AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00500_hpyl_reg_300.orf -o00500_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: HP1503 25 cation-transporting ATPase, P-type (copA) Input sequences: #1 HP0428 300 phage/colicin/tellurite resistance cluster terY protein #2 HP0429 124 H. pylori predicted coding region HP0429 #3 HP0430 85 H. pylori predicted coding region HP0430 #4 HP0640 62 poly(A) polymerase (papS) #5 HP0643 164 glutamyl-tRNA synthetase (gltX) #6 HP0791 24 cadmium-transporting ATPase, P-type (cadA) #7 HP0795 111 trigger factor (tig) #8 HP0796 28 H. pylori predicted coding region HP0796 #9 HP0797 118 flagellar sheath adhesin hpaA #10 HP0801 72 molybdopterin converting factor, subunit 1 (moaD) #11 HP0802 88 GTP cyclohydrolase II (ribA) #12 HP0803 88 H. pylori predicted coding region HP0803 #13 HP0804 170 GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase (ribA, ribB) #14 HP0805 81 lipooligosaccharide 5G8 epitope biosynthesis-associated protein (lex2B) #15 HP0906 259 H. pylori predicted coding region HP0906 #16 HP0907 50 hook assembly protein, flagella (flgD) #17 HP0909 51 H. pylori predicted coding region HP0909 #18 HP1101 65 glucose-6-phosphate dehydrogenase (g6pD) #19 HP1166 63 glucose-6-phosphate isomerase (pgi) #20 HP1365 83 response regulator #21 HP1368 300 type IIS restriction enzyme M2 protein (mod) #22 HP1483 26 gerC2 protein (gerC2) #23 HP1490 103 hemolysin #24 HP1491 138 phosphate permease #25 HP1506 127 glutamate permease (gltS) #26 HP1523 81 DNA recombinase (recG) Motif number 1 AAAATCATCAAAAAGAGTGCTGAAATGAATGT 1 127 1 AAAAGGTGTG 0.760503 -174 AATACTGGAATAAAGCGTTCTTCCATAGTGTA 1 250 0 TAAAGGTTTT 0.975659 -51 AATCCATAAATAAAGCGTTTTTGTGGCGTAAA 2 27 0 TAAAGGTTTT 0.975129 -98 ACAGATATACAAAAGTGGGATTTAAAGGGTTT 3 42 1 AAAAGGGGTT 0.958934 -44 TAAAGGGTTTAAAAGGGGAGTTTGAAGACGCT 3 64 1 AAAAGGGATT 0.854595 -22 CCTTTATTTAAAAATAGTTTTTGATTATACCT 5 137 0 AAAATGTTTT 0.685086 -28 TATTTTTAAATAAAGGGTTTTT 5 153 1 TAAAGGTTTT 0.97566 -12 CCAGTTTATAAAAAGCGGTTTTAATTCTAGTT 7 28 0 AAAAGGGTTT 0.980959 -84 TTTTGACAACAAAAGCGTGTTGGTTGCTTCGG 9 51 1 AAAAGGTGTG 0.760497 -68 ATGAGTGCTTTAAAGAGGTTTTAAAAATATTT 10 16 1 TAAAGGGTTT 0.983757 -57 ATCATGCTTTAAAAGATTTAATATAAGGGTAA 10 51 1 AAAAGTTTAT 0.57904 -22 AAGAAAATTATAAAGAGTTTTGATAGAATACC 11 24 1 TAAAGGTTTG 0.891828 -65 GCATCTTTTAAAAAAAGGTATTCTATCAAAAC 11 40 0 AAAAAGGTTT 0.767694 -49 GCTTGACTTAAAAAGAGTTTATTATACCTTAA 12 49 0 AAAAGGTTAT 0.910653 -40 GCTTAATGAGAACAGAGGTTTTTAAAACTATG 15 77 0 AACAGGGTTT 0.888515 -183 TATTTTTAAAAAATGGGGTTTTTCGTTTTAAA 15 127 1 AAATGGGTTT 0.840112 -133 CTAAAAATGCTAAAGGTGTTTTTAAAACGAAA 15 147 0 TAAAGTGTTT 0.890793 -113 GAGTTAAGCAAAAAGAGTTCCTTAAGACGCGT 15 187 0 AAAAGGTTCT 0.916923 -73 ATAAAGAAATAAAAGAGTTGTTTTAAAAAGGA 15 233 1 AAAAGGTTTT 0.986434 -27 TCTTCCTTCTTAAAGATGTCTTATTATAGAGC 16 25 0 TAAAGTGTTT 0.890794 -26 AAATCTTAATTAAAGGGGTATTC 18 2 0 TAAAGGGTTT 0.983774 -64 AAAACACTCTAAAAGGGTTATTG 18 53 1 AAAAGGTTTT 0.986841 -13 TATCTTTTATTTAAGGGGTATTG 19 51 1 TTAAGGGTTT 0.737222 -13 TAAAATAAAGCGGTGTCTTTTTTAAGG 20 6 1 TAAAGGGTTC 0.823039 -78 CCTTTATACTAAAAGCGGTTATAAAAAAACAC 20 40 0 AAAAGGGTAT 0.93879 -44 CTATGAAAAGGTTTTCTAAAACTTCAT 21 6 1 AAAAGTTTCT 0.597571 -295 CCCATGCAAAAAAAGATTTTTTTATTAGAAGA 21 129 1 AAAAGTTTTT 0.904504 -172 GCCACTCTTAAAAAGCGTTGTTTGATAAAAAT 24 61 0 AAAAGGTTTT 0.983728 -78 ACCTTGTTCTAATAGTGGTCTTATTCTATCCA 24 105 0 AATAGGGTTT 0.844887 -34 ***** *** ** Masking position 4 Map Score: 47.5726 Number of sites scoring better than the average of aligned sites = 1242 Number in coding regions = 1044 Number in noncoding regions = 198 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 2 TCAGCACTCTTTTTGATGATTTTATAAGCT 1 120 0 TTTTGATGAT 0.718061 -181 TAAAAGGGGAGTTTGAAGACGCT 3 73 1 GTTTGAAGAC 0.799205 -13 CTTTTTAGAATTTTTAAGGAATTTTG 4 7 0 TTTTTAAGGA 0.853459 -56 GCTGTTAGCTTTTTGATAACCAACCATAAA 5 15 1 TTTTGATAAC 0.894356 -150 AACGCCAAGCTTTTTATGGTTGGTTATCAA 5 27 0 TTTTTATGGT 0.749496 -138 GCCTATTCATGTTTGATAAAAACAGAACTA 5 83 1 GTTTGATAAA 0.541537 -82 AAGGATTTTTATAAGGGAGAAAAA 6 6 1 TTTTTATAAG 0.828801 -19 TTTTTTAAATTTTTGAAAACTAGAATTAAA 7 11 1 TTTTGAAAAC 0.90034 -101 TTAAAACCGCTTTTTATAAACTGGAATTAA 7 36 1 TTTTTATAAA 0.791065 -76 ATTTTAAATATTTTTAAAACCTCTTTAAAG 10 23 0 TTTTTAAAAC 0.554704 -50 TTATAAAGAGTTTTGATAGAATACCTTTTT 11 31 1 TTTTGATAGA 0.713961 -58 AGAATACCTTTTTTTAAAAGATGCGTTTTA 11 48 1 TTTTTAAAAG 0.801704 -41 TAAAAGATGCGTTTTAAAACTAATTTTAGG 11 62 1 GTTTTAAAAC 0.492293 -27 TGTTGTAATGTTTTTAAGGTATAATAAACT 12 36 1 TTTTTAAGGT 0.816513 -53 ATAATATTGAGTTTTATAGAAAAAAGAAAT 13 129 0 GTTTTATAGA 0.581063 -42 AGAACAGAGGTTTTTAAAACTATGGTTTCG 15 71 0 TTTTTAAAAC 0.554704 -189 ACAACTTTTATTTTTAAAAAATGGGGTTTT 15 119 1 TTTTTAAAAA 0.494804 -141 GCTAAAGGTGTTTTTAAAACGAAAAACCCC 15 141 0 TTTTTAAAAC 0.554704 -119 GGTTATCCTTTTTAAAACAACTCTTTTA 15 242 0 TTTTTAAAAC 0.554704 -18 AGCGGTGTCTTTTTTAAGGGAGTGTTTTTT 20 19 1 TTTTTAAGGG 0.828212 -65 AGGGAGTGTTTTTTTATAACCGCTTTTAGT 20 35 1 TTTTTATAAC 0.9076 -49 CTTCCTATGTTTTTTAAGGAGCGTTATAAT 21 61 0 TTTTTAAGGA 0.853459 -240 CTGACTCATTTTTTTAAAATACCCCCATTT 21 223 1 TTTTTAAAAT 0.793754 -78 GGTTTTTGAAGGCTTGATTTTTA 23 4 1 TTTTGAAGGC 0.893632 -100 GAAGGCTTGATTTTTAAAGTTAGGCTTAAT 23 18 1 TTTTTAAAGT 0.823864 -86 TTTTTAAAACTCTCTTTAAA 24 1 1 TTTTTAAAAC 0.554704 -138 AAAAAGCGTTGTTTGATAAAAATGGCTCAT 24 54 0 GTTTGATAAA 0.541537 -85 CAAACAACGCTTTTTAAGAGTGGCTCAAGG 24 69 1 TTTTTAAGAG 0.871688 -70 TAGAACAAGGTTTTTATGACGAT 24 126 1 TTTTTATGAC 0.930283 -13 TCCTTAATCATTTTTATGATAAGATAGTCA 26 42 0 TTTTTATGAT 0.809595 -40 ********** Masking position 6 Map Score: 39.7574 Number of sites scoring better than the average of aligned sites = 1756 Number in coding regions = 1349 Number in noncoding regions = 407 Number of orfs with sites within 600 bp upstream = 205 Fraction of orfs with sites within 600 bp upstream = 0.0329264 Motif number 3 GTCTTAAGGCAAAGAAATAAAAAGCAACACCA 1 16 0 AAAGATAAAA 0.841596 -285 AAACCCAATCAAAAAAATAAAGCACAATCTGA 1 164 0 AAAAATAAAG 0.883389 -137 TTTGTGGCGTAAAGATTTTAAATCATCCA 2 8 0 AAAGATTAAA 0.770563 -117 GCCAATTGCTCAAAAGCTAAAAG 3 2 0 CAAAATAAAA 0.600213 -84 TAAAAATTCTAAAAAGATATAATAACACAAAG 4 21 1 AAAAATATAA 0.798758 -42 GTTGGTTATCAAAAAGCTAACAGCGTTT 5 7 0 AAAAATAACA 0.819512 -158 TCTAGTTTTCAAAAATTTAAAAAA 7 3 0 AAAAATAAAA 0.897388 -109 CCTTAATGGCTAAAAAATTAAATTTTTGTATC 7 84 0 TAAAATTAAA 0.874909 -28 CCAATAATCTAAAGATGTTAGGGTAAAATAAC 9 18 1 AAAGATTAGG 0.601657 -101 TATAGAAGTCTAAAATATTACAATCAAGGATA 9 92 1 TAAAATTACA 0.784081 -27 AAGAGGTTTTAAAAATATTTAAAATCATGCTT 10 28 1 AAAAATTTAA 0.71501 -45 AATCATGCTTTAAAAGATTTAATATAAGGGTA 10 50 1 TAAAATTTAA 0.759912 -23 GAGCTTAAAATTTAAGAAAATTATAAA 11 6 1 TAAAATAAGA 0.85174 -83 AGAAAATTATAAAGAGTTTTGATAGAATACCT 11 25 1 AAAGATTTGA 0.441767 -64 ACACATTCAATAAAACTTAACGAGCCTC 12 7 0 TAAAATAACG 0.832673 -82 ATTATACCTTAAAAACATTACAACACATTCAA 12 29 0 AAAAATTACA 0.741614 -60 TTTATAGAAAAAAGAAATATAGCATGTTTAAT 13 115 0 AAAGATATAG 0.67624 -56 TTATTTGCATTAAGAATTAAGGCTAAC 14 65 1 TAAGATAAGG 0.75144 -17 TCCCACCATGTAAAATATAAAGAAATAAAAGA 15 217 1 TAAAATAAAG 0.905526 -43 AAGGCTGAAATAAGAAGTATGGTAAAATATCC 17 11 1 TAAGATATGG 0.578427 -41 ACCCCTTAAATAAAAGATATAATGCTGTATTA 19 38 0 TAAAATATAA 0.833932 -26 TGAAGTTTAATAAAAGGTAAAAATAAGA 21 283 1 TAAAATAAAA 0.917117 -18 AATTTTAACATAAAAGATTAAGCCTAACTTTA 23 32 0 TAAAATTAAG 0.858333 -72 ACGATAAATATAAAATATATAAAATCTCAGAA 23 62 0 TAAAATATAA 0.833932 -42 ACTTTAAACCTAAAACCTAACGATAAATATAA 23 81 0 TAAAATAACG 0.832673 -23 TATCTTAAAGTAAAATTTTAAAGAGAGTTTTA 24 15 0 TAAAATTAAA 0.874909 -124 ***** ***** Masking position 8 Map Score: 19.8428 Number of sites scoring better than the average of aligned sites = 1135 Number in coding regions = 789 Number in noncoding regions = 346 Number of orfs with sites within 600 bp upstream = 223 Fraction of orfs with sites within 600 bp upstream = 0.0358175 Motif number 4 AAATAAAAAGCAACACCACCAAT 1 4 0 CAACACCACC 0.930905 -297 AGCGTCTTCAAACTCCCCTTTTAAACCCT 3 67 0 AAACTCCCCT 0.914062 -19 TAATTGAATGAAACTCCCCCTATCATGCAA 13 31 0 AAACTCCCCC 0.977241 -140 TCTTTTTGCTTAACTCCCACCATGTAAAAT 15 203 1 TAACTCCCAC 0.644549 -57 GAATACCCCTTTAATTAAGA 18 1 1 GAATACCCCT 0.899637 -65 CAATACCCCTTAAATAAAAG 19 54 0 CAATACCCCT 0.969289 -10 GGTTATAAAAAAACACTCCCTTAAAAAAGA 20 26 0 AAACACTCCC 0.894671 -58 ATTAGCGCTACAATACCCCC 20 74 1 CAATACCCCC 0.992213 -10 TTAAGCGCTACAATACCCCCATGCAAAAAA 21 112 1 CAATACCCCC 0.992213 -189 CATTTTTTTAAAATACCCCCATTTCATTGT 21 229 1 AAATACCCCC 0.987704 -72 TATTATAATATAATACCCCCCTAAAAGAAC 25 79 0 TAATACCCCC 0.977301 -49 ********** Masking position 3 Map Score: 15.7167 Number of sites scoring better than the average of aligned sites = 399 Number in coding regions = 346 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 5 TCATTGAACCACTCGTATCTAACAATAAAAATACTGGAAT 1 271 0 TATAAATAAA 0.790798 -30 CACAACACAATTAAGTATTCTTTAGGTATAATCAAAAACTATTTTT 5 114 1 TATTAATCAA 0.858309 -51 TAAACTGGAATTAAAACAAATTAAGCTATAATGATACAAAAATTTA 7 52 1 TATTAATGAA 0.858308 -60 AGACCAATAATCTAAAGATGTTAGGGTAAAATAACATTTTGACAAC 9 15 1 TTTTAATAAA 0.790796 -104 TCTAACTCCCTAGTTTTATTCAATAATATTGAGTTTTA 13 143 0 TATTAATAAA 0.974623 -28 TAAGTCTGTTTGATATTGATTTTATTTGCATTAAGAATTAAGGCTA 14 44 1 TATTATTAAA 0.886766 -38 TTAGGTTTAATTAAATTTCGCTACAATTAAATAAAAACGATAATTT 15 24 0 TATTAATAAA 0.974577 -236 TTTTAAGCAAGTTTGCTCTATAATAAGACATCTTTAAG 16 3 1 TATTAATAAA 0.974624 -48 AATACCCCTTTAATTAAGATTTAATATATAATAATAACTCAAAAAC 18 12 1 TATTAATAAA 0.974623 -54 CGCTCTCGCTTAAAAGGTAATCGTCTTCTAATAAAAAAATCTTTTT 21 138 0 TACTAATAAA 0.848542 -163 ATTCTTTCATGCAAAACCCATTGAAGTTTAATAAAAGGTAAAAATA 21 262 1 GATTAATAAA 0.848542 -39 TAAAAATGGCTCATTATATGGTATCTTAAAGTAAAATTTTAAAGAG 24 22 0 TATTAGTAAA 0.868303 -117 TAAGAGTGGCTCAAGGGCTAATTGGATAGAATAAGACCACTATTAG 24 83 1 TATTAATAAA 0.974623 -56 GGGTATTATATTATAATAAGATAAATTTGATTAATAAGGATGCAAG 25 91 1 TATTATTAAA 0.886588 -37 * * * * ***** * Masking position 20 Map Score: 12.8911 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 21 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 TCGCGCCAAAAAACCCAATCAAAAAAATAAAG 1 174 0 AAACCCATAA 0.981138 -127 TAGATATTTTAAACCCTTTAAAGAGAAAGCAT 2 75 1 AAACCCTTAA 0.981138 -50 CTCCCCTTTTAAACCCTTTAAATCCCACTTTT 3 52 0 AAACCCTTAA 0.981138 -34 AGAACTACCACAACACAATTAAGTATTCTTTA 5 106 1 CAACACATAA 0.920089 -59 AAAAACATTACAACACATTCAATAAAACTTAA 12 19 0 CAACACATAA 0.920089 -70 ACAAATCGCTAAAGCCTCTAAATTAATTGAAT 13 52 0 AAAGCCTTAA 0.895934 -119 AATAACTCAAAAACACTCTAAAAGGGTTATTG 18 44 1 AAACACTTAA 0.953124 -22 CTTTCATGCAAAACCCATTGAAGTTTAATAAA 21 265 1 AAACCCATAA 0.981138 -36 ******* * ** Masking position 3 Map Score: 7.97041 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 95 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 CAGCACTCTTTTTGATGATTTTATAAGCTTT 1 118 0 TTTATGATTT 0.511398 -183 TGTGCTTTATTTTTTTGATTGGGTTTTTTGG 1 170 1 TTTTTGATTG 0.911663 -131 TTATTATATCTTTTTAGAATTTTTAAGGAAT 4 15 0 TTTTAGAATT 0.695715 -48 TATTAAATCTTTTAAAGCATGATTTTAAATA 10 43 0 TTTAAGCATG 0.644307 -30 CTCGTTAAGTTTTATTGAATGTGTTGTAATG 12 15 1 TTTTTGAATG 0.934243 -74 GGTTGCAAACTTTATTGCTTGACTTAAAAAG 12 66 0 TTTTTGCTTG 0.942916 -23 TCTTTGAGCATTTCTTGCATGATAGGGGGAG 13 17 1 TTTTTGCATG 0.957877 -154 AGCCTCTAAATTAATTGAATGAAACTCCCCC 13 41 0 TTATTGAATG 0.760951 -130 CGATTATTACTTTATTGCTTTATTTAGATAC 13 82 0 TTTTTGCTTT 0.882032 -89 GATATTGATTTTATTTGCATTAAGAATTAAG 14 55 1 TTATTGCATT 0.697538 -27 ACCTTTAGCATTTTTAGATTTGATCACGCGT 15 162 1 TTTTAGATTT 0.624179 -98 AAAAAAATCTTTTTTTGCATGGGGGTATTGT 21 121 0 TTTTTGCATG 0.957877 -180 *** ******* Masking position 2 Map Score: 8.53811 Number of sites scoring better than the average of aligned sites = 472 Number in coding regions = 429 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 8 ACTATGGAAGAACGCTTTATTCCAGTATTT 1 253 1 AACGCTTTAT 0.751126 -48 ACGCCACAAAAACGCTTTATTTATGGATTT 2 30 1 AACGCTTTAT 0.751126 -95 TAGAATTTTTAAGGAATTTTG 4 2 0 AAGGAATTTT 0.607765 -61 AAGGATTTTTATAAGGGAGA 6 1 1 AAGGATTTTT 0.782235 -24 CATGTTTAATAACGATTATTACTTTATTGC 13 95 0 AACGATTATT 0.82156 -76 CTTACATTCTAGCGCAAATTTTAGTAAAAT 14 18 0 AGCGCAAATT 0.78214 -64 ATTAAATAAAAACGATAATTTTAGAGAGAT 15 15 0 AACGATAATT 0.866553 -245 ATTTAATTGTAGCGAAATTTAATTAAACCT 15 38 1 AGCGAAATTT 0.779143 -222 CCTTATTAAAAAGGATATTTTACCATACTT 17 25 0 AAGGATATTT 0.835155 -27 CCTTTTTAATAAGGATATTTA 17 41 1 AAGGATATTT 0.835155 -11 GGGGTATTGTAGCGCTAATTGCCTTTATAC 20 63 0 AGCGCTAATT 0.892736 -21 AAACGAACGAAGCGCAATTTTATGAAGTTT 21 29 0 AGCGCAATTT 0.835078 -272 GGGGTATTGTAGCGCTTAATGAGCGGGCTT 21 101 0 AGCGCTTAAT 0.656459 -200 CCTAAAACCTAACGATAAATATAAAATATA 23 75 0 AACGATAAAT 0.677707 -29 TTTATCAAACAACGCTTTTTAAGAGTGGCT 24 64 1 AACGCTTTTT 0.903104 -75 GAGTGGCTCAAGGGCTAATTGGATAGAATA 24 86 1 AGGGCTAATT 0.821555 -53 ACATTGACTTAAGGAAATTTAATTG 26 6 0 AAGGAAATTT 0.686067 -76 ********** Masking position 1 Map Score: 13.8234 Number of sites scoring better than the average of aligned sites = 1285 Number in coding regions = 1125 Number in noncoding regions = 160 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 9 TGAAATGAATGTTTTAATCAGATTGTGCTTTA 1 147 1 GTTTAATCAA 0.944222 -154 TATGGCATTAGATTTAAGTAAATACACTATGG 1 228 1 GTTTAAGTAA 0.912074 -73 TGGTAGTTCTGTTTTTATCAAACATGAATAGG 5 84 0 GTTTTATCAA 0.824735 -81 GTATTCTTTAGGTATAATCAAAAACTATTTTT 5 128 1 GTATAATCAA 0.682631 -37 ATAAAAAGCGGTTTTAATTCTAGTTTTCAAAA 7 21 0 GTTTAATTCA 0.912074 -91 AGCTTAATTTGTTTTAATTCCAGTTTATAAAA 7 47 0 GTTTAATTCA 0.912074 -65 TTACTTTATTGCTTTATTTAGATACAAATCGC 13 75 0 GTTTATTTAA 0.77448 -96 GTTTCGTTTAGGTTTAATTAAATTTCGCTACA 15 45 0 GTTTAATTAA 0.964321 -215 TTATAAGCTAGTTTTAATTACAATTTTCAA 19 9 0 GTTTAATTAA 0.964321 -55 TTTTATAACCGCTTTTAGTATAAAGGCAATTA 20 46 1 GTTTTAGTAA 0.742503 -38 CGCTTCGTTCGTTTTCATTATAACGCTCCTTA 21 45 1 GTTTCATTAA 0.863293 -256 * ******** * Masking position 12 Map Score: 8.31921 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 75 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 10 TTTATTTCTTTGCCTTAAGACAAACCATAG 1 27 1 TGCCTTAAGA 0.864548 -274 GACTTAGACTTAGCTTAAGAGTTCCTGAAT 1 77 0 TAGCTTAAGA 0.870309 -224 TTTTAGCCAATTGCTCAAAAGCTAAAAG 3 9 0 TTGCTCAAAA 0.721478 -77 TTTGAGCAATTGGCTAAAAAATACAGATAT 3 20 1 TGGCTAAAAA 0.791932 -66 CAAAATTCCTTAAAAATTCTAAAAA 4 6 1 TTCCTTAAAA 0.886808 -57 TTTTTGATTATACCTAAAGAATACTTAATT 5 122 0 TACCTAAAGA 0.613016 -43 TTTTTCTCCCTTATAAAAATCCTT 6 9 0 TCCCTTATAA 0.588051 -16 TTTTCCTTAATGGCTAAAAAATTAAATTTT 7 90 0 TGGCTAAAAA 0.791932 -22 GAGCTTAAAATTTAAGAAAA 11 1 1 GAGCTTAAAA 0.608661 -88 GAGTTTATTATACCTTAAAAACATTACAAC 12 37 0 TACCTTAAAA 0.919808 -52 CTTTATTGCTTGACTTAAAAAGAGTTTATT 12 58 0 TGACTTAAAA 0.709892 -31 GCAAAAAGAGTTCCTTAAGACGCGTGATCA 15 182 0 TTCCTTAAGA 0.800955 -78 TAGAGCAAACTTGCTTAAAA 16 1 0 TTGCTTAAAA 0.899236 -50 TATATAATAATAACTCAAAAACACTCTAAA 18 36 1 TAACTCAAAA 0.395987 -30 TAATTAAAACTAGCTTATAATACAGCATTA 19 21 1 TAGCTTATAA 0.663449 -43 AAAAAAACACTCCCTTAAAAAAGACACCGC 20 20 0 TCCCTTAAAA 0.904406 -64 CTTAACGCTCTCGCTTAAAAGGTAATCGTC 21 159 0 TCGCTTAAAA 0.915087 -142 ********** Masking position 5 Map Score: 15.0712 Number of sites scoring better than the average of aligned sites = 482 Number in coding regions = 382 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 11 TGAAATGAATGTTTTAATCAGATTGTGCTT 1 147 1 GTTTTAATCA 0.952361 -154 CAACTTCATCGTTTAAATCCATAAATAAAG 2 44 0 GTTTAAATCC 0.666976 -81 TGGTAGTTCTGTTTTTATCAAACATGAATA 5 86 0 GTTTTTATCA 0.781789 -79 ATAAAAAGCGGTTTTAATTCTAGTTTTCAA 7 23 0 GTTTTAATTC 0.929253 -89 AGCTTAATTTGTTTTAATTCCAGTTTATAA 7 49 0 GTTTTAATTC 0.929253 -63 TAACTCCCTAGTTTTATTCAATAATATTGA 13 149 0 GTTTTATTCA 0.737744 -22 GTTTCGTTTAGGTTTAATTAAATTTCGCTA 15 47 0 GGTTTAATTA 0.793737 -213 AAAAACCTCTGTTCTCATTAAGCGCGAATA 15 86 1 GTTCTCATTA 0.652908 -174 TTATAAGCTAGTTTTAATTACAATTTTCAA 19 11 0 GTTTTAATTA 0.948594 -53 CGCTTCGTTCGTTTTCATTATAACGCTCCT 21 45 1 GTTTTCATTA 0.900199 -256 ********** Masking position 3 Map Score: 4.79033 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 92 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 ATCTTTTTAGAATTTTTAAGGAATTTTG 4 5 0 AATTTTTGAT 0.785863 -58 AACACAAAGAAATTTTAAGAGTAAAAAGC 4 44 1 AATTTTAAAA 0.861823 -19 TTTTTTAAATTTTTGAAAACTAGAATTAAAA 7 8 1 AATTTTTACT 0.406938 -104 TAAAAAATTAAATTTTTGTATCATTATAGCTTAA 7 72 0 AATTTTTAAT 0.852257 -40 ACAAAAATTTAATTTTTTAGCCATTAAGGAAAAA 7 87 1 AATTTTTGAT 0.785865 -25 AGAAGTCTAAAATATTACAATCAAGGATAGAACG 9 95 1 AATATTAAAA 0.32066 -24 GAGCTTAAAATTTAAGAAAATTATAAAGAGT 11 8 1 AAATTTAAAT 0.522431 -81 TTTTAAAACTAATTTTAGGAGTATCC 11 73 1 AATTTTAAAT 0.935314 -16 TTCTAGCGCAAATTTTAGTAAAATACGCATC 14 8 0 AATTTTAAAT 0.935306 -74 TAAAAACGATAATTTTAGAGAGATTGGC 15 5 0 AATTTTAGAT 0.901952 -255 GTTTTTATTTAATTGTAGCGAAATTTAATTAAAC 15 32 1 AATTGTAGAT 0.507829 -228 CGACAACTTTTATTTTTAAAAAATGGGGTTTTTC 15 117 1 TATTTTTAAT 0.448137 -143 AACGAAGCGCAATTTTATGAAGTTTTAGAAAACC 21 20 0 AATTTTAATT 0.537127 -281 GAAATGGGGGTATTTTAAAAAAATGAGTCAGTCA 21 220 0 TATTTTAAAT 0.669649 -81 TGCATGAAAGAATTTTACAATGAAATGGGGGTAT 21 241 0 AATTTTAAAA 0.861823 -60 AAAATCTCAGAATTTTAACATAAAAGATTAAGCC 23 40 0 AATTTTAAAA 0.861815 -64 CTTAAAGTAAAATTTTAAAGAGAGTTTTAAAAA 24 10 0 AATTTTAGAG 0.591988 -129 TAATAAGATAAATTTGATTAATAAGGATGCAAGT 25 104 1 AATTTGAAAA 0.41162 -24 ******* * ** Masking position 2 Map Score: 8.22007 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 220 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 13 CCTCTGTTCTCATTAAGCGCGAATAACGAC 15 91 1 CATTAAGCGC 0.980716 -169 AGTATAAAGGCAATTAGCGCTACAATACCC 20 62 1 CAATTAGCGC 0.980716 -22 AAAGCCCGCTCATTAAGCGCTACAATACCC 21 100 1 CATTAAGCGC 0.980716 -201 TTATTCTATCCAATTAGCCCTTGAGCCACT 24 87 0 CAATTAGCCC 0.949929 -52 ********** Masking position 6 Map Score: 1.09935 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 28 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 14 GGTGTTGCTTTTTATTTCTTTGCCTTAAGA 1 17 1 TTTATTTCTT 0.695354 -284 CAGATTGTGCTTTATTTTTTTGATTGGGTT 1 165 1 TTTATTTTTT 0.923782 -136 TTTGTATATCTGTATTTTTTAGCCAATTGC 3 25 0 TGTATTTTTT 0.823064 -61 TGTTGTGGTAGTTCTGTTTTTATCAAACAT 5 91 0 GTTCTGTTTT 0.565571 -74 ATACAAAAATTTAATTTTTTAGCCATTAAG 7 85 1 TTAATTTTTT 0.606302 -27 GCGTTCTTTTTTTATGCGTTAT 8 17 0 GTTCTTTTTT 0.861927 -12 ACATGCTATATTTCTTTTTTCTATAAAACT 13 120 1 TTTCTTTTTT 0.94208 -51 AACGACAACTTTTATTTTTAAAAAATGGGG 15 115 1 TTTATTTTTA 0.606302 -145 CTTTTATTTCTTTATATTTTACATGGTGGG 15 218 0 TTTATATTTT 0.630374 -42 AATAAAGCGGTGTCTTTTTTAAGGGAGTGT 20 14 1 TGTCTTTTTT 0.861927 -70 GACTTTTCTTTTTTCATGGCTTGT 22 13 0 TTTCTTTTTT 0.94208 -14 ********** Masking position 5 Map Score: 5.40568 Number of sites scoring better than the average of aligned sites = 364 Number in coding regions = 278 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 15 ********** No masking Map Score: 8.47978e-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