AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00860_hpyl_reg_300.orf -o00860_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -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 Input sequences: #1 HP0163 71 delta-aminolevulinic acid dehydratase (hemB) #2 HP0165 25 H. pylori predicted coding region HP0165 #3 HP0166 235 response regulator (ompR) #4 HP0168 46 H. pylori predicted coding region HP0168 #5 HP0170 74 H. pylori predicted coding region HP0170 #6 HP0171 60 peptide chain release factor RF-2 (prfB) #7 HP0174 300 H. pylori predicted coding region HP0174 #8 HP0243 205 neutrophil activating protein (napA) (bacterioferritin) #9 HP0246 188 flagellar basal-body P-ring protein (flgI) #10 HP0296 241 ribosomal protein L21 (rpl21) #11 HP0298 116 dipeptide ABC transporter, periplasmic dipeptide-binding protein (dppA) #12 HP0304 41 H. pylori predicted coding region HP0304 #13 HP0305 243 H. pylori predicted coding region HP0305 #14 HP0376 55 ferrochelatase (hemH) #15 HP0382 182 zinc-metallo protease (YJR117W) #16 HP0476 117 glutamyl-tRNA synthetase (gltX) #17 HP0601 163 flagellin A (flaA) #18 HP0602 117 endonuclease III #19 HP0603 44 H. pylori predicted coding region HP0603 #20 HP0604 65 uroporphyrinogen decarboxylase (hemE) #21 HP0640 62 poly(A) polymerase (papS) #22 HP0643 164 glutamyl-tRNA synthetase (gltX) #23 HP1223 65 H. pylori predicted coding region HP1223 Motif number 1 TATTTTTTAATGTTTTTAAACAATTCCTTT 3 20 0 TGTTTTTAAA 0.775066 -216 TTTAAGGCTTTGTTTTCATGGAATATTGAA 3 61 0 TGTTTTCATG 0.512781 -175 TTTGAATTTTTATTTTTAAGATATTTTCAA 3 116 1 TATTTTTAAG 0.953115 -120 ATTTTTAAGATATTTTCAAGGTATCTTTAA 3 127 1 TATTTTCAAG 0.883587 -109 CAAAGTTAATCGTTTTTAAAGTTGCAGAAA 3 193 1 CGTTTTTAAA 0.726775 -43 TTGCATCGAGAATTTTTGAATCTTCTTTAA 7 107 0 AATTTTTGAA 0.665662 -194 TAGTAAAACTCATTTTTAAGGGGGATAGTT 8 18 0 CATTTTTAAG 0.940095 -188 TATAAAACAAAATTTTAAAAAGATTAAATA 8 46 1 AATTTTAAAA 0.863984 -160 AAACCCCATTCAATTTAATATTATTTAATC 8 67 0 CAATTTAATA 0.416861 -139 TTTAGGCTTTTATTTTCATAAAAACCTTGA 8 162 0 TATTTTCATA 0.63161 -44 AGCCTAAAACAATTTTAAAAAAAGGACTTT 8 184 1 AATTTTAAAA 0.863984 -22 TTAAAATCTTTGATTTAAAGTTTATAAGAT 9 70 1 TGATTTAAAG 0.569404 -119 TAATTGAGCGTATTTTTATGCTATACTCAA 9 102 0 TATTTTTATG 0.897318 -87 TTAGGTTTAAAGTTTTTATAAAAGGCTTAT 9 129 1 AGTTTTTATA 0.512999 -60 GATTTAATCTCAATTTAAAGTTACATTTTA 10 160 1 CAATTTAAAG 0.759885 -82 AATAAGCGTTTATTTTAAAAAGAGCGTTCA 10 205 1 TATTTTAAAA 0.899314 -37 AAGAGCGTTCAATTTTTAAGGAATAGAA 10 224 1 AATTTTTAAG 0.935304 -18 AACGCTATTTTTAAAATAATCCATT 12 6 1 TATTTTTAAA 0.914401 -36 TCCTCGCCTTTATTTTAATGGATTATTTTA 12 22 0 TATTTTAATG 0.879441 -20 TAACGCTTATTATTTTAGTGTAAATAAGCA 13 196 0 TATTTTAGTG 0.656953 -48 AAAAAGAGACTATTTTTGAGCGTTTTTAAT 15 58 0 TATTTTTGAG 0.841969 -125 CATATTTATTTAATTTTATGGTTTTATGGT 15 93 1 TAATTTTATG 0.678209 -90 TTTTATGGTAAATTTTTGAAAAATTGTTAT 15 114 1 AATTTTTGAA 0.665662 -69 TTTTATTGGTAAATTTAATGGAGAAAGGAG 15 155 1 AAATTTAATG 0.556196 -28 ATCATACACTAATTTTAATAGAAAAAAGTG 16 38 1 AATTTTAATA 0.731943 -80 AAAGTGAAACCATTTTTAAGCCATTTTTGA 16 62 1 CATTTTTAAG 0.940095 -56 ATTTTTAAGCCATTTTTGAATACAATAAGA 16 73 1 CATTTTTGAA 0.683668 -45 AAGAGTATTTTATTTTTAAGGTTAGAACA 16 99 1 TATTTTTAAG 0.953115 -19 TATTATAGCCCATTTTCATGCTCCTTTAAA 17 38 1 CATTTTCATG 0.715806 -126 TTTAAAAGCAAAATTTAAAGGAGCATGAAA 17 51 0 AAATTTAAAG 0.744597 -113 TAAAGGGCTTTGTTTTAAAAGCAAAATTTA 17 64 0 TGTTTTAAAA 0.742347 -100 TAAAGTTTGAAATTTTAAAGGGCTTTGTTT 17 79 0 AATTTTAAAG 0.923596 -85 AATATTCATTTTAAAAAACAACTATG 20 7 1 CATTTTAAAA 0.873337 -59 ATCTTTTTAGAATTTTTAAGGAATTTTG 21 9 0 AATTTTTAAG 0.935304 -54 TAACACAAAGAAATTTTAAGAGTAAAAAGC 21 43 1 AAATTTTAAG 0.777117 -20 AATCAAAAACTATTTTTAAATAAAGGGTTT 22 143 1 TATTTTTAAA 0.914401 -22 AACATAACCTTATTTTAAAAACTAAGGATA 23 43 1 TATTTTAAAA 0.899314 -23 ********** Masking position 5 Map Score: 37.5015 Number of sites scoring better than the average of aligned sites = 1686 Number in coding regions = 1362 Number in noncoding regions = 324 Number of orfs with sites within 600 bp upstream = 254 Fraction of orfs with sites within 600 bp upstream = 0.0407967 Motif number 2 AAGGGGATAGAAAAAGCCAATTGTGGGGTT 1 28 1 AAAAAGCCAA 0.814361 -44 AGGAATTGTTTAAAAACATTAAAAAATAAG 3 22 1 TAAAAACATT 0.819872 -214 CTGCAACTTTAAAAACGATTAACTTTGTTA 3 190 0 AAAAACGATT 0.707083 -46 ACCTAATCTCTAAACGCCATTT 4 3 0 TAAACGCCAT 0.874894 -44 ATGGTTACTATAAAACGCTTTTTAAAACCA 5 38 1 TAAAACGCTT 0.92805 -37 AAACGCTTTTTAAAACCAATTGGCAAGGAA 5 50 1 TAAAACCAAT 0.882742 -25 ATAGCATTGTTAAAAGCCATT 6 2 0 TAAAAGCCAT 0.956002 -59 ATGCAATGCTAAAAAACCAAATATAAAGAA 7 202 0 AAAAAACCAA 0.628796 -99 AACAAAATTTTAAAAAGATTAAATAATATT 8 51 1 TAAAAAGATT 0.743017 -155 CAAATATTGATAAACCCCATTCAATTTAAT 8 78 0 TAAACCCCAT 0.843815 -128 TTTATTTTCATAAAAACCTTGATCGCTATC 8 154 0 TAAAAACCTT 0.910307 -52 TTTATGAAAATAAAAGCCTAAAACAATTTT 8 170 1 TAAAAGCCTA 0.927093 -36 TGAAACTTTATAAAAAGCTAATAAAAGGCT 9 36 1 TAAAAAGCTA 0.75723 -153 AAAAAGCTAATAAAAGGCTAAAATTAAAAT 9 47 1 TAAAAGGCTA 0.889839 -142 AAAGTTTTTATAAAAGGCTTATGCTAAAAT 9 137 1 TAAAAGGCTT 0.94349 -52 TTGTTTGTTAAAAAACCAATAAGGATTTGA 10 13 0 AAAAACCAAT 0.758543 -229 GAAACACCTATAAACGCAATAAAATATTTA 11 50 1 TAAACGCAAT 0.758237 -67 GAGTTTAAAATAAACGCAATTGTATCTCTT 13 111 1 TAAACGCAAT 0.758237 -133 CGCTTACAACTAAAACGATTCATTTTGATA 13 166 0 TAAAACGATT 0.852608 -78 CATGCTAAAATAAAACGATTAATAAAAAAT 14 31 0 TAAAACGATT 0.852608 -25 AAATTTACCATAAAACCATAAAATTAAATA 15 99 0 TAAAACCATA 0.815013 -84 GGCTTTGTTTTAAAAGCAAAATTTAAAGGA 17 59 0 TAAAAGCAAA 0.825006 -105 CCTTGTTATAAAAAACCCAAAGGCATCCTT 17 134 0 AAAAACCCAA 0.77216 -30 AAATTAAAGCAAAAAGCCAACGCTTAAAGC 18 41 0 AAAAAGCCAA 0.814361 -77 CGCCTATAATAAAAAGGAATCAAAAAGAGT 18 92 0 AAAAAGGAAT 0.720911 -26 AAACGCCTTTTAAAAGGCTTAAGATTAAGA 19 23 0 TAAAAGGCTT 0.94349 -22 TAAAACGCCTTTTAAAAGGCT 19 34 0 AAAACGCCTT 0.779253 -11 CTATGGAGTATAAAAACCATAATTAGACAA 20 32 1 TAAAAACCAT 0.893506 -34 TTAAAAATTCTAAAAAGATATAATAACACA 21 20 1 TAAAAAGATA 0.583133 -43 TAACCAACCATAAAAAGCTTGGCGTTAGCC 22 31 1 TAAAAAGCTT 0.865718 -134 AAAAACCCTTTATTTAAAAA 22 155 0 AAAAACCCTT 0.894442 -10 ********** Masking position 4 Map Score: 38.598 Number of sites scoring better than the average of aligned sites = 2316 Number in coding regions = 2020 Number in noncoding regions = 296 Number of orfs with sites within 600 bp upstream = 210 Fraction of orfs with sites within 600 bp upstream = 0.0337295 Motif number 3 TTTAGGGGACTAATTCTAGCATTTTATTATTA 3 154 0 TATTCTAGCT 0.948559 -82 TTATCGGCTGTCATTTTAGCGCAC 5 3 0 TATTTTAGCC 0.958334 -72 TTTGAACTTATCATTATAGCATTGTTAAAAGC 6 15 0 TATTATAGCT 0.976153 -46 TCAAAGATTTTAATTTTAGCCTTTTATTAGCT 9 51 0 TATTTTAGCT 0.983587 -138 ATAAGATTTTTGAGTATAGCATAAAAATACGC 9 93 1 TAGTATAGCT 0.885171 -96 TAAATTCTAATTATTTTAGCATAAGCCTTTTA 9 147 0 TATTTTAGCT 0.983587 -42 TATTTTGGAATACTTTTAGCTTGTTTGTTAAA 10 31 0 TCTTTTAGCT 0.918605 -211 ATAACGCTTATTATTTTAGTGTAAATAAGCAC 13 195 0 TATTTTAGTT 0.825235 -49 ATTAATCGTTTTATTTTAGCATGCACCA 14 38 1 TATTTTAGCT 0.983587 -18 TAAATTTTCTTTATTATAGCCCATTTTCATGC 17 27 1 TATTATAGCC 0.940157 -137 TTTCTTTGTGTTATTATATCTTTTTAGAATTT 21 24 0 TATTATATCT 0.76333 -39 * ******** * Masking position 8 Map Score: 13.9121 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 78 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 4 TGTGGGGTTAAAGAAAAACAATAAAGAGAGAAC 1 49 1 AAAAAAAATA 0.744596 -23 AAAACGATCAAAGGAATTGTTTAAAAACAT 3 7 1 ATAAAGGATT 0.857506 -229 AAAAACATTAAAAAATAAGACTTTATTTTTCAAT 3 33 1 AAAATAAATT 0.7813 -203 TATCATAGTTATTAATGGAAATTTAAGGCTTTGT 3 78 0 ATAATGGATT 0.660865 -158 AACTAACACCAAAAAAGACAATAAATATTATTAC 7 46 0 AAAAAGAATA 0.633049 -255 TCTTTCCAAAAAGAATAAAACTAACACCAAAAAA 7 64 0 AAAATAAATA 0.485609 -237 TCTTTTTGGAAAGAAAAAAAATGTTAAAGAAGAT 7 84 1 AAAAAAAATT 0.916891 -217 AAAACCAAATATAAAGAATAATAACCCTGGTAAC 7 186 0 ATAAGAAATA 0.5807 -115 GAGTTTTACTATAAAACAAAATTTTAAAAAGATT 8 37 1 ATAAACAATT 0.645194 -169 CAAAAATAAGATCAAAAAAATTTTTTATTAACTC 8 109 1 ATAAAAAATT 0.930567 -97 AAACAATTTTAAAAAAAGGACTTTTG 8 190 1 AAAAAAGATT 0.893291 -16 TTAAATCCACATTAAAAGAATTTTTTATTCAAAA 10 133 0 ATAAAAGATT 0.910471 -109 AATATGGTAGAAAAAAGAGACTATTTTTGAGCGT 15 65 0 AAAAAGAATT 0.86717 -118 GTTGATCCTAATCAAAAATAATCTCAATCATACA 16 12 1 ATAAAAAATT 0.930567 -106 ACTTTTTTCTATTAAAATTAGTGTATGATTGAGA 16 33 0 ATAAAATATT 0.568798 -85 TTTTGAATACAATAAGAGTATTTTATTTTTAAGG 16 86 1 AAAAGAGATT 0.765999 -32 AATGGGCTATAATAAAGAAAATTTATACCAAATC 17 18 0 AAAAAGAATT 0.86717 -146 ATAAAAAGGAATCAAAAAGAGTATTTTATTAAAA 18 80 0 ATAAAAAATT 0.930567 -38 AAGGCTTAAGATTAAGAAAAATCTAAAAA 19 6 0 ATAAGAAATT 0.839766 -39 CAATGATTTGATAAATAGGAATGTTTAAGGA 23 8 0 ATAATAGATT 0.767067 -58 ** ***** * * * Masking position 12 Map Score: 15.2732 Number of sites scoring better than the average of aligned sites = 394 Number in coding regions = 299 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 5 AAACAGAACCTTTATGAGTGGGGTTTTGA 6 42 0 ACCTTTAGAT 0.772883 -19 TGTTAGTTTTATTCTTTTTGGAAAGAAAAAAAA 7 72 1 ATCTTTTGGA 0.901134 -229 CAGGGTTATTATTCTTTATATTTGGTTTTTTAG 7 191 1 ATCTTTAATT 0.769321 -110 AATATTATTTAATCTTTTTAAAATTTTGTTTTA 8 48 0 ATCTTTTAAA 0.447632 -158 TTAATAAAAAATTTTTTTGATCTTATTTTTGTC 8 107 0 ATTTTTTATT 0.47445 -99 TTTTTTATTAACTCTTTTGGTGTAGGATAGCGA 8 129 1 ATCTTTTGTT 0.929994 -77 GATCAAATCCTTATTGGTTTTTTAACAAA 10 7 1 ACCTTATGGT 0.704828 -235 TGAATAAAAAATTCTTTTAATGTGGATTTAATC 10 136 1 ATCTTTTATT 0.826623 -106 AAGAGCGTTCAATTTTTAAGGAATAGAA 10 224 1 ATTTTTAGGA 0.545776 -18 AGGTTTAATTAACCTTTAAAGGTTACC 11 5 0 ACCTTTAAGT 0.683583 -112 AGGTTAATTAAACCTTTAGGTGTTTGTGAAACA 11 23 1 ACCTTTAGTT 0.925796 -94 TTAGATCTCTATCCTTTATAGAATTTGTTGTGG 11 84 1 ACCTTTAAGA 0.755495 -33 CATGCGCTTTAACCTTTTGATGAATGGTTCAGA 13 46 1 ACCTTTTATA 0.789022 -198 TTTATTTTAAACTCTTTTTGTAAATAATGCTGA 13 92 0 ATCTTTTGTA 0.885251 -152 GACAAACCTTTTTGTTTATAGCGGGTT 15 5 1 ACCTTTTGTT 0.947203 -178 TGGATAACACAGCTTTTTAGGATTAAAAACGCT 15 37 1 ACTTTTTGGT 0.793929 -146 AAAATAAAATACTCTTATTGTATTCAAAAATGG 16 82 0 ATCTTATGTT 0.601741 -36 TTAATAAAATACTCTTTTTGATTCCTTTTTATT 18 82 1 ATCTTTTGAT 0.795368 -36 TAATTAGACAAACCTTTAAGGATTT 20 51 1 ACCTTTAGGT 0.584684 -15 ATCTTTTTAGAATTTTTAAGGAATTTTG 21 6 0 ATTTTTAGGA 0.545776 -57 AAACGCTGTTAGCTTTTTGATAACCAACCATAA 22 11 1 ACTTTTTATA 0.414536 -154 ACAATTAAGTATTCTTTAGGTATAATCAAAAAC 22 120 1 ATCTTTAGTT 0.902743 -45 * ****** ** * Masking position 6 Map Score: 16.7247 Number of sites scoring better than the average of aligned sites = 965 Number in coding regions = 837 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 6 AAGACTTTATTTTTCAATATTCCATGAAAA 3 49 1 TTTTCAATAT 0.926942 -187 AAGCCTTAAATTTCCATTAATAACTATGAT 3 81 1 TTTCCATTAA 0.413186 -155 CTCTTAATCATTTTCAATACCTAATCTCTA 4 21 0 TTTTCAATAC 0.800352 -26 GGTTTTGAACTTATCATTATAGCATTGTTA 6 20 0 TTATCATTAT 0.726915 -41 ATTTTTTTTCTTTCCAAAAAGAATAAAACT 7 76 0 TTTCCAAAAA 0.545169 -225 CTCGATGCAATTATGAATATAATATTCGTA 7 127 1 TTATGAATAT 0.891401 -174 ACAACAATAATTACGAATATTATATTCATA 7 138 0 TTACGAATAT 0.764298 -163 CATAGTAAGCTTATCAATATGAGATTGATT 7 266 0 TTATCAATAT 0.932947 -35 TGAATGGGGTTTATCAATATTTGACAAAAA 8 85 1 TTATCAATAT 0.932947 -121 ATCAAGGTTTTTATGAAAATAAAAGCCTAA 8 161 1 TTATGAAAAT 0.727731 -45 TTTATAAGATTTTTGAGTATAGCATAAAAA 9 90 1 TTTTGAGTAT 0.45638 -99 AATGGGGTTATTTTGAATAAAAAATTCTTT 10 123 1 TTTTGAATAA 0.845502 -119 GAGATCTAAATTATAAATATTTTATTGCGT 11 63 0 TTATAAATAT 0.617832 -54 GTGCAAATGATTATCAAAATGAATCGTTTT 13 155 1 TTATCAAAAT 0.81921 -89 TAATGTGGTCTTATCAATAACGCTTATTAT 13 213 0 TTATCAATAA 0.908835 -31 TTATAACAATTTTTCAAAAATTTACCATAA 15 116 0 TTTTCAAAAA 0.751682 -67 TCCATTAAATTTACCAATAAAAGTGTAGGA 15 147 0 TTACCAATAA 0.801356 -36 TTTAAGCCATTTTTGAATACAATAAGAGTA 16 76 1 TTTTGAATAC 0.702784 -42 TTATGGTTGGTTATCAAAAAGCTAACAGCG 22 14 0 TTATCAAAAA 0.767431 -151 TAAAAATAGTTTTTGATTATACCTAAAGAA 22 131 0 TTTTGATTAT 0.588684 -34 CAAAAACTATTTTTAAATAAAGGGTTTTT 22 146 1 TTTTAAATAA 0.519509 -19 ********** Masking position 2 Map Score: 15.7384 Number of sites scoring better than the average of aligned sites = 644 Number in coding regions = 554 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 7 TATTCTAATAAGGAGTTAAGGGGTT 2 10 1 AAGGAGTTAA 0.942919 -16 GAAATCATTGAAGGAGTTAATTGAAGT 3 219 1 AAGGAGTTAA 0.942919 -17 ATTGTCTTTTTTGGTGTTAGTTTTATTCTT 7 58 1 TTGGTGTTAG 0.475278 -243 TCCTACACCAAAAGAGTTAATAAAAAATTT 8 126 0 AAAGAGTTAA 0.717906 -80 GATAGCGATCAAGGTTTTTATGAAAATAAA 8 154 1 AAGGTTTTTA 0.565518 -52 ATTAAACCTTTAGGTGTTTGTGAAACACCT 11 29 1 TAGGTGTTTG 0.894416 -88 ATTGCGTTTATAGGTGTTTCACAAACACCT 11 40 0 TAGGTGTTTC 0.815757 -77 TTATTTACAAAAAGAGTTTAAAATAAACGC 13 98 1 AAAGAGTTTA 0.751503 -146 TTAATGGAGAAAGGAGTTTGGAAT 15 169 1 AAGGAGTTTG 0.961937 -14 TTTTTATAACAAGGAGTTACAACA 17 150 1 AAGGAGTTAC 0.917464 -14 TTTTAAGAAAGGTGTTTGTATGGGGCTA 18 9 1 AAGGTGTTTG 0.955091 -109 ********** Masking position 7 Map Score: 5.94118 Number of sites scoring better than the average of aligned sites = 337 Number in coding regions = 265 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 8 AAATAAAGTCTTATTTTTTAATGTTTTTAA 3 31 0 TTATTTTTTA 0.913392 -205 AAATAAGACTTTATTTTTCAATATTCCATG 3 45 1 TTATTTTTCA 0.687441 -191 TTTTGAATTTTTATTTTTAAGATATTTTCA 3 115 1 TTATTTTTAA 0.789445 -121 GTTAGTTTTATTCTTTTTGGAAAGAAAAAA 7 73 1 TTCTTTTTGG 0.516729 -228 ACCAGGGTTATTATTCTTTATATTTGGTTT 7 189 1 TTATTCTTTA 0.514657 -112 TTTTTTGATCTTATTTTTGTCAAATATTGA 8 98 0 TTATTTTTGT 0.487377 -108 GTTATTAAGCTTATTTTGGAATACTTTTAG 10 44 0 TTATTTTGGA 0.721702 -198 TTAAATGGGGTTATTTTGAATAAAAAATTC 10 120 1 TTATTTTGAA 0.422534 -122 ACTAAAACGATTCATTTTGATAATCATTTG 13 158 0 TTCATTTTGA 0.588158 -86 TTCTAACGATTTATTTTTTATTAATCGTTT 14 19 1 TTATTTTTTA 0.913392 -37 AAAAAAGAGACTATTTTTGAGCGTTTTTAA 15 59 0 CTATTTTTGA 0.721702 -124 ATGATTGAGATTATTTTTGATTAGGATCAA 16 13 0 TTATTTTTGA 0.930015 -105 TAAGAGTATTTTATTTTTAAGGTTAGAACA 16 98 1 TTATTTTTAA 0.789445 -20 GGTATAAATTTTCTTTATTATAGCCCATTT 17 23 1 TTCTTTATTA 0.351863 -141 GCTTTTTGCTTTAATTTTTACTTCTTTTTT 18 54 1 TTAATTTTTA 0.598984 -64 TAATTTTTACTTCTTTTTTAATAAAATACT 18 65 1 TTCTTTTTTA 0.888918 -53 TAATAAAATACTCTTTTTGATTCCTTTTTA 18 83 1 CTCTTTTTGA 0.663044 -35 CTCTTTTTGATTCCTTTTTATTATAGGCGG 18 93 1 TTCCTTTTTA 0.487867 -25 TACTCCATAGTTGTTTTTTAAAATGAATAT 20 12 0 TTGTTTTTTA 0.606054 -54 GTTTATCCTTAGTTTTTAAAATAAGGTT 23 48 0 TTAGTTTTTA 0.556629 -18 ********** Masking position 5 Map Score: 11.2713 Number of sites scoring better than the average of aligned sites = 755 Number in coding regions = 614 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 9 GCTTTTTCTATCCCCTTCATTCCGCTCACT 1 15 0 TCCCCTTCAT 0.879061 -57 AAGTTCAAAACCCCACTCATAAAGGTTCTG 6 38 1 CCCCACTCAT 0.96421 -23 TGGATAACTATCCCCCTTAAAAATGAGTTT 8 13 1 TCCCCCTTAA 0.846252 -193 TATTGATAAACCCCATTCAATTTAATATTA 8 74 0 CCCCATTCAA 0.980873 -132 ACCCGCATTGTCCCACTCAAACCACTCGCA 10 77 0 TCCCACTCAA 0.967726 -165 TTCAAAATAACCCCATTTAACCCGCCATTA 10 110 0 CCCCATTTAA 0.933287 -132 AAAGCGTTAGCCCCATACAAACACCTTTCT 18 16 0 CCCCATACAA 0.914138 -102 ********** Masking position 9 Map Score: 3.59789 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 133 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 10 TATTGAAAATGATTAAGAGAAACGC 4 32 1 GATTAAGAGA 0.966472 -15 ATATGAGATTGATTAATAGAGTATAGAAGT 7 250 0 GATTAATAGA 0.906891 -51 TACTATGTAAGATTAAGGGACT 7 289 1 GATTAAGGGA 0.898678 -12 AGAATTTAGGGAATAAGAAAGGGTTTGA 9 171 1 GAATAAGAAA 0.912159 -18 GGGTTATTTTGAATAAAAAATTCTTTTAAT 10 127 1 GAATAAAAAA 0.665535 -115 AAAATAAAACGATTAATAAAAAATAAATCG 14 25 0 GATTAATAAA 0.889694 -31 AAAGGCTTAAGATTAAGAAAAATCTAAAAA 19 11 0 GATTAAGAAA 0.959791 -34 ********** Masking position 5 Map Score: 2.91685 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 26 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 11 CAAAGTTAATCGTTTTTAAAGTTGCAGAAA 3 193 1 CGTTTTTAAA 0.455666 -43 TACTATAAAACGCTTTTTAAAACCAATTGG 5 43 1 CGCTTTTTAA 0.911926 -32 CACTTTTACCCGCTTTGAAT 7 1 0 CGCTTTGAAT 0.764727 -300 GCCTTTTATTAGCTTTTTATAAAGTTTCAA 9 35 0 AGCTTTTTAT 0.902633 -154 TTTTAATTTTAGCCTTTTATTAGCTTTTTA 9 46 0 AGCCTTTTAT 0.904275 -143 TTTTAGCATAAGCCTTTTATAAAAACTTTA 9 136 0 AGCCTTTTAT 0.904275 -53 TTAAAATAAACGCTTATTATAGTGAGTATT 10 193 0 CGCTTATTAT 0.911926 -49 TCCTCGCCTTTATTTTAATGGATT 12 28 0 CGCCTTTATT 0.690856 -14 TTATCAATAACGCTTATTATTTTAGTGTAA 13 203 0 CGCTTATTAT 0.911926 -41 TATTTTTGAGCGTTTTTAATCCTAAAAAGC 15 48 0 CGTTTTTAAT 0.722794 -135 AATAACCGCCTATAATAAAAAGGAAT 18 102 0 CGCCTATAAT 0.870833 -16 TAAAACGCCTTTTAAAAGGCTTAAG 19 30 0 CGCCTTTTAA 0.913426 -15 GCTAACGCCAAGCTTTTTATGGTTGGTTAT 22 30 0 AGCTTTTTAT 0.902633 -135 ********** Masking position 5 Map Score: 11.3494 Number of sites scoring better than the average of aligned sites = 948 Number in coding regions = 847 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 12 ********** No masking Map Score: -6.49903e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 13 CCATGAAAACAAAGCCTTAAATTTCCATTAATA 3 70 1 AAAGCTAATT 0.833779 -166 TAACTATGATAATGTTTTGAATTTTTATTTTTA 3 101 1 AATGTTAATT 0.963435 -135 AGCTTTTTATAAAGTTTCAAATTAAATTGAGGT 9 22 0 AAAGTTAATT 0.95549 -167 ACTTTAAATCAAAGATTTTAATTTTAGCCTTTT 9 58 0 AAAGTTAATT 0.95549 -131 CTTATGCTAAAATAATTAGAATTTAGGGAATAA 9 154 1 AATATTAATT 0.854918 -35 AACGCAATAAAATATTTATAATTTAGATCTCTA 11 62 1 AATATTAATT 0.854918 -55 ATTTTTGAAAAATTGTTATAATTCCTACACTTT 15 125 1 AATTTTAATT 0.704208 -58 ATGGCTTAAAAATGGTTTCACTTTTTTCTATTA 16 53 0 AATGTTACTT 0.860719 -65 ATAATCGGTTAAAGTTTGAAATTTTAAAGGGCT 17 85 0 AAAGTTAATT 0.955464 -79 **** ** **** Masking position 7 Map Score: 4.34139 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 53 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 14 ********** No masking Map Score: -6.49903e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 15 ********** No masking Map Score: -6.49903e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0