AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00290_hinf_reg_300.orf -o00290_hinf_300.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 HI1396 84 H. influenzae predicted coding region HI1396 #14 HI1397 234 DNA polymerase III, chi subunit (holC) #15 HI1585 266 acetolactate synthase III large subunit (ilvI) #16 HI1586 300 conserved hypothetical integral membrane protein Motif number 1 GTGAATTTTTACCGCTCTTTTGGCTTATTT 2 74 0 ACCGCTCTTT 0.994896 -174 GCCAATTTTCACCGCACTTTTTTTCGTTTT 2 142 1 ACCGCACTTT 0.998852 -106 CTAAAAAACCACCGCACTTTTTATTTCTCT 4 137 1 ACCGCACTTT 0.998852 -112 TTAAATTTTAACCGCACTTTTGCAGCATTT 4 220 0 ACCGCACTTT 0.998852 -29 CAATTTTAAACCCGCACTTTATAAGTTGCG 7 235 1 CCCGCACTTT 0.992766 -66 GGAAAAACGCACCGCACTTTTGGA 7 287 1 ACCGCACTTT 0.998852 -14 AAAAAAACTAACCGCACTTTTGAAGTAAAA 8 51 1 ACCGCACTTT 0.998852 -35 GTGTTTTTCAACCGCACTTTAAATACTTTG 9 111 0 ACCGCACTTT 0.998852 -65 TCGAATTTTAACCGCACTTCCCTTAACGAA 9 142 1 ACCGCACTTC 0.992766 -34 CAAAAAAATTACCGCACTTTCAAATAATTA 11 106 1 ACCGCACTTT 0.998852 -194 CTAAAACCTAACCGCTCTTTAAGGATCAAA 12 202 1 ACCGCTCTTT 0.994896 -20 CTGAAAATCCACCGCGCTTTTATGATCTAT 14 114 0 ACCGCGCTTT 0.993915 -121 CCTTAAATTCACCGCACTTTTAAAAAAACG 15 239 0 ACCGCACTTT 0.998852 -28 ********** Masking position 8 Map Score: 58.3059 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 AAACCACAACAAAAAAATATGCAAACACAACATCA 1 241 1 AAAAAAAAAA 0.961937 -60 TATCCTATGTAAAAAAATGAAAAGAGTTTCAATAT 2 15 1 AAAAAAAAGA 0.793119 -233 ATCATCAGTCAATAAATAAGCCAAAAGAGCGGTAA 2 61 1 AATAAATAAA 0.903051 -187 AAAAGAGCGGTAAAAATTCACTAAATTTTTTAGGG 2 83 1 TAAAAATAAA 0.935114 -165 GCTTGGAGAGAAAAAAACGAAAAAAAGTGCGGTGA 2 150 0 AAAAAAAAAA 0.961937 -98 AAATTTATTGTAAAAAACAACTAAAAAACCACCGC 4 117 1 TAAAAAAAAA 0.91571 -132 TATTCCGTGAAAAAAAACTGATAAAATCCGCCACA 6 174 0 AAAAAAAAAA 0.961937 -127 AAAATTTCTATACAATTAGGCAAAAATTTTAGGGT 6 221 1 TACAATTAAA 0.430096 -80 TTATTTTTAATATAAAATGCCAAAAAATAGTTTGA 7 51 1 TATAAAAAAA 0.751145 -250 AGTTGTGGATAAAAAAACAGTCAGATGTAAATACC 7 200 1 AAAAAAAAGA 0.793119 -101 TTTTTTATCTAAAAAATACAGGAAAAACGCACCGC 7 267 1 AAAAAATAAA 0.971036 -34 CAAAGAGGGGAAAAATACAAAAAAACTAACCGCAC 8 33 1 AAAAATAAAA 0.835881 -53 CTTTTGAAGTAAAAAATAGGAAAAATAAT 8 67 1 AAAAAATAAA 0.971036 -19 TGATTTAAATAATAAATTCTCGAAATGATGCAATT 10 216 0 AATAAATAAA 0.903051 -85 AATTTCATTCAAAAAATAATATTAAGGAAGTAAA 10 277 1 AAAAAATTAA 0.68684 -24 TCCTTTTTGAAAAAAATCTGAAAAAACTTTAAAAC 11 18 1 AAAAAATAAA 0.971036 -282 TTTAGCGAACAAAAAAACACAAAAAAATTACCGCA 11 87 1 AAAAAAAAAA 0.961937 -213 CTTTGCCATAAATAATTATTTGAAAGTGCGGTAAT 11 113 0 AATAATTAAA 0.652443 -187 TCTTTATCTCAAAAAATCTTCTAAAATTTACAAGA 11 183 1 AAAAAATAAA 0.971036 -117 ACAAACATTTAACAAATCTTGTAAATTTTAGAAGA 11 199 0 AACAAATAAA 0.897026 -101 CAAAACAAGAAATAAATTATCTAAACTTAT 12 6 0 AATAAATAAA 0.903051 -216 ACCAGCTTGGTAAAAATTCACTAAATTGAGTAATG 12 118 0 TAAAAATAAA 0.935114 -104 CAAGCTGGTGTAAAAAAGTATTAAATCAATTGATA 12 144 1 TAAAAAAAAA 0.915707 -78 CTAGGATTTGTAAAAACTTTCTAAAACCTAACCGC 12 182 1 TAAAAACAAA 0.717152 -40 AGTGGAACGTAACAAAAACGTTAAAAATCAGTTTT 14 74 1 AACAAAAAAA 0.86784 -161 TATGCATTATTACAAATGTCTGAAAATCCACCGCG 14 128 0 TACAAATAAA 0.789239 -107 AATTTTAACGAAAAAACCCTAAAAAATAAATAATT 14 166 0 AAAAAACAAA 0.855034 -69 AATCTTACCCTATAAAAAGGGTAAAATTTTAACGA 14 190 0 TATAAAAAAA 0.751145 -45 GATCTCATTCAAAAATTTGAATAAAAAATAATATT 15 17 1 AAAAATTAAA 0.871076 -250 TGCCGCATTTTATAAAATAGTAAAAATATTATTTT 15 41 0 TATAAAAAAA 0.751145 -226 AATAAAAATAAAAAAATGCGACAAAATGCCGCATT 15 67 0 AAAAAATAAA 0.971036 -200 TTATTGATGGAAAAATTTATAAAAAACTAAATTTT 15 97 1 AAAAATTAAA 0.871076 -170 TAAAACAACAAAAAAATCAATTAAAAAAATATAAA 15 148 0 AAAAAATAAA 0.971036 -119 CCGCACTTTTAAAAAAACGAACAGATTATGTCAAT 15 223 0 AAAAAAAAGA 0.793119 -44 AAACTTTAATAAAAATATAAAGAAAATAAACACAA 16 21 0 AAAAATAAAA 0.835881 -280 ACAGATTTTATAAAAATTTTATAAACTTTAATAAA 16 43 0 TAAAAATAAA 0.935114 -258 ATCCACTCTGAAAAAATACTTATAATAATTGCGCC 16 128 0 AAAAAATTAA 0.68684 -173 ******* *** Masking position 5 Map Score: 62.4008 Number of sites scoring better than the average of aligned sites = 779 Number in coding regions = 525 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 3 TAAGCCAAAAGAGCGGTAAAAATTCACTAAATTT 2 77 1 GAGCGGTATT 0.979397 -171 ACGAAAAAAAGTGCGGTGAAAATTGGCTTATTTT 2 135 0 GTGCGGTATT 0.991283 -113 GAAATAAAAAGTGCGGTGGTTTTTTAGTTGTTTT 4 130 0 GTGCGGTTTT 0.99666 -119 TGCTGCAAAAGTGCGGTTAAAATTTAAGGTGATT 4 223 1 GTGCGGTATT 0.991283 -26 CACAAACGATGTGTGGCGGATTTTATCAGTTTTT 6 163 1 GTGTGGCTTT 0.931237 -138 CACATTTTGTGTGCGGCTAAGTTGTGGATAAAAA 7 181 1 GTGCGGCTTG 0.948465 -120 TCCAAAAGTGCGGTGCGTTTTTCCTGTATTT 7 280 0 GTGCGGTTTT 0.99666 -21 TACTTCAAAAGTGCGGTTAGTTTTTTTGTATTTT 8 44 0 GTGCGGTTTT 0.99666 -42 GTTAAGGGAAGTGCGGTTAAAATTCGATGTGTTT 9 135 0 GTGCGGTATT 0.991283 -41 TGCTCTCATTGAGTGGCGTTTTTTTCATCCCGAT 10 112 1 GAGTGGCTTT 0.849881 -189 TTATTTGAAAGTGCGGTAATTTTTTTGTGTTTTT 11 99 0 GTGCGGTTTT 0.99666 -201 GATCCTTAAAGAGCGGTTAGGTTTTAGAAAGTTT 12 195 0 GAGCGGTTTT 0.992047 -27 TTTGAGTATTGAGCAGTAGGTTTTGAATTAATTA 13 48 1 GAGCAGTTTT 0.875905 -37 GATCATAAAAGCGCGGTGGATTTTCAGACATTTG 14 117 1 GCGCGGTTTT 0.982516 -118 TTTTTTAAAAGTGCGGTGAATTTAAGGAGTGAAA 15 242 1 GTGCGGTTTA 0.967072 -25 ******* *** Masking position 13 Map Score: 37.265 Number of sites scoring better than the average of aligned sites = 859 Number in coding regions = 556 Number in noncoding regions = 303 Number of orfs with sites within 600 bp upstream = 227 Fraction of orfs with sites within 600 bp upstream = 0.03646 Motif number 4 TAAGCCAAAAGAGCGGTAAAAATTCACTAA 2 77 1 GAGCGGTAAA 0.909003 -171 ACGAAAAAAAGTGCGGTGAAAATTGGCTTA 2 139 0 GTGCGGTGAA 0.993919 -109 GAAATAAAAAGTGCGGTGGTTTTTTAGTTG 4 134 0 GTGCGGTGGT 0.962119 -115 TGCTGCAAAAGTGCGGTTAAAATTTAAGGT 4 223 1 GTGCGGTTAA 0.991856 -26 CACATTTTGTGTGCGGCTAAGTTGTGGATA 7 181 1 GTGCGGCTAA 0.950517 -120 TCCAAAAGTGCGGTGCGTTTTTCCTGT 7 284 0 GTGCGGTGCG 0.955253 -17 TACTTCAAAAGTGCGGTTAGTTTTTTTGTA 8 48 0 GTGCGGTTAG 0.98706 -38 AGTATTTAAAGTGCGGTTGAAAAACACATC 9 114 1 GTGCGGTTGA 0.985525 -62 GTTAAGGGAAGTGCGGTTAAAATTCGATGT 9 139 0 GTGCGGTTAA 0.991856 -37 TTATTTGAAAGTGCGGTAATTTTTTTGTGT 11 103 0 GTGCGGTAAT 0.925337 -197 GATCCTTAAAGAGCGGTTAGGTTTTAGAAA 12 199 0 GAGCGGTTAG 0.944722 -23 GATCATAAAAGCGCGGTGGATTTTCAGACA 14 117 1 GCGCGGTGGA 0.945075 -118 TTTTTTAAAAGTGCGGTGAATTTAAGGAGT 15 242 1 GTGCGGTGAA 0.993919 -25 ********** Masking position 4 Map Score: 28.3159 Number of sites scoring better than the average of aligned sites = 681 Number in coding regions = 418 Number in noncoding regions = 263 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 5 ATGCCAATTCACAAAAAAAAATAATTGCACAA 1 151 1 AAAAAAAAAT 0.886915 -150 ACTTTACGCAACAACAAAAAATCCTATAATCA 1 210 1 AAAAAAAAAT 0.886915 -91 GAAGAACAGGAATATTCAAAATAAGCCAATTT 2 118 1 ATATCAAAAT 0.891126 -130 GAGGTCTCTCAATAATAAAAATA 4 2 0 ATATAAAAAT 0.92788 -247 CTGTTCTGCAAAAATTGAAAATTTATTGTAAA 4 99 1 AAATGAAAAT 0.819596 -150 CAGCATTTTGACAATAGAAAATGTGGCATAGA 4 196 0 AAAAGAAAAT 0.754111 -53 CATTGACAAAAGTATAAAAAATCGGCATATTG 6 52 0 ATAAAAAAAT 0.89675 -249 GAATATAGCGTAAAAACAAAATTTCTATACAA 6 204 1 TAAACAAAAT 0.618972 -97 TTAAAAGTCGTTTACTCAAAATATTCTTCTCT 6 256 0 TTATCAAAAT 0.72714 -45 TTTGGCATTTTATATTAAAAATAAACCTACTT 7 43 0 TTATAAAAAT 0.807274 -258 AATACGAAACATAAATAAAAATCCTCTGTGTA 7 121 0 AAATAAAAAT 0.920748 -180 TGAAGTAAAAAATAGGAAAAATAAT 8 71 1 ATAGAAAAAT 0.669886 -15 CAGAGTTATCATAAATAAAAATTTCATCACAA 12 46 0 AAATAAAAAT 0.920748 -176 CCTACTGCTCAATACTCAAAATTGAAAGCGTT 13 36 0 ATATCAAAAT 0.891131 -49 TTCAAAAATTTGAATAAAAAATAATATTTTTA 15 24 1 TAAAAAAAAT 0.718578 -243 CATTTTATAAAATAGTAAAAATATTATTTTTT 15 39 0 ATATAAAAAT 0.92788 -228 AAATTTTTCCATCAATAAAAATAAAAAAATGC 15 83 0 ACATAAAAAT 0.816815 -184 AAAACCAAATATAAATGAAAATTTAGTTTTTT 15 117 0 AAATGAAAAT 0.819596 -150 CATAATACAAAGTAAAAAAAATTTGTCTAGCC 15 185 0 ATAAAAAAAT 0.896751 -82 TTTTATAAACTTTAATAAAAATATAAAGAAAA 16 30 0 TTATAAAAAT 0.807274 -271 ATTACCGTAAAACAAACAAAATGCCAACAGAT 16 72 0 ACAACAAAAT 0.65695 -229 * ** ******* Masking position 12 Map Score: 21.1978 Number of sites scoring better than the average of aligned sites = 410 Number in coding regions = 281 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 6 AAATTGAAACAAAGCAAAGAACAGCGATTTAAC 1 45 1 AACAAAAACA 0.729386 -256 TAAAAGAAAGTAGGCAAAGAAAACACGCCCCAG 1 77 0 TACAAAAAAA 0.932552 -224 ACGATGCCAATTCACAAAAAAAAATAATTGCAC 1 148 1 TTCAAAAAAA 0.7276 -153 AATATCACTTTACGCAACAACAAAAAATCCTAT 1 204 1 TACAACACAA 0.745666 -97 CTATAATCAAACCACAACAAAAAAATATGCAAA 1 233 1 ACCAACAAAA 0.687458 -68 AACAAAAAAATATGCAAACACAACATCATACAA 1 248 1 TACAAAACAA 0.809041 -53 TGGAGAGAAAAAAACGAAAAAAAGTGCGGTGAA 2 149 0 AACGAAAAAA 0.729386 -99 ACTTATCCCCAAAATAAAAACAACAGGAAACAA 2 220 1 AATAAAACAA 0.723217 -28 TTTATTGTAAAAAACAACTAAAAAACCACCGCA 4 120 1 AACAACAAAA 0.96194 -129 AACAATACGAAACATAAATAAAAATCCTCTGTG 7 123 0 AATAAAAAAA 0.895037 -178 AGAGGGGAAAAATACAAAAAAACTAACCGCACT 8 36 1 AACAAAAAAC 0.736966 -50 TCCCGAACTATATGCAAACACAACATCATAC 10 9 0 TACAAAACAA 0.809041 -292 ATGCAATTTTTAGCCAACTAAAAAGGAATAATG 10 191 0 TACAACAAAA 0.905374 -110 AGCGAACAAAAAAACACAAAAAAATTACCGCAC 11 90 1 AACACAAAAA 0.729386 -210 TGCCAGAGTTATCATAAATAAAAATTTCATCAC 12 48 0 ATTAAAAAAA 0.622263 -174 TTGAATTGATTTTTCAACTAAAAGATAACTGCA 12 87 1 TTCAACAAAA 0.648924 -135 TTATGAGTGGAACGTAACAAAAACGTTAAAAAT 14 69 1 AATAACAAAA 0.855091 -166 AAAGGGTAAAATTTTAACGAAAAAACCCTAAAA 14 177 0 ATTAACAAAA 0.532703 -58 TTTTTCCATCAATAAAAATAAAAAAATGCGACA 15 79 0 AAAAAAAAAA 0.604451 -188 AAAATATAAAAAACCAAATATAAATGAAAATTT 15 125 0 AACAAAATAA 0.681993 -142 TCTAGCCACTAAAACAACAAAAAAATCAATTAA 15 159 0 AACAACAAAA 0.96194 -108 CACATAATACAAAGTAAAAAAAATTTGTCTAGC 15 186 0 AATAAAAAAA 0.895037 -81 AAAGAAAATAAACACAAAAAAATATAT 16 5 0 AACAAAAAAT 0.654026 -296 CTTTAATAAAAATATAAAGAAAATAAACACAAA 16 20 0 AATAAAAAAA 0.895037 -281 AGATTACCGTAAAACAAACAAAATGCCAACAGA 16 73 0 AACAAAAAAA 0.97335 -228 ATAGTTGCCGAAATCAAATAAAAGTCGTTTTGT 16 186 1 AACAAAAAAA 0.97335 -115 AGCACGCCACCAACCAAACAAAACGACTTTTAT 16 203 0 CACAAAAAAA 0.785975 -98 ** **** **** Masking position 10 Map Score: 24.5054 Number of sites scoring better than the average of aligned sites = 563 Number in coding regions = 425 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 7 ATCGCTGTTCTTTGCTTTGTTTCAATTTTCTTAACGGC 1 35 0 TTTGTTTATT 0.974324 -266 TTTGTTGTGGTTTGATTATAGGATTTTTTGTTGTTGCG 1 216 0 TTTGTTATTT 0.603872 -85 GTATAGAAATTTTGTTTTTACGCTATATTCCGTGAAAA 6 196 0 TTTGTTTTTT 0.946854 -105 AAAAGTGCGGTTAGTTTTTTTGTATTTTTCCCCTCTTT 8 34 0 TTAGTTTATT 0.910743 -52 GTTACTCAAGTTCGGTTTCCCGAACTATATGCAAACAC 10 21 0 TTCGTTTATT 0.85684 -280 TCCATCGGGCTTTGTTTTAAAGTTTTTTCAGATTTTTT 11 28 0 TTTGTTTTTT 0.946854 -272 TACGGCAATATTTGCTTTTCACAAACATTTAACAAATC 11 216 0 TTTGTTTACT 0.827954 -84 TTTTCCTTAATCTGTTTTGAGTGAATATTAGTTTAGAC 11 269 0 TCTGTTTATT 0.827954 -31 TAATTTATTTCTTGTTTTGTCATATTGTGATGAAATTT 12 22 1 CTTGTTTATT 0.837364 -200 AGATTTATCAATTGATTTAATACTTTTTTACACCAGCT 12 146 0 ATTGTTTTTT 0.619912 -76 TAAAGAGCGGTTAGGTTTTAGAAAGTTTTTACAAATCC 12 185 0 TTAGTTTATT 0.910743 -37 AAATGAAAATTTAGTTTTTTATAAATTTTTCCATCAAT 15 99 0 TTAGTTTATT 0.910743 -168 TTCATTTATATTTGGTTTTTTATATTTTTTTAATTGAT 15 130 1 TTTGTTTATT 0.974324 -137 ATATATTTTTTTGTGTTTATTTTCTTTATATTTTTAT 16 10 1 TTTGGTTTTT 0.693195 -291 TGGCATTTTGTTTGTTTTACGGTAATCTCCCCAATCAC 16 78 1 TTTGTTTATT 0.974324 -223 ACGACTTTTATTTGATTTCGGCAACTATTCCTTTCTTT 16 176 0 TTTGTTTATT 0.974324 -125 **** *** * * * Masking position 7 Map Score: 16.6247 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 111 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 8 TATTTTGGGGATAAGTTCAGCATTGTAGCGAAAT 2 202 0 AAATCGCATT 0.965427 -46 GTTTGTATGATTAATTTCTTCGTTAATTGATAAA 3 17 0 TAATCTCGTT 0.66538 -55 TCTCTCCGAGTAAAATTTAGGGTTCGTTTGTATG 3 42 0 TAATTGGGTT 0.56063 -30 GAAAATAAGAGAATTTCGGCATTATAGCGAGAA 5 12 0 AAATCGCATT 0.965427 -23 CGAAATCAACACAAATTTTCCATTGACAAAAGTA 6 70 0 AAATTCCATT 0.72354 -231 AAACGACTTTTAAAATCTAGCATTGTTGTTAGTT 6 275 1 TAATTGCATT 0.928135 -26 CGATTTTAGCATAACTATATCGTTATTTCCTGCC 10 142 1 AAATTTCGTT 0.692534 -159 TAGTTGGCTAAAAATTGCATCATTTCGAGAATTT 10 204 1 AAATCTCATT 0.860419 -97 AAATAACCAGTAAAATATTGCATTCCATCGGGCT 11 55 0 TAATTGCATT 0.928135 -245 AAAACACAAAAAAATTACCGCACTTTCAAATAAT 11 100 1 AAATCGCACT 0.814962 -200 TTTATTTATGATAACTCTGGCATTGCGCTTGAAT 12 59 1 AAATTGCATT 0.952856 -163 AAATCAATTGATAAATCTAGGATTTGTAAAAACT 12 166 1 AAATTGGATT 0.798208 -56 TACTATTTTATAAAATGCGGCATTTTGTCGCATT 15 54 1 TAATCGCATT 0.946931 -213 * ** * * ***** Masking position 4 Map Score: 7.04193 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 227 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 9 TACGATGCCAATTCACAAAAAAAAATAATT 1 147 1 ATTCACAAAA 0.952316 -154 AGCGGTAAAAATTCACTAAATTTTTTAGGG 2 88 1 ATTCACTAAA 0.750829 -160 TTCTTCGTTAATTGATAAAATATTC 3 6 0 ATTGATAAAA 0.535257 -66 TTGAAAATTTATTGTAAAAAACAACTAAAA 4 113 1 ATTGTAAAAA 0.467088 -136 CACATTTTCTATTGTCAAAATGCTGCAAAA 4 203 1 ATTGTCAAAA 0.828607 -46 CTGTTGATTGATAGACAAAATAAAGGGCAT 6 22 1 ATAGACAAAA 0.891633 -279 CAAATTTTCCATTGACAAAAGTATAAAAAA 6 63 0 ATTGACAAAA 0.941354 -238 GAGGGGAAAAATACAAAAAAACTAACCGCA 8 37 1 ATACAAAAAA 0.649855 -49 CCCTTAACGAATAGAGAAAAATATT 9 161 1 ATAGAGAAAA 0.701097 -15 TAAATAATAAATTCTCGAAATGATGCAATT 10 216 0 ATTCTCGAAA 0.432727 -85 GCGAAATTTCATTCAAAAAATAATATTAAG 10 273 1 ATTCAAAAAA 0.783584 -28 GCGAACAAAAAAACACAAAAAAATTACCGC 11 91 1 AAACACAAAA 0.688789 -209 CTTGGTAAAAATTCACTAAATTGAGTAATG 12 118 0 ATTCACTAAA 0.750829 -104 CTACTGCTCAATACTCAAAATTGAAAGCGT 13 37 0 ATACTCAAAA 0.7551 -48 ATAGGGTAAGATTGAGAAAATAACGGGGCT 14 212 1 ATTGAGAAAA 0.820657 -23 TATGTGAAACATTGACATAATCTGTTCGTT 15 213 1 ATTGACATAA 0.548484 -54 TAAAGAAAATAAACACAAAAAAATATAT 16 9 0 AAACACAAAA 0.688789 -292 CTCCATAGTTAATCAGAAAAACTATGACAG 16 250 0 AATCAGAAAA 0.551749 -51 ********** Masking position 9 Map Score: 10.4559 Number of sites scoring better than the average of aligned sites = 470 Number in coding regions = 381 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 10 TTCTTCGTTAATTGATAAAATATTC 3 6 0 ATTGATAAAA 0.598696 -66 CGGCTAAGTTGTGGATAAAAAAACAGTCAG 7 194 1 GTGGATAAAA 0.806107 -107 CCTGTATTTTTTAGATAAAAAACCCGCAAC 7 259 0 TTAGATAAAA 0.688303 -42 TTTTCCCCTCTTTGCTAAAAAGGGGAACTC 8 17 0 TTTGCTAAAA 0.854975 -69 TCCTTTTTAGTTGGCTAAAAATTGCATCAT 10 197 1 TTGGCTAAAA 0.858268 -104 ATATTATTTTTTGAATGAAATTTCGCTTAA 10 269 0 TTGAATGAAA 0.635067 -32 CTGAGTCCTTTTTGAAAAAAATCTGAAAAA 11 13 1 TTTGAAAAAA 0.561957 -287 TGTTTTTTTGTTCGCTAAAATAACCAGTAA 11 76 0 TTCGCTAAAA 0.581348 -224 GATATGATGATTTGATGAAAATTCACTATC 11 155 1 TTTGATGAAA 0.849817 -145 AATTGAAAGCGTTGATAAAAGGTAATATCG 13 19 0 GTTGATAAAA 0.802282 -66 CTCCTATGAATTGAATGAAAATTAAAACGC 14 17 1 TTGAATGAAA 0.635067 -218 ATTCAAAAATTTGAATAAAAAATAATATTT 15 23 1 TTGAATAAAA 0.803709 -244 ATTTTTACTATTTTATAAAATGCGGCATTT 15 49 1 TTTTATAAAA 0.450109 -218 TTTTATAAACTTTAATAAAAATATAAAGAA 16 32 0 TTTAATAAAA 0.762673 -269 TTTATAAAATTTTTATAAAATCTGTTGGCA 16 53 1 TTTTATAAAA 0.450109 -248 ********** Masking position 8 Map Score: 5.26061 Number of sites scoring better than the average of aligned sites = 413 Number in coding regions = 304 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 11 TGAGCGTAGCGAGTTCAGCAAATTG 1 6 1 GTAGCGAGTT 0.724055 -295 CGATTTAACTGGGGCGTGTTTTCTTTGCCT 1 69 1 GGGGCGTGTT 0.951724 -232 GGAATGTAATGTTGCGATTTGTGCAATTAT 1 171 0 GTTGCGATTT 0.887961 -130 ATATTTTTTTGTTGTGGTTTGATTATAGGA 1 231 0 GTTGTGGTTT 0.648889 -70 CAAACGATGTGTGGCGGATTTTATCAGTTT 6 165 1 GTGGCGGATT 0.862432 -136 CAACTTATAAAGTGCGGGTTTAAAATTGGG 7 233 0 AGTGCGGGTT 0.67178 -68 CACTTTATAAGTTGCGGGTTTTTTATCTAA 7 249 1 GTTGCGGGTT 0.973961 -52 CCAAAAGTGCGGTGCGTTTTTCCTGTATTT 7 280 0 GGTGCGTTTT 0.919423 -21 CTCTCATTGAGTGGCGTTTTTTTCATCCCG 10 114 1 GTGGCGTTTT 0.951779 -187 GTTAAAATCACTTGCGTTTTAATTTTCATT 14 30 0 CTTGCGTTTT 0.702298 -205 TGTTTGGTTGGTGGCGTGCTCGAAAGGGGC 16 216 1 GTGGCGTGCT 0.85565 -85 ********** Masking position 10 Map Score: 4.67632 Number of sites scoring better than the average of aligned sites = 257 Number in coding regions = 220 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 12 TACTCGTGTAAAAGAAAGTAGGCAAAGAAA 1 88 0 AAAGAAAGTA 0.965036 -213 TACACGAGTAAAAGAAAGTAGGTCGTTCAT 1 108 1 AAAGAAAGTA 0.965036 -193 GACACAACCGAAAGTAAGTATCGTTATTTT 6 108 1 AAAGTAAGTA 0.893494 -193 TTAATAATATACAGGAAGTAAATGAGTAAC 10 64 0 ACAGGAAGTA 0.875635 -237 AAAATAATATTAAGGAAGTAAA 10 289 1 TAAGGAAGTA 0.826103 -12 ATAAAAATATAAAGAAAATAAACACAAAAA 16 18 0 AAAGAAAATA 0.781666 -283 GAAGAAGAAAAAAGAAAGGAATAGTTGCCG 16 166 1 AAAGAAAGGA 0.894657 -135 ********** Masking position 6 Map Score: 2.29368 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 23 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 13 GGTAGGGCTTGGAGAGAAAAAAACGAAAAA 2 161 0 GGAGAGAAAA 0.967789 -87 AATTTTACTCGGAGAGATTATTT 3 59 1 GGAGAGATTA 0.949312 -13 AAATTAATAGGGAGAGAAATAAAAAGTGCG 4 149 0 GGAGAGAAAT 0.843364 -100 AGCAGTAGGTTGAGAGATAAAGAAACAATA 7 149 0 TGAGAGATAA 0.810738 -152 TAATCTGTTTTGAGTGAATATTAGTTTAGA 11 270 0 TGAGTGAATA 0.715565 -30 GTGAATTTAAGGAGTGAAAA 15 257 1 GGAGTGAAAA 0.91666 -10 TGTAGTGATTGGGGAGATTACCGTAAAACA 16 90 0 GGGGAGATTA 0.83262 -211 AGGACAGAATAAGACCAGAAC 16 290 0 GGACAGAATA 0.83257 -11 ********** Masking position 7 Map Score: 1.9114 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 40 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 14 TGCCGTTAAGAAAATTGAAACAAAGCAAAG 1 34 1 AAAATTGAAA 0.889924 -267 CAAAAAATCCTATAATCAAACCACAACAAA 1 224 1 TATAATCAAA 0.495589 -77 ACAACAAAAAAATATGCAAACACAACATCA 1 246 1 AATATGCAAA 0.769436 -55 TCCTATGTAAAAAAATGAAAAGAGTTTCAA 2 17 1 AAAAATGAAA 0.702916 -231 TAGATTTCATTATATTGAAACTCTTTTCAT 2 31 0 TATATTGAAA 0.867761 -217 GAAGAACAGGAATATTCAAAATAAGCCAAT 2 118 1 AATATTCAAA 0.878814 -130 CTGTTCTGCAAAAATTGAAAATTTATTGTA 4 99 1 AAAATTGAAA 0.889924 -150 TGTGTGAGCCCATATTGAAAGAGCTTGTAA 6 137 0 CATATTGAAA 0.747226 -164 TTTGGCATTTTATATTAAAAATAAACCTAC 7 45 0 TATATTAAAA 0.531482 -256 TTTTATTCGTAATATGGAAAACGTTTTACA 7 95 1 AATATGGAAA 0.867075 -206 TTTCCCGAACTATATGCAAACACAACATCA 10 14 0 TATATGCAAA 0.607062 -287 ACTAAAAAGGAATAATGAAATTTTGGAAAC 10 178 0 AATAATGAAA 0.805765 -123 CTCAATACTCAAAATTGAAAGCGTTGATAA 13 31 0 AAAATTGAAA 0.889924 -54 GAATTGAATGAAAATTAAAACGCAAGTGAT 14 24 1 AAAATTAAAA 0.582914 -211 ********** Masking position 4 Map Score: 7.25732 Number of sites scoring better than the average of aligned sites = 338 Number in coding regions = 269 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 15 TTGTTGCGTAAAGTGATATTATGGGAATGT 1 194 0 AAGTGATATT 0.824009 -107 TTAAAATTTAAGGTGATTTT 4 239 1 AGGTGATTTT 0.874048 -10 ACCATTCCTGAAGTGATTTAAATAATAAAT 10 234 0 AAGTGATTTA 0.903715 -67 ATTGCGCTTGAATTGATTTTTCAACTAAAA 12 80 1 AATTGATTTT 0.934983 -142 TAGATTTATCAATTGATTTAATACTTTTTT 12 155 0 AATTGATTTA 0.819638 -67 ATTAAAACGCAAGTGATTTTAACACTTCCG 14 37 1 AAGTGATTTT 0.967428 -198 TATGTCACAAAACTGATTTTTAACGTTTTT 14 87 0 AACTGATTTT 0.939482 -148 ATATTTTTTTAATTGATTTTTTTGTTGTTT 15 151 1 AATTGATTTT 0.934983 -116 ACAAAATGCCAACAGATTTTATAAAAATTT 16 59 0 AACAGATTTT 0.709909 -242 ********** Masking position 6 Map Score: 6.51065 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 97 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912