AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00251_hpyl_reg_100.orf -o00251_hpyl_100.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 HP0056 300 delta-1-pyrroline-5-carboxylate dehydrogenase {Synechocystis sp.) #2 HP0329 248 NH(3)-dependent NAD+ synthetase (nadE) #3 HP0380 65 glutamate dehydrogenase (gdhA) #4 HP0382 182 zinc-metallo protease (YJR117W) #5 HP0408 165 H. pylori predicted coding region HP0408 #6 HP0417 168 methionyl-tRNA synthetase (metS) #7 HP0476 117 glutamyl-tRNA synthetase (gltX) #8 HP0512 290 glutamine synthetase (glnA) #9 HP0549 37 glutamate racemase (glr) #10 HP0550 263 transcription termination factor Rho (rho) #11 HP0643 164 glutamyl-tRNA synthetase (gltX) #12 HP0919 98 carbamoyl-phosphate synthase (glutamine-hydrolysing) (pyrAb) #13 HP0920 143 conserved hypothetical integral membrane protein #14 HP1234 300 conserved hypothetical integral membrane protein #15 HP1236 78 H. pylori predicted coding region HP1236 #16 HP1530 152 purine nucleoside phosphorylase (punB) #17 HP1531 42 H. pylori predicted coding region HP1531 Motif number 1 TGTAAATCCGTTTAATTTAAAATCGTTTCGTT 1 18 1 TTTAATTAAA 0.80038 -283 AATGTTATAATTTATTATTAAACGAAAAGTAA 1 75 1 TTTATTTTAA 0.803287 -226 CATTCCAACCTTTTTGAGTTTATCACGCATTT 1 158 0 TTTTTGGTTA 0.553882 -143 GGTAATGTTTTTTAATTTTAAATTTTGTTCTA 1 205 0 TTTAATTTAA 0.766939 -96 GAGCTTACCTTTTATTTAAGAATTTGACTTG 1 280 0 TTTTATTAAA 0.71079 -21 AAACGCATCGTTTAAGTGAAAAATTAGCTTTT 2 207 0 TTTAAGGAAA 0.845753 -42 AAACGATGCGTTTTTTCTATTATAATTTAAGG 2 226 1 TTTTTTTATA 0.452887 -23 TTTAAGTGTTTTTATTGTAACACTAAAAGGGT 3 25 0 TTTATTTAAA 0.841323 -41 AGCGGCATCCTTTATTGTTTTAAGTGTTTTTA 3 43 0 TTTATTTTTA 0.803089 -23 GACAAACCTTTTTGTTTATAGCGGGTTGGA 4 9 1 TTTTTGTTAA 0.880031 -174 TTTGAGCGTTTTTAATCCTAAAAAGCTGTGTT 4 42 0 TTTAATCTAA 0.567456 -141 TTTATTTAATTTTATGGTTTTATGGTAAATTT 4 97 1 TTTATGTTTA 0.894274 -86 TTCCTACACTTTTATTGGTAAATTTAATGGAG 4 146 1 TTTATTGTAA 0.792805 -37 AATTCTCAATTTTTATATTATAATACCCAATC 5 96 1 TTTTATTTAA 0.773363 -70 CTTTTATCCTTATAAGCGTCAATA 5 152 0 TTTATCTTAA 0.70404 -14 TATAATGAATTTTAAGCTAAAAACACCCCACA 6 54 1 TTTAAGTAAA 0.504931 -115 TTTAAACAAATTTAAGGTAACACGATTATAAA 6 146 1 TTTAAGTAAA 0.923599 -23 ATACACTAATTTTAATAGAAAAAAGTGAAACC 7 41 1 TTTAATGAAA 0.683023 -77 GTATTTTATTTTTAAGGTTAGAACA 7 103 1 TTTAAGTTAA 0.93684 -15 CAAGTATCCTTTATTTTTAAATTTAAACTTA 10 10 1 TTTATTTTAA 0.902914 -254 ATGCTATAATTTTAAGTTTAAATTTAAAAATA 10 22 0 TTTAAGTTAA 0.797237 -242 TTAGAGTGGTTTTAATTTATTATGACTTATGC 10 50 0 TTTAATTATA 0.739466 -214 TCAAATTTTATTTAACTTTAGAGTGGTTTTAA 10 67 0 TTTAACTTAA 0.750002 -197 TAGAAATCTCTTTTTGTTAAAAGGAAATTTA 10 243 1 TTTTTGTAAA 0.80138 -21 ATAGGCATCATTTAAGAGATTAGCACTTGGCT 11 57 0 TTTAAGGATA 0.701395 -108 TTAAAAATAGTTTTTGATTATACCTAAAGAAT 11 130 0 TTTTTGTTAA 0.879394 -35 GATTCGTGTTTTTATGTTTTCATATTTCTATA 14 94 1 TTTATGTTTA 0.894277 -207 ACTTAAAGTTTTTAAGCTTTAAACGCATAAAA 14 226 0 TTTAAGTTTA 0.773496 -75 GCTTAAAAACTTTAAGTCTTAATTAGAGATTT 14 241 1 TTTAAGCTTA 0.686877 -60 TAATTAGAGATTTTAGGTTAAACTACCCTAAA 14 260 1 TTTTAGTTAA 0.569021 -41 CCCTAAAATCTTTATGGGTAAAATGC 14 285 1 TTTATGGTAA 0.887847 -16 TTTTATCGTTTTTTAGATAAAACGCTTTTTAA 15 20 0 TTTTAGTAAA 0.514851 -59 GCATATTTTATTTATTTTTAGAGTGTATTTTA 15 47 0 TTTATTTTAA 0.905783 -32 ACACCTTAATTTTAAGGCTTCATTCACATTTC 16 64 0 TTTAAGCTTA 0.6869 -89 ****** *** * Masking position 3 Map Score: 40.9191 Number of sites scoring better than the average of aligned sites = 716 Number in coding regions = 508 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 2 CGATTTTAAATTAAACGGATTTACAAAAAATT 1 11 0 TTAAAGATTT 0.571857 -290 AATCGTTTCGTTCAATGGTTTTAAATTACACG 1 38 1 TTCAAGTTTT 0.677445 -263 CTTACCTTTTATTTAAGAATTTGACTTGATTG 1 276 0 ATTTAGATTT 0.624578 -25 TCCTTTATTGTTTTAAGTGTTTTTATTGTAAC 3 36 0 TTTTAGGTTT 0.960974 -30 AAGAGACTATTTTTGAGCGTTTTTAATCCTAA 4 53 0 TTTTGGGTTT 0.917676 -130 ATTTATTTAATTTTATGGTTTTATGGTAAATT 4 96 1 TTTTAGTTTT 0.854697 -87 ATAATACCCAATCAATGCGTTTAATTTCTGTT 5 115 1 ATCAAGGTTT 0.713197 -51 GAGCGTTAATTATAATGAATTTTAAGCTAAAA 6 44 1 TATAAGATTT 0.718012 -125 GCAACCACACTATTAGGATTTTTTGAAGAAAA 8 120 0 TATTAGTTTT 0.624578 -171 CACTCCTTGATTTAGCGGATTTTACCGCATGC 8 169 1 TTTAGGATTT 0.802971 -122 TTCATAACAATTAAAGGTGGTTA 8 278 1 TTAAAGGGTT 0.555255 -13 CTATTTTTAATTTAATGGGATTAATTAGGGAT 9 12 0 TTTAAGGATT 0.788797 -26 TTTATTTAACTTTAGAGTGGTTTTAATTTATT 10 61 0 TTTAGGGGTT 0.792072 -203 AATAGGCATCATTTAAGAGATTAGCACTTGGC 11 58 0 ATTTAGGATT 0.408347 -107 ACTATTTTTAAATAAAGGGTTTTT 11 151 1 AATAAGGTTT 0.750921 -14 AAGTATTTTTTATTAGGTTTTTGCGTGGCGTC 12 29 0 TATTAGTTTT 0.624577 -70 TTATCAATATTTTAAAGTATTTTTTATTAGGT 12 43 0 TTTAAGATTT 0.900027 -56 CAATTTCAATTTTAGGGGGTTTTGTTTGGTAT 13 38 1 TTTAGGGTTT 0.944631 -106 AGAAAACTCTTTTTAAGCTTTTTAAATCCC 14 9 0 TTTTAGTTTT 0.854697 -292 CTAGACCCTTTTTAAAGGGTTTGAATGCCACT 14 44 0 TTTAAGGTTT 0.974152 -257 TTCATATTTCTATAAGGAGTTTGAAATGCTGA 14 112 1 TATAAGGTTT 0.914231 -189 TATAACAATGTTCTAGGAGTTTTACCTTTTGT 14 169 0 TTCTAGGTTT 0.851734 -132 TCAATGCAACTTTTATGCGTTTAAAGCTTAAA 14 216 1 TTTTAGGTTT 0.960974 -85 TTAAGTCTTAATTAGAGATTTTAGGTTAAACT 14 252 1 ATTAGGTTTT 0.535458 -49 CCATAAAGATTTTAGGGTAGTTTAACCTAAAA 14 270 0 TTTAGGAGTT 0.476431 -31 ATTAATTCTTTAAAAAGCGTTTTATCTAAAAA 15 11 1 TAAAAGGTTT 0.61262 -68 AAGCCTTAAAATTAAGGTGTTTCTTTTAAGGG 16 76 1 ATTAAGGTTT 0.914231 -77 AAGGTGTTTCTTTTAAGGGTTTGTCTATAATG 16 89 1 TTTTAGGTTT 0.960974 -64 ***** * **** Masking position 11 Map Score: 30.8077 Number of sites scoring better than the average of aligned sites = 1990 Number in coding regions = 1686 Number in noncoding regions = 304 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 3 ATCCGTTTAATTTAAAATCGTTTCGTTCAAT 1 23 1 TTTAAAATGT 0.868303 -278 CGTGATAAACTCAAAAAGGTTGGAATGAGAA 1 163 1 TCAAAAAGTT 0.671639 -138 GTTTCACTTCTTTAAAAGTGCTCGTAGCTCA 2 161 0 TTTAAAAGGC 0.688337 -88 TTAAAAACGCTCAAAAATAGTCTCTTTTTTC 4 59 1 TCAAAAATGT 0.959035 -124 GGTAAATTTTTGAAAAATTGTTATAATTCCT 4 120 1 TGAAAAATGT 0.908077 -63 CTCAAAAAATTGAAAAAGAGTTCAAGGAATA 6 16 0 TGAAAAAGGT 0.934119 -153 TCTCTAAATTTTTAAAAGCATGTTAAAATTA 6 110 1 TTTAAAAGAT 0.592751 -59 TTGATCCTAATCAAAAATAATCTCAATCATA 7 13 1 TCAAAAATAT 0.782647 -105 CTTTTTTCTATTAAAATTAGTGTATGATTGA 7 35 0 TTAAAATTGT 0.695994 -83 CAAAAATGGCTTAAAAATGGTTTCACTTTTT 7 60 0 TTAAAAATGT 0.966106 -58 CTTATTGTATTCAAAAATGGCTTAAAAATGG 7 71 0 TCAAAAATGC 0.845294 -47 TCCCATTAAATTAAAAATAGTGTC 9 24 1 TTAAAAATGT 0.966106 -14 AACCCTTTATTTAAAAATAGTTTTTGATTAT 11 141 0 TTAAAAATGT 0.966106 -24 TTTAAAAAGCTTAAAAAGAGTTTTCTAATAG 14 15 1 TTAAAAAGGT 0.97614 -286 TTCAAACCCTTTAAAAAGGGTCTAGGAGTTT 14 51 1 TTAAAAAGGT 0.97614 -250 GAGTTTATTTTCAAAAAGGATTCGTGTTTTT 14 76 1 TCAAAAAGAT 0.837879 -225 ATTAATTCTTTAAAAAGCGTTTTATCTAAA 15 10 1 TTAAAAAGGT 0.97614 -69 ******** ** Masking position 6 Map Score: 23.2239 Number of sites scoring better than the average of aligned sites = 481 Number in coding regions = 383 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 4 AGTAAATGAAGCTAAAAACAATACAAATTA 1 102 1 GCTAAAAACA 0.970578 -199 AAAGCCACCCGCTTAAAACATGCTACAATC 1 251 1 GCTTAAAACA 0.860921 -50 CTTAAAACATGCTACAATCAAGTCAAATTC 1 262 1 GCTACAATCA 0.920248 -39 CTCCCATTATGGTAAAATAAATACTTGCTT 2 33 0 GGTAAAATAA 0.72078 -216 AGCTTTTCTTGCTATAATCATCGTTTCACT 2 184 0 GCTATAATCA 0.974026 -65 TATCCAACCCGCTATAAACAAAAAGGTTTG 4 13 0 GCTATAAACA 0.966071 -170 TGAATTTTAAGCTAAAAACACCCCACAAAT 6 59 1 GCTAAAAACA 0.970578 -110 AAAATTAAGAGATTTAAACAAATTTAAGGT 6 134 1 GATTTAAACA 0.480134 -35 AGATGCATGCGGTAAAATCCGCTAAATCAA 8 175 0 GGTAAAATCC 0.764268 -116 CCCCATAAATGCTATAATCACCCCTATCAA 8 238 1 GCTATAATCA 0.974026 -53 ATTCATGTTTGATAAAAACAGAACTACCAC 11 87 1 GATAAAAACA 0.850805 -78 GTATTCTTTAGGTATAATCAAAAACTATTT 11 128 1 GGTATAATCA 0.950457 -37 TGCATTGATTGGTAAAATCATGTTATAACA 14 194 0 GGTAAAATCA 0.956944 -107 ACTTATTCACGCTATAATAACGCC 16 5 0 GCTATAATAA 0.813276 -148 ********** Masking position 6 Map Score: 18.6231 Number of sites scoring better than the average of aligned sites = 345 Number in coding regions = 304 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 5 ATCGTGTAATTTAAAACCATTGAACGAAAC 1 42 0 TTAAAACCAT 0.682735 -259 TAATAATAAATTATAACATTCGCATCGTGT 1 65 0 TTATAACATT 0.877835 -236 TAAATGAAGCTAAAAACAATACAAATTATC 1 104 1 TAAAAACAAT 0.647522 -197 ATAAAAACACTTAAAACAATAAAGGATGCC 3 42 1 TTAAAACAAT 0.940689 -24 AGTGTAGGAATTATAACAATTTTTCAAAAA 4 126 0 TTATAACAAT 0.933118 -57 TAATTAACGCTCAAAAAATTGAAAAAGAGT 6 26 0 TCAAAAAATT 0.612695 -143 TGGGATGATATTATAAAAATTGGTGGGAAT 8 17 0 TTATAAAAAT 0.854468 -274 TTGAAGAAAATCAAAACAATCAATTTGTCA 8 100 0 TCAAAACAAT 0.8795 -191 ATAGGGGTGATTATAGCATTTATGGGGCAA 8 235 0 TTATAGCATT 0.752361 -56 CAAACTCAATTCATAACAATTAAAGGTGGT 8 269 1 TCATAACAAT 0.865238 -22 TTTGACTTTGTTAAAAAAATTATGATAGCA 10 94 1 TTAAAAAAAT 0.869699 -170 TAAAGCATTCTTAAAAAATTAGTGTAACCA 10 180 0 TTAAAAAATT 0.774653 -84 TTCAAACTCCTTATAGAAATATGAAAACAT 14 107 0 TTATAGAAAT 0.712844 -194 TAAAATCATGTTATAACAATGTTCTAGGAG 14 182 0 TTATAACAAT 0.933118 -119 AAAACGCTTTTTAAAGAATTAAT 15 4 0 TTAAAGAATT 0.592409 -75 ********** Masking position 5 Map Score: 12.661 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 252 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 6 AAAAACATTACCAATAAATGAGACTTAAAG 1 225 1 CCAATAAATG 0.951377 -76 TACCATAAAACCATAAAATTAAATAAATAT 4 94 0 CCATAAAATT 0.675246 -89 ATTAAATTTACCAATAAAAGTGTAGGAATT 4 144 0 CCAATAAAAG 0.840281 -39 ACTCCTTTCTCCATTAAATTTACCAATAAA 4 156 0 CCATTAAATT 0.876611 -27 ATTATAATACCCAATCAATGCGTTTAATTT 5 112 1 CCAATCAATG 0.892165 -54 CTTATCATTCCCACCAATTTTTATAATAT 8 10 1 CCCACCAATT 0.35538 -281 ATAATATCATCCCATAATTGTTCGCATTAT 8 33 1 CCCATAATTG 0.804967 -258 CTTTTTTTGCCCCATAAATGCTATAATCAC 8 229 1 CCCATAAATG 0.959647 -62 TAACCACCTTTAATTGTTATGAATTG 8 275 0 CCTTTAATTG 0.37558 -16 CTAATTAATCCCATTAAATTAAAAATAGTG 9 16 1 CCATTAAATT 0.876611 -22 TGATAACCAACCATAAAAAGCTTGGCGTTA 11 28 1 CCATAAAAAG 0.636417 -137 AAGTGCTAATCTCTTAAATGATGCCTATTC 11 61 1 CTCTTAAATG 0.604519 -104 AAACAAAACCCCCTAAAATTGAAATTGAAG 13 35 0 CCCTAAAATT 0.716473 -109 CATGATTTTACCAATCAATGCAACTTTTAT 14 202 1 CCAATCAATG 0.892165 -99 TATAGACAAACCCTTAAAAGAAACACCTTA 16 88 0 CCCTTAAAAG 0.87897 -65 ********** Masking position 7 Map Score: 9.78062 Number of sites scoring better than the average of aligned sites = 617 Number in coding regions = 547 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 7 TTTAAAATCGTTTCGTTCAATGGTTTTAAA 1 33 1 TTTCGTTCAA 0.89519 -268 TTCATTTACTTTTCGTTTAATAATAAATTA 1 82 0 TTTCGTTTAA 0.887431 -219 TTGTTTTTAGCTTCATTTACTTTTCGTTTA 1 93 0 CTTCATTTAC 0.939658 -208 AGAAAAAACGCATCGTTTAAGTGAAAAATT 2 214 0 CATCGTTTAA 0.777516 -35 CATGAATAGGCATCATTTAAGAGATTAGCA 11 64 0 CATCATTTAA 0.730781 -101 ATTGATAACGCTTCGTTTACATTCTTTCTT 12 67 1 CTTCGTTTAC 0.95249 -32 GTTATTCCTTTTTCATTCACCACTTATTCA 16 26 0 TTTCATTCAC 0.91364 -127 TTCATTCACATTTCATTCACATGTTATTCC 16 48 0 TTTCATTCAC 0.91364 -105 AATTTTAAGGCTTCATTCACATTTCATTCA 16 59 0 CTTCATTCAC 0.944044 -94 AATTAAGGTGTTTCTTTTAAGGGTTTGTCT 16 85 1 TTTCTTTTAA 0.601699 -68 ********** Masking position 6 Map Score: 6.98767 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 101 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 AAATATGGTAGAAAAAAGAGACTATTTTTG 4 70 0 GAAAAAAGAG 0.963263 -113 AAATTTAATGGAGAAAGGAGTTTGGAAT 4 165 1 GAGAAAGGAG 0.86307 -18 CGTCAATATTGAAAACAGAAATTAAACGCA 5 130 0 GAAAACAGAA 0.90522 -36 TAAAAATTTAGAGAATAGAGGTTGCATTTA 6 94 0 GAGAATAGAG 0.760772 -75 AATTTTAATAGAAAAAAGTGAAACCATTTT 7 48 1 GAAAAAAGTG 0.805201 -70 TGTATAGTTGGAAAAAGGAATAATGCGAAC 8 52 0 GAAAAAGGAA 0.924458 -239 TTTGAAAAAATAGGGGGGGACGC 12 4 1 GAAAAAATAG 0.80157 -95 ATTGAAGTCTGAAAATAGGATAATAGTTAC 13 12 0 GAAAATAGGA 0.726394 -132 ATAGAAATATGAAAACATAAAAACACGAAT 14 95 0 GAAAACATAA 0.595367 -206 AGTGGTGAATGAAAAAGGAATAACATGTGA 16 32 1 GAAAAAGGAA 0.924458 -121 TAATGGATGCGAAAAAAGGATTTTC 16 138 1 GAAAAAAGGA 0.893633 -15 ********** Masking position 5 Map Score: 6.15356 Number of sites scoring better than the average of aligned sites = 422 Number in coding regions = 379 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 9 TAACACAGCTTTTTAGGATTAAAAACGCTC 4 41 1 TTTTAGGATT 0.890826 -142 TGAAAAAGAGTTCAAGGAATAGACAG 6 7 0 TTCAAGGAAT 0.820847 -162 GCAACCACACTATTAGGATTTTTTGAAGAA 8 122 0 TATTAGGATT 0.669376 -169 AATCCGCTAAATCAAGGAGTGTTATTATGG 8 160 0 ATCAAGGAGT 0.806478 -131 ACATTCTTTCTTTAAGGATTAGTT 12 85 1 TTTAAGGATT 0.932611 -14 TTGAGTTGAATTCAAGGAGTAAAAC 13 129 1 TTCAAGGAGT 0.967338 -15 TTTAAAAAGGGTCTAGGAGTTTATTTTCAA 14 60 1 GTCTAGGAGT 0.784563 -241 TTCATATTTCTATAAGGAGTTTGAAATGCT 14 112 1 TATAAGGAGT 0.845582 -189 TATAACAATGTTCTAGGAGTTTTACCTTTT 14 171 0 TTCTAGGAGT 0.945836 -130 ACACCTTAATTTTAAGGCTTCATTCACATT 16 66 0 TTTAAGGCTT 0.742676 -87 AGGTGTTTCTTTTAAGGGTTTGTCTATAAT 16 90 1 TTTAAGGGTT 0.742676 -63 ********** Masking position 5 Map Score: 6.16879 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 180 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 10 ACATTCGCATCGTGTAATTTAAAACCATTGA 1 49 0 CGGTAATTTA 0.388916 -252 ATTTTGTTCTAGCGGTAATTAATTCTCATTC 1 185 0 AGGGTAATTA 0.457867 -116 ATTTATTGGTAATGTTTTTTAATTTTAAATT 1 213 0 AAGTTTTTTA 0.412785 -88 ACTTGATTGTAGCATGTTTTAAGCGGGTGGC 1 254 0 AGATGTTTTA 0.440808 -47 CAAATCTCCTAGCGTGTTTAAGCAAGTATTT 2 14 1 AGGTGTTTAA 0.869637 -235 TAACACTAAAAGGGTAATTAAGTTTTAAT 3 9 0 AGGTAATTAA 0.806072 -57 TATTGTTTTAAGTGTTTTTATTGTAACACTA 3 32 0 AGGTTTTTAT 0.56901 -34 ACTATTTTTGAGCGTTTTTAATCCTAAAAAG 4 49 0 AGGTTTTTAA 0.916918 -134 TACTAGCATGAGGGTGTTTTAGAAAGACTTA 5 23 1 AGGTGTTTTA 0.914417 -143 CAATTTTTTGAGCGTTAATTATAATGAATTT 6 35 1 AGGTTAATTA 0.748183 -134 GAATACAATAAGAGTATTTTATTTTTAAGGT 7 90 1 AGGTATTTTA 0.907936 -28 TAAATCAAGGAGTGTTATTATGGAAGCAGAC 8 152 0 AGGTTATTAT 0.471247 -139 TCCTTGATTTAGCGGATTTTACCGCATGCAT 8 172 1 AGGGATTTTA 0.737074 -119 TTAACTTTAGAGTGGTTTTAATTTATTATGA 10 57 0 AGGGTTTTAA 0.758287 -207 AATATTTTAAAGTATTTTTTATTAGGTTTTT 12 39 0 AGATTTTTTA 0.566001 -60 ATGTAAACGAAGCGTTATCAATATTTTAAAG 12 58 0 AGGTTATCAA 0.579583 -41 ACCTAGCTGTAGGGTTAATTAAAATTATTTA 13 98 1 AGGTTAATTA 0.748183 -46 AAGCTTAAAAAGAGTTTTCTAATAGTGGCAT 14 21 1 AGGTTTTCTA 0.765858 -280 TAAAGATTTTAGGGTAGTTTAACCTAAAATC 14 268 0 AGGTAGTTTA 0.608684 -33 TTATTTTTAGAGTGTATTTTATCGTTTTTTA 15 37 0 AGGTATTTTA 0.907936 -42 GCGTTATTATAGCGTGAATAAGTGGTGAATG 16 12 1 AGGTGAATAA 0.528582 -141 ** ******** Masking position 1 Map Score: 11.6921 Number of sites scoring better than the average of aligned sites = 1452 Number in coding regions = 1256 Number in noncoding regions = 196 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 11 CGAAAAGTAAATGAAGCTAAAAACAATACA 1 97 1 ATGAAGCTAA 0.651005 -204 ATTATAGCAAGAAAAGCTAATTTTTCACTT 2 196 1 GAAAAGCTAA 0.929098 -53 TTTTAATCCTAAAAAGCTGTGTTATCCAAC 4 35 0 AAAAAGCTGT 0.651005 -148 TTTTCTTCAAAAAATCCTAATAGTGTGGTT 8 120 1 AAAATCCTAA 0.764197 -171 GTGTAACCAAAAGATGCTAATAAGTGGCCC 10 159 0 AAGATGCTAA 0.853964 -105 ATAAAAATACAAAAAGCTAAAGCATTCTTA 10 197 0 AAAAAGCTAA 0.971545 -67 GTTGGTTATCAAAAAGCTAACAGCGTTT 11 9 0 AAAAAGCTAA 0.971545 -156 GACGCCACGCAAAAACCTAATAAAAAATAC 12 29 1 AAAAACCTAA 0.890547 -70 GGGATTTAAAAAGCTTAAAAAGAGTTT 14 8 1 AAAAAGCTTA 0.843318 -293 TAAGGAGTTTGAAATGCTGAAGCTTCTAGA 14 124 1 GAAATGCTGA 0.691767 -177 CTTGCTTTATAATAAGCTAATGGATGCGAA 16 121 1 AATAAGCTAA 0.843318 -32 ********** Masking position 4 Map Score: 6.60344 Number of sites scoring better than the average of aligned sites = 495 Number in coding regions = 406 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 12 ACAATACAAATTATCACTCAAATTCTTATCATT 1 119 1 TTTCATCAAT 0.951319 -182 CGGTAATTAATTCTCATTCCAACCTTTTTGAGT 1 171 0 TTTCATCCAC 0.986543 -130 TTTTTAAACATTATCGCTCCCATTATGGTAAAA 2 46 0 TTTCGTCCAT 0.867104 -203 AAAAGCTAATTTTTCACTTAAACGATGCGTTTT 2 207 1 TTTCATTAAC 0.80057 -42 TGAAAAATTGTTATAATTCCTACACTTTTATTG 4 130 1 TTTAATCCAC 0.864955 -53 ATCAAAAATAATCTCAATCATACACTAATTTTA 7 22 1 ATTCATCAAC 0.935266 -96 CTTATCATTCCCACCAATTTTTAT 8 2 1 TTTCATCCAC 0.986543 -289 AACAATCAATTTGTCATTCCTATCTATCAGAGG 8 83 0 TTTCATCCAT 0.969022 -208 ATAATCACCCCTATCAATCAAACTCAATTCATA 8 251 1 CTTCATCAAC 0.924279 -40 CTTCATTCACATTTCATTCACATGTTATTCCTT 16 46 0 ATTCATCAAT 0.858836 -107 ** *** *** ** Masking position 8 Map Score: 6.90619 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 51 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 13 CACCCGCTTAAAACATGCTACAATCAAGTCAAA 1 256 1 AAAATTACAA 0.665136 -45 GAAGTGAAACGATGATTATAGCAAGAAAAGCTA 2 182 1 GATATTAGCA 0.617708 -67 GCCTTAAATTATAATAGAAAAAACGCATC 2 230 0 AATATTAGAA 0.93921 -19 AAAATTAAATAAATATGGTAGAAAAAAGAGACT 4 77 0 AAAATTAGAA 0.953155 -106 AAAGAGTAAACATACTAGCATGAGGGTGTT 5 8 1 AAAATTAGCA 0.930994 -158 CATGCTTTTAAAAATTTAGAGAATAGAGGTTGC 6 99 0 AAATTGAGAA 0.546745 -70 ATCATACACTAATTTTAATAGAAAAAAGTGAAA 7 38 1 AATTTTAGAA 0.759359 -80 TTTATGGGGCAAAAAAAGTAGAATCTGTATCAA 8 214 0 AAAAATAGAA 0.666954 -77 AATTTAAACTTAAAATTATAGCATAAGTCATAA 10 30 1 TAAATTAGCA 0.589447 -234 TTGTTAAAAAAATTATGATAGCATAGCAAAGAA 10 101 1 AATATTAGCA 0.911068 -163 TTTTGTCTAGAATCATTCTAGAAGCTTCAGCAT 14 137 0 AATATTAGAA 0.93921 -164 AACAAAAGGTAAAACTCCTAGAACATTGTTATA 14 168 1 AAACTTAGAA 0.777429 -133 TGATTGGTAAAATCATGTTATAACAATGTTCTA 14 186 0 AATATTATAA 0.504367 -115 AAAATAAATAAAATATGCGAGAAAAATC 15 61 1 AAAATGAGAA 0.855198 -18 *** ** ***** Masking position 10 Map Score: 4.8803 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 209 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 14 ********** No masking Map Score: -5.91639e-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 AATCAAGTCAAATTCTTAAATAAAAGGTAAG 1 277 1 AATCTTAAAT 0.856576 -24 CGAGCACACCATTTCTTAATATTCTGCATGT 2 78 0 ATTCTTAATA 0.752003 -171 ATTAAAACTTAATTACCCTTTTAG 3 4 1 AAACTTAATT 0.856957 -62 AGCGTGGGGTAATTCTCAATTTTTATATTAT 5 86 1 AATCTCAATT 0.817638 -80 ATTTGTTTAAATCTCTTAATTTTAACATGCT 6 126 0 ATTCTTAATT 0.955654 -43 CAAGTGTTGAATTTCGTAATTCTTTGCTATG 10 122 0 ATTCGTAATT 0.8179 -142 TTTTGTATTTTTATCTTAATTGCAACAAACT 10 213 1 TTTCTTAATT 0.752015 -51 CCAAGTGCTAATCTCTTAAATGATGCCTATT 11 59 1 ATTCTTAAAT 0.856954 -106 ATACCTAAAGAATACTTAATTGTGTTGTGGT 11 112 0 AAACTTAATT 0.856945 -53 TAAAAACTTTAAGTCTTAATTAGAGATTTTA 14 244 1 AATCTTAATT 0.955645 -57 ** ******** Masking position 8 Map Score: 4.13429 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 14 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802