AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -irpoH_mpneu_opreg_300.orf -g0.400 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 grpE 22 heat shock protein GrpE; similar to GenBank Accession Number I64046, from H. influenzae #2 1673683 300 DnaJ homolog protein, from M. capricolum #3 dnaJ 45 heat shock protein DnaJ; similar to Swiss-Prot Accession Number P17631, from B. subtilis #4 pmd1 300 transport ATP-binding protein; similar to Swiss-Prot Accession Number P36619, from S. pombe #5 1673831 170 hypothetical protein (HI0671) homolog; similar to GenBank Accession Number F64156, from H. influenzae #6 ftsH 180 cell division protein FtsH; similar to Swiss-Prot Accession Number P37476, from B. subtilis #7 1673937 300 D02_orf128 Protein #8 groES 187 heat shock protein GroES; similar to Swiss-Prot Accession Number P28599, from B. subtilis #9 ackA 300 acetate kinase; similar to Swiss-Prot Accession Number P37877, from B. subtilis #10 clpB 175 ATP-dependent protease binding subunit ClpB; similar to GenBank Accession Number F64098, from H. influenzae #11 ileS 42 isoleucine-tRNA ligase; similar to GenBank Accession Number S40178, from S. aureus #12 lip3 117 triacylglycerol lipase (lip) 3; similar to GenBank Accession Number JC4111, from M. mycoides #13 1674088 300 putative lipoprotein, MG307 homolog, from M. genitalium #14 dnaK 55 heat shock protein DnaK; similar to GenBank Accession Number A49230, from E. rhusiopathiae #15 cbiO 157 abc transport ATP-binding protein; similar to Swiss-Prot Accession Number Q05596, from S. typhimurium #16 gap 30 glycerladehyde-3-phosphate dehydrogenase; similar to GenBank Accession Number S34254, from C. pasteurianum #17 lig 167 DNA ligase; similar to Swiss-Prot Accession Number P15042, from E. coli #18 grs1 21 glycyl-tRNA synthetase; similar to Swiss-Prot Accession Number P38088, from S. cerevisiae #19 sigA 52 RNA polymerase sigma-A factor; similar to Swiss-Prot Accession Number P06224, from B. subtilis #20 lon 70 ATP-dependent protease Lon; similar to Swiss-Prot Accession Number P37945, from B. subtilis #21 tig 24 trigger factor; similar to GenBank Accession Number C64088, from H. influenzae #22 rpl21 146 ribosomal protein L21; similar to Swiss-Prot Accession Number P26908, from B. subtilis #23 nrdE 23 ribonucleoside-diphosphate reductase; similar to Swiss-Prot Accession Number Q08698, from S. typhimurium #24 thyA 300 thymidylate synthase; similar to Swiss-Prot Accession Number P13954, from S. aureus Motif number 1 TGGAGTGTATTGATTTTGTCCTTATGAATTAAAACAGCA 2 131 1 TTTTTTTAAT 0.848735 -170 AGAGTTGGTATAATTTTATTAATTTATAAGCCATTGCAA 2 250 0 TTTTTTTTAA 0.965093 -51 TAGCCAAAGCTAGTTTTTAAGCGGTCTTATAATTAAAGC 4 261 1 TTTTTGTTTA 0.770089 -40 AAGCTTGCCTTCATTTTAATTTGGTTTAAGCCACCAATC 5 24 1 TTTTTGTTAA 0.916101 -147 GCCAAGCTTTGTCTTTTTTAGCTCTCAACATAAAAGGAA 5 106 1 GTTTTTTAAC 0.703971 -65 ATTAAGATGATTTTTTTGTGCTTTTTTACCAGGGAAACC 6 51 0 TTTTTTTTAC 0.898196 -130 CGAGTCCAATTAATTTTTTAGGGTTTAAAAGAAATTAGC 7 43 1 TTTTTGTAAA 0.916101 -258 GGTTTTTTAGTTGTTTTAAGTATTTGTTATTTCCAAACA 7 262 1 TTTTTTTTTA 0.894528 -39 TTAACGCCTGTGTTTTTTGAATTATTTACCTGTTCAAAA 9 53 0 TTTTTTTTAC 0.898196 -248 TAAGCATAGTAATTTTATTAATATTTAACTAACTTCTA 11 15 0 TTTTTTTTAA 0.965093 -28 TGTGTGCAAGGTGTTTTACTTTTCTTAAAAGGTAATT 12 91 1 GTTTTTTAAA 0.881686 -27 TTTCAAACGTTTTTTTTTTTTTTTTGAAAGAAATTGATT 13 86 0 TTTTTTTAAA 0.965093 -215 TCTCTTGGCTTAATTTTGTACATTTTAAACCACGATGGC 13 140 0 TTTTTTTAAA 0.965093 -161 AATTTTTGCTTTATTTTGGCACTTTAAAAGCTAGTTTTT 13 244 0 TTTTTTTAAA 0.965093 -57 GTTAAACTGCTCTTTTTTTATGTCTTATTTGACCTGTAA 15 44 1 TTTTTTTATT 0.632515 -114 TCAATTAGTCTTATTTTTAAAATTTAAAAATAAAAACTT 15 126 1 TTTTTTTAAA 0.965093 -32 GCCAACCAGGTGCTTTTAGGAAAATTTAATATGGAGCAG 17 107 0 TTTTTATTAA 0.676621 -61 ATAAAACCGTTTCTTTTGGTATTTTGTATAAACAAAATT 22 113 0 TTTTTTTTAT 0.848735 -34 CTGCTAAAACGGCTTTTTAGTGTCTTATAAGCGCTTAGA 24 83 1 GTTTTTTATA 0.695677 -218 GTTATTAACATTGTTTTAACAGGTTATTAACATTGTTTT 24 196 1 TTTTTGTTTA 0.770089 -105 CTCCATTAGCTCATTTTTGCAGTGTTAAAACCGCTTTAA 24 241 1 TTTTTTTAAA 0.965093 -60 TTAAACGCCTTTTTTTAAAGCTTTATAAGCTTTAAAGC 24 273 0 TTTTTTTTAA 0.965093 -28 * **** * * *** Masking position 7 Map Score: 23.2293 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 87 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 2 GTGTTAATTATAAAACTGCTTTGAT 3 5 0 TAAAATGCTT 0.85726 -41 GCTTTAATTATAAGACCGCTTAAAAACTAGC 4 269 0 TAAGACGCTT 0.811778 -32 TTTATCGAGTTAAAACCGTTTTCATTAGCGA 7 15 1 TAAAACGTTT 0.884782 -286 CCTTATTGGCAATAAACGCTTAATCTACTAG 8 49 1 AATAACGCTT 0.908299 -139 TTTCATTTATAAAGACGGTTTTGAGTTACTT 10 13 0 AAAGAGGTTT 0.642595 -163 AAAAAAAAAAAAAAAACGTTTGAAATTGTAA 13 100 1 AAAAACGTTT 0.928212 -201 GATAAGTAAGAAAAACTGCTTTAGTGCCCAC 13 196 0 AAAAATGCTT 0.910008 -105 TTTAGAGAGCAAAAACCGCGTTA 13 288 1 AAAAACGCGT 0.91822 -13 TTTGACCTGTAATAATGGTTTATAGACGTCT 15 71 1 AATAAGGTTT 0.71032 -87 AAAATGGTTTAAAAAGTGCTTAAAGACGTCT 15 94 0 AAAAATGCTT 0.910008 -64 GACTAATTGAAAAAATGGTTTAAAAAGTGCT 15 105 0 AAAAAGGTTT 0.897007 -53 TTAGAGTGCTAAAAAATGTGTTACAATTTAG 20 22 1 AAAAATGTGT 0.542579 -49 TTTCAATAAAACCGTTTCTTTTGGTAT 22 130 0 TAAAACGTTT 0.884782 -17 ATTGAGCTGCTAAAACGGCTTTTTAGTGTCT 24 77 1 TAAAAGGCTT 0.933656 -224 TTTAGTGTCTTATAAGCGCTTAGAAAGCCTT 24 98 1 TATAACGCTT 0.854691 -203 AAAATGGCACAGAAAAGGCTTTCTAAGCGCT 24 112 0 AGAAAGGCTT 0.715344 -189 AAACAATGTTAATAACCGCTTGTAAGCCCCC 24 181 0 AATAACGCTT 0.908299 -120 TTTGCAGTGTTAAAACCGCTTTAAAGCTTAT 24 256 1 TAAAACGCTT 0.954325 -45 TAAAGCTTTAAAAAAAGGCGTTTAA 24 286 1 AAAAAGGCGT 0.883214 -15 ***** ***** Masking position 11 Map Score: 23.603 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 217 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 3 CTCAACCTCCTGAGTGCAAATCAGGTGCTC 4 85 1 TGAGTGCAAA 0.916647 -216 CCTTTTATGTTGAGAGCTAAAAAAGACAAA 5 113 0 TGAGAGCTAA 0.950497 -58 TTAAATGCTTAAAGTGCAAATAAAAATAAT 8 132 0 AAAGTGCAAA 0.861308 -56 TAACTGTCAATGAGTGCTAAAACTTCATAT 9 222 0 TGAGTGCTAA 0.976129 -79 ATAAAGTAAAAGAGAGCCAACCCCCAAGTG 10 52 0 AGAGAGCCAA 0.901058 -124 AGTGCTAACGAGTGGGCTAAAGATTTACCT 10 94 0 AGTGGGCTAA 0.787903 -82 TCGAATGGCTTGAGTGCTAACGAGTGGGCT 10 106 0 TGAGTGCTAA 0.976129 -70 TCAAGCCATTCGAGTGCTAATTTTATATAA 10 123 1 CGAGTGCTAA 0.926388 -53 ACTAGCTTTTAAAGTGCCAAAATAAAGCAA 13 248 1 AAAGTGCCAA 0.870197 -53 TTTAACCTTTAGAGAGCAAAAACCGCGTTA 13 281 1 AGAGAGCAAA 0.894026 -20 TCAAACGCTAAAAGTGCTAACGATTTGTTT 14 14 1 AAAGTGCTAA 0.958499 -42 ATGTTTATGTGCTAAATATTATAAA 14 41 0 TATGTGCTAA 0.820698 -15 AATGGTTTAAAAAGTGCTTAAAGACGTCTA 15 93 0 AAAGTGCTTA 0.64974 -65 TGGTTGGCATTGTAAGCTAATCAGGGCTTT 17 138 1 TGTAAGCTAA 0.366911 -30 TCAAAGTATTAGAGTGCTAAAAAATGTGTT 20 14 1 AGAGTGCTAA 0.985256 -57 AAGAGGTTGAAGAATGCTAAATTGTAACAC 20 39 0 AGAATGCTAA 0.861662 -32 ACACTGCAAAAATGAGCTAATGGAGCCTTT 24 236 0 AATGAGCTAA 0.778335 -65 ********** Masking position 10 Map Score: 21.2049 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 65 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 4 GTGTTAATTATAAAACTGCTTTGAT 3 6 0 TAAAACTGCT 0.966462 -40 GCTTTAATTATAAGACCGCTTAAAAACTAG 4 270 0 TAAGACCGCT 0.940855 -31 TTTATCGAGTTAAAACCGTTTTCATTAGCG 7 15 1 TAAAACCGTT 0.802327 -286 ACTTTAAGCATTTAACTGCTAATTGTTAAT 8 147 1 TTTAACTGCT 0.715026 -41 AATAACTGTCAATGAGTGCTAAAACTTCAT 9 224 0 AATGAGTGCT 0.462113 -77 GATAAGTAAGAAAAACTGCTTTAGTGCCCA 13 197 0 AAAAACTGCT 0.931174 -104 TTTAGAGAGCAAAAACCGCGTTA 13 288 1 AAAAACCGCG 0.707783 -13 ACTCAAACGCTAAAAGTGCTAACGATTTGT 14 12 1 TAAAAGTGCT 0.930389 -44 AAGAGGGCAGTTAAACTGCTCTTTTTTTAT 15 35 1 TTAAACTGCT 0.877546 -123 AAAATGGTTTAAAAAGTGCTTAAAGACGTC 15 95 0 AAAAAGTGCT 0.862544 -63 ACTCAAAGTATTAGAGTGCTAAAAAATGTG 20 12 1 TTAGAGTGCT 0.565168 -59 TTTCAATAAAACCGTTTCTTTTGGTA 22 131 0 TAAAACCGTT 0.802327 -16 ATTGAGCTGCTAAAACGGCTTTTTAGTGTC 24 77 1 TAAAACGGCT 0.870682 -224 TTTAGTGTCTTATAAGCGCTTAGAAAGCCT 24 98 1 TATAAGCGCT 0.868525 -203 AAACAATGTTAATAACCGCTTGTAAGCCCC 24 182 0 AATAACCGCT 0.869911 -119 TTTGCAGTGTTAAAACCGCTTTAAAGCTTA 24 256 1 TAAAACCGCT 0.976008 -45 ********** Masking position 5 Map Score: 16.0171 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 198 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 5 ACGATTACCAAATTAAAGCTTTAGTGCCTA 2 69 0 AATTAAAGCT 0.877063 -232 TGTCCTTATGAATTAAAACAGCACTTACAG 2 147 1 AATTAAAACA 0.699382 -154 GCAGTTTTATAATTAACACTCGAATGATTA 3 17 1 AATTAACACT 0.903433 -29 GCGGTCTTATAATTAAAGCAAGTAGTTTTT 4 281 1 AATTAAAGCA 0.593021 -20 ATTTGATCTAAATAAAACCTGCTGCCAAGC 5 83 1 AATAAAACCT 0.863967 -88 GTGTTGTTAGAATAAAAACCAGTCAAATCA 6 143 1 AATAAAAACC 0.709222 -38 AAGTTTCAACAATAAAAACTAAAAACTCTA 7 126 0 AATAAAAACT 0.885324 -175 TGTGGTTAGTAATTAAAACTAA 8 3 0 AATTAAAACT 0.91928 -185 CCTTATTGGCAATAAACGCTTAATCTACTA 8 49 1 AATAAACGCT 0.79885 -139 TCCAAACCCAAATTTACCCTAAAAAAGGAC 12 55 1 AATTTACCCT 0.67421 -63 ATAAAGCAAAAATTTAACCTTTAGAGAGCA 13 269 1 AATTTAACCT 0.71587 -32 AAAATTTAAAAATAAAAACTTAAA 15 144 1 AATAAAAACT 0.885324 -14 AGTAGTAAAATATAAACTAATTAGAGGA 16 9 1 AATATAAACT 0.674873 -22 TTTTAAGATTAATTAACACT 18 12 1 AATTAACACT 0.903433 -10 AATTATAACAAATTAACCCCTGCTAAAGTC 22 52 0 AATTAACCCC 0.708584 -95 ********** Masking position 6 Map Score: 13.2548 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 94 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 CTTTGGCGGAATTGCTGTAAGTGCTGTTTTAA 2 159 0 ATTGTGAAGT 0.966153 -142 TTAACACTCGAATGATTAAAGTGATAA 3 29 1 AATGTTAAGT 0.938852 -17 CATCCCCATTATTGGTGGAAGTAAATGGACTT 4 129 1 ATTGTGAAGT 0.966153 -172 GGGTGAGGTCGATGGTTCAAGTCCATTTACTT 4 147 0 GATGTTAAGT 0.885728 -154 TTTAGTTTTTATTGTTGAAACTTTTTAAGCCT 7 133 1 ATTGTGAACT 0.928645 -168 CTAAAAAACCAATGCTGACAGTAGTAACGTTA 7 240 0 AATGTGCAGT 0.81824 -61 TGGTTTTTTAGTTGTTTTAAGTATTTGTTATT 7 261 1 GTTGTTAAGT 0.885728 -40 TTAGCAGTTAAATGCTTAAAGTGCAAATAAAA 8 137 0 AATGTTAAGT 0.938852 -51 CAAAAAAGACAATGATTAAGGTCTTATCATTA 9 113 1 AATGTTAGGT 0.707746 -188 CATGGGGGTAATTGGTGTAAGTAATGATAAGA 9 134 0 ATTGTGAAGT 0.966153 -167 ATGTGTGAACGATGTTGGAACTTCCAAACCCA 12 33 1 GATGTGAACT 0.8679 -85 AAAGAAATTGATTGCTTTAACTAACCTGCTTT 13 67 0 ATTGTTAACT 0.875005 -234 TTTAGTGCCCACTGGTGCAACTAGCTTAATCT 13 176 0 ACTGTGAACT 0.80018 -125 **** ** **** Masking position 6 Map Score: 13.0975 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 42 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 7 AATTTTATTAATTTATAAGCCATTGCAACA 2 248 0 ATTTATAAGC 0.839777 -53 GCCAAAGCTAGTTTTTAAGCGGTCTTATAA 4 263 1 GTTTTTAAGC 0.847282 -38 CAAGCTTTGTCTTTTTTAGCTCTCAACATA 5 108 1 CTTTTTTAGC 0.928632 -63 TTTTTTTGTGCTTTTTTACCAGGGAAACCA 6 50 0 CTTTTTTACC 0.855753 -131 ATGCTAATTTCTTTTAAACCCTAAAAAATT 7 54 0 CTTTTAAACC 0.893631 -247 GGAAAATTTAATTTTTAAGCCTAATGCTAA 7 77 0 ATTTTTAAGC 0.926139 -224 ATTGTTGAAACTTTTTAAGCCTTTAATGGG 7 143 1 CTTTTTAAGC 0.979719 -158 CTCTCTTTTACTTTATAACCACCAAAAAAG 10 66 1 CTTTATAACC 0.902102 -110 AATTTTGTACATTTTAAACCACGATGGCAT 13 138 0 ATTTTAAACC 0.68544 -163 TATTTTGGCACTTTAAAAGCTAGTTTTTAC 13 242 0 CTTTAAAAGC 0.884983 -59 TCTTTAAGCACTTTTTAAACCATTTTTTCA 15 99 1 CTTTTTAAAC 0.880206 -59 ATTGTAACACATTTTTTAGCACTCTAATAC 20 19 0 ATTTTTTAGC 0.771333 -52 ACAGAAAAGGCTTTCTAAGCGCTTATAAGA 24 105 0 CTTTCTAAGC 0.901117 -196 CTAATGGAGCCTTTTAAAACAATGTTAATA 24 220 0 CTTTTAAAAC 0.736614 -81 TTTTTTAAAGCTTTATAAGCTTTAAAGCGG 24 271 0 CTTTATAAGC 0.952809 -30 ********** Masking position 8 Map Score: 17.5347 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 113 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 8 GCAAGGGTGATAGCTTTGGCGGAATTGCTG 2 174 0 TAGCTTTGGC 0.962858 -127 CATATAAGATTAAGTTAGGCGTTT 4 5 0 TAAGTTAGGC 0.891353 -296 GCTTAAAAACTAGCTTTGGCTAAATTAATA 4 253 0 TAGCTTTGGC 0.962858 -48 TAAAAAAGACAAAGCTTGGCAGCAGGTTTT 5 96 0 AAAGCTTGGC 0.904675 -75 ATTACCTTTCTAACTTTGGCTGGTTTTGCA 6 88 1 TAACTTTGGC 0.978623 -93 GTCAAATAAAAAAGTTTGGCGCTTTAAATT 9 12 0 AAAGTTTGGC 0.943692 -289 TTTGAAATTGTAAGTTTGTCATGCCATCGT 13 118 1 TAAGTTTGTC 0.836394 -183 ACCCGCATCTTAACCTTGGCAAGGTTATGT 17 63 0 TAACCTTGGC 0.962858 -105 ********** Masking position 2 Map Score: 7.17451 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 22 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 TATGAATTAAAACAGCACTTACAGCAATTC 2 153 1 AACAGCACTT 0.969918 -148 ACGCAAACACAACCGCACTTTACCTAATTG 2 219 0 AACCGCACTT 0.921938 -82 TTTTTATTCTAACAACACTAAGGGTAACTA 6 131 0 AACAACACTA 0.916152 -50 ACGCTAATTTAGCAGCACTATTTCGGTAGT 8 94 1 AGCAGCACTA 0.980712 -94 AAAATAATTTAGCAACACTACCGAAATAGT 8 110 0 AGCAACACTA 0.944997 -78 AATGAAAGAGAGCAGCACTTGGGGGTTGGC 10 37 1 AGCAGCACTT 0.980708 -139 ********** Masking position 7 Map Score: 4.50358 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 26 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 10 TTGATTTTAGGCACTAAAGCTTTAATTTGG 2 62 1 GCACTAAAGC 0.970173 -239 CAAAATCAATACACTCCACCAAATTGGTGT 2 119 0 ACACTCCACC 0.929502 -182 AGGGTCTCAAACCCTCAACCTCCTGAGTGC 4 72 1 ACCCTCAACC 0.929502 -229 GGAAACCAACACACTAAACCATCGCATAAA 6 28 0 ACACTAAACC 0.954017 -153 TGCCAATAAGGCACTCAACCTTGTATATGT 8 30 0 GCACTCAACC 0.988827 -158 CCACTCGTTAGCACTCAAGCCATTCGAGTG 10 109 1 GCACTCAAGC 0.985372 -67 GCACCAGTGGGCACTAAAGCAGTTTTTCTT 13 190 1 GCACTAAAGC 0.970173 -111 ********** Masking position 8 Map Score: 7.80264 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 12 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 11 TCACTGCCAATTAGGTAAAGTGCGGTTGTG 2 212 1 TTAGGTAAAG 0.899708 -89 CAGGTTTTATTTAGATCAAATCTCAATTGG 5 74 0 TTAGATCAAA 0.854765 -97 TTGACAGTTATTAGAGAAAAAATGAGGACT 9 242 1 TTAGAGAAAA 0.86208 -59 TTGTTACCTATTAGATAAAA 9 291 1 TTAGATAAAA 0.958325 -10 AATAGGCCAATTATATAAAATTAGCACTCG 10 133 0 TTATATAAAA 0.721817 -43 ACTTAAATAGTTAGATAAAAGCAGGTTAGT 13 50 1 TTAGATAAAA 0.958325 -251 TAAAAGCAGGTTAGTTAAAGCAATCAATTT 13 65 1 TTAGTTAAAG 0.766843 -236 ATACTTATTTTTAGGTAAAAACTAGCTTTT 13 228 1 TTAGGTAAAA 0.940587 -73 ********** Masking position 3 Map Score: 2.86283 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 33 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 12 CTCAATTGGGAACAGTAAATGATTGGTGGC 5 53 0 AACAGTAAAT 0.669271 -118 CTCTCAACATAAAAGGAAAAGGGGGTGGCA 5 127 1 AAAAGGAAAA 0.914871 -44 GCCAAAGTTAGAAAGGTAATTAAGATGATT 6 78 0 GAAAGGTAAT 0.604877 -103 TCACTGGCATAACAGGAAAATTTAATTTTT 7 91 0 AACAGGAAAA 0.944867 -210 TCTTTTTTTGAACAGGTAAATAATTCAAAA 9 48 1 AACAGGTAAA 0.944867 -253 TAACCACCAAAAAAGGTAAATCTTTAGCCC 10 81 1 AAAAGGTAAA 0.914871 -95 ACCTTTTAAGAAAAGTAAAACACCTTGCAC 12 94 0 AAAAGTAAAA 0.650082 -24 TACTTTTCTTAAAAGGTAATT 12 107 1 AAAAGGTAAT 0.880104 -11 AGCGGATTAAAACAGGAATAGATTTACTTA 13 25 1 AACAGGAATA 0.706872 -276 ACATTGTTTTAACAGGTTATTAACATTGTT 24 203 1 AACAGGTTAT 0.622234 -98 ********** Masking position 4 Map Score: 3.44835 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 94 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 TTGTAAGTTTTAGCATCAACGCTTAAT 2 7 1 GTTTTAGCAC 0.920336 -294 CGCTGCCTTGATTTTAGGCACTAAAGCTTTA 2 55 1 ATTTTAGGCC 0.919981 -246 TAATTATATTAATTTAGCCAAAGCTAGTTTT 4 247 1 AATTTAGCCA 0.824154 -54 TTTTAATTTGGTTTAAGCCACCAATCATTTA 5 37 1 GTTTAAGCCC 0.776738 -134 GCTATTTAGAATTTTATGCGATGGTTTAGTG 6 16 1 ATTTTATGCA 0.227664 -165 CAGGCACGCTAATTTAGCAGCACTATTTCGG 8 89 1 AATTTAGCAC 0.929725 -99 AAATAAAAATAATTTAGCAACACTACCGAAA 8 114 0 AATTTAGCAC 0.929725 -74 AATATATGAAGTTTTAGCACTCATTGACAGT 9 219 1 GTTTTAGCAT 0.640264 -82 CTATTTTATCCCCTTTCTTTGTT 10 163 0 ATTTTATCCC 0.764565 -13 AAATGTACAAAATTAAGCCAAGAGATTAAGC 13 154 1 AATTAAGCCA 0.46794 -147 AATGTGTTACAATTTAGCATTCTTCAACCTC 20 36 1 AATTTAGCAT 0.670854 -35 GTATAAACAAAATTTAGGAACCGCAGAAGAC 22 96 0 AATTTAGGAC 0.844718 -51 CTAAAAAGCCGTTTTAGCAGCTCAATTAACT 24 72 0 GTTTTAGCAC 0.920336 -229 TGTAGGGCTCATTTTAGGCTCAAGCTAGGAA 24 141 0 ATTTTAGGCC 0.919981 -160 ********* * Masking position 6 Map Score: 6.40229 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 132 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 14 GAGTAATTTATTGTAATTCTAA 1 7 0 TAATTTGTAA 0.789485 -16 AGCCTAATGCTAATTTCTTTTAAACCCTAAAAA 7 57 0 TAATTTTTAA 0.816909 -244 ATTTAACTGCTAATTGTTAATAATTGGTAGAAT 8 156 1 TAATTTATAA 0.947025 -32 GTAATTGGTGTAAGTAATGATAAGACCTTAATC 9 126 0 TAAGTTATAA 0.918333 -175 ATTCGAGTGCTAATTTTATATAATTGGCCTATT 10 130 1 TAATTAATAA 0.675603 -46 AGAAGTTAGTTAAATATTAATAAAATTACTATG 11 16 1 TAAATTATAA 0.737155 -27 ACCAATTGGTGATAAGCGGATTAAA 13 3 1 CAATTTATAA 0.755326 -298 TACCTAAAAATAAGTATTGATAAGTAAGAAAAA 13 212 0 TAAGTTATAA 0.918333 -89 AGTGTTAATTAATCTTAAAAA 18 4 0 TAATTTTTAA 0.81687 -18 TAGCAGGGGTTAATTTGTTATAATTTCACGCTT 22 57 1 TAATTTATAA 0.947283 -90 AATTGGCTAATCATTAATAACGG 23 4 0 TAATCTATAA 0.852141 -20 AAAGGCTTTCTAAGCGCTTATAAGACACTAAAA 24 97 0 TAAGCTATAA 0.796062 -204 ***** * **** Masking position 3 Map Score: 6.21909 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 11 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 15 TTATAAATGAAAGAGAGCAGCACTTGGGGG 10 32 1 AAGAGAGCAG 0.985884 -144 TATAAAGTAAAAGAGAGCCAACCCCCAAGT 10 53 0 AAGAGAGCCA 0.933174 -123 ATTTAACCTTTAGAGAGCAAAAACCGCGTT 13 280 1 TAGAGAGCAA 0.904047 -21 GATCAATAAAAAGAGGGCAGTTAAACTGCT 15 25 1 AAGAGGGCAG 0.969196 -133 AAGACATAAAAAAAGAGCAGTTTAACTGCC 15 40 0 AAAAGAGCAG 0.930477 -118 ********** Masking position 4 Map Score: 0.0726476 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 2 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234