AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00350_hinf_reg_100.orf -o00350_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 HI0185 122 alcohol dehydrogenase, class III (adhC) #2 HI0195.1 26 conserved hypothetical transmembrane protein (aefA) #3 HI0197 84 penicillin-insensitive murein endopeptidase (mepA) #4 HI0199 46 lipid A biosynthesis (kdo)2-(lauroyl)-lipid IVA acyltransferase (msbB) #5 HI0301 300 hemolysin, putative #6 HI0329 37 conserved hypothetical protein #7 HI0330 98 opacity associated protein (oapA) #8 HI0331 59 opacity associated protein (oapB) #9 HI0468 300 ATP phosphoribosyltransferase (hisG) #10 HI0469 92 histidinol dehydrogenase (hisD) #11 HI0470 68 histidinol-phosphate aminotransferase (hisC) #12 HI0549 169 dimethyladenosine transferase (ksgA) #13 HI0916 107 outer membrane protein, putative #14 HI0961 74 hit-related protein #15 HI0962 28 isoleucyl-tRNA synthetase (isoleucine--tRNA ligase) (ileRS) #16 HI0963 34 riboflavin kinase / FMN adenylyltransferase (ribF) #17 HI0964 300 virulence factor (mviN) #18 HI0976 119 conserved hypothetical protein #19 HI0978 40 ribosomal protein L11 methyltransferase (prmA) #20 HI1024 49 hexulose-6-phosphate synthase, putative #21 HI1027 58 L-xylulose kinase (lyx) #22 HI1028 30 conserved hypothetical protein #23 HI1030 71 conserved hypothetical transmembrane protein #24 HI1031 175 conserved hypothetical protein #25 HI1062 85 (3R)-hydroxymyristol (acyl carrier protein) dehydrase (fabZ) #26 HI1064 56 conserved hypothetical protein #27 HI1527 84 lipid A biosynthesis lauroyl acyltransferase (htrB) #28 HI1617 138 aspartate aminotransferase (aspC) Motif number 1 AAAGCGCGCAAAAGTGCGGTTAAAATTAATTACA 4 16 1 AAAGTGTAAA 0.909826 -31 AATAAAATGTAATTAATTTTAACCGCA 4 30 0 AAAATATAAT 0.848852 -17 TCATATAAACAAAATAAGAATATTTTGTTGTCTA 5 115 1 AAAATGTATT 0.928412 -186 GTTTAAACCTAAAGTGCGGTTAAAAATACACAAT 5 171 0 AAAGTGTAAA 0.909826 -130 CGAAAAGAGGAAAATCAATAAAAAATAACCGCAC 5 210 0 AAAATAAAAA 0.836588 -91 GATTTTTTCTAAAATATGATAATTTTTCGCCGTC 5 252 1 AAAATGAATT 0.933867 -49 GATCCGATAAAATACACATAATTTTTTCGCCG 7 9 1 AAAATATAAT 0.848826 -90 TAGTAAAAATGTACTAAAAACACAATTTT 9 6 1 AAAATAAAAA 0.836588 -295 GAGTGTAATAAAAATCAGTGTAAAAGCAATAAAT 9 213 1 AAAATGTAAA 0.933458 -88 TTCCTATTTTAAAGTTGAGATAAAAGAAAACCCC 9 270 0 AAAGTATAAA 0.771851 -31 TCTCAACTTTAAAATAGGAAAAACATT 9 284 1 AAAATGAAAC 0.741958 -17 TTTAGGCGGAAAAGTTAAGAAAAACGGGCGGATT 12 11 1 AAAGTAAAAA 0.786426 -159 TTTAATAAGAAAAGTGCGGTTATTATAGGGGTTG 12 138 0 AAAGTGTATT 0.903209 -32 TCTGTCCTTAAAAGTTAGACTAAATAAGCAACAA 14 49 1 AAAGTGTAAA 0.909826 -26 TTAAAATGTAAAAATTGGAAAATAAA 15 13 1 AAAATGAATA 0.922039 -16 GAAAATAAGAGAATTTCGGCATTAT 16 20 0 AAAATGAATT 0.933868 -15 AAAAGTATAAAAAATCGGCATATTGATGCCCTTT 17 43 0 AAAATGTATT 0.928412 -258 GAAATTGCTGAAAGTGAGAAAATTAAATATCACC 18 53 0 AAAGTGAATT 0.910368 -67 AGTGCGGTAAAAATACGCAAAATTTTGAAAGGA 19 10 1 AAAATGAAAT 0.947998 -31 TCTAGATCACAAAATCAGTAAAATTATTTTAACA 24 46 1 AAAATGAAAT 0.947998 -130 CAATAAATGTAAAATAAATAAATTATTTATAAAT 24 85 0 AAAATAAATT 0.825627 -91 TACCTTACAAAAAATAAACAAATAAAATCTATCG 25 57 0 AAAATAAATA 0.798614 -29 TCTGGCTTAAAAAATTGGCTTATTCTATAAAATA 26 22 1 AAAATGTATT 0.928439 -35 ***** * **** Masking position 5 Map Score: 31.1329 Number of sites scoring better than the average of aligned sites = 923 Number in coding regions = 583 Number in noncoding regions = 340 Number of orfs with sites within 600 bp upstream = 263 Fraction of orfs with sites within 600 bp upstream = 0.0422422 Motif number 2 TGTTTTTCCTCTTAATTCATTGAC 1 109 0 TTTTCCTCTA 0.920469 -14 TTGTCTAGAATTTTCCCCTCTCCGTAAAAAT 5 142 1 TTTTCCCCTT 0.691834 -159 TTTTTATTGATTTTCCTCTTTTCGCGTTTTG 5 220 1 TTTTCCTCTT 0.943008 -81 AATCGCCCCTTTTTCTTTTTAAGTTCTTTTC 8 25 1 TTTTCTTTTA 0.836369 -35 TCGGAAGATATTTTATTATCTTCCAAACATA 9 184 0 TTTTATTATT 0.734781 -117 TATTTATTGCTTTTACACTGATTTTTATTAC 9 217 0 TTTTACACTA 0.785522 -84 TTTCGAGGGGTTTTCTTTTATCTCAACTTTA 9 264 1 TTTTCTTTTT 0.879625 -37 AATGTTTTTCCTATTTTAAAGTTGAG 9 285 0 TTTTCCTATT 0.9118 -16 TGTTTATTTTCCTTTGTATCCGTAAAA 10 76 0 TTTTCCTTTT 0.944107 -17 ATAACCGCACTTTTCTTATTAAATAGTACTT 12 149 1 TTTTCTTATA 0.757767 -21 GCACTTTTTGTTTTACAATGAATTTAA 14 7 0 TTTTACAATA 0.695889 -68 ATTTTCCAATTTTTACATTTTAAAA 15 5 0 TTTTACATTT 0.842401 -24 TATGCCGATTTTTTATACTTTTGTCAATGGA 17 55 1 TTTTATACTT 0.693738 -246 TCAACACAAATTTTCCATTGACAAAAGTATA 17 68 0 TTTTCCATTA 0.857863 -233 TTGTTTTTCCTTTCAAAATTTTGCG 19 26 0 TTTTCCTTTA 0.921967 -15 TGGGCTGGATTTTTATTATGTAAAATCCAGC 21 18 0 TTTTATTATT 0.734781 -41 ATGTGATTCGTTTTATATTATGGCGTTTTAC 23 27 0 TTTTATATTT 0.698103 -45 AATTTATTTATTTTACATTTATTGACTGAGC 24 95 1 TTTTACATTA 0.788978 -81 TGAAACGTAATTTTACTATATAAAATTAAGA 24 146 1 TTTTACTATT 0.864939 -30 TTTTTCCTCTCTTAATTTTATA 24 164 0 TTTTCCTCTT 0.943008 -12 ATTGAGTGCGTTTTATTTTTAGCTATAAATA 25 16 1 TTTTATTTTA 0.75998 -70 ACTTCAGTCATTTTATTTTATCAAGAAAGAT 28 77 0 TTTTATTTTT 0.819061 -62 ********* * Masking position 4 Map Score: 25.1167 Number of sites scoring better than the average of aligned sites = 713 Number in coding regions = 526 Number in noncoding regions = 187 Number of orfs with sites within 600 bp upstream = 190 Fraction of orfs with sites within 600 bp upstream = 0.0305172 Motif number 3 TTCACAATCAAAAATCCATTATTCACAAGTTA 5 61 1 AAAACATTAT 0.672012 -240 TGCGGTTAAAAATACACAATTTTTACGGAGAG 5 159 0 AATACAATTT 0.946095 -142 AAATGTACTAAAAACACAATTTTTTTCAAAAA 9 17 1 AAAACAATTT 0.958671 -284 TTAAAATTAAAAAAAGCAATTTTTTTGAAAAA 9 38 0 AAAACAATTT 0.958339 -263 TATTGCCTTAAAAATACACTTTAAAATTAAAA 9 58 0 AAAACACTTT 0.688921 -243 TTTGAGCGAGCATATACAATATGAATTTTATC 9 105 1 CATACAATAT 0.689308 -196 TGTTTGGAAGATAATAAAATATCTTCCGAGTG 9 186 1 ATAAAAATAT 0.67526 -115 TCGCCATTTAAATAATCAATATCTCAAAATGC 10 30 1 AATACAATAT 0.958689 -63 TTCATACAACAATACGAAATATGT 11 55 1 AATAAAATAT 0.863476 -14 TCTACGAAAGAAAAAATAATATTGTTCATGAA 12 62 1 AAAATAATAT 0.634541 -108 TTGTTCATGAAAAACTCAATTTGGCATAACCT 12 83 1 AAAACAATTT 0.958595 -87 GATGAAGAAAAAAGTTCAATTTA 13 2 0 AAAGCAATTT 0.803026 -106 TACTTTTGTCAATGGAAAATTTGTGTTGATTT 17 70 1 AATGAAATTT 0.469549 -231 ATATAGCGTAAAAACAAAATTTCTATACAATT 17 206 1 AAAAAAATTT 0.863468 -95 GTATTAATCAATATGCTGTCACCT 18 3 1 ATTACAATAT 0.852472 -117 TGAAAGTGAGAAAATTAAATATCACCTTCCTC 18 47 0 AAAAAAATAT 0.891675 -73 GTGCGGTAAAAATACGCAAAATTTTGAAAGGA 19 12 1 AATACAAAAT 0.735185 -29 TTCACAATATGAAATATTATCACAAGA 24 6 1 AATAAAATAT 0.862837 -170 TAAATTATTTATAAATCAATATGTTAAAATAA 24 69 0 ATAACAATAT 0.884238 -107 ATTTTATAGAATAAGCCAATTTTTTAAGCCAG 26 23 0 ATAACAATTT 0.85247 -34 TCTCTATTTGAATAACCAAAATTGTGGCGATT 27 20 1 AATACAAAAT 0.735191 -65 **** ****** Masking position 12 Map Score: 17.2661 Number of sites scoring better than the average of aligned sites = 339 Number in coding regions = 265 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 4 CAAAAATGATAAAAAAACACTTGCTTTAGAGT 1 28 1 AAAAACACTT 0.932333 -95 GTGCGGTTAAAAATACACAATTTTTACGGAGA 5 160 0 AAAAACAATT 0.977582 -141 AAAATGTACTAAAAACACAATTTTTTTCAAAA 9 16 1 AAAAACAATT 0.977584 -285 TTTAAAATTAAAAAAAGCAATTTTTTTGAAAA 9 39 0 AAAAGCAATT 0.891457 -262 ATATTGCCTTAAAAATACACTTTAAAATTAAA 9 59 0 AAAAACACTT 0.932333 -242 ATTATCTTCCAAACATACAATCACGCCTGAAA 9 169 0 AAAAACAATC 0.891457 -132 CTCGCCATTTAAATAATCAATATCTCAAAATG 10 29 1 AAAATCAATA 0.686454 -64 GCTTTCTACGAAAGAAAAAATAATATTGTTCA 12 58 1 AAAAAAAATA 0.600859 -112 ATTGTTCATGAAAAACTCAATTTGGCATAACC 12 82 1 AAAATCAATT 0.907162 -88 AATATAGCGTAAAAACAAAATTTCTATACAAT 17 205 1 AAAAAAAATT 0.870446 -96 TTCTACGCTAAAACATAGAATTGCAACAATTC 18 84 1 AAAAAGAATT 0.912225 -36 ATTAAAGACAGAATTATACTGCCTT 20 4 1 AAAAAGAATT 0.912225 -46 ACCTTACAAAAAATAAACAAATAAAATCTATC 25 58 0 AAAAACAAAT 0.822728 -28 *** * ****** Masking position 5 Map Score: 11.8941 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 117 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 ATGTAATTAATTTTAACCGCACTTTTGCGC 4 21 0 TTTTAACCGC 0.95889 -26 AATTGTGTATTTTTAACCGCACTTTAGGTT 5 170 1 TTTTAACCGC 0.95889 -131 AATCAATAAAAAATAACCGCACATTGGGTT 5 202 0 AAATAACCGC 0.966372 -99 ACAACCCCTATAATAACCGCACTTTTCTTA 12 137 1 TAATAACCGC 0.95889 -33 ATTTTGCGTATTTTTACCGCACT 19 4 0 TTTTTACCGC 0.895167 -37 TTATTCTATAAAATAACCGCTCAAGA 26 41 1 AAATAACCGC 0.966372 -16 AATTGTGGCGATTTTACCACAACTCAAATT 27 39 1 ATTTTACCAC 0.674432 -46 TGTAAAAAATGACCGCACTTTTTGAT 28 7 1 AAATGACCGC 0.898398 -132 ATTTTATAAAAATTAACCACGCTTTGATAT 28 49 0 AATTAACCAC 0.874554 -90 ********** Masking position 6 Map Score: 9.42311 Number of sites scoring better than the average of aligned sites = 471 Number in coding regions = 275 Number in noncoding regions = 196 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 6 AAGAAAAACGGGCGGATTATAGCCGTTTTTA 12 27 1 GGGGATTATA 0.87587 -143 AACGATGTGTGGCGGATTTTATCAGTTTTTT 17 167 1 GGGGATTTTA 0.975232 -134 TAACAACAATGCTAGATTTTAAAAGTCGTTT 17 275 0 GCAGATTTTA 0.973088 -26 TCAATAGGCTGGATTTTACATAATAAAA 21 8 1 GCGGATTTTA 0.982863 -51 TTTTTTATGGGCTGGATTTTTATTATGTAAA 21 25 0 GCGGATTTTT 0.911332 -34 CGTATAATCCGATAGATTTTATTTGTTTATT 25 48 1 GAAGATTTTA 0.958325 -38 TATTCAAATAGAGAGATTTTAAA 27 3 0 GAAGATTTTA 0.958325 -82 ATTTTATCAAGAAAGATTTTATAAAAATTAA 28 63 0 GAAGATTTTA 0.958324 -76 ** ******** Masking position 6 Map Score: 8.45301 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 35 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 GGAAAGCGCGCAAAAGTGCGGTTAAAATTAA 4 14 1 CAAAGTGCGG 0.995555 -33 GGGTTTAAACCTAAAGTGCGGTTAAAAATAC 5 176 0 CTAAGTGCGG 0.975692 -125 AGGTTTAAACCCAATGTGCGGTTATTTTTTA 5 195 1 CCAAGTGCGG 0.983468 -106 TTGAGAAGCTCAAAAGTGCGGCGAAAAAATT 7 30 0 CAAAGTGCGG 0.995555 -69 CTTAAAAAGAAAAAGGGGCGATTACTCGCCC 8 17 0 AAAAGGGCGA 0.931467 -43 AAAGTTAAGAAAAACGGGCGGATTATAGCCG 12 21 1 AAAAGGGCGG 0.985719 -149 TATTTAATAAGAAAAGTGCGGTTATTATAGG 12 143 0 GAAAGTGCGG 0.984523 -27 ATTGTAAAACAAAAAGTGCGATTGATTTGCT 14 19 1 AAAAGTGCGA 0.965284 -56 AATATTCATCAAAAAGTGCGGTCATTTTTTA 28 13 0 AAAAGTGCGG 0.992968 -126 **** ****** Masking position 4 Map Score: 19.5311 Number of sites scoring better than the average of aligned sites = 535 Number in coding regions = 319 Number in noncoding regions = 216 Number of orfs with sites within 600 bp upstream = 172 Fraction of orfs with sites within 600 bp upstream = 0.0276261 Motif number 8 CCCTTTAAACAAAAATGATAAAAAAACACT 1 19 1 AAAAATGATA 0.798078 -104 GTCATATAAACAAAATAAGAATATTTTGTT 5 114 1 CAAAATAAGA 0.709481 -187 GAAATATCCTAAAAATGAGAGATGGTTTGA 6 15 1 AAAAATGAGA 0.932204 -23 AATTAGCCACAAAATTGAGAAGCTCAAAAG 7 45 0 AAAATTGAGA 0.912594 -54 GCTAATTAATATAAATAAGAACAAGCATCA 7 68 1 ATAAATAAGA 0.743952 -31 AATACACTTTAAAATTAAAAAAAGCAATTT 9 48 0 AAAATTAAAA 0.661982 -253 TTCCTATTTTAAAGTTGAGATAAAAGAAAA 9 274 0 AAAGTTGAGA 0.737044 -27 GCTTAGATCTATAATTAATATC 11 3 0 ATAATTAATA 0.388069 -66 TTTAGGCGGAAAAGTTAAGAAAAACGGGCG 12 11 1 AAAGTTAAGA 0.773379 -159 CTACGAAAGAAAAAATAATATTGTTCATGA 12 63 1 AAAAATAATA 0.827948 -107 GAAAATAAGAGAATTTCGGC 16 25 0 GAAAATAAGA 0.709481 -10 TCCGTGAAAAAAAACTGATAAAATCCGCCA 17 176 0 AAAACTGATA 0.480102 -125 CATAATTTACAAAAATAAGAAAGCTCAGTC 24 118 0 AAAAATAAGA 0.943634 -58 TTTACTATATAAAATTAAGAGAGGAAAAA 24 157 1 AAAATTAAGA 0.927072 -19 ATTTATAGCTAAAAATAAAACGCACTCAAT 25 16 0 AAAAATAAAA 0.720605 -70 ********** Masking position 3 Map Score: 9.63241 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 112 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 9 TTGATGTGATAAGGATCTTTGCCCTCTTTT 5 20 1 AAGGATCTTT 0.843122 -281 CTTGTGAATAATGGATTTTTGATTGTGAAT 5 60 0 ATGGATTTTT 0.751446 -241 TAAACAAAATAAGAATATTTTGTTGTCTAG 5 120 1 AAGAATATTT 0.941573 -181 CTCTCATTTTTAGGATATTTCAAAT 6 6 0 TAGGATATTT 0.766239 -32 GTATTGTTGTATGAAAATTTGACTGCTTAC 11 40 0 ATGAAAATTT 0.673907 -29 TCATTTAATTAAGGATATTTATCAA 13 93 1 AAGGATATTT 0.953931 -15 TAGGGTAGAGAAGAATATTTTGAGTAAACG 17 250 1 AAGAATATTT 0.941573 -51 GCACTTTTTGATGAATATTTAAAAATATCA 28 25 1 ATGAATATTT 0.929122 -114 GTGTTGTGTGATGAATAGTTTTATACTTCA 28 102 0 ATGAATAGTT 0.753871 -37 ********** Masking position 5 Map Score: 3.9669 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 91 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 10 TTTTTTATCATTTTTGTTTAAAGGGAATAAA 1 13 0 TTTTGTTTAA 0.556639 -110 TGTTTTTCCTCTTAATTCATTGACA 1 108 0 TTTCTCTTAA 0.530412 -15 TATTTTTCCCTAATCTAAATGGT 2 14 0 TTTTCCCTAA 0.90628 -13 GCTTCTCAATTTTGTGGCTAATTAATATAAA 7 52 1 TTTTGGCTAA 0.59799 -47 CTTTTTAAGTTCTTTTCTCAAGGTAGGATTT 8 39 1 TCTTTCTCAA 0.477603 -21 TTTCTTAACTTTTCCGCCTAAA 12 2 0 TTTCGCCTAA 0.902185 -168 TCATTGTTAGGTTATGCCAAATTGAGTTTTT 12 92 0 GTTTGCCAAA 0.39929 -78 AAAACAACGTTCTCTGCCTAATTTAATTGGG 13 42 1 TCTTGCCTAA 0.955639 -66 TTTAATATTTTCTCTGCCCAATTAAATTAGG 13 58 0 TCTTGCCCAA 0.881879 -50 ATTGATTTGCTCTGTCCTTAAAAGTTAGACT 14 39 1 TCTTCCTTAA 0.90628 -36 TACCCTAAAATTTTTGCCTAATTGTATAGAA 17 226 0 TTTTGCCTAA 0.938498 -75 AATATTCTTCTCTACCCTAAAATTTTTGCCT 17 238 0 TCTCCCTAAA 0.652241 -63 TTCAGCAATTTCTACGCTAAAACATAGAATT 18 75 1 TCTCGCTAAA 0.747468 -45 GCAGTATAATTCTGTCTTTAAT 20 2 0 TCTTCTTTAA 0.529 -48 CGTTTTTCCTTAAATAATATGAG 20 37 0 TTTTCCTTAA 0.872613 -13 *** ******* Masking position 10 Map Score: 4.04135 Number of sites scoring better than the average of aligned sites = 440 Number in coding regions = 368 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 11 GCAAGTGTTTTTTTATCATTTTTGTTTAAAGGG 1 19 0 TTTTTCTTTT 0.730429 -104 GATTTTCCTCTTTTCGCGTTTTGCGATTTTTTC 5 228 1 TTTTGCTTTG 0.965557 -73 GTAATCGCCCCTTTTTCTTTTTAAGTTCTTTTC 8 23 1 CTTTTCTTTA 0.704559 -37 AAAAATTGCTTTTTTTAATTTTAAAGTGTATTT 9 46 1 TTTTTATTTA 0.812949 -255 TTATAGCCGTTTTTAGCTTTCTACGAAAGAAAA 12 43 1 TTTTGCTTTA 0.960318 -127 ATAGGGGTTGTTTTAGCTTTGTAAATCATTGTT 12 115 0 TTTTGCTTTA 0.960318 -55 GAGAACGTTGTTTTTGAGTTCTGATGAAGAAAA 13 23 0 TTTTGATTTG 0.889601 -85 TATTTTCCAATTTTTACATTTTAAAA 15 4 0 TTTTACTTTA 0.758396 -25 AATAAGAGAATTTCGGCATTATAGCGAGAAG 16 9 0 TTTCGCTTTA 0.884334 -26 TATGCCGATTTTTTATACTTTTGTCAATGGAAA 17 55 1 TTTTTATTTG 0.834288 -246 TCGTTTTATATTATGGCGTTTTACTGGAAACAT 23 18 0 TTATGCTTTA 0.720306 -54 TTGACTGAGCTTTCTTATTTTTGTAAATTATGA 24 116 1 TTTCTATTTG 0.613984 -60 TGTTTTTTCCTTCTGGCTTAAAAAA 26 3 1 TTTTTCTTTG 0.94599 -54 **** ** ** ** Masking position 9 Map Score: 7.69574 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 207 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 12 ACACTTGCTTTAGAGTGAACTCTAAAGTGT 1 44 1 TAGAGTGAAC 0.907736 -79 CTAATAACATTTGAGCGAGCATATACAATA 9 96 1 TTGAGCGAGC 0.978918 -205 ATGTAGTGCGAGCTTTGACTCGC 10 4 1 TAGTGCGAGC 0.913765 -89 TGAGCCCATATTGAAAGAGCTTGTAAAAAT 17 133 0 TTGAAAGAGC 0.822821 -168 CACACATCGTTTGTGTGAGCCCATATTGAA 17 148 0 TTGTGTGAGC 0.961922 -153 GAAGAATATTTTGAGTAAACGACTTTTAAA 17 259 1 TTGAGTAAAC 0.78308 -42 TTTACATTTATTGACTGAGCTTTCTTATTT 24 106 1 TTGACTGAGC 0.940554 -70 GGTTATTTTATAGAATAAGCCAATTTTTTA 26 29 0 TAGAATAAGC 0.728547 -28 ********** Masking position 8 Map Score: 0.979983 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 98 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 13 TGTGATAAGGATCTTTGCCCTCTTTTTACG 5 24 1 ATCTTTGCCC 0.846666 -277 AATATGAATTTTATCTGCACTTACCATCAT 9 122 1 TTATCTGCAC 0.775912 -179 AAAAACAACGTTCTCTGCCTAATTTAATTG 13 41 1 TTCTCTGCCT 0.957232 -67 GTTTAATATTTTCTCTGCCCAATTAAATTA 13 60 0 TTCTCTGCCC 0.993136 -48 GCGATTGATTTGCTCTGTCCTTAAAAGTTA 14 36 1 TGCTCTGTCC 0.891113 -39 CAAAATATTCTTCTCTACCCTAAAATTTTT 17 242 0 TTCTCTACCC 0.957232 -59 ********** Masking position 6 Map Score: 0.532623 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 55 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 14 ********** No masking Map Score: 4.45754e-12 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 15 GATCAATTCACAATCAAAAATCCATTATTCAC 5 55 1 CAATCAAATC 0.89019 -246 AGAGGAAAATCAATAAAAAATAACCGCACATT 5 207 0 CAATAAAATA 0.927305 -94 TTTTCGCCGTCAATAAGACATCAAACACAAAT 5 275 1 CAATAGAATC 0.969526 -26 ATTTTTAAGGCAATATAAGATCTAATAACATT 9 75 1 CAATAAAATC 0.963431 -226 GTTTGGAAGATAATAAAATATCTTCCGAGTGT 9 187 1 TAATAAAATC 0.773619 -114 TTTCATACAACAATACGAAATATGT 11 54 1 CAATAGAATA 0.93904 -15 TTCACAATATGAAATATTATCACAAG 24 5 1 CAATAGAATA 0.93904 -171 ***** ** *** Masking position 8 Map Score: 2.40092 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 8 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274