AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00051_hinf_reg_100.orf -o00051_hinf_100.ace -a/home/amcguire/genomes/ORF_hinf.txt -z/home/amcguire/genomes/hinf.fna -g0.38 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 HI0058 70 3-deoxy-D-manno-octulosonate cytidylyltransferase (kdsB) #2 HI0059 72 conserved hypothetical protein #3 HI0060 40 ABC transporter, ATP-binding protein (msbA) #4 HI0061 258 recombination protein (rec2) #5 HI0448 71 PTS system, fructose-specific IIA/FPr component (fruB) #6 HI0449 86 H. influenzae predicted coding region HI0449 #7 HI0451 71 conserved hypothetical protein #8 HI0452 50 conserved hypothetical protein #9 HI0453 26 conserved hypothetical protein #10 HI0454 54 conserved hypothetical protein #11 HI0457 69 conserved hypothetical protein #12 HI0458 70 stationary phase survival protein SurA, putative #13 HI0459 131 pyrimidine operon regulatory protein (pyrR) #14 HI0524 110 fructose-bisphosphate aldolase (fba) #15 HI0613 72 fuculokinase (fucK) #16 HI0614 181 L-fucose isomerase (fucI) #17 HI0678 165 triosephosphate isomerase (tpiA) #18 HI0740 300 phosphomannomutase (yhxB) #19 HI0982 95 6-phosphofructokinase (pfkA) #20 HI0985 300 DNA processing chain A (dprA) #21 HI1062 85 (3R)-hydroxymyristol (acyl carrier protein) dehydrase (fabZ) #22 HI1064 56 conserved hypothetical protein #23 HI1112 233 xylose isomerase (xylA) #24 HI1136 122 UDP-N-acetylmuramoylalanine--D-glutamate ligase (murD) #25 HI1137 21 cell division protein (ftsW) #26 HI1560 22 H. influenzae predicted coding region HI1560 #27 HI1561 106 peptide chain release factor 1 (prfA) #28 HI1645 233 fructose-1,6-bisphosphatase (fbp) #29 HI1711 59 PTS system, glucose-specific IIA component (crr) #30 HI1712 79 phosphoenolpyruvate-protein phosphotransferase (ptsI) #31 HI1713 158 phosphocarrier protein HPr (ptsH) #32 HI1716 196 undecaprenyl-phosphate alpha-N-acetylglucosaminyltransferase (rfe), putative Motif number 1 CTGAAATATTAAAGAATAAGGAATAAATT 1 52 1 AAAAAGGAAT 0.885574 -19 AGCAGTCAGGAACAAACTAAAATAACAAGACAGG 4 57 0 AAATAAAATA 0.559522 -202 GCTCCTTAATAATTTAAAAAGAAAGCTGCGGATG 5 44 0 AAAAAAGAAA 0.918137 -28 TTTGTAGAGAAATGGATAAAAATTTACCGCACTT 7 11 0 AAAAAAAATT 0.844611 -61 TTATGTTATAAAACCATAAAAAATTTGAGGTTAA 7 46 1 AAAAAAAAAT 0.906133 -26 TACTCAAAAATATAAAAGAAAACGACCGCACT 8 29 0 AAAAAGAAAA 0.884055 -22 TGGATAGTATAACGAACAAGAAAAATGGTGCAAA 13 38 1 AAAAAGAAAA 0.884055 -94 TTCAATGCACAAAGTATAAAGAAAATACGCCTAA 13 84 0 AAAAAAGAAA 0.918137 -48 TTTTGACCGAAAATTACTAAAAATTGAAAGAATC 16 24 1 AAATAAAAAT 0.678309 -158 TGTGAAAGAAAAATGATAAGGAAAACAGTAAGAA 16 125 0 AAAAAGGAAA 0.892242 -57 ACCTGTATGGAACCAATAAAAAATAACCAATT 17 9 0 AAAAAAAAAT 0.906133 -157 GAAGATCATAAAATTAAAAAAATTCTCACAGAAA 17 74 0 AAAAAAAATT 0.844613 -92 TATTCGTTGAAATAAATAAAAAATCGTCGTTAGA 18 71 0 AAAAAAAAAT 0.906133 -230 TATTTATTTCAACGAATAAGGATAACGCTATGAC 18 87 1 AAAAAGGATA 0.823395 -214 TTAACTAATAAACTTAATAAAATTAGCATATTTA 20 91 1 AAATAAAATT 0.542813 -210 AAATGTAAAAAATCCAATAAGAAAAATTTGTTGA 20 141 0 AAATAAGAAA 0.710128 -160 TACATTTTCAAAATAAGAAAAATTTTGCAATTTT 20 168 1 AAAAAAAATT 0.844615 -133 AATTCTTTTTAATGAATAAAAAATTGCAAAATTT 20 187 0 AAAAAAAAAT 0.906133 -114 AGAAACGATTAATTTAAAAGCATTTTGCGATGCA 20 230 0 AAAAAGCATT 0.641733 -71 CTAGATTTTCAAATAAAAAGGAAAAAAT 20 283 1 AAAAAGGAAA 0.892242 -18 GATACCTTACAAAAAATAAACAAATAAAATCTAT 21 59 0 AAAAAACAAA 0.821801 -27 CCAATTTTTTAAGCCAGAAGGAAAAAACA 22 6 0 AAAAAGGAAA 0.892242 -51 AAAACGTAATAATGGAGAAAGATTTTATAATTGA 23 85 0 AAAAAAGATT 0.855131 -149 GCAAATAATCAACATAGAAAAATTAAATAACATA 23 146 1 AAAAAAAATT 0.844615 -88 TTGGAGCGCAAATGCATAAAAACACTCCAAAATT 28 60 1 AAAAAAAACA 0.522711 -174 GTATTATGAAAAACTAAAAGGAAATT 28 218 1 AAAAAGGAAA 0.892242 -16 TTAACAAAGTAATAAATAAACAATAGCCATAAAA 30 38 0 AAAAAACAAT 0.811693 -42 ATACCTTCCGAAACAATTAACAAAGTAATAAATA 30 54 0 AAATAACAAA 0.501825 -26 AGCCTGAATTAAATCATAAAAATAAGCTAAATAG 31 38 0 AAAAAAAATA 0.853275 -121 ** * ******* Masking position 6 Map Score: 37.4576 Number of sites scoring better than the average of aligned sites = 796 Number in coding regions = 550 Number in noncoding regions = 246 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 2 AAGGTACAATGCGTGCAATTTTTACTATTAGA 3 10 1 TGCGGCTTTT 0.931294 -31 AGTTTGTTCCTGACTGCTATTTTAGGAACCCAA 4 73 1 TGACGCTTTT 0.994844 -186 GACAGTATAATGGCGGCGTTTTATTAACTTTAA 6 58 1 TGGCGCTTTA 0.918022 -29 ATGGTGCAAATGCCGTCGCTTTTTAGGCGTATT 13 62 1 TGCCTCTTTT 0.799519 -70 TTTGTATTGATGATGGCATTTTTGATGCCACCA 14 38 0 TGATGCTTTT 0.969798 -73 ATTATGTTTTTGACCGCACTTTTTTATAAAAAC 15 21 0 TGACGCTTTT 0.994844 -52 ATTTTTGTGATGCTCGCAGTTTTGCAACAAAAT 16 87 1 TGCTGCTTTT 0.926235 -95 TCCGCTAGTCTAACGACGATTTTTTATTTATTT 18 63 1 TAACACTTTT 0.719972 -238 GATAACGCTATGACAACACTTTTGGAGGTTGCA 18 107 1 TGACACTTTT 0.947323 -194 CGTGCAGAATTAACCGCACTTTTAGATGCCGCA 18 176 1 TAACGCTTTT 0.965016 -125 AAAAATAGTTTGACAGCCAGTTTTTTATTC 20 8 0 TGACGCGTTT 0.955832 -293 GCTATATTGAGTGCGTTTTATTTTTAGCTA 21 8 1 TGAGGCTTTA 0.882272 -78 ATTTTATAATTGAAAGCCTTTTTTAAAGTGTGA 23 65 0 TGAAGCTTTT 0.927051 -169 TGGGCTACCATAACCGCACTTTATTAAGCCAAA 28 20 0 TAACGCTTTA 0.856379 -214 TTCACATTTATTACTGCAATTTTTAGAAACTAT 28 110 0 TTACGCTTTT 0.916088 -124 CCATTCAAGATGGTTGCTATTTTAACGTAAAAT 29 24 0 TGGTGCTTTT 0.896053 -36 CGGTCAAAATTGACCGCACTTTTACGCCTATCT 32 62 0 TGACGCTTTT 0.994844 -135 CGGTCAATTTTGACCGCATTTTTTATAAAAATA 32 79 1 TGACGCTTTT 0.994844 -118 **** ** **** Masking position 11 Map Score: 29.365 Number of sites scoring better than the average of aligned sites = 503 Number in coding regions = 374 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 3 TCGCGTTATTTTATCCGCACTTATTAGAAAG 2 44 1 TTTCCGCACT 0.983486 -29 TGGATAAAAATTTACCGCACTT 7 2 0 TTACCGCACT 0.997 -70 ATAAAAGAAAACGACCGCACTTTGCGACCGT 8 19 0 ACACCGCACT 0.969982 -32 CATTATGTTTTTGACCGCACTTTTTTATAAA 15 24 0 TTACCGCACT 0.997 -49 TCGTGCAGAATTAACCGCACTTTTAGATGCC 18 175 1 TTACCGCACT 0.997 -126 TTGGGCTACCATAACCGCACTTTATTAAGCC 28 23 0 ATACCGCACT 0.991847 -211 GCGGTCAAAATTGACCGCACTTTTACGCCTA 32 65 0 TTACCGCACT 0.997 -132 GCGGTCAATTTTGACCGCATTTTTTATAAAA 32 78 1 TTACCGCATT 0.97376 -119 ** ******** Masking position 9 Map Score: 19.8869 Number of sites scoring better than the average of aligned sites = 611 Number in coding regions = 351 Number in noncoding regions = 260 Number of orfs with sites within 600 bp upstream = 184 Fraction of orfs with sites within 600 bp upstream = 0.0295535 Motif number 4 TTTTAGGAACCCAATTTTTGCGGGCGGTAT 4 92 1 CCAATTTTTG 0.914764 -167 AACGGTTGCTTCAAATTTTGCGATCCATAT 4 180 0 TCAAATTTTG 0.962499 -79 ATTTAACCTCAAATTTTTTATGGTTTTA 7 54 0 TCAAATTTTT 0.93425 -18 TACAAATTCTTCAAATTGTGGGCTTATCCC 14 65 1 TCAAATTGTG 0.756853 -46 ACCGATTCTTTCAATTTTTAGTAATTTTCG 16 31 0 TCAATTTTTA 0.801366 -151 TTAAATATAGTCAATTTTTGTGATGCTCGC 16 74 1 TCAATTTTTG 0.958905 -108 CAGTAAGAAATGAAATTTTGTTGCAAAACT 16 104 0 TGAAATTTTG 0.947931 -78 TCTTTCTGTGAGAATTTTTTTAATTTTATG 17 72 1 AGAATTTTTT 0.725007 -94 AGAATAGGGGCGAAATTTTGGTATAGTAAG 17 113 1 CGAAATTTTG 0.891072 -53 CGGCTAATTATCAATTTTTTGATCTACTTA 18 15 0 TCAATTTTTT 0.927363 -286 CAAAATCCCGTCAAATTTTGCTAGAGCAGA 19 18 1 TCAAATTTTG 0.962499 -78 ACCCTAATCAACAAATTTTTCTTATTGGAT 20 134 1 ACAAATTTTT 0.806068 -167 TTCATTAAAAAGAATTTTTGCGATCTGCAT 20 205 1 AGAATTTTTG 0.828142 -96 ATAGAATAAGCCAATTTTTTAAGCCAGAAG 22 20 0 CCAATTTTTT 0.854526 -37 CTCTAGGTGATGAAATTTTTCGTATTTTTG 23 203 0 TGAAATTTTT 0.909456 -31 GTAATAAATGTGAATTTTTTGTGATAAAGA 28 129 1 TGAATTTTTT 0.900087 -105 CATAAAATTGTGAAATTTTATGGCTATTGT 30 23 1 TGAAATTTTA 0.76017 -57 ********** Masking position 6 Map Score: 18.8658 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 296 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 5 GTTGTTTGTTTTAGCAAGTAAATTTTCCTGAAAAAT 4 133 1 TTGCTAATTT 0.708464 -126 TCTCTAAGCCTAGGCTAGTTTTATTTAAATATGCAA 4 209 0 TAGCTTTTTT 0.977832 -50 ATTTGTTTCATCCGCAGCTTTCTTTTTAAATTATTA 5 36 1 TCGCTTTTTT 0.911553 -36 AAGGGGCAATTAAGCCCCTTTATTTTTGATACTTTG 11 11 0 TAGCTTTTTT 0.977832 -59 CGTCGCTTTTTAGGCGTATTTTCTTTATACTTTGTG 13 75 1 TAGCTTTTTT 0.977831 -57 ATACCAAAATTTCGCCCCTATTCTTTGCAGAAGATC 17 101 0 TTGCTATTTT 0.853224 -65 TTTGGTATAGTAAGCAAGTTAATTTTATCAACTATG 17 129 1 TAGCTTATTT 0.948556 -37 AAATTGATAATTAGCCGTTTTCATTTNGTTAGATTT 18 28 1 TTGCTTTTTT 0.97101 -273 AAACTATTTTTTGGCATTTTATATTAAAAATAAACC 20 30 1 TTGCTTATTA 0.708464 -271 TGATGAAGTGTAAGTAGGTTTATTTTTAATATAAAA 20 46 0 TAGTTTTTTT 0.825627 -255 ATTGGTTAAATATGCTAATTTTATTAAGTTTATTAG 20 95 0 TAGCTTTTTA 0.884421 -206 TAAGAAAAATTTTGCAATTTTTTATTCATTAAAAAG 20 181 1 TTGCTTTATT 0.754072 -120 TTTCATCAATTATGTTATTTAATTTTTCTATGTTGA 23 154 0 TAGTTTATTT 0.664356 -80 TATAGCTAGGTTCGCTCTTTCACTTTTGAAAGAGCG 24 15 1 TTGCTTCTTT 0.863158 -108 TCGGCTAGAATACGCCGATTTTATTTTCGGTGACTT 27 77 1 TAGCTTTTTT 0.977832 -30 ** ** *** *** Masking position 9 Map Score: 14.3464 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 129 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 6 AATTTATTCCTTATTCTTTAAT 1 59 0 TTTATTCCTT 0.886251 -12 TGCGGTAAATTTTTATCCATTTCTCTACAA 7 14 1 TTTTATCCAT 0.466036 -58 AATTATTTTTCCTTATGCCTAAGG 10 41 0 ATTTTTCCTT 0.740387 -14 AATTTGGTTTCCTTTGATGGAATG 13 5 1 TGGTTTCCTT 0.881027 -127 ACTTGTGTTTCCTTTTTATGTTTA 14 97 0 GTGTTTCCTT 0.641209 -14 CATTTCTTACTGTTTTCCTTATCATTTTTC 16 122 1 TGTTTTCCTT 0.945988 -60 GAACAAATGGTGTTTTCATTGAATTAGAGT 16 158 0 TGTTTTCATT 0.744562 -24 CTTATTGGATTTTTTACATTTTCAAAATAA 20 154 1 TTTTTACATT 0.564585 -147 TTTGCAATTTTTTATTCATTAAAAAGAATT 20 191 1 TTTATTCATT 0.564585 -110 CTCTCCCTCGTTTTTTCCATACTAGATTTT 20 262 1 TTTTTTCCAT 0.834133 -39 ATTTTTTCCTTTTTATTTGAA 20 290 0 TTTTTTCCTT 0.96664 -11 GTTGATACCTTACAAAAAATA 21 75 0 TTGATACCTT 0.469712 -11 TGTTTTTTCCTTCTGGCTTAAA 22 3 1 TTTTTTCCTT 0.96664 -54 TTTTTACCTTTTGGCTTAAT 28 1 1 TTTTTACCTT 0.886251 -233 ATTTGCCTTATGTTATCCTTTACAAAAAAT 32 163 1 TGTTATCCTT 0.752458 -34 ********** Masking position 10 Map Score: 11.4792 Number of sites scoring better than the average of aligned sites = 471 Number in coding regions = 320 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 7 TAGGCTAGTTTTATTTAAATATGCAAACGGTTG 4 202 0 TTTTAATATG 0.852679 -57 ATGGCGGCGTTTTATTAACTTTAATCGGGT 6 67 1 TTTTAATTTA 0.620033 -20 TTTTCCCAGCTTTATCAATAGTATTTCAATGCA 13 109 0 TTTCAAAGTA 0.527473 -23 TCATATACATTTCCTTAAATATAGTCAATTTTT 16 60 1 TTTTAATATA 0.875849 -122 CTGTGAGAATTTTTTTAATTTTATGATCTTCTG 17 77 1 TTTTAATTTA 0.620032 -89 GCAAGTTAATTTTATCAACTATGGAGAAACAAA 17 142 1 TTTCAATATG 0.912614 -24 TCTTATGCCCATTTTCAATTATGGTTAAAAGTA 19 65 1 ATTCAATATG 0.69305 -31 CTACTTACACTTCATCAAATATACATTTAACTA 20 65 1 TTTCAATATA 0.927163 -236 ATATGCTAATTTTATTAAGTTTATTAGTTAAAT 20 89 0 TTTTAATTTA 0.620033 -212 TAGGGTTGTATTGGTTAAATATGCTAATTTTAT 20 107 0 TTTTAATATG 0.852679 -194 AAACTAACTTTTCATCAATTATGTTATTTAATT 23 166 0 TTTCAATATG 0.912614 -68 AAAGTTAGTTTTTCACAAAAATACGAAAAATTT 23 188 1 TTACAAAATA 0.383718 -46 ACTCCAAAATTTATTCAAAAATAAGCGATAGTT 28 83 1 TTTCAAAATA 0.891626 -151 TCATAATACGTTGATCAATTATAGGGAATCTGG 28 194 0 TTTCAATATA 0.927163 -40 TCAAAGCAAAATAATCAAGAATAAACACTAAAA 31 72 0 ATTCAAAATA 0.640124 -87 CGACTAATCAATAATTAAAAATATAAAACCAGA 31 126 0 ATTTAAAATA 0.496424 -33 CGCCCGTATTTTTATAAAAAATGCGGTCAAAAT 32 85 0 TTTAAAAATG 0.370959 -112 AAAATAGGGCTTCGTTAAAAATATATTTCTAGG 32 127 1 TTTTAAAATA 0.820134 -70 ** **** **** Masking position 2 Map Score: 10.8309 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 199 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 8 GCTGAAATATTAAAGAATAAGGAATAAATT 1 51 1 TAAAGAATAA 0.567569 -20 AGCAGCTTATTGAAAAACAA 5 1 0 TGAAAAACAA 0.58659 -71 CCTTAATAATTTAAAAAGAAAGCTGCGGAT 5 45 0 TTAAAAAGAA 0.72708 -27 TACTCAAAAATATAAAAGAAAAC 8 38 0 TCAAAAATAT 0.867067 -13 CAAAGTATCAAAAATAAAGGGGCTTAA 11 8 1 TCAAAAATAA 0.949056 -62 AAAGAGAAAATAAAAAACAACAAAAGGGGC 11 40 0 TAAAAAACAA 0.707512 -30 AAAAGTGCGGTCAAAAACATAATGATTTTT 15 31 1 TCAAAAACAT 0.750101 -42 CTCAGCGCAGTCAAAAATCATTATGTTTTT 15 43 0 TCAAAAATCA 0.702606 -30 ATGGAACCAATAAAAAATAACCAATT 17 7 0 TAAAAAATAA 0.840164 -159 GCATTTTATATTAAAAATAAACCTACTTAC 20 43 1 TTAAAAATAA 0.893982 -258 TTTTTATTCATTAAAAAGAATTTTTGCGAT 20 199 1 TTAAAAAGAA 0.72708 -102 TGGGTAAATCACAAATAAAGCGTCTGAG 27 9 1 TCACAAATAA 0.702606 -98 CAAAATTTATTCAAAAATAAGCGATAGTTT 28 87 1 TCAAAAATAA 0.949056 -147 AGCAAAATAATCAAGAATAAACACTAAAAA 31 71 0 TCAAGAATAA 0.823062 -88 TAATCAATAATTAAAAATATAAAACCAGAA 31 125 0 TTAAAAATAT 0.746989 -34 TAGGGCTTCGTTAAAAATATATTTCTAGGT 32 131 1 TTAAAAATAT 0.746989 -66 ********** Masking position 6 Map Score: 10.3381 Number of sites scoring better than the average of aligned sites = 347 Number in coding regions = 230 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 9 AAATGGATAAAAATTTACCGCACTT 7 5 0 AAATTACCGC 0.981742 -67 AATATAAAAGAAAACGACCGCACTTTGCGAC 8 22 0 AAAACACCGC 0.932376 -29 AACTCGTGCAGAATTAACCGCACTTTTAGAT 18 172 1 GAATTACCGC 0.963348 -129 AAATGCTTTTAAATTAATCGTTTCTCTCCCT 20 239 1 AAATTATCGT 0.633388 -62 CTTATTCTATAAAATAACCGCTCAAGA 22 40 1 AAAATACCGC 0.965761 -17 TATAATTTTAAAATTTATAGCAATTAAGAAG 24 95 1 AAATTATAGC 0.776298 -28 ATTTTAGGGAAAATTGACAGCGAAAAGGAAA 27 47 0 AAATTACAGC 0.913707 -60 GCAATTTTTAGAAACTATCGCTTATTTTTGA 28 97 0 GAAACATCGC 0.688355 -137 AATGCGGTCAAAATTGACCGCACTTTTACGC 32 68 0 AAATTACCGC 0.981742 -129 ***** ***** Masking position 7 Map Score: 5.99279 Number of sites scoring better than the average of aligned sites = 732 Number in coding regions = 478 Number in noncoding regions = 254 Number of orfs with sites within 600 bp upstream = 201 Fraction of orfs with sites within 600 bp upstream = 0.032284 Motif number 10 AAGGATTAATCCCCAGTTGTTTTG 1 4 1 GATTATCCCC 0.919019 -67 TAATATTTCAGCTTTATCGGCAAGCAATCAA 1 32 0 GCTTATCGGC 0.978302 -39 AACTCGCGTTATTTTATCCGCACTTATTAGA 2 41 1 ATTTATCCGC 0.670048 -32 TGGTCGATTTGTTTCATCCGCAGCTTTCTTT 5 30 1 GTTTATCCGC 0.911605 -42 AGGCTTCCTTGCTTAATCCCCTTTAGACAGT 6 33 1 GCTTATCCCC 0.988699 -54 TATGCCTAAGGCTTGAACGCCATAGACGATA 10 21 0 GCTTAACGCC 0.965093 -34 AAATAAAGGGGCTTAATTGCCCCTTTTGTTG 11 22 1 GCTTATTGCC 0.895586 -48 TGCTTCTGCCGCTTTATCTCCGCCTTTTGCG 18 205 0 GCTTATCTCC 0.943711 -96 CCTATTTTTCACTTCAACGCCCGTATTTTTA 32 104 0 ACTTAACGCC 0.844823 -93 **** ****** Masking position 6 Map Score: 4.69233 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 174 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 11 TCTGATATTTATACCGCCCGCAAAAATTGGGTTC 4 98 0 ATCGCCGAAA 0.906297 -161 TATTTTTACGATATGGATCGCAAAATTTGAAGCA 4 170 1 ATTGACGAAA 0.978731 -89 ACAAATGACCATTTTGACCGAAAATTACTAAAAA 16 13 1 ATTGACGAAA 0.978692 -169 AAAGATGATTATCTTGAGCTAAAAAGCTACAATT 17 43 0 ATTGACTAAA 0.888322 -123 GCATTTTGCGATGCAGATCGCAAAAATTCTTTTT 20 211 0 ATCGACGAAA 0.951886 -90 TTATTTGAAAATCTAGTATGGAAAAAACGAGGGA 20 265 0 ATTGTTGAAA 0.778733 -36 GCCCAAGTTTATTTGGAGCGCAAATGCATAAAAA 28 48 1 ATTGACGAAA 0.978715 -186 ATTATAGGGAATCTGGAGTGTAAACTCTAATGGC 28 176 0 ATTGATGAAA 0.951548 -58 AATAGCAACCATCTTGAATGGATAGGAGATTAAA 29 36 1 ATTGATGATA 0.734281 -24 ATTCTTGATTATTTTGCTTTGAAAAAGGATACTA 31 83 1 ATTGCTTAAA 0.623982 -76 ** * ** ** *** Masking position 12 Map Score: 6.22098 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 54 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 12 CAAAATTTGAAGCAACCGTTTGCATATTTA 4 190 1 AGCAACCGTT 0.820195 -69 GACCGCACTTTGCGACCGTTTGGGATA 8 8 0 TGCGACCGTT 0.931029 -43 GCATTTTTGATGCCACCATCAATATGTTAT 14 26 0 TGCCACCATC 0.964062 -85 GCATCAAAAATGCCATCATCAATACAAATT 14 43 1 TGCCATCATC 0.776763 -68 GTTGCAAAACTGCGAGCATCACAAAAATTG 16 85 0 TGCGAGCATC 0.907976 -97 CCAAATTGTAAGCGACCATCAAAACGCGCA 18 244 0 AGCGACCATC 0.980888 -57 CTTTTGAAAGAGCGACCTTTTTTACGTTAG 24 37 1 AGCGACCTTT 0.831913 -86 ACGTTAAAATAGCAACCATCTTGAATGGAT 29 29 1 AGCAACCATC 0.945481 -31 ********** Masking position 5 Map Score: 2.50529 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 55 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 13 ACTTTTCCCTTGTTAGAACTG 9 16 0 CTTTTCCCTT 0.843229 -11 AATTATTTTTCCTTATGCCTAAGG 10 41 0 ATTTTTCCTT 0.798155 -14 CCGCACTTTTCCTCTATAACATATT 14 6 1 CTTTTCCTCT 0.785185 -105 TTTCCTTATCATTTTTCTTTCACACTCTAA 16 135 1 ATTTTTCTTT 0.827785 -47 ATTTTTTCCTTTTTATTTGAAA 20 289 0 TTTTTCCTTT 0.705627 -12 AACATTTTCCTCTCTAGGTGATG 23 221 0 ATTTTCCTCT 0.904976 -13 TGGAAATATAAATTTCCTTTACTAACGTAA 24 58 0 AATTTCCTTT 0.925232 -65 TGAGATTCTTAATTTCCTTTTCGCTGTCAA 27 35 1 AATTTCCTTT 0.925232 -72 TTTCGCTGTCAATTTTCCCTAAAATCGGCT 27 53 1 AATTTTCCCT 0.616242 -54 AATTTCCTTTTAGTTTTTCA 28 224 0 AATTTCCTTT 0.925232 -10 ATTCTTGATTATTTTGCTTTGAAAAAGGAT 31 83 1 ATTTTGCTTT 0.838419 -76 TTTCTAGGTAAATTTGCCTTATGTTATCCT 32 152 1 AATTTGCCTT 0.756143 -45 ********** Masking position 5 Map Score: 7.69472 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 103 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 14 AAGGATTAATCCCCAGTTGTTTTGATTGCTT 1 11 1 CCCAGTTGTT 0.969153 -60 AGTTTTTCAACTCGCGTTTTCGATAATCAAT 2 14 0 CCGCGTTTTC 0.855758 -59 GATAAAATAACGCGAGTTTTTCAACTCGCGT 2 28 0 CCGAGTTTTT 0.944271 -45 GGCTTAATTGCCCCTTTTGTTGTTTTTTATT 11 31 1 CCCTTTTGTT 0.615008 -39 ACGGCATTTGCACCATTTTTCTTGTTCGTTA 13 47 0 CCCATTTTTC 0.873198 -85 TCAATGAAAACACCATTTGTTCTGCA 16 166 1 CCCATTTGTT 0.91018 -16 GTTAATTCTGCACGAGTTTCTGCGTCAGGAT 18 159 0 CCGAGTTTCT 0.744164 -142 ATAGTTTGACAGCCAGTTTTTTATTC 20 6 0 ACCAGTTTTT 0.732636 -295 TCGTTTCTCTCCCTCGTTTTTTCCATACTAG 20 256 1 CCTCGTTTTT 0.82487 -45 CTAGTTATTGCTCCAGTTGTTAGTTTTCACA 23 39 1 CCCAGTTGTT 0.969153 -195 TTCACTTCAACGCCCGTATTTTTATAAAAAA 32 97 0 CCCCGTATTT 0.734783 -100 TTTAACGAAGCCCTATTTTTCACTTCAACGC 32 115 0 CCTATTTTTC 0.575553 -82 * ********* Masking position 7 Map Score: 2.67879 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 234 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 15 AATCGCTATCTAATAGTAAAAATT 3 27 0 ATCCTTCTAT 0.850343 -14 GTTTTTTATTTTCTCTTTCTTATAGCTT 11 52 1 TTCCTTCTAT 0.947314 -18 TTTTCCCAGCTTTATCAATAGTATT 13 117 0 TTCCACTTAT 0.803004 -15 TCATTTTTCTTTCACACTCTAATTCAATGAAAA 16 143 1 TTCCATCTAT 0.971593 -39 GTTGTTAGTTTTCACACTTTAAAAAAGGCTTTC 23 54 1 TTCCATTTAA 0.864455 -180 TATAGCTAGGTTCGCTCTTTCACTTTTGAAAGA 24 15 1 TTCCTTTTAC 0.737944 -108 TGTGATAAAGATCTCATTCTGATAATCTGCCAT 28 148 1 ATCCATCTAT 0.915232 -86 GCCATAAAATTTCACAATTTTATGGCTAAGTAA 30 14 0 TTCCATTTAT 0.94573 -66 TTATTTATTATTCACAATCTCAATCG 31 4 0 TTCCATCTAA 0.926008 -155 *** ** *** ** Masking position 10 Map Score: 1.32123 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 52 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925