AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02010_hpyl_reg_300.orf -o02010_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 HP0251 300 oligopeptide ABC transporter, permease protein (oppC) #2 HP0296 241 ribosomal protein L21 (rpl21) #3 HP0298 116 dipeptide ABC transporter, periplasmic dipeptide-binding protein (dppA) #4 HP0473 225 molybdenum ABC transporter, periplasmic molybdate-binding protein (modA) #5 HP0474 21 molybdenum ABC transporter, permease protein (modB) #6 HP0686 247 iron(III) dicitrate transport protein (fecA) #7 HP0687 143 iron(II) transport protein (feoB) #8 HP0807 193 iron(III) dicitrate transport protein (fecA) #9 HP0811 300 H. pylori predicted coding region HP0811 #10 HP0813 132 conserved hypothetical protein #11 HP0818 68 osmoprotection protein (proWX) #12 HP0890 217 conserved hypothetical protein #13 HP1169 212 glutamine ABC transporter, permease protein (glnP) #14 HP1172 48 glutamine ABC transporter, periplasmic glutamine-binding protein (glnH) #15 HP1253 31 tryptophanyl-tRNA synthetase (trpS) #16 HP1254 116 biotin synthesis protein (bioC) #17 HP1400 300 iron(III) dicitrate transport protein (fecA) #18 HP1466 134 conserved hypothetical integral membrane protein #19 HP1563 240 alkyl hydroperoxide reductase (tsaA) #20 HP1564 139 outer membrane protein #21 HP1574 74 riboflavin synthase alpha subunit (ribC) #22 HP1576 21 ABC transporter, ATP-binding protein (abc) Motif number 1 ATTATCTTAAAATTAGAAAGTTTCTTTTA 1 3 0 AATAAACTTT 0.842981 -298 GCTTAATAGCAAATTAAGAATGATTATCTTAAAATTA 1 25 0 AAATAGTTAT 0.763081 -276 ATTTTTTATTCAAAATAACCCCATTTAACCCGCCATT 2 111 0 CAAAAATTTA 0.692376 -131 ATTAAATCCACATTAAAAGAATTTTTTATTCAAAATA 2 131 0 CATAAATTTT 0.842992 -111 TATTCCTTAAAAATTGAACGCTCTTTTTAAAATAAAC 2 212 0 AAATAATTTT 0.941992 -30 TAGAGATCTAAATTATAAATATTTTATTGCGTTTATA 3 58 0 AATAAATTAT 0.81506 -59 AAACTTTTAGAAAAATAACCGATCTTAGGGTGTAACT 4 35 0 AAAAAACTTA 0.691885 -191 AGATTGGAAGAAAAATAAAAATTTTTTAATATTTCTA 6 66 0 AAAAAATTTT 0.943332 -182 TTATTTAGATAATATTAATGACTTTTTTATCAAAAAT 6 130 0 AATTAATTTT 0.927295 -118 GATATAACTAAAAATTAGAAAAACTTTAATGCGGAGC 7 106 1 AAATAGCTTT 0.795924 -38 TTATCAAAACCATTTGAAAAAAGTTTTTTGCGTTTTT 8 65 0 CATTAATTTT 0.836525 -129 TCAAACTTCAAAATTTAAGTTAATTTTAATAATTATT 8 122 1 AAATAATTTT 0.833448 -72 TATAACTTAGCATTTTAATCAACTTTTTCATTAAAAT 9 45 0 CATTAATTTT 0.836525 -256 TACCAAAAAAAAAAAAAACGATGTTATTTGAACTTTA 9 136 1 AAAAAATTAT 0.848729 -165 TCTTTTTTATAAAATGAAACACTTTTTAAGTTTATTT 9 191 1 AAATAATTTT 0.879383 -110 AATTGTTTCAAATTATAGCGATTCTTTCTTTTAAACA 9 244 0 AATAAGCTTT 0.763822 -57 CTCAACCAACAATAATAGAAGCGCTATTCTAGTCAAA 10 34 1 AATAAGCTAT 0.515726 -99 ATCATAGCGCAAAAATAAGGCGATTTTGACTAGAATA 10 58 0 AAAAAATTTT 0.943389 -75 TATGATTTTCAATAATAATGACTTTTTAAAACTAGTT 10 89 1 AATAAATTTT 0.930469 -44 CTGCAACCAACATTAAAGAATGCCTTTAGCATTTTAA 11 12 1 CATAAGCTTT 0.564723 -57 ATGCCTTTAGCATTTTAAAACCCCTTTATCCAAATAA 11 31 1 CATTAACTTT 0.672431 -38 CCCCTTTATCCAAATAAGTTTGGTTATA 11 51 1 CAATAGTTAT 0.563716 -18 ATATTGAGTGAATATTAGAGGAATTTTAAAAATAATA 12 94 1 AATTAGTTTT 0.884832 -124 CATTGTTGTTAATTTCAGCCAGTTTTTTTATTATAAT 13 38 1 AATTAGTTTT 0.884835 -175 AATTGGGGTGAATAAGAGCTGTTTTTAAACATGGTGC 13 152 1 AATAAGTTTA 0.726371 -61 CTATACCTTAAAAATTAATGACGCTTTAAAGCACCAT 13 182 0 AAATAACTTT 0.866908 -31 CTTTTTTTGAAATTAGAATCATCTTTTTAGCAAACTT 14 14 0 AATAAATTTT 0.930478 -35 ATTCTAATTTCAAAAAAAGGTGTTTTT 14 32 1 CAAAAATTTT 0.870872 -17 AAACTAAGATAAATTAAAATATTAAAA 15 1 1 AAATAGTTAA 0.514713 -31 CCACGCTTGAAATTAAAACTAAATTTTAGTGTATTCT 16 72 0 AATAAATTTT 0.93047 -45 GAAAAGTTAAACCGCTTTTAGCGTCAAAG 17 3 1 AAATAATTTT 0.94157 -298 AAATCAAAAAAAAAAAAAAAAGATTTTCATGGGATTA 17 126 1 AAAAAATTTT 0.943389 -175 GGATTAATAAAATTTTAAGAATTTTTATGATAAAATT 17 157 1 AATTAATTTA 0.807705 -144 TAAGTAATAAAAACAAAAAAAACTTAATAATGTGCGG 17 194 0 AAAAAATTAA 0.648817 -107 TTTACTTGAAAAATTTAAACCATTTTTCAATCTCTCA 17 258 1 AAATAATTTT 0.941318 -43 ATCCTTTATTAAACAGAGTATTGTTTAACCTTTTGTT 18 25 1 AAAAAGTTTA 0.771668 -110 TCGTTTTAACAAACAAAATTTTGTTAATAGATTTTAC 18 82 1 AAAAAATTAA 0.648817 -53 ACAAGCAGTAAAAATGAAACTATTTTTCACAAAATCC 19 63 1 AAATAATTTT 0.505686 -178 AAAGCATAGTAAATTAAATCTGTTTTTAGGTTTAATT 19 174 1 AAATAATTTT 0.86682 -67 GATCCAACAAAATTTTAAAACACTTAAGGAGTTACGA 19 213 1 AATTAATTAA 0.580383 -28 GCGAAGAATCAAAAAGAAAGGATTTAACCAAGAAAGA 20 39 0 AAAAAATTAA 0.648817 -101 *** * ** **** Masking position 7 Map Score: 46.6269 Number of sites scoring better than the average of aligned sites = 1789 Number in coding regions = 1428 Number in noncoding regions = 361 Number of orfs with sites within 600 bp upstream = 226 Fraction of orfs with sites within 600 bp upstream = 0.0362994 Motif number 2 TTTTAGCTTGTTTGTTAAAAAACCAATAAGG 2 19 0 TTTTTAAAAA 0.944824 -223 AATAAGCGTTTATTTTAAAAAGAGCGTTCAA 2 205 1 TATTTAAAAA 0.944286 -37 TTCTATTCCTTAAAAATTGAACGCTC 2 226 0 TTCTTAAAAA 0.837528 -16 CCTTTAGGTGTTTGTGAAACACCTATAAACG 3 35 1 TTTTGAAACA 0.836881 -82 AAATTAAAACTTTTAGAAAAATAACCGATCT 4 47 0 TTTAGAAAAA 0.851508 -179 AATCTTCATCTTTGATAAAAAATTAAAACTT 4 66 0 TTTATAAAAA 0.917648 -160 TACCTATTTGTATCTTAAAAATTTGTATTTT 4 167 0 TATTTAAAAA 0.946911 -59 TAATGGGGTGAATTTTAAACAAATAAAGGGC 6 37 0 AATTTAAACA 0.7881 -211 CCCCATTAGAAATATTAAAAAATTTTTATTT 6 60 1 AATTTAAAAA 0.896463 -188 TTCCAATCTTTTCTATAAACATTCGCATTAA 6 94 1 TTCATAAACA 0.580396 -154 AATCGGTATTTTTGATAAAAAAGTCATTAAT 6 123 1 TTTATAAAAA 0.917648 -125 TTAGCTTAAATTTTTGAAAAATTATTATTTA 6 160 0 TTTTGAAAAA 0.525791 -88 TTACCACCTTTTATGAAAAATGTTCTTTTT 6 228 0 TTTTGAAAAA 0.890841 -20 GCGAGACAAGAATGTTAAAAAATGAAAGGAG 7 17 0 AATTTAAAAA 0.896463 -127 TATAACTAAAAATTAGAAAAACTTTAATGCG 7 108 1 AATAGAAAAA 0.784228 -36 GTTTTTTGCGTTTTTTAAACAGCCGTTAAGC 8 49 0 TTTTTAAACA 0.880706 -145 AACCGATGCATACTATAAAAATAATTATTAA 8 147 0 TACATAAAAA 0.763039 -47 AGAAAAACAGAATGTTAAAAATAAAGTTCAA 9 163 0 AATTTAAAAA 0.896463 -138 AAGTGTTTCATTTTATAAAAAAGAAAAACAG 9 184 0 TTTATAAAAA 0.915621 -117 GAATCGCTATAATTTGAAACAATTTAAATCT 9 257 1 AATTGAAACA 0.71425 -44 TTGGAATGTTTTTTACAAAAAACATTTTTAA 12 36 0 TTTACAAAAA 0.660046 -182 ATATTAGAGGAATTTTAAAAATAATAAGAGA 12 105 1 AATTTAAAAA 0.89644 -113 AATTTTGGATTATAATAAAAAAACTGGCTGA 13 52 0 TATATAAAAA 0.917667 -161 AACGCTATACCTTAAAAATTAATGACGC 13 195 0 TACTTAAAAA 0.837545 -18 AGATGATTCTAATTTCAAAAAAAGGTGTTTT 14 27 1 AATTCAAAAA 0.668046 -22 AATGCCTAAAATTTAGAAAAAATCACGCTTG 16 21 1 ATTAGAAAAA 0.783965 -96 TGCGGAATTTTATCATAAAAATTCTTAAAAT 17 168 0 TATATAAAAA 0.917667 -133 GGTGTGATTTTACTTGAAAAATTTAAACCAT 17 250 1 TACTGAAAAA 0.775703 -51 TAATTAATCCTTTATTAAACAGAGTATTGTT 18 19 1 TTTTTAAACA 0.884562 -116 AAATAGTCGTTTTAACAAACAAAATTTTGTT 18 76 1 TTTACAAACA 0.527608 -59 ATTTTAGGATTTTGTGAAAAATAGTTTCATT 19 75 0 TTTTGAAAAA 0.890841 -166 GGTGGAGTATAATCTTAAAAAGTTAATGAAA 19 122 0 AATTTAAAAA 0.896463 -119 TTAATTCAAAAATGATAAAAAGATAAAACGA 20 96 0 AATATAAAAA 0.843943 -44 AAAAACCCCTTTATTAAAAAAAATTAATTC 20 120 0 TTTTTAAAAA 0.944824 -20 *** ******* Masking position 7 Map Score: 45.2615 Number of sites scoring better than the average of aligned sites = 1123 Number in coding regions = 842 Number in noncoding regions = 281 Number of orfs with sites within 600 bp upstream = 187 Fraction of orfs with sites within 600 bp upstream = 0.0300353 Motif number 3 AGTATTTGCTAAAATGTAACTTTAAATTGAGATTAAA 2 162 0 AAAAAAAAAT 0.840154 -80 ATAAAAAATTAAAACTTTTAGAAAAATAACCGATCTT 4 46 0 AAAATTAAAT 0.490287 -180 TGTATCTTAAAAATTTGTATTTTAAAAGTTTGAGGCG 4 153 0 AAATTAAAAA 0.703378 -73 ATAATTTTTCAAAAATTTAAGCTAAAACTAATAATGG 6 166 1 AAAATAAAAA 0.932586 -82 AATAAAAGCGAGACAAGAATGTTAAAAAATGAAAGGA 7 18 0 AGACAAAAAA 0.509398 -126 TTTAATCTAAAAACGATATAACTAAAAATTAGAAAAA 7 92 1 AAACATAAAA 0.811113 -52 ATTTGTTATCAAAACCATTTGAAAAAAGTTTTTTGCG 8 70 0 AAAATTAAAA 0.83275 -124 GCAAATAAATAAAATCAAACTTCAAAATTTAAGTTAA 8 108 1 AAAAAAAAAA 0.964548 -86 TGCATACTATAAAAATAATTATTAAAATTAACTTAAA 8 135 0 AAAAATAAAA 0.907342 -59 GCCGAGCATTATACCAAAAAAAAAAAAAACGATGTTA 9 125 1 ATACAAAAAA 0.697418 -176 ATAAAAAAGAAAAACAGAATGTTAAAAATAAAGTTCA 9 164 0 AAAAAAAAAA 0.964548 -137 TATTAAATAAATAAATAAACTTAAAAAGTGTTTCATT 9 203 0 ATAAAAAAAA 0.840154 -98 TCTTTCTTTTAAACACCAATATTAAATAAATAAATAA 9 222 0 AAACAAAAAT 0.697418 -79 ATTATTATTGAAAATCATAGCGCAAAAATAAGGCGAT 10 71 0 AAAATAAAAA 0.932586 -62 TTGGTGTTAAAAATGTTTTTTGTAAAAAACATTCCAA 12 30 1 AAATTTAAAA 0.460474 -188 AATGGGCGAGAAAAAAGAAAGCCAAAAGGTGGCGGTT 12 149 1 AAAAAAAAAA 0.964548 -69 ATAAAGTTTGCTAAAAAGATGATTCTA 14 1 1 ATAATTAAAA 0.490287 -48 AAACTAAGATAAATTAAAATATTAAAATTAG 15 11 1 AAATAAAAAA 0.823435 -21 TAAAATCAGCAAAATCAAAAAAAAAAAAAAAAGATTT 17 115 1 AAAAAAAAAA 0.964548 -186 ACACAATGATAAAACAAAAGGTTAAACAATACTCTGT 18 37 0 AAAAAAAAAC 0.703065 -98 CAGATTAGGTAAAATCTATTAACAAAATTTTGTTTGT 18 90 0 AAAAATAAAA 0.907342 -45 ACAAAATCCTAAAATATTAAAGAAAATATTTTTTCAT 19 91 1 AAAATAAAAT 0.727706 -150 TATAATCTTAAAAAGTTAATGAAAAAATATTTTCTTT 19 109 0 AAAAAAAAAA 0.964548 -132 TTGTTGGATCAAAATTAAACCTAAAAACAGATTTAAT 19 186 0 AAAAAAAAAA 0.964548 -55 AGATAAAACGATACGAAAACTTTAAAACTAAGCGAAG 20 70 0 ATACAAAAAA 0.697418 -70 CTTTATTAAAAAAAATTAATTCAAAAATGATAAAAAG 20 105 0 AAAAAAAAAA 0.964548 -35 CATACTAAATAAAACCATAGGATAAAAGC 21 3 0 AAAATAAAAA 0.932586 -72 **** ** **** Masking position 14 Map Score: 33.7132 Number of sites scoring better than the average of aligned sites = 890 Number in coding regions = 686 Number in noncoding regions = 204 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 4 TTAATTTGCTATTAAGCGTTTCAAAAAAGCA 1 45 1 ATTAAGCGTT 0.841461 -256 TACTAGCAAGAAAACGGGTTTGATCCATAAA 1 225 0 AAAACGGGTT 0.827044 -76 ATTGTTTTTCATCAAGGGAGTTTGAGC 1 284 1 ATCAAGGGGT 0.710652 -17 TTAAAAAACCAATAAGGATTTGATC 2 5 0 AATAAGGATT 0.696199 -237 TACTCACTATAATAAGCGTTTATTTTAAAAA 2 195 1 AATAAGCGTT 0.856038 -47 AAGGCTAGCCATAAAGGGTTTTTAAGCCCTT 6 12 1 ATAAAGGGTT 0.972868 -236 TTTTAAACAAATAAAGGGCTTAAAAACCCTT 6 25 0 ATAAAGGGTT 0.972869 -223 ATTCTGTTTTAAAAAGCGCTTAACGGCTGTT 8 32 1 AAAAAGCGTT 0.906679 -162 AAATAAACTTAAAAAGTGTTTCATTTTATAA 9 197 0 AAAAAGTGTT 0.709752 -104 TATTGATGGGATAAAGGGGGTTTT 9 287 1 ATAAAGGGGT 0.928784 -14 ACTTATTTGGATAAAGGGGTTTTAAAATGCT 11 39 0 ATAAAGGGTT 0.972869 -30 AACTTCCCATAATAAGGGCTTGGGTTTTCCA 13 111 1 AATAAGGGTT 0.960917 -102 TCTAATTTCAAAAAAAGGTGTTTTT 14 34 1 AAAAAAGGGT 0.593139 -15 TGAGAGATTGAAAAATGGTTTAAATTTTTCA 17 264 0 AAAAATGGTT 0.694471 -37 CTCTCAAAACATTAAGGAGTTT 17 289 1 ATTAAGGATT 0.671646 -12 TACTCTGTTTAATAAAGGATTAATTATTTTT 18 14 0 AATAAAGGTT 0.710406 -121 ATTTTTTTTAATAAAGGGGTTTTT 20 126 1 ATAAAGGGTT 0.972869 -14 ******** ** Masking position 4 Map Score: 19.0877 Number of sites scoring better than the average of aligned sites = 657 Number in coding regions = 565 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 5 AAATTGACATCTTTTAAGCAAAATGTTATAATG 1 78 1 CTTTACAAAA 0.964588 -223 CCTTATTGGTTTTTTAACAAACAAGCTAAAAGT 2 19 1 TTTTAAAACA 0.740826 -223 TTAAAAGAATTTTTTATTCAAAATAACCCCATT 2 123 0 TTTTACAAAA 0.549986 -119 TAGGGTGTAACTTTAATTCAACAAGAAGGATTT 4 14 0 CTTTACAACA 0.967332 -212 AAATCTTCATCTTTGATAAAAAATTAAAACTTT 4 65 0 CTTTAAAAAA 0.731305 -161 TTAACCAACATTTTCACTCTAAAATCTTCATCT 4 86 0 TTTTACTAAA 0.776088 -140 CACTTATTAGTATTTAACCAACATTTTCACTCT 4 99 0 TATTACAACA 0.577045 -127 CCGCCTCAAACTTTTAAAATACAAATTTTTAAG 4 152 1 CTTTAATACA 0.578434 -74 TATTAATGACTTTTTTATCAAAAATACCGATTA 6 122 0 TTTTTCAAAA 0.462449 -126 GAAAAATGTTCTTTTTTACAACAATGTGAAATT 6 211 0 CTTTTCAACA 0.847274 -37 TTACCACCTTTTATGAAAAATGTTCTTTTT 6 228 0 CTTTAAAAAA 0.847419 -20 ATAGTGCTGACTTTTAATCTAAAAACGATATAA 7 80 1 CTTTACTAAA 0.873373 -64 GTTAAGCGCTTTTTAAAACAGAATGTTAGTTTT 8 23 0 TTTTACAGAA 0.571217 -171 CGTCAGGACATTTTAATGAAAAAGTTGATTAAA 9 36 1 TTTTAAAAAA 0.731851 -265 CTTCGCCGAGCATTATACCAAAAAAAAAAAAAA 9 121 1 CATTTCAAAA 0.332547 -180 GCGATTCTTTCTTTTAAACACCAATATTAAATA 9 231 0 CTTTACACCA 0.906142 -70 AAAACCCCCTTTATCCCATCAATAGATTTAA 9 280 0 CTTTTCATCA 0.254891 -21 CTTGGAATGTTTTTTACAAAAAACATTTTTAAC 12 35 0 TTTTAAAAAA 0.565216 -183 AGTTTTTTTATTATAATCCAAAATTTCTTTGAA 13 58 1 TTATACAAAA 0.421823 -155 ATTAATGACGCTTTAAAGCACCATGTTTAAAAA 13 173 0 CTTTACACCA 0.906147 -40 ACCACCGCCTTTAACGCACCACGCTTGAAAT 16 96 0 CTTTACACCA 0.906147 -21 ACAAGACACTCTTTGACGCTAAAAGCGGTTTAA 17 17 0 CTTTACTAAA 0.87528 -284 AAATCCCCATTTTTGACACACAACGAGCCTATA 17 66 0 TTTTACACAA 0.800092 -235 TGGTTTAAATTTTTCAAGTAAAATCACACCAAT 17 247 0 TTTTATAAAA 0.367689 -54 TTAGGTTTAATTTTGATCCAACAAAATTTTAAA 19 199 1 TTTTACAACA 0.935071 -42 CGGCTTAATTCTTTTAACCAAGAGAGTTCTTTC 20 12 1 CTTTACAAGA 0.778474 -128 GATACGAAAACTTTAAAACTAAGCGAAGAATCA 20 65 0 CTTTACTAAG 0.341427 -75 **** * ***** Masking position 4 Map Score: 21.9034 Number of sites scoring better than the average of aligned sites = 985 Number in coding regions = 857 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 6 GTCAGGGGTTCGAACCCCCTACACTCCACC 1 173 1 CGAACCCCCT 0.983422 -128 GCTCAAACTCCCTTGATGAAAAA 1 288 0 CAAACTCCCT 0.97768 -13 ACCCACAAAACAAACCGCCTCAAACTTTTA 4 138 1 CAAACCGCCT 0.906799 -88 AGAACTCCCTTTGATTAAAT 4 216 0 AGAACTCCCT 0.958747 -10 AAAGGGCTTAAAAACCCTTTATGGCTAGCC 6 14 0 AAAACCCTTT 0.70319 -234 AAAACCCCCTTTATCCCATC 9 291 0 AAAACCCCCT 0.984148 -10 ACTCCAAACTCCCTTCAAACTAGT 10 119 0 CAAACTCCCT 0.97768 -14 TTAGCATTTTAAAACCCCTTTATCCAAATA 11 37 1 AAAACCCCTT 0.905343 -32 TTATCTAACGCCAACTCTCTTATTATTTTT 12 121 0 CCAACTCTCT 0.742397 -97 TAACCAAGAAAGAACTCTCTTGGTTAAAAG 20 22 0 AGAACTCTCT 0.85199 -118 AAAAACCCCTTTATTAAAAA 20 130 0 AAAAACCCCT 0.830269 -10 ********** Masking position 4 Map Score: 11.3736 Number of sites scoring better than the average of aligned sites = 486 Number in coding regions = 411 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 7 GCTTAATTTTATTTGGGGTGTTAGCTCAGC 1 114 1 ATTTGGGGTG 0.619365 -187 ATCAAATCCTTATTGGTTTTTTAACAAACA 2 12 1 TATTGGTTTT 0.439023 -230 ATGGCGGGTTAAATGGGGTTATTTTGAATA 2 112 1 AAATGGGGTT 0.950942 -130 TAATTAAACCTTTAGGTGTTTGTGAAACAC 3 27 1 TTTAGGTGTT 0.505842 -90 TTATTGCGTTTATAGGTGTTTCACAAACAC 3 42 0 TATAGGTGTT 0.878457 -75 AAATGATTGGAATTGGTGATTATACCTATT 4 190 0 AATTGGTGAT 0.703535 -36 TTAATATTTCTAATGGGGTGAATTTTAAAC 6 48 0 TAATGGGGTG 0.902536 -200 ATTTATTTAATATTGGTGTTTAAAAGAAAG 9 228 1 TATTGGTGTT 0.943679 -73 TTGATGGGATAAAGGGGGTTTT 9 289 1 AAAGGGGGTT 0.75353 -12 CTTATTTGGATAAAGGGGTTTTAAAATGCT 11 39 0 TAAAGGGGTT 0.893178 -30 CCTTAATTAAAATTGGTGTTAAAAATGTTT 12 18 1 AATTGGTGTT 0.943679 -200 AACTTCTAACAATTGGGGTGAATAAGAGCT 13 142 1 AATTGGGGTG 0.919929 -71 TAATTTCAAAAAAAGGTGTTTTT 14 36 1 AAAAGGTGTT 0.85349 -13 TGTGTGTCAAAAATGGGGATTTTTCACTAG 17 77 1 AAATGGGGAT 0.733002 -224 ATTACTTAATAATTGGCGTTCGTTATTGGT 17 223 1 AATTGGCGTT 0.777496 -78 TGGCGTTCGTTATTGGTGTGATTTTACTTG 17 236 1 TATTGGTGTG 0.888945 -65 TGTATTTCCTTAATGGTGTTATAATCGCTC 19 36 0 TAATGGTGTT 0.931059 -205 TTTTTTTTAATAAAGGGGTTTTT 20 127 1 TAAAGGGGTT 0.893178 -13 ********** Masking position 5 Map Score: 19.2867 Number of sites scoring better than the average of aligned sites = 482 Number in coding regions = 406 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 8 AAGATGTCAATTTGATGCTTTTTTGAAACGCTTA 1 57 0 TTTTGTTTTT 0.954299 -244 TCAAACCCGTTTTCTTGCTAGTATTACCCATAAT 1 233 1 TTTTGTAGTT 0.636393 -68 GATCAAATCCTTATTGGTTTTTTAACAAACAAG 2 10 1 CTTTGTTTTT 0.725886 -232 TTATAAATATTTTATTGCGTTTATAGGTGTTTCA 3 49 0 TTTTGGTTTT 0.920612 -68 AGGCGGTTTGTTTTGTGGGTGTATCCCACTTATT 4 124 0 TTTTGGTGTT 0.919091 -102 TTGAAAAAAGTTTTTTGCGTTTTTTAAACAGCCG 8 55 0 TTTTGGTTTT 0.920612 -139 AATAACATCGTTTTTTTTTTTTTTGGTATAATGC 9 130 0 TTTTTTTTTT 0.708051 -171 GTCCTCTCCATTTAATGATTGTTTAATCATTGTT 13 11 1 TTTTGTTGTT 0.953391 -202 CGTCAAAGAGTGTCTTGTGTGTTTTGAGAACGCA 17 32 1 TGTTGGTGTT 0.590264 -269 TTTTTTTGATTTTGCTGATTTTACTCAATCTCTA 17 104 0 TTTTGTTTTC 0.725886 -197 TGAAAATCTTTTTTTTTTTTTTTTGATTTTGCTG 17 121 0 TTTTTTTTTT 0.708051 -180 TTATTAAGTTTTTTTTGTTTTTATTACTTAATAA 17 201 1 TTTTGTTTTT 0.954299 -100 TAACCTTTTGTTTTATCATTGTGTTAAAATAGTC 18 50 1 TTTTCTTGTT 0.786089 -85 TAGTTTCATTTTTACTGCTTGTATTTCCTTAATG 19 51 0 TTTTGTTGTT 0.953391 -190 TTCTTTAATATTTTAGGATTTTGTGAAAAATAGT 19 81 0 TTTGGTTTTT 0.725886 -160 TTTCGTATCGTTTTATCTTTTTATCATTTTTGAA 20 89 1 TTTTCTTTTT 0.789537 -51 *** ** **** * Masking position 3 Map Score: 14.892 Number of sites scoring better than the average of aligned sites = 287 Number in coding regions = 240 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 9 CTTTAAATTGAGATTAAATCCACATTAAAA 2 150 0 AGATTAAATC 0.751698 -92 CTTTAAAGGTTAATTAAACCTTTAGGTGTT 3 17 1 TAATTAAACC 0.662378 -100 CTTTGATAAAAAATTAAAACTTTTAGAAAA 4 58 0 AAATTAAAAC 0.850533 -168 AATTGCAAATAAATAAAATCAAACTTCAAA 8 104 1 AAATAAAATC 0.851979 -90 ATTTTATAAAAAAGAAAAACAGAATGTTAA 9 176 0 AAAGAAAAAC 0.446212 -125 AATTTGAAACAATTTAAATCTATTGATGGG 9 267 1 AATTTAAATC 0.665861 -34 AGTTTGATGAAAGGAAAATC 10 1 0 AAGGAAAATC 0.552617 -132 ACCACGCTTGAAATTAAAACTAAATTTTAG 16 80 0 AAATTAAAAC 0.850533 -37 GAAAAGTTAAACCGCTTTTAGCG 17 4 1 AAGTTAAACC 0.898878 -297 AATTATTAAGTAATAAAAACAAAAAAAACT 17 207 0 TAATAAAAAC 0.442946 -94 TAAATTTTTCAAGTAAAATCACACCAATAA 17 245 0 AAGTAAAATC 0.849359 -56 TTACTTGAAAAATTTAAACCATTTTTCAAT 17 259 1 AATTTAAACC 0.670219 -42 CTCTCAGATTAGGTAAAATCTATTAACAAA 18 101 0 AGGTAAAATC 0.657155 -34 AAAGCATAGTAAATTAAATCTGTTTTTAGG 19 174 1 AAATTAAATC 0.899038 -67 TGTTGGATCAAAATTAAACCTAAAAACAGA 19 192 0 AAATTAAACC 0.900738 -49 AGTTCTTTCTTGGTTAAATCCTTTCTTTTT 20 36 1 TGGTTAAATC 0.390673 -104 GTAACATACTAAATAAAACCATAGGATAAA 21 14 0 AAATAAAACC 0.854337 -61 TCGGAATGTAAAGTTAAAACG 22 11 1 AAGTTAAAAC 0.847891 -11 ********** Masking position 6 Map Score: 14.7865 Number of sites scoring better than the average of aligned sites = 340 Number in coding regions = 250 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 10 CGAGCATTATAACATTTTGCTTAAAAGATGT 1 84 0 AACATTTGCT 0.663617 -217 AGGTTAATTAAACCTTTAGGTGTTTGTGAAA 3 23 1 AACCTTAGGT 0.553553 -94 AATAAATCCTTCTTGTTGAATTAAAG 4 6 1 ATCCTTTTGT 0.900296 -220 TTATAAATTTCACATTGTTGTAAAAAAGAAC 6 206 1 CACATTTTGT 0.787245 -42 TTCATTTTTTAACATTCTTGTCTCGCTTTTA 7 22 1 AACATTTTGT 0.90442 -122 TTCTAAAACTAACATTCTGTTTTAAAAAGCG 8 19 1 AACATTTGTT 0.891426 -175 ATGTTATTTGAACTTTATTTTTAACATTCTG 9 156 1 AACTTTTTTT 0.650648 -145 CTTTATTTTTAACATTCTGTTTTTCTTTTTT 9 168 1 AACATTTGTT 0.891426 -133 TGATTGTTTAATCATTGTTGTTAATTTCAGC 13 26 1 ATCATTTTGT 0.881373 -187 AAAAACACCTTTTTTTGAAATTAGAA 14 33 0 CACCTTTTTT 0.761086 -16 TCCCATGAAAATCTTTTTTTTTTTTTTTTGA 17 129 0 ATCTTTTTTT 0.593995 -172 AGTATTGTTTAACCTTTTGTTTTATCATTGT 18 41 1 AACCTTTGTT 0.911173 -94 CTTTTGTTTTATCATTGTGTTAAAATAGTCG 18 54 1 ATCATTTGTT 0.86887 -81 AACGATCCTTTTTGTATGATTTATG 19 5 1 ATCCTTTTGT 0.900296 -236 TTATCTTTTTATCATTTTTGAATTAATTTTT 20 101 1 ATCATTTTGA 0.388652 -39 GATTGTTATTCTCCTTATGTTAGAATGTTTG 21 50 0 CTCCTTTGTT 0.759134 -25 ****** **** Masking position 6 Map Score: 7.66032 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 191 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 11 CCCCTACACTCCACCATTATTACGCTTATTCT 1 188 1 CCCCATATTA 0.906118 -113 TTACGCTTATTCTCTTTCTTTATGGATCAAAC 1 207 1 TCCTTTTTTA 0.806636 -94 TTGCTAGTATTACCCATAATTAATTATAATCT 1 247 1 TACCATATTA 0.824518 -54 CCCATTTAACCCGCCATTATTAACCCGCATTG 2 97 0 CCCCATATTA 0.906118 -145 TAGCAAATACTCACTATAATAAGCGTTTATTT 2 188 1 TCCTATATAA 0.431904 -54 AGAACTCCCTTTGATTAAATGATTGGA 4 209 0 TCCTTTATTA 0.898839 -17 TGCTCGCCTTTTTTATGCGTT 5 7 0 TCCCTTTTTA 0.934824 -15 AAATTTATAATAACCATTATTAGTTTTAGCTT 6 184 0 TACCATATTA 0.824504 -64 CATTCTTGTCTCGCTTTTATTATATAACAATT 7 34 1 TCCTTTATTA 0.898839 -110 AAAGAAAGAATCGCTATAATTTGAAACAATTT 9 250 1 TCCTATATTT 0.60662 -51 CTAGTCAAAATCGCCTTATTTTTGCGCTATGA 10 62 1 TCCCTTTTTT 0.713411 -71 TGTTTCTCCTTAATTAAAATTGGTGT 12 5 1 TCCCTTATTA 0.968304 -213 ACGCTTTAAAGCACCATGTTTAAAAACAGCTC 13 167 0 GCCCATTTTA 0.711173 -46 TAGTGAAAAATCCCCATTTTTGACACACAACG 17 74 0 TCCCATTTTG 0.676615 -227 AAAAATAATTAATCCTTTATTAAACAGAGTAT 18 14 1 AACCTTATTA 0.489719 -121 AAAAACCCCTTTATTAAAAAAAATTA 20 124 0 ACCCTTATTA 0.861873 -16 ** **** **** Masking position 7 Map Score: 7.73575 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 219 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 12 TTGGTTTTTTAACAAACAAGCTAAAAGTAT 2 24 1 AACAAACAAG 0.734188 -218 ATTAGTATTTAACCAACATTTTCACTCTAA 4 97 0 AACCAACATT 0.941154 -129 CGCATTCTAAAACTAACATTCTGTTTTAAA 8 15 1 AACTAACATT 0.801015 -179 AACTCATCTCAACCAACAATAATAGAAGCG 10 27 1 AACCAACAAT 0.904122 -106 CCTGCAACCAACATTAAAGAATGCC 11 6 1 AACCAACATT 0.941154 -63 TGTTTTTTACAAAAAACATTTTTAACACCA 12 31 0 AAAAAACATT 0.775816 -187 TGTTTTTTGTAAAAAACATTCCAAGAACTA 12 43 1 AAAAAACATT 0.775816 -175 ACAATGATTAAACAATCATTAAATGGAGAG 13 14 0 AACAATCATT 0.847872 -199 TAGTCGTTTTAACAAACAAAATTTTGTTAA 18 79 1 AACAAACAAA 0.650787 -56 TGTTACAATAATCAAACATTCTAACATAAG 21 38 1 ATCAAACATT 0.74054 -37 TAAGGAGAATAACAATCAATT 21 64 1 AACAATCAAT 0.766691 -11 ********** Masking position 5 Map Score: 6.81689 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 57 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 13 GAACCCCCTACACTCCACCATTATTACGCT 1 184 1 CACTCCACCA 0.907618 -117 CGCATTGTCCCACTCAAACCACTCGCAATT 2 74 0 CACTCAAACC 0.950988 -168 CCAACATTTTCACTCTAAAATCTTCATCTT 4 85 0 CACTCTAAAA 0.843272 -141 TAATGCGGAGCATTCAAACCCA 7 132 1 CATTCAAACC 0.908054 -12 ATAACGCATTCTAAAACTAACATTCT 8 7 1 CATTCTAAAA 0.732517 -187 TTGTAAAAAACATTCCAAGAACTATATATT 12 49 1 CATTCCAAGA 0.783521 -169 TAACGCACACTCCAACCCAATCCCAGA 12 201 0 CACTCCAACC 0.968264 -17 CTATGCTTTCCACTCAATCAGCGGAAACAT 19 153 0 CACTCAATCA 0.808268 -88 AATAATCAAACATTCTAACATAAGGAGAAT 21 44 1 CATTCTAACA 0.922918 -31 ********** Masking position 4 Map Score: 1.62248 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 97 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 14 AGAAACTTTCTAATTTTAAGATAATCATTC 1 15 1 TAATTTTAAG 0.418822 -286 ACACCCCAAATAAAATTAAGCGAGCATTAT 1 105 0 TAAAATTAAG 0.677116 -196 AATTTAAAGTTACATTTTAGCAAATACTCA 2 171 1 TACATTTTAG 0.342216 -71 TAAAAAATTAAAACTTTTAGAAAAATAACC 4 52 0 AAACTTTTAG 0.770469 -174 ATCAAAGATGAAGATTTTAGAGTGAAAATG 4 81 1 AAGATTTTAG 0.684674 -145 TAATTTTTCAAAAATTTAAGCTAAAACTAA 6 167 1 AAAATTTAAG 0.92025 -81 AAAGTTTTTCTAATTTTTAGTTATATCGTT 7 103 0 TAATTTTTAG 0.396473 -41 AAAATTAGAAAAACTTTAATGCGGAGCATT 7 116 1 AAACTTTAAT 0.390381 -28 ATCAAACTTCAAAATTTAAGTTAATTTTAA 8 121 1 AAAATTTAAG 0.92025 -73 ATATATTAGTAAAAATTAAGTAATATTGAG 12 72 1 AAAAATTAAG 0.826262 -146 GCTATACCTTAAAAATTAATGACGCTTTAA 13 190 0 AAAAATTAAT 0.452668 -23 TGATTTTTTCTAAATTTTAGGCATTTAAGG 16 16 0 TAAATTTTAG 0.822642 -101 GTATTCTTAGCAAATTTTAGATAAGATCAA 16 49 0 CAAATTTTAG 0.588002 -68 AAATTAAAACTAAATTTTAGTGTATTCTTA 16 70 0 TAAATTTTAG 0.822642 -47 AAAAATTCTTAAAATTTTATTAATCCCATG 17 153 0 AAAATTTTAT 0.646552 -148 TTTTACTTGAAAAATTTAAACCATTTTTCA 17 257 1 AAAATTTAAA 0.518194 -44 CAATCTCTCAAAACATTAAGGAGTTT 17 285 1 AAACATTAAG 0.602805 -16 TATTTTCTTTAATATTTTAGGATTTTGTGA 19 89 0 AATATTTTAG 0.443224 -152 TTGATCCAACAAAATTTTAAAACACTTAAG 19 211 1 AAAATTTTAA 0.495058 -30 TCTTGGTTAAAAGAATTAAGCCGA 20 5 0 AAGAATTAAG 0.495385 -135 CTTTATTAAAAAAAATTAATTCAAAAATGA 20 112 0 AAAAATTAAT 0.452668 -28 ********** Masking position 6 Map Score: 7.72409 Number of sites scoring better than the average of aligned sites = 1034 Number in coding regions = 845 Number in noncoding regions = 189 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 15 TCAATTTGATGCTTTTTTGAAACGCTTAATAGC 1 52 0 GCTTTTAAAC 0.976161 -249 CATTTAACCCGCCATTATTAACCCGCATTGTCC 2 94 0 GCTTATAACC 0.563587 -148 AAAATTGAACGCTCTTTTTAAAATAAACGCTTA 2 207 0 GCTTTTAAAA 0.803366 -35 TGAAAAATGTTCTTTTTTACAACAATGTGAAAT 6 212 0 TCTTTTCAAC 0.61168 -36 CAGCCGTTAAGCGCTTTTTAAAACAGAATGTTA 8 28 0 GCTTTTAAAA 0.803366 -166 AAAGTTTTTTGCGTTTTTTAAACAGCCGTTAAG 8 50 0 GCTTTTAAAC 0.976161 -144 CAATAATAATGACTTTTTAAAACTAGTTTGAAG 10 98 1 GATTTTAAAC 0.814655 -35 GAATGCCTTTAGCATTTTAAAACCCCTTTATCC 11 29 1 AGTTTTAAAC 0.515014 -40 TTTACAAAAAACATTTTTAACACCAATTTTAAT 12 23 0 ACTTTTACAC 0.89809 -195 AAGTTTATGAGCCGTTTTGCCACTATTCAAAGA 13 83 0 GCTTTTCCAC 0.884463 -130 GTGAATAAGAGCTGTTTTTAAACATGGTGCTTT 13 159 1 GCTTTTAAAC 0.976161 -54 TGAAAAATCCCCATTTTTGACACACAACGAGCC 17 70 0 CCTTTTACAC 0.798788 -231 AAATAATTAATCCTTTATTAAACAGAGTATTGT 18 16 1 TCTTATAAAC 0.610716 -119 TGTTAAAACGACTATTTTAACACAATGATAAAA 18 60 0 ACTTTTACAC 0.89809 -75 GATTTATGGAGCGATTATAACACCATTAAGGAA 19 28 1 GCTTATACAC 0.884048 -213 TTGATCCAACAAAATTTTAAAACACTTAAGGAG 19 211 1 AATTTTAAAC 0.55819 -30 ** **** **** Masking position 6 Map Score: 13.0806 Number of sites scoring better than the average of aligned sites = 837 Number in coding regions = 738 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918