AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00970_hinf_reg_300.orf -o00970_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) Input sequences: #1 HI0078 102 cysteinyl-tRNA synthetase (cysS) #2 HI0110 166 seryl-tRNA synthetase (serS) #3 HI0274 300 glutamyl-tRNA synthetase (gltX) #4 HI0317 218 aspartyl-tRNA synthetase (aspS) #5 HI0365 225 conserved hypothetical protein #6 HI0366 101 fimbrial biogenesis and twitching motility protein, putative #7 HI0367 71 conserved hypothetical protein #8 HI0622 300 polypeptide deformylase (def) #9 HI0623 92 methionyl-tRNA formyltransferase (fmt) #10 HI0637 128 tryptophanyl-tRNA synthetase (trpS) #11 HI0727.1 260 cyaY protein (cyaY) #12 HI0729 84 prolyl-tRNA synthetase (proS) #13 HI0814 187 alanyl-tRNA synthetase (alaS) #14 HI0815 101 universal stress protein A (uspA) #15 HI0817 170 conserved hypothetical protein #16 HI0819 37 galactokinase (galK) #17 HI0820 207 galactose-1-phosphate uridylyltransferase (galT) #18 HI0836 181 lysyl-tRNA synthetase analog (genX) #19 HI0921 248 leucyl-tRNA synthetase (leuS) #20 HI0924 300 glycyl-tRNA synthetase, beta chain (glyS) #21 HI0927 265 glycyl-tRNA synthetase, alpha chain (glyQ) #22 HI0963 34 riboflavin kinase / FMN adenylyltransferase (ribF) #23 HI0964 300 virulence factor (mviN) #24 HI1211 300 lysyl-tRNA synthetase (lysU) #25 HI1276 102 methionyl-tRNA synthetase (metG) #26 HI1302 147 asparaginyl-tRNA synthetase (asnS) #27 HI1310 24 H. influenzae predicted coding region HI1310 #28 HI1311 148 phenylalanyl-tRNA synthetase, alpha subunit (pheS) #29 HI1312 33 phenylalanyl-tRNA synthetase, beta subunit (pheT) #30 HI1354 300 glutaminyl-tRNA synthetase (glnS) #31 HI1367 284 threonyl-tRNA synthetase (thrS) #32 HI1394 221 conserved hypothetical protein #33 HI1396 84 H. influenzae predicted coding region HI1396 #34 HI1397 234 DNA polymerase III, chi subunit (holC) #35 HI1583 79 arginyl-tRNA synthetase (argS) #36 HI1610 200 tyrosyl tRNA synthetase (tyrS) #37 HI1612 43 conserved hypothetical transmembrane protein Motif number 1 AAGTGCTATAAAAGTGCGGTTTGTTTTTAT 1 63 1 AAAGTGCGGT 0.997181 -40 ATTCTAATACAAAGTGCGGTCAATTTTTCT 2 52 1 AAAGTGCGGT 0.997181 -115 CTTCTAAATAAAAAAGCGGATTTTATGCTT 3 225 0 AAAAAGCGGA 0.810209 -76 TACAGCGGAAAAAGTGCGGTAAAATATCAG 5 34 0 AAAGTGCGGT 0.997181 -192 AGATCGCAAAAAAGTGCGGTAAGATTTTCT 5 84 1 AAAGTGCGGT 0.997181 -142 CAATCATTTCAAAAAACGGTGGGCTTAAGC 9 34 1 AAAAAACGGT 0.773951 -59 TAATTGATAGGAAGTAGGGTGGGCTTAAGC 9 56 0 GAAGTAGGGT 0.689082 -37 TAAATCTGATAAAATGCGGCAAATTATAAA 11 227 0 AAAATGCGGC 0.831217 -34 GTGTTAAAAGTGCGGTTAAAAATGAC 12 7 1 AAAGTGCGGT 0.997181 -78 AGTATAACAAAAAGTGCGGTCATTTTTAAC 12 25 0 AAAGTGCGGT 0.997181 -60 CGCTATTTGAGAAGTGCGGTTAAAATTTAA 13 48 0 GAAGTGCGGT 0.986441 -140 ATAGCGTCGTGAAGTGCGGTTTTATTTTGG 13 72 1 GAAGTGCGGT 0.986441 -116 AGAGAAATAAAAAGTGCGGTGGTTTTTTAG 19 137 0 AAAGTGCGGT 0.997181 -112 AAATGCTGCAAAAGTGCGGTTAAAATTTAA 19 220 1 AAAGTGCGGT 0.997181 -29 CCTCTTTAGCAAAGAGGGGTAGGGGAGATT 20 60 0 AAAGAGGGGT 0.980462 -241 CCTCTTTGCTAAAGAGGGGAATTCTTGAAT 20 73 1 AAAGAGGGGA 0.872329 -228 CCTCTTTGCTAAAGAGGGGATTGGATCTTT 20 203 0 AAAGAGGGGA 0.872329 -98 CCTCTTTAGCAAAGAGGGGTAGGGGCGATT 20 216 1 AAAGAGGGGT 0.980462 -85 ATAAAGGCGAAAAATGCGGTTGAAAATCAG 21 189 0 AAAATGCGGT 0.984041 -77 GGAAAGTGCGGTATGTTAAGTT 25 3 1 AAAGTGCGGT 0.997181 -100 AGTCCTAAATAAAATAGGGTAAAGCCTTAT 26 34 0 AAAATAGGGT 0.652582 -114 ACATCACATTAAAAAGCGGTATCGCCGTGA 30 28 1 AAAAAGCGGT 0.969091 -273 ATAAATGCACAAAGTGCGGTAAGTTTTTTG 30 124 0 AAAGTGCGGT 0.997181 -177 TGGGTATTTAAAAGTGCGGTTATTCTAGCC 31 25 1 AAAGTGCGGT 0.997181 -260 AAGTAGGGCAAAAGTGCGGTTAATTTTTAT 31 206 1 AAAGTGCGGT 0.997181 -79 TTTGATCCTTAAAGAGCGGTTAGGTTTTAG 32 202 0 AAAGAGCGGT 0.994472 -20 ATAGATCATAAAAGCGCGGTGGATTTTCAG 34 114 1 AAAGCGCGGT 0.974037 -121 AGAAATATACAAAGAACGGTATCATAACCG 35 23 1 AAAGAACGGT 0.951562 -57 ********** Masking position 3 Map Score: 88.2001 Number of sites scoring better than the average of aligned sites = 1701 Number in coding regions = 1166 Number in noncoding regions = 535 Number of orfs with sites within 600 bp upstream = 333 Fraction of orfs with sites within 600 bp upstream = 0.0534854 Motif number 2 TAAGCTCGTAAAATGAAATAAAAACAAACCGCACTTTTATAGCA 1 66 0 AAAAACCGCC 0.997887 -37 CCAACGTATAAAAATAAAGAAAAATTGACCGCACTTTGTATTAG 2 55 0 AAAAACCGCC 0.997887 -112 TCACCTTAAAAAATAGGCTGATATTTTACCGCACTTTTTCCGCT 5 17 1 AAAAACCGCC 0.997887 -209 CGGAATTGAAAAACGATAGAAAATCTTACCGCACTTTTTTGCGA 5 87 0 AAAAACCGCC 0.997887 -139 TTGGACTTTAAAATTTAGCCTCCATTTACCGCCTAATTATTTGA 7 30 1 AAATACCGCT 0.868321 -42 GTATAACAAAAAGTGCGGTCATTTTTAACCGCACTTTTAACAC 12 10 0 AAGAACCGCC 0.981474 -75 GAATAATCTGAAATAACTTAAATTTTAACCGCACTTCTCAAATA 13 31 1 AAAAACCGCC 0.997887 -157 GGCTTTTTGCCAAAACTCCAAAATAAAACCGCACTTCACGACGC 13 75 0 CAAAACCGCC 0.989848 -113 TTTATTGTAAAAAACAACTAAAAAACCACCGCACTTTTTATTTC 19 120 1 AAAAACCGCC 0.997887 -129 TTGACAATAGAAAATGTGGCATAGAATACCGTAAAATGGCAAAA 19 177 0 AAAAACCGTA 0.772829 -72 AAAATCACCTTAAATTTTAACCGCACTTTTGCAGCA 19 223 0 AATAACCGCC 0.972786 -26 CTAGTTTGAAAAACTTTAACTTAACATACCGCACTTTCC 25 6 0 AAATACCGCC 0.992536 -97 TTGGTAAGCTAAACATTCAAAAAACTTACCGCACTTTGTGCATT 30 107 1 AAAAACCGCC 0.997887 -194 AAAGATTGTAAAAACTTGCCATAAAAAACCGCCACGAAATTATC 30 164 0 AAAAACCGCA 0.976362 -137 TATCTCTTAAAAATAAAGGCTAGAATAACCGCACTTTTAAATAC 31 28 0 AAATACCGCC 0.992536 -257 TGTTCATTTAAAATTCTATAAAAATTAACCGCACTTTTGCCCTA 31 209 0 AAAAACCGCC 0.997887 -76 GGATTTGTAAAAACTTTCTAAAACCTAACCGCTCTTTAAGGATC 32 185 1 AAAAACCGCC 0.997887 -37 TGCATTATTACAAATGTCTGAAAATCCACCGCGCTTTTATGATC 34 117 0 CAAAACCGCC 0.989848 -118 TGAATAATAAAAATAATCGGTTATGATACCGTTCTTTGTATATT 35 26 0 AAATACCGTC 0.916329 -54 *** * ***** * Masking position 18 Map Score: 56.7202 Number of sites scoring better than the average of aligned sites = 653 Number in coding regions = 417 Number in noncoding regions = 236 Number of orfs with sites within 600 bp upstream = 197 Fraction of orfs with sites within 600 bp upstream = 0.0316415 Motif number 3 TTCCCTCTAAAAAATTAAGGGTTGTATTAT 1 17 1 AAAATTAAGG 0.468941 -86 CTCGTAAAATGAAATAAAAACAAACCGCAC 1 76 0 GAAATAAAAA 0.745098 -27 CCAACGTATAAAAATAAAGAAAAATTGACC 2 69 0 AAAATAAAGA 0.898655 -98 CAAACTTAGTAAAATTAAGAAAACTTTTTA 3 29 1 AAAATTAAGA 0.616337 -272 TAAACAAAATTTAATAAAAAGGTATTGACT 3 181 0 TTAATAAAAA 0.602422 -120 GTTTGACTTCTAAATAAAAAAGCGGATTTT 3 231 0 TAAATAAAAA 0.871764 -70 ATAAATATTCAAAATAAAGGCTTTTTTGTG 4 78 0 AAAATAAAGG 0.829762 -141 ATTTTTGAGCATAATTAAAAGAGTACAAAG 4 190 1 ATAATTAAAA 0.445383 -29 TTATCTAAGTTAAATAAAAACAGAAGGACC 8 96 1 TAAATAAAAA 0.871764 -205 TTACTTATTGAAAATTAAAATTAGACACTT 8 184 0 AAAATTAAAA 0.782745 -117 CCAAAACTCCAAAATAAAACCGCACTTCAC 13 80 0 AAAATAAAAC 0.745098 -108 ACCCATAATAAAAATAAAAACTAAGTCGCC 13 151 0 AAAATAAAAA 0.952124 -37 GCCATTATTTATAATAAAAATGTCATTACA 15 11 1 ATAATAAAAA 0.815927 -160 TAAACCTTTGTAAATAAAAAAGCCATCGCT 15 119 0 TAAATAAAAA 0.871764 -52 TCTTTGTCACAAAATAAGAAAATAAGCAAA 17 117 0 AAAATAAGAA 0.851754 -91 AGGTCTCTCAATAATAAAAATA 19 3 0 ATAATAAAAA 0.815927 -246 AATAGGGAGAGAAATAAAAAGTGCGGTGGT 19 144 0 GAAATAAAAA 0.745098 -105 TGATAACGAGAAAATAAGAATTTAAATCTA 20 255 1 AAAATAAGAA 0.851754 -46 ACAGAATTTTTAAATAAGAGAAACAAA 20 284 1 TAAATAAGAG 0.519134 -17 AAACTATACTAAAATAAAACTTAAAATCTA 21 116 1 AAAATAAAAC 0.745098 -150 GAAAATAAGAGAATTTCGGCA 22 24 0 AAAATAAGAG 0.759511 -11 ATTGATAGACAAAATAAAGGGCATCAATAT 23 28 1 AAAATAAAGG 0.829762 -273 GTAAACAAAGAAAATAAAAATTTCTTATTA 24 259 1 AAAATAAAAA 0.952124 -42 TTTTTATAAATTAATAAGAAATTTTTATTT 24 270 0 TTAATAAGAA 0.304475 -31 TGGCTTATCAAAAATAAAAATGGAATAACG 28 35 0 AAAATAAAAA 0.952124 -114 TTTTCTCTATAAAATAAAAAACCGAGTAAT 28 112 0 AAAATAAAAA 0.952124 -37 ATACTAGATTTAAATAAAAGATTGTAAAAA 30 194 0 TAAATAAAAG 0.788885 -107 AATCTAAGGGAAAATAAAGGTTCATCTCCT 30 239 0 AAAATAAAGG 0.829762 -62 TTCTCTCGTTAAAATAAAAAAATATTCGGC 30 280 0 AAAATAAAAA 0.952124 -21 TTATCTCTTAAAAATAAAGGCTAGAATAAC 31 43 0 AAAATAAAGG 0.829762 -242 AGAGTTATCATAAATAAAAATTTCATCACA 32 47 0 TAAATAAAAA 0.871764 -175 GAATTGAATGAAAATTAAAACGCAAGTGAT 34 24 1 AAAATTAAAA 0.782745 -211 AAAACCCTAAAAAATAAATAATTAAATATG 34 159 0 AAAATAAATA 0.497538 -76 TTCAAATTGAATAATAAAAATAATCGGTTA 35 47 0 ATAATAAAAA 0.815927 -33 ********** Masking position 5 Map Score: 37.6506 Number of sites scoring better than the average of aligned sites = 520 Number in coding regions = 284 Number in noncoding regions = 236 Number of orfs with sites within 600 bp upstream = 206 Fraction of orfs with sites within 600 bp upstream = 0.0330871 Motif number 4 CTAGATCGCAAATATTTTCAATTACAGCGGAAAA 5 52 0 AATTTCATTA 0.598306 -174 GTTTCCGTTAAATATAGCATTTTTAACCTAGCTT 10 30 1 AATTAATTTT 0.6649 -99 AATTAATAGTAATTTTTTCATTTTTTCTTTCTCA 11 154 1 AATTTCTTTT 0.940436 -107 AATTTGCCGCATTTTATCAGATTTAAACAGGAAA 11 232 1 ATTTAAATTT 0.428941 -29 AAGTCGCCCTATTTTTGCATATTTTTGAAATTTA 13 125 0 ATTTTAATTT 0.6649 -63 ACTAGATCACAATTTAAACATTTTTA 14 3 0 AATTACTTTT 0.856681 -99 AGTATAAATTAATGTAATCGTTTACATTGATAAA 17 170 1 AATTACTTTA 0.598306 -38 ATGCCCACACAATATTACCCTTTTAGGGGATTTA 18 40 0 AATTTCTTTT 0.94044 -142 CTCTCAACTCAATCTTAGCTTTTTTGAGGTAGAT 18 143 0 AATTTCTTTT 0.940441 -39 TTTTACAATAAATTTTCAATTTTTGCAGAACAGA 19 98 0 AATTTATTTT 0.839777 -151 CTCCCTATTAATTTTTGCCATTTTACGGTATTCT 19 165 1 ATTTTCTTTT 0.940441 -84 TTTTTTGATTAATTTAATAGATTTCGATTGTTTA 21 83 0 AATTAAATTT 0.428941 -183 TCAAGTAAGTAATTTTGAATATTTAGGTAGATTT 21 139 0 AATTTAATTT 0.664898 -127 TTTCAACCGCATTTTTCGCCTTTATCCCTTTTAC 21 194 1 ATTTTCTTTA 0.797346 -72 TGTGTGGCGGATTTTATCAGTTTTTTTTCACGGA 23 172 1 ATTTAATTTT 0.6649 -129 ATTGTTTACCTTTTTTATAAATTA 24 287 0 ATTTTCTTTT 0.940441 -14 TTATTATTCTCTTTTTTAGCATACAA 25 87 0 ATTTTCTTTT 0.940441 -16 ATTAATATTGAATATACGCGATTTT 26 2 0 AATTACATTT 0.693517 -146 TTTTCGCATTATTCTTTTACTTTTTAAGGACTTG 28 70 1 ATTTTATTTT 0.839779 -79 ATAGCCGAATATTTTTTTATTTTAACGAGAGAAA 30 277 1 ATTTTATTTA 0.566357 -24 TCAGAAAAACATTATTTCCTTTTTGTAAAATATG 31 82 1 ATTTTCTTTT 0.940441 -203 CACAAAACTGATTTTTAACGTTTTTGTTACGTTC 34 78 0 ATTTTCTTTT 0.940441 -157 TTTTCGTTAAAATTTTACCCTTTTTATAGGGTAA 34 187 1 AATTTCTTTT 0.940441 -48 TTTTTGAGGAATTATTTTCATTTAACTATTGACA 36 15 1 ATTTTCTTTA 0.797346 -186 TATTATAGGGATTCTTAGCAATTTGTGAATAAAA 36 145 0 ATTTTCATTT 0.856681 -56 AATTTTTTCCTTTTCTAAAAATTT 37 1 1 AATTTCTTTT 0.940441 -43 *** ** * **** Masking position 5 Map Score: 28.1448 Number of sites scoring better than the average of aligned sites = 430 Number in coding regions = 318 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 5 AACCCTTAATTTTTTAGAGGGAAAACAAA 1 3 0 TTTTGAAAAA 0.764543 -100 AAATAAAGGCTTTTTTGTGCCATATCATCAGATTTTT 4 60 0 TTTTGATATA 0.92771 -159 TGCGACAGATTTTTGAGCATAATTAAAAGAGTACAAA 4 182 1 TTTTGATTAA 0.759425 -37 TTACCGCACTTTTTCCGCTGTAATTGAAAATATTTGC 5 42 1 TTTTGAATTA 0.790888 -184 TACCGCACTTTTTTGCGATCTAGATCGCAAATATTTT 5 68 0 TTTTGAGATG 0.741894 -158 AAGTAAGTAATTTTTCAACTCATATGAAGTCACATTC 8 208 1 TTTTAATATA 0.830941 -93 GTTTTAGTTATTTTGGGAATGATATTAGATAATAGAT 11 22 1 TTTTGATATA 0.928047 -239 AGCTTGATCTTTTTCAGGAAAATATAAAGAACCTTTT 11 73 1 TTTTGATATA 0.92804 -188 TTTTGCATATTTTTGAAATTTATAAAAAGGCTTTTTG 13 110 0 TTTTAATAAA 0.692217 -78 AATGCTAACATTTTGAGCAATAAAAAACTGTGTACTA 14 33 0 TTTTGAAAAA 0.764123 -69 AAGCAAAATTTTTTATGATTTAGTTCATACTTATGAA 17 87 0 TTTTGAGTTA 0.885814 -121 TATTTTCTTATTTTGTGACAAAGATCACGGTTTATTT 17 123 1 TTTTGAGATA 0.935608 -85 CATTGTGCCATTTTTCGTTACAAATTAATAACGTNTT 18 71 1 TTTTGAAATA 0.876291 -111 CAATCTTAGCTTTTTTGAGGTAGATCACAAAATCCGA 18 131 0 TTTTGAGATA 0.935479 -51 AATTTTCAATTTTTGCAGAACAGATTAGAACAAAGGA 19 85 0 TTTTAAGATA 0.847028 -164 ACTTTAACGTTTTTTGAAAGCAGATAATTTAATCTCT 20 143 0 TTTTAAGATA 0.846721 -158 TAGTATAGTTTTTTTTGATTAATTTAATAGATTTCGA 21 90 0 TTTTGATTTA 0.873197 -176 TTTAGGTAGATTTTAAGTTTTATTTTAGTATAGTTTT 21 115 0 TTTTGATTTA 0.8732 -151 AATACCAACATTTTTAATCACATTAGATCAACGATT 21 240 1 TTTTAATTAA 0.546067 -26 TTATCAGTTTTTTTTCACGGAATATAGCGTAAAAACA 23 185 1 TTTTAATATG 0.492989 -116 TAGGCAAAAATTTTAGGGTAGAGAAGAATATTTTGAG 23 237 1 TTTTGAGAAA 0.869454 -64 TAAGTTAAAGTTTTTCAAACTAGAAAAAATCCCCTAT 25 27 1 TTTTAAGAAA 0.708267 -76 TAAGCACAATTTTTGTATGCTAAAAAAGAGAATAATA 25 75 1 TTTTAAAAAA 0.527763 -28 TTAGGACTCATTTTTAAGGCGATTTTATTGTTCATAA 26 56 1 TTTTAATTTA 0.724086 -92 ATGAAGGAAATTTTCCATAAAAATATAGTGTTGGTGC 26 96 0 TTTTAAATAA 0.39784 -52 TCGCCACGCATTTTTTGCCTAATTTCGCTCGTTCAAT 31 154 1 TTTTGATTTG 0.576684 -131 TAAAAATCAGTTTTGTGACATAGATCATAAAAGCGCG 34 95 1 TTTTGAGATA 0.935603 -140 TAATAAAACCTTTTAAAACATAATTTAGGAAATAATA 36 174 1 TTTTAAATTA 0.590384 -27 TTTCTAAAAATTTTTAGCAGTATATCAAATTT 37 22 1 TTTTGATATA 0.928045 -22 **** * **** * Masking position 12 Map Score: 28.1685 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 213 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 6 TAAGCATAAAATCCGCTTTTTTATTTAGAAGTCAA 3 224 1 ATCCTTTATT 0.494669 -77 GTAGTAGAATAACGACTAATATTTTATTGAAGATA 3 266 1 AACCATTTTT 0.859215 -35 TTTGTGCCATATCATCAGATTTTTTGTTATATTAT 4 49 0 ATCCATTTTT 0.946226 -170 TATGGCACAAAAAAGCCTTTATTTTGAATATTTAT 4 73 1 AAACTTTTTT 0.66994 -146 GCGGTAAAATATCAGCCTATTTTTTAAGGTGACCA 5 14 0 ATCCATTTTT 0.946226 -212 TCAAGTTCACATACCCCTATGTTTTCATACAAATT 6 32 1 ATACATTTTT 0.929937 -70 AAATAAGAAAATAAGCAAAATTTTTTATGATTTAG 17 101 0 ATACAATTTT 0.899592 -107 GTAGATCACAAAATCCGATACTTTCCATCTTTAG 18 114 0 AAACTATTT 0.020487 -68 AAAATCACCTTAAATTTTAACCGCACTT 19 231 0 ATCCAATTTT 0.922352 -18 AAGAATTTAAATCTACAGAATTTTTAAATAAGAGA 20 270 1 ATCCAATTTT 0.922352 -31 AAAACTTAAAATCTACCTAAATATTCAAAATTACT 21 131 1 ATCCAATATT 0.599779 -135 TATAATGCCGAAATTCTCTTATTTTC 22 19 1 AAACTTTTTT 0.669944 -16 TTGTCTATCAATCAACAGAAATTTTAGGA 23 5 0 ATCCAATTTT 0.922352 -296 AAGGGCATCAATATGCCGATTTTTTATACTTTTGT 23 44 1 ATACATTTTT 0.929937 -257 TCTCACCGAAATCAACACAAATTTTCCATTGACAA 23 75 0 ATCCAATTTT 0.922352 -226 TTAAAGTAAGATAAGCACAATTTTTGTATGCTAAA 25 64 1 ATACAATTTT 0.899592 -39 TTTGTATAGAATAGCCGAATATTTTTTTATTTTAA 30 267 1 ATACATTTTT 0.929937 -34 ATTGTTAAATAAATGCCCATATTTTACAAAAAGGA 31 98 0 AAACATTTTT 0.821538 -187 GAACGGTATCATAACCGATTATTTTTATTATTCAA 35 36 1 ATACTTTTTT 0.854071 -44 TTCCCCACAGATAGGCGTTTTTTTTTATTCACAAA 36 123 1 ATACTTTTTT 0.854072 -78 *** * ** **** Masking position 12 Map Score: 21.6955 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 116 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 7 TGCGGTCAATTTTTCTTTATTTTTATACGTTG 2 66 1 TTTTTTATTT 0.746531 -101 TTTTATTAAATTTTGTTTAATTGTCGTAAAAA 3 192 1 TTTTTTAATT 0.707981 -109 TATTTATTACTTTTCTTTGCTTTTTTGATTGA 4 101 1 TTTTTTGCTT 0.615586 -118 TTCTTTGCTTTTTTGATTGATTTGTCAGCATA 4 113 1 TTTTTTGATT 0.884774 -106 TTTGGGAATTTATTCATTATTTAATCAAATAA 8 154 1 TATTTTATTT 0.347442 -147 AATTTCTCTTGTTTTTAAGGGTAG 8 287 0 TTTCTTGTTT 0.876209 -14 TGTGTGCCTGTTTTAGTTATTTTGGGAATGAT 11 13 1 TTTTTTATTT 0.746531 -248 ATAAGCAAAATTTTTTATGATTTAGTTCATAC 17 94 0 TTTTATGATT 0.478779 -114 TCATAAAAAATTTTGCTTATTTTCTTATTTTG 17 106 1 TTTTTTATTT 0.746531 -102 TTATTTTTACTTTCTATTGATTGGAGGATATC 18 11 0 TTTCTTGATT 0.853511 -171 TGCGGTGGTTTTTTAGTTGTTTTTTACAATAA 19 121 0 TTTTTTGTTT 0.903177 -128 TTTGTTTCTCTTATTTAAAAATTCTG 20 285 0 TTTCTTATTT 0.690865 -16 ATTTAATAGATTTCGATTGTTTAAACCTTTCT 21 74 0 TTTCTTGTTT 0.876209 -192 TTTAGTATAGTTTTTTTTGATTAATTTAATAG 21 97 0 TTTTTTGATT 0.884774 -169 TCCTAAAATTTCTGTTGATTGATAGACAAA 23 9 1 TTTCTTGATT 0.853511 -292 CAATGGAAAATTTGTGTTGATTTCGGTGAGAC 23 79 1 TTTGTTGATT 0.67335 -222 GAAATTTTTATTTTCTTTGTTTACTTTAGGAG 24 251 0 TTTTTTGTTT 0.903177 -50 GCGGTAAGTTTTTTGAATGTTTAGCTTACCAA 30 107 0 TTTTATGTTT 0.527389 -194 TTAGATAATTTATTTCTTGTTTTGTCATATTG 32 17 1 TATTTTGTTT 0.627742 -205 ATCCTAGATTTATCAATTGATTTAATACTTTT 32 157 0 TATCTTGATT 0.51286 -65 AGCAGTAGGTTTTGAATTAATTAAAGAGGATA 33 59 1 TTTGTTAATT 0.394254 -26 **** ****** Masking position 8 Map Score: 17.9493 Number of sites scoring better than the average of aligned sites = 373 Number in coding regions = 269 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 8 TTGTGGAATAATACAACCCTTAATTTTTTAG 1 23 0 ATAAACCCTT 0.872982 -80 GTTGAAATGAAAACAACCTTATTCTAGCGTG 2 126 0 AAAAACCTTA 0.680314 -41 ATATGGCACAAAAAAGCCTTTATTTTGAATA 4 72 1 AAAAGCCTTT 0.911618 -147 TTGTCAGCATAAATAACCTTTTTATCTCTCT 4 134 1 AAAAACCTTT 0.918952 -85 AGCACAGCTAATAAAACATTTATAGGAATGT 8 239 0 ATAAACATTT 0.634318 -62 TTTCCGTTAAATATAGCATTTTTAACCTAGC 10 31 1 ATAAGCATTT 0.612059 -98 AGGAAAATATAAAGAACCTTTTACGCCACAT 11 88 1 AAAAACCTTT 0.918849 -173 GCGGCAAATTATAAAGCCTTTCTCAAGCTTG 11 211 0 ATAAGCCTTT 0.931432 -50 GAGTTTTGGCAAAAAGCCTTTTTATAAATTT 13 101 1 AAAAGCCTTT 0.911618 -87 TGCCCACACAATATTACCCTTTTAGGGGATT 18 42 0 ATATACCCTT 0.563264 -140 TTTTTAAGAGATAAAGCCTTTAGTCAGAAAA 31 59 1 ATAAGCCTTT 0.931432 -226 TAAATGAACGATATTACCTTTTATCAACGCT 33 11 1 ATATACCTTT 0.73702 -74 AATTTTAACGAAAAAACCCTAAAAAATAAAT 34 170 0 AAAAACCCTA 0.494774 -65 AATCCCTATAATAAAACCTTTTAAAACATAA 36 166 1 ATAAACCTTT 0.937245 -35 *** ******* Masking position 3 Map Score: 11.1172 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 77 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 9 TTTTGAGCATAATTAAAAGAGTACAAAGGAT 4 192 1 AATTAAAGAG 0.685255 -27 CTTCCTGCCCAATTAAAAGGAGGAAAA 6 85 1 AATTAAAGGA 0.923989 -17 GCTAATAAAACATTTATAGGAATGTGACTTC 8 233 0 CATTATAGGA 0.756633 -68 ACGTTATGGTAATTGATAGGAAGTAGGGTGG 9 64 0 AATTATAGGA 0.955183 -29 TAAGTACTAAAATTAATAGTAATTTTTTCAT 11 144 1 AATTATAGTA 0.807575 -117 ATTTACGATAAATTGAAAGCGGTTACTTTCA 17 60 1 AATTAAAGCG 0.830665 -148 TTTACCACCAAATTTATAGAGGTCTCTCAAT 19 21 0 AATTATAGAG 0.792412 -228 AGAACAAAGGAATTCATAGCAAGCCAATATA 19 65 0 AATTATAGCA 0.904361 -184 AAATGGCAAAAATTAATAGGGAGAGAAATAA 19 157 0 AATTATAGGG 0.950945 -92 TTCTTGAATAAATTGATAGTAACTGGCTCAT 20 94 1 AATTATAGTA 0.807575 -207 CTCGGATTTGAATTAAAAGGATAACAACAA 29 14 1 AATTAAAGGA 0.923989 -20 GCCAGCTCCCATTTGATAGGAAATTTTGCTG 30 71 0 ATTTATAGGA 0.677179 -230 CAATACTCAAAATTGAAAGCGTTGATAAAAG 33 28 0 AATTAAAGCG 0.830665 -57 ATTTTCATTCAATTCATAGGAGTACAGA 34 8 0 AATTATAGGA 0.955183 -227 **** ****** Masking position 6 Map Score: 9.19138 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 34 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 10 AAAATTAAGAAAACTTTTTAGAGAAGTGGT 3 39 1 AAACTTTTTA 0.857769 -262 TTTCAGTCAATACCTTTTTATTAAATTTTG 3 177 1 TACCTTTTTA 0.633513 -124 CAGCATAAATAACCTTTTTATCTCTCTTGG 4 138 1 AACCTTTTTA 0.949705 -81 CGTTAAATATAGCATTTTTAACCTAGCTTT 10 35 1 AGCATTTTTA 0.785262 -94 TTTGGCAAAAAGCCTTTTTATAAATTTCAA 13 105 1 AGCCTTTTTA 0.896797 -83 TCACAATTTAAACATTTTTA 14 1 0 AACATTTTTA 0.888223 -101 AATTAGTGTAAACCTTTGTAAATAAAAAAG 15 127 0 AACCTTTGTA 0.764239 -44 TTAAATCTACAGAATTTTTAAATAAGAGAA 20 276 1 AGAATTTTTA 0.538732 -25 CGATTGTTTAAACCTTTCTATATGATACGC 21 63 0 AACCTTTCTA 0.896797 -203 GTATAATACCAACATTTTTAATCACATTAG 21 236 1 AACATTTTTA 0.888223 -30 GCGTAAAAACAAAATTTCTATACAATTAGG 23 211 1 AAAATTTCTA 0.538732 -90 GGATTTGTAAAAACTTTCTAAAACCTAACC 32 185 1 AAACTTTCTA 0.735122 -37 TTAAAATTTTACCCTTTTTATAGGGTAAGA 34 193 1 ACCCTTTTTA 0.764239 -42 CCTATAATAAAACCTTTTAAAACATAATTT 36 170 1 AACCTTTTAA 0.633513 -31 TCCTTTTCTAAAAATTTTTAGCAGTATATC 37 18 1 AAAATTTTTA 0.717349 -26 ********** Masking position 10 Map Score: 8.00477 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 73 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 11 TCTAGCGTGCTTTCTTCAAATAAACCAGTTTA 2 103 0 TTTTCAAATA 0.736217 -64 AAAAGTAATAAATATTCAAAATAAAGGCTTTT 4 83 0 AATTCAAAAT 0.746017 -136 CTCTTTTAATTATGCTCAAAAATCTGTCGCAA 4 181 0 TATTCAAAAA 0.817072 -38 GTGCAGGTGTTTTTATCAAAAACTCACAACGA 5 189 0 TTTTCAAAAA 0.882638 -37 AAATTTAATCAAATAATTAGGCGGT 7 57 0 TTTTCAAATA 0.736227 -15 TTATTCATTATTTAATCAAATAAGTGTCTAAT 8 163 1 TTTTCAAATA 0.736227 -138 GTTATTTCAGATTATTCAAAAAACAATTTCTT 13 16 0 ATTTCAAAAA 0.817053 -172 ACAGTTTTTTATTGCTCAAAATGTTAGCATTG 14 39 1 ATTTCAAAAT 0.831829 -63 GTAAATTATTTATGATCAAAATATAAGATTTA 17 34 0 TATTCAAAAT 0.831831 -174 CCACATTTTCTATTGTCAAAATGCTGCAAAAG 19 202 1 TATTCAAAAT 0.831829 -47 AATCTATTAAATTAATCAAAAAAAACTATACT 21 94 1 ATTTCAAAAA 0.817073 -172 AATCTACCTAAATATTCAAAATTACTTACTTG 21 140 1 AATTCAAAAT 0.746017 -126 TACCAACATTTTTAATCACATTAGATCAACGA 21 242 1 TTTTCACATT 0.496566 -24 TTAAAAGTCGTTTACTCAAAATATTCTTCTCT 23 256 0 TTTTCAAAAT 0.892816 -45 TAAATAAAAATTTCATCACAATATGACAAAAC 32 35 0 TTTTCACAAT 0.726638 -187 CCTACTGCTCAATACTCAAAATTGAAAGCGTT 33 36 0 AATTCAAAAT 0.746021 -49 GTTTTTTCCTATGTTCAAATTGAATAATAAA 35 59 0 TATTCAAATT 0.647293 -21 AATGAAAATAATTCCTCAAAAAAATA 36 5 0 ATTTCAAAAA 0.817073 -196 GGCGTTTTTTTTTATTCACAAATTGCTAAGAA 36 136 1 TTTTCACAAA 0.705895 -65 *** ******* Masking position 6 Map Score: 15.9878 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 232 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 12 GTTGAGATTAAATTACGTTAAGGATAACCA 4 12 0 AATTACGTTA 0.619927 -207 CAAGAGAGATAAAAAGGTTATTTATGCTGA 4 137 0 AAAAAGGTTA 0.658392 -82 AGCGGAATTGAAAAACGATAGAAAATCTTA 5 103 0 AAAAACGATA 0.906809 -123 TTTAGACATAAAAACGTTATTAATTTGTA 18 89 0 AAAACGTTA 0.94287 -93 TCTGCTTTCAAAAAACGTTAAAGTAGAACA 20 156 1 AAAAACGTTA 0.94287 -145 ATTAATCAAAAAAAACTATACTAAAATAAA 21 104 1 AAAAACTATA 0.627164 -162 AGCTTGTAAAAATAACGATACTTACTTTCG 23 116 0 AATAACGATA 0.794909 -185 TTCTAGTTTGAAAAACTTTAACTTAACATA 25 22 0 AAAAACTTTA 0.740462 -81 AATAACGATATGTTGTAATT 27 1 1 AATAACGATA 0.794909 -24 CTTTAGTCAGAAAAACATTATTTCCTTTTT 31 76 1 AAAAACATTA 0.618021 -209 GGAACGTAACAAAAACGTTAAAAATCAGTT 34 77 1 AAAAACGTTA 0.94287 -158 ********** Masking position 5 Map Score: 5.3945 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 61 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 13 TTTCCTTACTTTTTTCGTTGAAATGAAAAC 2 143 0 TTTTTCGTTG 0.884096 -24 TATCATCAGATTTTTTGTTATATTATGCCG 4 45 0 TTTTTTGTTA 0.583315 -174 TCTCTCTTGGTTTTCCGCTATAATTGCGAC 4 158 1 TTTTCCGCTA 0.729251 -61 TTACCGCACTTTTTCCGCTGTAATTGAAAA 5 42 1 TTTTCCGCTG 0.745019 -184 TAATTGCGAATTTTTCGTTGTGAGTTTTTG 5 175 1 TTTTTCGTTG 0.884096 -51 AACTTTTTCCTTGTTATAATCTA 17 4 1 TTTTTCCTTG 0.906973 -204 CATTGTGCCATTTTTCGTTACAAATTAATA 18 71 1 TTTTTCGTTA 0.875491 -111 TACCCTAAAATTTTTGCCTAATTGTATAGA 23 227 0 TTTTTGCCTA 0.733766 -74 CGCTATTCCATTTTTTCTTG 28 1 0 TTTTTTCTTG 0.659983 -148 AATTTTGCTGTTTTTGCCTGCATTCACGGC 30 51 0 TTTTTGCCTG 0.749361 -250 TGAACCTTTATTTTCCCTTAGATTTGTATA 30 245 1 TTTTCCCTTA 0.778489 -56 CGCCACGCATTTTTTGCCTAATTTCGCTCG 31 155 1 TTTTTGCCTA 0.733766 -130 TGTTTTTTCCTTATACAGTGGTC 31 272 0 TTTTTCCTTA 0.899874 -13 TTTTTAGGGTTTTTTCGTTAAAATTTTACC 34 176 1 TTTTTCGTTA 0.875491 -59 GTTTTTTCCTATGTTCAAATT 35 69 0 TTTTTTCCTA 0.636728 -11 AATTTTTTCCTTTTCTAAAAATT 37 4 1 TTTTTCCTTT 0.558424 -40 ********** Masking position 4 Map Score: 10.8444 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 105 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 14 CTAAATAAAAAAGCGGATTTTATGCTTATT 3 222 0 AAGCGGATTT 0.89262 -79 CCGCATAATCTAGCGGAATTGAAAAACGAT 5 114 0 TAGCGGAATT 0.730324 -112 CCGATGGTAGTGTGGGGTTTCCCCATGTGA 8 37 1 TGTGGGGTTT 0.693582 -264 TGTCGAAAGATATGGGGTTTTAGCTTTTGG 8 129 1 TATGGGGTTT 0.676297 -172 AGCTTGTGAAAGGCGGATTTACCGATAAGT 11 187 0 AGGCGGATTT 0.900061 -74 ATTACCCTTTTAGGGGATTTATTTTTACTT 18 31 0 TAGGGGATTT 0.944063 -151 GATGGAAANGTATCGGATTTTGTGATCTAC 18 119 1 TATCGGATTT 0.882923 -63 AAACGATGTGTGGCGGATTTTATCAGTTTT 23 166 1 TGGCGGATTT 0.962022 -135 GCCGTATTAGACGGGGATTTAGATCGATTT 24 101 1 ACGGGGATTT 0.772616 -200 TTACTTTAAATAGGGGATTTTTTCTAGTTT 25 43 0 TAGGGGATTT 0.944063 -60 TTTCTCGGATTTGAATTAAAAG 29 3 1 TCTCGGATTT 0.810263 -31 GATAATTTCGTGGCGGTTTTTTATGGCAAG 30 164 1 TGGCGGTTTT 0.78091 -137 ********** Masking position 9 Map Score: 5.7709 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 126 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 15 TGGGAGAGCACCTCCCTTACAAGGAGGGGG 3 95 0 CCTCCCTTAC 0.890317 -206 ATGGGGAAACCCCACACTACCATCGGCATT 8 33 0 CCCACACTAC 0.928556 -268 CTGGCTAAAGCCCACCCTACGTT 9 4 0 CCCACCCTAC 0.979443 -89 TGGGCTTAAGCCCACCCTACTTCCTATCAA 9 53 1 CCCACCCTAC 0.979443 -40 AGCGAGTAAATCTCCCCTACCCCTCTTTGC 20 52 1 TCTCCCCTAC 0.944664 -249 TTCTGCCAAATCGCCCCTACCCCTCTTTGC 20 224 0 TCGCCCCTAC 0.909204 -77 ATACGCCTCCCTCCACTACATCACATTAA 30 10 1 CCTCCACTAC 0.944664 -291 ********** Masking position 9 Map Score: 3.59465 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 5 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863