AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00561_hinf_reg_100.orf -o00561_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 Purged sequences: HI1137 21 cell division protein (ftsW) Input sequences: #1 HI0123 274 phosphatidylglycerophosphate synthase (pgsA) #2 HI0160 156 phosphatidylserine decarboxylase proenzyme (psd) #3 HI0185 122 alcohol dehydrogenase, class III (adhC) #4 HI0195.1 26 conserved hypothetical transmembrane protein (aefA) #5 HI0197 84 penicillin-insensitive murein endopeptidase (mepA) #6 HI0199 46 lipid A biosynthesis (kdo)2-(lauroyl)-lipid IVA acyltransferase (msbB) #7 HI0211 44 phosphatidylglycerophosphatase B (pgpB) #8 HI0301 300 hemolysin, putative #9 HI0329 37 conserved hypothetical protein #10 HI0330 98 opacity associated protein (oapA) #11 HI0331 59 opacity associated protein (oapB) #12 HI0334 77 GTP pyrophosphokinase (relA) #13 HI0425 146 phosphatidylserine synthase (pssA) #14 HI0604 300 adenylate cyclase (cyaA) #15 HI0605 73 glycerol-3-phosphate dehydrogenase (NAD+) (gpsA) #16 HI0678 165 triosephosphate isomerase (tpiA) #17 HI0685_HI0686 292 HI0685: anaerobic glycerol-3-phosphate dehydrogenase, subunit A (glpA), HI0686: glycerol-3-phosphatase transporter (glpT) #18 HI0687 99 conserved hypothetical protein #19 HI0688 94 H. influenzae predicted coding region HI0688 #20 HI0690 229 glycerol uptake facilitator protein (glpF) #21 HI0734 85 1-acyl-glycerol-3-phosphate acyltransferase (plsC) #22 HI0748 248 glycerol-3-phosphate acyltransferase (plsB) #23 HI0916 107 outer membrane protein, putative #24 HI0920 248 conserved hypothetical protein #25 HI1136 122 UDP-N-acetylmuramoylalanine--D-glutamate ligase (murD) #26 HI1139 137 UDP-N-acetylmuramate--alanine ligase (murC) #27 HI1140 71 D-alanine--D-alanine ligase (ddlB) #28 HI1303 147 riboflavin synthase, beta chain (ribH) #29 HI1527 84 lipid A biosynthesis lauroyl acyltransferase (htrB) #30 HI1716 196 undecaprenyl-phosphate alpha-N-acetylglucosaminyltransferase (rfe), putative Motif number 1 GCCACCTAAGGTCGCTTTTTATAAATAATT 1 191 0 GTCGCTTTTT 0.691575 -84 AGAAAAATTGACCGCACTTTAGCTAAAGAT 1 255 0 ACCGCACTTT 0.992101 -20 TCAAAGGGAAATCACATTTTTTATTGGATA 2 45 1 ATCACATTTT 0.815587 -112 ATTAATTTTAACCGCACTTTTGCGCGCTTT 6 16 0 ACCGCACTTT 0.992101 -31 TGTATTTTTAACCGCACTTTAGGTTTAAAC 8 175 1 ACCGCACTTT 0.992101 -126 ATAAAAAATAACCGCACATTGGGTTTAAAC 8 197 0 ACCGCACATT 0.875903 -104 TAATTTTTTCGCCGCACTTTTGAGCTTCTC 10 29 1 GCCGCACTTT 0.993193 -70 TGTGACATAAATCACAATTTTTCGAAAAAT 14 211 0 ATCACAATTT 0.497716 -90 TGTGATTTATGTCACATTTTTTTGCATTTA 14 225 1 GTCACATTTT 0.837089 -76 GCCAAAATTAACAACATTTTGAGTGTAAAA 17 204 0 ACAACATTTT 0.519844 -89 GTTAATTTTGGCCGCACTTCCCTACAATGA 17 222 1 GCCGCACTTC 0.958966 -71 CAATTTGCCCACCGCCTTTTTTAAGCTAA 18 10 0 ACCGCCTTTT 0.919704 -90 AAATTGCTTAGTCGCCTTTTTTGTAACTAT 18 34 1 GTCGCCTTTT 0.776206 -66 CTTCATTTCAACCGCACTTCTAAGGAGTGA 20 207 1 ACCGCACTTC 0.95264 -23 TGTGTATTAAGTCACATTTTGTCGCCAAAT 22 83 1 GTCACATTTT 0.837089 -166 TTAAATTTTAACCGCACTTTTGCAGCATTT 24 20 1 ACCGCACTTT 0.992101 -229 CCGCACTTTTGCAGCATTTTGACAATAGAA 24 31 1 GCAGCATTTT 0.82836 -218 GGTATTCTATGCCACATTTTCTATTGTCAA 24 49 0 GCCACATTTT 0.951725 -200 CTAAAAAACCACCGCACTTTTTATTTCTCT 24 103 0 ACCGCACTTT 0.992101 -146 CGTAAAAAAGGTCGCTCTTTCAAAAGTGAA 25 33 0 GTCGCTCTTT 0.812226 -90 GCGAATTTTAACCGCACTTTTAGTTGAGTT 26 91 1 ACCGCACTTT 0.992101 -47 TGGTAAAATCGCCACAATTTTGGTTATTCA 29 28 0 GCCACAATTT 0.815401 -57 GTCAAAATTGACCGCACTTTTACGCCTATC 30 63 0 ACCGCACTTT 0.992101 -134 GTCAATTTTGACCGCATTTTTTATAAAAAT 30 81 1 ACCGCATTTT 0.984872 -116 ********** Masking position 9 Map Score: 49.3168 Number of sites scoring better than the average of aligned sites = 1959 Number in coding regions = 1367 Number in noncoding regions = 592 Number of orfs with sites within 600 bp upstream = 367 Fraction of orfs with sites within 600 bp upstream = 0.0589464 Motif number 2 CTTTAGCTAAAGTGCGGTCAATTTTTCT 1 257 1 AGTGCGGTAA 0.997523 -18 AGCGCGCAAAAGTGCGGTTAAAATTAATTAC 6 18 1 AGTGCGGTAA 0.997523 -29 TTAAACCTAAAGTGCGGTTAAAAATACACAA 8 172 0 AGTGCGGTAA 0.997523 -129 TTAAACCCAATGTGCGGTTATTTTTTATTGA 8 199 1 TGTGCGGTAT 0.932247 -102 GAAGCTCAAAAGTGCGGCGAAAAAATTATGT 10 26 0 AGTGCGGCAA 0.992201 -73 ATTAAAGACTAGTGCGTTAGTTTACAATATT 13 113 0 AGTGCGTTGT 0.811294 -34 ATTGTAGGGAAGTGCGGCCAAAATTAACAAC 17 219 0 AGTGCGGCAA 0.992201 -74 ACTCCTTAGAAGTGCGGTTGAAATGAAGAGT 20 204 0 AGTGCGGTGA 0.995106 -26 ATGCTGCAAAAGTGCGGTTAAAATTTAAGGT 24 17 0 AGTGCGGTAA 0.997523 -232 AGAAATAAAAAGTGCGGTGGTTTTTTAGTTG 24 105 1 AGTGCGGTGT 0.984911 -144 CTCAACTAAAAGTGCGGTTAAAATTCGCAAC 26 88 0 AGTGCGGTAA 0.997523 -50 TAGGCGTAAAAGTGCGGTCAATTTTGACCGC 30 65 1 AGTGCGGTAA 0.997523 -132 TTTTATAAAAAATGCGGTCAAAATTGACCGC 30 78 0 AATGCGGTAA 0.963672 -119 ******** ** Masking position 3 Map Score: 39.5442 Number of sites scoring better than the average of aligned sites = 1080 Number in coding regions = 679 Number in noncoding regions = 401 Number of orfs with sites within 600 bp upstream = 264 Fraction of orfs with sites within 600 bp upstream = 0.0424028 Motif number 3 GTTTTCTCTTTATTTTTTCCATTGCCTAATACCG 1 93 0 TTTTTTCTTG 0.671218 -182 CTTAGGTGGCTTTTTTTATCATCAGAGATAATTT 1 211 1 TTTTTTCTCA 0.869318 -64 TTTTTATTCCCTTTAAACAAAAATG 3 2 1 TTTATTCTTA 0.743129 -121 TGTTTTTCCTCTTAATTCATTGAC 3 109 0 TTTTTTTTTA 0.952924 -14 ATGCGCGCGTTATTTTTGTTATCAAGGGGCGAGC 7 21 1 TTTTTTTTCA 0.920661 -24 TGCGGTTATTTTTTATTGATTTTCCTCTTTTCGC 8 211 1 TTTATTTTTC 0.788393 -90 TGATGCTTGTTCTTATTTATATTAATTAGCCACA 10 64 0 TTTATTTTTA 0.834617 -35 AGTAATCGCCCCTTTTTCTTTTTAAGTTCTTTTC 11 22 1 CTTTTTTTTA 0.835178 -38 GAAAAAAGGCTTTTTTTCGTTATAATGCTCACAA 13 62 0 TTTTTTTATA 0.834618 -85 CGAAAAAAAGCCTTTTTTCTATTAATAAGCACGT 13 77 1 CTTTTTTTTA 0.835178 -70 GATAGCTTGATATTTTTCTTATCAACGCAAAGTA 14 49 0 TTTTTTTTCA 0.920661 -252 TATAAAAATCTATATTTTCTATTATTAGTGGATA 14 79 0 TTATTTTTTA 0.483654 -222 TCTGTGAGAATTTTTTTAATTTTATGATCTTCTG 16 76 1 TTTTTTTTTA 0.952924 -90 TTTACTTTCTTATTTTTTATTTTCTTTTATGATT 17 80 0 TTTTTTTTTC 0.937282 -213 ACATTTTTGATTTTTTTTACTTTCTTATTTTTTA 17 95 0 TTTTTTCTTC 0.895473 -198 CTTTTTATATTATTTTTTCTTACATTTTGGGAAT 17 257 1 TTTTTTTACA 0.743129 -36 ATGATACTTATCTTTTTATTATTCTTATGATAGT 18 59 0 TTTTTTTTTC 0.937282 -41 AGCCCTTTGGTGTTTTTATCGTCCAAAAACTCAA 22 149 0 TTTTTTCTCC 0.830826 -100 TAAATTGAACTTTTTTCTTCATCAGAACTCAAA 23 10 1 CTTTTTTATC 0.482573 -98 CCACCGCACTTTTTATTTCTCTCCCTATTAATTT 24 91 0 TTTATTTTCC 0.681103 -158 GTTTTTTAGTTGTTTTTTACAATAAATTTTCAAT 24 124 1 TTTTTTCATA 0.743126 -125 TATTTTTATTATTGAGAGACCTCT 24 235 0 TTTTTTTTTG 0.780763 -14 GAAAGAGCGACCTTTTTTACGTTAGTAAAGGAAA 25 42 1 CTTTTTCTTA 0.743903 -81 TTTCTTTCTTCTTAATTGCTATAA 25 109 0 TTCTTTTTTA 0.718699 -14 CAGTCATAAGTATTTTTTATATCCAAAAGTGCTA 26 37 1 TTTTTTTTCC 0.895473 -101 TTCGCAACGTTTTTATTTCTAATATTAGCACTTT 26 62 0 TTTATTTATA 0.557161 -76 TTATTTTTCCTTTTCTCCCAATGAC 26 123 0 TTTTTTTTTC 0.937282 -15 TTTCTATCCTGTTTTTCTTCTTACTGATGATAC 27 49 0 TTTTTTTTTA 0.952924 -23 TTTAAGGCGATTTTATTGTTCATAACCCGCACCA 28 67 0 TTTATTTATA 0.557162 -81 CTTTTACGCCTATCTTTTATTTTACCAGTGGTAT 30 43 0 TTCTTTTTTA 0.718699 -154 AACGAAGCCCTATTTTTCACTTCAACGCCCGTAT 30 109 0 TTTTTTCTCA 0.869318 -88 * ***** * *** Masking position 7 Map Score: 34.819 Number of sites scoring better than the average of aligned sites = 541 Number in coding regions = 346 Number in noncoding regions = 195 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 4 TTTATAAATAATTGATAAAATTAAAGCTCGTT 1 172 0 ATGTAAAATT 0.831985 -103 GCGCAAAAGTGCGGTTAAAATTAATTACATTT 6 21 1 GGGTAAAATT 0.978172 -26 TTTTTACGGAGAGGGGAAAATTCTAGACAACA 8 140 0 GGGGAAAATT 0.977727 -161 AACCTAAAGTGCGGTTAAAAATACACAATTTT 8 168 0 GGGTAAAAAT 0.92213 -133 TGTCTTATTGACGGCGAAAAATTATCATATTT 8 263 0 AGGGAAAAAT 0.855392 -38 TTAGCCAAAAAATGCTAAAATTTGTGAGCATT 13 41 1 ATGTAAAATT 0.831978 -106 TTGATTGTTGATAGGTAAAATTTATAGTATTT 14 183 1 AAGTAAAATT 0.831987 -118 GCAAAGAATAGGGGCGAAATTTTGGTATAGTA 16 109 1 GGGGAAATTT 0.84705 -57 TTTCTCCATAGTTGATAAAATTAACTTGCTTA 16 139 0 GTGTAAAATT 0.906638 -27 TTAAAAAGTTGGAGAAAAAATT 17 1 0 GAGAAAAATT 0.685117 -292 ACTGTTTCAAAAGGGTAAATTTAGATGACACA 17 36 0 AGGTAAATTT 0.742461 -257 CGTTTGAGCGAATGCGAAAATTATTGTGATCA 17 153 1 ATGGAAAATT 0.829083 -140 GTAGGGAAGTGCGGCCAAAATTAACAACATTT 17 215 0 GGGCAAAATT 0.939506 -78 AAAACACCAAAGGGCTAAAAATAGTTCTATTC 22 167 1 AGGTAAAAAT 0.857925 -82 AACTTATAACAAAGAGAAAATTTATT 22 233 1 AAGGAAAATT 0.829083 -16 CTGCAAAAGTGCGGTTAAAATTTAAGGTGATT 24 13 0 GGGTAAAATT 0.978172 -236 ATACCGTAAAATGGCAAAAATTAATAGGGAGA 24 74 1 AGGAAAAATT 0.836599 -175 AACTAAAAGTGCGGTTAAAATTCGCAACGTTT 26 84 0 GGGTAAAATT 0.978172 -54 TATAAAAAATGCGGTCAAAATTGACCGCACTT 30 74 0 GGGCAAAATT 0.939506 -123 TACGGGCGTTGAAGTGAAAAATAGGGCTTCGT 30 110 1 GAGGAAAAAT 0.715405 -87 * ** ******* Masking position 12 Map Score: 25.5885 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 289 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 5 ATTAACTTATAGGGCAAAAATAACTATGGTT 1 27 1 AGGGCAAAAT 0.898507 -248 GCGCAAAAGTGCGGTTAAAATTAATTACATT 6 21 1 GCGGTAAAAT 0.979477 -26 AACCTAAAGTGCGGTTAAAAATACACAATTT 8 169 0 GCGGTAAAAA 0.956699 -132 TGTCTTATTGACGGCGAAAAATTATCATATT 8 264 0 ACGGCAAAAA 0.921917 -37 GCTCAAAAGTGCGGCGAAAAAATTATGTGTA 10 23 0 GCGGCAAAAA 0.976233 -76 GCAAAGAATAGGGGCGAAATTTTGGTATAGT 16 109 1 GGGGCAAATT 0.766219 -57 GTAGGGAAGTGCGGCCAAAATTAACAACATT 17 216 0 GCGGCAAAAT 0.988855 -77 CCTTAGAAGTGCGGTTGAAATGAAGAGTGTT 20 201 0 GCGGTGAAAT 0.882731 -29 AAAACACCAAAGGGCTAAAAATAGTTCTATT 22 167 1 AGGGCAAAAA 0.803859 -82 CTGCAAAAGTGCGGTTAAAATTTAAGGTGAT 24 14 0 GCGGTAAAAT 0.979477 -235 ATACCGTAAAATGGCAAAAATTAATAGGGAG 24 74 1 ATGGCAAAAT 0.690231 -175 AACTAAAAGTGCGGTTAAAATTCGCAACGTT 26 85 0 GCGGTAAAAT 0.979477 -53 TATAAAAAATGCGGTCAAAATTGACCGCACT 30 75 0 GCGGTAAAAT 0.979477 -122 ***** ***** Masking position 8 Map Score: 20.7948 Number of sites scoring better than the average of aligned sites = 478 Number in coding regions = 321 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 6 ATAAGTTAATTTAAATAAGGAAATAT 1 4 0 TTAAAGGAAA 0.920308 -271 ATTGGATAACTCAATAAAGGAAATTATCCGCTA 2 67 1 TCTAAGGAAA 0.956826 -90 CGCCTCTTTTTTTAACAAGGAAAGATA 2 140 1 TTAAAGGAAA 0.920302 -17 TTTACCATTTAGATTAGGGAAAAATA 4 10 1 TATAGGGAAA 0.899736 -17 ACAGCCATTTTTACTCAGGGAAACCCT 13 5 0 TTTAGGGAAA 0.969945 -142 TCTCTTCCCTTTACTTAGGGAAAACACTCTTCA 20 179 1 TTTAGGGAAA 0.969939 -51 GAATTTGTTATACTTCAAGGAAATTTTATATAG 21 54 1 TATAAGGAAA 0.934758 -32 AACCCATCATTTAATTAAGGATATTTATCAA 23 87 1 TTTAAGGATA 0.920308 -21 CTTTTTTACGTTAGTAAAGGAAATTTATATTTC 25 53 1 TTTAAGGAAA 0.980968 -70 TAAAATTATATCATTGATGGAAATATAAATTTC 25 72 0 TCTATGGAAA 0.777466 -51 ATAGTTTACCTTAATGAAGGAAATTTTCCATAA 28 23 1 TTTAAGGAAA 0.980968 -125 CCTAAAATTTTTTGTAAAGGATAACATAAGGCA 30 166 0 TTTAAGGATA 0.920307 -31 ** * ******* Masking position 7 Map Score: 13.9238 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 26 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 AATTATTTATAAAAAGCGACCTTAGGTGGC 1 191 1 AAAAAGCGAC 0.703761 -84 CTGATGATAAAAAAAGCCACCTAAGGTCGC 1 206 0 AAAAAGCCAC 0.957154 -69 TATTTATATTAATTAGCCACAAAATTGAGA 10 55 0 AATTAGCCAC 0.718081 -44 TTTGGCTAAAAAACAGCCATTTTTACTCAG 13 20 0 AAACAGCCAT 0.708815 -127 TTATAACGAAAAAAAGCCTTTTTTCTATTA 13 71 1 AAAAAGCCTT 0.857288 -76 ATCTTGAGCTAAAAAGCTACAATTACCTGT 16 37 0 AAAAAGCTAC 0.738661 -129 CAATATCACAAAATCGCTTTCTTTTACACT 17 183 1 AAATCGCTTT 0.444506 -110 GAGTGTTTTGAAATAGCCTCCTTATTTGAA 20 129 0 AAATAGCCTC 0.951576 -101 AAAATCACCTTAAATTTTAAC 24 2 1 AAATCACCTT 0.423683 -247 AAAAACAACTAAAAAACCACCGCACTTTTT 24 111 0 AAAAAACCAC 0.721803 -138 GGCTATTTATAAAACGCCACAACCC 26 6 0 AAAACGCCAC 0.953092 -132 GGCGTTTTATAAATAGCCTCAGTCATAAGT 26 18 1 AAATAGCCTC 0.951576 -120 ATGAACAATAAAATCGCCTTAAAAATGAGT 28 78 1 AAATCGCCTT 0.863559 -70 AGTTGTGGTAAAATCGCCACAATTTTGGTT 29 33 0 AAATCGCCAC 0.959248 -52 ********** Masking position 2 Map Score: 10.1664 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 286 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 8 TAAAGCTCGTTAGCATCTATTTTAGGGATTC 1 152 0 TAGCACTATT 0.71499 -123 GCTTTAATTTTATCAATTATTTATAAAAAGC 1 177 1 TATCATTATT 0.88837 -98 GGCGTGATTATAGCAATTTTTGTTATAGTTC 2 113 0 TAGCATTTTT 0.92696 -44 AGTGTTTTTTTATCATTTTTGTTTAAAGGGA 3 18 0 TATCATTTTG 0.944314 -105 GGCGAAAAATTATCATATTTTAGAAAAAATC 8 252 0 TATCAATTTT 0.757651 -49 CTTTTGAGCTTCTCAATTTTGTGGCTAATTA 10 45 1 TCTCATTTTG 0.744321 -54 TCACAAATTTTAGCATTTTTTGGCTAAAAAA 13 37 0 TAGCATTTTT 0.92696 -110 CCTTACTCAATATCACTTATTAAGGAAT 14 8 0 TATCATTATT 0.88837 -293 AAGTTAATTTTATCAACTATGGAGAAACAAA 16 144 1 TATCACTATG 0.770224 -22 AAAAGATAAGTATCATTTTTGGGAAAAGTAA 18 77 1 TATCATTTTG 0.944314 -23 TTGTTTAGATTAGCACATATTGAGATCGAAT 21 27 1 TAGCAATATT 0.618584 -59 TACAATAAATTTTCAATTTTTGCAGAACAGA 24 141 1 TTTCATTTTT 0.740251 -108 AGGTTCGCTCTTTCACTTTTGAAAGAGCGAC 25 22 1 TTTCATTTTG 0.775963 -101 TTTCTAATATTAGCACTTTTGGATATAAAAA 26 50 0 TAGCATTTTG 0.939114 -88 ***** ***** Masking position 5 Map Score: 8.61065 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 71 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 9 CATAGTTATTTTTGCCCTATAAGTTAATTT 1 25 0 TTTGCCCTAT 0.804678 -250 TTATTTGTTGTTTTCTCTTTATTTTTTCCA 1 106 0 TTTTCTCTTT 0.863518 -169 AAAAAATGTGATTTCCCTTTGACTATCTTC 2 37 0 ATTTCCCTTT 0.795761 -120 TTTTTATTCCCTTTAAACAAAAAT 3 5 1 TATTCCCTTT 0.68843 -118 ATAGCAACAGTTTACACTTTAGAGTTCACT 3 57 0 TTTACACTTT 0.779229 -66 TTTACCATTTAGATTAGGGA 4 1 1 TTTACCATTT 0.739073 -26 GATAAGGATCTTTGCCCTCTTTTTACGAGA 8 27 1 TTTGCCCTCT 0.864361 -274 TGTCTAGAATTTTCCCCTCTCCGTAAAAAT 8 143 1 TTTCCCCTCT 0.829107 -158 TTTTATTGATTTTCCTCTTTTCGCGTTTTG 8 221 1 TTTCCTCTTT 0.818341 -80 TCTATACTTATTTCCTCTTTTACTAGATAA 15 45 1 TTTCCTCTTT 0.818341 -29 GTCATCTAAATTTACCCTTTTGAAACAGTA 17 39 1 TTTACCCTTT 0.954972 -254 CCCTACAATGATTACACTTTTTATATTATT 17 241 1 ATTACACTTT 0.320199 -52 TAATAAATTCTCTTCCCTTTACTTAGGGAA 20 171 1 TCTTCCCTTT 0.766072 -59 AGAACTATTTTTAGCCCTTTGGTGTTTTTA 22 165 0 TTAGCCCTTT 0.661421 -84 AATAAATTTTCTCTTTGTTATAAGTT 22 233 0 TTTTCTCTTT 0.863518 -16 CCTATTAATTTTTGCCATTTTACGGTATTC 24 72 0 TTTGCCATTT 0.784792 -177 TTACAATAAATTTTCAATTTTTGCAGAACA 24 140 1 TTTTCAATTT 0.393552 -109 TTATTTTTCCTTTTCTCCCAATGA 26 124 0 TTTTCCTTTT 0.606801 -14 TTAATAAGGCTTTACCCTATTTTATTTAGG 28 108 0 TTTACCCTAT 0.761902 -40 ********** Masking position 8 Map Score: 11.3718 Number of sites scoring better than the average of aligned sites = 426 Number in coding regions = 314 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 10 AGTTTGATGTGATAAGGATCTTTGCCCTCT 8 17 1 GATAAGGATC 0.802177 -284 TTTATATGACGAAAAGTATCTATGTTGTGG 8 94 0 GAAAAGTATC 0.953282 -207 CGGTTATTCGGTACAATATCCACCCAAAAT 12 13 1 GTACAATATC 0.696744 -65 GCGTTGATAAGAAAAATATCAAGCTATCCA 14 55 1 GAAAAATATC 0.949653 -246 ATAGGTTACCGAAAGATATCTATACTTATT 15 27 1 GAAAGATATC 0.799596 -47 AAATTATTGTGATCAATATCACAAAATCGC 17 170 1 GATCAATATC 0.886301 -123 ATAATAAAAAGATAAGTATCATTTTTGGGA 18 71 1 GATAAGTATC 0.925994 -29 AATAGGTATAGTTAAATATCTGGTTCAATT 19 36 1 GTTAAATATC 0.841562 -59 TTGATAAATATCCTTAATTAAA 23 96 0 GATAAATATC 0.922472 -12 CTTAGTATTAGAAAAGTATCATCAGTAAGA 27 34 1 GAAAAGTATC 0.953282 -38 ********** Masking position 8 Map Score: 7.97491 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 65 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 11 TGCTATAATCACGCCTCTTTTTTTAACAAG 2 129 1 ACGCCTCTTT 0.913543 -28 GCTCGCCCCTTGATAACAAAAA 7 33 0 TCGCCCCTTG 0.944108 -12 GGGCGAGTAATCGCCCCTTTTTCTTTTTAA 11 17 1 TCGCCCCTTT 0.978812 -43 TACCAAAATTTCGCCCCTATTCTTTGCAGA 16 106 0 TCGCCCCTAT 0.978812 -60 AATTGCTTAGTCGCCTTTTTTGTAACTATC 18 35 1 TCGCCTTTTT 0.742432 -65 AGAATTGCTAACGCCCTTAATAAAACCAAT 19 63 0 ACGCCCTTAA 0.845736 -32 ACGATAAACTACGCCCCTAACTTAC 29 70 1 ACGCCCCTAA 0.9526 -15 TTTCACTTCAACGCCCGTATTTTTATAAAA 30 99 0 ACGCCCGTAT 0.913737 -98 ********** Masking position 8 Map Score: 4.80179 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 24 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 12 GAATATTACCTGTTGTTGCGAAGATAGTCAAA 2 18 1 TGTTTTGCAA 0.701787 -139 AAAGTATCTATGTTGTGGATAACTTGTGAATA 8 80 0 TGTTTGGAAA 0.799573 -221 AGCTTCTCAATTTTGTGGCTAATTAATATAAA 10 51 1 TTTTTGGCAA 0.916231 -48 GGAAGTTGCTTGCTCTTCATCAACAAGGGGGT 12 53 1 TGCTTTCACA 0.419827 -25 AATTTTAGCATTTTTTGGCTAAAAAACAGCCA 13 31 0 TTTTTGGCAA 0.916239 -116 TCAAAATGACTTTTTTACCTAAGAGTGGTAGG 14 155 0 TTTTTACCAA 0.611381 -146 TTCGCCCCTATTCTTTGCAGAAGATCATAAAA 16 95 0 TTCTTGCAAA 0.895592 -71 AAATGAAGAGTGTTTTCCCTAAGTAAAGGGAA 20 183 0 TGTTTCCCAA 0.762631 -47 TTAAGTCACATTTTGTCGCCAAATTTTCTAAA 22 89 1 TTTTTCGCAA 0.722734 -160 CTAAAAATAGTTCTATTCACAAACTGCTTTTT 22 181 1 TTCTTTCAAA 0.71197 -68 AATTGAACTTTTTTCTTCATCAGAACTCAAAA 23 13 1 TTTTTTCACA 0.496572 -95 AAAAACAACGTTCTCTGCCTAATTTAATTGGG 23 41 1 TTCTTGCCAA 0.946346 -67 GTTTAATATTTTCTCTGCCCAATTAAATTAGG 23 58 0 TTCTTGCCAA 0.946346 -50 TTTTACGGTATTCTATGCCACATTTTCTATTG 24 53 0 TTCTTGCCCA 0.873379 -196 TGTTCTAATCTGTTCTGCAAAAATTGAAAATT 24 148 0 TGTTTGCAAA 0.864967 -101 AACACTATATTTTTATGGAAAATTTCCTTCAT 28 36 0 TTTTTGGAAA 0.841865 -112 **** **** ** Masking position 6 Map Score: 6.35162 Number of sites scoring better than the average of aligned sites = 460 Number in coding regions = 397 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 13 TAGAGTATACTACCCTAGGTACAGGA 5 6 0 TACCCAGGTA 0.903286 -79 TAGGGTAGTATACTCTAGGTTAGTTCTTCAA 5 20 1 TACTCAGGTT 0.921393 -65 TAGGTAAGTATATCCTAGGTTCAGTCCTATT 5 49 0 TATCCAGGTT 0.921091 -36 TGTTTACCCCCGATTCCCAAAATGT 17 278 0 TACCCCGATT 0.948199 -15 TGGGTATGTTTACCCACGGTTGTGAGGGATA 20 11 0 TACCCCGGTT 0.989078 -219 TGGGTAAACATACCCACGGTTAACTAGGTTT 20 26 1 TACCCCGGTT 0.989078 -204 ***** ***** Masking position 2 Map Score: 2.93276 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 6 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 14 AACTTATAGGGCAAAAATAACTATGGTTTCA 1 30 1 GCAAAAAAAC 0.815353 -245 TTAGGCAATGGAAAAAATAAAGAGAAAACAA 1 98 1 GAAAAAAAAA 0.530675 -177 AAAAAATAAAGAGAAAACAACAAATAATTCT 1 109 1 GAGAAAAAAC 0.879115 -166 AAACAAAAATGATAAAAAAACACTTGCTTTA 3 25 1 GATAAAAAAC 0.646692 -98 GGAAAATCAATAAAAAATAACCGCACATTGG 8 205 0 TAAAAAAAAC 0.957352 -96 TATCATATTTTAGAAAAAATCGCAAAACGCG 8 242 0 TAGAAAAATC 0.519419 -59 CTAATTAATATAAATAAGAACAAGCATCAGA 10 69 1 TAAATAAAAC 0.749725 -30 ATCCTACCTTGAGAAAAGAACTTAAAAAGAA 11 37 0 GAGAAAAAAC 0.879115 -23 ATTTTTTGGCTAAAAAACAGCCATTTTTACT 13 23 0 TAAAAAAAGC 0.727685 -124 ATGGAACCAATAAAAAATAACCAATT 16 6 0 TAAAAAAAAC 0.957352 -160 TAAAAGAAAATAAAAAATAAGAAAGTAAAAA 17 85 1 TAAAAAAAAG 0.637493 -208 AATAAGAAAGTAAAAAAAATCAAAAATGTGA 17 100 1 TAAAAAAATC 0.760724 -193 CAAAATGTAAGAAAAAATAATATAAAAAGTG 17 255 0 GAAAAAAAAT 0.665983 -38 GAGAATTTATTAAAAAAGAATACGGAGTGTT 20 152 0 TAAAAAAAAT 0.676612 -78 TACACAGATTTAAAAAATAACAGTTGCAACT 22 58 0 TAAAAAAAAC 0.957352 -191 TCATCAGAACTCAAAAACAACGTTCTCTGCC 23 29 1 TCAAAAAAAC 0.822496 -79 AAAAAACAACTAAAAAACCACCGCACTTTTT 24 111 0 TAAAAAACAC 0.704171 -138 AAATTTATTGTAAAAAACAACTAAAAAACCA 24 122 0 TAAAAAAAAC 0.957352 -127 GCTAATATTAGAAATAAAAACGTTGCGAATT 26 67 1 GAAATAAAAC 0.740578 -71 ******* *** Masking position 6 Map Score: 18.1116 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 91 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 15 TTTTTGCCCTATAAGTTAATTTAAATAAGGA 1 16 0 ATAATTAATT 0.538051 -259 GTAGTATACTCTAGGTTAGTTCTTCAATAGG 5 24 1 CTAGTTAGTT 0.91125 -61 TATTGCGTAAATAGCTTAATTCTGCCGATAT 14 110 0 ATAGTTAATT 0.804992 -191 AGGATAGTACCTAGTTTTATTGCGTAAATAG 14 127 0 CTAGTTTATT 0.882985 -174 TCCTCTTTTACTAGATAAATTGTAGAT 15 57 1 CTAGTAAATT 0.915344 -17 GTTAGAACACCTAGATTGATTATGATGTTAC 20 92 0 CTAGTTGATT 0.863806 -138 GCCAAATTTTCTAAATTAGTTGAGATCGGAT 22 106 1 CTAATTAGTT 0.743398 -143 CGTTCTCTGCCTAATTTAATTGGGCAGAGAA 23 49 1 CTAATTAATT 0.870762 -59 AAGAGCGAACCTAGCTATATTTA 25 3 0 CTAGTATATT 0.773594 -120 AAATATATTTCTAGGTAAATTTGCCTTATGT 30 145 1 CTAGTAAATT 0.915344 -52 **** ****** Masking position 6 Map Score: 2.09016 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 50 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049