AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00300_hpyl_reg_300.orf -o00300_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 Purged sequences: HP0510 21 dihydrodipicolinate reductase (dapB) Input sequences: #1 HP0180_HP0181 257 HP0180: apolipoprotein N-acyltransferase (cute), HP0181: H. pylori predicted coding region HP0181 #2 HP0194 214 triosephosphate isomerase (tpi) #3 HP0213 95 glucose inhibited division protein (gidA) #4 HP0282 50 H. pylori predicted coding region HP0282 #5 HP0289 66 toxin-like outer membrane protein #6 HP0290 47 diaminopimelate decarboxylase (dap decarboxylase) (lysA) #7 HP0497 228 sodium- and chloride-dependent transporter #8 HP0500 57 DNA polymerase III beta-subunit (dnaN) #9 HP0502 45 H. pylori predicted coding region HP0502 #10 HP0503 88 H. pylori predicted coding region HP0503 #11 HP0505 140 H. pylori predicted coding region HP0505 #12 HP0506 203 conserved hypothetical secreted protein #13 HP0566 115 diaminopimelate epimerase (dapF) #14 HP0625 119 protein E (gcpE) #15 HP0813 132 conserved hypothetical protein #16 HP0818 68 osmoprotection protein (proWX) #17 HP0820 173 H. pylori predicted coding region HP0820 #18 HP1010 300 polyphosphate kinase (ppk) #19 HP1011 36 dihydroorotate dehydrogenase (pyrD) #20 HP1190 61 histidyl-tRNA synthetase (hisS) #21 HP1227 73 cytochrome c553 #22 HP1228 150 invasion protein (invA) #23 HP1492 138 conserved hypothetical nifU-like protein Motif number 1 TGGGTGTTTGTTTTAAGACGCTATGACTATCTTTAT 1 73 0 TTTTAAGATA 0.961494 -185 GGGTAGTTTTTTTTAAGTTGTGTTATTATTTTCAAA 1 151 0 TTTTAAGTTT 0.952574 -107 AGATTGATTTTTTTAAGGGTAGTTTTTTTTAAGTTG 1 167 0 TTTTAAGTTT 0.952574 -91 AATTTTGAGTTTTTAGGAGCAGTTTTT 2 2 0 TTTTAGGTTT 0.936822 -213 CGTCAAGCGATTTTAGGTTAATTTTGAGTTTTTAGG 2 21 0 TTTTAGGTTG 0.850547 -194 AAATTTACATTTTTTAAACGCTATTAGATATAATAA 2 154 1 TTTTTAAATA 0.70064 -61 AATGAGAGAGTTTTTGGCTACTATCTAGGAAATGAG 5 28 1 TTTTTGGATT 0.785188 -39 TATTGTATAATTTTAAGAAAATTTCATTATTTAAGT 7 22 0 TTTTAAGTTA 0.97531 -207 GCTCTGTATTTTTTAGGTATTTTTAAAGTGGGTTTT 7 91 1 TTTTAGGTTA 0.96684 -138 GCTGTATTAGTTTTTAAAATCTTTAAAGATCTTAAG 7 136 0 TTTTTAATTA 0.787344 -93 AAAAGCGTTCTTTTAYGCTATAATTAAGACCAAAAA 8 11 1 TTTTAYGATA 0.961494 -47 TAATTTTCTCTTTTAGGATTAACTAAAGCGTTTATT 10 32 0 TTTTAGGCTA 0.902972 -57 AAATATCATTTTTTAGGGGCTAATGATAAAGTAAAA 11 94 1 TTTTAGGATA 0.948535 -47 CATTTGATAATTTTTGGTTCAGTTTAATGGGGATAA 13 15 0 TTTTTGGTTA 0.919174 -101 AAAAGAGCGTTTTTTAGCTAACATTTGATAATTTTT 13 36 0 TTTTTAGATT 0.831964 -80 ATGATAAGCCTTTTTGATTTTAATTATAAGTTAAAA 13 88 0 TTTTTGAATA 0.633414 -28 AACGCTTAAATTTTAGGTAAGATTAACTATTCCATT 14 30 0 TTTTAGGTTA 0.966847 -90 TTCAAACTAGTTTTAAAAAGTCATTATTATTGAAAA 15 94 0 TTTTAAAATA 0.85718 -39 GCCTTTAGCATTTTAAAACCCCTTTATCCAAATAAG 16 33 1 TTTTAAATTA 0.904713 -36 TTTTAAGGCTGATTTAAAAATTCTGG 17 1 1 TTTTAAGTTA 0.97531 -173 GTTTGAAGTTTTTTTAGCGGGTTTTTCATTGAATGG 17 79 1 TTTTTAGTTT 0.886781 -95 GCTAAAAAAATTTTAAGCGATCTTTTAGGGTTAAAT 18 15 1 TTTTAAGTTT 0.952574 -286 GACCATGACTTTTTAAAAAAGCTTCAATGATTATCA 18 213 1 TTTTAAATTA 0.904713 -88 AACAAACTGATTTTTAAACATGATGATTTAAAGGAT 18 270 1 TTTTTAAATA 0.70064 -31 TTTTTAAAGATTTTAAGCTAAAATTTTAGCATACAA 20 21 1 TTTTAAGATT 0.926989 -41 TTCATTTTAAGCAAAACTTAAACTTGTAAT 21 5 1 TTTTAAGCTA 0.926501 -69 AATTGTATCATTTTAAGATCATTTTGATAAGTAGAG 21 38 1 TTTTAAGTTG 0.885172 -36 AAACAACGCTTTTTAAGAGTGGCTCAAGGGCTAATT 23 54 0 TTTTAAGCTA 0.926501 -85 TAAAGTAAAATTTTAAAGAGAGTTTTAAAAA 23 118 1 TTTTAAATTT 0.828406 -21 ******* ** * Masking position 4 Map Score: 47.17 Number of sites scoring better than the average of aligned sites = 1128 Number in coding regions = 902 Number in noncoding regions = 226 Number of orfs with sites within 600 bp upstream = 197 Fraction of orfs with sites within 600 bp upstream = 0.0316415 Motif number 2 GATTTAAGAGTAATGGGTGTTTGTTTTAAGAC 1 90 0 TAATGGGTTT 0.570416 -168 TGTTTTTGCGTCAAGCGATTTTAGGTTAATTT 2 33 0 TCAAGGTTTT 0.651462 -182 AATTCAATTCAAAGGGGCTATTGTTTAAAATT 2 127 1 AAAGGGTATT 0.703339 -88 TAGGTATTTTTAAAGTGGGTTTTTTCTTAAAT 7 104 1 TAAAGGGTTT 0.955752 -125 AAAAGCGTTCTTTTAYGCTATA 8 1 1 AAAAGGTCTT 0.879429 -57 TTAGCCCCTAAAAAATGATATTTTTCATCTTT 11 85 0 AAAAAGTATT 0.575537 -56 ACTCAATTCATAAAGAGTTTTTACTTTATCAT 11 116 0 TAAAGGTTTT 0.948723 -25 TATAGCTTTATGAAGCGCGTTTTATTGATGCA 12 86 0 TGAAGGGTTT 0.8843 -118 TTTTATCCTTAAAAGAGCGTTTTTTAGCTAAC 13 50 0 AAAAGGGTTT 0.964885 -66 ATTATAAGTTAAAAGAGGTTTTTTATCCTTAA 13 70 0 AAAAGGTTTT 0.96095 -46 CAACAATAATAGAAGCGCTATTCTAGTCAAAA 15 40 1 AGAAGGTATT 0.795503 -93 AGCGCAAAAATAAGGCGATTTTGACTAGAATA 15 58 0 TAAGGGTTTT 0.757075 -75 AAAACTAGTTTGAAGGGAGTTTGGAGT 15 116 1 TGAAGGGTTT 0.884354 -17 CTTATTTGGATAAAGGGGTTTTAAAATGCTAA 16 37 0 TAAAGGTTTT 0.948935 -32 AGTTTTACAAAAAAGAGTTTTTAAACAACAAC 18 72 1 AAAAGGTTTT 0.944723 -229 TCCGCAATCAAAAAGGGAGATTGTAGCGCGAG 18 112 0 AAAAGGGATT 0.942741 -189 TCATGGTCGGAGTAGCGGGATTCAAACCCACG 18 189 0 AGTAGGGATT 0.475186 -112 AAATCTTTAAAAAAGGGCTATTG 20 2 0 AAAAGGTATT 0.906482 -60 TCTCCGTTTTAATAGCGTTATTTGGGCGCTAT 22 15 1 AATAGGTATT 0.592113 -136 TGGGCGCTATTAAAATGAGTTTCAAGCCCTTT 22 37 1 TAAAAGGTTT 0.674052 -114 AAAAATTAAGAAAAAAGGGCTTGAAACTCATT 22 50 0 AAAAAGGCTT 0.528834 -101 ACCTTGTTCTAATAGTGGTCTTATTCTATCCA 23 23 1 AATAGGTCTT 0.610481 -116 GCCACTCTTAAAAAGCGTTGTTTGATAAAAAT 23 67 1 AAAAGGTGTT 0.763843 -72 AGTAAAATTTTAAAGAGAGTTTTAAAAA 23 121 1 TAAAGGGTTT 0.955752 -18 ***** * **** Masking position 11 Map Score: 32.6962 Number of sites scoring better than the average of aligned sites = 1534 Number in coding regions = 1335 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 3 TGTTTTAGTGTATTATAGCTATATTTTAAT 1 214 0 TATTATAGCT 0.791491 -44 CCTTATTATATCTAATAGCGTTTAAAAAAT 2 162 0 TCTAATAGCG 0.904977 -53 ACGATCCTTATTTTATAGGTGGTAACTATC 2 192 0 TTTTATAGGT 0.817027 -23 TAATCTTGGATATAATGGCGTAATCATTTT 4 22 1 TATAATGGCG 0.783492 -29 TTCGTTCAAATTTTATGGTTAGGTTTTTCT 6 28 1 TTTTATGGTT 0.417218 -20 TTGCTCTGTATTTTTTAGGTATTTTTAAAG 7 89 1 TTTTTTAGGT 0.680718 -140 TTTCTTTATCTTTAATGGGGACATCATAAC 11 35 0 TTTAATGGGG 0.809772 -106 AAAAATATCATTTTTTAGGGGCTAATGATA 11 92 1 TTTTTTAGGG 0.855906 -49 TTTTATCTCGTCTTATAGCGTTGGGTATTT 12 36 0 TCTTATAGCG 0.93158 -168 CTGGCCTTGTTTTTATAGCTTTATGAAGCG 12 101 0 TTTTATAGCT 0.904897 -103 ATCGTTTTTCTTTAATGGCTTATGTTATAC 12 144 1 TTTAATGGCT 0.765025 -60 TTTGGTTCAGTTTAATGGGGATAATTTC 13 9 0 TTTAATGGGG 0.809772 -107 TAAAAGAGCGTTTTTTAGCTAACATTTGAT 13 43 0 TTTTTTAGCT 0.819593 -73 CAAGAAAGAGTATAATAGCGCATAAGAATT 14 81 1 TATAATAGCG 0.880916 -39 TGTTTGAAGTTTTTTTAGCGGGTTTTTCAT 17 78 1 TTTTTTAGCG 0.926778 -96 CGCTTAAAATTTTTTTAGCGTTT 18 4 0 TTTTTTAGCG 0.926778 -297 TTTTAAGCGATCTTTTAGGGTTAAATGAAG 18 25 1 TCTTTTAGGG 0.75314 -276 CCCTCTCCGTTTTAATAGCGTTATTTGGGC 22 12 1 TTTAATAGCG 0.948829 -139 TGAAACTCATTTTAATAGCGCCCAAATAAC 22 31 0 TTTAATAGCG 0.948829 -120 ATTAAGATGGTATTATAGTGTATACTAGCT 22 102 0 TATTATAGTG 0.619282 -49 AGGTCTTTATTTTAGCTCTTTCTTGTT 22 134 0 TATTTTAGCT 0.644436 -17 AAAACCTTGTTCTAATAGTGGTCTTATTCT 23 20 1 TCTAATAGTG 0.594291 -119 ********** Masking position 6 Map Score: 29.9294 Number of sites scoring better than the average of aligned sites = 775 Number in coding regions = 697 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 4 AAGTAACGCTAAATCAATATAATTCAAACCCTAAACC 1 11 1 AAAAAATTAA 0.801168 -247 TCACACTCTTTAGACTTGAAATTTGAAAATAATAACA 1 130 1 TAGTATTTAA 0.70525 -128 AATCAATCTAAAATTCTTAAATTAAAATATAGCTATA 1 194 1 AAATATTAAA 0.769988 -64 AAACAATCTCAAGGTTTCAAAATTTAGCC 1 239 1 AAGTAATTAG 0.802659 -19 AACTGCTCCTAAAAACTCAAAATTAACCTAAAATCGC 2 14 1 AAATAATTAC 0.880583 -201 TAGCGTTTAAAAAATGTAAATTTTAAACAATAGCCCC 2 140 0 AAATATTTAA 0.940387 -75 TGATTTTTCTAAAATCTTAGTTTTGAAAAAGTTTTAT 3 50 0 AAATATTTAA 0.940387 -46 AGAAAAACCTAACCATAAAATTTGAACGAA 6 28 0 AAATAATAAA 0.846273 -20 TAATTTTAAGAAAATTTCATTATTTAAGTAAGGGGAA 7 14 0 AAATAATTAA 0.962882 -215 AAAATCTTTAAAGATCTTAAGATTTAAGAAAAAACCC 7 120 0 AAGTAATTAA 0.934678 -109 CATCGCTCTTTAATTTTAATCATTGACAAGGAGTTTG 7 192 1 TAATAATTAC 0.669722 -37 GGATTAACTAAAGCGTTTATTATTAAAGCATCACACT 10 16 0 AAGTAATTAA 0.934678 -73 TAAAAGATGAAAAATATCATTTTTTAGGGGCTAATGA 11 83 1 AAATATTTAG 0.817655 -58 ATAAGCCATTAAAGAAAAACGATACAAGTTTAAAGCC 12 130 0 AAAAAATAAA 0.460938 -74 GAAATTATCCCCATTAAACTGAACCAAA 13 2 1 AAATCATTAA 0.68362 -114 TTTCATACCATAACGCTTAAATTTTAGGTAAGATTAA 14 40 0 TAATATTTAG 0.552187 -80 TAGTTTTAAAAAGTCATTATTATTGAAAATCATAGCG 15 86 0 AAGTAATTAA 0.934678 -47 TTAGCGCTTGTAGCAATAACCATTCAAGCTTGCGGTT 17 126 0 TAGTAATTAA 0.797355 -48 AGTTTTATTCAAAAAATGAAGTTTTACAAAAAAGAGT 18 53 1 AAATATTTAC 0.817655 -248 TTATATAATGAAATGATAATCATTGAAGCTTTTTTAA 18 225 0 AAATAATTAA 0.962882 -76 GAAATCCTTTAAATCATCATGTTTAAAAATCAGTTTG 18 272 0 AAATATTTAA 0.940387 -29 TTCAAATCATAAAAGATAAGGATTTAA 19 20 1 AAATAATTAA 0.962882 -17 ATTTTAAGCTAAAATTTTAGCATACAAATACAAGGAA 20 30 1 AAATAATAAA 0.846273 -32 TATGGTATCTTAAAGTAAAATTTTAAAGAGAGTTTTA 23 108 1 TAAAATTTAA 0.402553 -31 *** * * *** ** Masking position 13 Map Score: 25.6184 Number of sites scoring better than the average of aligned sites = 525 Number in coding regions = 389 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 5 ATAACACAACTTAAAAAAAACTACCCTTAAA 1 161 1 TTAAAAAAAC 0.677926 -97 TCTAAAATTCTTAAATTAAAATATAGCTATA 1 200 1 TTAAATTAAA 0.540061 -58 ATAATTTTTCTTATAAACAAAACCTAAATTG 2 90 1 TTATAAAAAA 0.725948 -125 GAACGAAGCATTATAGCAAAAAAG 6 4 0 TTATAGCAAA 0.407082 -44 ATCTTAAGATTTAAGAAAAAACCCACTTTAA 7 113 0 TTAAGAAAAA 0.926616 -116 TTTAAAGATTTTAAAAACTAATACAGCAATA 7 145 1 TTAAAAATAA 0.586721 -84 TTGTCAATGATTAAAATTAAAGAGCGATGTC 7 190 0 TTAAAATAAA 0.915943 -39 TAYGCTATAATTAAGACCAAAAATTCAAGGG 8 24 1 TTAAGACAAA 0.799583 -34 GTGTGATGCTTTAATAATAAACGCTTTAGTT 10 17 1 TTAATAAAAA 0.661282 -72 TAGTTAATCCTAAAAGAGAAAATTATGGCAT 10 43 1 TAAAAGAAAA 0.53814 -46 GATGTCCCCATTAAAGATAAAGAAAAATTTG 11 40 1 TTAAAGAAAA 0.942118 -101 TACGGATTGATTAAAAAGAAAATACCCAACG 12 17 1 TTAAAAAAAA 0.952036 -187 ACATAAGCCATTAAAGAAAAACGATACAAGT 12 138 0 TTAAAGAAAA 0.942144 -66 AAACGCTCTTTTAAGGATAAAAAACCTCTTT 13 60 1 TTAAGGAAAA 0.911963 -56 TAACTTATAATTAAAATCAAAAAGGCTTATC 13 91 1 TTAAAATAAA 0.917159 -25 CTATTCCATTTTAAGATTAAAGTAGCCCT 14 9 0 TTAAGATAAA 0.87504 -111 AAATCAAAAATTAAGAAAAAAGGGCTTGAAA 22 56 0 TTAAGAAAAA 0.926616 -95 AAGAATGCCATTAAAATCAAAAATTAAGAAA 22 69 0 TTAAAATAAA 0.917159 -82 ATATGGTATCTTAAAGTAAAATTTTAAAGAG 23 107 1 TTAAAGTAAA 0.900813 -32 ******* *** Masking position 1 Map Score: 19.3718 Number of sites scoring better than the average of aligned sites = 539 Number in coding regions = 406 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 6 CCAATTCACACTCTTTAGACTTGAAATTTGAAA 1 125 1 CCTTTAGTTG 0.900969 -133 TAAACAATAGCCCCTTTGAATTGAATTTTTTCT 2 121 0 CCCTTTGTTG 0.407431 -94 TTTATTTTACCCTTTAAAATTACTAACCTCCA 3 10 1 CCTTTAATTA 0.964017 -86 AGAAAAAACCCACTTTAAAAATACCTAAAAAAT 7 98 0 CCTTTAAATA 0.801277 -131 AAGGACATCGCTCTTTAATTTTAATCATTGACA 7 187 1 CCTTTAATTA 0.964026 -42 CCAAGTGTGATGCTTTAATAATAAACGCTTTAG 10 13 1 TCTTTAAATA 0.540437 -76 GTTCAAATTTTTCTTTATCTTTAATGGGGACAT 11 41 0 TCTTTATTTA 0.800566 -100 AAAGAGTTTTTACTTTATCATTAGCCCCTAAAA 11 104 0 TCTTTATTTA 0.800566 -37 AACAAGGCCAGGCTTTAAACTTGTATCGTTTTT 12 120 1 GCTTTAATTG 0.736264 -84 GATAAAAAACCTCTTTTAACTTATAATTAAAAT 13 75 1 CCTTTTATTA 0.896669 -41 AGGGCTACTTTAATCTTAAAATGGAATA 14 6 1 TCTTTAATTA 0.886286 -114 CATACCATAACGCTTAAATTTTAGGTAAGATTA 14 41 0 CCTTAAATTA 0.682782 -79 TAGTCAAAATCGCCTTATTTTTGCGCTATGATT 15 63 1 CCCTTATTTG 0.759351 -70 GCTAAAGGCATTCTTTAATGTTGGTTGCAGG 16 9 0 TCTTTAATTG 0.884191 -60 GCTACAATCTCCCTTTTTGATTGCGGAGTATGG 18 117 1 CCTTTTTTTG 0.814059 -184 GAGTTTCAAGCCCTTTTTTCTTAATTTTTGATT 22 53 1 CCTTTTTTTA 0.817162 -98 TTTTAAAACTCTCTTTAAAATTTTACTTTAAGA 23 115 0 CCTTTAATTT 0.772986 -24 * ****** *** Masking position 5 Map Score: 11.6859 Number of sites scoring better than the average of aligned sites = 518 Number in coding regions = 438 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 7 GAATTTTAGATTGATTTTTTTAAGGGTAGT 1 180 0 TTGATTTTTT 0.750391 -78 TAGGTTAATTTTGAGTTTTTAGGAGCAGTT 2 14 0 TTGAGTTTTT 0.638129 -201 CCCCTTTGAATTGAATTTTTTCTCAATTTA 2 114 0 TTGAATTTTT 0.917901 -101 TAATGGCGTAATCATTTTTTAGGAAGT 4 34 1 ATCATTTTTT 0.391546 -17 TAATGCTTCGTTCAAATTTTATGGTTAGGT 6 22 1 TTCAAATTTT 0.810952 -26 TACTTAAATAATGAAATTTTCTTAAAATTA 7 21 1 ATGAAATTTT 0.815404 -208 AATAATCCCCTTGAATTTTTGGTCTTAATT 8 32 0 TTGAATTTTT 0.917901 -26 AAGTAGTGAGTTCAAATTTTTCTTTATCTT 11 53 0 TTCAAATTTT 0.810952 -88 GATGAAAAATATCATTTTTTAGGGGCTAAT 11 88 1 ATCATTTTTT 0.391546 -53 TTAGAGCTGTTTGAAGTTTTTTTAGCGGGT 17 71 1 TTGAAGTTTT 0.937515 -103 AAAAGATCGCTTAAAATTTTTTTAGCGTTT 18 11 0 TTAAAATTTT 0.591749 -290 TTAGGGTTAAATGAAGTTTTATTCAAAAAA 18 39 1 ATGAAGTTTT 0.875688 -262 TATTCAAAAAATGAAGTTTTACAAAAAAGA 18 58 1 ATGAAGTTTT 0.875688 -243 ATGATAATCATTGAAGCTTTTTTAAAAAGT 18 220 0 TTGAAGCTTT 0.6555 -81 CAATTACAAGTTTAAGTTTTGCTTAAAATG 21 13 0 TTTAAGTTTT 0.567258 -61 AAAACTCTCTTTAAAATTTTACTTTAAGAT 23 114 0 TTAAAATTTT 0.591749 -25 ********** Masking position 4 Map Score: 11.5306 Number of sites scoring better than the average of aligned sites = 621 Number in coding regions = 545 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 8 TAAATCAATATAATTCAAACCCTAAACCCAAACC 1 20 1 TATAAACCTA 0.339222 -238 GCGAGATATATGAGAGAAAGGTTTGGGTTTAGGG 1 39 0 TGAAAAGGTT 0.763263 -219 GCAGTGTTTTTGCGTCAAGCGATTTTAGGTTAAT 2 35 0 TGTAAGCGTT 0.945412 -180 AAAATTTACATTTTTTAAACGCTATTAGATATAA 2 153 1 TTTAAACGTA 0.309979 -62 CGCTATTAGATATAATAAGGGATAGTTACCACCT 2 172 1 TAAAAGGGTA 0.896705 -43 CTTTTAGGATTAACTAAAGCGTTTATTATTAAAG 10 25 0 TATAAGCGTT 0.915041 -64 TTTATTAGTATAACATAAGCCATTAAAGAAAAAC 12 147 0 TAAAAGCCTT 0.773825 -57 AATACAGATTTGATTGAAGGCATTAAACAACTGC 12 180 1 TGTAAGGCTT 0.846192 -24 CTATGATAAGCCTTTTTGATTTTAA 13 101 0 TAAAAGCCTT 0.773825 -15 ATCTTACCTAAAATTTAAGCGTTATGGTATGAAA 14 43 1 AATAAGCGTA 0.55147 -77 CAACCAACAATAATAGAAGCGCTATTCTAGTCAA 15 36 1 TAAAAGCGTA 0.896705 -97 CAAACTTATTTGGATAAAGGGGTTTTAAAATGCT 16 39 0 TGTAAGGGTT 0.945412 -30 GAATGGTTATTGCTACAAGCGCTAAAAAGCATGT 17 138 1 TGAAAGCGTA 0.933152 -36 TTAAACATGATGATTTAAAGGATTTCTA 18 283 1 TGTAAAGGTT 0.763263 -18 CTTAAAATCTTTAAAAAAGGGCTATTG 20 4 0 TTAAAGGGTA 0.707015 -58 TCAAAAATTAAGAAAAAAGGGCTTGAAACTCATT 22 50 0 AGAAAGGGTT 0.710388 -101 AGACCACTATTAGAACAAGGTTTTTATGACGAT 23 10 0 TAAAAGGTTT 0.395994 -129 TTTTTAAGAGTGGCTCAAGGGCTAATTGGATAGA 23 47 0 TGTAAGGGTA 0.933152 -92 ** * ***** ** Masking position 13 Map Score: 10.12 Number of sites scoring better than the average of aligned sites = 1493 Number in coding regions = 1284 Number in noncoding regions = 209 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 9 CCATTACTCTTAAATCATGCCAATTCACACTC 1 106 1 TAAATCATCA 0.69684 -152 TTGAAATTTGAAAATAATAACACAACTTAAAA 1 145 1 AAAATAATCA 0.912726 -113 ATAATACACTAAAACAATCTCAAGGTTTCAAA 1 228 1 AAAACAATCA 0.767659 -30 GTTTATAAGAAAAATTATTTCAAATGTAGTAG 2 76 0 AAAATTATCA 0.952237 -139 ATGCTACAATAAAACTTTTTCAAAACTAAGAT 3 42 1 AAAACTTTCA 0.562641 -54 AGATTTTAGAAAAATCATATCAAAATAGGAAA 3 70 1 AAAATCATCA 0.955752 -26 AAATTTTCTTAAAATTATACAATATGTAACTT 7 34 1 AAAATTATAA 0.716109 -195 AGTTAAAATAATCCCCTTGAATTTTT 8 42 0 AAAATAATCC 0.642261 -16 CCTAAAAGAGAAAATTATGGCATTAGCCAAGA 10 51 1 AAAATTATCA 0.952237 -38 AACTGAACCAAAAATTATCAAATGTTAGCTAA 13 27 1 AAAATTATAA 0.716109 -89 TCCTTTCATCAAACTCATCTCAACCAACAATA 15 16 1 AAACTCATCA 0.773077 -117 ATTATTATTGAAAATCATAGCGCAAAAATAAG 15 76 0 AAAATCATCG 0.787595 -57 ATTTTAAGCTAAAATTTTAGCATACAAATACA 20 30 1 AAAATTTTCA 0.802838 -32 ******** ** Masking position 3 Map Score: 6.39897 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 107 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 10 AAAAACACTGCCTTAATTCTACTACATTTGA 2 58 1 CCTTAATCTA 0.727649 -157 AAATTACTAACCTCCATGCTACAATAAAACT 3 27 1 CCTCCATCTA 0.924792 -69 AAAAGCGTTCTTTTAYGCTATAATTAAGAC 8 10 1 CTTTTAYCTA 0.664724 -48 CCAAGATGAGCCTTTAATCATC 10 77 1 CCTTTAACAT 0.734983 -12 TTGTTTAATGCCTTCAATCAAATCTGTATTT 12 179 0 CCTTCAACAA 0.972073 -25 GATTTTCCTTTCATCAAACTCATCTCA 15 7 1 CCTTTCACAA 0.804322 -126 CTCCAAACTCCCTTCAAACTAGTTTTAAAAA 15 111 0 CCTTCAACTA 0.953537 -22 CCTGCAACCAACATTAAAGAA 16 1 1 CCTGCAACAA 0.902392 -68 TTTTAAAACCCCTTTATCCAAATAAGTTTGG 16 43 1 CCTTTATCAA 0.948368 -26 AGCTCTAATTCTTCTATGCAAACGCCCACCA 17 48 0 CTTCTATCAA 0.6683 -126 TTATAAAGCCCCTCCATTCAATGAAAAACCC 17 97 0 CCTCCATCAA 0.954245 -77 ******* *** Masking position 3 Map Score: 3.72688 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 151 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 11 CCTAAAAACTCAAAATTAACCTAAAATCGCT 2 21 1 CAAAATAACC 0.624274 -194 AGTTAAAATAATCCCCTTGAATTT 8 44 0 TAAAATATCC 0.794414 -14 TCCCAAACATTTAAATCAGCGAGAGAGC 9 28 1 TTAAATAGCG 0.697984 -18 TGGCATTAGCCAAGATGAGCCTTTAATCATC 10 68 1 CAAGATAGCC 0.905636 -21 GTTTTTACTTTATCATTAGCCCCTAAAAAAT 11 101 0 TATCATAGCC 0.909964 -40 TTTATTAGTATAACATAAGCCATTAAAGAAA 12 150 0 TAACATAGCC 0.957119 -54 CTATGATAAGCCTTTTTGATTT 13 104 0 TATGATAGCC 0.909964 -12 CATTTTAAGATTAAAGTAGCCCT 14 3 0 TTAAAGAGCC 0.78823 -117 GCCAGAATTTTTAAATCAGCCTTAAAA 17 7 0 TTAAATAGCC 0.946943 -167 TAAGATACCATATAATGAGCCATTTTTATCA 23 89 0 TATAATAGCC 0.946943 -50 ****** **** Masking position 5 Map Score: 1.99502 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 230 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 12 CCATTTATGAGAAACCACCATGCATCAATA 12 66 1 GAAACCACCA 0.980081 -138 GTTATGGTATGAAACCACCAAGAAAGAGTA 14 63 1 GAAACCACCA 0.980081 -57 CAAACTCATCTCAACCAACAATAATAGAAG 15 25 1 TCAACCAACA 0.925284 -108 CCTGCAACCAACATTAAAGAATG 16 4 1 GCAACCAACA 0.980081 -65 ********** Masking position 4 Map Score: 0.572054 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 23 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 13 TTGATTTAATCAAATGAGAGAGTTTTTGGC 5 16 1 CAAATGAGAG 0.840658 -51 TACTATCTAGGAAATGAGAGGGTAGCATTT 5 46 1 GAAATGAGAG 0.733868 -21 TTTCATTATTTAAGTAAGGGGAATTA 7 7 0 TAAGTAAGGG 0.748324 -222 TTTTTATCCTTAAAAGAGCGTTTTTTAGCT 13 53 0 TAAAAGAGCG 0.759941 -63 ATGAAACCACCAAGAAAGAGTATAATAGCG 14 71 1 CAAGAAAGAG 0.89869 -49 TGAAGTTTTACAAAAAAGAGTTTTTAAACA 18 69 1 CAAAAAAGAG 0.93405 -232 TACTCCGCAATCAAAAAGGGAGATTGTAGC 18 117 0 TCAAAAAGGG 0.713104 -184 TTAAAATCTTTAAAAAAGGGCTATTG 20 7 0 TAAAAAAGGG 0.922592 -55 CAAAAATTAAGAAAAAAGGGCTTGAAACTC 22 53 0 GAAAAAAGGG 0.889137 -98 CTTAATCAAACAAGAAAGAGCTAAAATAAA 22 126 1 CAAGAAAGAG 0.89869 -25 AAGTAAAATTTTAAAGAGAGTTTTAAAAA 23 120 1 TTAAAGAGAG 0.591441 -19 ********** Masking position 7 Map Score: 2.85513 Number of sites scoring better than the average of aligned sites = 617 Number in coding regions = 543 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 14 ********** No masking Map Score: -4.71557e-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: -4.71557e-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