AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -icrp_hpyl_opreg_300.orf -g0.389 -x5 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 = 0.389 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HP0097 104 H. pylori predicted coding region HP0097 #2 HP0098 203 threonine synthase (thrC) #3 HP0133 180 serine transporter (sdaC) #4 HP0166 235 response regulator (ompR) #5 HP0168 46 H. pylori predicted coding region HP0168 #6 HP0170 74 H. pylori predicted coding region HP0170 #7 HP0171 60 peptide chain release factor RF-2 (prfB) #8 HP0174 300 H. pylori predicted coding region HP0174 #9 HP0359 300 H. pylori predicted coding region HP0359 #10 HP0360 216 UDP-glucose 4-epimerase #11 HP0473 225 molybdenum ABC transporter, periplasmic molybdate-binding protein (modA) #12 HP0474 21 molybdenum ABC transporter, permease protein (modB) #13 HP0588 184 ferrodoxin-like protein #14 HP0654 296 conserved hypothetical protein #15 HP0655 82 protective surface antigen D15 #16 HP0664 37 H. pylori predicted coding region HP0664 #17 HP0723 128 L-asparaginase II (ansB) #18 HP0745 300 conserved hypothetical protein #19 HP0813 132 conserved hypothetical protein #20 HP0818 68 osmoprotection protein (proWX) #21 HP0942 40 D-alanine glycine permease (dagA) #22 HP0943 21 D-amino acid dehydrogenase (dadA) #23 HP0944 300 translation initiation inhibitor, putative #24 HP1024 167 co-chaperone-curved DNA binding protein A (CbpA) #25 HP1027 159 ferric uptake regulation protein (fur) #26 HP1075 134 conserved hypothetical secreted protein #27 HP1108 259 pyruvate ferredoxin oxidoreductase, gamma subunit #28 HP1112 109 adenylosuccinate lyase (purB) #29 HP1113 65 outer membrane protein (omp24) #30 HP1180 300 pyrimidine nucleoside transport protein (nupC) #31 HP1430 37 conserved hypothetical ATP-binding protein #32 HP1431 253 16S rRNA (adenosine-N6,N6-)-dimethyltransferase (ksgA) #33 HP1441 120 peptidyl-prolyl cis-trans isomerase B, cyclosporin-type rotamase (ppi) Motif number 1 TCAAACTCCTTTCATTCAGTTTAAT 1 90 0 AAACCCTTAT 0.965157 -15 GCAAAATTTTAAACCGCATTATAGTATTATAAG 2 50 1 AAACGCTTTA 0.815221 -154 GTTCTCATTAAAAAACCATTTAAGGTTACATTC 2 124 1 AAAACCTTAA 0.979755 -80 TAATCTCAAAAAACCCCAATCATAAAAAGCTTT 3 110 1 AAACCCATAT 0.88705 -71 AATTGGTTTTAAAAAGCGTTTTATAGTAACCAT 6 38 0 AAAAGCTTTA 0.843161 -37 GATAAGTTCAAAACCCCACTCATAAAGGTTCTG 7 35 1 AAACCCCTAT 0.771526 -26 ATGTTATACCAAAAACCCTAAAAATTTAAGCTC 9 41 1 AAAACCTAAA 0.749784 -260 ATAAGCCCTTAAAAGCCAATAAAGATGAAATTA 10 105 1 AAAACCATAA 0.932075 -112 AATTTTCTTAAAAAATCCTTAAATAATAAATGG 10 145 1 AAAATCTTAA 0.937962 -72 AAAACCCCTTTTAAAATGAAAAAA 10 203 0 AAACCCTTAA 0.975362 -14 AATAAATTCTAAAATGCTTTAATAGTAGGAACT 13 84 0 AAAAGCTTAT 0.904276 -101 ATTTTATCATAAAAATCTATTTAATGAGAATTA 14 149 1 AAAATCATTA 0.631338 -148 TATAATATGTAAAAAGCATTCTTAAATCTAAAA 14 232 1 AAAAGCTTTT 0.790404 -65 TAGTATAGTAAAACATCGTTAAAATAAATTTAA 17 20 0 AAACTCTTAA 0.925189 -109 ATTAAAAAAGAAAAACCAATCATGAATATTTT 18 10 0 AAAACCATAT 0.905671 -291 AACTTGCGCAAAACGCCATTCAATTTCTCATGA 18 110 1 AAACCCTTAA 0.975362 -191 TTCCATTATAAAACCCCTTTTAAAAATGATTTG 18 154 1 AAACCCTTAA 0.975362 -147 TTGCTTTTTTAAAAACCATTATTTTACTCAAAA 18 266 0 AAAACCTTTT 0.931022 -35 ACTAGTTTTAAAAAGTCATTATTATTGAAAATC 19 92 0 AAAATCTTTT 0.808646 -41 ACTCCAAACTCCCTTCAAACTAGTTTTA 19 115 0 AAACCCTTAA 0.975362 -18 TTAGCATTTTAAAACCCCTTTATCCAAATAAGT 20 37 1 AAAACCTTAT 0.971316 -32 AAAAACTCCTTAATAAACTAGGGT 21 27 0 AAAATCTTAT 0.913636 -14 AAACTCAAACAAAACCCGTTTAAGAATTTCTAA 23 145 1 AAAACCTTAA 0.979756 -156 AAATGAGCGCAAAACGCCATGAATTTTCATCTT 23 210 0 AAAAGCATAA 0.792867 -91 GATTGAAACTCCTATGATGATGTGTTAT 23 283 0 AAACCCATAT 0.88705 -18 TATTTTAGTTAAAATTCCTTTTAATTGCGCTGA 24 39 1 AAAATCTTTA 0.857924 -129 AATGGTAATAAAAAATCAATATTTTTGGATTGA 25 37 1 AAAATCATTT 0.545006 -123 AAACATAGATAAAACTCATTATTATTTTAATTC 25 68 0 AAAATCTTTT 0.80866 -92 TTCTAGTTATAAAAATCATTTTACGGATAAGGA 25 127 1 AAAATCTTTA 0.857821 -33 AAAAAACCTTTTAAATAGAATTGA 26 2 1 AAAACCTTAA 0.979757 -133 AAACTTTAAAAAACCCCCTTAAAAAGGTTTTTA 26 68 1 AAACCCTTAA 0.975362 -67 CGTTCTTAATAAAAACCACTAATATTTATTTTA 27 63 0 AAAACCCTAT 0.805006 -197 TTTTCCTATAAAAATTCCTAAAAAGATATTGTT 27 155 1 AAAATCTAAA 0.483495 -105 TTGATTCTTTAAACCCCTTTAAAGTAACATAAA 28 61 1 AAACCCTTAA 0.975362 -49 AAAACCCCTTAAAACTTCAATTT 29 53 0 AAAACCTTAA 0.979757 -13 ACCTTTCTTAAAAATCCATTAAAATTACATTAA 30 65 0 AAAACCTTAA 0.979757 -236 GAGATTATACAAAAACCTTTCTTAAAAATCCAT 30 79 0 AAAACCTTTT 0.931168 -222 ATTTTGATTTAAACTTCATTTAATATCCGTTTA 30 208 1 AAACTCTTAA 0.925189 -93 CTTTGAATGAAAAAAGCTATAATAAAGAAGTTG 32 166 1 AAAAGCATAT 0.728137 -88 **** ** ** ** Masking position 3 Map Score: 66.3178 Number of sites scoring better than the average of aligned sites = 1445 Number in coding regions = 1218 Number in noncoding regions = 227 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 2 GAATAAGGGCTTAAAAAAGAT 1 2 0 TTAAAAAAGA 0.888818 -103 TTAAACTGGATTAAAAAGACGATCAATCGT 2 96 1 TTAAAAAGAC 0.789479 -108 TTATCCAAAAATAAAAAGGAATCATTTT 2 186 1 ATAAAAAGGA 0.915488 -18 ATAATAACGCTTAAAAAAAGATTAATAAAG 3 21 0 TTAAAAAAAG 0.486132 -160 CTTTAACACGATAAAAGGGCGGTTTAATAG 3 160 1 ATAAAAGGGC 0.87883 -21 TTCTGCAACTTTAAAAACGATTAACTTTGT 4 192 0 TTAAAAACGA 0.868014 -44 GCCAATTGGTTTTAAAAAGCGTTTTATAGT 6 44 0 TTTAAAAAGC 0.654372 -31 GACACGACTGATAAAAAGAAAAAATTTAAG 9 272 1 ATAAAAAGAA 0.512775 -29 TTTTTTCATTTTAAAAGGGGTTTT 10 203 1 TTAAAAGGGG 0.95499 -14 AACGCATAAAAAAGGCGAGCA 12 6 1 ATAAAAAAGG 0.768977 -16 TTAGAATTTATTAAAAAAGGCTTGCTACAA 13 105 1 TTAAAAAAGG 0.906868 -80 CAATAGGGGGTTAAAAGGGGATATTTTTAT 14 203 1 TTAAAAGGGG 0.95499 -94 AATGTTTATCTTTAAAACGAAAGGGCAATT 14 272 1 TTTAAAACGA 0.561155 -25 CTAATCATTCTTAAAAACGCTAAAAATTA 15 10 0 TTAAAAACGC 0.889019 -73 TACAATCAGCTTAAAAAGGATATAAA 16 22 1 TTAAAAAGGA 0.96941 -16 TAAAATAAATTTAAAAAGGGTTA 17 4 0 TTAAAAAGGG 0.974747 -125 CGCGAAGCCATTAAAAAAGAAAAACCAATC 18 22 0 TTAAAAAAGA 0.888818 -279 CAAATCATTTTTAAAAGGGGTTTTATAATG 18 157 0 TTAAAAGGGG 0.95499 -144 ATAATGGTTTTTAAAAAAGCAAAAAAGAGT 18 277 1 TTAAAAAAGC 0.906868 -24 CAAACTAGTTTTAAAAAGTCATTATTATTG 19 98 0 TTAAAAAGTC 0.532673 -35 AAACTAGGGTTTAAAAAAGAAATTCC 21 7 0 TTAAAAAAGA 0.888818 -34 TTTATTAAAGGGACTATCAGC 22 4 1 ATTAAAGGGA 0.536555 -18 ATAAGCCATAATAAAAGGGCTTGCAAGCGA 23 81 1 ATAAAAGGGC 0.87883 -220 TTCAGCGCAATTAAAAGGAATTTTAACTAA 24 43 0 TTAAAAGGAA 0.628576 -125 ATCAATTCTATTTAAAAGGTTTTTT 26 6 0 TTTAAAAGGT 0.53623 -129 TAAAGTTTTCATAAAAAGGAACGAAAAATG 26 46 0 ATAAAAAGGA 0.915488 -89 AAAAACCCCCTTAAAAAGGTTTTTAGGTAT 26 76 1 TTAAAAAGGT 0.856046 -59 TTTATGTTACTTTAAAGGGGTTTAAAGAAT 28 64 0 TTTAAAGGGG 0.804893 -46 TTTTGTTTTTATAAAAACGCGCC 29 4 0 ATAAAAACGC 0.732498 -62 TTTCAATTTTTTAAAAAGGCA 31 2 0 TTAAAAAGGC 0.974747 -36 AGAAGTTGCATTAAAAAGGAAAGACAAATC 32 191 1 TTAAAAAGGA 0.96941 -63 ATATTATACCTTAAAAAGGGGATTTGTCTT 32 211 0 TTAAAAAGGG 0.974747 -43 ********** Masking position 5 Map Score: 38.9262 Number of sites scoring better than the average of aligned sites = 1569 Number in coding regions = 1277 Number in noncoding regions = 292 Number of orfs with sites within 600 bp upstream = 201 Fraction of orfs with sites within 600 bp upstream = 0.032284 Motif number 3 TTATAGTATTATAAGCATAAATCAAAAATTAAACTGGATTAAA 2 68 1 ATAAAAATAA 0.78456 -136 AGCATACCCTAAAAGAGCGAATGTAACCTTAAATGGTTTTTTA 2 132 0 AAAAAAATAA 0.910055 -72 AAAACGATCAAAGGAATTGTTTAAAAACATTAA 4 1 1 AAAAAAATTA 0.78456 -235 AAAATATCTTAAAAATAAAAATTCAAAACATTATCATAGTTAT 4 100 0 AAAAAAAATA 0.831355 -136 AACTAACACCAAAAAAGACAATAAATATTATTACAACATCTGA 8 37 0 AAAAAATATA 0.773673 -264 GGAAAGAAAAAAAATGTTAAAGAAGATTCAAAAATTCTCGATG 8 91 1 AAAAAAAAAA 0.931956 -210 ATGCAATGCTAAAAAACCAAATATAAAGAATAATAACCCTGGT 8 189 0 AAAAAAAAAA 0.931956 -112 TTTGCGCAATATAAAGAACAAAGCAAATAAAAAATCTCAATCC 9 142 1 ATAAAAAAAA 0.831355 -159 CACGACTGATAAAAAGAAAAAATTTAAGGAGAAAACG 9 274 1 AAAAAAAAAA 0.931956 -27 TTAAAAGCCAATAAAGATGAAATTATAGATTAAATTTTCTTAA 10 113 1 ATAAAATTAA 0.715999 -104 ATCTTTGATAAAAAATTAAAACTTTTAGAAAAATAACCGATCT 11 47 0 AAAAAATAAA 0.90474 -179 TAATTATAGCATAAATGATAATGAAAAAGTAAATGAGAGTATG 14 44 1 ATAAAAATAA 0.78456 -253 TGAGAGTATGAAAATTTTTAAAAATTTACAAAAATGAGAAAGA 14 77 1 AAAAAATAAA 0.90474 -220 CAAACAAAATAAAAGAATCAACAATTTCAAAAATATTCTCATT 17 84 0 AAAAAATAAA 0.90474 -45 CGAAGCCATTAAAAAAGAAAAACCAATCATGAATATTTT 18 7 0 AAAAAAATAA 0.910055 -294 TTTATAATGGAAAACAACGAAAATCATGAGAAATTGAATGGCG 18 123 0 AAAAAAAGAA 0.634629 -178 TAATAAATTAATAAATAAAAACATGATTTTTAAGGTTTTGAGT 18 231 1 ATAAAAATAA 0.784557 -70 AAGGGGTTTTAAAATGCTAAAGGCATTCTTTAATGTTGGTTGC 20 14 0 AAAAAATTAA 0.875253 -55 AGTGTCTGTAAAAATGCTCAAAAGCATTTTCTATAATAAGCCA 23 46 1 AAAAAAATTA 0.78456 -255 ATATGGGTAAAAAATATACAATACCTTATAATAAGATGAAAAT 23 178 1 AAAAAATATA 0.773673 -123 GTTCTTAATAAAAACCACTAATATTTATTTTAAACTTTGTTAT 27 52 0 AAAAAATTAA 0.875253 -208 TTATACAAGAAAAACTATTAATGTGTCTTATAACAATATCTTT 27 176 0 AAAAAATAAA 0.90474 -84 GCGCGTTTTTATAAAAACAAAACTATAAAATAAGCGCTAAAAA 29 12 1 ATAAAATAAA 0.773673 -54 CTACCTTGACAAAAAAATAAAAGAATGAGATTATACAAAAACC 30 95 0 AAAAAATATA 0.773673 -206 TTTTGCTAAAAAAAAGATTAAACGGATATTAAATGAAGTTTAA 30 216 0 AAAAAAATAA 0.910055 -85 TGCCTTTTTAAAAAATTGAAATAAAGGAATAAAAGTT 31 10 1 AAAAAAAAAA 0.931956 -28 ATTTCATTTTATAATGCAAAATCTAACCAATTATTAACGAAAA 32 56 1 ATAAAAAATA 0.639545 -198 **** ** * * ** Masking position 11 Map Score: 34.2005 Number of sites scoring better than the average of aligned sites = 923 Number in coding regions = 711 Number in noncoding regions = 212 Number of orfs with sites within 600 bp upstream = 163 Fraction of orfs with sites within 600 bp upstream = 0.0261805 Motif number 4 ATCGTGGATTTTAGAAAATAAATGCGTGCCCA 3 67 1 TTAGAAAAAA 0.820522 -114 TCATGGAATATTGAAAAATAAAGTCTTATTTT 4 44 0 TTGAAAAAAA 0.855012 -192 TGAAAATATCTTAAAAATAAAAATTCAAAACA 4 113 0 TTAAAAAAAA 0.93078 -123 CAAGGTATCTTTAATAATAAAATGCTAGAATT 4 143 1 TTAATAAAAA 0.872639 -93 TTTATTCTTTTTGGAAAGAAAAAAAATGTTAA 8 79 1 TTGGAAAAAA 0.667219 -222 AAGCGAAAAGTTATAAAGCAAAAGAGATTTTG 9 114 1 TTATAAAAAA 0.847166 -187 AAAACCCCTTTTAAAATGAAAAAATAACAACT 10 195 0 TTAAAATAAA 0.919521 -22 CCTCAAACTTTTAAAATACAAATTTTTAAGAT 11 155 1 TTAAAATAAA 0.919166 -71 TAGTAGGAACTTAAAATTAAAATGAGAAGATA 13 63 0 TTAAAATAAA 0.918653 -122 GGACCACCTTTTGAAATTAAAAGATTTTATAG 17 50 0 TTGAAATAAA 0.832851 -79 CGCGAAGCCATTAAAAAAGAAAAACCAATCAT 18 20 0 TTAAAAAAAA 0.930791 -281 AAAAGGGGTTTTATAATGGAAAACAACGAAAA 18 143 0 TTATAATAAA 0.824872 -158 AACTAATAAATTAATAAATAAAAACATGATTT 18 228 1 TTAATAAAAA 0.872637 -73 TAAAAAGTCATTATTATTGAAAATCATAGCGC 19 85 0 TTATTATAAA 0.705834 -48 AAACTAGGGTTTAAAAAAGAAATTCC 21 5 0 TTAAAAAAAA 0.930791 -36 TTATTATGGCTTATTATAGAAAATGCTTTTGA 23 63 0 TTATTATAAA 0.70585 -238 TGCAATCAAATTAATAAAGAAATAAAAAATGA 23 237 0 TTAATAAAAA 0.87265 -64 CGACAATCCTTAAAATCAAAATGGGATTTAT 28 89 0 TTAAAATAAA 0.919521 -21 GGAAGTAGGATTGATAATAAAAGTTTAATGTA 30 41 1 TTGATAAAAA 0.750298 -260 ACTCCTTTAATTGAAATTTAAATTCTAGCTCA 32 15 1 TTGAAATAAA 0.831713 -239 GGATTTCATTTTATAATGCAAAATCTAACCAA 32 54 1 TTATAATAAA 0.82486 -200 ATCTAACCAATTATTAACGAAAAAGATTTTAA 32 76 1 TTATTAAAAA 0.738507 -178 GTATTAAAAATTAGTATTAAAATCTTTTTCGT 32 92 0 TTAGTATAAA 0.663731 -162 AGAAGTTGCATTAAAAAGGAAAGACAAATCCC 32 191 1 TTAAAAAAAA 0.930792 -63 ******* *** Masking position 2 Map Score: 31.8422 Number of sites scoring better than the average of aligned sites = 338 Number in coding regions = 234 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 5 GAATTTCCTTATTATAGTGTAGTTTGACTT 1 51 0 ATTATAGTGT 0.602464 -54 TTTAAACCGCATTATAGTATTATAAGCATA 2 57 1 ATTATAGTAT 0.827481 -147 TTTAAGCGTTATTATAGCTTGTGCGGGTTA 3 36 1 ATTATAGCTT 0.927464 -145 AAGAGCTTTCATTGTAGCATAAAGCTTTTT 3 133 0 ATTGTAGCAT 0.964966 -48 TAGGGGACTAATTCTAGCATTTTATTATTA 4 154 0 ATTCTAGCAT 0.862059 -82 TGAACTTATCATTATAGCATTGTTAAAAGC 7 15 0 ATTATAGCAT 0.971041 -46 AATAACAACTATTATAACATCTTAATCCCA 10 175 0 ATTATAACAT 0.624612 -42 AGTTCCTACTATTAAAGCATTTTAGAATTT 13 84 1 ATTAAAGCAT 0.729358 -101 TTTGCCTAAAATTGTAGCAAGCCTTTTTTA 13 116 0 ATTGTAGCAA 0.806125 -69 TTGTCCCATAATTATAGCATAAATGATAAT 14 36 1 ATTATAGCAT 0.971041 -261 AAAGATAAACATTGTAGCATTTTTAGATTT 14 255 0 ATTGTAGCAT 0.964966 -42 TCCTTAATAGATTTTAGCTTGAGTGTTGTT 15 56 0 ATTTTAGCTT 0.618994 -27 TGGCACACAGATTATAGCGTATTAAACCAA 18 200 1 ATTATAGCGT 0.913795 -101 TTTTATTACCATTGTCGCATTTTAATGTAA 25 20 0 ATTGTCGCAT 0.766385 -140 ATGCAAGGCTATTGTAGTTTAGTTTTGCTA 30 251 0 ATTGTAGTTT 0.600224 -50 CAACTTCTTTATTATAGCTTTTTTCATTCA 32 169 0 ATTATAGCTT 0.927464 -85 CAAATGCTCTATTATAGCAACAAATTAAAA 33 74 0 ATTATAGCAA 0.835051 -47 ********** Masking position 3 Map Score: 18.2949 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 42 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 6 GAAATTATCCAAAAATAAAAAGGAATCATTT 2 182 1 AAAATAAAAA 0.763446 -22 ATTGTTTAAAAACATTAAAAAATAAGACTTT 4 26 1 AACTTAAAAA 0.885635 -210 AAAATATCTTAAAAATAAAAATTCAAAACAT 4 112 0 AAAATAAAAA 0.763446 -124 TGATTTCTGCAACTTTAAAAACGATTAACTT 4 195 0 AACTTAAAAA 0.885635 -41 TTCTTTTTGGAAAGAAAAAAAATGTTAAAGA 8 83 1 AAAAAAAAAA 0.693012 -218 CTAAAAAACCAAATATAAAGAATAATAACCC 8 193 0 AAAATAAAGA 0.813393 -108 TTATACCAAAAACCCTAAAAATTTAAGCTCC 9 44 1 AACCTAAAAA 0.873659 -257 GAAAAGTTATAAAGCAAAAGAGATTTTGCGC 9 118 1 AAACAAAAGA 0.852918 -183 AAGCATTCTTAAATCTAAAAATGCTACAATG 14 245 1 AAACTAAAAA 0.859912 -52 CATTCTTAAAAACGCTAAAAATTA 15 4 0 AACCTAAAAA 0.873659 -79 TCGTTAAAATAAATTTAAAAAGGGTTA 17 7 0 AAATTAAAAA 0.873002 -122 CCACCTTTTGAAATTAAAAGATTTTATAGTA 17 48 0 AAATAAAAGA 0.86656 -81 CCCTTCAAACAAAATAAAAGAATCAACAATT 17 101 0 AAATAAAAGA 0.86656 -28 TTTTACTCAAAACCTTAAAAATCATGTTTTT 18 247 0 AACTTAAAAA 0.885635 -54 GGTTTTTAAAAAAGCAAAAAAGAGTTTGG 18 282 1 AAACAAAAAA 0.811094 -19 CCTGCAACCAACATTAAAGAATGCCTTTAG 20 10 1 AACTTAAAGA 0.912732 -59 TTGATTGACTAACACTAAAGATTTATGATAG 24 116 1 AACCTAAAGA 0.903283 -52 TTTTTATGAAAACTTTAAAAAACCCCCTTAA 26 59 1 AACTTAAAAA 0.885635 -76 CTACTATTTGAAACTAAAAGATCGCTAATTA 26 105 0 AAATAAAAGA 0.86656 -30 CCTTGACAAAAAAATAAAAGAATGAGATTAT 30 104 0 AAATAAAAGA 0.86656 -197 CTAATGCAAGAAATTAAAAGATGCAAGGCTA 30 270 0 AAATAAAAGA 0.86656 -31 ACCAATTATTAACGAAAAAGATTTTAATACT 32 81 1 AACAAAAAGA 0.774506 -173 *** ******* Masking position 7 Map Score: 27.6105 Number of sites scoring better than the average of aligned sites = 691 Number in coding regions = 533 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 7 TGGTTTTTTAATGAGAACGATTGATCGTCTTT 2 110 0 ATGAAACGTT 0.838773 -94 CGCACAAGCTATAATAACGCTTAAAAAAAGAT 3 29 0 ATAAAACGTT 0.871624 -152 ATTAATAACTATGATAATGTTTTGAATTTTTA 4 96 1 ATGAAATGTT 0.863652 -140 TTCTGCAACTTTAAAAACGATTAACTTTGTTA 4 190 0 TTAAAACGTT 0.921209 -46 AGATTAGGTATTGAAAATGATTAAGAGAAACG 5 24 1 TTGAAATGTT 0.91602 -23 AATGGCTTTTAACAATGCTATAATGATAAG 7 9 1 TTAAAATGTA 0.618187 -52 GCTTATCAATATGAGATTGATTAATAGAGTAT 8 256 0 ATGAATTGTT 0.418751 -45 GGCTAATGGCTTGATAAAGCTTAGATTTTATC 14 125 1 TTGAAAAGTT 0.848892 -172 ATTTTTAGATTTAAGAATGCTTTTTACATATT 14 235 0 TTAAAATGTT 0.934363 -62 TTTAGCGTTTTTAAGAATGATTAGTTATAATA 15 16 1 TTAAAATGTT 0.934363 -67 ATGATTAGTTATAATAACGCTACTAACAACAC 15 32 1 ATAAAACGTA 0.43574 -51 TAAAATAAATTTAAAAAGGGTTA 17 2 0 TTAAAAGGTT 0.831467 -127 AAAACCCCTTTTAAAAATGATTTGAGCCACAC 18 163 1 TTAAAATGTT 0.934363 -138 GGTTTTGAGTAAAATAATGGTTTTTAAAAAAG 18 264 1 AAAAAATGTT 0.586267 -37 TGGCTTATTATAGAAAATGCTTTTGAGCATTT 23 57 0 TAGAAATGTT 0.651533 -244 ATCAAGTTTATTGATAATGCTTTTAGATAATG 24 89 0 TTGAAATGTT 0.91602 -79 GGATCACCTTTAAAATAGTTTTATTAGAATA 24 147 0 TTAAATAGTT 0.454709 -21 AAAAACCCCCTTAAAAAGGTTTTTAGGTATAA 26 76 1 TTAAAAGGTT 0.831467 -59 ACCTTAAATAATAACAAAGTTTAAAATAAATA 27 42 1 ATAAAAAGTT 0.809799 -218 GTGGTTTTTATTAAGAACGCTTGTCTTTTTAG 27 77 1 TTAAAACGTT 0.921209 -183 TAATGGATTTTTAAGAAAGGTTTTTGTATAAT 30 77 1 TTAAAAAGTT 0.879976 -224 TAGTTTTGCTAAAAAAAAGATTAAACGGATAT 30 230 0 AAAAAAAGTT 0.421902 -71 **** **** ** Masking position 11 Map Score: 20.208 Number of sites scoring better than the average of aligned sites = 403 Number in coding regions = 308 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 8 GCCCAAAACCACCCCTTAATCTCAAAAAAC 3 94 1 ACCCCTTAAT 0.915851 -87 ACTTCAATTAACTCCTTCAATGATTTCTGC 4 216 0 ACTCCTTCAA 0.683259 -20 AAAAATTTAAGCTCCTTAGAACAAATATAA 9 60 1 GCTCCTTAGA 0.55602 -241 TTAACTCAAAGCTCCTTGATGGAAGATTAA 9 188 0 GCTCCTTGAT 0.737045 -113 CGTTTTCTCCTTAAATTTTTTCTTT 9 286 0 TCTCCTTAAA 0.77274 -15 TCATTCTCCTTTGTGCTAAAAGCT 13 171 0 TCTCCTTTGT 0.552627 -14 AGTATCTCCTTTGTGTTGGTTTAA 14 5 1 TCTCCTTTGT 0.552627 -292 ATTGATGCCAACCCCTTTTTTTACCTAATT 14 177 0 ACCCCTTTTT 0.590925 -120 AACCTGCCCCTTCAAACAAAATAAA 17 114 0 GCCCCTTCAA 0.738815 -15 GCATTTTAAAACCCCTTTATCCAAATAAGT 20 40 1 ACCCCTTTAT 0.905428 -29 AAAAACTCCTTAATAAACTAGGGT 21 27 0 ACTCCTTAAT 0.859047 -14 CTTTAAAAAACCCCCTTAAAAAGGTTTTTA 26 71 1 CCCCCTTAAA 0.651373 -64 AAATCAAATCACACCTTAAATAATAACAAA 27 30 1 ACACCTTAAA 0.413804 -230 GGTAATATGTCTCCTTAATATCGTATAAA 27 241 0 TCTCCTTAAT 0.805095 -19 GCGCAAAAAAGCCCCTTGATTTAATTAAAG 28 13 0 GCCCCTTGAT 0.833486 -97 GTGCGATTTTTCCCCTTGATTCTTTAAACC 28 46 1 TCCCCTTGAT 0.822068 -64 GATTCTTTAAACCCCTTTAAAGTAACATAA 28 63 1 ACCCCTTTAA 0.8874 -47 AAAACCCCTTAAAACTTCAATTT 29 53 0 ACCCCTTAAA 0.899589 -13 GATGACTCCTTTAATTGAAATTTA 32 5 1 ACTCCTTTAA 0.815264 -249 GAAAGACAAATCCCCTTTTTAAGGTATAAT 32 209 1 TCCCCTTTTT 0.494709 -45 ********** Masking position 6 Map Score: 15.2096 Number of sites scoring better than the average of aligned sites = 559 Number in coding regions = 453 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 9 TTGACTTAAAATTAAGATTTTATTAGGAATA 1 27 0 ATAAGATTTT 0.936943 -78 ATAATCCTTTATTAATCTTTTTTTAAGCGTT 3 15 1 ATAATCTTTT 0.729291 -166 TCATTGTAGCATAAAGCTTTTTATGATTGGG 3 124 0 ATAAGCTTTT 0.924264 -57 ATTAAATTGGATTGAGATTTTTTATTTGCTT 9 162 0 ATGAGATTTT 0.71837 -139 AATAAATGGGATTAAGATGTTATAATAGTTG 10 169 1 ATAAGATGTT 0.668436 -48 TTTATCAAAGATGAAGATTTTAGAGTGAAAA 11 78 1 ATAAGATTTT 0.936943 -148 AACTTTTAAAATACAAATTTTTAAGATACAA 11 160 1 ATCAAATTTT 0.601506 -66 AGGGCTTTAAATGCAGCTTTTAGCACAAAGG 13 157 1 ATCAGCTTTT 0.848852 -28 AAATGAGAGTATGAAAATTTTTAAAAATTTA 14 74 1 ATAAAATTTT 0.766358 -223 AAAACCAATCATGAATATTTT 18 1 0 ATAATATTTT 0.766358 -300 CTTTTAGATAATGCAGATTTTAAACCCGTTT 24 71 0 ATCAGATTTT 0.872412 -97 AAGTTTATTGATAATGCTTTTAGATAATGCA 24 87 0 ATATGCTTTT 0.527669 -81 GTAATAAAAAATCAATATTTTTGGATTGAAT 25 41 1 ATAATATTTT 0.766357 -119 TTAAAATTACATTAAACTTTTATTATCAATC 30 49 0 ATAAACTTTT 0.729291 -252 ATTATTAACGAAAAAGATTTTAATACTAATT 32 85 1 AAAAGATTTT 0.576266 -169 ** ******** Masking position 1 Map Score: 8.94506 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 120 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 10 TCCTTTCATTCAGTTTAATTTTCGTTTAGAAT 1 77 0 CATTTAATTT 0.890519 -28 CTTTTTAATCCAGTTTAATTTTTGATTTATGC 2 82 0 CATTTAATTT 0.890519 -122 CATTAAAAAACCATTTAAGGTTACATTCGCTC 2 129 1 CCTTTAAGTT 0.59288 -75 AAAATGATTCCTTTTTATTTTTGGATAATTTC 2 182 0 CTTTTATTTT 0.561851 -22 CTAATTCTAGCATTTTATTATTAAAGATACCT 4 145 0 CATTTATTTT 0.890524 -91 AATCTCAATCCAATTTAATCTTCCATCAAGGA 9 174 1 CATTTAATTT 0.890519 -127 CATCTTAATCCCATTTATTATTTAAGGATTTT 10 156 0 CCTTTATTTT 0.919893 -61 AGTATCTTCTCATTTTAATTTTAAGTTCCTAC 13 61 1 CATTTAATTT 0.890519 -124 GCTTGCAAGCCCTTTTATTATGGCTTATTATA 23 77 0 CCTTTATTTG 0.663449 -224 ACCATTGTCGCATTTTAATGTAACTTATAAGA 25 11 0 CATTTAATTA 0.756085 -149 TATTTTATGGCCATTTATTCTAAAAAGACAAG 27 96 0 CCTTTATTTA 0.813989 -164 AGGCTGAATTCAATTTATTTTATACGATATTA 27 223 1 CATTTATTTA 0.75609 -37 GCGATTTTTCCCCTTGATTCTTTAAACCCCTT 28 48 1 CCTTGATTTT 0.59288 -62 ACATAAATCCCATTTTGATTTTAAGGATTGTC 28 87 1 CATTTGATTT 0.670092 -23 CATTTAATATCCGTTTAATCTTTTTTTTAGCA 30 224 1 CCTTTAATTT 0.919892 -77 GGCTAAAATACCATTTGTTTTAATTTGTTGCT 33 57 1 CCTTTGTTTA 0.522143 -64 ** ****** ** Masking position 5 Map Score: 11.0077 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 86 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 11 TTACTATGATGAAATTTTTTGCCCTTTGCGG 2 20 1 GAATTTTTTG 0.777221 -184 CCCTTTGCGGCAAAATTTTAAACCGCATTAT 2 41 1 CAAATTTTAA 0.788003 -163 CTAAGGAGCTTAAATTTTTAGGGTTTTTGGT 9 48 0 TAATTTTTAG 0.563202 -253 TATCAAAGATGAAGATTTTAGAGTGAAAATG 11 80 1 GAAATTTTAG 0.870619 -146 TTTTAAAATACAAATTTTTAAGATACAAATA 11 163 1 CAATTTTTAA 0.788328 -63 ATGAGAGTATGAAAATTTTTAAAAATTTACA 14 76 1 GAAATTTTTA 0.529363 -221 TCCATAATGAGAATATTTTTGAAATTGTTGA 17 79 1 GAAATTTTTG 0.777221 -50 GCGTTTTGCGCAAGTTTTTAGGCGATGCGTT 18 95 0 CAATTTTTAG 0.920299 -206 GATTTAAACTCAATATTTTAGTTAAAATTCC 24 26 1 CAAATTTTAG 0.920214 -142 AATAAAAAATCAATATTTTTGGATTGAATTA 25 43 1 CAAATTTTTG 0.853691 -117 CTTAAAACTTCAATTTTTTAGCGCTTATTTT 29 38 0 CAATTTTTAG 0.920299 -28 TCCTTTATTTCAATTTTTTAAAAAGGCA 31 8 0 CAATTTTTAA 0.788336 -30 *** ******* Masking position 3 Map Score: 6.56258 Number of sites scoring better than the average of aligned sites = 269 Number in coding regions = 239 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 12 AATTTTGCCGCAAAGGGCAAAAAATTTCATCA 2 26 0 CAAGGCAAAA 0.901886 -178 CAAGTCGTAGCATACCCTAAAAGAGCGAATGT 2 151 0 CATCCTAAAA 0.544637 -53 CAAGCTATAATAACGCTTAAAAAAAGATTAAT 3 25 0 TAAGCTAAAA 0.745584 -156 TCCATGAAAACAAAGCCTTAAATTTCCATTAA 4 69 1 CAAGCTTAAA 0.743799 -167 GGATAACATGCAATGCTAAAAAACCAAATATA 8 207 0 CAAGCAAAAA 0.890886 -94 TCACTGGCATCAAGGGTCAAAATATAG 9 6 0 CAAGGCAAAA 0.901886 -295 TTGTTCTTTATATTGCGCAAAATCTCTTTTGC 9 131 0 TATGCCAAAA 0.640547 -170 ATATAAAGAACAAAGCAAATAAAAAATCTCAA 9 150 1 CAAGCAATAA 0.381914 -151 AGCGTGAACGCATCGCCTAAAAACTTGCGCAA 18 89 1 CATGCTAAAA 0.898395 -212 TATTGAAAATCATAGCGCAAAAATAAGGCGAT 19 71 0 CATGCCAAAA 0.925827 -62 GTGTCTGTAAAAATGCTCAAAAGCATTTTCTA 23 47 1 AAAGCCAAAA 0.620827 -254 TTGATGACAACAAAGCCTAAAACTCAAACAAA 23 126 1 CAAGCTAAAA 0.953484 -175 TAAATAATAACAAAGTTTAAAATAAATATTAG 27 46 1 CAAGTTAAAA 0.555114 -214 AAAAATCGCACAAGGCGCAAAAAAGCCCCTTG 28 25 0 CAAGCCAAAA 0.966596 -85 TTTAAAGAATCAAGGGGAAAAATCGCACAAGG 28 42 0 CAAGGAAAAA 0.721732 -68 CGACAATCCTTAAAATCAAAATGGG 28 95 0 CAACCTAAAA 0.734942 -15 CTTATGAGACCAGCGCTCTAAACCAGCTGAGC 30 137 0 CAGGCCTAAA 0.392617 -164 CCTACAACACTATCGGCTAAAATACCATTTGT 33 43 1 TATGGTAAAA 0.286513 -78 *** ** ***** Masking position 2 Map Score: 10.6381 Number of sites scoring better than the average of aligned sites = 580 Number in coding regions = 533 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 13 ATGATGAAATTTTTTGCCCTTTGCGGCAAA 2 25 1 TTTTTGCCCT 0.800346 -179 TCGGCTGTCATTTTAGCGCAC 6 2 0 TTTTAGCGCA 0.963033 -73 AGCAAAAGAGATTTTGCGCAATATAAAGAA 9 130 1 ATTTTGCGCA 0.829938 -171 TAAATGCAGCTTTTAGCACAAAGGAGAATG 13 164 1 TTTTAGCACA 0.694754 -21 TAATTTTTAGCGTTTTTAAGAATG 15 5 1 TTTTAGCGTT 0.672419 -78 ATTGAATGGCGTTTTGCGCAAGTTTTTAGG 18 104 0 GTTTTGCGCA 0.930125 -197 AATCGCCTTATTTTTGCGCTATGATTTTCA 19 70 1 TTTTTGCGCT 0.968709 -63 AATTCATGGCGTTTTGCGCTCATTTTTTAT 23 218 1 GTTTTGCGCT 0.930125 -83 TTTAAACCCGTTTCAGCGCAATTAAAAGGA 24 54 0 TTTCAGCGCA 0.830681 -114 TCAAGGGGCTTTTTTGCGCCTTGTGCGATT 28 24 1 TTTTTGCGCC 0.918828 -86 AACTTCAATTTTTTAGCGCTTATTTTATAG 29 34 0 TTTTAGCGCT 0.963033 -32 ********** Masking position 3 Map Score: 8.3094 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 386 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 14 AAATCTTAATTTTAAGTCAAACTACACTAT 1 38 1 TTTAAGTCAA 0.849265 -67 CCGCAAGTCTTTTAACTCAAAGCTCCTTGA 9 199 0 TTTAACTCAA 0.914954 -102 AGGGTGTAACTTTAATTCAACAAGAAGGAT 11 16 0 TTTAATTCAA 0.905775 -210 ACTAAACACTTTTTACTCAATTCAAAAGAA 13 34 0 TTTTACTCAA 0.793474 -151 AAAACCATTATTTTACTCAAAACCTTAAAA 18 258 0 TTTTACTCAA 0.793474 -43 CATCGTGGATTTAAACTCAATATTTTAGTT 24 19 1 TTAAACTCAA 0.515372 -149 AAATCTTTAGTGTTAGTCAATCAAGTTTAT 24 110 0 TGTTAGTCAA 0.368252 -58 TCATTATTATTTTAATTCAATCCAAAAATA 25 56 0 TTTAATTCAA 0.905775 -104 AGCCCCTTGATTTAATTAAAGGG 28 4 0 TTTAATTAAA 0.327683 -106 TTAAATGAAGTTTAAATCAAAATCATGGTG 30 201 0 TTTAAATCAA 0.673274 -100 CTTTTATTCCTTTATTTCAATTTTTTAAAA 31 16 0 TTTATTTCAA 0.530578 -22 TTATAGCTTTTTTCATTCAAAGATGTTAGT 32 158 0 TTTCATTCAA 0.814069 -96 GTCTTTCCTTTTTAATGCAACTTCTTTATT 32 186 0 TTTAATGCAA 0.62377 -68 GATAAGCTTTTGTCATTCAAATGCTCTATT 33 91 0 TGTCATTCAA 0.562781 -30 ********** Masking position 9 Map Score: 4.1998 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 218 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 15 TTATAGCTTGTGCGGGTTAAATCGTGGATTT 3 47 1 TGCGGGTTAA 0.816802 -134 ATCAGTCGTGTCTTGGTTGAGAAATCCTAAA 9 253 0 TCTTGGTTAG 0.827855 -48 AGAGTGAAAATGTTGGTTAAATACTAATAAG 11 99 1 TGTTGGTTAA 0.967367 -127 ATCTCCTTTGTGTTGGTTTAAGTTGTCCCAT 14 14 1 TGTTGGTTAA 0.967367 -283 TTAATTTATTAGTTGGTTTAATACGCTATAA 18 211 0 AGTTGGTTAA 0.915628 -90 CTTCTATTATTGTTGGTTGAGATGAGTTTGA 19 24 0 TGTTGGTTAG 0.966729 -109 CATTCTTTAATGTTGGTTGCAGG 20 3 0 TGTTGGTTCA 0.887306 -66 AAGGTAGCTCAGCTGGTTTAGAGCGCTGGTC 30 131 1 AGCTGGTTAG 0.85762 -170 ******** ** Masking position 7 Map Score: 1.55843 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 47 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617