AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00240_hinf_reg_300.orf -o00240_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 Input sequences: #1 HI0011 105 DNA polymerase III, psi subunit (holD) #2 HI0075 280 anaerobic ribonucleoside-triphosphate reductase (nrdD) #3 HI0132 165 uridine kinase (udk) #4 HI0137 60 DNA polymerase III, epsilon subunit (dnaQ) #5 HI0205 292 H. influenzae predicted coding region HI0205 #6 HI0229 298 polynucleotide phosphorylase (pnp) #7 HI0272 23 orotate phosphoribosyltransferase (pyrE) #8 HI0273 300 ribonuclease PH (rph) #9 HI0280 214 uridine phosphorylase (udp) #10 HI0457 69 conserved hypothetical protein #11 HI0458 70 stationary phase survival protein SurA, putative #12 HI0459 131 pyrimidine operon regulatory protein (pyrR) #13 HI0514 241 DNA-directed RNA polymerase, beta' chain (rpoC) #14 HI0515 300 DNA-directed RNA polymerase, beta chain (rpoB) #15 HI0518 83 purine-nucleoside phosphorylase (deoD) #16 HI0519 98 transport protein, putative #17 HI0521 212 conserved hypothetical protein #18 HI0530 231 O-sialoglycoprotein endopeptidase (gcp) #19 HI0583 93 2',3'-cyclic-nucleotide 2'-phosphodiesterase (cpdB) #20 HI0584 71 hydrolase #21 HI0586 66 H. influenzae predicted coding region HI0586 #22 HI0587 99 peptidase E (pepE) #23 HI0739 300 DNA polymerase III, alpha subunit (dnaE) #24 HI0787 300 H. influenzae predicted coding region HI0787 #25 HI0788 280 ribosomal protein L14 (rpL14) #26 HI0792 36 ribosomal protein S8 (rpS8) #27 HI0798.1 28 ribosomal protein L36 (rpL36) #28 HI0799 139 ribosomal protein S13 (rpS13) #29 HI0801 27 ribosomal protein S4 (rpS4) #30 HI0802 31 DNA-directed RNA polymerase, alpha chain (rpoA) #31 HI0856 148 DNA polymerase I (polA) #32 HI0876 300 nucleoside diphosphate kinase (ndk) #33 HI0900 100 glutamate 5-kinase (gamma-glutamyl kinase) (proB) #34 HI0901 80 conserved hypothetical protein #35 HI0921 248 leucyl-tRNA synthetase (leuS) #36 HI0922 49 rare lipoprotein B, putative #37 HI0953 124 DNA/pantothenate metabolism flavoprotein (dfp) #38 HI0954 47 deoxyuridinetriphosphatase (dut) #39 HI0993 191 chromosomal replication initiator protein (dnaA) #40 HI0994 27 transferrin-binding protein 1 precursor (tbp1) #41 HI0995 97 transferrin-binding protein 2 precursor (tbp2) #42 HI1077 300 CTP synthetase (pyrG) #43 HI1158 73 thioredoxin reductase (trxB) #44 HI1159 284 conserved hypothetical protein #45 HI1161 300 conserved hypothetical protein #46 HI1219 279 cytidylate kinase 1 (cmkA) #47 HI1220 75 ribosomal protein S1 (rpS1) #48 HI1221 122 integration host factor, beta-subunit (himD) #49 HI1222 74 conserved hypothetical protein #50 HI1224 23 orotidine 5'-phosphate decarboxylase (pyrF) #51 HI1228 123 uracil phosphoribosyltransferase (upp) #52 HI1230 147 adenine phosphoribosyltransferase (apt) #53 HI1231 113 dihydrolipoamide dehydrogenase (lpdA) #54 HI1232 62 dihydrolipoamide acetyltransferase (aceF) #55 HI1233 299 pyruvate dehydrogenase, E1 component (aceE) #56 HI1243 90 16s pseudouridylate 516 synthase (rsuA) #57 HI1244 197 H. influenzae predicted coding region HI1244 #58 HI1350 273 cytidine deaminase (cdd) #59 HI1397 234 DNA polymerase III, chi subunit (holC) #60 HI1401 229 dihydroorotate dehydrogenase (pyrD) #61 HI1402 32 H. influenzae predicted coding region HI1402 #62 HI1403 32 H. influenzae predicted coding region HI1403 #63 HI1404 300 H. influenzae predicted coding region HI1404 #64 HI1644 233 pseudouridylate synthase I (truA) #65 HI1646 300 cytidylate kinase 2 (cmkB) #66 HI1655 71 antigen #67 HI1658 56 hemolysin, putative #68 HI1659 179 ribonucleoside-diphosphate reductase, alpha chain (nrdA) #69 HI1660 141 ribonucleoside diphosphate reductase, beta chain (nrdB) #70 HI1742 62 DNA-directed RNA polymerase, omega chain (rpoZ) #71 HI1743 249 guanylate kinase (gmk) Motif number 1 CGTGAAATTCACCGCACTTTTCTTTATAAT 3 114 1 ACCGCACTTT 0.998525 -52 CGAAAAAATGACCGCACTTTGGGCGTTTAA 6 207 0 ACCGCACTTT 0.998525 -92 TAACTTTTTGACCGCACTTCTTTTTTTACT 9 66 1 ACCGCACTTC 0.988431 -149 GAGAATTTTGACCGCACTTCGGCGATTTCA 13 172 0 ACCGCACTTC 0.988431 -70 GAAATTTTTAACCGCACTTTAAACCTTTAA 13 203 1 ACCGCACTTT 0.998525 -39 CGTTAAAATGACCGCACTCTGAACCTTACT 14 221 0 ACCGCACTCT 0.977458 -80 GTCATTTTTTACCGCACTTTTTAATTGATT 15 19 0 ACCGCACTTT 0.998525 -65 GTAAAAAATGACCGCACTTTATTCATTTTT 15 37 1 ACCGCACTTT 0.998525 -47 GCGAATTTTCACCGCACTTTTTGTAAACGT 16 11 0 ACCGCACTTT 0.998525 -88 TAAAAAATTGACCGCACTTTATTTAAGTGC 20 17 1 ACCGCACTTT 0.998525 -55 ATAAAAACAGACCGCACTTAAATAAAGTGC 20 30 0 ACCGCACTTA 0.969063 -42 GCAAAATTTAACCGCACTTTAAGGATTTTC 23 280 1 ACCGCACTTT 0.998525 -21 GTTAAAATTTACCGCACTTTTGGAATTATA 25 102 0 ACCGCACTTT 0.998525 -179 CTAAAAAACCACCGCACTTTTTATTTCTCT 35 137 1 ACCGCACTTT 0.998525 -112 TTAAATTTTAACCGCACTTTTGCAGCATTT 35 220 0 ACCGCACTTT 0.998525 -29 TTCCAACCGTACTTTTACCTAAAAA 38 6 1 ACCGTACTTT 0.947376 -42 GACAATTTTTACCGCACTTTTCTCTATTAC 39 151 1 ACCGCACTTT 0.998525 -41 TCGATTTTTGACCGCACTTTTGGTTGATTT 42 225 1 ACCGCACTTT 0.998525 -76 TCTAAAATCTTCCGCACTTTGCTAAAATCA 44 32 1 TCCGCACTTT 0.96695 -253 TTCTTTTTTTACCGCACTTTTGAGCATTAT 52 126 1 ACCGCACTTT 0.998525 -22 AAAAATATTGACCGCACTTTTACGGTCTTT 53 74 0 ACCGCACTTT 0.998525 -40 ATGTTTTTTGACCGCAGTTTTCATCAA 54 8 0 ACCGCAGTTT 0.963876 -55 GTGTTTTATGACCGCACTTTAAAAGGAACA 54 39 1 ACCGCACTTT 0.998525 -24 CAAAAAAATTACCGCACTTTCAAATAATTA 55 106 1 ACCGCACTTT 0.998525 -194 CTGAAAATCCACCGCGCTTTTATGATCTAT 59 114 0 ACCGCGCTTT 0.977458 -121 GTCAATTTTCACCGCACTTTAAAGGTAAGG 60 169 0 ACCGCACTTT 0.998525 -61 GTGAAAATTGACCGCACTTTCTTACAGTAA 60 187 1 ACCGCACTTT 0.998525 -43 GGCTACCATAACCGCACTTTATTAAGCCAA 64 204 1 ACCGCACTTT 0.998525 -30 TGAATTTTTCACCGCACTTTGAAGGA 68 7 0 ACCGCACTTT 0.998525 -173 ACAAATTTTTACCGCACTTTTTCTTATTTT 68 37 1 ACCGCACTTT 0.998525 -143 GTAAAAAATCACCGCACTTTTGATGATTTT 71 176 1 ACCGCACTTT 0.998525 -74 ********** Masking position 8 Map Score: 151.581 Number of sites scoring better than the average of aligned sites = 1115 Number in coding regions = 700 Number in noncoding regions = 415 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 2 ATAAAGAAAAGTGCGGTGAATTTCACGTTA 3 110 0 GTGCGGTAAT 0.993836 -56 AACGCCCAAAGTGCGGTCATTTTTTCGAAAG 6 210 1 GTGCGGTATT 0.985793 -89 AAAAAAAGAAGTGCGGTCAAAAAGTTAAACG 9 62 0 GTGCGGTAAA 0.995439 -153 AATCGCCGAAGTGCGGTCAAAATTCTCCGAA 13 175 1 GTGCGGTAAA 0.995439 -67 AAGGTTTAAAGTGCGGTTAAAAATTTCGGAG 13 199 0 GTGCGGTAAA 0.995439 -43 AAGGTTCAGAGTGCGGTCATTTTAACGGTCA 14 224 1 GTGCGGTATT 0.985793 -77 CAATTAAAAAGTGCGGTAAAAAATGACCGCA 15 22 1 GTGCGGTAAA 0.995439 -62 AATGAATAAAGTGCGGTCATTTTTTACCGCA 15 33 0 GTGCGGTATT 0.985793 -51 TTTACAAAAAGTGCGGTGAAAATTCGCCGAC 16 14 1 GTGCGGTAAA 0.995439 -85 CTTAAATAAAGTGCGGTCAATTTTTTACTAT 20 13 0 GTGCGGTAAT 0.993836 -59 AATCCTTAAAGTGCGGTTAAATTTTGCCGTA 23 276 0 GTGCGGTAAA 0.995439 -25 AATTCCAAAAGTGCGGTAAATTTTAACTGGA 25 105 1 GTGCGGTAAT 0.993836 -176 GAAATAAAAAGTGCGGTGGTTTTTTAGTTGT 35 133 0 GTGCGGTGTT 0.836614 -116 TGCTGCAAAAGTGCGGTTAAAATTTAAGGTG 35 223 1 GTGCGGTAAA 0.995439 -26 ATAGAGAAAAGTGCGGTAAAAATTGTCGGAG 39 147 0 GTGCGGTAAA 0.995439 -45 TCAACCAAAAGTGCGGTCAAAAATCGAAGAT 42 221 0 GTGCGGTAAA 0.995439 -80 ATGCTCAAAAGTGCGGTAAAAAAAGAAACGT 52 122 0 GTGCGGTAAA 0.995439 -26 GACCGTAAAAGTGCGGTCAATATTTTTAACG 53 77 1 GTGCGGTAAT 0.993836 -37 TTGATGAAAACTGCGGTCAAAAAACATTGTG 54 11 1 CTGCGGTAAA 0.9084 -52 TCCTTTTAAAGTGCGGTCATAAAACACAATG 54 35 0 GTGCGGTATA 0.989466 -28 TTATTTGAAAGTGCGGTAATTTTTTTGTGTT 55 102 0 GTGCGGTATT 0.985793 -198 TACCTTTAAAGTGCGGTGAAAATTGACCGCA 60 172 1 GTGCGGTAAA 0.995439 -58 CTGTAAGAAAGTGCGGTCAATTTTCACCGCA 60 183 0 GTGCGGTAAT 0.993836 -47 GCTTAATAAAGTGCGGTTATGGTAGCCCAAG 64 200 0 GTGCGGTATG 0.92255 -34 TCCTTCAAAGTGCGGTGAAAAATTCAACAA 68 10 1 GTGCGGTAAA 0.995439 -170 ATAAGAAAAAGTGCGGTAAAAATTTGTTGAA 68 33 0 GTGCGGTAAA 0.995439 -147 ATCATCAAAAGTGCGGTGATTTTTTACGGTA 71 172 0 GTGCGGTATT 0.985793 -78 ******* *** Masking position 7 Map Score: 107.27 Number of sites scoring better than the average of aligned sites = 622 Number in coding regions = 360 Number in noncoding regions = 262 Number of orfs with sites within 600 bp upstream = 184 Fraction of orfs with sites within 600 bp upstream = 0.0295535 Motif number 3 TAGTGTTAATTTCTTTTATTAATCTTTGCTAAAATGGTGCGT 1 43 0 TTTTTATTAA 0.877673 -63 CAACAACTTAATTTGATATTTTTCTAATAAAATCAATCTTTA 2 131 1 ATTTTTTTAA 0.772885 -150 TGATTATCTTTTTAGATCTATATATAGTGCAATCCGCATTTC 2 222 1 TTTTATTTAA 0.782329 -59 AGCTTACTTTTTTCTCTGTATATATAGACAAAAAGCCTGCGA 5 76 1 TTTTATTTAA 0.782329 -217 TCAAGCAAAATTGCAAGTTTTGTATGCATAAAGTAGGTTGTA 5 130 1 TTGTTTTTAA 0.632429 -163 TAGCCATCATTACATTATATTTCATATAAAAGAACCTAATT 6 10 1 TTTTATTAAA 0.748494 -289 ACAATGATAATTAAGTTGGTAATGTGAAATAAAGTTAGCCAT 6 94 1 TTTGTATTAA 0.507104 -205 AATGTTTTCCTTAAAATTTATATTAAAAACAATGCCTTATTT 6 267 0 TTTTATTAAA 0.732039 -32 TCTAGCACGCTTTAGTTTTTATTTTTGTTAAAATTCGCTAAG 8 220 0 TTTTTATTAA 0.877712 -81 CATTATTTCTTTTTTGTTTTTCTGATAACGAATAATAAGTAA 9 91 0 TTTTTTTAAA 0.918795 -124 TTTTCTAAAAATATTTTATTTCTTTTCTTGAAAATAAGATTT 9 156 1 ATTTTTTTAA 0.772898 -59 AATTTTTCCTTATTTTTAATAATGAATAAAAATGAA 15 58 0 TTTTTTTAAA 0.91868 -26 ATTCGGCTTATTCTACTTGTTTTCTTATGAAAAGTCGGCGAA 16 36 0 TTTGTTTTAA 0.720291 -63 TAATTGCAATTTAAAATTTTATTTTTGCCAAAGCACCTGTGT 18 38 1 TTTTTATTAA 0.877712 -194 AAGGACGCAATTCTAATCTATTTTTAGGGAAAAAGTAAAGGA 18 99 1 TTTTATTTAA 0.826468 -133 TCTAACGACGATTTTTTATTTATTTCAACGAATAAGGATAAC 23 76 0 ATTTTTTTAA 0.772898 -225 TATCATTGCCTTTCTCTTTTTCTTTTGATAAAATCCGCCGCC 25 172 1 TTTTTTTTAA 0.947273 -109 TGCTTATCCTTTTACTTTAAATGAACAA 27 4 0 TTTTTATTAA 0.87771 -25 TGCAACCAATTTTGTTTATAATTTTTTACAAAATACGATAAA 32 148 0 TTTTAATTAA 0.655673 -153 TGAAACAATCTTGAGCTATTTTTATAGGAAAAATTTAAGGTA 34 41 1 TTTTTTTTAA 0.933469 -40 GCGGTGGTTTTTTAGTTGTTTTTTACAATAAATTTTCAATTT 35 110 0 TTTTTTTAAA 0.918795 -139 AAAAGGATCCTTATTGTTTTTGTAATAGAGAAAAGTGCGGTA 39 160 0 TTTTTTTAAA 0.918793 -32 CATATTTTAATATTTGTCTCAACCAACACATCTCTT 42 5 1 TTTTTTTTAA 0.947268 -296 ACTTATTGCATTATATTATTACTTAACTACAAACAAGGATTC 43 39 1 TTTTTATAAA 0.818845 -35 TAAAATTTAATTAAAATATTTTTGATTAAAAAGTTTATTTTG 49 16 1 TTTTTTTAAA 0.918794 -59 CCTCTACCATTTTGTATTTTTTTAATCTAGAATTTGTCAATT 51 62 1 TTTTTTTAAA 0.918723 -62 TTTTCCTCTCTTTCTATTTTTTTATGATAGAATGCCAATCTA 52 77 1 TTTTTTTTAA 0.947199 -71 CGGTAATTTTTTTGTGTTTTTTTGTTCGCTAAAATAACCAGT 55 78 0 TTTTTTTTAA 0.947273 -222 TGCAGCCTTTTTTGTTTCGTTCTAAAAGCAAAAACCTGTAAA 56 27 1 TTTGTTTAAA 0.618586 -64 TTAAAATCACTTGCGTTTTAATTTTCATTCAATTCATAGGAG 59 17 0 TTTTAATTAA 0.65512 -218 AATTTCCTTTTAGTTTTTCATAATACGTTGATC 64 2 1 ATTTTATTAA 0.576206 -232 GATTATCAGAATGAGATCTTTATCACAAAAAATTCACATTTA 64 80 1 ATTTTTTAAA 0.681867 -154 CGTGCTTAATTTCAGTTTTTTGTATAAACGAAGTGTAGAACG 65 84 1 TTTTTTTTAA 0.947028 -217 TTACCGCACTTTTTCTTATTTTTCTAAATAAAAAATTTTAAT 68 45 1 TTTTTTTTAA 0.945243 -135 AATAAAAAATTTTAATTTTTATTCTCACAAAAACCGTTTATT 68 71 1 TTTTTATTAA 0.877598 -109 TTTATTTAGCTTTCCCTGTTTATCAGGGGAAACTATCAAAGA 69 81 0 TTTTTTTAAA 0.918795 -61 TAAATAAATGATAAGTTCTATTTAAAGGATAAATAAA 69 115 1 ATTTATTAAA 0.362527 -27 AGATTTTCACCTTTTATTTAAGTTAAACAAATCTGTT 71 6 1 TTTTTATAAA 0.818782 -244 TCACCGCACTTTTGATGATTTTTTATAGAGAAATCTGCATAA 71 184 1 TTGTTTTAAA 0.520058 -66 ** * *** * * ** Masking position 13 Map Score: 41.7693 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 145 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 4 AACGTTTTTAAAAATTCACTT 1 95 1 AAAATCACTT 0.619712 -11 TGAAAAGTATAAAATTCGCAGGCTTTTTGTC 5 102 0 AAAATCGCAG 0.866641 -191 TATTTTTGTTAAAATTCGCTAAGATATTGAT 8 212 0 AAAATCGCTA 0.862405 -89 AAGTATAAAGAAAATACGCCTAAAAAGCGAC 12 76 0 AAAATCGCCT 0.934198 -56 AAGTGCGGTCAAAATTCTCCGAAATTTTTAA 13 183 1 AAAATCTCCG 0.689364 -59 GCATTCATTTAAAATTTACCGCCTTAAAATT 14 25 1 AAAATTACCG 0.72323 -276 TTACCGCCTTAAAATTAGCAAAGATTTAGAT 14 40 1 AAAATAGCAA 0.590559 -261 AAGTGCGGTGAAAATTCGCCGACTTTTCATA 16 22 1 AAAATCGCCG 0.978141 -77 CGAATATCAAAAAATAAACCGTATCAGGAGA 22 16 0 AAAATAACCG 0.890583 -84 TTTTTCGTTGAAAATTAACCTTTTCTAAGCG 22 61 1 AAAATAACCT 0.720849 -39 ATTTGTTTGAAAAATTCGCTATAATACCGCT 23 237 1 AAAATCGCTA 0.862405 -64 AAGAAACGTCAAAATTAGCAGAGGATAAATT 24 195 1 AAAATAGCAG 0.717228 -106 TATCGAATGAAAAATAAACTGCAGAAAAAAT 25 45 0 AAAATAACTG 0.667196 -236 TAATCCAGTTAAAATTTACCGCACTTTTGGA 25 108 0 AAAATTACCG 0.72323 -173 TTCTTTTGATAAAATCCGCCGCCTATCTGCC 25 191 1 AAAATCGCCG 0.978141 -90 GCACAAGCAGAAAATGAACCTTTCTGGCGTT 32 11 1 AAAATAACCT 0.720849 -290 AAATCCCCCTAAAATTTGCCGTTACTATACC 33 11 1 AAAATTGCCG 0.848652 -90 ATTAAAATGCGCCAGATAGATTAA 39 4 1 AAAATCGCCA 0.962188 -188 AGAACAGAAAAAAATGCGCCAGTATTGTATA 39 47 0 AAAATCGCCA 0.962188 -145 TCCTACAGACAAAATCAACCAAAAGTGCGGT 42 235 0 AAAATAACCA 0.822332 -66 GCACTTTGCTAAAATCAGCCATTATTTTTTT 44 45 1 AAAATAGCCA 0.908525 -240 CGATAAAAGGAAAATCAGCCATGTTTTATCC 44 81 0 AAAATAGCCA 0.908525 -204 GTAGTGCCAAAAAATCCGCCGATTCTTTATG 44 196 0 AAAATCGCCG 0.978141 -89 TTTGTAACCCAAAATAAACTTTTTAATCAAA 49 36 0 AAAATAACTT 0.388766 -39 TGATTTGATGAAAATTCACTATCTTTATCTC 55 162 1 AAAATCACTA 0.744954 -138 TTCTCTTATTAAAATTCGCTAGGCATTTTAC 56 64 0 AAAATCGCTA 0.862405 -27 CAAATGTCTGAAAATCCACCGCGCTTTTATG 59 120 0 AAAATCACCG 0.954241 -115 ATGGCATTAGTAAATACGCCAG 62 21 1 TAAATCGCCA 0.540759 -12 TTTATCACAAAAAATTCACATTTATTACTGC 64 98 1 AAAATCACAT 0.490007 -136 ***** ***** Masking position 5 Map Score: 29.1769 Number of sites scoring better than the average of aligned sites = 400 Number in coding regions = 294 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 5 AATAAAAGAAATTAACACTATTTTTCAAGCAACG 1 65 1 ATTAATTTTT 0.668258 -41 ATATGTAGTGTTTTAGACCTTTTTGTCGTAAGAT 2 181 0 TTTTACTTTT 0.793743 -100 TCATCACGGTATTATTTCTATTTTTCAAGTAGGA 3 44 0 ATTATTTTTT 0.718796 -122 ATCATTCACAATTTATTTTGTTTTACGATATAAT 5 184 1 ATTTATTTTT 0.750388 -109 AAACATTTTCATTATTTCTTTTTTGTTTTTCTGA 9 108 0 ATTATTTTTT 0.718796 -107 TTTTTAGAAAATTTTTTTCTCTTTCAAACATTTT 9 133 0 ATTTTCCTTT 0.829193 -82 TTCTAAAAATATTTTATTTCTTTTCTTGAAAATA 9 158 1 ATTTTTTTTT 0.792303 -57 AAGCCCCTTTATTTTTGATACTTTG 10 2 0 ATTTTTCTTT 0.777975 -68 TTTGTTGTTTTTTATTTTCTCTTTCTTATAGCTT 10 46 1 TTTATCCTTT 0.750353 -24 CTCCGAAATTTTTAACCGCACTTTAAACCTTTAA 13 199 1 TTTAACCTTT 0.703144 -43 TATTGCTTAATTTAACCGTGTTTTTGATAGAAAG 14 96 1 TTTAATTTTT 0.650504 -205 TGCGGTCATTTTTTACCGCACTTTTTAATTGATT 15 19 0 TTTTACCTTT 0.779487 -65 AATTTTTCCTTATTTTTAATAATGAA 15 68 0 TTTTTTTTTT 0.778992 -16 ATTTATTACCTTTTATATTCCGTT 17 1 1 ATTTACTTTT 0.806386 -212 AACTGACAAAATTATTTCTGTTTTTGCATCTTTC 17 47 0 ATTATTTTTT 0.718796 -166 AAATAAAAATATTTTTACTCCTTTCTTTTAAGAA 19 13 1 ATTTTTCTTT 0.777975 -81 TGCGGTCTGTTTTTATAGCCTTTTAAAGGAAGAA 20 44 1 TTTTACTTTT 0.793743 -28 TTTTTTCTTCCTTTAAAAGGCTAT 20 58 0 TTTTTTCTTT 0.76402 -14 AAAACGGCTAATTATCAATTTTTTGATCTACTTA 23 140 1 ATTATTTTTT 0.718796 -161 TACGGCAAAATTTAACCGCACTTTAAGGATTTTC 23 276 1 TTTAACCTTT 0.703144 -25 AAGTACCATTATTAAAAATATTTTTTTCAGTATT 24 57 0 ATTAATTTTT 0.668258 -244 TCCAGTTAAAATTTACCGCACTTTTGGAATTATA 25 102 0 ATTTACCTTT 0.792776 -179 TTTATCCTCTCTTTGGTTTTAAGC 30 18 0 TTTATCCTTT 0.750353 -14 GCAACGGCATTTTTATCGTATTTTGTAAAAAATT 32 137 1 TTTTATTTTT 0.735288 -164 GTGCGGTGGTTTTTTAGTTGTTTTTTACAATAAA 35 120 0 TTTTTTTTTT 0.778992 -129 CTCCCTATTAATTTTTGCCATTTTACGGTATTCT 35 165 1 ATTTTCTTTT 0.840892 -84 CACCTTAAATTTTAACCGCACTTTTGCAGCATTT 35 220 0 TTTAACCTTT 0.703144 -29 CTCCGACAATTTTTACCGCACTTTTCTCTATTAC 39 147 1 TTTTACCTTT 0.779487 -45 AATTGTTCGCATTATCATTTTTTTTTTGTAATAA 41 47 0 ATTATTTTTT 0.718796 -51 CATTTTACTGATTATAAACTTTTTGC 43 3 0 ATTATCTTTT 0.779802 -71 TTTTAGGTACATTATCTATGTTTTTTAATATTTC 45 178 0 ATTATTTTTT 0.718796 -123 AACCTCTACCATTTTGTATTTTTTTAATCTAGAA 51 60 1 ATTTTTTTTT 0.792303 -64 TTTTACTCTCCTTTTGACTCTTAA 51 110 0 TTTTATCTTT 0.718425 -14 GGGGATTTTTATTTTCCTCTCTTTCTATTTTTTT 52 66 1 ATTTTCCTTT 0.829193 -82 ACGTTTCTTTTTTTACCGCACTTTTGAGCATTAT 52 122 1 TTTTACCTTT 0.779487 -26 TGCGGTCAATATTTTTAACGTTTTTACGAGGTAA 53 88 1 ATTTTCTTTT 0.840892 -26 TTTTTGTTCCTTTTAAAGTGCGGT 54 49 0 TTTTTCTTTT 0.830027 -14 TCGGGCTTTGTTTTAAAGTTTTTTCAGATTTTTT 55 28 0 TTTTATTTTT 0.735288 -272 TGCGGTAATTTTTTTGTGTTTTTTTGTTCGCTAA 55 88 0 TTTTTTTTTT 0.778992 -212 TATTGCGTCGATTATATCTGTTTTTTATTCAAAA 57 46 1 ATTATTTTTT 0.718796 -152 TACAGTTATAATTTTTAATATTTTTCCTAAGGAT 58 245 1 ATTTTTTTTT 0.792303 -29 CACAAAACTGATTTTTAACGTTTTTGTTACGTTC 59 78 0 ATTTTCTTTT 0.840892 -157 TGCATATTTAATTATTTATTTTTTAGGGTTTTTT 59 157 1 ATTATTTTTT 0.718796 -78 TTTCGTTAAAATTTTACCCTTTTTATAGGGTAAG 59 188 1 ATTTTCTTTT 0.840892 -47 TAGAGCTTAATTTTACAATATTTTCCATTAATTA 60 86 1 TTTTATTTTT 0.735288 -144 TTGAAATGTTTTTAAAAACCTTTTTCTATGTGGT 65 219 1 TTTAACTTTT 0.720566 -82 AATTAACTCCTTTTTAGATTAAATT 67 42 0 ATTAACTTTT 0.736205 -15 TTCAACAAATTTTTACCGCACTTTTTCTTATTTT 68 33 1 TTTTACCTTT 0.779487 -147 TTTATTTATCCTTTAAATAGAACT 69 128 0 TTTATTCTTT 0.684489 -14 TGCGGTGATTTTTTACGGTACTTTTTCATTCTAA 71 158 0 TTTTATCTTT 0.718425 -92 ***** * **** Masking position 3 Map Score: 52.9411 Number of sites scoring better than the average of aligned sites = 1080 Number in coding regions = 717 Number in noncoding regions = 363 Number of orfs with sites within 600 bp upstream = 265 Fraction of orfs with sites within 600 bp upstream = 0.0425634 Motif number 6 CAACAACTTAATTTGATATTTTTCTAATAAAATCAATCTTT 2 131 1 ATTTATTAAA 0.820742 -150 CACGTTATTTTTTCACTTGAATTTTAAAAACTGTGAACTT 3 77 0 TTTTATTAAA 0.92103 -89 TATAAACCTCATTTAACTGATATTTTATCAAGCTAAAATAC 5 261 0 ATTTATTAAA 0.820742 -32 AAGGCATTGTTTTTAATATAAATTTTAAGGAAAACATT 6 271 1 TTTTATTAGA 0.646097 -28 TTAGCAAAGATTTAGATTGATTTTTAATCAATCTTGACCTT 14 54 1 TTTAATTAAA 0.433226 -247 TTTACCGCACTTTTTAATTGATTAAGATAAA 15 1 0 TTTTATAAAA 0.296518 -83 CACTTTATTCATTTTTATTCATTATTAAAAATAAGGAAAAA 15 51 1 ATTTTTTAAA 0.301683 -33 AGTCGGCGAATTTTCACCGCACTTTTTGTAAACGT 16 5 0 TTTTATTTAA 0.552611 -94 GTGCGGTCTGTTTTTATAGCCTTTTAAAGGAAGAAAAAA 20 43 1 TTTTATTAGA 0.646097 -29 TTACGGCAAAATTTAACCGCACTTTAAGGATTTTCA 23 275 1 ATTTATTAAT 0.429374 -26 TGCAACGGCATTTTTATCGTATTTTGTAAAAAATTATAAAC 32 136 1 TTTTATTTAA 0.552593 -165 TACCACCAAATTTATAGAGGTCTCTCAATAATAAAAATA 35 9 0 TTTAATTAAA 0.433225 -240 GTGCGGTGGTTTTTTAGTTGTTTTTTACAATAAATTTTCAA 35 113 0 TTTTATTAAT 0.657556 -136 TTAGAAGATCTTTTCACGCATTTATTGTAAAATCTCCGACA 39 114 1 TTTTATTGAA 0.660086 -78 CATATTTTAATATTTGTCTCAACCAACACATCTCT 42 5 1 TTTTATTACA 0.405129 -296 AGTGCGGAAGATTTTAGAAACGTTTTACCATTTCTATTA 44 9 0 ATTTATTAAT 0.429373 -276 TAATCACATCTTTTAATCTAACTCTGAGGATATTTT 46 6 0 TTTTATTAAT 0.657558 -274 AGATGTGATTATTTTATGGATTTATATGCAAAGCATATACC 46 36 1 ATTTATTTAA 0.326159 -244 GCATATACCTATTTTAAGAAAATGTGATCAATATCTCATAA 46 68 1 ATTTATTAAA 0.820692 -212 ATTTTATGGATTTTAATGTGGATGTTATTAACTTAAATTAA 47 32 1 TTTTATTAAA 0.92116 -44 ATCAAAAATATTTTAATTAAATTTTAATCAA 49 1 0 TTTTATTAAA 0.921146 -74 GCTGAGTCCTTTTTGAAAAAAATCTGAAAAAACTTTAAAAC 55 12 1 TTTTATTAAA 0.920199 -288 CAATATTTGCTTTTCACAAACATTTAACAAATCTTGTAAAT 55 208 0 TTTTATTAAA 0.921147 -92 TCGACGCAATATTTCAATCCTGTTTCAAGAAAATGGAGCAC 57 16 0 ATTTATTAAA 0.820741 -182 ATCTGTTTTTTATTCAAAAAATTGTGACGAACTGCAAACTT 57 61 1 TATTATTAAA 0.296535 -137 GAACTGCAAACTTTTACAACTTTATAACAAAATTTTTTTGA 57 89 1 CTTTATTAAA 0.463009 -109 TTAGCCTTGTTTGTTAAGAAATTGTAATAAATAGAAGCTAT 58 124 1 TTGTATTAAA 0.362121 -150 AAGATCACAGTTTTAATGAATATTTAATCAAACTATCGCGG 58 178 1 TTTTATTAAA 0.921146 -96 TCCACCGCGCTTTTATGATCTATGTCACAAAACTGATTTTT 59 96 0 TTTTTTTAAA 0.529896 -139 GCGCGGTGGATTTTCAGACATTTGTAATAATGCATATTTAA 59 127 1 TTTTATTAAT 0.657557 -108 AATTATTTATTTTTTAGGGTTTTTTCGTTAAAATTTTACCC 59 166 1 TTTTATTGAA 0.660124 -69 TCATTAATACATTTTAATTATGTATAAAAAACGGCTAGTTT 60 40 0 ATTTATTAAA 0.819448 -190 TCCTTTTAGTTTTTCATAATACGTTGATCAATTATAGGGAA 64 15 1 TTTTAGTAAA 0.384526 -219 TTTTAAAAACATTTCAAGGTTTTTTTAATAACTATTGTGGC 65 195 0 ATTTATTAAA 0.820723 -106 TTTGTTGAATTTTTCACCGCACTTTGAAGGA 68 1 0 TTTTATTAGA 0.646097 -179 TTACCGCACTTTTTCTTATTTTTCTAAATAAAAAATTTTAA 68 45 1 TTTTTTTAAA 0.529896 -135 GTAATAAATTTTTTGATTTGATTCTTGACAATAGATAACTT 68 120 0 TTTTATTGAA 0.660123 -60 **** * * * * ** Masking position 15 Map Score: 22.9007 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 75 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 7 TTGCTTTATTAATTTGGTGGAGATAATCGGGATCGA 8 145 0 AAGTGGAGAA 0.920012 -156 GCTCCCCCGTAAACGGGTGGAGCCAAGGGATCAGCA 13 31 0 AAGTGGAGAA 0.920012 -211 TTCCCTCGCAAAGCAGGGGAAGGCAAGAGGAACAAC 13 125 1 AAGGGAAGAA 0.966746 -117 CAATTTTGAAAACGTGAGGAAGATCACAGTTTTAGA 17 135 0 AAGGGAAGCA 0.765301 -78 TAAATAGATCAATAAGAGGAAGCTAAATTATCATTG 25 144 1 AAGGGAAGAA 0.966746 -137 TTATCAAAAGAAAAAGAGAAAGGCAATGATAATTTA 25 167 0 AAGGAAAGAA 0.840523 -114 TCTGTTCTATAATCTGCTTAAGTGAAAGGTCAAACT 39 70 1 AAGTTAAGAA 0.81017 -122 TCCAAGGATAAAAAGGATTAAGCCAAAACTAGCATT 42 133 1 AAGTTAAGAA 0.81017 -168 TCCCCCCATAAATGGGTGGAGCCAAGATTAGAGGT 45 10 1 AAGTGGAGAA 0.920012 -291 TAAAACCTCTAATAAGCAGAAGGCAAGTTATCATTA 45 57 0 AAGAGAAGAA 0.83404 -244 CTTCCCCCACAAGCAGGGGAAGGCAAGTTTTTAAAA 45 88 0 AAGGGAAGAA 0.966746 -213 CTCCCCCCATAAATGGGTGGAGCCAAGATAATTGAT 45 258 1 AAGTGGAGAA 0.920012 -43 AAAAAAATAGAAAGAGAGGAAAATAAAAATCCCCAA 52 64 0 AAGGGAAAAA 0.575884 -84 TATTCACTCAAAACAGATTAAGGAAAACCT 55 280 1 AAGTTAAGAA 0.81017 -20 TCAATTATTCAACTAGAAAAAGGAAATTATT 58 6 0 AAGAAAAGAA 0.476745 -268 AAGATAATGTGTTTGAGAAAAGATCGCAAGT 68 159 0 AAGTTGAGAA 0.730838 -21 TCTTCCCCATAAGTTGGGGAAGACAATAGGGGCGT 69 10 0 AAGGGAAGAA 0.966746 -132 TTCCCCTGATAAACAGGGAAAGCTAAATAAATGATA 69 92 1 AAGGAAAGAA 0.840523 -50 ** * ***** ** Masking position 11 Map Score: 17.6152 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 94 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 ATCACTTTCGAATTTGAGAATATTCTTTTAGTA 5 33 0 ATTTAGAAAT 0.939198 -260 ATTCGAAAGTGATTTGAGAATATAGCTTACTTT 5 53 1 GTTTAGAAAT 0.693951 -240 GAAATAAAATATTTTTAGAAAATTTTTTTCTCT 9 145 0 ATTTAGAAAT 0.925349 -70 GGAAGATCACAGTTTTAGAAAATAAACATTATG 17 121 0 ATTTAGAAAT 0.935653 -92 TTTAGGTAATAAATTAAGAAAATCA 18 217 1 AATTAGAAAT 0.793261 -15 ACTTAAGAGAAATTTCTGAAGATCTTGGTTTTG 24 87 1 ATTTTGAAAT 0.552301 -214 TCAAATATTTAATTTAAGGAAATCAA 31 4 0 ATTTAGGAAT 0.663427 -145 GTTAATGCCAATTTTAAGAACTTGGAAAGGATT 33 78 1 ATTTAGAATT 0.604509 -23 CAAACTTGGATTTTTTAGAAGATCTTTTCACGC 39 100 1 TTTTAGAAAT 0.729562 -92 TATCATTATTTATTTTAGAACCTCTAATCTTGG 45 32 0 TTTTAGAACT 0.420032 -269 GCATATACCTATTTTAAGAAAATGTGATCAATA 46 68 1 ATTTAGAAAT 0.925349 -212 TTATTAACTTAAATTAAGAAGATTATTTAT 47 56 1 AATTAGAAAT 0.794449 -20 AAATCTTGTAAATTTTAGAAGATTTTTTGAGAT 55 188 0 ATTTAGAAAT 0.939523 -112 TTATAGGGTAAGATTGAGAAAATAACGGGGCTA 59 210 1 AATTAGAAAT 0.791179 -25 TATTACTGCAATTTTTAGAAACTATCGCTTATT 64 120 1 ATTTAGAACT 0.794521 -114 CTTTTTCTTAAATTTCAGAAAATCTAACCACAT 65 246 0 ATTTAGAAAT 0.842729 -55 * *** **** ** Masking position 5 Map Score: 12.2598 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 20 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 TTCAAGTAGGATTCAAACATTTTATCCAATAAG 3 22 0 ATTAAATTTT 0.808662 -144 TTTCTTTATAATTGCAAGAATTTTCCTTACATC 3 132 1 ATTAAAATTT 0.407859 -34 TTCTTTTAGTAATTAAACATTTAGAGGAAGGTT 5 11 0 AATAAATTTA 0.7876 -282 CAAGAAAAGAAATAAAATATTTTTAGAAAATTT 9 153 0 AATAAATTTT 0.892161 -62 TCTTTTCTTGAAAATAAGATTTTTCCTAAGGGC 9 176 1 AAAAAATTTT 0.705528 -39 ATTTAATTGCAATTTAAAATTTTATTTTTGCCA 18 35 1 AATAAATTTT 0.892165 -197 TTAAATAAAAATATTTTTACTCCTTTC 19 5 1 ATAAAATTTT 0.550694 -89 ACAAATACTGAAAAAAATATTTTTAATAATGGT 24 54 1 AAAAAATTTT 0.705528 -247 AATATCAGCCATTCAAATATTTAATTTAAGGAA 31 16 0 ATTAAATTTA 0.654484 -133 TGGCGGGTTTAATGTAAAATTTATGACGAATAT 31 64 0 AATAAATTTA 0.7876 -85 GGCGTTTACCATTTGAAGATTTTCATCGTTCAC 32 36 1 ATTAAATTTT 0.808662 -265 GTTCTGCAAAAATTGAAAATTTATTGTAAAAAA 35 101 1 AATAAATTTA 0.7876 -148 ATATTTCATCACTCCAAAATTTTATTTCGCATA 45 152 0 ACTAAATTTT 0.673828 -149 TTTAGGTTGAAATTGAACATTTATCCCCCCTCA 45 215 1 AATAAATTTA 0.7876 -86 TATCTCATAAAATTTAACATTTTGNTTCCATTT 46 99 1 AATAAATTTT 0.892165 -181 TTAAAATTTAATTAAAATATTTTTGATTAAAAA 49 15 1 ATTAAATTTT 0.808662 -60 AGCCCGATGGAATGCAATATTTTACTGGTTATT 55 55 1 AATAAATTTT 0.892166 -245 TTACAACTTTATAACAAAATTTTTTTGATGCGA 57 102 1 ATAAAATTTT 0.550697 -96 AATTATATTGAATAGAACAATTTCACTTCAAAT 58 84 0 AATAAAATTT 0.574172 -190 TGTACTTATTAAATCAAAATTTATTGTTAGCCG 58 216 0 AAAAAATTTA 0.518159 -58 GCATAAAAACACTCCAAAATTTATTCAAAAATA 64 149 0 ACTAAATTTA 0.480763 -85 TATTTTTCTAAATAAAAAATTTTAATTTTTATT 68 61 1 AATAAATTTT 0.892166 -119 TCAAGAATCAAATCAAAAAATTTATTACTTGCG 68 133 1 AATAAAATTT 0.574172 -47 *** ** ***** Masking position 11 Map Score: 16.2774 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 139 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 10 TTCGCGCCAGCTCCCCCGTAAACGGGTGGAGCCAAG 13 40 0 CCCCTAAGGG 0.952504 -202 AACGTCCCCTTTGAAAATGGTTTCGTATTG 17 193 0 TCCCGAATGG 0.858142 -20 TGCGCGATTTTACCCTGTTTAAGCGGTTTTAACCAG 18 177 0 TCCCTAACGG 0.931137 -55 TCCCCCCATAAATGGGTGGAGCCAAG 45 1 1 TCCCTAAGGG 0.992196 -300 AAACTTGCCTTCCCCTGCTTGTGGGGGAAGGTGCCC 45 94 1 TCCCTGTGGG 0.960649 -207 TGGGGGAAGGTGCCCGAAGGGAAGGGGGATATAGGG 45 115 1 TCCCGGAGGG 0.974873 -186 TGGGGGGAGCTGCCGAAGGTGAGGGGGGATAAATGT 45 231 0 TCCGGGAGGG 0.777795 -70 CTTCGGCAGCTCCCCCCATAAATGGGTGGAGCCAAG 45 249 1 TCCCTAAGGG 0.992196 -52 AAACGTATAATACCCATATCAAAGGGAGGGCATTAG 58 43 0 TCCCTAAGGG 0.992197 -231 GTTAAAATTTTACCCTTTTTATAGGGTAAGATTGAG 59 192 1 TCCCTATGGG 0.981534 -43 TTTTGGCTAAATCCCAGTGCATTGGGCGAATTGCGG 63 83 0 ACCCGATGGG 0.789502 -218 CCTATTGTCTTCCCCAACTTATGGGGAAGATAGCAC 69 16 1 TCCCTATGGG 0.981532 -126 TTTGATAGTTTCCCCTGATAAACAGGGAAAGCTAAA 69 83 1 TCCCTAAAGG 0.901216 -59 TGTCAAAAATTACTCTATTGAAAGGGCGTTATAATA 70 23 0 TCTCTAAGGG 0.885581 -40 * *** * ** *** Masking position 3 Map Score: 14.1866 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 16 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 11 AATCTTTGCTAAAATGGTGCGTAATTTTAA 1 35 0 AAAATGGTGC 0.963329 -71 TATATAGACAAAAAGCCTGCGAATTTTATA 5 96 1 AAAAGCCTGC 0.798505 -197 AAATAAAAACTAAAGCGTGCTAGAATAGTG 8 238 1 TAAAGCGTGC 0.699874 -63 ACGAACAAGAAAAATGGTGCAAATGCCGTC 12 49 1 AAAATGGTGC 0.963329 -83 CTGATTACTATAAATGGTGCTGATCCCTTG 13 14 1 TAAATGGTGC 0.912768 -228 TTTATTACCTAAAATGTTGCGCGATTTTAC 18 200 0 AAAATGTTGC 0.773111 -32 TTCTATTGTCAAAATGCTGCAAAAGTGCGG 35 209 1 AAAATGCTGC 0.946757 -40 ATACCTATAAAAAATGGTGCGTGAATTTTA 36 30 0 AAAATGGTGC 0.963329 -20 TAGATAAAGGCTGCATTGCAGCCT 56 5 1 TAAAGGCTGC 0.868833 -86 AACGAAACAAAAAAGGCTGCAATGCAGCCT 56 18 0 AAAAGGCTGC 0.943277 -73 CTGTTTCAAGAAAATGGAGCACTTATT 57 8 0 AAAATGGAGC 0.769472 -190 ********** Masking position 4 Map Score: 8.17483 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 37 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 12 AGCAAAGATTAATAAAAGAAATTAACACTAT 1 55 1 AATAAAGAAA 0.766251 -51 ATCCTACTTGAAAAATAGAAATAATACCGTG 3 43 1 AAAAAAGAAA 0.853409 -123 GAATTTTAACAAAAATAAAAACTAAAGCGTG 8 226 1 AAAAAAAAAA 0.770718 -75 GATAACGAATAATAAGTAAAAAAAGAAGTGC 9 79 0 AATAATAAAA 0.607013 -136 TCGTTATCAGAAAAACAAAAAAGAAATAATG 9 102 1 AAAAAAAAAA 0.770718 -113 AACAAAAAAGAAATAATGAAAATGTTTGAAA 9 115 1 AAATATGAAA 0.649448 -100 TCTTATTTTCAAGAAAAGAAATAAAATATTT 9 164 0 AAGAAAGAAA 0.381697 -51 GGAAAGATGCAAAAACAGAAATAATTTTGTC 17 46 1 AAAAAAGAAA 0.853409 -167 AAATAGTAAAAAATTGACCGC 20 1 1 AAATATAAAA 0.516841 -71 CCTTTAAGTTAATAAGAAAAAGTTGTATTGA 21 37 0 AATAAAAAAA 0.654309 -30 TATTCGTTGAAATAAATAAAAAATCGTCGTT 23 84 1 AATAATAAAA 0.607013 -217 ACACCTAAACAAATACTGAAAAAAATATTTT 24 46 1 AAATATGAAA 0.649448 -255 TAAACTGCAGAAAAAATGAAATGCTCTCTTC 25 31 0 AAAAATGAAA 0.826114 -250 GCACTTTTGGAATTATAAAAATATCCTCATC 25 88 0 AATTAAAAAA 0.424658 -193 TTATCAAAAGAAAAAGAGAAAGGCAATGATA 25 172 0 AAAAAAGAAA 0.853409 -109 GAGGTCTCTCAATAATAAAAATA 35 3 0 AATAAAAAAA 0.654309 -246 TCTGTTCTGCAAAAATTGAAAATTTATTGTA 35 98 1 AAAAATGAAA 0.826114 -151 TGGTTGAGACAAATATTAAAATATG 42 5 0 AAATATAAAA 0.516841 -296 TGGAGTGATGAAATATTAAAAAACATAGATA 45 169 1 AAATATAAAA 0.516841 -132 TCTATCATAAAAAAATAGAAAGAGAGGAAAA 52 77 0 AAAAAAGAAA 0.853409 -71 AAAGTGCGGTAAAAAAAGAAACGTTTTTAGA 52 115 0 AAAAAAGAAA 0.853409 -33 AGCGAATTTTAATAAGAGAAAACATA 56 75 1 AATAAAGAAA 0.766251 -16 TTTCACTTCAAATTATAGAAACGTATAATAC 58 66 0 AATTAAGAAA 0.56108 -208 TCCTTAGGAAAAATATTAAAAATTATAACTG 58 247 0 AAATATAAAA 0.516841 -27 ACGTATTATGAAAAACTAAAAGGAAATT 64 8 0 AAAAATAAAA 0.732845 -226 CGTTTATACAAAAAACTGAAATTAAGCACGC 65 83 0 AAAAATGAAA 0.826114 -218 TGTCCAATTTAATAATAGAAAAAAGAGCTAC 65 136 1 AATAAAGAAA 0.766251 -165 TATTTAGAAAAATAAGAAAAAGTGCGGTAAA 68 44 0 AATAAAAAAA 0.654309 -136 TTGTGAGAATAAAAATTAAAATTTTTTATTT 68 70 0 AAAAATAAAA 0.732845 -110 ***** ***** Masking position 5 Map Score: 28.9097 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 246 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 13 ATAAATTGTGAATGATAATTAAAAGGAATAC 5 169 0 AATGATAATA 0.831708 -124 CTGTCGAAACAATGATAATTAAGTTGGTAAT 6 86 1 AATGATAATA 0.831708 -213 ACATCCACACAATGACAAATTCACCGTTATT 14 131 1 AATGACAATT 0.886863 -170 CCTGTGTGTAAATGACAAATTTAATAAAGGA 18 73 1 AATGACAATT 0.886863 -159 TTCGTCAAACAATTATAATTTTTCGTTGAAA 22 43 1 AATTATAATT 0.584777 -57 AGATCAAAAAATTGATAATTAGCCGTTTTCA 23 138 0 ATTGATAATA 0.551371 -163 TATCTGTATCATTGATAAGTTCTTCTGGGAA 24 224 0 ATTGATAATT 0.778282 -77 AGAGAAAGGCAATGATAATTTAGCTTCCTCT 25 158 0 AATGATAATT 0.933841 -123 GAACTTAAAAAATTATAAGTTGACATTATTA 41 22 1 AATTATAATT 0.584777 -76 ACAAATGTTGAATGATAAATTAAGTATTAAA 42 83 0 AATGATAATT 0.933841 -218 GAACAATATCAAGGACAATTTATTCTTGGAA 44 241 1 AAGGACAATT 0.754015 -44 TAAAATAAATAATGATAACTTGCCTTCTGCT 45 48 1 AATGATAATT 0.933841 -253 TGGAGAATGAAAGGATAATTTGTATGGGA 46 261 1 AAGGATAATT 0.846616 -19 TAAAAAACAAATTGACAAATTCTAGATTAAA 51 82 0 ATTGACAATT 0.660948 -42 AAGCTAAATAAATGATAAGTTCTATTTAAAG 69 111 1 AATGATAATT 0.933841 -31 GTTCTATTTAAAGGATAAATAAA 69 129 1 AAGGATAATA 0.658998 -13 ******** ** Masking position 5 Map Score: 10.5586 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 55 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 14 TTAAAATACTTGCCATTCTACACAACAACC 4 19 0 TGCCATTCTA 0.902739 -42 AAATAAAGTTAGCCATTAAAGCCAAACATC 6 120 1 AGCCATTAAA 0.473805 -179 AGCGCTTGAATGGCATTCAAGAGGTCGTCG 8 113 1 TGGCATTCAA 0.9267 -188 TAAGGTGAATTGGCATTCTATCCTTTACTT 18 131 0 TGGCATTCTA 0.936086 -101 GCCGCCTATCTGCCATTCTATCTGAATAGT 25 208 1 TGCCATTCTA 0.902739 -73 GCATAATATCAGCCATTCAAATATTTAATT 31 23 0 AGCCATTCAA 0.761408 -126 TGAAAAATGTGGGCATTATAGCGTAATTTA 31 111 0 GGGCATTATA 0.639896 -38 TATTAATTTTTGCCATTTTACGGTATTCTA 35 170 1 TGCCATTTTA 0.723671 -79 AAATAGCGTTGGGCATTCAATAAAATTAAA 37 61 1 GGGCATTCAA 0.844631 -64 AAGTATGTAGTGGCATTTAATACTTAATTT 42 68 1 TGGCATTTAA 0.781053 -233 AATGTTAATATGGCATTAAAAATCTTTA 46 193 0 TGGCATTAAA 0.781053 -87 GTTTTTAGATTGGCATTCTATCATAAAAAA 52 94 0 TGGCATTCTA 0.936086 -54 AAAATTCGCTAGGCATTTTACAGGTTTTTG 56 55 0 AGGCATTTTA 0.622086 -36 ********** Masking position 5 Map Score: 6.8456 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 55 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 15 TTGCAAGAATTTTCCTTACATCGAAACACGA 3 143 1 TTTCCTTAAT 0.891874 -23 AATTTGGTTTCCTTTGATGGAATGTTTT 12 8 1 TTTCCTTTAT 0.915704 -124 TAATCAATCTTGACCTTTTATTGCTTAATTT 14 78 1 TGACCTTTAT 0.693762 -223 ATTTATTACCTTTTATATTCCGTTTT 17 6 1 TTACCTTTAT 0.915704 -207 TTTTTGCATCTTTCCTTTTATGATAAAACGG 17 30 0 TTTCCTTTAT 0.915704 -183 CTCTCTTCTCTTACCTTAGATAAATTCA 25 8 0 TTACCTTAAT 0.891874 -273 TTGATTTCCTTAAATTAAATATTTG 31 5 1 TTTCCTTAAT 0.891874 -144 CATTCGCTCATCACCATAAATTACGCTATAA 31 95 1 TCACCATAAT 0.463899 -54 TATCGTTTTACCTTAAATTTTTCCTATA 34 63 0 TTACCTTAAT 0.891874 -18 AAAATCACCTTAAATTTTAACCGCA 35 234 0 TCACCTTAAT 0.821788 -15 CATGGCTGATTTTCCTTTTATCGTTGAGATC 44 89 1 TTTCCTTTAT 0.915704 -196 CCATACAAATTATCCTTTCATTCTCCAAATT 46 257 0 TATCCTTTAT 0.60451 -23 TTTACAATATTTTCCATTAATTATTTCTTTA 60 97 1 TTTCCATTAT 0.670885 -133 AGATTTTCACCTTTTATTTAAGTTAAA 71 7 1 TCACCTTTAT 0.858615 -243 ******** ** Masking position 10 Map Score: 7.04317 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 64 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912