AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00790_hpyl_reg_300.orf -o00790_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: HP0791 24 cadmium-transporting ATPase, P-type (cadA) HP1552 23 Na+/H+ antiporter (nhaA) Input sequences: #1 HP0795 111 trigger factor (tig) #2 HP0796 28 H. pylori predicted coding region HP0796 #3 HP0797 118 flagellar sheath adhesin hpaA #4 HP0801 72 molybdopterin converting factor, subunit 1 (moaD) #5 HP0802 88 GTP cyclohydrolase II (ribA) #6 HP0803 88 H. pylori predicted coding region HP0803 #7 HP0804 170 GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase (ribA, ribB) #8 HP0805 81 lipooligosaccharide 5G8 epitope biosynthesis-associated protein (lex2B) #9 HP0906 259 H. pylori predicted coding region HP0906 #10 HP0907 50 hook assembly protein, flagella (flgD) #11 HP0909 51 H. pylori predicted coding region HP0909 #12 HP0925 155 recombinational DNA repair protein (recR) #13 HP1038 128 3-dehydroquinase type II (aroQ) #14 HP1039 30 H. pylori predicted coding region HP1039 #15 HP1040 140 ribosomal protein S15 (rps15) #16 HP1227 73 cytochrome c553 #17 HP1228 150 invasion protein (invA) #18 HP1365 83 response regulator #19 HP1368 300 type IIS restriction enzyme M2 protein (mod) #20 HP1483 26 gerC2 protein (gerC2) #21 HP1490 103 hemolysin #22 HP1491 138 phosphate permease #23 HP1503 25 cation-transporting ATPase, P-type (copA) #24 HP1506 127 glutamate permease (gltS) #25 HP1523 81 DNA recombinase (recG) #26 HP1550 62 protein-export membrane protein (secD) #27 HP1551 47 conserved hypothetical secreted protein #28 HP1553 248 helicase Motif number 1 AAAAGCGGTTTTAATTCTAGTTTTCAAAAATTTAAAAAA 1 11 0 TAATTTCAAA 0.548479 -101 TTAATTTGTTTTAATTCCAGTTTATAAAAAGCGGTTTTA 1 37 0 TAATTATAAA 0.943481 -75 CTTAATGGCTAAAAAATTAAATTTTTGTATCATTATAGC 1 76 0 AAATTTTTGA 0.374742 -36 TTAAATATTTTTAAAACCTCTTTAAAGCACTCATAATTT 4 11 0 TAATTAAAGA 0.811252 -62 TTAAATCTTTTAAAGCATGATTTTAAATATTTTTAAAAC 4 33 0 TAATTTAAAA 0.876177 -40 TACCTTTTTTTAAAAGATGCGTTTTAAAACTAATTTTAG 5 52 1 TAATTTTAAA 0.933147 -37 ATTGCTTGACTTAAAAAGAGTTTATTATACCTTAAAAAC 6 45 0 TAATTATTAA 0.840572 -44 TTTTTTCTATAAAACTCAATATTATTGAATAAAACTAGG 7 134 1 AAATTATTGA 0.417515 -37 ACAATTAAATAAAAACGATAATTTTAGAGAGATTGGC 9 9 0 AAATTTTAGG 0.597787 -251 GCGCTTAATGAGAACAGAGGTTTTTAAAACTATGGTTTC 9 72 0 AAATTTTAAA 0.788857 -188 GCGAATAACGACAACTTTTATTTTTAAAAAATGGGGTTT 9 109 1 AAATTTTAAA 0.788857 -151 CTAAAAATGCTAAAGGTGTTTTTAAAACGAAAAACCCCA 9 140 0 TAATTAAAAG 0.868908 -120 TATAAAGAAATAAAAGAGTTGTTTTAAAAAGGATAACC 9 232 1 TAATTTTAAA 0.933147 -28 CTCTTCCTTCTTAAAGATGTCTTATTATAGAGCAAACTT 10 19 0 TAATTATTAA 0.840575 -32 AGAAGTATGGTAAAATATCCTTTTTAATAAGGATATTTA 11 23 1 TAATTTTAAA 0.933147 -29 GAAAAAGCGCTTAATGAAGCGTTTAAATGGAAGTGTTAT 12 40 0 TAATTTAAAG 0.847147 -116 ATTATTTAATTAAACCCCCTTTTAAAAAACAATAAAAGC 12 81 1 TAATTAAAAA 0.894321 -75 ATCATACGCTTAAACTTTATATTATAATAAGCCTAAAAA 15 50 0 TAATTATAAA 0.943481 -91 CATTATAGCGTAAAATAAGCTTTTTTGTATCATACGCTT 15 78 0 TAATTTTTGA 0.690887 -63 GGTAATTTAATAAAGTTCGCATTATAGCGTAAAATAAGC 15 97 0 TAATTATAGG 0.86912 -44 AATTACAAGTTTAAGTTTTGCTTAAAATGAA 16 3 0 TAATTAAAAG 0.868908 -71 CCTCTACTTATCAAAATGATCTTAAAATGATACAATTAC 16 36 0 TAATTAAAAG 0.868908 -38 CCCTTTTTTCTTAATTTTTGATTTTAATGGCATTCTTAA 17 63 1 TAATTTTAAG 0.916196 -88 TCTTGTTTGATTAAGATGGTATTATAGTGTATACTAGCT 17 102 0 TAATTATAGG 0.86912 -49 CGGTTATAAAAAAACACTCCCTTAAAAAAGACACCGCTT 18 18 0 AAATTAAAAA 0.693736 -66 CCCATGCAAAAAAAGATTTTTTTATTAGAAGACGATTAC 19 129 1 AAATTATTAA 0.585284 -172 ACATAAAAGATTAAGCCTAACTTTAAAAATCAAGCCTTC 21 18 0 TAATTTAAAA 0.876177 -86 ATATGGTATCTTAAAGTAAAATTTTAAAGAGAGTTTTAA 22 14 0 TAATTTTAAG 0.916196 -125 GCCATTTTTATCAAACAACGCTTTTTAAGAGTGGCTCAA 22 58 1 TAATTTTTAG 0.775435 -81 ATCGTCATAAAAACCTTGTTCTAATAGTGGTCTTAT 22 113 0 TAATTCTAAA 0.639007 -26 CGCCCTTAAATTAAGGATTAAAAAA 23 7 1 TAATTAAAAA 0.894318 -19 TCCTTATTAATCAAATTTATCTTATTATAATATAATACC 24 92 0 TAATTATTAA 0.840575 -36 ATAAAAACGATTAAACGAGCGTTAAAAAGTT 26 3 0 TAATTAAAAG 0.868908 -60 AAAAGATGTTTTAATCTCAAATTATAGCATTTTTAG 27 8 0 TAATTATAGA 0.894496 -40 * ** ****** * Masking position 12 Map Score: 44.6054 Number of sites scoring better than the average of aligned sites = 1207 Number in coding regions = 897 Number in noncoding regions = 310 Number of orfs with sites within 600 bp upstream = 217 Fraction of orfs with sites within 600 bp upstream = 0.0348538 Motif number 2 TTTTGTATCATTATAGCTTAATTTGTTTTAA 1 62 0 TTATACTTAA 0.935737 -50 TTTTTTCCTTAATGGCTAAAAA 1 100 0 TTTTTCTTAA 0.910007 -12 CAAAATGTTATTTTACCCTAACATCTTTAGA 3 25 0 TTTTACCTAA 0.869964 -94 AAAGAGTTTATTATACCTTAAAAACATTACA 6 39 0 TTATACTTAA 0.935737 -50 CTATATTTCTTTTTTCTATAAAACTCAATAT 7 125 1 TTTTTTATAA 0.725816 -46 AAAATTATCGTTTTTATTTAATTGTAGCGAA 9 23 1 TTTTTTTTAA 0.783974 -237 TAAGGAACTCTTTTTGCTTAACTCCCACCAT 9 195 1 TTTTTCTTAA 0.910007 -65 TTTTATTTCTTTATATTTTACATGGTGGGAG 9 216 0 TTATATTTAC 0.58857 -44 AAAAAGGATATTTTACCATACTTCTTATTTC 11 17 0 TTTTACATAC 0.807467 -35 GTTATTCCTTAAAATTGAGATA 12 2 1 TTATTCTTAA 0.876096 -154 TAGCATAAGTTTTTATCTTACCCCTTAAATC 13 67 0 TTTTACTTAC 0.850933 -62 TGAGACCACATTATAGCATAAGTTTTTATCT 13 80 0 TTATACATAA 0.853694 -49 TTTAGGCTTATTATAATATAAAGTTTAAGCG 15 52 1 TTATATATAA 0.479233 -89 AAAGTTCGCATTATAGCGTAAAATAAGCTTT 15 94 0 TTATACGTAA 0.716974 -47 TTTCAAGCCCTTTTTTCTTAATTTTTGATTT 17 56 1 TTTTTCTTAA 0.910007 -95 TAAGGGAGTGTTTTTTTATAACCGCTTTTAG 18 33 1 TTTTTTATAA 0.725816 -51 TTATAACCGCTTTTAGTATAAAGGCAATTAG 18 48 1 TTTTATATAA 0.806975 -36 AATCTCAGAATTTTAACATAAAAGATTAAGC 21 41 0 TTTTACATAA 0.938587 -63 CTCTTTAAAATTTTACTTTAAGATACCATAT 22 22 1 TTTTATTTAA 0.883078 -117 TAGGGGGGTATTATATTATAATAAGATAAAT 24 86 1 TTATATATAA 0.479233 -42 GATTAAGGTTTTTTAGCTTAAGTAAAAAAGG 28 180 1 TTTTACTTAA 0.954897 -69 TTTGTCTTTATTATAACCTAAAAGCCTTTTT 28 204 0 TTATACCTAA 0.823045 -45 ***** ***** Masking position 4 Map Score: 29.2631 Number of sites scoring better than the average of aligned sites = 305 Number in coding regions = 210 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 3 TTTTTTCCTTAATGGCTAAAAAA 1 99 0 TTTCCTTAAT 0.665517 -13 ATTTTTAAAACCTCTTTAAAGCACTCATAA 4 14 0 CCTCTTTAAA 0.807023 -59 CTCTTTATAATTTTCTTAAATTTTAAGCTC 5 11 0 TTTTCTTAAA 0.922788 -78 ATAGAATACCTTTTTTTAAAAGATGCGTTT 5 46 1 TTTTTTTAAA 0.827866 -43 TATAATAAACTCTTTTTAAGTCAAGCAATA 6 55 1 TCTTTTTAAG 0.795842 -34 TGTAGCGAAATTTAATTAAACCTAAACGAA 9 45 1 TTTAATTAAA 0.388024 -215 AAACCTCTGTTCTCATTAAGCGCGAATAAC 9 88 1 TCTCATTAAG 0.844124 -172 AGCAAAAAGAGTTCCTTAAGACGCGTGATC 9 183 0 GTTCCTTAAG 0.879122 -77 GGTTATCCTTTTTAAAACAACTCTTT 9 244 0 CCTTTTTAAA 0.750555 -16 ATAGAGCAAACTTGCTTAAAA 10 2 0 CTTGCTTAAA 0.760494 -49 GATCTCTTCCTTCTTAAAGATGTCTTAT 10 33 0 CCTTCTTAAA 0.88211 -18 TAAATATCCTTATTAAAAAGGATATTT 11 35 0 CCTTATTAAA 0.750483 -17 GTTATTCCTTAAAATTGAGATAG 12 4 1 ATTCCTTAAA 0.543373 -152 CATTTAAACGCTTCATTAAGCGCTTTTTCA 12 50 1 CTTCATTAAG 0.81595 -106 TTTCATATTATTTAATTAAACCCCCTTTTA 12 75 1 TTTAATTAAA 0.388024 -81 GGCTTTTATTGTTTTTTAAAAGGGGGTTTA 12 91 0 GTTTTTTAAA 0.689975 -65 ATAATGCGAACTTTATTAAATTACCAATTA 15 111 1 CTTTATTAAA 0.770687 -30 AAGTTTAAGTTTTGCTTAAAATGAA 16 6 0 TTTGCTTAAA 0.813093 -68 TCAAGCCCTTTTTTCTTAATTTTTGATTTT 17 58 1 TTTTCTTAAT 0.588744 -93 CTCTTTCTTGTTTGATTAAGATGGTATTAT 17 116 0 TTTGATTAAG 0.618573 -35 AAAGCGGTGTCTTTTTTAAGGGAGTGTTTT 18 17 1 CTTTTTTAAG 0.768494 -67 TCATTATAACGCTCCTTAAAAAACATAGGA 19 59 1 GCTCCTTAAA 0.868253 -242 AACAAAGCCCGCTCATTAAGCGCTACAATA 19 97 1 GCTCATTAAG 0.714746 -204 GACTGACTCATTTTTTTAAAATACCCCCAT 19 221 1 TTTTTTTAAA 0.827866 -80 TATTTTTACCTTTTATTAAACTTCAATGGG 19 278 0 TTTTATTAAA 0.819312 -23 TTTTTAAAACTCTCTTTAAAATTTTACTTT 22 11 1 TCTCTTTAAA 0.851418 -128 ATCAAACAACGCTTTTTAAGAGTGGCTCAA 22 67 1 GCTTTTTAAG 0.643215 -72 CAATTAAATTTCCTTAAGTCAATGTATA 25 9 1 TTTCCTTAAG 0.940143 -73 TTAATTTCCTTAAAAGATGTTTTA 27 34 0 TTTCCTTAAA 0.943191 -14 GAGAATTCTCCTTAAAGTTATTTTGG 28 7 1 TCTCCTTAAA 0.934426 -242 TGATTCTTAATTTTCTTAAGAACACCTAAT 28 58 1 TTTTCTTAAG 0.918728 -191 AAAAGCCTTTTTTACTTAAGCTAAAAAACC 28 186 0 TTTACTTAAG 0.718006 -63 ********** Masking position 6 Map Score: 30.6767 Number of sites scoring better than the average of aligned sites = 858 Number in coding regions = 669 Number in noncoding regions = 189 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 4 ATCATTATAGCTTAATTTGTTTTAATTCCAGT 1 55 0 CTTAATTTTT 0.792306 -57 AAATTTAATTTTTTAGCCATTAAGGAAAAAA 1 91 1 TTTTAGCTTA 0.564009 -21 TATCAAAACTCTTTATAATTTTCTTAAATTTT 5 17 0 CTTTATATTT 0.717737 -72 AGGTTGCAAACTTTATTGCTTGACTTAAAAAG 6 66 0 CTTTATTTTG 0.603441 -23 GGGAGTTTCATTCAATTAATTTAGAGGCTTTA 7 43 1 TTCAATTTTT 0.478686 -128 AATTTAGAGGCTTTAGCGATTTGTATCTAAAT 7 60 1 CTTTAGCTTT 0.923717 -111 ACGATTATTACTTTATTGCTTTATTTAGATAC 7 82 0 CTTTATTTTT 0.874149 -89 TTAAAAACACCTTTAGCATTTTTAGATTTGAT 9 154 1 CTTTAGCTTT 0.923717 -106 AAAACAACTCTTTTATTTCTTTATATTTTACA 9 225 0 TTTTATTTTT 0.839724 -35 CTAAAAGGGCTTTTATTGTTTTTTAAAAGGGG 12 96 0 TTTTATTTTT 0.839724 -60 TTTTTATCGGTTTTAGGGTGTGG 14 2 1 TTTTATCTTT 0.942903 -29 AAACTTGTAATTGTATCATTTTAAGATCATTT 16 30 1 TTGTATCTTT 0.662829 -44 TAAAATGAGTTTCAAGCCCTTTTTTCTTAATT 17 47 1 TTCAAGCTTT 0.615501 -104 AGGTCTTTATTTTAGCTCTTTCTTGTTTGAT 17 130 0 TTTTAGCTTT 0.90132 -21 TAAAGTTAGGCTTAATCTTTTATGTTAAAATT 21 32 1 CTTAATCTTA 0.630037 -72 AATTCTGAGATTTTATATATTTTATATTTATC 21 60 1 TTTTATATTT 0.6573 -44 CTAGCCAATCCTTAATCATTTTTATGATAAGA 25 48 0 CTTAATCTTT 0.923219 -34 TTAACGCTCGTTTAATCGTTTTTATTGGCGCG 26 17 1 TTTAATCTTT 0.900691 -46 TTTGTCGTTTTTCTATCATTTTAATAGGAACA 28 128 0 TTCTATCTTT 0.840505 -121 GCTAAAAAACCTTAATCTTTTGCTATAATCGT 28 165 0 CTTAATCTTG 0.724836 -84 ******* *** Masking position 10 Map Score: 14.4012 Number of sites scoring better than the average of aligned sites = 1117 Number in coding regions = 911 Number in noncoding regions = 206 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 5 AGTTTATAAAAAGCGGTTTTAATTCTAGTTT 1 27 0 AAGCGGTTTA 0.93041 -85 GAGTGCTTTAAAGAGGTTTTAAAAATATTTA 4 18 1 AAGAGGTTTA 0.634263 -55 TCTTGCATGATAGGGGGAGTTTCATTCAATT 7 29 1 TAGGGGGATT 0.827915 -142 TGTTCTCATTAAGCGCGAATAACGACAACTT 9 95 1 AAGCGCGATA 0.744593 -165 TTTTTAAAAAATGGGGTTTTTCGTTTTAAAA 9 129 1 ATGGGGTTTT 0.895449 -131 AAAAATGCTAAAGGTGTTTTTAAAACGAAAA 9 146 0 AAGGTGTTTT 0.638434 -114 ACGCTTCATTAAGCGCTTTTTCATATTATTT 12 57 1 AAGCGCTTTT 0.878698 -99 TGTTTTTTAAAAGGGGGTTTAATTAAATAAT 12 81 0 AAGGGGGTTA 0.968677 -75 AAGCCACTAAAAGGGCTTTTATTGTTTTTTA 12 103 0 AAGGGCTTTA 0.912434 -53 CATCAAGGGGTTTGACATTAGTCAA 13 5 1 AAGGGGTTGA 0.847553 -124 GACATTAGTCAAGCGGTAGTTTCTTGTGATT 13 24 1 AAGCGGTATT 0.915806 -105 GATTCGTTCTTAGGGGGATTTAAGGGGTAAG 13 51 1 TAGGGGGATT 0.827915 -78 AGGGGGATTTAAGGGGTAAGATAAAAACTTA 13 62 1 AAGGGGTAGA 0.753295 -67 TGTCTTTTTTAAGGGAGTGTTTTTTTATAAC 18 24 1 AAGGGAGTTT 0.721613 -60 TTTATACTAAAAGCGGTTATAAAAAAACACT 18 39 0 AAGCGGTTTA 0.93041 -45 GGGGGTATTGTAGCGCTAATTGCCTTTATAC 18 63 0 TAGCGCTATT 0.43206 -21 CTTTTTTTGCATGGGGGTATTGTAGCGCTTA 19 113 0 ATGGGGGTTT 0.902885 -188 TTACAATGAAATGGGGGTATTTTAAAAAAAT 19 230 0 ATGGGGGTTT 0.902885 -71 AGAGTGGCTCAAGGGCTAATTGGATAGAATA 22 85 1 AAGGGCTATT 0.894486 -54 TCGTTCTTTTAGGGGGGTATTATATTATAAT 24 77 1 AGGGGGGTTT 0.845045 -51 ******** ** Masking position 3 Map Score: 19.0027 Number of sites scoring better than the average of aligned sites = 1375 Number in coding regions = 1168 Number in noncoding regions = 207 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 6 GCGTTCTTTTTTTATGCGTTA 2 18 0 CGTTCTTTTT 0.746731 -11 TTTAGATTATTGGTCTTTTT 3 1 0 TGGTCTTTTT 0.947412 -118 AACATGCTATATTTCTTTTTTCTATAAAAC 7 119 1 ATTTCTTTTT 0.698862 -52 CTCTCTAAAATTATCGTTTTTATTTAATTG 9 17 1 TTATCGTTTT 0.638488 -243 AAAATAAAAGTTGTCGTTATTCGCGCTTAA 9 103 0 TTGTCGTTAT 0.872861 -157 AAAATGGGGTTTTTCGTTTTAAAAACACCT 9 136 1 TTTTCGTTTT 0.894817 -124 GGTAGGTGGTTTGTCTTTTTAGGCTTATTA 15 35 1 TTGTCTTTTT 0.956398 -106 TCAAGCCCTTTTTTCTTAATTTTTGATTTT 17 58 1 TTTTCTTAAT 0.406545 -93 AGGTCTTTATTTTAGCTCTT 17 141 0 AGGTCTTTAT 0.606023 -10 AAATAAAGCGGTGTCTTTTTTAAGGGAGTG 18 13 1 GTGTCTTTTT 0.805097 -71 AATTGCGCTTCGTTCGTTTTCATTATAACG 19 40 1 CGTTCGTTTT 0.707737 -261 GACTTTTCTTTTTTCATGGCTTG 20 14 0 TTTTCTTTTT 0.911956 -13 GTTCTAATAGTGGTCTTATTCTATCCAATT 22 102 0 TGGTCTTATT 0.757675 -37 TCGTAGGGTTTTGTCGTTTTTCTATCATTT 28 139 0 TTGTCGTTTT 0.947412 -110 AATTCTAATTTTGTCTTTATTATAACCTAA 28 214 0 TTGTCTTTAT 0.89315 -35 ********** Masking position 4 Map Score: 10.1702 Number of sites scoring better than the average of aligned sites = 638 Number in coding regions = 552 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 7 AATGATACAAAAATTTAATTTTTTAGCCATTA 1 81 1 ATTTAATTTT 0.501124 -31 TTGTTATAGAAGTCTAAAATATTACAATCAAG 3 88 1 ACTAAAATAT 0.422634 -31 TTACCCTTATATTAAATCTTTTAAAGCATG 4 53 0 ATTAAATCTT 0.442828 -20 TCTTTATAATTTTCTTAAATTTTAAGCTC 5 8 0 TCTTAAATTT 0.7271 -81 GATGCGTATTTTACTAAAATTTGCGCTAGAAT 8 11 1 TCTAAAATTT 0.577303 -71 GTTAGCCTTAATTCTTAATGCAAAT 8 67 0 ACTTAATTCT 0.773611 -15 TTTGTATCATACGCTTAAACTTTATATTATAA 15 62 0 ACTTAAACTT 0.918935 -79 ATTTTAAGCAAAACTTAAACTTGTAATTGTAT 16 14 1 ACTTAAACTT 0.891539 -60 CAAGCCCTTTTTTCTTAATTTTTGATTTTAAT 17 59 1 TCTTAATTTT 0.80478 -92 ATGAAAAGGTTTTCTAAAACTTCATAAAATTG 19 13 1 TCTAAAACTT 0.639011 -288 CAGTCAAGGCAATCTAAATTTTCAATGAGTCA 19 194 0 ACTAAATTTT 0.875247 -107 GGTTTTTGAAGGCTTGATTTTTAAAGTTAGG 21 10 1 ACTTGATTTT 0.605538 -94 TTTTAAAGTTAGGCTTAATCTTTTATGTTAAA 21 29 1 ACTTAATCTT 0.945293 -75 AACTTTAAACCTAAAACCTAACGATAAAT 21 85 0 ACTAAAACCT 0.594728 -19 TTTTTTAATCCTTAATTTAAGGGCG 23 7 0 ACTTAATTTA 0.508799 -19 ACCCTAGCCAATCCTTAATCATTTTTATGATA 25 51 0 ACTTAATCAT 0.741163 -31 TGCTCATTTGATTCTTAATTTTCTTAAGAACA 28 50 1 ACTTAATTTT 0.931894 -199 TAAGCTAAAAAACCTTAATCTTTTGCTATAAT 28 168 0 ACTTAATCTT 0.946513 -81 * ********* Masking position 5 Map Score: 10.9657 Number of sites scoring better than the average of aligned sites = 382 Number in coding regions = 278 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 8 TCTAGTTTTCAAAAATTTAAAAAA 1 3 0 AAATTTAAAA 0.69749 -109 GGGTAAAATAACATTTTGACAACAAAAGCGTG 3 38 1 AATTTGACAA 0.880005 -81 ATAGAAGTCTAAAATATTACAATCAAGGATAG 3 93 1 AATATTACAA 0.899329 -26 ATGATTTTAAATATTTTTAAAACCTCTTTAAA 4 24 0 AATTTTAAAA 0.924738 -49 ACTCCTAAAATTAGTTTTAAAACGCATCTTTT 5 63 0 TATTTTAAAA 0.680761 -26 TTATACCTTAAAAACATTACAACACATTCAAT 6 28 0 AACATTACAA 0.584891 -61 AAACGAAACCATAGTTTTAAAAACCTCTGTTC 9 68 1 AATTTTAAAA 0.924738 -192 ACGACAACTTTTATTTTTAAAAAATGGGGTTT 9 116 1 TATTTTAAAA 0.680761 -144 GTTTAATTAAATAATATGAAAAAGCGCTTAAT 12 64 0 AATATGAAAA 0.727935 -92 TCTTAAAATGATACAATTACAAGTTTAAGTTT 16 24 0 AAAATTACAA 0.62636 -50 TGACTGACTCATTTTTTTAAAATACCCCCATT 19 220 1 ATTTTTAAAA 0.529368 -81 TTTGCATGAAAGAATTTTACAATGAAATGGGG 19 245 0 AATTTTACAA 0.94549 -56 AATTTTAAAGAGAGTTTTAAAAA 22 2 0 AATTTTAAAA 0.924738 -137 TTCCTTGCATACAGTATTACAAATTGGAGCTG 24 25 0 AATATTACAA 0.899329 -103 AAGTCAATGTATAATTTGACTATCTTATCATA 25 26 1 AATTTGACTA 0.401683 -56 * * ******** Masking position 9 Map Score: 8.80496 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 214 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 9 ATATAGCATGTTTAATAACGATTATTACTT 7 101 0 TTTAATAACG 0.880152 -70 TAATTGGTAATTTAATAAAGTTCGCATTAT 15 111 0 TTTAATAAAG 0.591171 -30 CCCTCTCCGTTTTAATAGCGTTATTTGGGC 17 12 1 TTTAATAGCG 0.963001 -139 TGAAACTCATTTTAATAGCGCCCAAATAAC 17 31 0 TTTAATAGCG 0.963001 -120 AATTTTTGATTTTAATGGCATTCTTAAAGC 17 75 1 TTTAATGGCA 0.783846 -76 CGGTGTCTTTTTTAAGGGAGTGTTTTTTTA 18 21 1 TTTAAGGGAG 0.853359 -63 AACAACGCTTTTTAAGAGTGGCTCAAGGGC 22 71 1 TTTAAGAGTG 0.674208 -68 AGAACAAGGTTTTTATGACGAT 22 127 1 TTTTATGACG 0.62234 -12 TAATCCTTAATTTAAGGGCG 23 1 0 TTTAAGGGCG 0.96727 -25 TTTAATCGTTTTTATTGGCGCGCTTCTTTT 26 27 1 TTTATTGGCG 0.853809 -36 ********** Masking position 3 Map Score: 5.96681 Number of sites scoring better than the average of aligned sites = 725 Number in coding regions = 665 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 10 AATTCCAGTTTATAAAAAGCGGTTTTAATT 1 34 0 TATAAAAAGC 0.764605 -78 GGAATTAAAACAAATTAAGCTATAATGATA 1 58 1 CAAATTAAGC 0.839248 -54 AGACAAATAACGCATAAAAAAAG 2 4 1 CAAATAACGC 0.892252 -25 AAATAACGCATAAAAAAAGAACGC 2 15 1 TAAAAAAAGA 0.766292 -14 AACATTTTGACAACAAAAGCGTGTTGGTTG 3 47 1 CAACAAAAGC 0.77478 -72 ACGCATCTTTTAAAAAAAGGTATTCTATCA 5 44 0 TAAAAAAAGG 0.657921 -45 GATTTGTATCTAAATAAAGCAATAAAGTAA 7 77 1 TAAATAAAGC 0.927511 -94 CAAATTTTAGTAAAATACGCATC 8 4 0 TAAAATACGC 0.79229 -78 TTTTAAAAAACAATAAAAGCCCTTTTAGTG 12 100 1 CAATAAAAGC 0.698892 -56 AACTTTATATTATAATAAGCCTAAAAAGAC 15 47 0 TATAATAAGC 0.512627 -94 CATTATAGCGTAAAATAAGCTTTTTTGTAT 15 87 0 TAAAATAAGC 0.881326 -54 TAATAGCGCCCAAATAACGCTATTAAAACG 17 19 0 CAAATAACGC 0.892252 -132 AGAAAGAGCTAAAATAAAGACCT 17 138 1 AAAATAAAGA 0.312189 -13 TAAAATAAAGCGGTGTCTTTT 18 2 1 AAAATAAAGC 0.760465 -82 TACCCCCATGCAAAAAAAGATTTTTTTATT 19 125 1 CAAAAAAAGA 0.805125 -176 CCATTTTTATCAAACAACGCTTTTTAAGAG 22 59 1 CAAACAACGC 0.718154 -80 ACCCTACCCCTAAAAGAAGCGCGCCAATAA 26 38 0 TAAAAGAAGC 0.769876 -25 TTAGCTTAAGTAAAAAAGGCTTTTAGGTTA 28 192 1 TAAAAAAGGC 0.769876 -57 ********** Masking position 7 Map Score: 8.74842 Number of sites scoring better than the average of aligned sites = 1442 Number in coding regions = 1271 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 11 GAGTGCTTTAAAGAGGTTTTAAAAATATTT 4 18 1 AAGAGGTTTT 0.637879 -55 AGAAAATTATAAAGAGTTTTGATAGAATAC 5 25 1 AAAGAGTTTT 0.766539 -64 TTTTTTAAAAGATGCGTTTTAAAACTAATT 5 57 1 GATGCGTTTT 0.442156 -32 GAGGCTCGTTAAGTTTTATTGAATGTG 6 8 1 GTTAAGTTTT 0.444713 -81 TGAATGTGTTGTAATGTTTTTAAGGTATAA 6 30 1 GTAATGTTTT 0.477602 -59 ATTCAATAATATTGAGTTTTATAGAAAAAA 7 134 0 ATTGAGTTTT 0.637411 -37 TTTTTAAAAAATGGGGTTTTTCGTTTTAAA 9 129 1 ATGGGGTTTT 0.833637 -131 AAAGCCACTAAAAGGGCTTTTATTGTTTTT 12 105 0 AAAGGGCTTT 0.603311 -51 CTTTTTTAAGGGAGTGTTTTTTTATAACCG 18 27 1 GGAGTGTTTT 0.495416 -57 CTATGAAAAGGTTTTCTAAAACTTC 19 6 1 AAAAGGTTTT 0.816158 -295 ATTAAACTTCAATGGGTTTTGCATGAAAGA 19 264 0 AATGGGTTTT 0.867493 -37 TATATTTATCGTTAGGTTTTAGGTTTAAAG 21 82 1 GTTAGGTTTT 0.772341 -22 AAAATTTTAAAGAGAGTTTTAAAAA 22 6 0 AGAGAGTTTT 0.61685 -133 CACTATTAGAACAAGGTTTTTATGACGAT 22 120 1 ACAAGGTTTT 0.596972 -19 TCTTTTAGGGGTAGGGTTTTCT 26 51 1 GTAGGGTTTT 0.947498 -12 TGCTATAATCGTAGGGTTTTGTCGTTTTTC 28 147 0 GTAGGGTTTT 0.947498 -102 TAGCAAAAGATTAAGGTTTTTTAGCTTAAG 28 172 1 TTAAGGTTTT 0.446564 -77 CTTAAGTAAAAAAGGCTTTTAGGTTATAAT 28 196 1 AAAGGCTTTT 0.472489 -53 ********** Masking position 8 Map Score: 4.3933 Number of sites scoring better than the average of aligned sites = 1753 Number in coding regions = 1525 Number in noncoding regions = 228 Number of orfs with sites within 600 bp upstream = 170 Fraction of orfs with sites within 600 bp upstream = 0.0273049 Motif number 12 TTAAGCTATAATGATACAAAAATTTAATTT 1 72 1 ATGATACAAA 0.898519 -40 ATTACAATCAAGGATAGAACG 3 108 1 AGGATAGAAC 0.827147 -11 ATAAAGAGTTTTGATAGAATACCTTTTTTT 5 33 1 TTGATAGAAT 0.872877 -56 GTTTAAGCGTATGATACAAAAAAGCTTATT 15 74 1 ATGATACAAA 0.898519 -67 TGATCTTAAAATGATACAATTACAAGTTTA 16 29 0 ATGATACAAT 0.920171 -45 TGGGTTTTGCATGAAAGAATTTTACAATGA 19 252 0 ATGAAAGAAT 0.770731 -49 AAGGGCTAATTGGATAGAATAAGACCACTA 22 95 1 TGGATAGAAT 0.795448 -44 TCCTATTAAAATGATAGAAAAACGACAAAA 28 131 1 ATGATAGAAA 0.935084 -118 ********** Masking position 6 Map Score: 2.21058 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 91 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 ATTTTTGTATCATTATAGCTTAATTTGTTTT 1 64 0 CATTTAGCTT 0.813386 -48 AACAGACTTACATTCTAGCGCAAATTTTAGT 8 23 0 CATTTAGCGC 0.991321 -59 AAAGATGTCTTATTATAGAGCAAACTTGCTT 10 15 0 TATTTAGAGC 0.725524 -36 TGAGATAGCACATTATAACACTTCCATTTAA 12 26 1 CATTTAACAC 0.864286 -130 ATAACACTTCCATTTAAACGCTTCATTAAGC 12 40 1 CATTAAACGC 0.810139 -116 AATGAGACCACATTATAGCATAAGTTTTTAT 13 82 0 CATTTAGCAT 0.813386 -47 ATAAAGTTCGCATTATAGCGTAAAATAAGCT 15 96 0 CATTTAGCGT 0.961852 -45 AGGTCTTTATTTTAGCTCTTTCTTGTTT 17 133 0 TATTTAGCTC 0.864286 -18 GGGGGTATTGTAGCGCTAATTGCCTT 18 68 0 TATTTAGCGC 0.973573 -16 CGTTCGTTTTCATTATAACGCTCCTTAAAAA 19 50 1 CATTTAACGC 0.973573 -251 TGCATGGGGGTATTGTAGCGCTTAATGAGCG 19 106 0 TATTTAGCGC 0.973573 -195 AACTTTTTAACGCTCGTTTAATC 26 3 1 CTTTTAACGC 0.810139 -60 **** ****** Masking position 7 Map Score: 14.9297 Number of sites scoring better than the average of aligned sites = 314 Number in coding regions = 278 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 14 ********** No masking Map Score: 5.35339e-13 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: 5.35339e-13 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