AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i03010_hinf_reg_300.orf -o03010_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: 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 HI0518 83 purine-nucleoside phosphorylase (deoD) #8 HI0519 98 transport protein, putative #9 HI0521 212 conserved hypothetical protein #10 HI0531 231 ribosomal protein S21 (rpS21) #11 HI0546 28 primosomal replication protein N (priB) #12 HI0547 198 ribosomal protein S6 (rpS6) #13 HI0548 169 translation initiation factor 1 (infA) #14 HI0580 156 ribosomal protein S7 (rpS7) #15 HI0581 181 ribosomal protein S12 (rps12) #16 HI0582 300 glucose inhibited division protein (gidA) #17 HI0638 128 conserved hypothetical protein #18 HI0639 22 adenylosuccinate lyase (purB) #19 HI0640 271 ribosomal protein L10 (rpL10) #20 HI0641 54 ribosomal protein L7/L12 (rpL7/L12) #21 HI0758 176 ribosomal protein L31 (rpL31) #22 HI0775 205 transcriptional regulator #23 HI0776 190 ribosomal protein S10 (rpS10) #24 HI0787 300 H. influenzae predicted coding region HI0787 #25 HI0788 280 ribosomal protein L14 (rpL14) #26 HI0792 36 ribosomal protein S8 (rpS8) #27 HI0798.1 28 ribosomal protein L36 (rpL36) #28 HI0799 139 ribosomal protein S13 (rpS13) #29 HI0801 27 ribosomal protein S4 (rpS4) #30 HI0802 31 DNA-directed RNA polymerase, alpha chain (rpoA) #31 HI0803 40 ribosomal protein L17 (rplQ) #32 HI0880 212 ribosomal protein L21 (rpL21) #33 HI0908 79 H. influenzae predicted coding region HI0908 #34 HI0909 124 preprotein translocase SecA subunit (secA) #35 HI0910 64 mutator mutT protein (mutT) #36 HI0911 108 glutathione-regulated potassium efflux system protein (kefC) #37 HI0912 100 H. influenzae predicted coding region HI0912 #38 HI0913 144 ribosomal protein S2 (rpS2) #39 HI0951 213 ribosomal protein L28 (rpL28) #40 HI0952 124 DNA repair protein (radC) #41 HI0965 300 ribosomal protein S20 (rpS20) #42 HI0997 300 H. influenzae predicted coding region HI0997 #43 HI0998 180 ribosomal protein L34 (rpL34) #44 HI1219 279 cytidylate kinase 1 (cmkA) #45 HI1220 75 ribosomal protein S1 (rpS1) #46 HI1316 300 H. influenzae predicted coding region HI1316 #47 HI1317 81 conserved hypothetical protein #48 HI1318 267 translation initiation factor 3 (infC) #49 HI1319 138 ribosomal protein L35 (rpL35) #50 HI1320 66 ribosomal protein L20 (rpL20) #51 HI1443 300 ribosomal protein L13 (rpL13) #52 HI1472 67 iron chelatin ABC transporter, periplasmic-binding protein, putative #53 HI1475 227 H. influenzae predicted coding region HI1475 #54 HI1476 227 transcriptional regulatory protein #55 HI1630 166 ribosomal protein L25 (rpL25) Motif number 1 GATTATATAAAAAGTGCGGTTGTTTTTCAA 6 37 0 AAAGTGCGGT 0.997869 -136 AATCAATTAAAAAGTGCGGTAAAAAATGAC 7 19 1 AAAGTGCGGT 0.997869 -65 AAAAATGAATAAAGTGCGGTCATTTTTTAC 7 37 0 AAAGTGCGGT 0.997869 -47 ACGTTTACAAAAAGTGCGGTGAAAATTCGC 8 11 1 AAAGTGCGGT 0.997869 -88 TTTAATAAGAAAAGTGCGGTTATTATAGGG 13 19 1 AAAGTGCGGT 0.997869 -151 TAAAAAAACAAAAGTGCGGTAAATTTTAAT 15 20 1 AAAGTGCGGT 0.997869 -162 AAAAAGAAAAGTGCGGTTAAAAATGCT 21 8 1 AAAGTGCGGT 0.997869 -169 CCTAAAAGAAAAGGTGCGGGTT 24 3 0 AAGGTGCGGG 0.966879 -298 TATAATTCCAAAAGTGCGGTAAATTTTAAC 25 102 1 AAAGTGCGGT 0.997869 -179 TTATCAGTTAAAAGTGCGGTGCATTTTACC 32 21 1 AAAGTGCGGT 0.997869 -192 TGAACAATCAAAGTGCGGTGATTTTTCAC 35 10 1 AAAGTGCGGT 0.997869 -55 AGGTATGAAAAAGGTGCGGTGAAAAATCAC 35 28 0 AAGGTGCGGT 0.991519 -37 TTTATACCATAAAGTGCGGTTAAAAACCAG 38 21 0 AAAGTGCGGT 0.997869 -124 TAAAATCCATAAAATGCGGGGTTGAGGAT 45 17 0 AAAATGCGGG 0.860717 -59 ATTGCTAACAAAAGTGCGGTAGT 51 4 0 AAAGTGCGGT 0.997869 -297 AACGAAAAAGAAAGTGCGGTAATTTTTTGT 51 51 1 AAAGTGCGGT 0.997869 -250 ********** Masking position 5 Map Score: 68.5822 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 TGTTTTACGATATAATACGAGGCATCCAGCTGTTTTA 5 75 0 TAAATCGAAC 0.562753 -218 TTGAAAAGTATAAAATTCGCAGGCTTTTTGTCTATAT 5 180 1 TAAATCGCCT 0.989962 -113 GCACTTTTTATATAATCCGTGCCCATTATGAGCCGTT 6 50 1 TAAATCGTCT 0.813197 -123 AAAGTGCGGTGAAAATTCGCCGACTTTTCATAAGAAA 8 21 1 GAAATCGCCT 0.895648 -78 GTTAAGTTAATAAAATTCGGCTTATTCTACTTGTTTT 8 55 0 TAAATCGGAC 0.581478 -44 TACCATTGCGTACAATACGAAACCATTTTCAAAGGGG 9 181 1 TAAATCGACT 0.916663 -32 AAAAAATCGGTATAATCCGCAACCCTTAGCCACATTG 12 98 1 TAAATCGCCT 0.989962 -101 TAAAAACGGCTATAATCCGCCCGTTTTTCTTAACTTT 13 133 1 TAAATCGCTT 0.857213 -37 TCCTGAAGATTAAAATACGGAGAAATTCGCA 14 136 1 TAAATCGGAT 0.85049 -21 GTAAAACTATTAGAATTCGCCGTCTATTTCTATATAG 15 96 1 TAAATCGCCT 0.989962 -86 ATTTTTTCAGTATAATTCGCAACCTATTTGGTGCCAA 21 74 1 TAAATCGCCT 0.989962 -103 CGCGTGAGTGAATAATACGCCATAATTGGCACCAAAT 21 99 0 AAAATCGCAT 0.735053 -78 TGTCTTTCTATAGAATCTACGAGCTCTCAATATGAGA 23 37 1 TAAATTACCT 0.552651 -154 TTTCTTTTGATAAAATCCGCCGCCTATCTGCCATTCT 25 190 1 TAAATCGCCT 0.989962 -91 AAAATTCGGGTAAAATGCACCGCACTTTTAACTGATA 32 22 0 TAAATCACAT 0.818956 -191 GATTTTTCCGTAGAATTTGCGACCTATTTATATGAAT 32 134 1 TAAATTGCCT 0.928077 -79 AGATTTCCGTTACAATACACGCAATTTTCATAATAAA 33 42 1 TAAATCACAT 0.818956 -38 ACAAAGTCAGTATAATTTGCGACCTTTAATATAGTAA 39 82 1 TAAATTGCCT 0.928077 -132 AAAAAACTGATAAAATCCGCCACACATCGTTTGTGTG 41 122 1 TAAATCGCAT 0.979274 -179 ATTCTAGTCATAAAATACGCGTTCGTCAAATAAGAAA 43 109 0 TAAATCGCCC 0.96014 -72 TAGAAGAATATAGAATATGATAAAGATTSSTTTAATG 44 173 1 TAAATTGAAT 0.408094 -107 AAATTCTCACTATAATGCGCAAAATTTGGAGAATGAA 44 235 1 TAAATCGCAT 0.979274 -45 GTGAATACTATAGAATTCGCGAGACTTTGCTCGTTCC 48 30 1 TAAATCGCAT 0.979274 -238 AAAAAACGAGTATAATACGCCGACCCTGTAAATGTGC 51 160 1 TAAATCGCCT 0.989962 -141 ** *** *** * * Masking position 6 Map Score: 34.758 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 96 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 3 TATAATCACGCCTCTTTTTTTAACAAGGAAAGATA 1 6 0 CCTTTTTAAA 0.721355 -151 GTGATTTCCCTTTGACTATCTTCGCAACAACAGGTAATAT 1 118 1 TTTTTCTAAA 0.89741 -39 TACTTTTTTCTCTGTATATATAGACAAAAAGCCTGCGAAT 5 194 0 TCTTTATAAA 0.751552 -99 AACCTTCCTCTAAATGTTTAATTACTAAAAGAATATTC 5 265 0 TCTTTTTAAA 0.937795 -28 TTCGGCTTATTCTACTTGTTTTCTTATGAAAAGTCGGCGA 8 37 0 TCTTTTTAAA 0.937795 -62 TGATTTTCTTAATTTATTACCTAAAATGTTGCGCGA 10 7 1 TCTTTATTAA 0.402282 -225 GCATTCTATCCTTTACTTTTTCCCTAAAAATAGATTAGAA 10 104 1 CTTTTTTAAA 0.768421 -128 ACAATATCGACCTTCTTTTTTGTTCAAAAAGAACTCAAAC 12 43 1 CCTTTTTAAA 0.721355 -156 TATAGCCGTTTTTAGCTTTCTACGAAAGAAAAAATAATAT 13 107 0 TTTTTCTAAA 0.89741 -63 TTTACCGCACTTTTGTTTTTTTATAAAAAACT 15 3 0 TTTTTTTAAA 0.950795 -179 TGTCAGGTGTTTTAAATTTCTGTAGAATAACGCCAATTTT 16 246 1 TTTTTCTAAA 0.897409 -55 ATCTATCTCTATTTATTCTGATCAAAAAATTGGCG 16 276 0 TCTTTATAAA 0.782051 -25 GAATTTGGCTCTTTTTTCAACAATATTCTTTAC 19 4 1 TTTTTTTAAA 0.950796 -268 AGCTTGTTTATCTGCATTTTTTCAGTATAATTCGCAACCT 21 59 1 TCTTTTTTAA 0.73875 -118 TCAGTATTTGTTTAGGTGTTATGTCAATAACACCTAAAAG 24 25 0 TTTTTTAAAA 0.863843 -276 TTTTCTGCAGTTTATTTTTCATTCGATAAATTTTTGAGAG 25 48 1 TTTTTCAAAA 0.741725 -233 TCATTGCCTTTCTCTTTTTCTTTTGATAAAATCCGCCGCC 25 174 1 TCTTTCTAAA 0.8722 -107 ATGAAGGGAATTTTTTTATTTTATTATAAATAAAATCTTG 32 84 1 TTTTTTTAAA 0.950672 -129 TCGTCTCGTTGTTTATTATGAAAATTGCGTGTA 33 57 0 TCTTTTTTAA 0.738748 -23 TTTTTCTGTTTTTTGTGAAGAATATTGCTATT 34 3 1 TTTTTTTAAA 0.950795 -122 TTTTTTAAAATATCGCTATTTCAATAGCAATATTCTTCAC 34 25 0 TATTTTTAAA 0.676864 -100 AATTATTTTTTATCTATAAAAATATTAAATTTTAACTT 37 9 1 TTTTTAAAAA 0.528439 -92 ATCACGTAAATTTTTATTTTAAGGCAATAA 37 81 1 TTTTTTAAAA 0.863369 -20 ACTGACTTTGTTTTCATTTCTCAAGTGTAAATGCGATTTT 39 53 0 TTTTTCTTAA 0.621319 -161 AGGTATATGCTTTGCATATAAATCCATAAAATAATCACAT 44 38 0 TTTTTAAAAA 0.600423 -242 CTGCACCTTATTTATCTTTTAAAATAGGAATAAAC 47 57 1 TTTTTTAAAA 0.818601 -25 GCGGTAATTTTTTGTGTATTTTTATAGAAAGATAAATGCG 51 66 1 TTTTTTTAAA 0.937809 -235 ATACAATAGATTTGTTTTTTAGCGCAAAAAATTAGCATTT 51 116 1 TTTTTTAAAA 0.863369 -185 TTGCCCCTTTTTTTATTCTTAGGGAAAGAAAACTAAGAAA 53 105 0 TTTTTTAAAA 0.863842 -123 TAATCTATTGTTTTACTATTTCGAATAAAAACAATGACTT 54 114 1 TTTTTTTTAA 0.781704 -114 ATTTTAATCTTTTCAAATCAAAAAGCCTAGA 55 2 1 TTTTTTTAAA 0.950773 -165 GATTATAGAATATCCTTATTTTCAAATCAAACTTTTTTCT 55 39 0 TATTTTTAAA 0.676864 -128 CGCCTGCGATTTTCTTTCTTTTAACATTAATTTAAAGAGA 55 129 1 TTTTTTTAAA 0.950672 -38 *** * *** * ** Masking position 9 Map Score: 32.5395 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 196 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 4 TATCTTTCCTTGTTAAAAAAAGAGGCGTGAT 1 10 1 TTTTAAAAAA 0.873408 -147 TTTTTATTCATTATTAAAAATAAGGAAAAATT 7 62 1 TTTTAAAATA 0.917736 -22 ATGCAAACGGTTACTCAAAATAAATATGTTTT 9 92 0 TTCTAAAATA 0.920473 -121 CTTTACTTTTTCCCTAAAAATAGATTAGAATT 10 114 1 TCCTAAAATA 0.871018 -118 AGTTTTTTATAAAAAAACAAAAGTGCG 15 6 1 TTATAAAAAA 0.764921 -176 GAATAGAATGTTGTTCAAAAAATCTACTTCTA 15 130 0 TTTTAAAAAA 0.873408 -52 GTAAAGAATATTGTTGAAAAAAGAGCCAAATT 19 12 0 TTTTAAAAAA 0.873408 -260 AAGGATTGTTTAAAACACTATCAAAAT 22 189 0 TTTTAAAACA 0.748491 -17 TTAAGTACCATTATTAAAAATATTTTTTTCAG 24 61 0 TTTTAAAATA 0.917736 -240 GAATATCAAATTAATTAAAATATAGGAGTGCA 28 116 1 TTATAAAATA 0.839702 -24 TGCACAATAATTTTTTAAAATATCGCTATTTC 34 43 0 TTTTAAAATA 0.826928 -82 TTATTTTTTATCTATAAAAATATTAAATTTTA 37 13 1 TCATAAAATA 0.753495 -88 TAAAAGTCGTTTACTCAAAATATTCTTCTCTA 41 33 1 TTCTAAAATA 0.920473 -268 CAAATTATCATCATTTAAAAAATTTAATCCTA 42 147 0 TCTTAAAAAA 0.799809 -154 AGTTTTACTAAAAAAATGATCTGCCC 42 285 0 TTCTAAAAAA 0.878425 -16 GAAACGGAAATTTTTAAAAAAAACTTCAAACG 43 81 0 TTTTAAAAAA 0.806883 -100 TTGATCACATTTTCTTAAAATAGGTATATGCT 44 67 0 TTCTAAAATA 0.918951 -213 ACCTTATTTATCTTTTAAAATAGGAATAAAC 47 61 1 TCTTAAAATA 0.862861 -21 AAAAATCTTTTCGCTAAAAATAAAAGATTTCA 48 83 0 TCCTAAAATA 0.871018 -185 CATTTATCTTTCTATAAAAATACACAAAAAAT 51 72 0 TCATAAAATA 0.753495 -229 AAATTAGCATTTTATGAAAAAACGAGTATAAT 51 144 1 TTATAAAAAA 0.764921 -157 TGATATTTTCTTACTTAAAATAAGGATGTGCG 52 46 1 TTCTAAAATA 0.920453 -22 TGGGCGGGAATTATTGAAAACAGGGGCTTTGG 53 152 0 TTTTAAAACA 0.749714 -76 ** ** ****** Masking position 5 Map Score: 25.5384 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 136 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 5 TTATAGCAATTTTTGTTATAGTTCCAACCTTTT 1 41 1 TTTTTATAGT 0.753205 -116 TTTTGCTTTTTGATTTAGTTCTCAAACTAA 4 8 1 TTTTTTTAGT 0.888996 -28 TTTAGTTTTCCTCTAATTGGGTAATAAC 6 155 0 TTTTTCTAAT 0.894693 -18 ATAAATATGTTTTTGATATAAATGAACTGACAA 9 72 0 TTTTTATAAT 0.812181 -141 ACCTCAATGAGTTTAATTTAATTGCAATTTAAA 10 200 0 GTTTTTTAAT 0.773342 -32 TAATCCGCCCGTTTTTCTTAACTTTTCCGCCTA 13 145 1 GTTTCTTAAT 0.653636 -25 GTGCGGTAAATTTTAATCTAGTTTTAATCCTAG 15 33 1 TTTTTCTAGT 0.857065 -149 AATATAGCATTTTTAACCTAGCTTTTGAACTCG 17 77 0 TTTTCCTAGT 0.768328 -52 AACCCGCACCTTTTCTTTTAGGTGTTATTGACA 24 11 1 TTTTTTTAGT 0.888996 -290 TGCTTATCCTTTTACTTTAAATGAACAA 27 7 0 TTTTTTTAAT 0.919011 -22 AATTTTTTTATTTTATTATAAATAAAATCTTGC 32 92 1 TTTTTATAAT 0.812163 -121 ATACTAAATCTTTTAATATAACTTTAAACCACA 36 17 0 TTTTTATAAT 0.812181 -92 AATTTCGTTATTTTACTTTAATTTTATTGAATG 40 39 1 TTTTTTTAAT 0.919012 -86 TACCCTAAAATTTTTGCCTAATTGTATAGAAAT 41 63 1 TTTTCCTAAT 0.824534 -238 TAATCACATCTTTTAATCTAACTCTGAGGATAT 44 14 0 TTTTTCTAAT 0.894692 -266 TCAGCAAATCTTTTTGTTTAAGTTTGACTTAAA 49 29 1 TTTTTTTAAT 0.919012 -110 TGCAGTTGTCTTTTCATTTAAGTCAAACTTAAA 49 45 0 TTTTTTTAAT 0.919012 -94 CTAATCGTACGTTTTGCTTAAATAACGGC 50 7 0 GTTTCTTAAT 0.653636 -60 GGCGTTTTCTTTTTTGTTTAAATTCTTAGTTTT 53 33 1 TTTTTTTAAT 0.919012 -195 AAAGATCTGATTTTTTCTTAGTTTTCTTTCCCT 53 92 1 TTTTCTTAGT 0.815823 -136 **** ***** * Masking position 9 Map Score: 17.078 Number of sites scoring better than the average of aligned sites = 225 Number in coding regions = 155 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 6 TCAATAAAGGAAATTATCCGCTAACTAAAAA 1 70 0 AAATTTCCGC 0.951846 -87 AAGTGCTTGAAAAACAACCGCACTTTTTATA 6 31 1 AAAACACCGC 0.849062 -142 AGTGCGGTAAAAAATGACCGCACTTTATTCA 7 31 1 AAAATACCGC 0.974723 -53 AACAACCCCTATAATAACCGCACTTTTCTTA 13 24 0 ATAATACCGC 0.892901 -146 CGTTTTTCTTAACTTTTCCGCCTAAA 13 154 1 AACTTTCCGC 0.689165 -16 AACTAGATTAAAATTTACCGCACTTTTGTTT 15 25 0 AAATTACCGC 0.951846 -157 ATTTTTAAAGAAAATGATCGCATTTTCACAA 16 49 1 AAAATATCGC 0.643004 -252 TGGAATTATAAAAATATCCTCATCCTCTCAA 25 81 0 AAAATTCCTC 0.771285 -200 AATCCAGTTAAAATTTACCGCACTTTTGGAA 25 107 0 AAATTACCGC 0.951846 -174 TTTTCTTTTGATAAAATCCGCCGCCTATCTG 25 189 1 ATAAATCCGC 0.674619 -92 AATTCGGGTAAAATGCACCGCACTTTTAACT 32 26 0 AAATGACCGC 0.742497 -187 AAATACTCCGCTTAATTGTGT 32 202 0 AAATATCCGC 0.830958 -11 GGTGCGGTGAAAAATCACCGCACTTTGATTG 35 15 0 AAAATACCGC 0.974723 -50 AAAAAAACTGATAAAATCCGCCACACATCGT 41 121 1 ATAAATCCGC 0.674619 -180 GTTTTTTTTAAAAATTTCCGTTTCTTATTTG 43 89 1 AAAATTCCGT 0.643004 -92 AAAATATCCTCAGAGTTAGAT 44 1 1 AAAATTCCTC 0.771285 -279 GATTTGCTGAAAAATCTCAGCAAAATTC 49 8 0 AAAATTCAGC 0.643004 -131 AAATACACAAAAAATTACCGCACTTTCTTTT 51 56 0 AAAATACCGC 0.974723 -245 ***** ***** Masking position 1 Map Score: 14.7806 Number of sites scoring better than the average of aligned sites = 659 Number in coding regions = 413 Number in noncoding regions = 246 Number of orfs with sites within 600 bp upstream = 190 Fraction of orfs with sites within 600 bp upstream = 0.0305172 Motif number 7 AAGAGGCGTGATTATAGCAATTTTTGTTATAGTTC 1 30 1 AATAATTTTT 0.86688 -127 CTTTTCAAGCAAAATTGCAAGTTTTGTATGCATAA 5 153 0 AATAAGTTTT 0.420264 -140 CAATGGTAACAAAATAGACAATTTTGAAAACGTGA 9 154 0 AATCAATTTT 0.525034 -59 AACCGAAAAACTATTATCAATTTTCAAA 11 5 0 AATCAATTTT 0.718226 -24 AGGGTTGCGGATTATACCGATTTTTTACGCTCCG 12 89 0 AATGATTTTT 0.587987 -110 TTTTTCATGAACAATATTATTTTTTCTTTCGTAGA 13 94 1 AATATTTTTT 0.654027 -76 TATTGTTATTATTAAGATCTTTTTTGGTTGTGAGT 16 128 0 AAACTTTTTT 0.377852 -173 ATTTCTGTAGAATAACGCCAATTTTTTGATCAGAA 16 261 1 AAACAATTTT 0.564188 -40 GATGGTGAACAGAATAAGAATTTTTCTTGCTTCTG 19 169 1 AATAATTTTT 0.865688 -103 TTCGTGTAAAATCATCAGCATTTTTAACCGCACTT 21 19 0 AATCATTTTT 0.801345 -158 AATGCAGATAAACAAGCTCTATTTTCGTGTAAAAT 21 42 0 AAACTATTTT 0.277346 -135 AAGTACCATTATTAAAAATATTTTTTTCAGTATTT 24 56 0 AAATATTTTT 0.401982 -245 AAGAGAAGAGAGCATTTCATTTTTTCTGCAGTTTA 25 27 1 AATATTTTTT 0.658404 -254 CAATCCGCAAATGAAGGGAATTTTTTTATTTTATT 32 74 1 AAAAATTTTT 0.768106 -139 TACTCGCCAAAATATTTGTATTTTTTGCATTATTG 36 76 1 AATTATTTTT 0.556648 -33 TTTATCTATAAAAATATTAAATTTTAACTTCTCGT 37 19 1 AATAAATTTT 0.541918 -82 ACCGAAAGTAAGTATCGTTATTTTTACAAGCTCTT 41 171 0 AATTATTTTT 0.569346 -130 TCTCACCGAAATCAACACAAATTTTCCATTGACAA 41 210 1 AAAAAATTTT 0.676775 -91 AAAGGGCATCAATATGCCGATTTTTTATACTTTTG 41 242 0 AATGATTTTT 0.587952 -59 TTGTCTATCAATCAACAGAAATTTTAGGAGT 41 280 1 AAAAAATTTT 0.676775 -21 ACAGAGGTAGATGATGAAAAATTTTTAGGTGTTAT 42 62 1 AATAAATTTT 0.804608 -239 TATGGCAAGTAGGATTAAATTTTTTAAATGATGAT 42 138 1 AATATTTTTT 0.658545 -163 TCGTCAAATAAGAAACGGAAATTTTTAAAAAAAAC 43 89 0 AAAAAATTTT 0.676327 -92 AAATGGAACAAAATGTTAAATTTTATGAGATATT 44 97 0 AATAAATTTT 0.762118 -183 GTTTTTTCATAAAATGCTAATTTTTTGCGCTAAAA 51 132 0 AATAATTTTT 0.86122 -169 AACACTGGGTATCAAACTAATTTTTGGTAATTAAT 51 274 1 AAAAATTTTT 0.768087 -27 AAATCAACCAAAGATCTGATTTTTTCTTAGTTTTC 53 83 1 AATATTTTTT 0.658354 -145 * ** ******* Masking position 4 Map Score: 15.2955 Number of sites scoring better than the average of aligned sites = 374 Number in coding regions = 271 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 8 GCGGAGCGTWAAAAAATCGGTATAATCCGCAA 12 88 1 AAAAACGGTA 0.86477 -111 TAAAAAAGCTCCAGTTTAAATGT 15 169 0 AAAAACTCCA 0.816183 -13 AAATGCAGATAAACAAGCTCTATTTTCGTGTA 21 46 0 AAAAACTCTA 0.511765 -131 TGATACCCGTAAAGAAACGTCAAAATTAGCAG 24 184 1 AAAAACGTCA 0.897302 -117 ATCGAATGAAAAATAAACTGCAGAAAAAATGA 25 43 0 AAAAACTGCA 0.919353 -238 GTAATCGGTAAAAAAATGGTCAATATTATAAA 39 14 0 AAAAAGGTCA 0.884665 -200 ACAAAAGTATAAAAAATCGGCATATTGATGCC 41 241 1 AAAAACGGCA 0.964399 -60 TTGATAGACAAAATAAAGGGCATCAATATGCC 41 259 0 AAAAAGGGCA 0.959647 -42 ATCAGTAGAAAAAAAATGGCCATGGGCAGATC 42 262 1 AAAAAGGCCA 0.90256 -39 GAAATTTTTAAAAAAAACTTCAAACGAATATT 43 75 0 AAAAACTTCA 0.786183 -106 TAATCGTTATAAAGAATGGTTAGAAGAAAAGG 46 67 1 AAAAAGGTTA 0.644223 -234 TTTAAAAGATAAATAAGGTGCAGAGATAACAA 47 48 0 AAAAAGTGCA 0.909156 -34 AACCGTAAAAAAAGCACCGGCAGTAAATCGCC 48 148 1 AAACACGGCA 0.786115 -120 CCTAAGAATAAAAAAAGGGGCAATGCACCGCC 53 122 1 AAAAAGGGCA 0.959647 -106 AAGGTACAGCAAAAAAGGTGTATTAA 54 5 0 AAAAAGTGTA 0.702606 -223 *** ** ***** Masking position 6 Map Score: 9.64556 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 111 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 9 GTTATAGTTCCAACCTTTTTAGTTAGCGGA 1 55 1 CAACCTTTTT 0.733578 -102 CGTAATGTAGTAGGCTTTTT 3 28 1 TAGGCTTTTT 0.911224 -10 ATAAAATTCGCAGGCTTTTTGTCTATATAT 5 189 1 CAGGCTTTTT 0.922422 -104 ATTTTACACACAAGATTTTTAAAGAAAATG 16 35 1 CAAGATTTTT 0.822885 -266 CGCATTTTCACAAGATTTTTGGATCCTATA 16 67 1 CAAGATTTTT 0.822885 -234 TCAGAAACTCTAGGCTTTTTTAATGTTCGA 17 50 1 TAGGCTTTTT 0.911224 -79 CCGTTAAATATAGCATTTTTAACCTAGCTT 17 86 0 TAGCATTTTT 0.819272 -43 GTAAAATCATCAGCATTTTTAACCGCACTT 21 19 0 CAGCATTTTT 0.840032 -158 TTAACATTTTTCTTGCCAAGA 28 2 1 TAACATTTTT 0.672336 -138 GGTCATAGGTTAAGATTTTTCTGAGAAGGA 31 14 1 TAAGATTTTT 0.800429 -27 TTGCCATAGGTAGGATTTTTCCGTAGAATT 32 121 1 TAGGATTTTT 0.898588 -92 AACTTTTTTCTAGGCTTTTTGATTTGAAAA 55 20 0 TAGGCTTTTT 0.911224 -147 ********** Masking position 2 Map Score: 8.51137 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 45 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 10 CGTGATTATAGCAATTTTTGTTATAGTTCCA 1 36 1 GCAATTTTTT 0.91526 -121 AAGCAAAATTGCAAGTTTTGTATGCATAAAG 5 151 0 GCAAGTTTTT 0.820361 -142 CAAAAAGCCTGCGAATTTTATACTTTTCAAG 5 179 0 GCGAATTTTT 0.442143 -114 AAAAACAACCGCACTTTTTATATAATCCGTG 6 40 1 GCACTTTTTT 0.847274 -133 AATTTTTAGTGCAAGATTCATTGCACCACAC 6 103 0 GCAAGATTCT 0.655882 -70 AATTTTCACCGCACTTTTTGTAAACGT 8 7 0 GCACTTTTTT 0.847274 -92 TATAATAACCGCACTTTTCTTATTAAATAGT 13 15 0 GCACTTTTCT 0.909173 -155 GCTTTGCGCTGCAAATTTTCTCAATGAGAAA 14 83 1 GCAAATTTTT 0.669623 -74 AAACCCATCAGCAATATTTCTCATTGAGAAA 14 99 0 GCAATATTTT 0.714152 -58 ATTTTTAACCGCACTTTTCTTTTT 21 4 0 GCACTTTTCT 0.909173 -173 AAAAGGAGGTGCAAGTTACCTGTTATATAGT 23 144 0 GCAAGTTACT 0.398254 -47 TACAATACACGCAATTTTCATAATAAACAAC 33 52 1 GCAATTTTCT 0.951193 -28 TATTTCAATAGCAATATTCTTCACAAAAAAC 34 18 0 GCAATATTCT 0.818444 -107 AAGTGTAAATGCGATTTTCCTGAATGTAATC 39 40 0 GCGATTTTCT 0.884004 -174 TCTGCCCATGGCCATTTTTTTTCTACTGATA 42 261 0 GCCATTTTTT 0.61174 -40 AGGCGACCCAGCAATTTTCCTAAAAACCGCT 55 103 0 GCAATTTTCT 0.951193 -64 TGGGTCGCCTGCGATTTTCTTTCTTTTAACA 55 124 1 GCGATTTTCT 0.884004 -43 ********* * Masking position 7 Map Score: 13.7213 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 143 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 11 CTCGTATTATATCGTAAAACAAAATAAATT 5 91 1 ATCGTAAAAC 0.785387 -202 AACCGAAAAACTATTATCAAT 11 18 0 ACCGAAAAAC 0.810481 -11 CTGGTTGCGGAGCGTWAAAAAATCGGTATA 12 82 1 AGCGTWAAAA 0.936717 -117 TTTCGTAGAAAGCTAAAAACGGCTATAATC 13 120 1 AGCTAAAAAC 0.690747 -50 GAAAATTTGCAGCGCAAAGCGCTTTTGACT 14 73 0 AGCGCAAAGC 0.747776 -84 TTGACAATAAAGCGTAAAACTATTAGAATT 15 83 1 AGCGTAAAAC 0.959603 -99 AATCCTTAATACCTTAAAACTGTTCACACA 17 15 1 ACCTTAAAAC 0.599178 -114 TAGTTAAGCTTAAAACCAAAGAGAGG 30 7 1 AGCTTAAAAC 0.811553 -25 TGCGATGCATATCGTAAAAATAGCGTTGGG 40 72 0 ATCGTAAAAA 0.695157 -53 CACGGAATATAGCGTAAAAACAAAATTTCT 41 90 0 AGCGTAAAAA 0.936717 -211 TCATTGATGAAGCGAAAAAATATATTCAAG 46 213 1 AGCGAAAAAA 0.884754 -88 TTTTATTTTTAGCGAAAAGATTTTTACTAT 48 90 1 AGCGAAAAGA 0.690247 -178 GATTATTAAAACCGTAAAAAAAGCACCGGC 48 139 1 ACCGTAAAAA 0.837081 -129 TTTGTTTTTTAGCGCAAAAAATTAGCATTT 51 126 1 AGCGCAAAAA 0.864215 -175 ********** Masking position 6 Map Score: 8.32879 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 118 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 12 TACGCGTATAGCGGTATTTTAGCTTGATAAA 5 35 0 GCGTATTTTA 0.854781 -258 AGTAGAATAAGCCGAATTTTATTAACTTAAC 8 61 1 GCGAATTTTA 0.683026 -38 CTAAAATGTTGCGCGATTTTACCCTGTTTAA 10 31 1 GCCGATTTTA 0.864446 -201 GGTTAAAAATGCTATATTTAACGGAAACGTT 17 92 1 GCATATTTAA 0.61324 -37 AACCCTATTTGCAAGCTTTTATTTTAA 23 7 0 GCAGCTTTTA 0.717996 -184 TATGCACTCCTATATTTTAATTAATTTGA 28 121 0 CCATATTTTA 0.592798 -19 CCTACCTATGGCAAGATTTTATTTATAATAA 32 104 0 GCAGATTTTA 0.936833 -109 TATTGAAATAGCGATATTTTAAAAAATTATT 34 39 1 GCATATTTTA 0.931923 -86 TAACAACAATGCTAGATTTTAAAAGTCGTTT 41 14 1 GCAGATTTTA 0.936833 -287 CTAGAATTGCGCTCTATTTTATTCACTCTTA 43 139 1 GCCTATTTTA 0.854781 -42 TAGGAATTTGGCGAAATTTTACGGACGTAAG 53 184 0 GCAAATTTTA 0.833651 -44 GTTTCATTTGGCTATATTTTAATCTATTGTT 54 95 1 GCATATTTTA 0.931923 -133 ** ******** Masking position 11 Map Score: 6.58296 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 95 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 13 TTATCAAGCTAAAATACCGCTATACGCGTA 5 36 1 AAAATACCGC 0.89267 -257 GTGCGGTAAAAAATGACCGCACTTTATTCA 7 32 1 AAATGACCGC 0.938604 -52 ACTAGATTAAAATTTACCGCACTTTTGTTT 15 25 0 AATTTACCGC 0.93946 -157 TTTTTAAAGAAAATGATCGCATTTTCACAA 16 50 1 AAATGATCGC 0.725486 -251 ATCCAGTTAAAATTTACCGCACTTTTGGAA 25 107 0 AATTTACCGC 0.93946 -174 ATTCGGGTAAAATGCACCGCACTTTTAACT 32 26 0 AATGCACCGC 0.895976 -187 ATAATTTTTTAAAATATCGCTATTTCAATA 34 39 0 AAAATATCGC 0.589789 -86 GTGCGGTGAAAAATCACCGCACTTTGATTG 35 15 0 AAATCACCGC 0.957023 -50 AATACACAAAAAATTACCGCACTTTCTTTT 51 56 0 AAATTACCGC 0.957839 -245 AAAAAGGGGCAATGCACCGCCAAAGCCCCT 53 133 1 AATGCACCGC 0.895976 -95 ********** Masking position 6 Map Score: 6.53463 Number of sites scoring better than the average of aligned sites = 407 Number in coding regions = 280 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 14 GCAACATGCAACTATTACGGATAATATACA 54 43 0 ACTATTACGG 0.980226 -185 GCCAAATGAAACTATTACGGTGTATTTTAT 54 77 0 ACTATTACGG 0.980226 -151 CTATTGTTTTACTATTTCGAATAAAAACAA 54 118 1 ACTATTTCGA 0.805159 -110 CTTAATTAGTTCTATTACGGGTAATAATTT 54 151 1 TCTATTACGG 0.924412 -77 AATAATTACAACTATTACGGGATTAAAAAC 54 182 0 ACTATTACGG 0.980226 -46 TAATTATTCAACTATTACGACTAAAGAGGT 54 204 1 ACTATTACGA 0.943663 -24 ********** Masking position 5 Map Score: 4.26539 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 2 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 15 AATATAGCTTACTTTTTTCTCTGTATATATAGACAAA 5 206 0 ATTTTTTATA 0.373458 -87 GAATTTGAGAATATTCTTTTAGTAATTAAACATTTAG 5 257 1 ATTTTTAATT 0.909912 -36 TTTATGGTTTAAATTGTTTTGCTAATTTAGACGTTTG 14 32 0 ATTTTTAATT 0.909912 -125 ATATATAAAGATCTTATTATTGTTATTATTAAGATCT 16 143 0 ATTTTTTATT 0.881252 -158 CATCTAACTTTATTTATTTTAGGAATTGATTGTT 20 31 1 TTTTTTAATT 0.67209 -24 AATATAAGATACTTATTTGTTGATATTCTTTCTTTTA 22 33 0 ATATTTTATT 0.690898 -173 TTCTTTTACGAAATTCTTTTTGCTATTTTTAATATCA 22 124 0 ATTTTTTATT 0.881252 -82 ATTATTAAAAATATTTTTTTCAGTATTTGTTTAGGTG 24 47 0 ATTTTTTATT 0.881252 -254 TATCATTGATAAGTTCTTCTGGGAATTTATCCTCTGC 24 212 0 ATTTTTAATT 0.909913 -89 AGAATTTGCGACCTATTTATATGAATTTTTAAGTGTG 32 145 1 ATATTTAATT 0.752604 -68 TCGTCTCGTTGTTTATTATGAAAATTGCGTGTATTG 33 54 0 TTTTTTAATT 0.672109 -26 CTACCTCTGTACGTAATTTTTCAAATTGAATTTTGGC 42 35 0 ATATTTAATT 0.752604 -266 AGCAAAGTGCATATATTTTTTAATATTCGTTTGAAGT 43 54 1 ATATTTTATT 0.690898 -127 ATTCGTTTGAAGTTTTTTTTAAAAATTTCCGTTTCTT 43 78 1 ATTTTTAATT 0.909875 -103 TCCATTTCTTACATTTTTATTACTATTTGTGTTTAGT 44 125 1 ATTTTTTATT 0.881252 -155 ATCATATTCTATATTCTTCTATTAATGCTATAACTAA 44 157 0 ATTTTTAATG 0.688741 -123 CTCCTATGTAATATTTTTCTAAAATGAACTAATCGT 50 32 0 ATTTTTAATG 0.688741 -35 ACGGGCGTTTTCTTTTTTGTTTAAATTCTTAGTTTTT 53 30 1 TTTTTTAATT 0.672109 -198 AGAACTAATTAAGTCATTGTTTTTATTCGAAATAGTA 54 127 0 ATCTTTTATT 0.501721 -101 * ** ** * **** Masking position 8 Map Score: 10.1352 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 90 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665