AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00290_hinf_reg_100.orf -o00290_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: HI0962 28 isoleucyl-tRNA synthetase (isoleucine--tRNA ligase) (ileRS) HI0989 23 3-isopropylmalate dehydratase small subunit (leuD) Input sequences: #1 HI0682 300 ketol-acid reductoisomerase (ilvC) #2 HI0737 247 acetohydroxy acid synthase II, putative #3 HI0738 71 dihydroxyacid dehydratase (ilvD) #4 HI0921 248 leucyl-tRNA synthetase (leuS) #5 HI0963 34 riboflavin kinase / FMN adenylyltransferase (ribF) #6 HI0964 300 virulence factor (mviN) #7 HI0986 300 2-isopropylmalate synthase (leuA) #8 HI0987 85 3-isopropylmalate dehydrogenase (beta-IPM dehydrogenase) (leuB) #9 HI0988 175 3-isopropylmalate dehydratase, alpha subunit (leuC) #10 HI1193 300 branched-chain-amino-acid transaminase (ilvE) #11 HI1233 299 pyruvate dehydrogenase, E1 component (aceE) #12 HI1394 221 conserved hypothetical protein #13 HI1585 266 acetolactate synthase III large subunit (ilvI) Motif number 1 AAATAAGCCAAAAGAGCGGTAAAAATTCAC 2 74 1 AAAGAGCGGT 0.995455 -174 AAAACGAAAAAAAGTGCGGTGAAAATTGGC 2 142 0 AAAGTGCGGT 0.998978 -106 AGAGAAATAAAAAGTGCGGTGGTTTTTTAG 4 137 0 AAAGTGCGGT 0.998978 -112 AAATGCTGCAAAAGTGCGGTTAAAATTTAA 4 220 1 AAAGTGCGGT 0.998978 -29 CGCAACTTATAAAGTGCGGGTTTAAAATTG 7 235 0 AAAGTGCGGG 0.994077 -66 TCCAAAAGTGCGGTGCGTTTTTCC 7 287 0 AAAGTGCGGT 0.998978 -14 TTTTACTTCAAAAGTGCGGTTAGTTTTTTT 8 51 0 AAAGTGCGGT 0.998978 -35 CAAAGTATTTAAAGTGCGGTTGAAAAACAC 9 111 1 AAAGTGCGGT 0.998978 -65 TTCGTTAAGGGAAGTGCGGTTAAAATTCGA 9 142 0 GAAGTGCGGT 0.994077 -34 TAATTATTTGAAAGTGCGGTAATTTTTTTG 11 106 0 AAAGTGCGGT 0.998978 -194 TTTGATCCTTAAAGAGCGGTTAGGTTTTAG 12 202 0 AAAGAGCGGT 0.995455 -20 CGTTTTTTTAAAAGTGCGGTGAATTTAAGG 13 239 1 AAAGTGCGGT 0.998978 -28 ********** Masking position 3 Map Score: 56.7141 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 2 TGCCGTTAAGAAAATTGAAACAAAGCAAAGAACA 1 34 1 AAAATTAAAA 0.822955 -267 AAACCACAACAAAAAAATATGCAAACACAACATC 1 241 1 AAAAAAACAA 0.825746 -60 ATCCTATGTAAAAAAATGAAAAGAGTTTCAATAT 2 16 1 AAAAAAAAGA 0.877525 -232 AAAGAGCGGTAAAAATTCACTAAATTTTTTAGGG 2 84 1 AAAAATAAAA 0.980743 -164 CTTGGAGAGAAAAAAACGAAAAAAAGTGCGGTGA 2 150 0 AAAAAAAAAA 0.973132 -98 CCCCAAAATAAAAACAACAGGAAACAAACACC 2 226 1 AAAACAAAAA 0.735338 -22 AATTTATTGTAAAAAACAACTAAAAAACCACCGC 4 118 1 AAAAAAAAAA 0.973132 -131 TTCCATTGACAAAAGTATAAAAAATCGGCATATT 6 53 0 AAAAGTAAAA 0.796206 -248 ATTCCGTGAAAAAAAACTGATAAAATCCGCCACA 6 174 0 AAAAAAGAAA 0.929365 -127 AAACAATACGAAACATAAATAAAAATCCTCTGTG 7 123 0 AAACATAAAA 0.915995 -178 GTTGTGGATAAAAAAACAGTCAGATGTAAATACC 7 201 1 AAAAAAGAGA 0.72244 -100 TTTTTATCTAAAAAATACAGGAAAAACGCACCGC 7 268 1 AAAAATAAAA 0.980743 -33 CAAAGAGGGGAAAAATACAAAAAAACTAACCGCA 8 33 1 AAAAATAAAA 0.980743 -53 TTTTGAAGTAAAAAATAGGAAAAATAAT 8 68 1 AAAAATGAAA 0.948722 -18 CCTTTTTGAAAAAAATCTGAAAAAACTTTAAAAC 11 19 1 AAAAATGAAA 0.948722 -281 TTGTTCGCTAAAATAACCAGTAAAATATTGCATT 11 65 0 AAATAAAAAA 0.774856 -235 TTTAGCGAACAAAAAAACACAAAAAAATTACCGC 11 87 1 AAAAAAAAAA 0.973132 -213 CTTTATCTCAAAAAATCTTCTAAAATTTACAAGA 11 184 1 AAAAATTAAA 0.741081 -116 TGCTTTTCACAAACATTTAACAAATCTTGTAAAT 11 208 0 AAACATAAAA 0.915995 -92 CAATATGACAAAACAAGAAATAAATTATCTAAAC 12 15 0 AAACAAAAAA 0.885771 -207 CTTTTAGTTGAAAAATCAATTCAAGCGCAATGCC 12 77 0 AAAAATACAA 0.869511 -145 CCAGCTTGGTAAAAATTCACTAAATTGAGTAATG 12 118 0 AAAAATAAAA 0.980743 -104 AAGCTGGTGTAAAAAAGTATTAAATCAATTGATA 12 145 1 AAAAAAAAAA 0.973132 -77 ATCTCATTCAAAAATTTGAATAAAAAATAATATT 13 18 1 AAAATTAAAA 0.822955 -249 ATAAAAATAAAAAAATGCGACAAAATGCCGCATT 13 67 0 AAAAATGAAA 0.948722 -200 TTATTGATGGAAAAATTTATAAAAAACTAAATTT 13 97 1 AAAAATAAAA 0.980743 -170 ATAAAAAACCAAATATAAATGAAAATTTAGTTTT 13 119 0 AAATATAAAA 0.828752 -148 AAAACAACAAAAAAATCAATTAAAAAAATATAAA 13 148 0 AAAAATAAAA 0.980743 -119 CGCACTTTTAAAAAAACGAACAGATTATGTCAAT 13 223 0 AAAAAAAAGA 0.877525 -44 ****** * *** Masking position 3 Map Score: 53.7482 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 232 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 3 AAAATCCTATAATCAAACCACAACAAAAAAATA 1 227 1 AAAACCACAA 0.657736 -74 AATTTAGTGAATTTTTACCGCTCTTTTGGCTTA 2 77 0 ATTACCGCTC 0.821991 -171 AAATAAGCCAATTTTCACCGCACTTTTTTTCGT 2 136 1 ATCACCGCAC 0.988673 -112 AAACAACTAAAAAACCACCGCACTTTTTATTTC 4 131 1 AACACCGCAC 0.993649 -118 ATCACCTTAAATTTTAACCGCACTTTTGCAGCA 4 223 0 ATAACCGCAC 0.987724 -26 AAAACTGATAAAATCCGCCACACATCGTTTGTG 6 163 0 AACGCCACAC 0.904367 -138 TTTTATCCACAACTTAGCCGCACACAAAATGTG 7 181 0 AAAGCCGCAC 0.983864 -120 AATACCCAATTTTAAACCCGCACTTTATAAGTT 7 229 1 TTACCCGCAC 0.778944 -72 TTTTTTAGATAAAAAACCCGCAACTTATAAAGT 7 250 0 AAACCCGCAA 0.795987 -51 AATACAGGAAAAACGCACCGCACTTTTGGA 7 281 1 AACACCGCAC 0.993648 -20 AAATACAAAAAAACTAACCGCACTTTTGAAGTA 8 45 1 AAAACCGCAC 0.993114 -41 TTCGATGTGTTTTTCAACCGCACTTTAAATACT 9 114 0 TTAACCGCAC 0.923895 -62 AACACATCGAATTTTAACCGCACTTCCCTTAAC 9 136 1 ATAACCGCAC 0.987724 -40 TCGGGATGAAAAAAACGCCACTCAATGAGAGCA 10 112 0 AACGCCACTC 0.686262 -189 AAAACACAAAAAAATTACCGCACTTTCAAATAA 11 100 1 AATACCGCAC 0.972813 -200 AACTTTCTAAAACCTAACCGCTCTTTAAGGATC 12 196 1 AAAACCGCTC 0.970894 -26 TTCACTCCTTAAATTCACCGCACTTTTAAAAAA 13 242 0 AACACCGCAC 0.993649 -25 ** ******** Masking position 8 Map Score: 34.3698 Number of sites scoring better than the average of aligned sites = 1233 Number in coding regions = 825 Number in noncoding regions = 408 Number of orfs with sites within 600 bp upstream = 288 Fraction of orfs with sites within 600 bp upstream = 0.0462576 Motif number 4 ATGCCAATTCACAAAAAAAAATAATTGCACAA 1 151 1 AAAAAAAAAT 0.933725 -150 ACTTTACGCAACAACAAAAAATCCTATAATCA 1 210 1 AAAAAAAAAT 0.933725 -91 TAATCAAACCACAACAAAAAAATATGCAAACA 1 236 1 AAAAAAAAAA 0.883415 -65 TCCTATGTAAAAAAATGAAAAGAGTTTCAATA 2 17 1 AAATGAAAAG 0.594641 -231 GAAGAACAGGAATATTCAAAATAAGCCAATTT 2 118 1 ATATCAAAAT 0.734476 -130 GAGGTCTCTCAATAATAAAAATA 4 2 0 ATATAAAAAT 0.886535 -247 CTGTTCTGCAAAAATTGAAAATTTATTGTAAA 4 99 1 AAATGAAAAT 0.876643 -150 ATTGTAAAAAACAACTAAAAAACCACCGCACT 4 123 1 AAATAAAAAA 0.897077 -126 TAATAGGGAGAGAAATAAAAAGTGCGGTGGTT 4 143 0 AAATAAAAAG 0.769861 -106 CAGCATTTTGACAATAGAAAATGTGGCATAGA 4 196 0 AAAAGAAAAT 0.860689 -53 CATTGACAAAAGTATAAAAAATCGGCATATTG 6 52 0 ATAAAAAAAT 0.871673 -249 GAATATAGCGTAAAAACAAAATTTCTATACAA 6 204 1 TAAACAAAAT 0.585185 -97 TTAAAAGTCGTTTACTCAAAATATTCTTCTCT 6 256 0 TTATCAAAAT 0.438944 -45 TTTGGCATTTTATATTAAAAATAAACCTACTT 7 43 0 TTATAAAAAT 0.688455 -258 AATACGAAACATAAATAAAAATCCTCTGTGTA 7 121 0 AAATAAAAAT 0.941879 -180 AGAGGGGAAAAATACAAAAAAACTAACCGCAC 8 36 1 ATAAAAAAAA 0.7851 -50 ACCGCACTTTTGAAGTAAAAAATAGGAAAAAT 8 61 1 TAATAAAAAA 0.711415 -25 TCCCTTAACGAATAGAGAAAAATATT 9 160 1 ATAAGAAAAA 0.615691 -16 AGCGAACAAAAAAACACAAAAAAATTACCGCA 11 90 1 AAAACAAAAA 0.728455 -210 ACAATATGACAAAACAAGAAATAAATTATCTA 12 18 0 AAAAAGAAAT 0.500404 -204 CAGAGTTATCATAAATAAAAATTTCATCACAA 12 46 0 AAATAAAAAT 0.941879 -176 TTCAAAAATTTGAATAAAAAATAATATTTTTA 13 24 1 TAAAAAAAAT 0.799387 -243 CATTTTATAAAATAGTAAAAATATTATTTTTT 13 39 0 ATATAAAAAT 0.886535 -228 TTCCATCAATAAAAATAAAAAAATGCGACAAA 13 77 0 AAATAAAAAA 0.897077 -190 AAAACCAAATATAAATGAAAATTTAGTTTTTT 13 117 0 AAATGAAAAT 0.876643 -150 AACAAAAAAATCAATTAAAAAAATATAAAAAA 13 145 0 TAATAAAAAA 0.711415 -122 AGCCACTAAAACAACAAAAAAATCAATTAAAA 13 157 0 AAAAAAAAAA 0.883415 -110 CATAATACAAAGTAAAAAAAATTTGTCTAGCC 13 185 0 ATAAAAAAAT 0.871673 -82 * ** ******* Masking position 4 Map Score: 32.1156 Number of sites scoring better than the average of aligned sites = 822 Number in coding regions = 546 Number in noncoding regions = 276 Number of orfs with sites within 600 bp upstream = 210 Fraction of orfs with sites within 600 bp upstream = 0.0337295 Motif number 5 GTAAAAATTCACTAAATTTTTTAGGGGAAGA 2 92 1 ATAAATTTTT 0.765241 -156 ATTCAAAATAAGCCAATTTTCACCGCACTTT 2 131 1 ACCAATTTTC 0.888711 -117 TCAGCATTGTAGCGAAATTTCGAGTCATTGG 2 189 0 ACGAAATTTC 0.896567 -59 ACAAACGAACCCTAAATTTTACTCGGAGAGA 3 45 1 CTAAATTTTA 0.7121 -27 TATAGTTTACCACCAAATTTATAGAGGTCTC 4 26 0 CCCAAATTTA 0.611901 -223 TGTTTTTTACAATAAATTTTCAATTTTTGCA 4 105 0 ATAAATTTTC 0.902005 -144 AAAATCACCTTAAATTTTAACCGCACTTT 4 230 0 CTAAATTTTA 0.7121 -19 TCCTAAAATTTCTGTTGATTGA 6 2 1 CTAAAATTTC 0.836915 -299 CCGAAATCAACACAAATTTTCCATTGACAAA 6 74 0 CCAAATTTTC 0.891915 -227 ATAGCGTAAAAACAAAATTTCTATACAATTA 6 208 1 ACAAAATTTC 0.888772 -93 TCTTCTCTACCCTAAAATTTTTGCCTAATTG 6 233 0 CTAAAATTTT 0.645056 -68 AGATGTAAATACCCAATTTTAAACCCGCACT 7 222 1 ACCAATTTTA 0.738767 -79 TGAAAAACACATCGAATTTTAACCGCACTTC 9 131 1 ACGAATTTTA 0.806871 -45 AAAAAGGAATAATGAAATTTTGGAAACAGGG 10 174 0 ATGAAATTTT 0.72208 -127 GTGTAGATTAAGCGAAATTTCATTCAAAAAA 10 262 1 ACGAAATTTC 0.896567 -39 AGATAAAGATAGTGAATTTTCATCAAATCAT 11 161 0 ATGAATTTTC 0.908968 -139 TACTCAATTTAGTGAATTTTTACCAAGCTGG 12 121 1 ATGAATTTTT 0.779547 -101 ATTATTTTTTATTCAAATTTTTGAATGAGAT 13 18 0 ATCAAATTTT 0.637509 -249 TTTATAAAAAACTAAATTTTCATTTATATTT 13 112 1 ATAAATTTTC 0.902005 -155 * ********* Masking position 8 Map Score: 14.4326 Number of sites scoring better than the average of aligned sites = 406 Number in coding regions = 326 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 6 TTAACGGCAATTTGCTGAACTCGCTACGCTCA 1 11 0 TTTGCTGATC 0.716213 -290 ATTTCGCTACAATGCTGAACTTATCCCCAAAA 2 202 1 AATGCTGATT 0.940229 -46 CAATATAACTTATGATATAGTTTACCACCAAA 4 40 0 TATGATAATT 0.419251 -209 TACGGTATTCTATGCCACATTTTCTATTGTCA 4 188 1 TATGCCAATT 0.897184 -61 TAACCGCACTTTTGCAGCATTTTGACAATAGA 4 210 0 TTTGCAGATT 0.638757 -39 TTCTCGCTATAATGCCGAAATTCTCTTATTTT 5 12 1 AATGCCGATT 0.966833 -23 AGGGCATCAATATGCCGATTTTTTATACTTTT 6 45 1 TATGCCGTTT 0.742886 -256 AACTAACAACAATGCTAGATTTTAAAAGTCGT 6 277 0 AATGCTAATT 0.884614 -24 ACGATATAGTTATGCTAAAATCGGGATGAAAA 10 133 0 TATGCTAATC 0.778476 -168 AAATTCTCGAAATGATGCAATTTTTAGCCAAC 10 206 0 AATGATGATT 0.707521 -95 AGCCCGATGGAATGCAATATTTTACTGGTTAT 11 55 1 AATGCAAATT 0.800912 -245 AAAAGCAAATATTGCCGTATTCGTGTTTAGCC 11 235 1 ATTGCCGATC 0.884611 -65 ATTCAAGCGCAATGCCAGAGTTATCATAAATA 12 61 0 AATGCCAATT 0.934388 -161 TAAATTGAGTAATGCAGTTATCTTTTAGTTGA 12 100 0 AATGCAGTTC 0.499327 -122 AATGCGACAAAATGCCGCATTTTATAAAATAG 13 56 0 AATGCCGATT 0.966935 -211 TATGTGAAACATTGACATAATCTGTTCGTTTT 13 213 1 ATTGACAATC 0.365019 -54 ******* * ** Masking position 3 Map Score: 10.1693 Number of sites scoring better than the average of aligned sites = 555 Number in coding regions = 496 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 7 ACGCAACAACAAAAAATCCTATAATCAAACC 1 215 1 AAAAAACCTA 0.881477 -86 AAATTATCCTATGTAAAAAAA 2 1 1 AAATTACCTA 0.472194 -247 ATCAGTCAATAAATAAGCCAAAAGAGCGGTA 2 64 1 AAATAACCAA 0.922666 -184 GGAATATTCAAAATAAGCCAATTTTCACCGC 2 126 1 AAATAACCAA 0.922666 -122 GCTTGGAGAGAAAAAAACGAAAAAAAGTGCG 2 154 0 AAAAAACGAA 0.860726 -94 AAAAAACAACTAAAAAACCACCGCACTTTTT 4 128 1 TAAAAACCAC 0.616632 -121 TATTCCGTGAAAAAAAACTGATAAAATCCGC 6 178 0 AAAAAACTGA 0.718081 -123 TTTATATTAAAAATAAACCTACTTACACTTC 7 36 0 AAATAACCTA 0.720627 -265 ATTTTTAATATAAAATGCCAAAAAATAGTTT 7 53 1 TAAAATCCAA 0.507157 -248 CAGTCAGATGTAAATACCCAATTTTAAACCC 7 217 1 TAAATACCAA 0.84028 -84 GGAAAAATACAAAAAAACTAACCGCACTTTT 8 41 1 AAAAAACTAA 0.916063 -45 GGGATATTTCTAAATAACTAAGGGTGGAGAT 9 64 0 TAAATACTAA 0.625341 -112 TCCTTTTTGAAAAAAATCTGAAAAAACTTTA 11 18 1 AAAAAACTGA 0.718081 -282 TTTGTTCGCTAAAATAACCAGTAAAATATTG 11 69 0 AAAATACCAG 0.558527 -231 TTAGCGAACAAAAAAACACAAAAAAATTACC 11 88 1 AAAAAAACAA 0.602922 -212 AACAAGAAATAAATTATCTAAACTTAT 12 7 0 AAATTACTAA 0.567631 -215 GAAAAATTTATAAAAAACTAAATTTTCATTT 13 106 1 TAAAAACTAA 0.827954 -161 TAAAAAAATATAAAAAACCAAATATAAATGA 13 131 0 TAAAAACCAA 0.938152 -136 CTAAAACAACAAAAAAATCAATTAAAAAAAT 13 153 0 AAAAAATCAA 0.602922 -114 CCGCACTTTTAAAAAAACGAACAGATTATGT 13 227 0 AAAAAACGAA 0.860726 -40 ****** **** Masking position 3 Map Score: 11.8268 Number of sites scoring better than the average of aligned sites = 842 Number in coding regions = 695 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 8 GATTTGTGCAATTATTTTTTTTTGTGAATT 1 156 0 ATTATTTTTT 0.922708 -145 GTTGTGTTTGCATATTTTTTTGTTGTGGTT 1 242 0 CATATTTTTT 0.731576 -59 GAATATTTTATCAATTAACGA 3 2 1 AATATTTTAT 0.833983 -70 TTCTCTCCCTATTAATTTTTGCCATTTTAC 4 161 1 ATTAATTTTT 0.540119 -88 TGGCTGTCAAACTATTTTTTGGCATTTTAT 7 62 0 ACTATTTTTT 0.889302 -239 ATTATTTTTCCTATTTTTTA 8 76 0 ATTATTTTTC 0.834649 -10 AATATTTTTCTCTATTCGTT 9 166 0 AATATTTTTC 0.887634 -10 CTTCCTTAATATTATTTTTTGAATGAAATT 10 277 0 ATTATTTTTT 0.922708 -24 GATGGAATGCAATATTTTACTGGTTATTTT 11 60 1 AATATTTTAC 0.679906 -240 TAAATTTTAGAAGATTTTTTGAGATAAAGA 11 183 0 AAGATTTTTT 0.717102 -117 CAATTGATTTAATACTTTTTTACACCAGCT 12 146 0 AATACTTTTT 0.731564 -76 TAGTAAAAATATTATTTTTTATTCAAATTT 13 29 0 ATTATTTTTT 0.922708 -238 TAATATTTTTACTATTTTATAAAATGCGGC 13 45 1 ACTATTTTAT 0.683559 -222 TTTGGTTTTTTATATTTTTTTAATTGATTT 13 140 1 TATATTTTTT 0.647749 -127 TGGCTAGACAAATTTTTTTTACTTTGTATT 13 184 1 AATTTTTTTT 0.631048 -83 ********** Masking position 6 Map Score: 8.78405 Number of sites scoring better than the average of aligned sites = 280 Number in coding regions = 193 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 9 TTAAGAAAATTGAAACAAAGCAAAGAACAG 1 39 1 TGAAACAAAG 0.93796 -262 TTTACTCGTGTAAAAGAAAGTAGGCAAAGA 1 90 0 TAAAAGAAAG 0.955774 -211 TTTACACGAGTAAAAGAAAGTAGGTCGTTC 1 106 1 TAAAAGAAAG 0.955774 -195 CAGAACAGATTAGAACAAAGGAATTCATAG 4 77 0 TAGAACAAAG 0.93796 -172 GAAAAAACTTTAAAACAAAGCCCGATGGAA 11 37 1 TAAAACAAAG 0.976386 -263 ATGTTTCACATAATACAAAGTAAAAAAAAT 13 195 0 TAATACAAAG 0.910719 -72 ********** Masking position 5 Map Score: 3.83078 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 18 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 10 AATCATCAGTCAATAAATAAGCCAAAAGAG 2 60 1 CAATAAATAA 0.729299 -188 ATAAAAACAACAGGAAACAAACACC 2 233 1 CAGGAAACAA 0.949124 -15 GTTGAGAGATAAAGAAACAATACGAAACAT 7 141 0 AAAGAAACAA 0.72901 -160 TAATAATATACAGGAAGTAAATGAGTAACA 10 63 0 CAGGAAGTAA 0.949124 -238 GGAAACAGGGCAGGAAATAACGATATAGTT 10 154 0 CAGGAAATAA 0.970541 -147 AAATTTCATTCAAAAAATAATATTAAGGAA 10 276 1 CAAAAAATAA 0.729299 -25 AAATAATATTAAGGAAGTAAA 10 290 1 AAGGAAGTAA 0.810139 -11 TATGACAAAACAAGAAATAAATTATCTAAA 12 16 0 CAAGAAATAA 0.954066 -206 ********** Masking position 5 Map Score: 2.91579 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 66 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 11 TTGAAACAAAGCAAAGAACAGCGATTTAAC 1 48 1 GCAAAGAACA 0.819968 -253 AAGAAAGTAGGCAAAGAAAACACGCCCCAG 1 77 0 GCAAAGAAAA 0.936717 -224 AAAAAAATATGCAAACACAACATCATACAA 1 251 1 GCAAACACAA 0.976938 -50 TTCAATATGGGCTCACACAAACGATGTGTG 6 148 1 GCTCACACAA 0.875504 -153 CAACTTAGCCGCACACAAAATGTGAGAGCA 7 175 0 GCACACAAAA 0.959358 -126 CGAACTATATGCAAACACAACATCATAC 10 9 0 GCAAACACAA 0.976938 -292 GGTTATTTTAGCGAACAAAAAAACACAAAA 11 81 1 GCGAACAAAA 0.927675 -219 ********** Masking position 5 Map Score: 3.47555 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 45 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 GCGTAGCGAGTTCAGCAAATTGCCGTTAAG 1 14 1 TTCAGCAAAT 0.915306 -287 ATGATTAGATTTCATTATATTGAAACTCTT 2 36 0 TTCATTATAT 0.649365 -212 GCGGTAAAAATTCACTAAATTTTTTAGGGG 2 89 1 TTCACTAAAT 0.933453 -159 CTACTTACACTTCATCAAATATACATTTAA 7 19 0 TTCATCAAAT 0.948518 -282 AGAGCAGCGTTTAACCAAATCGGTTTAATA 10 88 0 TTAACCAAAT 0.789817 -213 ATAGTGAATTTTCATCAAATCATCATATCA 11 154 0 TTCATCAAAT 0.948518 -146 TTGGTAAAAATTCACTAAATTGAGTAATGC 12 117 0 TTCACTAAAT 0.933453 -105 ********** Masking position 4 Map Score: 3.33813 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 91 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 13 TAAATAAAAATCCTCTGTGTAAAACGTTTT 7 112 0 TCCTCTGTGT 0.879177 -189 TTTATCGAGTTCCCCTTTTTAGCAAAGAGG 8 11 1 TCCCCTTTTT 0.908901 -75 TTTGTATTTTTCCCCTCTTTGCTAAAAAGG 8 24 0 TCCCCTCTTT 0.975394 -62 TACTTGCCTTCCTCCGTTTACGGGGGAAG 9 10 1 TCCTCCGTTT 0.928868 -166 GGGTGGAGATTGCCCCCTTCCGCCCTTCAG 9 44 0 TGCCCCCTTC 0.861404 -132 AAATACTTTGTCCCCCCTGTTTATTGGGGA 9 91 0 TCCCCCCTGT 0.96989 -85 CGTTATTTCCTGCCCTGTTTCCAAAATTTC 10 162 1 TGCCCTGTTT 0.943588 -139 ********** Masking position 8 Map Score: 0.915014 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 56 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 14 TGTTTTCTTTGCCTACTTTCTTTTACACGA 1 85 1 GCCTACTTTC 0.97297 -216 TCGATGAACGACCTACTTTCTTTTACTCGT 1 111 0 ACCTACTTTC 0.983965 -190 AAATAACGATACTTACTTTCGGTTGTGTCT 6 107 0 ACTTACTTTC 0.939192 -194 TTAAAAATAAACCTACTTACACTTCATCAA 7 31 0 ACCTACTTAC 0.960453 -270 ********** Masking position 5 Map Score: 0.798641 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 3 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 15 AAAAAAATGAAAAGAGTTTCAATATAATGAAATCT 2 25 1 AAGTTTAAAT 0.930719 -223 TTATTTTTACAAGCTCTTTCAATATGGGCTCACAC 6 131 1 AACTTTAAAT 0.930719 -170 ATTTTGAGTAAACGACTTTTAAAATCTAGCATTGT 6 266 1 AAGTTTAAAT 0.930719 -35 CCTCTGTGTAAAACGTTTTCCATATTACGAATAAA 7 96 0 AACTTTCAAT 0.955174 -205 CGTTTAACCAAATCGGTTTAATAATATACAGGAAG 10 76 0 AACTTTATAT 0.706526 -225 GCTTTGTTTTAAAGTTTTTTCAGATTTTTTTCAAA 11 23 0 AAGTTTCAAT 0.955174 -277 TGCTTTTCACAAACATTTAACAAATCTTGTAAATT 11 207 0 AACTTACAAT 0.79247 -93 TAGGTTTTAGAAAGTTTTTACAAATCCTAGATTTA 12 177 0 AAGTTTCAAT 0.955174 -45 ** * *** ** ** Masking position 2 Map Score: 1.52789 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 84 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542