AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i199_trans1_hinf_reg_300.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -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 HI0250 153 single-stranded DNA binding protein (ssb) #2 HI0349 84 adenylate kinase (adk) #3 HI0350 141 permease, putative #4 HI0351 172 UDP-glucose 4-epimerase (galE) #5 HI0352 300 conserved hypothetical protein #6 HI0514 241 DNA-directed RNA polymerase, beta' chain (rpoC) #7 HI0515 300 DNA-directed RNA polymerase, beta chain (rpoB) #8 HI0517 172 ribosomal protein L11 (rpL11) #9 HI0518 83 purine-nucleoside phosphorylase (deoD) #10 HI0519 98 transport protein, putative #11 HI0521 212 conserved hypothetical protein #12 HI0546 28 primosomal replication protein N (priB) #13 HI0547 198 ribosomal protein S6 (rpS6) #14 HI0548 169 translation initiation factor 1 (infA) #15 HI0579 83 elongation factor G (fusA) #16 HI0580 156 ribosomal protein S7 (rpS7) #17 HI0581 181 ribosomal protein S12 (rps12) #18 HI0582 300 glucose inhibited division protein (gidA) #19 HI0632 300 elongation factor Tu (tufB) #20 HI0638 128 conserved hypothetical protein #21 HI0639 22 adenylosuccinate lyase (purB) #22 HI0640 271 ribosomal protein L10 (rpL10) #23 HI0641 54 ribosomal protein L7/L12 (rpL7/L12) #24 HI0713 300 trigger factor (tig) #25 HI0714 122 ATP-dependent Clp protease, proteolytic subunit (clpP) #26 HI0716 237 preprotein translocase SecE subunit (secE) #27 HI0775 205 transcriptional regulator #28 HI0776 190 ribosomal protein S10 (rpS10) #29 HI0781 25 ribosomal protein S19 (rpS19) #30 HI0787 300 H. influenzae predicted coding region HI0787 #31 HI0788 280 ribosomal protein L14 (rpL14) #32 HI0792 36 ribosomal protein S8 (rpS8) #33 HI0798.1 28 ribosomal protein L36 (rpL36) #34 HI0799 139 ribosomal protein S13 (rpS13) #35 HI0801 27 ribosomal protein S4 (rpS4) #36 HI0802 31 DNA-directed RNA polymerase, alpha chain (rpoA) #37 HI0803 40 ribosomal protein L17 (rplQ) #38 HI0861 191 virulence-associated protein (vacB) #39 HI0862 135 conserved hypothetical protein #40 HI1573 300 pyruvate kinase, type II (pykA) #41 HI1574 33 replicative DNA helicase (dnaB) #42 HI1618 95 ABC transporter, ATP-binding protein #43 HI1624 89 H. influenzae predicted coding region HI1624 #44 HI1644 233 pseudouridylate synthase I (truA) #45 HI1722 135 methionine aminopeptidase (map) Motif number 1 TTATCTAAAAAAGTGCGGTTATTTTGCCTGA 1 117 0 AAGTGCGGTA 0.998163 -37 AAGTGCGGTAAAAATTATAAA 2 1 1 AAGTGCGGTA 0.998163 -84 TGATAAAGCATAGTGCGGTCAAATTTTTTAT 2 27 0 TAGTGCGGTA 0.974925 -58 AAAGTGCGGTTAATTTTAGTTG 3 130 0 AAGTGCGGTA 0.998163 -12 GAAATCGCCGAAGTGCGGTCAAAATTCTCCG 6 173 1 AAGTGCGGTA 0.998163 -69 TAAAGGTTTAAAGTGCGGTTAAAAATTTCGG 6 201 0 AAGTGCGGTA 0.998163 -41 GTAAGGTTCAGAGTGCGGTCATTTTAACGGT 7 222 1 GAGTGCGGTA 0.982942 -79 ATTATATAAAAAGTGCGGTTGTTTTTCAAGC 8 35 0 AAGTGCGGTG 0.993917 -138 ATCAATTAAAAAGTGCGGTAAAAAATGACCG 9 20 1 AAGTGCGGTA 0.998163 -64 AAAATGAATAAAGTGCGGTCATTTTTTACCG 9 35 0 AAGTGCGGTA 0.998163 -49 CGTTTACAAAAAGTGCGGTGAAAATTCGCCG 10 12 1 AAGTGCGGTA 0.998163 -87 TTAATAAGAAAAGTGCGGTTATTATAGGGGT 14 20 1 AAGTGCGGTA 0.998163 -150 AAAAAAACAAAAGTGCGGTAAATTTTAATCT 17 21 1 AAGTGCGGTA 0.998163 -161 TTACAAACAAAAGTGCGGTCAAAAATGATTT 24 134 0 AAGTGCGGTA 0.998163 -167 GATTGAATAAAAGTGCGGTCGCTCTTTTTAA 25 27 1 AAGTGCGGTG 0.993917 -96 TTAATCGCAAAAGTGCGGTTGTTTTCACCAG 26 13 1 AAGTGCGGTG 0.993917 -225 ATAATTCCAAAAGTGCGGTAAATTTTAACTG 31 103 1 AAGTGCGGTA 0.998163 -178 AAAGTATGAAAAGCGCGGTAAAAATT 38 6 0 AAGCGCGGTA 0.982027 -186 CAGTTTTAAAAAGTGCGGAGAGTTTGACACT 38 162 0 AAGTGCGGAA 0.973591 -30 TGGCTTAATAAAGTGCGGTTATGGTAGCCCA 44 202 0 AAGTGCGGTA 0.998163 -32 ********* * Masking position 2 Map Score: 90.8018 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 ATCTAAAAAAGTGCGGTTATTTTGCCTGAAATT 1 113 0 GTGCGGTATT 0.995136 -41 AAGTGCGGTAAAAATTATAAAAAAT 2 3 1 GTGCGGTAAT 0.993392 -82 ATAAAGCATAGTGCGGTCAAATTTTTTATAATT 2 23 0 GTGCGGTAAT 0.993392 -62 AAAGTGCGGTTAATTTTAGTTGTATT 3 126 0 GTGCGGTATT 0.995136 -16 TCACTATTTTGTGTGGTAAGAATGGTGATTTTC 4 111 0 GTGTGGTAAT 0.862828 -62 AATCGCCGAAGTGCGGTCAAAATTCTCCGAAAT 6 175 1 GTGCGGTAAT 0.993392 -67 AAGGTTTAAAGTGCGGTTAAAAATTTCGGAGAA 6 197 0 GTGCGGTAAA 0.949917 -45 AAGGTTCAGAGTGCGGTCATTTTAACGGTCATT 7 224 1 GTGCGGTATT 0.995136 -77 TATATAAAAAGTGCGGTTGTTTTTCAAGCACTT 8 31 0 GTGCGGTGTT 0.984006 -142 AATGAATAAAGTGCGGTCATTTTTTACCGCACT 9 31 0 GTGCGGTATT 0.995136 -53 TTTACAAAAAGTGCGGTGAAAATTCGCCGACTT 10 14 1 GTGCGGTAAT 0.993392 -85 AATAAGAAAAGTGCGGTTATTATAGGGGTTGTT 14 22 1 GTGCGGTATT 0.995136 -148 AAAAACAAAAGTGCGGTAAATTTTAATCTAGTT 17 23 1 GTGCGGTATT 0.995136 -159 ACAAACAAAAGTGCGGTCAAAAATGATTTTCTT 24 130 0 GTGCGGTAAA 0.949917 -171 TTGAATAAAAGTGCGGTCGCTCTTTTTAATAAA 25 29 1 GTGCGGTGTT 0.984006 -94 AATCGCAAAAGTGCGGTTGTTTTCACCAGATTT 26 15 1 GTGCGGTGTT 0.984006 -223 AATTCCAAAAGTGCGGTAAATTTTAACTGGATT 31 105 1 GTGCGGTATT 0.995136 -176 AGTATGAAAAGCGCGGTAAAAATT 38 2 0 GCGCGGTAAT 0.937951 -190 GTTTTAAAAAGTGCGGAGAGTTTGACACTGTAA 38 158 0 GTGCGGAATT 0.9328 -34 GCTTAATAAAGTGCGGTTATGGTAGCCCAAGTT 44 198 0 GTGCGGTAGT 0.972319 -36 ******* * * * Masking position 6 Map Score: 67.4942 Number of sites scoring better than the average of aligned sites = 667 Number in coding regions = 386 Number in noncoding regions = 281 Number of orfs with sites within 600 bp upstream = 202 Fraction of orfs with sites within 600 bp upstream = 0.0324446 Motif number 3 GATTGATTGATTGATTGATT 5 1 0 TTGATTGATT 0.986496 -300 GATTGATTGATTGATTGATTGATTGATTGA 5 17 0 TTGATTGATT 0.986496 -284 GATTGATTGATTGATTGATTGATTGATTGA 5 29 0 TTGATTGATT 0.986496 -272 GATTGATTGATTGATTGATTGATTGATTGA 5 41 0 TTGATTGATT 0.986496 -260 GATTGATTGATTGATTGATTGATTGATTGA 5 53 0 TTGATTGATT 0.986496 -248 GATTGATTGATTGATTGATTGATTGATTGA 5 65 0 TTGATTGATT 0.986496 -236 GATTGATTGATTGATTGATTGATTGATTGA 5 77 0 TTGATTGATT 0.986496 -224 GATTGATTGATTGATTGATTGATTGATTGA 5 97 0 TTGATTGATT 0.986496 -204 ATGACAGACTTTGATTGATTGATTGATTGA 5 109 0 TTGATTGATT 0.986496 -192 AGCAAAGATTTAGATTGATTTTTAATCAAT 7 56 1 TAGATTGATT 0.968293 -245 ATAAAAGGTCAAGATTGATTAAAAATCAAT 7 69 0 AAGATTGATT 0.750358 -232 ACCGCACTTTTTAATTGATTAAGATAAA 9 9 0 TTAATTGATT 0.816409 -75 AGAAATTTGTTAGATTGACTAACACAGGCG 22 72 0 TAGATTGACT 0.816677 -200 ATAAAGGAACTAGATTGATATTAAAAATAG 27 109 1 TAGATTGATA 0.750358 -97 ********** Masking position 4 Map Score: 30.9005 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 ATTGATTGATTGATTGATTGATT 5 4 0 TGATTGATTG 0.993387 -297 ATTGATTGATTGATTGATTGATTGATTGAT 5 20 0 TGATTGATTG 0.993387 -281 ATTGATTGATTGATTGATTGATTGATTGAT 5 32 0 TGATTGATTG 0.993387 -269 ATTGATTGATTGATTGATTGATTGATTGAT 5 44 0 TGATTGATTG 0.993387 -257 ATTGATTGATTGATTGATTGATTGATTGAT 5 56 0 TGATTGATTG 0.993387 -245 ATTGATTGATTGATTGATTGATTGATTGAT 5 68 0 TGATTGATTG 0.993387 -233 ATTGATTGATTGATTGATTGATTGATTGAT 5 84 0 TGATTGATTG 0.993387 -217 ATTGATTGATTGATTGATTGATTGATTGAT 5 96 0 TGATTGATTG 0.993387 -205 TGACAGACTTTGATTGATTGATTGATTGAT 5 108 0 TGATTGATTG 0.993387 -193 ********** Masking position 5 Map Score: 30.7979 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 5 TTGCCTGAAATTTTTTAAAAGATCTATATATT 1 93 0 TTTTTAAAGA 0.568319 -61 AAAAACCTCATTTTTTATCTAAAAAAGTGCGG 1 130 0 TTTTTATTAA 0.821121 -24 TAGCAACAGGTTTTTTATTTTATTGAAAATCA 4 87 1 TTTTTATTTA 0.571073 -86 AATAAATATGTTTTTGATATAAATGAACTGAC 11 74 0 TTTTTATTAA 0.821121 -139 GTTTGAGTTCTTTTTGAACAAAAAAGAAGGTC 13 51 0 TTTTTAAAAA 0.891193 -148 AAAAATAATATTGTTCATGAAAAACTCAATTT 14 86 0 TTGTTATAAA 0.898755 -84 TAAGTTTTTGAATTTAAAGGGCTTCA 15 5 1 TTTTTAATTA 0.489598 -79 TATTATAACCTTGTTTATTTAATATCAGTTTA 15 62 0 TTGTTATTAA 0.779931 -22 AGTTTTTTATAAAAAAACAAAAGT 17 3 1 TTTTTATAAA 0.842954 -179 GAATAGAATGTTGTTCAAAAAATCTACTTCTA 17 130 0 TTGTTAAAAA 0.863306 -52 ACACACAAGATTTTTAAAGAAAATGATCGCAT 18 40 1 TTTTTAAAAA 0.891193 -261 TAACGCCAATTTTTTGATCAGAATAAATAGAG 18 273 1 TTTTTATAGA 0.691746 -28 GTAAAGAATATTGTTGAAAAAAGAGCCAAATT 22 12 0 TTGTTAAAAA 0.863306 -260 GTTTCCTTAATTTTTAATGATAATAATTATTA 24 13 1 TTTTTATATA 0.769313 -288 CCGAACACGTTTGTTAAATAAAAAGACGCTCA 24 240 0 TTGTTAAAAA 0.864768 -61 GCGGTCGCTCTTTTTAATAAAAGCGATCGCAT 25 41 1 TTTTTATAAA 0.918855 -82 TTTCTTACCTTTTTCATTAAAACTGCTAATT 25 102 0 TTTTTATAAA 0.919982 -21 GCAACCGAAATTGTTGATAAAAAGAAAAATAC 26 156 1 TTGTTATAAA 0.898736 -82 AAAGGGTGTTTTTTTAATCTTAACGGAGCACT 31 256 1 TTTTTATTTA 0.571073 -25 TTGTTCATTTAAAGTAAAAGGA 33 1 1 TTGTTATTAA 0.779931 -28 ATCAAGTCATTTTTTAAGGAAATTG 43 4 0 TTTTTAGAAA 0.609401 -86 TACTCCTTGTTTGTTTAAGAAAATCTAGGCGT 43 62 0 TTGTTAAAAA 0.863306 -28 TTCCTTTTAGTTTTTCATAATACGTTGATCAA 44 14 1 TTTTTATATA 0.769301 -220 CTATCGCTTATTTTTGAATAAATTTTGGAGTG 44 141 1 TTTTTAAAAA 0.891193 -93 TTATCTCACTTTTTTGAAAAAACTTTACGAGA 45 112 0 TTTTTAAAAA 0.817788 -24 ***** ** *** Masking position 5 Map Score: 26.1864 Number of sites scoring better than the average of aligned sites = 308 Number in coding regions = 184 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 6 ATCCAGTTAAAATATATAGATCTTTTAAAAAATTTC 1 83 1 AATATTTTTT 0.73903 -71 TTTTAGATAAAAAATGAGGTTTTTTT 1 138 1 AAAATTTTTT 0.628186 -16 AGTGCGGTCAAATTTTTTATAATTTTTACCGCACTT 2 11 0 AATTTATTTT 0.683007 -74 ACGTTTTGTATTAATGGAGATTTTTT 2 69 1 TTAATTTTTT 0.374777 -16 TATTCTCTAATATTTGTTTTTCTTTTTTAGGAAGAA 3 11 1 TATTTTTTTT 0.762813 -131 ATTTTTGTAAAAATTAGGGGATTTTTAATCATTCCC 3 63 0 AAATTATTTT 0.562412 -79 AGTGCGGTTAATTTTAGTTGTATTTTAGAAATTTCG 3 114 0 ATTTTTTTTT 0.803515 -28 AGACTAAAAAATTATATCACTATTTTGTGTGGTAAG 4 124 0 ATTATTTTTT 0.655394 -49 TGCGGTTAAAAATTTCGGAGAATTTTGACCGCACTT 6 183 0 AATTTATTTT 0.683038 -59 TTTATTGCTTAATTTAACCGTGTTTTTGATAGAAAG 7 94 1 AATTTTTTTT 0.858953 -207 AATTCACCGTTATTTGTCGTTGTTTTGCTCAAGTTG 7 148 1 TATTTTTTTT 0.762813 -153 GTGCGGTCATTTTTTACCGCACTTTTTAATTGATTA 9 18 0 TTTTTATTTT 0.433173 -66 AATTTTTCCTTATTTTTAATAATGAA 9 68 0 AATTTTTTTT 0.858915 -16 AGTGCGGTGAAAATTCGCCGACTTTTCATAAGAAAA 10 23 1 AAATTATTTT 0.562484 -76 AAAATTCGGCTTATTCTACTTGTTTTCTTATGAAAA 10 45 0 TTATTTTTTT 0.563019 -54 TGAACTGACAAAATTATTTCTGTTTTTGCATCTTTC 11 47 0 AAATTTTTTT 0.784064 -166 ACGGTTACTCAAAATAAATATGTTTTTGATATAAAT 11 82 0 AAAATTTTTT 0.619317 -131 AGGGTTGCGGATTATACCGATTTTTTACGCTCCGC 13 88 0 ATTATTTTTT 0.655479 -111 TGCGAATTTCTCCGTATTTTAATCTTCAGG 16 137 0 AATTTTTTTT 0.858953 -20 ACTAGATTAAAATTTACCGCACTTTTGTTTTTTTAT 17 19 0 AATTTATTTT 0.683038 -163 TATTATTGTTATTATTAAGATCTTTTTTGGTTGTGA 18 130 0 ATTATTTTTT 0.655479 -171 GAATTTGGCTCTTTTTTCAACAATATT 22 2 1 AATTTTTTTT 0.858954 -270 GATTTTGTACTTATTATACTTTTTTTTGATATTGAT 24 72 0 TTATTTTTTT 0.563019 -229 AGTGCGGTCAAAAATGATTTTCTTTTATGCTCATAT 24 118 0 AAAATTTTTT 0.628186 -183 TCTTTCGTTATAATTGAGCGTCTTTTTATTTAACAA 24 226 1 TAATTTTTTT 0.65738 -75 GGTATAAGTTATTTTGATAGTGTTTTAAACAATCCT 27 179 1 ATTTTTTTTT 0.803516 -27 TTAAGTACCATTATTAAAAATATTTTTTTCAGTATT 30 57 0 TTATTTTTTT 0.563018 -244 ATCCAGTTAAAATTTACCGCACTTTTGGAATTATAA 31 101 0 AATTTATTTT 0.683038 -180 CAGTGATGACTTTTTATAGATATTTTTAAAGTATGA 38 28 0 TTTTTTTTTT 0.683509 -164 ATCACTGTATATTTTAAGGATATTTTAAAATTGAAG 38 93 0 ATTTTTTTTT 0.803515 -99 TATTTTTTACAGTTTTAAAAAGTGCG 38 176 0 TATTTATTTT 0.53228 -16 TACTCCGTCAATAATTACAAAATTTTAAAGGTGTTA 40 271 0 ATAATATTTT 0.285087 -30 ATTGCAGTAATAAATGTGAATTTTTTGTGATAAAGA 44 96 0 TAAATTTTTT 0.47164 -138 TTTTTGAATAAATTTTGGAGTGTTTTTATGCATTTG 44 151 1 AATTTTTTTT 0.858954 -83 TTTTATCTCACTTTTTTGAAAAAACTT 45 119 0 TTTATTTTTT 0.501186 -17 ***** * **** Masking position 5 Map Score: 31.431 Number of sites scoring better than the average of aligned sites = 1006 Number in coding regions = 653 Number in noncoding regions = 353 Number of orfs with sites within 600 bp upstream = 271 Fraction of orfs with sites within 600 bp upstream = 0.0435271 Motif number 7 CTAATATTTGTTTTTCTTTTTTAGGAAGAA 3 17 1 TTTTTCTTTT 0.881899 -125 AGCAACAGGTTTTTTATTTTATTGAAAATC 4 88 1 TTTTTATTTT 0.766531 -85 GTTGCAATCAATTTTATTTTGAAGATCATT 5 210 1 ATTTTATTTT 0.766531 -91 AAAAATACTTTTTTTATTTTCTTGCCAAGA 5 244 0 TTTTTATTTT 0.766531 -57 ATTTATTACCTTTTATATTCCGTTTTATC 11 10 1 CTTTTATATT 0.539211 -203 GTTTTTGCATCTTTCCTTTTATGATAAAAC 11 32 0 CTTTCCTTTT 0.864651 -181 AATAACCGCACTTTTCTTATTAAATAGTAC 14 13 0 CTTTTCTTAT 0.587139 -157 ATTTACCGCACTTTTGTTTTTTTATAAAAA 17 14 0 CTTTTGTTTT 0.686962 -168 GTCAAAAATGATTTTCTTTTATGCTCATAT 24 118 0 ATTTTCTTTT 0.881899 -183 CGATTGTAGCATTTTCTTTTCGCCTTGCCT 26 71 0 ATTTTCTTTT 0.881899 -167 TTCTTGCGTATTTTTCTTTTTATCAACAAT 26 165 0 TTTTTCTTTT 0.881899 -73 TATTTGCAAGCTTTTATTTTAA 28 3 0 CTTTTATTTT 0.892035 -188 CTTGCACCTCCTTTTCTATTTTGAAGTTAG 28 160 1 CTTTTCTATT 0.726885 -31 AACCCGCACCTTTTCTTTTAGGTGTTATT 30 10 1 CTTTTCTTTT 0.949473 -291 AGAAGAGAGCATTTCATTTTTTCTGCAGTT 31 30 1 ATTTCATTTT 0.527445 -251 TGCCTTTCTCTTTTTCTTTTGATAAAATCC 31 178 1 TTTTTCTTTT 0.881899 -103 CGCTCTTTTATTTTAACATATTTA 41 20 0 CTTTTATTTT 0.892035 -14 AATTTCCTTTTAGTTTTTCAT 44 2 1 ATTTCCTTTT 0.7174 -232 ********** Masking position 4 Map Score: 15.7574 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 197 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 8 GATCTATATATTTTAACTGGATATTTGCACA 1 74 0 TTTAACTGGA 0.974183 -80 GTCAATTGATTTTAAACTTGTTCCATTACCT 5 145 0 TTTAACTTGT 0.629811 -156 CGCAAAGCGCTTTTGACTGGAGTTTATGGTT 16 60 0 TTTGACTGGA 0.856147 -97 TTGAATAACATTTAAACTGGAGCTTTTTTA 17 162 1 TTTAACTGGA 0.974183 -20 AAATCTTGTGTGTAAAATGGAAAGTTATTAA 18 22 0 TGTAAATGGA 0.702823 -279 TCTTTTAGATGGATCCTGATGGG 19 3 1 TTTAGATGGA 0.8257 -298 TAACCTAGCTTTTGAACTCGAACATTAAAAA 20 66 0 TTTAACTCGA 0.830109 -63 ATTGAATCCGTTTTAAATGGAAATGTAAAAA 26 119 0 TTTAAATGGA 0.937479 -119 GTATCTTATATTTCAAATGGATATGTTTCTT 27 58 1 TTTAAATGGA 0.937479 -148 GTGCGGTAAATTTTAACTGGATTATTTAGTA 31 115 1 TTTAACTGGA 0.974183 -166 TTAAGGATATTTTAAAATTGAAGAACTTAAC 38 85 0 TTTAAATTGA 0.767986 -107 TTATAGATATTTTTAACTTGAACACAAGTAT 40 103 1 TTTAACTTGA 0.892817 -198 GGCTCAGTTATTTAAGCTGGTTTTGTTTACT 40 165 0 TTTAGCTGGT 0.708866 -136 *** ******* Masking position 8 Map Score: 10.1401 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 57 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 9 AAAATTCTCCGAAATTTTTAACCGCACTTT 6 193 1 GAAATTTTTA 0.792794 -49 CTAAATCTTTGCTAATTTTAAGGCGGTAAA 7 39 0 GCTAATTTTA 0.828223 -262 GAGATAGGTCGATATTGTTACAATATCGAC 13 24 1 GATATTGTTA 0.661167 -175 GGATTATACCGATTTTTTACGCTCCGCAA 13 86 0 GATTTTTTA 0.114218 -113 GGTTAAAAATGCTATATTTAACGGAAACGT 20 92 1 GCTATATTTA 0.623909 -37 ATTGCATTTTGATAATTTTAAAATATGACT 24 164 0 GATAATTTTA 0.792805 -137 TTATCAAAATGCAATTTTTAATCACTCTTT 24 179 1 GCAATTTTTA 0.828223 -122 AAGTGCGGTCGCTCTTTTTAATAAAAGCGA 25 37 1 GCTCTTTTTA 0.72456 -86 CTATGTTGATGCTATTTTCAATAGGCAAGG 26 49 1 GCTATTTTCA 0.72456 -189 AATTCTTTTTGCTATTTTTAATATCAATCT 27 120 0 GCTATTTTTA 0.950951 -86 AGAGGATGAGGATATTTTTATAATTCCAAA 31 84 1 GATATTTTTA 0.938974 -197 ACTTTTTATAGATATTTTTAAAGTATGAAA 38 26 0 GATATTTTTA 0.938974 -166 ATATTTTAAGGATATTTTAAAATTGAAGAA 38 91 0 GATATTTTAA 0.584815 -101 AATATACAGTGATAATTTTATCCCCGTCTT 38 116 1 GATAATTTTA 0.792805 -76 CGTGATTATAGATATTTTTAACTTGAACAC 40 98 1 GATATTTTTA 0.938974 -203 ATTTATTACTGCAATTTTTAGAAACTATCG 44 117 1 GCAATTTTTA 0.828223 -117 ********** Masking position 8 Map Score: 11.7457 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 94 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 10 TTGACTATAGTTTATTACCTAAAGATTATG 5 171 1 TTTATTACCT 0.907 -130 CTTTTTTTATTTTCTTGCCAAGAAAATAAT 5 237 0 TTTCTTGCCA 0.873825 -64 ATCTTGACCTTTTATTGCTTAATTTAACCG 7 84 1 TTTATTGCTT 0.72845 -217 TAAGCCGAATTTTATTAACTTAACTAATCT 10 68 1 TTTATTAACT 0.552362 -31 ATTTATTACCTTTTATATTCC 11 2 1 TTTATTACCT 0.907 -211 GAATTTTTCGTTCCTTGCCTTTGCAGATTG 13 134 1 TTCCTTGCCT 0.842473 -65 TCCGCCCGTTTTTCTTAACTTTTCCGCCTA 14 148 1 TTTCTTAACT 0.756409 -22 AATAAGAATTTTTCTTGCTTCTGGGCGCCG 22 181 1 TTTCTTGCTT 0.870979 -91 TTATTAAGCGTTTCTTACTTCATCTAACTT 23 11 1 TTTCTTACTT 0.83011 -44 TTTCTTACCTTTTTCATTAA 25 113 0 TTTCTTACCT 0.96085 -10 ATCTAGTTCCTTTATTGCCTATCAAGGATC 27 94 0 TTTATTGCCT 0.930912 -112 AATGCTCTCTTCTCTTACCTTAGATAAATT 31 13 0 TCTCTTACCT 0.794701 -268 TTAACATTTTTCTTGCCAAGAACCAGTT 34 9 1 TTTCTTGCCA 0.873825 -131 ********** Masking position 5 Map Score: 7.64198 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 173 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 11 ATGATCGCAAAATTTACATTTATTTCATACTTTTG 1 20 0 AATATTATTT 0.821048 -134 TTGACGAGAAAGCTGCATTCATTTAAAATTTACC 7 10 1 AATATTATTT 0.82105 -291 AATTAGCAAAGATTTAGATTGATTTTTAATCAATC 7 52 1 GATATTATTT 0.729093 -249 AAAGGATCAATAGATCCATTCTTTTTTTGTCAGGT 18 219 1 TATATTTTTT 0.621173 -82 ATCTATCTCTATTTATTCTGATCAAAAA 18 283 0 TATATTATTC 0.803036 -18 GTCTTAGGATTAGGTAAATTAATTCCGAGTAATCG 22 222 1 TATATTATTC 0.803025 -50 TTACTTCATCTAACTTTATTTATTTTAGGAATTGA 23 25 1 TATATTATTT 0.928083 -30 ACATATTAAATAATTCAATTTATTTAATCAATATC 24 46 1 TATATTATTT 0.928082 -255 TTGTTACCTCAATTAATTTGCACTCGGTC 24 282 0 TATATTATTT 0.928083 -19 TCTAAAGGTTTAAATACATTCCTTTGGGTTTTAGT 26 212 1 TATATTCTTT 0.817269 -26 CCGCCTAAGAAAGATGTATTTCTTTTACGAAATTC 27 145 0 AATATTCTTT 0.613918 -61 ATTTGGGTCATAGATTAATTAATTTCATCAACGGC 30 147 1 TATATTATTT 0.928083 -154 TGCACTCCTATATTTTAATTAATTTGATATTCTGA 34 113 0 TATATTATTT 0.928082 -27 ** * *** **** Masking position 8 Map Score: 6.49121 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 39 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 12 ATGTAAATTTTGCGATCATTATCGCATATTTT 1 36 1 TCGATCTTAT 0.934369 -118 ATTTTATTTTGAAGATCATTATTTTCTTGGCA 5 220 1 GAGATCTTAT 0.619088 -81 AGGTTCAGAGTGCGGTCATTTTAACGGTCATT 7 225 1 TCGGTCTTTT 0.851102 -76 ATGAATAAAGTGCGGTCATTTTTTACCGCACT 9 31 0 TCGGTCTTTT 0.851102 -53 GCAACCAGTTTGAGTTCTTTTTGAACAAAAAA 13 58 0 TAGTTCTTTT 0.602672 -141 CTTGTGAAAATGCGATCATTTTCTTTAAAAAT 18 49 0 TCGATCTTTT 0.942834 -252 AGTAACCTTATTCGATCCTTATGGAAACAGGT 18 99 0 TCGATCTTAT 0.934369 -202 TTGTTATTATTAAGATCTTTTTTGGTTGTGAG 18 129 0 TAGATCTTTT 0.922706 -172 ATAACAATAATAAGATCTTTATATATAAAAAG 18 154 1 TAGATCTTAT 0.91154 -147 TATTAGTAAATAAGATCTCTTTTTATATATAA 18 172 0 TAGATCCTTT 0.790417 -129 CAAATAAAAATGCGATCGCTTTTATTAAAAAG 25 50 0 TCGATCCTTT 0.838986 -73 ATTTGAAATATAAGATACTTATTTGTTGATAT 27 44 0 TAGATATTAT 0.404307 -162 ATTATCAGAATGAGATCTTTATCACAAAAAAT 44 81 1 TAGATCTTAT 0.91154 -153 * ***** **** Masking position 6 Map Score: 7.07157 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 86 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 13 GTGCCCATTATGAGCCGTTTGTGGCTCATA 8 68 1 TGAGCCGTTT 0.97553 -105 CGGGCGGATTATAGCCGTTTTTAGCTTTCT 14 126 0 ATAGCCGTTT 0.901972 -44 TTTTGCTAATTTAGACGTTTGGCCTTACTT 16 23 0 TTAGACGTTT 0.737304 -134 ACTATTAGAATTCGCCGTCTATTTCTATAT 17 101 1 TTCGCCGTCT 0.790806 -81 GATAAAATAATTAGCAGTTTTAATGAAAAA 25 94 1 TTAGCAGTTT 0.737304 -29 TCTCAATATGAGAGCCGTTTAATGTAATCA 28 61 1 AGAGCCGTTT 0.935874 -130 CTTAAATAACTGAGCCGTTTTTGATTTCCA 40 180 1 TGAGCCGTTT 0.97553 -121 TAACGCCATTTGCGCCGTTTCAGCTTTCAG 42 69 0 TGCGCCGTTT 0.957582 -27 ********** Masking position 8 Map Score: 4.10033 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 47 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 14 ATAAATCCCCCCTCAGTCTTCGCGCCAGCT 6 64 0 CCTCAGTCTT 0.729408 -178 GTTGATGAAGCCTTACCCTTATATAAACTG 15 39 1 CCTTACCCTT 0.95324 -45 ATGGCTATTACCTTAGCCTTCCAAGCTAAT 19 67 1 CCTTAGCCTT 0.933312 -234 AGTTGGTAGAGCGCACCCTTGGTAAGGGTG 19 144 1 GCGCACCCTT 0.768023 -157 GAACCGCCGACCTCACCCTTACCAAGGGTG 19 157 0 CCTCACCCTT 0.975641 -144 TCTTATAATTCCTCATCCTTATATCAATCA 19 208 1 CCTCATCCTT 0.970732 -93 ATAAAAATATCCTCATCCTCTCAAAAATTT 31 75 0 CCTCATCCTC 0.885703 -206 TGCTTATCCTTTTACTTTAAA 33 18 0 GCTTATCCTT 0.856579 -11 GATCTTATCCTTCTCAGAAAAA 37 29 0 TCTTATCCTT 0.686486 -12 ********** Masking position 5 Map Score: 1.47652 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 19 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 15 ATAAAAAATGAGGTTTTTTT 1 144 1 AGGTTTTTTT 0.751936 -10 TTTTAGCAACAGGTTTTTTATTTTATTGAA 4 84 1 AGGTTTTTTA 0.699511 -89 TTATGGAAACAGGTGTTATAGGATCCAAAA 18 83 0 AGGTGTTATA 0.910537 -218 TTTTTTTGTCAGGTGTTTTAAATTTCTGTA 18 240 1 AGGTGTTTTA 0.910537 -61 CTTTTCTTTTAGGTGTTATTGACATAACAC 30 20 1 AGGTGTTATT 0.929838 -281 GTATTTGTTTAGGTGTTATGTCAATAACAC 30 32 0 AGGTGTTATG 0.85653 -269 CGTCCCGAAAGGGTGTTTTTTTAATCTTAA 31 249 1 GGGTGTTTTT 0.77876 -32 AAAATTTTAAAGGTGTTATTTTACTTCGCT 40 259 0 AGGTGTTATT 0.929838 -42 ********** Masking position 6 Map Score: 2.12995 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 25 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555