AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00340_hinf_reg_100.orf -o00340_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 HI0195.1 26 conserved hypothetical transmembrane protein (aefA) #2 HI0197 84 penicillin-insensitive murein endopeptidase (mepA) #3 HI0199 46 lipid A biosynthesis (kdo)2-(lauroyl)-lipid IVA acyltransferase (msbB) #4 HI0301 300 hemolysin, putative #5 HI0329 37 conserved hypothetical protein #6 HI0330 98 opacity associated protein (oapA) #7 HI0331 59 opacity associated protein (oapB) #8 HI0366 101 fimbrial biogenesis and twitching motility protein, putative #9 HI0367 71 conserved hypothetical protein #10 HI0468 300 ATP phosphoribosyltransferase (hisG) #11 HI0469 92 histidinol dehydrogenase (hisD) #12 HI0470 68 histidinol-phosphate aminotransferase (hisC) #13 HI0471 111 imidazoleglycerol-phosphate dehydratase / histidinol-phosphatase (hisB) #14 HI0472 65 amidotransferase (hisH) #15 HI0473 35 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (hisA) #16 HI0549 169 dimethyladenosine transferase (ksgA) #17 HI0675 110 aminoacyl-histidine dipeptidase (pepD) #18 HI0831 142 monofunctional biosynthetic peptidoglycan transglycosylase #19 HI0916 107 outer membrane protein, putative #20 HI0949 300 aminotransferase #21 HI0961 74 hit-related protein #22 HI0962 28 isoleucyl-tRNA synthetase (isoleucine--tRNA ligase) (ileRS) #23 HI0963 34 riboflavin kinase / FMN adenylyltransferase (ribF) #24 HI0964 300 virulence factor (mviN) #25 HI0976 119 conserved hypothetical protein #26 HI0978 40 ribosomal protein L11 methyltransferase (prmA) #27 HI1139 137 UDP-N-acetylmuramate--alanine ligase (murC) #28 HI1140 71 D-alanine--D-alanine ligase (ddlB) #29 HI1143 83 cell division protein (ftsZ) #30 HI1144 38 UDP-3-0-(3-hydroxymyristoyl) N-acetylglucosamine deacetylase (lpxC) #31 HI1166 87 histidinol-phosphate aminotransferase (hisH) #32 HI1167 190 phosphoserine aminotransferase (serC) #33 HI1527 84 lipid A biosynthesis lauroyl acyltransferase (htrB) Motif number 1 AAAGCGCGCAAAAGTGCGGTTAAAATTAATTACATTT 3 16 1 AAAGGGAAAT 0.989337 -31 TTGATCTCGTAAAAAGAGGGCAAAGATCCTTATCACA 4 24 0 AAAGGGAAAT 0.989337 -277 GTTTAAACCTAAAGTGCGGTTAAAAATACACAATTTT 4 168 0 AAAGGGAAAT 0.989337 -133 CGCAAAACGCGAAAAGAGGAAAATCAATAAAAAATAA 4 216 0 GAAGGGAATA 0.839748 -85 GAGAAGCTCAAAAGTGCGGCGAAAAAATTATGTGTAT 6 22 0 AAAGGGAAAA 0.990195 -77 ACTTAAAAAGAAAAAGGGGCGATTACTCGCCCAAAAA 7 12 0 AAAGGGATTT 0.918307 -48 ATTAGGCGGTAAATGGAGGCTAAATTTTAAAGTCCAA 9 30 0 AAAGGGAAAT 0.989309 -42 ATCTCAACTTTAAAATAGGAAAAACATT 10 283 1 TAATGGAAAT 0.605143 -18 TTGAAAGAGCGGTTAATTTTTGTCGTATTT 14 4 1 AAAGGGAATT 0.98053 -62 TTTAATAAGAAAAGTGCGGTTATTATAGGGGTTGTTT 16 135 0 AAAGGGATTA 0.924441 -35 TTTTTACTGAAAATATTGACGAAATAATAGCATAAAA 17 75 0 AAATGAAAAA 0.668719 -36 AATAAGTGAGAAAGTGCGGTAAAAATTCGC 18 4 0 AAAGGGAAAT 0.989337 -139 ATTTAGTCCTAAATGGTGGAAAAAAAACTGGCAGCGA 18 38 1 AAAGGGAAAA 0.990195 -105 AACAAAGCAAAAACGGCGAAAAAAAAACAAAAGACAA 18 76 0 AAAGGAAAAA 0.932894 -67 GGGTTACGTCAAAACGGGGACAATTGTATATTTTTTT 20 87 0 AAAGGGAATT 0.98053 -214 TCCAATGGGCAAACTAGGGTAAAAACAAAAAAGCTGA 20 154 1 AAAAGGAAAA 0.816771 -147 TAAAACCTTCTAAAAGAGGTGAAAAAAAATAAGTCGG 20 267 0 TAAGGGAAAA 0.919912 -34 TCTGTCCTTAAAAGTTAGACTAAATAAGCAACAATT 21 49 1 AAATGAAAAA 0.668746 -26 TTTAAAATGTAAAAATTGGAAAATAAA 22 12 1 AAATGGAATA 0.888398 -17 GAAATTGCTGAAAGTGAGAAAATTAAATATCACCTTC 25 50 0 AAAGGAATTA 0.627448 -70 AACTCAACTAAAAGTGCGGTTAAAATTCGCAACGTTT 27 84 0 AAAGGGAAAT 0.989337 -54 ATCATTCATAAAATAGAGGGTAAATTTTGACGATTGA 32 67 0 AAAGGGAAAT 0.989334 -124 TGAATAACCAAAATTGTGGCGATTTTACCACAACTCA 33 28 1 AAAGGGATTA 0.924255 -57 *** * ** *** * Masking position 12 Map Score: 43.5626 Number of sites scoring better than the average of aligned sites = 774 Number in coding regions = 490 Number in noncoding regions = 284 Number of orfs with sites within 600 bp upstream = 203 Fraction of orfs with sites within 600 bp upstream = 0.0326052 Motif number 2 ATTAATTTTAACCGCACTTTTGCGCGCTTT 3 16 0 ACCGCACTTT 0.99816 -31 TGTATTTTTAACCGCACTTTAGGTTTAAAC 4 175 1 ACCGCACTTT 0.99816 -126 ATAAAAAATAACCGCACATTGGGTTTAAAC 4 197 0 ACCGCACATT 0.988444 -104 TAATTTTTTCGCCGCACTTTTGAGCTTCTC 6 29 1 GCCGCACTTT 0.992174 -70 ACAAAAATTAACCGCTCTTTCAA 14 4 0 ACCGCTCTTT 0.988444 -62 CCCTATAATAACCGCACTTTTCTTATTAAA 16 142 1 ACCGCACTTT 0.99816 -28 GCGAATTTTTACCGCACTTTCTCACTTATT 18 11 1 ACCGCACTTT 0.99816 -132 GAGCAAATCAATCGCACTTTTTGTTTTACA 21 21 0 ATCGCACTTT 0.981547 -54 GCGAATTTTAACCGCACTTTTAGTTGAGTT 27 91 1 ACCGCACTTT 0.99816 -47 ********** Masking position 9 Map Score: 30.668 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 3 AATAAAATGTAATTAATTTTAACCGC 3 31 0 AAAATAATAA 0.562596 -16 TCATATAAACAAAATAAGAATATTTTGTTGTCT 4 115 1 AAAATGATAT 0.730055 -186 AGTGCGGTTAAAAATACACAATTTTTACGGAGA 4 160 0 AAAATACATT 0.757959 -141 ATATTTTAGAAAAAATCGCAAAACGCGAAAAGA 4 236 0 AAAAAGCAAA 0.933973 -65 GATTTTTTCTAAAATATGATAATTTTTCGCCGT 4 252 1 AAAATGAAAT 0.829251 -49 GATCCGATAAAATACACATAATTTTTTCGCC 6 9 1 AAAATACTAA 0.789307 -90 TAGTAAAAATGTACTAAAAACACAATTT 10 6 1 AAAATACAAA 0.87059 -295 CTTTAAAATTAAAAAAAGCAATTTTTTTGAAAA 10 39 0 AAAAAGCATT 0.868153 -262 TATTGCCTTAAAAATACACTTTAAAATTAAAAA 10 57 0 AAAATACTTA 0.678397 -244 TCTCAACTTTAAAATAGGAAAAACATT 10 284 1 AAAATGAAAA 0.85454 -17 GAATTTTGCAAAAATACGACAAAAATTAACCGC 14 19 0 AAAATGAAAA 0.85454 -47 GTAGAAAGCTAAAAACGGCTATAATCCGCCCGT 16 34 0 AAAAAGCATA 0.888454 -136 TCTACGAAAGAAAAAATAATATTGTTCATGAAA 16 62 1 AAAAAAAATT 0.470569 -108 TCGAGAAATAAAAAATTGCGTAAGGATAACCCG 17 34 1 AAAAAGCTAA 0.88735 -77 GCAACAAAGCAAAAACGGCGAAAAAAAAACAAA 18 82 0 AAAAAGCAAA 0.933973 -61 TACAAAGCGAAAAATCAGCAACAAAGCAAAAAC 18 99 0 AAAATGCACA 0.829463 -44 TATTGCAAAAAAAATATACAATTGTCCCCGTTT 20 80 1 AAAATACATT 0.757959 -221 GCTACTTATTAAAAAAAGCGTTTCAGCTTTTTT 20 180 0 AAAAAGCTTT 0.785717 -121 ATTGTAAAACAAAAAGTGCGATTGATTTGCTCT 21 19 1 AAAAAGCATT 0.868153 -56 TTAAAATGTAAAAATTGGAAAATAAA 22 13 1 AAAATGAAAT 0.829251 -16 GAAAATAAGAGAATTTCGGCATTA 23 21 0 AAAATGAAAT 0.829252 -14 AAAAGTATAAAAAATCGGCATATTGATGCCCTT 24 44 0 AAAATGCTAT 0.887348 -257 AAGAGCTTGTAAAAATAACGATACTTACTTTCG 24 116 0 AAAAAACATA 0.757959 -185 AAAAACTGATAAAATCCGCCACACATCGTTTGT 24 164 0 AAAATGCACA 0.829463 -137 AATATAGCGTAAAAACAAAATTTCTATACAATT 24 205 1 AAAAAAATTT 0.330949 -96 AGTGCGGTAAAAATACGCAAAATTTTGAAAGG 26 10 1 AAAATGCAAA 0.944784 -31 TTTTGGATATAAAAAATACTTATGACTGAGGCT 27 32 0 AAAAAACTAT 0.719121 -106 TTGTAGATGAAAAATTAAAATAA 29 1 0 AAAATAATAA 0.562596 -83 CGATTGATTAAAAAAAAGCTAAATTACGGCACA 32 41 0 AAAAAGCAAA 0.933973 -150 TTATCACTACAAAAATCGATAATCAATGCTTTT 32 129 0 AAAAAGAAAT 0.800592 -62 TTGTAGTGATAAAAAAGACATCATTATTTTCAT 32 150 1 AAAAAACTCA 0.468181 -41 ***** ** *** Masking position 4 Map Score: 30.2581 Number of sites scoring better than the average of aligned sites = 1553 Number in coding regions = 1245 Number in noncoding regions = 308 Number of orfs with sites within 600 bp upstream = 257 Fraction of orfs with sites within 600 bp upstream = 0.0412785 Motif number 4 GAAAAGAACTTAAAAAGAAAAAGGGGCGATT 7 25 0 TAAAAGAAAA 0.852448 -35 ATTTTACGGATACAAAGGAAAATAAACA 11 75 1 TAAAAGGAAA 0.829231 -18 ATACAAACAGTATAAAACTAAATAATCTCGA 13 40 0 TAAAAACTAA 0.772146 -72 ATACTGTTTGTATAAAGCAAATGATAAACCT 13 58 1 TAAAAGCAAA 0.978569 -54 TTTTCTTTCGTAGAAAGCTAAAAACGGCTAT 16 45 0 TAAAAGCTAA 0.966862 -125 AACAATGATTTACAAAGCTAAAACAACCCCT 16 115 1 TAAAAGCTAA 0.966862 -55 AAACGGCGAAAAAAAAACAAAAGACAACTCG 18 72 0 AAAAAACAAA 0.608163 -71 AAAAATCAGCAACAAAGCAAAAACGGCGAAA 18 92 0 AAAAAGCAAA 0.930378 -51 ATGGAATAGGTACAAAGCGAAAAATCAGCAA 18 111 0 TAAAAGCGAA 0.914299 -32 AACGGCTAAATAAAAAGCAAACGTTTCTAAT 20 19 0 TAAAAGCAAA 0.978569 -282 GTTTGACTCGTAAGAAGCTAAATTTACTTTT 20 47 1 TAGAAGCTAA 0.894393 -254 GTATCATCAGTAAGAAGAAAAACAGGATAGA 28 49 1 TAGAAGAAAA 0.626439 -23 GATTGATTAAAAAAAAGCTAAATTACGGCAC 32 42 0 AAAAAGCTAA 0.895167 -149 ATTATTTTCATAAAAAGCAAGGAAATACA 32 172 1 TAAAAGCAAG 0.869465 -19 ** ******** Masking position 6 Map Score: 15.0647 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 151 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 CGGAGAGGGGAAAATTCTAGACAACAAAATATTCTTA 4 129 0 AAAATTAAAA 0.827156 -172 ATGGAGGCTAAATTTTAAAGTCCAATACTTGATTTGG 9 18 0 AATTTTTATA 0.564513 -54 CTAAAAACACAATTTTTTTCAAAAAAATTGCTTTTTT 10 24 1 AATTTTAAAA 0.890631 -277 GTAAGCAGTCAAATTTTCATACAACAATACGAAATAT 12 40 1 AAATTTAAAA 0.94079 -29 AAGAAAAAATAATATTGTTCATGAAAAACTCAATTTG 16 69 1 AATATTAAAA 0.7104 -101 ACCTTAGTTTAAATTTATCGAGAAATAAAAAATTGCG 17 17 1 AAATTTAATA 0.863734 -94 GAGAAATAAAAAATTGCGTAAGGATAACCCGAAATGG 17 36 1 AAATTGAAAA 0.640571 -75 GCCTTGCGATAAATTTACTGTTTATAAAACAGACACA 20 228 0 AAATTTTAAA 0.863739 -73 AAATCAACACAAATTTTCCATTGACAAAAGTATAAAA 24 65 0 AAATTTTAAA 0.863739 -236 CGTAAAAACAAAATTTCTATACAATTAGGCAAAAATT 24 212 1 AAATTTAATA 0.863735 -89 ATTAGGCAAAAATTTTAGGGTAGAGAAGAATATTTTG 24 235 1 AATTTTTAAA 0.764665 -66 AAAATACGCAAAATTTTGAAAGGAAAAACAA 26 20 1 AAATTTAAAA 0.94079 -21 CAAAAGTGCTAATATTAGAAATAAAAACGTTGCGAAT 27 60 1 AATATTAAAA 0.7104 -78 GATTGATTGAAAATCTTAGTATTAGAAAAGTATCATC 28 20 1 AAATCTAAAA 0.654154 -52 TAAGCTGACTAAATATATAAAATATAAATTCCCTTTA 29 34 0 AAATATAAAA 0.560668 -50 TACTACGCCCAAATTTATTTAAAAATACATACTAACC 31 36 1 AAATTTAATA 0.863419 -52 AACCCATATCAATATTTATAAATACAACT 31 69 1 AATATTAAAA 0.7104 -19 ACCACAACTCAAATTTACGATAAACTACGCCCCTAAC 33 54 1 AAATTTTATA 0.716611 -31 ****** * * ** Masking position 14 Map Score: 11.8727 Number of sites scoring better than the average of aligned sites = 372 Number in coding regions = 231 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 6 CCCTCTCCGTAAAAATTGTGTATTTTTAACC 4 157 1 AAAAATTTGT 0.961072 -144 AGTGCGGCGAAAAAATTATGTGTATTTTATC 6 16 0 AAAAATTTGT 0.961072 -83 TTTTTTTGAAAAAAATTGTGTTTTTAGTACA 10 20 0 AAAAATTTGT 0.961072 -281 TCGAGAAATAAAAAATTGCGTAAGGATAACC 17 34 1 AAAAATTCGT 0.809333 -77 TCCTAAAATTTCTGTTGATTGATAG 24 5 1 AAAATTTTGT 0.927663 -296 TTGTCAATGGAAAATTTGTGTTGATTTCGGT 24 75 1 AAAATTTTGT 0.927663 -226 CTAATTGTATAGAAATTTTGTTTTTACGCTA 24 209 0 AGAAATTTGT 0.809077 -92 TCTCTACCCTAAAATTTTTGCCTAATTGTAT 24 230 0 AAAATTTTGC 0.831137 -71 TTTTTCCTTTCAAAATTTTGCGTATTTTTAC 26 17 0 CAAAATTTGC 0.841391 -24 TTACTACGCCCAAATTTATTTAAAAATACAT 31 35 1 CAAATTTTTT 0.499027 -53 CTGAAATCAAAAAAATTCTTTCTATCATTCA 32 96 0 AAAAATTTTT 0.772869 -95 TTTGAATAACCAAAATTGTGGCGATTTTACC 33 26 1 CAAAATTTGG 0.74245 -59 ******* *** Masking position 4 Map Score: 8.24606 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 110 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 7 AATTATCATATTTTAGAAAAAATCGCAAAA 4 246 0 TTTTAGAAAA 0.614706 -55 AAATCCTACCTTGAGAAAAGAACTTAAAA 7 41 0 CTTGAGAAAA 0.693064 -19 ACCCCTATGTTTTCATACAAATTAAAGCAT 8 44 1 TTTCATACAA 0.761715 -58 CGCCTAATTATTTGATTAAATTT 9 59 1 TTTGATTAAA 0.869128 -13 AAGCAATTTTTTTGAAAAAAATTGTGTTTT 10 27 0 TTTGAAAAAA 0.629854 -274 GCAGTCAAATTTTCATACAACAATACGAAA 12 44 1 TTTCATACAA 0.761715 -25 TCGTCAATATTTTCAGTAAAAAGGAGCAAT 17 90 1 TTTCAGTAAA 0.92043 -21 TTTTGATTAAAACCTTCTAAA 20 290 0 TTTGATTAAA 0.869128 -11 AGAAGAATATTTTGAGTAAACGACTTTTAA 24 258 1 TTTGAGTAAA 0.90878 -43 TAAGTTTCAGAAAATACCTAGTAA 30 5 1 TTTCAGAAAA 0.937637 -34 AATTTTGACGATTGATTAAAAAAAAGCTAA 32 52 0 ATTGATTAAA 0.596079 -139 TCTTTCTATCATTCATAAAATAGAGGGTAA 32 81 0 ATTCATAAAA 0.692445 -110 ATTTTTTTGATTTCAGTAAAAAGCATTGAT 32 111 1 TTTCAGTAAA 0.92043 -80 ACATCATTATTTTCATAAAAAGCAAGGAAA 32 167 1 TTTCATAAAA 0.878537 -24 ********** Masking position 5 Map Score: 8.56024 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 207 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 8 GGATCTTTGCCCTCTTTTTACGAGATCAAT 4 32 1 CCTCTTTTTA 0.850954 -269 TTTTCCTCCTTTTAATTGGGCAGG 8 88 0 CCTCCTTTTA 0.958418 -14 TAAAATTTAGCCTCCATTTACCGCCTAATT 9 38 1 CCTCCATTTA 0.975057 -34 GCTGGGTTATCATCCATTTTACGGATACAA 11 60 1 CATCCATTTT 0.721607 -33 ACCACCTCCTATTTAAGTCACAGA 13 5 1 CCTCCTATTT 0.711357 -107 AATTGCTCCTTTTTACTGAAAATA 17 97 0 GCTCCTTTTT 0.69373 -14 AGTTTTTTTTCCACCATTTAGGACTAAATA 18 37 0 CCACCATTTA 0.906538 -106 AATATTAAACCCATCATTTAATTAAGGATA 19 80 1 CCATCATTTA 0.70611 -28 ATATTGATGCCCTTTATTTTGTCTATCAAT 24 28 0 CCTTTATTTT 0.668708 -273 TCTACTACCTTCATTTACTAGGTATTT 30 22 0 CCTTCATTTA 0.906396 -17 CAAAATTTACCCTCTATTTTATGAATGATA 32 75 1 CCTCTATTTT 0.890695 -116 ********** Masking position 8 Map Score: 6.18897 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 109 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 9 GTATTTCTTCCTGCCCAATTAAAAGGAGGA 8 79 1 CTGCCCAATT 0.982468 -23 CCTCCATTTACCGCCTAATTATTTGATTAA 9 48 1 CCGCCTAATT 0.945712 -24 CGGCTATAATCCGCCCGTTTTTCTTAACTT 16 22 0 CCGCCCGTTT 0.877148 -148 TTGTTAGGTTATGCCAAATTGAGTTTTTCA 16 90 0 ATGCCAAATT 0.799186 -80 AGACAACTCGCTGCCAGTTTTTTTTCCACC 18 52 0 CTGCCAGTTT 0.902812 -91 ACAACGTTCTCTGCCTAATTTAATTGGGCA 19 45 1 CTGCCTAATT 0.972706 -63 AATATTTTCTCTGCCCAATTAAATTAGGCA 19 56 0 CTGCCCAATT 0.982468 -52 CCTAAAATTTTTGCCTAATTGTATAGAAAT 24 224 0 TTGCCTAATT 0.799186 -77 TTCTCCGTTACTGCCAGATAAGCTGACTAA 29 59 0 CTGCCAGATA 0.822507 -25 ********** Masking position 9 Map Score: 5.6035 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 51 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 10 TCCTGTACCTAGGGTAGTATACTCTA 2 7 1 ACCTAGGGTA 0.989102 -78 TGAAGAACTAACCTAGAGTATACTACCCTA 2 20 0 ACCTAGAGTA 0.975773 -65 ATAGGACTGAACCTAGGATATACTTACCTA 2 50 1 ACCTAGGATA 0.975776 -35 TAATTCACATACCTAGAATA 8 1 0 ACCTAGAATA 0.947028 -101 CCAATGGGCAAACTAGGGTAAAAACAAAAA 20 155 1 AACTAGGGTA 0.945624 -146 ********** Masking position 5 Map Score: 3.432 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 3 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 11 AAGGGGCGATTACTCGCCCAAAAAA 7 5 0 TCTCGCCCAA 0.970043 -55 TAAGTATTTCTTCCTGCCCAATTAAAAGGAG 8 76 1 TCCTGCCCAA 0.970043 -26 TAGCCTCCATTTACCGCCTAATTATTTGATT 9 45 1 TACCGCCTAA 0.890712 -27 ATATTGTATATGCTCGCTCAAATGTTATTAG 10 96 0 TCTCGCTCAA 0.76045 -205 TTTCTTAACTTTTCCGCCTAAA 16 2 0 TTCCGCCTAA 0.97062 -168 AAAACAACGTTCTCTGCCTAATTTAATTGGG 19 42 1 TTCTGCCTAA 0.943867 -66 TTTAATATTTTCTCTGCCCAATTAAATTAGG 19 58 0 TTCTGCCCAA 0.97062 -50 TACCCTAAAATTTTTGCCTAATTGTATAGAA 24 226 0 TTTTGCCTAA 0.89538 -75 TTATTTTTCCTTTTCTCCCAATGACAAAACT 27 117 0 TTTCTCCCAA 0.764078 -21 * ********* Masking position 10 Map Score: 5.15708 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 189 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 12 CATTTAGATTAGGGAAAAATA 1 16 1 AGGAAAAATA 0.82182 -11 TGTCTTATTGACGGCGAAAAATTATCATATT 4 264 0 AGGCGAAAAA 0.945491 -37 GCTCAAAAGTGCGGCGAAAAAATTATGTGTA 6 23 0 GGGCGAAAAA 0.762451 -76 TTAATTGGGCAGGAAGAAATACTTAATATGC 8 70 0 AGAAGAAATA 0.755746 -32 GCCCAATTAAAAGGAGGAAAA 8 91 1 AGGAGGAAAA 0.715398 -11 CATCCATTTTACGGATACAAAGGAAAATAAA 11 70 1 AGGATACAAA 0.488235 -23 TATAACATACACGGAGAAAAAT 13 100 1 AGGAGAAAAA 0.963363 -12 CCGATTGTAAAAGGATAAAAAA 14 54 1 AGGATAAAAA 0.908922 -12 CTTTCTACGAAAGAAAAAATAATATTGTTCA 16 59 1 AGAAAAAATA 0.497033 -111 GTTTAAATTTATCGAGAAATAAAAAATTGCG 17 23 1 ACGAGAAATA 0.485796 -88 TCCACCATTTAGGACTAAATAAGTGAGAAAG 18 27 0 AGACTAAATA 0.436508 -116 GTCCTAAATGGTGGAAAAAAAACTGGCAGCG 18 43 1 GGGAAAAAAA 0.608456 -100 CAAAGCAAAAACGGCGAAAAAAAAACAAAAG 18 80 0 AGGCGAAAAA 0.945491 -63 GAATAGGTACAAAGCGAAAAATCAGCAACAA 18 108 0 AAGCGAAAAA 0.43363 -35 TTGAGTTCTGATGAAGAAAAAAGTTCAATTT 19 12 0 AGAAGAAAAA 0.849255 -96 TACGAGTCAAACGGCTAAATAAAAAGCAAAC 20 28 0 AGGCTAAATA 0.783342 -273 CCATTGACAAAAGTATAAAAAATCGGCATAT 24 54 0 AGTATAAAAA 0.345333 -247 AAAATTTTGAAAGGAAAAACAA 26 29 1 AGGAAAAACA 0.550573 -12 ATTGGGAGAAAAGGAAAAATAA 27 126 1 AGGAAAAATA 0.82182 -12 TATCATCAGTAAGAAGAAAAACAGGATAGAA 28 50 1 AGAAGAAAAA 0.849255 -22 CGATTTTTGTAGTGATAAAAAAGACATCATT 32 144 1 ATGATAAAAA 0.305795 -47 * ********* Masking position 9 Map Score: 14.6 Number of sites scoring better than the average of aligned sites = 565 Number in coding regions = 441 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 13 TCAAGTATTGGACTTTAAAATTTAGCCTCC 9 23 1 GACTTTAAAA 0.909492 -49 CTTAAAAATACACTTTAAAATTAAAAAAAG 10 54 0 CACTTTAAAA 0.925634 -247 TAATAAAAATCAGTGTAAAAGCAATAAATA 10 218 1 CAGTGTAAAA 0.792958 -83 CTTTTATCTCAACTTTAAAATAGGAAAAAC 10 278 1 AACTTTAAAA 0.658187 -23 AAATTCGACCGATTGTAAAAGGATAAAAAA 14 46 1 GATTGTAAAA 0.89425 -20 TTAAATTCATTGTAAAACAAAAAGTGC 21 8 1 CATTGTAAAA 0.91285 -67 CCAATTTTTACATTTTAAAA 22 1 0 CATTTTAAAA 0.906262 -28 TATTGAAAGAGCTTGTAAAAATAACGATAC 24 125 0 GCTTGTAAAA 0.784299 -176 AACAATGCTAGATTTTAAAAGTCGTTTACT 24 272 0 GATTTTAAAA 0.886431 -29 AACAACTCCCTTTAAAATAAATAAAAT 32 8 1 CCCTTTAAAA 0.84257 -183 ********** Masking position 6 Map Score: 5.24433 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 94 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 14 AGTGCGGTTAAAATTAATTACATTTTATT 3 28 1 AAATTAATTA 0.765328 -19 GTTCTTATTTATATTAATTAGCCACAAAAT 6 60 0 ATATTAATTA 0.931535 -39 AAATTAAAGCATATTAAGTATTTCTTCCTG 8 62 1 ATATTAAGTA 0.833433 -40 GCATTTTGAGATATTGATTATTTAAATGGC 11 32 0 ATATTGATTA 0.918985 -61 GATATTAATTATAGATCTAAG 12 2 1 ATATTAATTA 0.931535 -67 AGGTGACAGCATATTGATTAATAC 25 5 0 ATATTGATTA 0.918985 -115 ********** Masking position 5 Map Score: 2.01934 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 30 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 15 AGACATCAAACACAAATCAAT 4 290 1 CACAAATCAA 0.952615 -11 AGCATTGCCAAATCAAGTATTGGACT 9 7 1 GCCAAATCAA 0.800718 -65 TTTTCTTCATCAGAACTCAAAAACAACGTT 19 23 1 CAGAACTCAA 0.937508 -85 TTGTGTCTCACCGAAATCAACACAAATTTT 24 85 0 CCGAAATCAA 0.948671 -216 CTCCCAATGACAAAACTCAACTAAAAGTGC 27 104 0 CAAAACTCAA 0.790618 -34 TACATACTAACCCATATCAATATTTATAAA 31 61 1 CCCATATCAA 0.813104 -27 ATGCTTTTTACTGAAATCAAAAAAATTCTT 32 107 0 CTGAAATCAA 0.823033 -84 GCGATTTTACCACAACTCAAATTTACGATA 33 46 1 CACAACTCAA 0.951703 -39 ********** Masking position 4 Map Score: 2.40577 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 71 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802