AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00400_hpyl_reg_300.orf -o00400_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 HP0153 98 recombinase (recA) #2 HP0282 50 H. pylori predicted coding region HP0282 #3 HP0289 66 toxin-like outer membrane protein #4 HP0290 47 diaminopimelate decarboxylase (dap decarboxylase) (lysA) #5 HP0403 80 phenylalanyl-tRNA synthetase, alpha subunit (pheS) #6 HP0654 296 conserved hypothetical protein #7 HP0655 82 protective surface antigen D15 #8 HP0774 23 tyrosyl-tRNA synthetase (tyrS) #9 HP0777 107 uridine 5'-monophosphate (UMP) kinase (pyrH) #10 HP0778 127 H. pylori predicted coding region HP0778 #11 HP1038 128 3-dehydroquinase type II (aroQ) #12 HP1039 30 H. pylori predicted coding region HP1039 #13 HP1040 140 ribosomal protein S15 (rps15) #14 HP1253 31 tryptophanyl-tRNA synthetase (trpS) #15 HP1254 116 biotin synthesis protein (bioC) #16 HP1279 300 anthranilate isomerase (trpC) #17 HP1282 222 anthranilate synthase component I (trpE) #18 HP1283 97 H. pylori predicted coding region HP1283 #19 HP1284 69 conserved hypothetical protein #20 HP1285 169 conserved hypothetical secreted protein #21 HP1360 28 4-hydroxybenzoate octaprenyltransferase (ubiA) #22 HP1361 56 competence locus E (comE3) #23 HP1365 83 response regulator #24 HP1368 300 type IIS restriction enzyme M2 protein (mod) #25 HP1378 300 competence lipoprotein (comL) #26 HP1379 41 ATP-dependent protease (lon) #27 HP1380 38 prephenate dehydrogenase (tyrA) Motif number 1 CCTAAAATCTATTATAATAAAAGGACTTACC 1 32 0 ATTATATAAA 0.845296 -67 TGATTTGTTTATTCTATCAAATCCTAGCCTA 1 59 0 ATTCTACAAA 0.880974 -40 TGATTACGCCATTATATCCAAGATTAAGGCT 2 17 0 ATTATACCAA 0.767231 -34 CTCTCATTTGATTAAATCAAAGGGA 3 5 0 ATTAAACAAA 0.51029 -62 TGAACGAAGCATTATAGCAAAAAAG 4 5 0 ATTATACAAA 0.966535 -43 CTTATATTTTATTTTTAAAAAGCTATAATAC 5 52 0 ATTTTTAAAA 0.758355 -29 TTGTCCCATAATTATAGCATAAATGATAATG 6 36 1 ATTATACATA 0.865548 -261 GAGTATGAAAATTTTTAAAAATTTACAAAAA 6 80 1 ATTTTTAAAA 0.758355 -217 GTTCTTTCTCATTTTTGTAAATTTTTAAAAA 6 91 0 ATTTTTTAAA 0.522061 -206 TAAAGCTTAGATTTTATCATAAAAATCTATT 6 139 1 ATTTTACATA 0.819357 -158 CTTTTTACATATTATATAAAAATATCCCCTT 6 217 0 ATTATAAAAA 0.940353 -80 ATAACTAATCATTCTTAAAAACGCTAAAAAT 7 13 0 ATTCTTAAAA 0.533901 -70 TAGTAGCGTTATTATAACTAATCATTCTTAA 7 26 0 ATTATACTAA 0.799028 -57 AATTAATAAAATTTTAATAAAACTTGTGATT 9 73 0 ATTTTATAAA 0.793658 -35 CGTTTGCCCCATGATAACAAAACTCTTTTTA 10 50 1 ATGATACAAA 0.814174 -78 ATGAGACCACATTATAGCATAAGTTTTTATC 11 81 0 ATTATACATA 0.865548 -48 TTTTAGGCTTATTATAATATAAAGTTTAAGC 13 51 1 ATTATATATA 0.549306 -90 GTTTAAGCGTATGATACAAAAAAGCTTATTT 13 74 1 ATGATAAAAA 0.70516 -67 ATCAAGCGTGATTTTTTCTAAATTTTAGGCA 15 23 0 ATTTTTCTAA 0.442655 -94 TTCTTAGCAAATTTTAGATAAGATCAAGCGT 15 45 0 ATTTTAATAA 0.604609 -72 TCAATCTGTAATTCTTTCAAATCATAGGGGG 16 71 0 ATTCTTCAAA 0.677262 -230 GTGTTTAGATATTTTAGAAAATAAAGGCAAG 16 126 1 ATTTTAAAAA 0.917411 -175 ATGTCTTGGAATTTTTGAAAACGCTCACTCA 17 133 1 ATTTTTAAAA 0.759 -90 ATAAACTCGTATTTTACAAGAAATAGATAAA 17 183 0 ATTTTAAAGA 0.671298 -40 CGAATGTGTGATTATAGTAGAAAGTCTCTTA 18 17 0 ATTATATAGA 0.501325 -81 TTTTTGTCATGTTTTAGCAAAAATCGTTCTT 19 27 0 GTTTTACAAA 0.806818 -43 GATTTTTTGTATTATACCTTAAAACAGATGA 20 84 0 ATTATACTTA 0.469825 -86 AGGTGTTGTTATGATAAAAAAGACCTTTGCA 20 125 1 ATGATAAAAA 0.705154 -45 ACTAAAAGCGGTTATAAAAAAACACTCCCTT 23 34 0 GTTATAAAAA 0.763848 -50 ATTTTATGAAGTTTTAGAAAACCTTTTCATA 24 12 0 GTTTTAAAAA 0.695104 -289 CATAGGAAGTATTATAACAAAGCCCGCTCAT 24 82 1 ATTATACAAA 0.966534 -219 AAATGGGGGTATTTTAAAAAAATGAGTCAGT 24 222 0 ATTTTAAAAA 0.91719 -79 GCGAAAATTGATTTTACCAAAATTGTTTG 25 9 0 ATTTTACAAA 0.953161 -292 AGTTATTGGGATTATATCCAAAACTAGCGAA 25 35 0 ATTATACCAA 0.767231 -266 TAACCGAATCATTATAAAATATAATAAGGAG 25 83 1 ATTATAAATA 0.778471 -218 ATAACCATGAGTTATTCAAAAATTTAACTTT 25 266 1 GTTATTAAAA 0.478458 -35 AACCATACACATTATAACAGAGAGATGAAAA 26 21 1 ATTATACAGA 0.841521 -21 ****** **** Masking position 2 Map Score: 34.6169 Number of sites scoring better than the average of aligned sites = 692 Number in coding regions = 494 Number in noncoding regions = 198 Number of orfs with sites within 600 bp upstream = 209 Fraction of orfs with sites within 600 bp upstream = 0.0335689 Motif number 2 TATCAAATCCTAGCCTAAAATCTATTATAATAAA 1 42 0 TGCCTAAAAA 0.820936 -57 ACTTCCTAAAAAATGATTACGCCATT 2 35 0 TCCTAAAAAA 0.857866 -16 ATAAAAGAAAAACCTTAAAAGGGAGCAAAAAAGC 5 11 0 ACCTTAAAAA 0.963819 -70 CTTAGATTTTATCATAAAAATCTATTTAATGAGA 6 144 1 ACATAAAAAA 0.776277 -153 TACAATGTTTATCTTTAAAACGAAAGGGCAATTT 6 269 1 ACTTTAAAAA 0.601388 -28 CATTCTTAAAAACGCTAAAAATTA 7 1 0 ACGCTAAAAA 0.631455 -82 CTGAGAATGTAGGCTTAAAATTCAGAAAGGGTGT 9 18 1 AGCTTAAAAA 0.926584 -90 CCCCTTAAATCCCCCTAAGAACGAATCACAAGAA 11 44 0 CCCCTAAGAA 0.682882 -85 TTTAAGGGGTAAGATAAAAACTTATGCTATAATG 11 69 1 AGATAAAAAA 0.621556 -60 AAACTCGCCACACCCTAAAACCGATAAAAA 12 7 0 CCCCTAAAAA 0.888757 -24 TATTATAATAAGCCTAAAAAGACAAACCACCTAC 13 36 0 ACCTAAAAAA 0.927173 -105 GATTCCTTAAATGCCTAAAATTTAGAAAAAATCA 15 12 1 AGCCTAAAAA 0.906286 -105 TTGCTAAGAATACACTAAAATTTAGTTTTAATTT 15 66 1 TCACTAAAAA 0.725263 -51 TTAAGCCATAAAGCTAAAGATTTAAAAGAGGGTG 16 205 1 AGCTAAAGAA 0.618941 -96 AGATTGTAAAAGCATAAAAAGGAATTTTCTAACC 17 47 1 ACATAAAAAA 0.776277 -176 CAATTTCTTTACGCTAAAAATAAACTCGTATTTT 17 199 0 AGCTAAAAAA 0.857674 -24 AATCCACGCAAACATTAAGAATAAACGAATGTGT 18 39 0 ACATTAAGAA 0.662021 -59 TACATTGTTGAACACTAAAAAATAGGAGCTGTTT 18 74 1 ACACTAAAAA 0.847755 -24 TTTTGTATTATACCTTAAAACAGATGATTAGGAG 20 77 0 TCCTTAAAAA 0.926689 -93 AAAAAAACACTCCCTTAAAAAAGACACCGCTTTA 23 16 0 TCCTTAAAAA 0.926689 -68 CATTATAACGCTCCTTAAAAAACATAGGAAGTAT 24 60 1 CCCTTAAAAA 0.912486 -241 CTTAACGCTCTCGCTTAAAAGGTAATCGTCTTCT 24 155 0 TGCTTAAAAA 0.854723 -146 * ******** * Masking position 7 Map Score: 21.2667 Number of sites scoring better than the average of aligned sites = 835 Number in coding regions = 707 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 3 GTTGTATTATAGCTTTTTAAAAATAAAATA 5 49 1 AGCTTTTTAA 0.686198 -32 ATAAAATCTAAGCTTTATCAAGCCATTAGC 6 126 0 AGCTTTATCA 0.635314 -171 TAAACATTGTAGCATTTTTAGATTTAAGAA 6 250 0 AGCATTTTTA 0.750551 -47 TAATTTTTAGCGTTTTTAAGAATGATTA 7 9 1 AGCGTTTTTA 0.978578 -74 TGTTGTTAGTAGCGTTATTATAACTAATCA 7 33 0 AGCGTTATTA 0.959229 -50 TTTTAGCTTGAGTGTTGTTAGTAGCGTTAT 7 45 0 AGTGTTGTTA 0.932372 -38 ATTCAGAAAGGGTGTTTTTAAGCAAGATTA 9 37 1 GGTGTTTTTA 0.869026 -71 TACAATCACAAGTTTTATTAAAATTTTATT 9 70 1 AGTTTTATTA 0.772596 -38 AAGTAAAAAGAGTTTTGTTATCATGGGGCA 10 54 0 AGTTTTGTTA 0.81392 -74 AAAGCACTCAAGCGTGTTTAGATATTTTAG 16 113 1 AGCGTGTTTA 0.836704 -188 CTAATGAGTGAGCGTTTTCAAAAATTCCAA 17 138 0 AGCGTTTTCA 0.914247 -85 CTCACTCATTAGCGTATTTATTGCCCATTT 17 156 1 AGCGTATTTA 0.775639 -67 CTGTATAGTTAGCGTTTTTAATTCAAAATG 20 24 0 AGCGTTTTTA 0.978578 -146 GATGATTAGGAGTGTTTTTACCATTAACCG 20 59 0 AGTGTTTTTA 0.954112 -111 CCATTAGGTAGGTGTTGTTATGATAAAAAA 20 116 1 GGTGTTGTTA 0.8148 -54 CCTTTGCATCAGTTTTATTAGGATTGAGTT 20 148 1 AGTTTTATTA 0.772596 -22 TTTTTAAGGGAGTGTTTTTTTATAACCGCT 23 29 1 AGTGTTTTTT 0.598005 -55 TTTTTTAAGGAGCGTTATAATGAAAACGAA 24 52 0 AGCGTTATAA 0.780213 -249 TTAATGAGCGGGCTTTGTTATAATACTTCC 24 86 0 GGCTTTGTTA 0.754097 -215 ********** Masking position 5 Map Score: 20.8181 Number of sites scoring better than the average of aligned sites = 1354 Number in coding regions = 1167 Number in noncoding regions = 187 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 4 AGTAAAATCCTTTTGTGATAGGGTAA 1 5 1 AAATCTTTGT 0.74702 -94 GTGATAGGGTAAGTCCTTTTATTATAATAGAT 1 25 1 AAGTCTTTAT 0.866513 -74 TAAATTACCTTATTGAATTTGAT 1 86 0 AAATTCTTAT 0.806157 -13 TCTTTTATTAAAGTTGTATTATAGCTTTTTAA 5 37 1 AAGTTTTTAT 0.673144 -44 TCTCCTTTTTAAATCGCATTATTGACTAATGC 10 12 1 AAATCCTTAT 0.928991 -116 CCATGATAACAAAACTCTTTTTACTTTTAGTT 10 58 1 AAAACCTTTT 0.609424 -70 TTAAAATCCTTTTTTGTATCGCATG 10 113 0 AAATCTTTTT 0.934024 -15 ATGATACAAAAAAGCTTATTTTACGCTATAAT 13 84 1 AAAGCTTTTT 0.906689 -57 TCATACTCTAAAATTCCGTTATTTTTCAATTC 16 13 0 AAATTCTTAT 0.806153 -288 TTTAAAAACCAAAGCGCCTTATGCGCATTTGC 16 258 1 AAAGCCTTAT 0.900168 -43 GGTGGTTAGAAAATTCCTTTTTATGCTTTTAC 17 52 0 AAATTCTTTT 0.823295 -171 CACCAAATTGAAAGCTTCTTTTCGCACAACCA 17 83 1 AAAGCTTTTT 0.90688 -140 GCTAAAAATAAACTCGTATTTTACAAGAAATA 17 189 0 AACTCTTTTT 0.67369 -34 ATTATAGTAGAAAGTCTCTTATCAAAT 18 6 0 AAAGTTTTAT 0.733916 -92 AACTGATGCAAAGGTCTTTTTTATCATAACAA 20 130 0 AAGGTTTTTT 0.613475 -40 AAAAGTCATTTTATTAGGGATCAA 21 3 1 AAGTCTTTAT 0.866513 -26 TCTAATAAAAAAATCTTTTTTTGCATGGGGGT 24 126 0 AAATCTTTTT 0.934024 -175 TAATCCCAGTAAATCTCATTTTAGCGGTAGGT 25 153 1 AAATCCTTTT 0.936043 -148 ***** * **** Masking position 9 Map Score: 16.085 Number of sites scoring better than the average of aligned sites = 646 Number in coding regions = 521 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 5 GATATAATGGCGTAATCATTTTTTAGGAAGT 2 30 1 CTAATCATTT 0.769897 -21 TCCCTTTGATTTAATCAAATGA 3 2 1 CCTTTGATTT 0.849224 -65 TAGCCAAAAACTCTCTCATTTGATTAAATCA 3 17 0 CCTCTCATTT 0.979593 -50 TAAATGCTACCCTCTCATTTCCTAGATAGT 3 47 0 CCTCTCATTT 0.979593 -20 TTTACTTTTTCATTATCATTTATGCTATAAT 6 46 0 CTTATCATTT 0.893467 -251 AAAATTTTCATACTCTCATTTACTTTTTCAT 6 64 0 TCTCTCATTT 0.691553 -233 AGCCGGTGTTCTTTCTCATTTTTGTAAATTT 6 98 0 CTTCTCATTT 0.954762 -199 GGTTAAATTGCCCTTTCGTTTTAAAGATAAA 6 276 0 CCTTTCGTTT 0.92387 -21 GATCCCTTCTCATTAATTAATAAAA 9 93 0 CTTCTCATTA 0.820239 -15 TGACTAATGCCCTAATCGTTTGCCCCATGAT 10 34 1 CTAATCGTTT 0.680376 -94 TGATTTGCCCCCCTATGATTTGAAAGAATTA 16 63 1 CCTATGATTT 0.849224 -238 GCGCATAAGGCGCTTTGGTTTTTAAATGCTC 16 253 0 CCTTTGGTTT 0.781819 -48 GGCTTAGCCTTATGATTTTTTGCAAATG 16 283 0 CTTATGATTT 0.712349 -18 TTTGAAAACGCTCACTCATTAGCGTATTTAT 17 146 1 CCACTCATTA 0.805457 -77 ACTATAATCACACATTCGTTTATTCTTAATG 18 30 1 CCATTCGTTT 0.828809 -68 GCGCTTCGTTCGTTTTCATTATAACGCTCCT 24 44 1 CTTTTCATTA 0.644534 -257 AACTCCTTAACGCTCTCGCTTAAAAGGTAAT 24 163 0 CCTCTCGCTT 0.774032 -138 ATTGCCTTGACTGACTCATTTTTTTAAAATA 24 213 1 CGACTCATTT 0.691013 -88 * ********* Masking position 6 Map Score: 14.9725 Number of sites scoring better than the average of aligned sites = 420 Number in coding regions = 371 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 GCTTTTTTGCTCCCTTTTAA 5 1 1 GCTTTTTTGC 0.967449 -80 TTAAAATCCTTTTTTGTATCGCATGGT 10 111 0 CCTTTTTTGT 0.816112 -17 CGTAAAATAAGCTTTTTTGTATCATACGCT 13 79 0 GCTTTTTTGT 0.958481 -62 ACGCTTGAGTGCTTTCTTGTGCGTTTTCAA 16 98 0 GCTTTCTTGT 0.967449 -203 TTAGCCTTATGATTTTTTGCAAATGCGCAT 16 278 0 GATTTTTTGC 0.906898 -23 CCCATTTATCTATTTCTTGTAAAATACGAG 17 179 1 TATTTCTTGT 0.690208 -44 ACCTAATGGGGATTTTTTGTATTATACCTT 20 95 0 GATTTTTTGT 0.88326 -75 ATTGTAAAATTCTTTCATGCAAAACCCATT 24 254 1 TCTTTCATGC 0.734444 -47 AATAATGCCTGCTTTCATGCCAAATT 27 7 0 GCTTTCATGC 0.923598 -32 ********** Masking position 5 Map Score: 6.0059 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 234 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 7 AGGGTAAGTCCTTTTATTATAATAGATTTTA 1 30 1 CTTTATTATA 0.745575 -69 CTTTTTTGCTATAATGCTTCGTT 4 3 1 TTTTGCTATA 0.933338 -45 TAAGGTTTTTCTTTTATTAAAGTTGTATTAT 5 28 1 CTTTATTAAA 0.66512 -53 TTCATTATCATTTATGCTATAATTATGGGAC 6 38 0 TTTTGCTATA 0.933335 -259 AAGATAAAAACTTATGCTATAATGTGGTCTC 11 79 1 CTTTGCTATA 0.894325 -50 ACGCTTAAACTTTATATTATAATAAGCCTAA 13 53 0 TTTTATTATA 0.828993 -88 AAAAGCTTATTTTACGCTATAATGCGAACTT 13 93 1 TTTCGCTATA 0.855484 -48 TCAAGCGTGATTTTTTCTAAATTTTAGGCAT 15 22 0 TTTTTCTAAA 0.551701 -95 CAATTTCTTTACGCTAAAAATAAACTCG 17 205 0 TTTCGCTAAA 0.800366 -18 GATAAGAGACTTTCTACTATAATCACACATT 18 15 1 TTTTACTATA 0.92013 -83 ATAAGAACGATTTTTGCTAAAACATGACAAA 19 25 1 TTTTGCTAAA 0.904664 -45 ATGGGGATTTTTTGTATTATACCTTAAAACA 20 89 0 TTTTATTATA 0.829004 -81 GCTAATTGCCTTTATACTAAAAGCGGTTATA 23 49 0 TTTTACTAAA 0.885901 -35 GCTTCGTTCGTTTTCATTATAACGCTCCTTA 24 46 1 TTTCATTATA 0.67211 -255 TTATTTTTACCTTTTATTAAACTTCAATGGG 24 278 0 CTTTATTAAA 0.66512 -23 *** ******* Masking position 9 Map Score: 14.6869 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 80 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 8 CCTATTGATGCCAACCCCTTTTTTTACCTAAT 6 178 0 CCACCCTTTT 0.881171 -119 ATCACAAGAAACTACCGCTTGACTAATGTCAA 11 22 0 ACACCCTTGA 0.804976 -107 AACGACCTCCTAATTGGTAATTT 13 128 0 ACACCCCTAA 0.945739 -13 ACCACCGCCTTTAACGCACCAC 15 105 0 ACACCCCTTT 0.976017 -12 CACATTCGCCACAACCACCATTGTATGCGAAT 16 158 0 ACACCCCATT 0.967279 -143 AGTCATGCTCACACCCTCTTTTAAATCTTTAG 16 218 0 ACCCCCTTTT 0.786012 -83 GAATTTTCTAACCACCACCAAATTGAAAGCTT 17 68 1 ACACCCCAAA 0.926798 -155 TTCTTTTCGCACAACCACATTTTTAAGAGAGC 17 98 1 ACACCCATTT 0.84073 -125 TGAACTTCTTACGACCCCCAAAGAATACCTG 22 36 1 ACACCCCAAA 0.926798 -21 GTGTTTTTTTATAACCGCTTTTAGTATAAAGG 23 40 1 ATACCCTTTT 0.627536 -44 ATTTTTTTAAAATACCCCCATTTCATTGTAAA 24 230 1 AAACCCCATT 0.699632 -71 AAAGACGCCACCTACCGCTAAAATGAGATTTA 25 162 0 CCACCCTAAA 0.697614 -139 ** *** ***** Masking position 6 Map Score: 5.90752 Number of sites scoring better than the average of aligned sites = 268 Number in coding regions = 231 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 9 CGTTTAAGCCTTAATCTTGGATATA 2 6 1 AAGCCTTAAT 0.849566 -45 ACTGATTTCCTTAATAGATTTTAGC 7 68 0 TTTCCTTAAT 0.880176 -15 GTTCATTCCTTAATTAGGGCTTA 8 10 0 ATTCCTTAAT 0.933342 -14 TTATTGACTAATGCCCTAATCGTTTGCCCC 10 30 1 ATGCCCTAAT 0.893279 -98 TCTAAAATCAATGCCTTAATCTGGTAGGTG 13 13 1 ATGCCTTAAT 0.972844 -128 TGATTCCTTAAATGCCTAAAAT 15 3 1 ATTCCTTAAA 0.815671 -114 ATGCGAATCCTTGCCTTTATTTTCTAAAAT 16 136 0 TTGCCTTTAT 0.855876 -165 TTTTTGTATTATACCTTAAAACAGATGATT 20 82 0 ATACCTTAAA 0.636541 -88 GTAGCGCTAATTGCCTTTATACTAAAAGCG 23 55 0 TTGCCTTTAT 0.855876 -29 ********** Masking position 7 Map Score: 4.94625 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 135 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 GCTTTTTTGCTCCCTTTTAAGGTTT 5 6 1 TTTGCTCCCT 0.979577 -75 TCCAAGACATTCTGCTCTCTTAAAAATGTG 17 113 0 TCTGCTCTCT 0.931841 -110 TGACAAAAAATTTGATCTCTTAGGCGGAGT 19 49 1 TTTGATCTCT 0.95558 -21 TGTTTCCTCACTTCATTTTGAA 20 3 1 TTTCCTCACT 0.929 -167 TGATTTGATCCCTAATAAAATGA 21 16 0 TTTGATCCCT 0.958716 -13 GTGGTTTTATTTTGCTCATTCCTCAACTCC 25 110 0 TTTGCTCATT 0.800879 -191 TTTTCATCTCTCTGTTATAAT 26 31 0 TTTCATCTCT 0.900772 -11 ********** Masking position 6 Map Score: 2.35894 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 109 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 11 TTCTTAAAAACGCTAAAAATTA 7 2 0 CGTAAAAATT 0.759937 -81 TGAGAATGTAGGCTTAAAATTCAGAAAGGGT 9 19 1 GGTTAAAATT 0.745131 -89 TTGTATCATACGCTTAAACTTTATATTATAA 13 62 0 CGTTAAACTT 0.97835 -79 GAAAAAATCACGCTTGATCTTATCTAAAATT 15 36 1 CGTTGATCTT 0.941913 -81 TAACGCACCACGCTTGAAATTAAAACTAAAT 15 85 0 CGTTGAAATT 0.945397 -32 ATCACACATTCGTTTATTCTTAATGTTTGCG 18 36 1 CGTTATTCTT 0.747774 -62 TTTCAGGGGGCGTTTGAACTTCTTACGACCC 22 22 1 CGTTGAACTT 0.977921 -35 TATAATGATTCGGTTAAACTTCCATCATGGT 25 68 0 CGTTAAACTT 0.978348 -233 ** ******** Masking position 4 Map Score: 3.1335 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 62 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 12 GGTAAAAAAAGGGGTTGGCATCAATAGGGGG 6 182 1 GGGTTGGCAT 0.906636 -115 ATTTAAGAATGCTTTTTACATATTATATAAA 6 228 0 GCTTTTACAT 0.881885 -69 CATCAAGGGGTTTGACATTAGTCAAGCG 11 8 1 GGTTTGACAT 0.979123 -121 AAGGCGCTTTGGTTTTTAAATGCTCTAAAGT 16 247 0 GGTTTTAAAT 0.913753 -54 ATGTTTGCGTGGATTTTACATTGTTGAACAC 18 58 1 GGTTTTACAT 0.974898 -40 AAACTTCAATGGGTTTTGCATGAAAGAATTT 24 260 0 GGTTTTGCAT 0.963146 -41 TAATGTGTATGGTTTTGAAATATC 26 4 0 GGTTTGAAAT 0.927505 -38 ** ******** Masking position 10 Map Score: 2.94078 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 50 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 13 GTTTTAGGGTGTGGCGAGTTT 12 20 1 GTGGCGGTTT 0.991647 -11 AATTTCAAGCGTGGTGCGTTAAAGGCGGTGG 15 95 1 GTGGTGGTTA 0.941231 -22 TGTGGCGAATGTGGCGAGTTTGTTGTATTTA 16 177 1 GTGGCGGTTT 0.991647 -124 TAAAATAAAGCGGTGTCTTTTTTAAGGGAG 23 10 1 GCGGTGCTTT 0.942183 -74 TTAGCGGTAGGTGGCGTCTTTTTGGTGCGGC 25 173 1 GTGGCGCTTT 0.98788 -128 ****** **** Masking position 9 Map Score: 1.94275 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 14 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 14 CCTATCACAAAAGGATTTTACT 1 3 0 AAGGATTTTA 0.903339 -96 TTTTATTATAATAGATTTTAGGCTAGGATT 1 41 1 ATAGATTTTA 0.716141 -58 GTAAATTTTTAAAAATTTTCATACTCTCAT 6 76 0 AAAAATTTTC 0.505816 -221 TTCTCATTAAATAGATTTTTATGATAAAAT 6 149 0 ATAGATTTTT 0.523107 -148 GATTTCCTTAATAGATTTTAGCTTGAGTGT 7 60 0 ATAGATTTTA 0.716141 -23 TAAAAGTAAAAAGAGTTTTGTTATCATGGG 10 57 0 AAGAGTTTTG 0.775102 -71 CGATACAAAAAAGGATTTTAA 10 117 1 AAGGATTTTA 0.903339 -11 CATCAAGGGGTTTGACATTAGTCA 11 5 1 AAGGGGTTTG 0.796724 -124 CTTGAGCGCTAAAGATTTTGATTTGCCCCC 16 45 1 AAAGATTTTG 0.926169 -256 ACGCCCCCTGAAAAGTTTTGTCTT 22 5 0 AAAAGTTTTG 0.709199 -52 CTATGAAAAGGTTTTCTAAAACTTCA 24 7 1 AAAGGTTTTC 0.785358 -294 CCATGCAAAAAAAGATTTTTTTATTAGAAG 24 130 1 AAAGATTTTT 0.732376 -171 CGAGAGCGTTAAGGAGTTTGACTCATTGAA 24 176 1 AAGGAGTTTG 0.826751 -125 TTTTGCATGAAAGAATTTTACAATGAAATG 24 248 0 AAGAATTTTA 0.687923 -53 TTAAACTTCAATGGGTTTTGCATGAAAGAA 24 263 0 ATGGGTTTTG 0.847647 -38 ********** Masking position 1 Map Score: 7.57072 Number of sites scoring better than the average of aligned sites = 1157 Number in coding regions = 1014 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 15 AGAAAAACCTAACCATAAAATTTGAACG 4 30 0 AAATAACATA 0.937743 -18 AAGCTATAATACAACTTTAATAAAAGAAAAACCTT 5 29 0 AAATTAAAAA 0.807457 -52 GAAAATTTTTAAAAATTTACAAAAATGAGAAAGAA 6 86 1 AAATTACAAA 0.928581 -211 TTTAAGCAAGATTAGGTTACAATCACAAGTTTTAT 9 53 1 ATATTACATA 0.674602 -55 ATTAATTAATAAAATTTTAATAAAACTTGTGATTG 9 72 0 AAATTAAAAA 0.807457 -36 AAAGTTTCTTACAACTTAACTAAAAGTAAAAAGAG 10 72 0 AAATAACAAA 0.916257 -56 AAGATAAATTAAAATATTAAAATTAG 14 16 1 AAATTAAATA 0.852359 -16 GATTTTTGCTAAAACATGACAAAAAATTTGATCTC 19 33 1 AAATGACAAA 0.800027 -37 TTTGCATGAAAGAATTTTACAATGAAATGGGGGTA 24 242 0 AAATTACATA 0.947085 -59 GAAGTTTAATAAAAGGTAAAAATAAGA 24 284 1 AAATAAAATA 0.829294 -17 TATAATCCCAATAACTTAACCATGATGGAAGTTTA 25 50 1 AAATAACATA 0.937741 -251 GAAAGATAAGAAAAAATAACCATGAGTTATTCAAA 25 251 1 AAATAACATA 0.937743 -50 * ** **** ** * Masking position 9 Map Score: 8.58712 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 58 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035