGGTAAA 0.94706 -29 GACCGTAAAAGTGCGGTCAATATTTTTAACGTTT 62 77 1 GTGCGGTATT 0.99766 -37 TCCTTTTAAAGTGCGGTCATAAAACACAATGTTT 63 32 0 GTGCGGTAAA 0.94706 -31 TTATTTGAAAGTGCGGTAATTTTTTTGTGTTTTT 64 99 0 GTGCGGTATT 0.99766 -201 GATCATAAAAGCGCGGTGGATTTTCAGACATTTG 65 117 1 GCGCGGTGTT 0.837198 -118 TCAATAAAAAGTGCGGTTAATTTTAACCGCACTT 71 17 1 GTGCGGTATT 0.99766 -49 CACTTTAAAAGTGCGGTCAGATCTAAAGATGTTT 74 11 0 GTGCGGTACT 0.964681 -59 CACTTTTAAAGTGCGGTTGTTTTTTTCGTAAATT 74 32 1 GTGCGGTGTT 0.989709 -38 TAAACCTAAAGTGCGGTGAAAAATCACCACACTT 76 15 1 GTGCGGTAAT 0.98886 -114 TCCTTCAAAGTGCGGTGAAAAATTCAACAAATT 79 10 1 GTGCGGTAAT 0.98886 -170 ATAAGAAAAAGTGCGGTAAAAATTTGTTGAATTT 79 30 0 GTGCGGTATT 0.99766 -150 TCTTTTAAAAGTGCGGTAAAAAATAAAGGTATTT 83 11 1 GTGCGGTAAT 0.98886 -250 ATCATCAAAAGTGCGGTGATTTTTTACGGTACTT 85 169 0 GTGCGGTATT 0.99766 -81 ******* * ** Masking position 7 Map Score: 156.405 Number of sites scoring better than the average of aligned sites = 502 Number in coding regions = 292 Number in noncoding regions = 210 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 3 GATTGATTGATTGATTGATT 15 1 0 TTGATTGATT 0.981601 -300 GATTGATTGATTGATTGATTGATTGATTGA 15 13 0 TTGATTGATT 0.981601 -288 GATTGATTGATTGATTGATTGATTGATTGA 15 25 0 TTGATTGATT 0.981601 -276 GATTGATTGATTGATTGATTGATTGATTGA 15 37 0 TTGATTGATT 0.981601 -264 GATTGATTGATTGATTGATTGATTGATTGA 15 49 0 TTGATTGATT 0.981601 -252 GATTGATTGATTGATTGATTGATTGATTGA 15 61 0 TTGATTGATT 0.981601 -240 GATTGATTGATTGATTGATTGATTGATTGA 15 73 0 TTGATTGATT 0.981601 -228 GATTGATTGATTGATTGATTGATTGATTGA 15 85 0 TTGATTGATT 0.981601 -216 GATTGATTGATTGATTGATTGATTGATTGA 15 97 0 TTGATTGATT 0.981601 -204 ATGACAGACTTTGATTGATTGATTGATTGA 15 109 0 TTGATTGATT 0.981601 -192 AGCAAAGATTTAGATTGATTTTTAATCAAT 20 56 1 TAGATTGATT 0.840026 -245 ACCGCACTTTTTAATTGATTAAGATAAA 21 9 0 TTAATTGATT 0.764576 -75 ACTTTTATTGTTGATTTATTCTTTTTGTAT 25 54 0 TTGATTTATT 0.764576 -65 GATAAAGTAATTGATTGATTTTTTAGCGGT 39 192 1 TTGATTGATT 0.981601 -109 ********** Masking position 4 Map Score: 34.7818 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 4 GGGTTATAGGTTTTGAGAAAAAATAGTCTATGG 2 42 0 TTTTGAAAAA 0.870455 -239 AAAGATTGATTTTATTAGAAAAATATCAAATTA 2 139 0 TTTAAAAAAA 0.821158 -142 AAACTTGCAATTTTGCTTGAAAAGTATAAAATT 4 117 0 TTTTTGAAAA 0.645933 -176 CAGATTTCACTTTATTTTGAAAACGAAATTTTA 5 54 0 TTTATGAAAA 0.711483 -76 AATTAGGTTCTTTTATATGAAATATAATGTAAT 7 19 0 TTTTAGAAAT 0.65566 -280 ACAATCAATTTTTAGGAGGAAAATACTGTCGAA 7 61 1 TTTAAGAAAA 0.812175 -238 TTCCTTAAAATTTATATTAAAAACAATGCCTTA 7 270 0 TTTATAAAAA 0.737976 -29 AATTAAAGGATTTTTGTAAAAATTAGGGGATTT 13 75 0 TTTTTAAAAT 0.562707 -67 AGAATGGTGATTTTCAATAAAATAAAAAACCTG 14 93 0 TTTTAAAAAT 0.678527 -80 TGTCAGTTCATTTATATCAAAAACATATTTATT 23 73 1 TTTATAAAAA 0.737976 -140 AGTCAGCGAATTTTACGTAAAAAATCTAAAATA 24 112 0 TTTTGAAAAA 0.870455 -51 ATTTAAATAAAAATGGAAATAACT 25 2 1 TTTATAAAAT 0.642951 -117 AAAAGGTTAATTTTCAACGAAAAATTATAATTG 29 52 0 TTTTAGAAAA 0.492248 -48 TAAATCACAATTTTTCGAAAAATACTATAAATT 30 201 0 TTTTGAAAAT 0.79758 -100 TTCGTCAATATTTTCAGTAAAAAGGAGCAATT 33 10 0 TTTTGAAAAA 0.828039 -101 TTAGTTTAAATTTATCGAGAAATAAAAAATTGC 33 79 0 TTTAGGAAAT 0.819909 -32 TTTTGTCGGTTTTTTCATAAAAAATACCGCACT 35 49 0 TTTTAAAAAA 0.496919 -102 TATAGTGCAATTTACTTAGAAAATTTTAACCCC 35 123 1 TTTATGAAAA 0.713529 -28 TAACGGATTTTTTATAAGGAAAACATA 36 63 1 TTTAAGAAAA 0.800825 -17 CGCACAATTATTTTCGATAAAAAAGAGCCCTTA 37 14 0 TTTTAAAAAA 0.503864 -95 CGCTTTAATATTTACGGCAAAATTTAACCGCAC 38 264 1 TTTAGAAAAT 0.839866 -37 ATACTCCCTATTTTCAAAAAAAAGATTTTGTAA 39 246 0 TTTTAAAAAA 0.503864 -55 GAATGGCGGGTTTAATGTAAAATTTATGACGAA 46 67 0 TTTAGAAAAT 0.839868 -82 TTGTTTATAATTTTTTACAAAATACGATAAAAA 47 146 0 TTTTAAAAAT 0.67729 -155 AAATTGAAAATTTATTGTAAAAAACAACTAAAA 52 110 1 TTTAGAAAAA 0.899327 -139 TTTTCACGCATTTATTGTAAAATCTCCGACAAT 54 124 1 TTTAGAAAAT 0.839866 -68 ATTTTTAAAGTTTATGGTAAAATGCACGCCAAT 57 29 0 TTTAGAAAAT 0.839866 -60 GTTGAAAATTTTTAATAGGAAAAAATA 57 72 1 TTTAAGAAAA 0.812175 -17 CGTTTGCTATTTTACAAAAAAAAGGCTGAAGTT 58 155 0 TTTAAAAAAA 0.822667 -56 CTTTATCGTATTTTTTGAAAAATTAAACTATTT 59 132 1 TTTTGAAAAT 0.79758 -83 TTTAAGTCTATTTTTAGTAAAAATAGTTTAATT 59 152 0 TTTTGAAAAA 0.822295 -63 TGCTGAGTCCTTTTTGAAAAAAATCTGAAAAAA 64 11 1 TTTTAAAAAA 0.496919 -289 ATTCACTATCTTTATCTCAAAAAATCTTCTAAA 64 175 1 TTTATAAAAA 0.737976 -125 AGGGTAAAATTTTAACGAAAAAACCCTAAAAAA 65 175 0 TTTAGAAAAA 0.899682 -60 AAGCTCAAGATTTAGGAGAAAAA 67 1 0 TTTAAAAAAA 0.832801 -179 TTATATCGGGTTTTAAGAAAAATACTTGTGTTC 68 122 0 TTTTGAAAAT 0.797895 -179 TTTTCTCGCTTTTAAAGCGAAAAGTGTATTGAG 69 27 1 TTTAGGAAAA 0.88617 -181 ATAGTTAAAATTTTTCAAAAAAATTTGTAAGAA 69 124 0 TTTTAAAAAA 0.496919 -84 TGTTGTGATGTTTAAGGGGAAAAA 71 52 1 TTTAGGAAAA 0.88617 -14 CTAAATGGCTTTTATAGGAAAATACCATTGCAA 73 65 0 TTTAGAAAAT 0.839866 -96 ACGCCACGTTTTTAATTAGAAAATTGAGAAAAT 73 135 1 TTTATGAAAA 0.727576 -26 TCTCGTTAAATTTACGAAAAAAACAACCGCACT 74 41 0 TTTAAAAAAA 0.822667 -29 TTTTCGTAAATTTAACGAGAAATATT 74 54 1 TTTAGGAAAT 0.819911 -16 CGTCAAATACTTTTTTACAAAAAAAGTAATTTT 75 61 1 TTTTAAAAAA 0.496919 -240 ATTAAAATTTTTTATTTAGAAAAATAAGAAAAA 79 54 0 TTTATGAAAA 0.711483 -126 TTTATCTCACTTTTTTGAAAAAACTTTACGAGA 81 12 1 TTTTGAAAAA 0.822295 -124 CAATCCAGTTTTTTCCTAGAAATCGTGCTATAA 81 45 0 TTTTTGAAAT 0.530116 -91 TTTGCTATTTTTTAAAAAGAAATAAAAATCCTC 82 79 0 TTTAAGAAAT 0.716762 -46 TTGATGATTTTTTATAGAGAAATCTGCATAATA 85 195 1 TTTAGGAAAT 0.819909 -55 **** * ***** Masking position 10 Map Score: 60.3888 Number of sites scoring better than the average of aligned sites = 412 Number in coding regions = 269 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 5 ATTGATTGATTGATTGATTGATT 15 4 0 TGATTGATTG 0.984476 -297 ATTGATTGATTGATTGATTGATTGATTGAT 15 20 0 TGATTGATTG 0.984476 -281 ATTGATTGATTGATTGATTGATTGATTGAT 15 32 0 TGATTGATTG 0.984476 -269 ATTGATTGATTGATTGATTGATTGATTGAT 15 44 0 TGATTGATTG 0.984476 -257 ATTGATTGATTGATTGATTGATTGATTGAT 15 56 0 TGATTGATTG 0.984476 -245 ATTGATTGATTGATTGATTGATTGATTGAT 15 72 0 TGATTGATTG 0.984476 -229 ATTGATTGATTGATTGATTGATTGATTGAT 15 84 0 TGATTGATTG 0.984476 -217 ATTGATTGATTGATTGATTGATTGATTGAT 15 96 0 TGATTGATTG 0.984476 -205 TGACAGACTTTGATTGATTGATTGATTGAT 15 108 0 TGATTGATTG 0.984476 -193 ATAGATAAAGTAATTGATTGATTTTTTAGC 39 189 1 TAATTGATTG 0.847105 -112 ********** Masking position 5 Map Score: 27.0313 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 28 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 GTGGGTTATTGGTTAAAATTACGCACCATT 1 23 1 GGTTAAAATT 0.754156 -83 CAAGCAACGTTTTTAAAAATTCACTT 1 90 1 TTTTAAAAAT 0.462573 -16 ATAAGTTGAAGTTAAAAAATATTGCGACGA 5 94 0 GTTAAAAAAT 0.613587 -36 CACTTTGGGCGTTTAAAAATTTCTTTTGAT 7 193 0 GTTTAAAAAT 0.596077 -106 CGGTAAAAATTATAAAAAATTTGACCGCAC 12 16 1 TATAAAAAAT 0.667122 -69 TTAGGGGAATGATTAAAAATCCCCTAATTT 13 59 1 GATTAAAAAT 0.761527 -83 AAAGGATTTTTGTAAAAATTAGGGGATTTT 13 74 0 TGTAAAAATT 0.658143 -68 TTGTAGAACAATTAAAAAATACTTTTTTTA 15 258 0 ATTAAAAAAT 0.508153 -43 TTTAAAGTGCGGTTAAAAATTTCGGAGAAT 19 196 0 GGTTAAAAAT 0.838244 -46 AGCTGCATTCATTTAAAATTTACCGCCTTA 20 21 1 ATTTAAAATT 0.362373 -280 GGTCAAGATTGATTAAAAATCAATCTAAAT 20 63 0 GATTAAAAAT 0.761527 -238 TAAAAAGTGCGGTAAAAAATGACCGCACTT 21 26 1 GGTAAAAAAT 0.847934 -58 TTTTATTCATTATTAAAAATAAGGAAAAAT 21 63 1 TATTAAAAAT 0.650658 -21 TAAAAGTCTGTGTTAAAATTTTCAAAATTT 25 77 1 TGTTAAAATT 0.641473 -42 AAATAGTAAAAAATTGACCGCACT 27 5 1 AGTAAAAAAT 0.783926 -67 TCAAAAGCTAGGTTAAAAATGCTATATTTA 31 82 1 GGTTAAAAAT 0.838244 -47 TTTATCGAGAAATAAAAAATTGCGTAAGGA 33 72 0 AATAAAAAAT 0.690944 -39 TTTAAGGGGTTAAAATTTTCTAAGTAA 35 134 0 GGTTAAAATT 0.754156 -17 ATGTTTTCCTTATAAAAAATCCGTTAAAAA 36 59 0 TATAAAAAAT 0.667122 -21 CGTTGAAATAAATAAAAAATCGTCGTTAGA 38 88 1 AATAAAAAAT 0.690944 -213 CGATTGCGTGAATAAAAAATGTTAAGTAGA 38 166 0 AATAAAAAAT 0.690944 -135 TAATTAAAAGTATAAAAATTTCCGAGTTTA 39 54 1 TATAAAAATT 0.542615 -247 GTTCATAAGGTTTTAAAATTTATTAGCAAT 39 161 1 TTTTAAAATT 0.337532 -140 TAAGTACCATTATTAAAAATATTTTTTTCA 40 62 0 TATTAAAAAT 0.650658 -239 TAAATAATCCAGTTAAAATTTACCGCACTT 41 113 0 AGTTAAAATT 0.666212 -168 TATCGTATTTTGTAAAAAATTATAAACAAA 47 150 1 TGTAAAAAAT 0.764832 -151 AGGAAAATCAGGTAAAAAATCACCGCACTT 48 89 0 GGTAAAAAAT 0.847934 -103 TTTTACCAAAAGTAAAAAATAA 49 3 0 AGTAAAAAAT 0.783926 -109 GTTAAACAATAATTAAAATTGAAAAATACT 49 33 0 AATTAAAATT 0.551531 -79 TTCATTAAATAGTTAAAAATAAGCGATGAG 50 157 0 AGTTAAAAAT 0.771257 -31 GGGAATTGCAGGTAAAAAATAGCCGTACTT 51 44 1 GGTAAAAAAT 0.847934 -52 GCAAAAGTGCGGTTAAAATTTAAGGTGATT 52 227 1 GGTTAAAATT 0.754156 -22 GGGTGTGTGGATTTAAAATTCACGCACCAT 53 17 1 ATTTAAAATT 0.362373 -33 ATACCTATAAAAAATGGTGCGTGAA 53 35 0 TATAAAAAAT 0.667122 -15 AGAAAAGTGCGGTAAAAATTGTCGGAGATT 54 144 0 GGTAAAAATT 0.767485 -48 TTTTATCCTTTATAAAAATTGGCGTGCATT 57 12 1 TATAAAAATT 0.542615 -77 TATTTTTTCCTATTAAAAATTTTCAACATT 57 69 0 TATTAAAAAT 0.650658 -20 TTCATTTTAATTTTAAAAATGTCATTAAAT 67 80 1 TTTTAAAAAT 0.462573 -100 GATCAATTGAAATAAAAATTGGGCAGATTA 67 150 0 AATAAAAATT 0.569598 -30 CTTGTGTTCAAGTTAAAAATATCTATAATC 68 101 0 AGTTAAAAAT 0.771257 -200 ATATTAGCCAGATAAAAAATCGGTGCACAT 68 227 0 GATAAAAAAT 0.774576 -74 TTTTGTTGATAGTTAAAATTTTTCAAAAAA 69 135 0 AGTTAAAATT 0.666212 -73 CAAATTAAGGGGTTAAAAATTCGTGCGCAT 69 175 0 GGTTAAAAAT 0.838244 -33 ACAAAAGTGCGGTTAAAATTAACCGCACTT 71 25 0 GGTTAAAATT 0.754156 -41 GACCTATTCTTATAAAAATTGTGCTTAGGA 73 16 1 TATAAAAATT 0.542615 -145 TGTTTAAATGAATAAAAAATAAGTGATATG 75 118 0 AATAAAAAAT 0.690944 -183 ATTTATTGYTAATTAAAATTTATTTGACAA 75 216 1 AATTAAAATT 0.551531 -85 GAAAAAGTGCGGTAAAAATTTGTTGAATTT 79 30 0 GGTAAAAATT 0.767485 -150 TATTTTTCTAAATAAAAAATTTTAATTTTT 79 61 1 AATAAAAAAT 0.690944 -119 TTTTTGTGAGAATAAAAATTAAAATTTTTT 79 74 0 AATAAAAATT 0.569598 -106 TAGATAACTTATTTAAAAATAAACGGTTTT 79 100 0 ATTTAAAAAT 0.489824 -80 TTTATTTCTTTTTAAAAAATAGCAAACGTT 82 86 1 TTTAAAAAAT 0.480829 -39 TTAAAAGTGCGGTAAAAAATAAAGGTATTT 83 15 1 GGTAAAAAAT 0.847934 -246 CAGATTTCTCTATAAAAAATCATCAAAAGT 85 191 0 TATAAAAAAT 0.667122 -59 ********** Masking position 5 Map Score: 51.8245 Number of sites scoring better than the average of aligned sites = 465 Number in coding regions = 308 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 7 GTTTTCCGTTGCAATCAATTTTATTTTGAAGA 15 203 1 GCAATCATTT 0.688598 -98 TAAACATTATGCAAACGGTTACTCAAAATAAA 23 100 0 GCAAACGTTC 0.929313 -113 TAAATATCAGGAAAACGTTTCCGTTAAATATA 31 104 0 GAAAACGTTC 0.550369 -25 TTTTATTCACGCAATCGGTTATCCGAGCCAAT 38 179 1 GCAATCGTTT 0.9166 -122 CTATATTTAAGCAAACGTTTGCGTTATAATTC 50 126 1 GCAAACGTTC 0.499975 -62 GGAGCAACCTGCAATCGCTTAACAGATGTGCG 58 70 0 GCAATCGTTA 0.809672 -141 TTGTAAAATAGCAAACGATTTTATCCCCTGTC 58 171 1 GCAAACGTTT 0.926795 -40 TTTACGCAAACGTTTTCTTTTTGGCTT 60 6 1 GCAAACGTTC 0.523295 -81 AATTTTGATTGCAAGCAATTTCATTTTAATTT 67 61 1 GCAAGCATTC 0.817785 -119 TAACAATATCGCAAACGTTTGCTTGATGATAT 67 119 1 GCAAACGTTC 0.499975 -61 AAGCCATTTAGCAAACGTTTGCCTGATATATG 73 87 1 GCAAACGTTC 0.499975 -74 TTAAAAAATAGCAAACGTTTGCTTTATTTGAT 82 97 1 GCAAACGTTC 0.499975 -28 ATCTAAATCCGCAAACAGTTCCAAAGGAGACC 83 182 0 GCAAACATTC 0.964775 -79 ******* ** * Masking position 4 Map Score: 18.5612 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 14 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 ATATGTAGTGTTTTAGACCTTTTTGTCGTAAGAT 2 181 0 TTTTCTTTTT 0.915634 -100 AGCCTGCGAATTTTATACTTTTCAAGCAAAATTG 4 109 1 TTTTCTTTCA 0.598462 -184 CCATCTCTCATTTTTAGGATATTTCAAAT 8 6 0 TTTTGTATTT 0.651071 -32 TAATTGCCCCTTTTGTTGTTTTTTATTTTCTCTT 16 35 1 TTTTGTTTTT 0.886105 -35 TGCCGTCGCTTTTTAGGCGTATTTTCTTTATACT 18 72 1 TTTTCTATTT 0.722449 -60 ATAAAAATATTTTTACTCCTTTCTTTTAAGAATC 26 15 1 TTTTCTTTCT 0.699125 -79 TTTTTTCTTCCTTTAAAAGGCTATAA 27 56 0 TTTTCTTTAA 0.727223 -16 TATGTCACATTTTTTTGCATTTATACTCCCTAAG 30 232 1 TTTTCTTTAT 0.806067 -69 AACGGAAACGTTTTCCTGATATTTACTA 31 111 1 TTTTGTATTT 0.651071 -18 ATAGAAATTATTTTATTCCTTTTAAGAATTCCAC 34 128 1 TTTTCTTTTA 0.874394 -156 GTGCGGTAAATTTTTGAGCTGTTTTAA 35 4 0 TTTTGTGTTT 0.669044 -147 TTTCAGTGCATTTTGTCGGTTTTTTCATAAAAAA 35 58 0 TTTTGTTTTT 0.886105 -93 TCTATGCGACTTTTCGTGATTTATCCACTAAAAT 37 51 1 TTTTGTTTAT 0.748714 -58 ACTCGGAAATTTTTATACTTTTAATTAATTTAAG 39 47 0 TTTTCTTTAA 0.727223 -254 TGCAACGGCATTTTTATCGTATTTTGTAAAAAAT 47 136 1 TTTTCTATTT 0.722449 -165 AGTTTCATAATTTTATCCTTATTTTTGCCCACAT 50 20 1 TTTTCTATTT 0.722449 -168 AGTGCGGTGGTTTTTTAGTTGTTTTTTACAATAA 52 121 0 TTTTGTGTTT 0.669044 -128 TCCCTATTAATTTTTGCCATTTTACGGTATTCTA 52 166 1 TTTTCTTTTA 0.874394 -83 TTTTTATCCTTTATAAAAATTGGC 57 1 1 TTTTCTTTAT 0.806067 -88 CTATTAAAAATTTTCAACATTTTATCTTATTTTT 57 56 0 TTTTCTTTTA 0.874394 -33 GTGCGGTCAATTTTTGAGGTGTTTTT 59 199 1 TTTTGTGTTT 0.669044 -16 GCGGTCAATATTTTTAACGTTTTTACGAGGTAAA 62 89 1 TTTTCTTTTT 0.915634 -25 TTTTTGTTCCTTTTAAAGTGCGGTC 63 48 0 TTTTCTTTTA 0.874394 -15 TCGGGCTTTGTTTTAAAGTTTTTTCAGATTTTTT 64 28 0 TTTTGTTTTT 0.886105 -272 TGCGGTAATTTTTTTGTGTTTTTTTGTTCGCTAA 64 88 0 TTTTGTTTTT 0.886105 -212 ACAAAACTGATTTTTAACGTTTTTGTTACGTTCC 65 77 0 TTTTCTTTTT 0.915634 -158 ATTATTTATTTTTTAGGGTTTTTTCGTTAAAATT 65 167 1 TTTTGTTTTT 0.886105 -68 TTCGTTAAAATTTTACCCTTTTTATAGGGTAAGA 65 189 1 TTTTCTTTTA 0.874394 -46 TTTCCAAAAGTTTTAAGCGTATAATGTGCACCGA 68 204 1 TTTTCTATAA 0.390001 -97 AATTACAAAATTTTAAAGGTGTTATTTTACTTCG 68 261 0 TTTTGTGTTA 0.564584 -40 TTTTTTACCTTTCAAATTTTCTCG 69 1 1 TTTTCTTTCA 0.598462 -207 ACCTTTCAAATTTTCTCGCTTTTAAAGCGAAAAG 69 17 1 TTTTGTTTTA 0.833062 -191 ATCACTTATTTTTTATTCATTTAAACAACTTATA 75 121 1 TTTTCTTTAA 0.727223 -180 TACTTTACTCTTTTTCGGCTTTAATCTCAATGAT 76 59 0 TTTTGTTTAA 0.656489 -70 AGATTTTCACCTTTTATTTAAGTTAAA 85 4 1 TTTTCTTTAT 0.806067 -246 ATCACCGCACTTTTGATGATTTTTTATAGAGAAA 85 183 1 TTTTGTTTTT 0.886105 -67 **** * ***** Masking position 10 Map Score: 39.9682 Number of sites scoring better than the average of aligned sites = 396 Number in coding regions = 279 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 9 GATATTGATCACAAAATCAAAAATATTTGAG 2 91 1 AAAAATCAAA 0.399557 -190 GAAAAGAACTTAAAAAGAAAAAGGGGCGATT 10 25 0 TAAAAGAAAA 0.872095 -35 CAATATCCACCCAAAATAAAAGCGACAGGAA 11 26 1 CAAAATAAAA 0.598287 -52 TCTTCTTCCTAAAAAAGAAAAACAAATATTA 13 18 0 AAAAAGAAAA 0.872095 -124 GTGATTTTCAATAAAATAAAAAACCTGTTGC 14 89 0 AAAAATAAAA 0.700686 -84 ATAATGATCTTCAAAATAAAATTGATTGCAA 15 211 0 TAAAATAAAA 0.700686 -90 TTTCTTGGCAAGAAAATAAAAAAAGTATTTT 15 242 1 AAAAATAAAA 0.700686 -59 TATAAGAAAGAGAAAATAAAAAACAACAAAA 16 45 0 AAAAATAAAA 0.700686 -25 TCATTATTAAAAATAAGGAAAAATT 21 69 1 AATAAGGAAA 0.720949 -15 CGCCGACTTTTCATAAGAAAACAAGTAGAAT 22 38 1 TATAAGAAAA 0.739942 -61 CCGTTTTATCATAAAAGGAAAGATGCAAAAA 23 30 1 AAAAAGGAAA 0.86094 -183 TTACTCACCCTAATAAGGAAAACTCT 26 78 1 TATAAGGAAA 0.720949 -16 CCCTTTAAGTTAATAAGAAAAAGTTGTATTG 28 38 0 TATAAGAAAA 0.739942 -29 TACTTTGCGTTGATAAGAAAAATATCAAGCT 30 49 1 TATAAGAAAA 0.739942 -252 AACGGATTTTTTATAAGGAAAACATA 36 64 1 TATAAGGAAA 0.720949 -16 CGGAAATCTAACNAAATGAAAACGGCTAATT 38 122 1 ANAAATGAAA 0.680065 -179 TCAAAATAAAACAATAAGATT 39 290 0 TAAAATAAAA 0.700686 -11 TCAATAACACCTAAAAGAAAAGGTGCGGGTT 40 11 0 CAAAAGAAAA 0.812659 -290 TAAACTGCAGAAAAAATGAAATGCTCTCTTC 41 31 0 AAAAATGAAA 0.680065 -250 GCGGATTTTATCAAAAGAAAAAGAGAAAGGC 41 179 0 TAAAAGAAAA 0.872095 -102 ATTTAGATCACAAAAAGGAAAATCAGGTAAA 48 103 0 CAAAAGGAAA 0.797523 -89 TCATCTTTAAACAAAAGGAAAGCAA 49 97 1 AAAAAGGAAA 0.86094 -15 AGAGGTCTCTCAATAATAAAAATA 52 4 0 CATAATAAAA 0.383288 -245 CCCTGTCATTTCATAAGGAAACACA 58 196 1 TATAAGGAAA 0.720949 -15 AAAATAAAGCCAAAAAGAAAACGTTTGCGTA 60 13 0 CAAAAGAAAA 0.812659 -74 TAAATGTTTGTGAAAAGCAAATATTGCCGTA 64 223 1 TAAAAGCAAA 0.65965 -77 ATTTTTAAAATTAAAATGAAATTGCTTGCAA 67 69 0 TAAAATGAAA 0.680065 -111 AAATGAACGCATAAAAGAAAAAATAGGATTA 75 189 0 AAAAAGAAAA 0.872095 -112 TCTCAATGATATAAAAGAAAAAGTGTGGTGA 76 38 0 AAAAAGAAAA 0.872095 -91 ATCTCATAACTTAAAAGCAAACAAAA 77 6 0 TAAAAGCAAA 0.65965 -66 TTATTTAGAAAAATAAGAAAAAGTGCGGTAA 79 45 0 AATAAGAAAA 0.739942 -135 * ********* Masking position 6 Map Score: 24.1915 Number of sites scoring better than the average of aligned sites = 490 Number in coding regions = 334 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 10 TTATTGGTTAAAATTACGCACCATTTTAGCAAAGAT 1 28 1 AAATTCCTTT 0.605185 -78 TGAAAAGTATAAAATTCGCAGGCTTTTTGTCTATAT 4 97 0 AAAATCCTTT 0.963047 -196 TTATAATGCTCTTATTATTGATAGTGTA 6 92 0 ATAATCCTAT 0.435353 -18 AACATCCTGTATAATGCACGGGCTTTATTTTCTACA 7 144 1 ATAATCCTTT 0.761352 -155 ATCTTTCGAAAAAATGACCGCACTTTGGGCGTTTAA 7 207 0 AAAATACTTT 0.819199 -92 GATCCGATAAAATACACATAATTTTTTCGCCGCA 9 9 1 AAAATCCTTT 0.960677 -90 GGAATGATTAAAAATCCCCTAATTTTTACAAAAATC 13 64 1 AAAATCCTTT 0.939275 -78 CGAAATTTCTAAAATACAACTAAAATTAACCGCACT 13 114 1 AAAATCAAAT 0.139328 -28 AAGTGCGGTCAAAATTCTCCGAAATTTTTAACCGCA 19 183 1 AAAATCCATT 0.82774 -59 AGTGCGGTAAAAAATGACCGCACTTTATTCATTTTT 21 31 1 AAAATACTTT 0.819199 -53 AAGTGCGGTGAAAATTCGCCGACTTTTCATAAGAAA 22 22 1 AAAATCCTTT 0.955194 -77 TGAAAGAAAAAAAATCCTCCTTATATAGAAACCGCA 24 40 0 AAAATCCTAT 0.867026 -123 TTTTTTACGTAAAATTCGCTGACTTTCGTATAATAA 24 121 1 AAAATCCTTT 0.930877 -42 TTTGTATAGTAGAATGCGAAAAATTTAGTTATTTCC 25 25 0 AGAATCATTT 0.262844 -94 AGTCTGTGTTAAAATTTTCAAAATTTATTTATAAAA 25 81 1 AAAATTCTTT 0.635994 -38 CTTTCTTTTAAGAATCCGCTATTTTTCTTAGAATAA 26 33 1 AGAATCCTTT 0.725418 -61 AATTTTTCGAAAAATACTATAAATTTTACCTATCAA 30 190 0 AAAATCATTT 0.75313 -111 AAAAACCGACAAAATGCACTGAAAATATTGGATCCT 35 68 1 AAAATCCAAT 0.545291 -83 TTTATCCACTAAAATAACCGCACTTTTGTTCTTGTT 37 70 1 AAAATACTTT 0.819199 -39 TTTATGTTCAAACATACTCCCTATTTTCAAAAAAAA 39 256 0 AACATCCTTT 0.557316 -45 TTCTTTTGATAAAATCCGCCGCCTATCTGCCATTCT 41 191 1 AAAATCCTAT 0.867026 -90 AAATTACGCTATAATGCCCACATTTTTCAGTTTAAA 46 112 1 ATAATCCTTT 0.759396 -37 AATTTTTTACAAAATACGATAAAAATGCCGTTGCAG 47 135 0 AAAATCAAAT 0.139294 -166 AATCAGGTAAAAAATCACCGCACTTTTTTATTGTTA 48 78 0 AAAATACTTT 0.819199 -114 AAGTGCGGTAAAAATACGATAAATTTCAGGCATAAA 50 67 0 AAAATCATTT 0.649625 -121 TTGCAGGTAAAAAATAGCCGTACTTTTTTTAAATTA 51 49 1 AAAATGCTTT 0.515264 -47 AGAACAGAAAAAAATGCGCCAGTATTGTATAGATAT 54 42 0 AAAATCCATT 0.827743 -150 AGTTTATGGTAAAATGCACGCCAATTTTTATAAAGG 57 18 0 AAAATCCATT 0.827792 -71 TTTCCTATTAAAAATTTTCAACATTTTATCTTATTT 57 58 0 AAAATTCTTT 0.644888 -31 CGGTAAGGAAAAAATACAAACTTTATCGTATTTTTT 59 112 1 AAAATCATAT 0.46813 -103 AAAACACAAAAAAATTACCGCACTTTCAAATAATTA 64 100 1 AAAATACTTT 0.819199 -200 TGATTTGATGAAAATTCACTATCTTTATCTCAAAAA 64 162 1 AAAATCCTTT 0.963144 -138 AAAATCTTCTAAAATTTACAAGATTTGTTAAATGTT 64 195 1 AAAATTCTTT 0.644946 -105 CAAATGTCTGAAAATCCACCGCGCTTTTATGATCTA 65 115 0 AAAATCCCTT 0.596629 -120 ATTCGTGCGCATATTACCCGATTTTTGTTGATAGTT 69 151 0 ATATTCCTTT 0.157836 -57 AGTGCGGTGAAAAATCACCACACTTTTTCTTTTATA 76 24 1 AAAATACTTT 0.820097 -105 AGTGCGGTGAAAAATTCAACAAATTTTTACCGCACT 79 19 1 AAAATCATTT 0.777991 -161 AACTTATTTAAAAATAAACGGTTTTTGTGAGAATAA 79 89 0 AAAATACTTT 0.816313 -91 TACCCGCGGTAAAATACCTTTATTTTTTACCGCACT 83 20 0 AAAATCTTTT 0.378118 -241 TAGTTTTATAAAAATGCTCGTGCTATACTCTGTGCG 85 82 0 AAAATCCTAT 0.867011 -168 AGTACCGTAAAAAATCACCGCACTTTTGATGATTTT 85 170 1 AAAATACTTT 0.819199 -80 ***** * * *** Masking position 5 Map Score: 46.0516 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 230 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 11 TCACAAAATCAAAAATATTTGAGAAAAGCT 2 99 1 AAAAATATTT 0.844101 -182 GTTGAAGTTAAAAAATATTGCGACGAGATT 5 90 0 AAAAATATTG 0.801869 -40 CCTGTTGCTAAAAAGTATTGTTGTAGCGAG 14 67 0 AAAAGTATTG 0.851078 -106 AGAAAATAAAAAAAGTATTTTTTAATTGTT 15 252 1 AAAAGTATTT 0.886092 -49 CTAAAATAGGAAAAATATTTTGTCAGAATT 24 90 0 AAAAATATTT 0.844101 -73 TTAAATAAAAATATTTTTACTCCTTT 26 7 1 AAAAATATTT 0.844101 -87 TTTTCAATTGAAAAGTGTTTTTCAGAAAGA 34 43 0 AAAAGTGTTT 0.766891 -241 TTTTCAATTGAAAAGTGTTTTTCATCATAG 34 59 1 AAAAGTGTTT 0.766891 -225 TGCAACCTCCAAAAGTGTTGTCATAGCGTT 38 49 1 AAAAGTGTTG 0.707286 -252 AAATACTGAAAAAAATATTTTTAATAATGG 40 56 1 AAAAATATTT 0.844101 -245 TGCCATAGCAAAAAATATTCGTCATAAATT 46 50 1 AAAAATATTC 0.679033 -99 ACTTTTGGTAAAAAGTATTTTTCAATTTTA 49 20 1 AAAAGTATTT 0.886092 -92 TCTCAATTTCAAAAATATTC 58 1 0 AAAAATATTC 0.679033 -210 TAAAAACGTTAAAAATATTGACCGCACTTT 62 84 0 AAAAATATTG 0.801869 -30 TTTTTTGTAAAAAAGTATTTGACGAGGATC 75 55 0 AAAAGTATTT 0.886092 -246 ********** Masking position 4 Map Score: 11.3055 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 74 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 12 TTGAAAACGAAATTTTAGGATTTATGCTAT 5 41 0 AATTTTAGGA 0.811355 -89 AGAACAATCAATTTTTAGGAGGAAAATACT 7 58 1 ATTTTTAGGA 0.811355 -241 TTTAATATAAATTTTAAGGAAAACATT 7 282 1 ATTTTAAGGA 0.911414 -17 ACCATCTCTCATTTTTAGGATATTTCAAAT 8 11 0 ATTTTTAGGA 0.811355 -27 TTCGCCTTTCAATTAAAGGATTTTTGTAAA 13 88 0 AATTAAAGGA 0.658778 -54 ATTTAACCGCACTTTAAGGATTTTCA 38 285 1 ACTTTAAGGA 0.853501 -16 ACTTTTAATTAATTTAAGGACATAACAATG 39 35 0 AATTTAAGGA 0.911414 -266 TCAAATATTTAATTTAAGGAAATCAA 46 7 0 AATTTAAGGA 0.911414 -142 AAAGGGTAAAATTTTAACGAAAAAACCCTA 65 180 0 ATTTTAACGA 0.648922 -55 AAGCTCGCATATTTTAAGGATTTAGTTTAA 72 34 0 ATTTTAAGGA 0.911414 -29 TACCATTGCAACTTTAAGGATAAAATTTTA 73 46 0 ACTTTAAGGA 0.853501 -115 TTTTTTCGTAAATTTAACGAGAAATATT 74 52 1 AATTTAACGA 0.648922 -18 GATAAGTTCTATTTAAAGGATAAATAAA 80 124 1 ATTTAAAGGA 0.658778 -18 GCGGGATTGAAATTTTAGGAAAGTAGGAAA 81 111 1 AATTTTAGGA 0.811355 -25 ********** Masking position 7 Map Score: 11.4484 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 13 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 GTAAACATTGTGATATTGATCACAAAATCAAAAA 2 80 1 TGATTATCAA 0.92305 -201 GGCATCCAGCTGTTTTAGGTCAAATTTACGCGTA 4 222 1 TGTTTGTCAA 0.812437 -71 TGTGTGGATGTGCTTTCTATCAAAAACACGGTTA 20 108 0 TGCTTATCAA 0.806766 -193 GTTTATTTTTTGATATTCGTCAAACAATTATAAT 29 28 1 TGATTGTCAA 0.950817 -72 CGAAAAATTGTGATTTATGTCACATTTTTTTGCA 30 217 1 TGATTGTCAA 0.950817 -84 AATTGAAAAGTGTTTTTCATCATAGATGGCATTA 34 64 1 TGTTTATCAA 0.729663 -220 CTTACTTCAATGATCTTGATAACATTAAATTAGC 47 272 0 TGATTATAAA 0.757207 -29 CCTAAAACTATGATTTAGATCACAAAAAGGAAAA 48 112 0 TGATTATCAA 0.923346 -80 CGCGCTTTTATGATCTATGTCACAAAACTGATTT 65 98 0 TGATTGTCAA 0.950817 -137 TTGATCTCAATAAAAAGTGCGGTTA 71 2 1 TGATTATAAA 0.757452 -64 AACGTTTGCCTGATATATGTAAGATGTGCTATTC 73 100 1 TGATTGTAAA 0.833633 -61 CTAATTTTGATGATCCTCGTCAAATACTTTTTTA 75 44 1 TGATCGTCAA 0.738228 -257 CAAATCTGTTTGCTTTGAGTAATACTGCTCACTC 85 38 1 TGCTTGTAAA 0.634625 -212 AATGATGATTTGATATAGATCACAAAAAAGTAGT 85 126 0 TGATTATCAA 0.92305 -124 **** * **** * Masking position 12 Map Score: 8.1497 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 24 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 14 CATAGACTATTTTTTCTCAAAACCTATAAC 2 43 1 TTTTTCTCAA 0.484951 -238 TTGTTGAGAGCTTTTCTCAAATATTTTTGA 2 107 0 CTTTTCTCAA 0.87892 -174 TACTAAAAGAATATTCTCAAATTCGAAAGT 4 33 1 ATATTCTCAA 0.624638 -260 AAAGTAAGCTATATTCTCAAATCACTTTCG 4 56 0 ATATTCTCAA 0.624638 -237 TTTTTAAGTTCTTTTCTCAAGGTAGGATTT 10 40 1 CTTTTCTCAA 0.87892 -20 CATAATGTTTATTTTCTAAAACTGTGATCT 23 121 1 ATTTTCTAAA 0.660578 -92 GAATTAAGCTATTTACGCAATAAAACTAGG 30 119 1 ATTTACGCAA 0.615602 -182 GGTAGTGCATCTTTACGCAAAATTTAAACT 34 253 1 CTTTACGCAA 0.634673 -31 TTATTGATCTATTTACTAAATAATCCAGTT 41 129 0 ATTTACTAAA 0.543612 -152 TAGCCCCGTTATTTTCTCAATCTTACCCTA 65 213 0 ATTTTCTCAA 0.869988 -22 ATAAAAGTAACTTTACTCAATTAAACTAAA 72 14 1 CTTTACTCAA 0.816268 -49 GCTATTTTCTCAATTTTCTAATT 73 148 0 ATTTTCTCAA 0.869988 -13 TTCTCGTTAAATTTACGAAAAAAACAACCG 74 45 0 ATTTACGAAA 0.317767 -25 TCTATACCCACTATTCTAAAAAAACACAAC 75 266 1 CTATTCTAAA 0.344275 -35 TACTTGCGATCTTTTCTCAAACACATTATC 79 158 1 CTTTTCTCAA 0.87892 -22 AAGCCGTAGGATTTACTAAATTTCCAATAA 82 13 1 ATTTACTAAA 0.543612 -112 ********** Masking position 4 Map Score: 6.35095 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 95 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 15 TCTTTAAGGTGGGCTTTAGCCTGCCT 6 6 1 AAGGGGGCTT 0.769217 -104 TAAAAAGAAAAAGGGGCGATTACTCGCCCAA 10 15 0 AAGGGCGATT 0.930516 -45 TTCTTTTCTCAAGGTAGGATTT 10 48 1 AAGGAGGATT 0.562629 -12 CTTCATCAACAAGGGGGTATT 11 67 1 AAGGGGTATT 0.765767 -11 CTTTAATTGAAAGGCGAAATTTCTAAAATAC 13 100 1 AAGGGAAATT 0.670304 -42 AAAACAACAAAAGGGGCAATTAAGCCCCTTT 16 26 0 AAGGGCAATT 0.929289 -44 CGCGAAGACTGAGGGGGGATTTATATCCTAA 19 70 1 GAGGGGGATT 0.859827 -172 GTTTCTATATAAGGAGGATTTTTTTTCTTTC 24 44 1 AAGGGGATTT 0.688177 -119 TTTCAGTAAAAAGGAGCAATT 33 1 0 AAGGGCAATT 0.929289 -110 AATTTAAACTAAGGTGCAATT 33 100 1 AAGGGCAATT 0.929289 -11 AATTTAAACTAAGGTGCAATT 34 273 1 AAGGGCAATT 0.929289 -11 CTTTACAAAAGAGGGGGAATTGCAGGTAAAA 51 30 1 GAGGGGAATT 0.857543 -66 AACCGAATAAAAGGCGGAAATT 76 117 1 AAGGGGAAAT 0.671176 -12 TTATTAGATAATGGCGGGATTGAAATTTTAG 81 98 1 ATGGGGGATT 0.675316 -38 **** ****** Masking position 11 Map Score: 7.21446 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 46 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925