AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i03010_hinf_reg_100.orf -o03010_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: HI0158 22 ribosomal protein L32 (rpL32) HI0781 25 ribosomal protein S19 (rpS19) Input sequences: #1 HI0159 156 conserved hypothetical protein #2 HI0201 36 ribosomal protein L19 (rpL19) #3 HI0202 37 tRNA (guanine-N1)-methyltransferase (trmD) #4 HI0203 35 conserved hypothetical protein #5 HI0204 292 ribosomal protein S16 (rpS16) #6 HI0517 172 ribosomal protein L11 (rpL11) #7 HI0531 231 ribosomal protein S21 (rpS21) #8 HI0546 28 primosomal replication protein N (priB) #9 HI0547 198 ribosomal protein S6 (rpS6) #10 HI0580 156 ribosomal protein S7 (rpS7) #11 HI0581 181 ribosomal protein S12 (rps12) #12 HI0640 271 ribosomal protein L10 (rpL10) #13 HI0641 54 ribosomal protein L7/L12 (rpL7/L12) #14 HI0758 176 ribosomal protein L31 (rpL31) #15 HI0776 190 ribosomal protein S10 (rpS10) #16 HI0788 280 ribosomal protein L14 (rpL14) #17 HI0792 36 ribosomal protein S8 (rpS8) #18 HI0798.1 28 ribosomal protein L36 (rpL36) #19 HI0799 139 ribosomal protein S13 (rpS13) #20 HI0801 27 ribosomal protein S4 (rpS4) #21 HI0802 31 DNA-directed RNA polymerase, alpha chain (rpoA) #22 HI0803 40 ribosomal protein L17 (rplQ) #23 HI0880 212 ribosomal protein L21 (rpL21) #24 HI0913 144 ribosomal protein S2 (rpS2) #25 HI0951 213 ribosomal protein L28 (rpL28) #26 HI0965 300 ribosomal protein S20 (rpS20) #27 HI0998 180 ribosomal protein L34 (rpL34) #28 HI1219 279 cytidylate kinase 1 (cmkA) #29 HI1220 75 ribosomal protein S1 (rpS1) #30 HI1319 138 ribosomal protein L35 (rpL35) #31 HI1320 66 ribosomal protein L20 (rpL20) #32 HI1443 300 ribosomal protein L13 (rpL13) #33 HI1472 67 iron chelatin ABC transporter, periplasmic-binding protein, putative #34 HI1475 227 H. influenzae predicted coding region HI1475 #35 HI1630 166 ribosomal protein L25 (rpL25) Motif number 1 GATTATATAAAAAGTGCGGTTGTTTTTCAA 6 37 0 AAAGTGCGGT 0.99757 -136 TAAAAAAACAAAAGTGCGGTAAATTTTAAT 11 20 1 AAAGTGCGGT 0.99757 -162 AAAAAGAAAAGTGCGGTTAAAAATGCT 14 8 1 AAAGTGCGGT 0.99757 -169 TATAATTCCAAAAGTGCGGTAAATTTTAAC 16 102 1 AAAGTGCGGT 0.99757 -179 TTATCAGTTAAAAGTGCGGTGCATTTTACC 23 21 1 AAAGTGCGGT 0.99757 -192 TTTATACCATAAAGTGCGGTTAAAAACCAG 24 21 0 AAAGTGCGGT 0.99757 -124 TAAAATCCATAAAATGCGGGGTTGAGGAT 29 17 0 AAAATGCGGG 0.936717 -59 ATTGCTAACAAAAGTGCGGTAGT 32 4 0 AAAGTGCGGT 0.99757 -297 TTTTCGTTGTAAAATGGGGTAAATCATTGC 32 29 0 AAAATGGGGT 0.901872 -272 AACGAAAAAGAAAGTGCGGTAATTTTTTGT 32 51 1 AAAGTGCGGT 0.99757 -250 ********** Masking position 5 Map Score: 34.5522 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 ATATAGACAAAAAGCCTGCGAATTTTATACTTTTCAA 5 180 0 AGGCGATTTA 0.990037 -113 AACGGCTCATAATGGGCACGGATTATATAAAAAGTGC 6 50 0 AGACGATTTA 0.798044 -123 CAATGTGGCTAAGGGTTGCGGATTATACCGATTTTTT 9 98 0 AGGCGATTTA 0.990037 -101 TGCGAATTTCTCCGTATTTTAATCTTCAGGA 10 136 0 ATCCGATTTA 0.75223 -21 AAAAAAACAAAAGTGCGGTAAATTTTAATCTAGTTTT 11 21 1 ATGTAATTTA 0.738362 -161 CTATATAGAAATAGACGGCGAATTCTAATAGTTTTAC 11 96 0 AGGCGATTTA 0.990037 -86 TTGGCACCAAATAGGTTGCGAATTATACTGAAAAAAT 14 74 0 AGGCGATTTA 0.990037 -103 ATTTGGTGCCAATTATGGCGTATTATTCACTCACGCG 14 99 1 ATGCGATTTT 0.940479 -78 TCTCATATTGAGAGCTCGTAGATTCTATAGAAAGACA 15 37 0 AGGTAATTTA 0.844818 -154 ATAATTCCAAAAGTGCGGTAAATTTTAACTGGATTAT 16 103 1 ATGTAATTTA 0.738362 -178 AGAATGGCAGATAGGCGGCGGATTTTATCAAAAGAAA 16 190 0 AGGCGATTTA 0.990037 -91 TATCAGTTAAAAGTGCGGTGCATTTTACCCGAATTTT 23 22 1 ATGTGATTTA 0.92196 -191 ATCAATCCGCAAATGAAGGGAATTTTTTTATTTTATT 23 72 1 ATGGGATTTT 0.780326 -141 ATTCATATAAATAGGTCGCAAATTCTACGGAAAAATC 23 134 0 AGGCAATTTA 0.959574 -79 TTACTATATTAAAGGTCGCAAATTATACTGACTTTGT 25 82 0 AGGCAATTTA 0.959574 -132 GCTTATATTTAATTATTGGAGATTATT 25 197 1 ATGGAATTTT 0.459031 -17 CACACAAACGATGTGTGGCGGATTTTATCAGTTTTTT 26 122 0 ATGCGATTTA 0.980956 -179 TTTCTTATTTGACGAACGCGTATTTTATGACTAGAAT 27 109 1 GGGCGATTTA 0.900532 -72 TTCATTCTCCAAATTTTGCGCATTATAGTGAGAATTT 28 235 0 ATGCGATTTA 0.980956 -45 AAGTGCGGTAATTTTTTGTGTATTTTTATAGAAAGAT 32 62 1 ATGTGATTTT 0.783739 -239 GCACATTTACAGGGTCGGCGTATTATACTCGTTTTTT 32 160 0 AGGCGATTTA 0.990037 -141 TACGGACGTAAGTGGGCGGGAATTATTGAAAACAGGG 34 159 0 AGGGGATTTT 0.872652 -69 * * *** *** ** Masking position 13 Map Score: 35.6916 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 129 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 3 TCACGCCTCTTTTTTTAACAAGGAAAGATA 1 6 0 TTTTAAAGAA 0.871687 -151 CTTTATTGAGTTATCCAATAAAAAATGTGATTTCC 1 92 1 TTATAAAAAA 0.93143 -65 AAATTGCAAGTTTTGTATGCATAAAGTAGGTTGTA 5 142 0 TTTTATAAAA 0.804198 -151 ACACAGGTGCTTTGGCAAAAATAAAATTTTAAATT 7 173 1 TTTGAAAAAA 0.776209 -59 GTTTGAGTTCTTTTTGAACAAAAAAGAAGGTCGAT 9 48 0 TTTTAAAAAA 0.907661 -151 CGCTGCAAATTTTCTCAATGAGAAATATTGCTGAT 10 89 1 TTTCAAAAAA 0.596721 -68 AGTTTTTTATAAAAAAACAAAAGTGCGGTAA 11 7 1 TTATAAAAAA 0.937272 -175 TCTCAAAAATTTATCGAATGAAAAATAAACTGCAG 16 52 0 TTATAAAAAA 0.93143 -229 TTTACCGCACTTTTGGAATTATAAAAATATCCTCA 16 90 0 TTTTAAAAAA 0.958477 -191 GCGGCGGATTTTATCAAAAGAAAAAGAGAAAGGCA 16 178 0 TTATAAAAAA 0.937184 -103 AAAAAACTGCTTTTGAAAGGCAAAAACAGCGGGGC 24 53 0 TTTTAACAAA 0.759923 -92 TCAAAAGCAGTTTTTTAATTACTAACAACACACAC 24 72 1 TTTTAAATAA 0.60178 -73 TCAACACAAATTTTCCATTGACAAAAGTATAAAAA 26 221 1 TTTTATAAAA 0.761125 -80 TATGTAATATTTTTCTAAAATGAACTAATCGTAC 31 30 0 TTTTAAAGAA 0.871839 -37 ATTTACCCCATTTTACAACGAAAAAGAAAGTGCGG 32 35 1 TTTTAAAAAA 0.965631 -266 TTGTGTATTTTTATAGAAAGATAAATGCGTGTTAA 32 77 1 TTATAAAAAA 0.937282 -224 ATACACATATTTATATAATGATAAACTATGTAC 33 9 0 TTATAAAAAA 0.937172 -59 ATTTTAATCTTTTCAAATCAAAAAGCCTAGAAAA 35 10 1 TTTTAAAAAA 0.904689 -157 **** ** * *** Masking position 2 Map Score: 21.3136 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 110 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 4 ATTATCATTCACAATTTATTTTGTTTTACGATATAA 5 97 0 ACTTTTTTTT 0.720365 -196 TGAGAATATAGCTTACTTTTTTCTCTGTATATATAG 5 211 0 GCACTTTTTT 0.720796 -82 GCCGTTTGTGGCTCATATTTTTGTGTGGTGCAATGA 6 81 1 GCATTTTTTT 0.939011 -92 AATTTACCGCACTTTTGTTTTTTTATAAAAAACT 11 9 0 ACTTTTTTTT 0.720365 -173 GGTTAAAAATGCTGATGATTTTACACGAAAATAGAG 14 25 1 GCATTTTTCC 0.751444 -152 CAGGTAACTTGCACCTCCTTTTCTATTTTGAAGTTA 15 153 1 GCCTTTTTTT 0.927005 -38 AGAGAAGAGAGCATTTCATTTTTTCTGCAGTTTATT 16 28 1 GCTTTTTTTT 0.972158 -253 CATTTTTTCTGCAGTTTATTTTTCATTCGATAAATT 16 44 1 GCTTTTTTCT 0.96397 -237 AATTATCATTGCCTTTCTCTTTTTCTTTTGATAAAA 16 169 1 GCTTCTTTTT 0.928758 -112 TGCTTATCCTTTTACTTTAAATGAACA 18 12 0 GCATTTTTCT 0.921859 -17 TATAAATCGCCCCGCTGTTTTTGCCTTTCAAAAGCA 24 45 1 CCCTTTTTCT 0.526181 -100 GCATATTGATGCCCTTTATTTTGTCTATCAATCAAC 26 260 1 GCTTTTTTTT 0.972158 -41 TTAGCAAAGTGCATATATTTTTTAATATTCGTTTGA 27 52 1 GCATTTTTAT 0.568482 -129 GACTAGAATTGCGCTCTATTTTATTCACTCTTAATT 27 137 1 GCTCTTTTTC 0.600055 -44 AGATTTTTCAGCAAATCTTTTTGTTTAAGTTTGACT 30 22 1 GCATTTTTTT 0.939011 -117 TGCCCAACATGCAGTTGTCTTTTCATTTAAGTCAAA 30 51 0 GCTTCTTTCT 0.909001 -88 TTTTGAAAAGGCGATTTAATTTGCCTTATGATGGAA 30 106 1 GCTTATTTCT 0.656847 -33 AAAAATTACCGCACTTTCTTTTTCGTTGTAAAATGG 32 42 0 GCTTTTTTCT 0.96397 -259 TATTTAACACGCATTTATCTTTCTATAAAAATACAC 32 79 0 GCTTCTTTTT 0.928758 -222 ATTTAAACGGGCGTTTTCTTTTTTGTTTAAATTCTT 34 24 1 GCTTTTTTTT 0.972158 -204 GCGGTGCATTGCCCCTTTTTTTATTCTTAGGGAAAG 34 117 0 GCCTTTTTTC 0.764953 -111 TCGCCAAATTCCTATTTCTTTTGTTTTCTTTGTTTT 34 201 1 CCTTTTTTTT 0.799388 -27 TGGGTCGCCTGCGATTTTCTTTCTTTTAACATTAAT 35 124 1 GCTTCTTTTT 0.928758 -43 ** ** **** * * Masking position 10 Map Score: 27.7101 Number of sites scoring better than the average of aligned sites = 310 Number in coding regions = 230 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 5 CAACCTTTTTAGTTAGCGGATAATTTCCTTTATTGA 1 65 1 ATAGAAATTT 0.840724 -92 TATAAACCTCATTTAACTGATATTTTATCAAGCTAA 5 12 1 ATAGAATTTT 0.929683 -281 TATTACCTAAAATGTTGCGCGATTTTACCCTGTTTA 7 25 1 ATTGCATTTT 0.769287 -207 AGGGTTGCGGATTATACCGATTTTTTACGCTCCGC 9 88 0 ATTGATTTTT 0.872817 -111 TATGGTTTAAATTGTTTTGCTAATTTAGACGTTTGG 10 31 0 ATTGCAATTT 0.571081 -126 TTTCGTGTAAAATCATCAGCATTTTTAACCGCACTT 14 19 0 ATAGCTTTTT 0.596894 -158 AATTTTTGAGAGGATGAGGATATTTTTATAATTCCA 16 76 1 AGTGAATTTT 0.686649 -205 CTATATTTTAATTAATTTGATATTCTGATCTTGAAA 19 105 0 ATAGAATTCT 0.669604 -35 ATTTTACCCGAATTTTCAGACTTTCTGAAATCAATC 23 43 1 ATTGATTTCT 0.512666 -170 TCAATCCGCAAATGAAGGGAATTTTTTTATTTTATT 23 73 1 ATAGATTTTT 0.863893 -140 TTTGCGACCTATTTATATGAATTTTTAAGTGTGGAC 23 149 1 ATAGATTTTT 0.863893 -64 GGAAAACACAATTAAGCGGAGTATTT 23 197 1 ATAGATATTT 0.717035 -16 TTTTTGCCTAATTGTATAGAAATTTTGTTTTTACGC 26 73 1 ATTGAATTTT 0.934621 -228 TTTATACTTTTGTCAATGGAAAATTTGTGTTGATTT 26 218 0 TTAGAAATTT 0.343438 -83 AAAGGGCATCAATATGCCGATTTTTTATACTTTTGT 26 241 0 ATTGATTTTT 0.872703 -60 TTTGTCTATCAATCAACAGAAATTTTAGGAGT 26 279 1 ATAGAATTTT 0.929683 -22 TTCGTCAAATAAGAAACGGAAATTTTTAAAAAAAAC 27 89 0 AGAGAATTTT 0.669604 -92 TTTTAATCTAACTCTGAGGATATTTT 28 1 0 ATTGAATTTT 0.934621 -279 CAAAATGTTAAATTTTATGAGATATTGATCACATTT 28 87 0 ATTGAATATT 0.435122 -193 AATTTTGCGCATTATAGTGAGAATTTGGTAATCCTG 28 225 0 ATTGAAATTT 0.850906 -55 AAATTTGGAGAATGAAAGGATAATTTGTATGGGA 28 256 1 ATAGAAATTT 0.840724 -24 ATTAACTTAAATTAAGAAGATTATTTAT 29 58 1 ATAGATATTT 0.717035 -18 GAATTTTGCTGAGATTTTTCAGCAAATC 30 3 1 ATTGAATTTT 0.934621 -136 TATAAATATGTGTATAATGATATTTTCTTACTTAAA 33 29 1 TTTGAATTTT 0.586205 -39 AAGAAATAGGAATTTGGCGAAATTTTACGGACGTAA 34 185 0 ATTGAATTTT 0.933731 -43 * * * ** ***** Masking position 16 Map Score: 27.38 Number of sites scoring better than the average of aligned sites = 278 Number in coding regions = 193 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 6 GCGTATAGCGGTATTTTAGCTTGATAAAATATCAGTTAA 5 24 0 GTTTTTAATA 0.41108 -269 CTCAATGAGTTTAATTTAATTGCAATTTAAAATTTTATT 7 192 0 TTATTTAAAA 0.950301 -40 AGTTTTTTATAAAAAAACAAAAGTGCGGTA 11 2 1 GTTTTTAAAA 0.667097 -180 GAGCATATTGTTTAATTATTGACAATAAAGCGTAAAACT 11 65 1 TTAATTAAAA 0.701821 -117 CGAAAGGGTGTTTTTTTAATCTTAACGGAGCACTAAT 16 254 1 TTTTTTAAAA 0.869971 -27 TTGTTCATTTAAAGTAAAAGGATAAGCA 18 4 1 TTATTTAAAA 0.86702 -25 ATGGCAAGATTTTATTTATAATAAAATAAAAAAATTCCC 23 89 0 TTATTTAAAA 0.518817 -124 AAAGCAGTTTTTTAATTACTAACAACACACACATATTAA 24 75 1 TTAATTAAAA 0.708915 -70 AAAATTTCTGTTGATTGATAGACAAAATAAAGGGCATCA 26 266 0 TTATTGAAAA 0.659886 -35 TTTAATTTACCTAAATACAATTAAGAGTGA 27 161 0 TTATTTAATA 0.859143 -20 GATTATTTTATGGATTTATATGCAAAGCATATACCTATT 28 42 1 TGATTTAAAA 0.659314 -238 ATGATAAAGATTSSTTTAATGCCATATTAACATTAGCAG 28 189 1 TTSTTTAATA 0.87004 -91 AATAATCTTCTTAATTTAAGTTAATAACATCCACATTAA 29 44 0 TTATTTAATA 0.807567 -32 CAGTTGTCTTTTCATTTAAGTCAAACTTAAACAAAAAGA 30 37 0 TTATTTAAAA 0.950661 -102 GCCGTTATTTAAGCAAAACGTACGATTAGTTC 31 4 1 GTATTTAAAA 0.853043 -63 ATCTATTGTATTTATTTAACACGCATTTATCTTTCTATA 32 88 0 TTATTTACAA 0.659994 -213 CCATCGTACATTATTTTATCGAGATCGCACTCGAAGGGG 32 203 1 TTTTTTAATA 0.699004 -98 TATACACATATTTATATAATGATAAACTATGTAC 33 6 0 TTATATAAAA 0.567042 -62 AGATCTTTGGTTGATTTAGTCAAAATGAACCAGAAAAAC 34 61 0 TTATTTAAAA 0.776156 -167 GCGATTTTCTTTCTTTTAACATTAATTTAAAGAGAACAT 35 134 1 TTTTTTAAAA 0.865775 -33 ** ***** ** * Masking position 8 Map Score: 15.6427 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 112 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 7 ATAAACCTCATTTAACTGATATTTTATCAAGCTA 5 13 1 TTTACTGTTT 0.968686 -280 ATGAGTTTAATTTAATTGCAATTTAAAATTTTAT 7 193 0 TTTATTGTTT 0.670788 -39 GCAAAGCGCTTTTGACTGGAGTTTATGGTTTAAA 10 56 0 TTTGCTGTTT 0.807591 -101 TGCGAATTTCTCCGTATTTTAATCTTCAGG 10 137 0 TTTCCCGTTT 0.699784 -20 AAAGCTCCAGTTTAAATGTTATTCAAGAATAGAA 11 154 0 TTTAATGTTC 0.509977 -28 CATCAGCATTTTTAACCGCACTTTTCTTTTT 14 8 0 TTTACCGTTT 0.944993 -169 ATAGAGCTTGTTTATCTGCATTTTTTCAGTATAA 14 55 1 TTTACTGTTT 0.968686 -122 AGCATTTCATTTTTTCTGCAGTTTATTTTTCATT 16 37 1 TTTTCTGTTT 0.877383 -244 TGCGGTAAATTTTAACTGGATTATTTAGTAAATA 16 116 1 TTTACTGTAT 0.68879 -165 TGCGGTGCATTTTACCCGAATTTTCAGACTTTCT 23 35 1 TTTACCGTTT 0.944993 -178 TTGCGACCTATTTATATGAATTTTTAAGTGTGGA 23 150 1 TTTAATGTTT 0.907531 -63 CTTAATTGTGTTTTCCTGCTTTTTAGCAGTCCAC 23 179 0 TTTTCTGTTT 0.877383 -34 TAAACTGGTTTTTAACCGCACTTTATGGTATAAA 24 17 1 TTTACCGTTT 0.944993 -128 ATTTCTCAAGTGTAAATGCGATTTTCCTGAATGT 25 44 0 TGTAATGTTT 0.509977 -170 AATGCTAGATTTTAAAAGTCGTTTACTCAAAATA 26 21 1 TTTAAAGTTT 0.725198 -280 TGTGGCGGATTTTATCAGTTTTTTTTCACGGAAT 26 112 0 TTTACAGTTT 0.892681 -189 TATCGTTATTTTTACAAGCTCTTTCAATATGGGC 26 160 0 TTTAAAGTTT 0.725198 -141 GAATTTTGCTGAGATTTTTCAGCAAAT 30 4 1 TTTTCTGTTT 0.877383 -135 AAAACGCCCGTTTAAATGGCGTTTAAATCT 34 7 0 TTTAATGTTT 0.907531 -221 **** *** *** Masking position 3 Map Score: 20.2223 Number of sites scoring better than the average of aligned sites = 325 Number in coding regions = 222 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 8 ATCGCGCAACATTTTAGGTAATAAATTAAGA 7 17 0 ATTTTAGGAA 0.963768 -215 TTCTAATCTATTTTTAGGGAAAAAGTAAAGG 7 113 0 TTTTTAGGAA 0.856319 -119 AACTTTATTTATTTTAGGAATTGATTGTT 13 36 1 ATTTTAGGAT 0.932412 -19 TTAGGCAAAAATTTTAGGGTAGAGAAGAATA 26 53 0 ATTTTAGGTA 0.771681 -248 ATCAACAGAAATTTTAGGAGT 26 290 1 ATTTTAGGGT 0.722076 -11 AGATGTGATTATTTTATGGATTTATATGCAA 28 36 1 ATTTTATGAT 0.795614 -244 GCATATACCTATTTTAAGAAAATGTGATCAA 28 68 1 ATTTTAAGAA 0.839667 -212 CANACCCCGCATTTTATGGATTTTAATGTGG 29 22 1 ATTTTATGAT 0.795614 -54 AAAAATTAGCATTTTATGAAAAAACGAGTAT 32 142 1 ATTTTATGAA 0.882427 -159 TATCAAACTAATTTTTGGTAATTAATTA 32 283 1 ATTTTTGGAA 0.754962 -18 GCACATCCTTATTTTAAGTAAGAAAATATCA 33 46 0 ATTTTAAGAA 0.83969 -22 CTTTGAGCGGTTTTTAGGAAAATTGCTGGGT 35 98 1 TTTTTAGGAA 0.856318 -69 ******** ** Masking position 5 Map Score: 6.58808 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 105 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 9 TCCAACCTTTTTAGTTAGCGGATAATTTCCTT 1 63 1 TTAGTGCGGA 0.803898 -94 CTATCTTAGTTTGAGAACTAAATCAAA 4 19 0 TTAGTGAGAA 0.702196 -17 ATATAGACAAAAAGCCTGCGAATTTTATACTT 5 185 0 AAAGCGCGAA 0.947506 -108 CTATATAGAAATAGACGGCGAATTCTAATAGT 11 101 0 ATAGCGCGAA 0.972066 -81 TTGGCACCAAATAGGTTGCGAATTATACTGAA 14 79 0 ATAGTGCGAA 0.967787 -98 TTAAAATAAAAGCTTGCAAATAGGGTTGTC 15 9 1 AAAGTGCAAA 0.834047 -182 AGAATGGCAGATAGGCGGCGGATTTTATCAAA 16 195 0 ATAGCGCGGA 0.930347 -86 GACGTATAGGATAGTTGGAGAAAGAAA 20 11 1 ATAGTGAGAA 0.868974 -17 TTGATTTCAGAAAGTCTGAAAATTCGGGTAAA 23 45 0 AAAGCGAAAA 0.562401 -168 ATTCATATAAATAGGTCGCAAATTCTACGGAA 23 139 0 ATAGTGCAAA 0.906456 -74 TTACTATATTAAAGGTCGCAAATTATACTGAC 25 87 0 AAAGTGCAAA 0.834048 -127 TCAAAAGCAGTTAGGCTGCGTAGTGTGCCCAA 30 80 0 TTAGCGCGTA 0.635171 -59 **** * ***** Masking position 3 Map Score: 5.13999 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 70 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 10 AAGTAAGCTATATTCTCAAATCACTTTCGA 5 229 1 TATTCTCAAA 0.759211 -64 ACTAAAAGAATATTCTCAAATTCGAAAGTG 5 250 0 TATTCTCAAA 0.759211 -43 AACTATTATCAATTTTCAAA 8 1 0 AATTTTCAAA 0.725563 -28 ATCAGCCACCAATCTGCAAAGGCAAGGAAC 9 143 0 AATCTGCAAA 0.770573 -56 AGAAAAACCTCAAAATGAAGCCAC 14 163 0 AAACCTCAAA 0.809719 -14 ATCGCAATTCTAACTTCAAAATAGAAAAGG 15 169 0 TAACTTCAAA 0.726679 -22 AATGAAAAATAAACTGCAGAAAAAATGAAA 16 41 0 AAACTGCAGA 0.439758 -240 ATTTTACCCGAATTTTCAGACTTTCTGAAA 23 43 1 AATTTTCAGA 0.571673 -170 TTCTGAAATCAATCCGCAAATGAAGGGAAT 23 65 1 AATCCGCAAA 0.822706 -148 TTTTTAAAAAAAACTTCAAACGAATATTAA 27 73 0 AAACTTCAAA 0.754905 -108 AAAATATCCTCAGAGTTAGATTAA 28 5 1 TATCCTCAGA 0.800222 -275 GCATTTATCCTCANACCCCGCATTT 29 6 1 TATCCTCANA 0.888074 -70 AGAATATCCTTATTTTCAAATCAAACTTTT 35 43 0 TATTTTCAAA 0.695322 -124 ********** Masking position 8 Map Score: 4.19489 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 140 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 11 TGAGTTATCCAATAAAAAATGTGATTTCCCTTTGAC 1 98 1 AAAAATGATT 0.910725 -59 TATACTTTTCAAGCAAAATTGCAAGTTTTGTATGCA 5 156 0 ACAAATAAGT 0.565991 -137 CTTTGGCAAAAATAAAATTTTAAATTGCAATTAAAT 7 182 1 AAAAATAATT 0.84252 -50 GCCCAGAAGCAAGAAAAATTCTTATTCTGTTCACCA 12 171 0 AAAAATTATT 0.681158 -101 TATCAAATTAATTAAAATATAGGAGTGCATA 19 119 1 AAAAATGAGT 0.863977 -21 ACCGAAATCAACACAAATTTTCCATTGACAAAAGTA 26 214 1 ACAAATCATT 0.66579 -87 TCAGAGTTAGATTAAAAGATGTGATTATTTTATGGA 28 20 1 AAAAATGATT 0.941877 -260 AAGAAATGGAACAAAATGTTAAATTTTATGAGATA 28 99 0 AAAAATAATT 0.844364 -181 CCGTTATTTAAGCAAAACGTACGATTAGTTCATTNT 31 12 1 AAAAATGATT 0.943031 -55 TGACTAAATCAACCAAAGATCTGATTTTTTCTTAGT 34 78 1 ACAAATGATT 0.905043 -150 CAAAAAGCCTAGAAAAAAGTTTGATTTGAAAATAAG 35 29 1 AAAAATGATT 0.941877 -138 * **** * **** Masking position 7 Map Score: 3.17536 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 47 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 12 TTTCAAGCACTTCTTAAATCCGATAGAAGA 6 13 0 TTCTTAAATC 0.420943 -160 TGATTTTCTTAATTTATTACCTAAA 7 6 1 TTCTTAATTT 0.812258 -226 ATAAGAATTTTTCTTGCTTCTGGGCGCCGA 12 182 1 TTCTTGCTTC 0.703749 -90 TATTAAGCGTTTCTTACTTCATCTAACTTT 13 12 1 TTCTTACTTC 0.926548 -43 CAATCGCAATTCTAACTTCAAAATAGAAA 15 172 0 TTCTAACTTC 0.573083 -19 AAAATAACGATACTTACTTTCGGTTGTGTC 26 182 1 TACTTACTTT 0.620025 -119 TTGNTTCCATTTCTTACATTTTTATTACTA 28 120 1 TTCTTACATT 0.757973 -160 ATAAATAATCTTCTTAATTTAAGTTAATAA 29 56 0 TTCTTAATTT 0.812258 -20 TAATGATATTTTCTTACTTAAAATAAGGAT 33 43 1 TTCTTACTTA 0.707362 -25 TTTGTTTAAATTCTTAGTTTTTCTGGTTCA 34 45 1 TTCTTAGTTT 0.871845 -183 ATCTGATTTTTTCTTAGTTTTCTTTCCCTA 34 96 1 TTCTTAGTTT 0.871845 -132 TTCTTTTGTTTTCTTTGTTTTG 34 216 1 TTCTTTGTTT 0.603842 -12 GCCTGCGATTTTCTTTCTTTTAACATTAAT 35 130 1 TTCTTTCTTT 0.774548 -37 ********** Masking position 4 Map Score: 4.77566 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 87 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 13 TTTTTAGTTAGCGGATAATTTCCTTTATTG 1 70 1 GCGGATAATT 0.867349 -87 ACCTCATTTAACTGATATTTTATCAAGCTA 5 17 1 ACTGATATTT 0.651671 -276 ATAAATTGTGAATGATAATTAAAAGGAATA 5 114 1 AATGATAATT 0.833195 -179 ACCATCTACGTAGGATAATTAAGATTACTC 12 145 0 TAGGATAATT 0.666718 -127 TTGAGAGGATGAGGATATTTTTATAATTCC 16 81 1 GAGGATATTT 0.860242 -200 AGAGAAAGGCAATGATAATTTAGCTTCCTC 16 159 0 AATGATAATT 0.833195 -122 CGCACTTTTAACTGATAAATGATGAAAA 23 9 0 ACTGATAAAT 0.4405 -204 ATCTAACTCTGAGGATATTTT 28 2 0 GAGGATATTT 0.860242 -278 TGGAGAATGAAAGGATAATTTGTATGGGA 28 261 1 AAGGATAATT 0.905888 -19 TGCGGGGTTGAGGATAAATGC 29 3 0 GAGGATAAAT 0.72147 -73 ATATGTGTATAATGATATTTTCTTACTTAA 33 34 1 AATGATATTT 0.749087 -34 ********** Masking position 5 Map Score: 3.07755 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 100 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 14 CGGATAATTTCCTTTATTGAGTTATCCAAT 1 81 1 CCTTTATTGA 0.930529 -76 TGTTTGATCCTTTATTGATCCTAGATGT 2 19 0 CCTTTATTGA 0.930529 -18 AGAATTGCGTCCTTTATTAAATTTGTCATT 7 140 1 CCTTTATTAA 0.753919 -92 TTAAACGGCTCTCATATTGAGAGCTCGTAG 15 53 0 CTCATATTGA 0.817351 -138 TTAATGTAATCATTTATTGAACGGGCATGA 15 79 1 CATTTATTGA 0.81904 -112 ATTTAGCTTCCTCTTATTGATCTATTTACT 16 142 0 CTCTTATTGA 0.877737 -139 TAACAACACACACATATTAACAAGGCTTAA 24 94 1 CACATATTAA 0.505822 -51 TTTGTGTGAGCCCATATTGAAAGAGCTTGT 26 151 1 CCCATATTGA 0.929776 -150 ********** Masking position 6 Map Score: 1.05902 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 38 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 15 GCATAAAGTAGGTTGTATTCCTTTTAATTAT 5 128 0 GGTTGTTTCC 0.979873 -165 TAAAAAGTGCGGTTGTTTTTCAAGCACTTCT 6 29 0 GGTTGTTTTC 0.978309 -144 TTGCAAATAGGGTTGTCTTTCTATAGAATCT 15 24 1 GGTTGTTTTC 0.978307 -167 ACTTACTTTCGGTTGTGTCTCACCGAAATCA 26 193 1 GGTTGTTCTC 0.95309 -108 TAAGATTAATGGTTGTGTTCATAAGAACACT 32 249 1 GGTTGTTTCA 0.90319 -52 ****** **** Masking position 6 Map Score: 0.764065 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 14 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701