AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00640_aful_reg_100.orf -o00640_aful_100.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: AF0672 27 medium-chain acyl-CoA ligase (alkK-3) AF1641 31 enoyl-CoA hydratase (fad-4) Input sequences: #1 AF0196 131 medium-chain acyl-CoA ligase (alkK-1) #2 AF0197 86 acetyl-CoA synthetase (acs-1) #3 AF0366 218 acetyl-CoA synthetase (acs-2) #4 AF0438 79 3-ketoacyl-CoA thiolase (acaB-8) #5 AF0439 82 transcriptional regulatory protein, AsnC family #6 AF0442 300 succinoglycan biosynthesis regulator (exsB) #7 AF0498 197 acyl-coA dehydrogenase (acd-3) #8 AF0673 155 mercuric resistance operon regulatory protein (merR) #9 AF0677 165 acetyl-CoA synthetase (acs-3) #10 AF0685 140 enoyl-CoA hydratase (fad-2) #11 AF0845 73 acyl-CoA dehydrogenase (acd-5) #12 AF0846 112 Na+/H+ antiporter (nhe2) #13 AF0968 205 3-ketoacyl-CoA thiolase (acaB-10) #14 AF0973 108 bile acid-inducible operon protein F (baiF-1) #15 AF1026 150 acyl-CoA dehydrogenase (acd-7) #16 AF1141 35 acyl-CoA dehydrogenase (acd-8) #17 AF1142 221 glucose-1-phosphate cytidylyltransferase (rfbF) #18 AF1287_AF1289 600 AF1287: acetyl-CoA synthetase (acs-6), AF1289: conserved hypothetical protein #19 AF1540 143 succinyl-CoA synthetase, beta subunit (sucC-1) #20 AF1642 50 histidyl-tRNA synthetase (hisS) #21 AF1699 102 pyruvate ferredoxin oxidoreductase, subunit gamma (porG) #22 AF2057 35 acyl-CoA dehydrogenase (acd-10) #23 AF2186 65 succinyl-CoA synthetase, beta subunit (sucC-2) #24 AF2187 174 A. fulgidus predicted coding region AF2187 #25 AF2216 131 methylmalonyl-CoA decarboxylase, biotin carboxyl carrier subunit (mmdC) #26 AF2219 137 methylmalonyl-CoA mutase, subunit alpha, C-terminus (mcmA2) #27 AF2244 300 acyl-CoA dehydrogenase (acd-11) #28 AF2275 63 acyl-CoA dehydrogenase (acd-12) #29 AF2277 49 DNA polymerase, bacteriophage-type #30 AF2389-C 300 acetyl-CoA synthetase, putative #31 AF2426 85 conserved hypothetical protein #32 AF2429 30 enoyl-CoA hydratase (fad-5) Motif number 1 GTTCACCTCCAATTTATAACATTTAATGAGCAAA 2 62 0 ATTATAATTT 0.94372 -25 TTTGCGCAAAAGTGTTTTAATTTTCGCAAAAATT 3 98 1 ATTTTTATTT 0.81557 -121 GTAGTCGTGTAATATTTAATGTTTTCGTGAAATA 4 48 0 ATTTTAATTT 0.943026 -32 GTAAACTAAAAATATAAAAATTTTATGTTTGCCA 5 50 0 ATTAAAATTT 0.90189 -33 GCTATATCTGATTCTTAAAATTTTAAAGATAAAA 7 121 1 ATTTAAATTT 0.90189 -77 TATACTAAGGACTATATAAATTTTTTTGCATTTA 8 44 1 ATTATAATTT 0.94372 -112 CGGCTTTAGGACTTTATAATATTTCCCATCTAAT 8 120 0 ATTATAATTT 0.94373 -36 TCTCATTTTCAAAATATAAGATTTGCCACTTTGT 11 40 0 AATATAATTT 0.761734 -34 ATTTTTATTTTTATATTTTTGTTTTTAACA 13 7 1 ATTTATATTT 0.7088 -199 TATTTCTACAATTTTTTAAAGTTTGAAATCGAAA 14 11 1 ATTTTAATTT 0.943026 -98 GTAATTTTCAAATGTATAAGTTTTTCGATTTCAA 14 33 0 ATTATAATTT 0.94372 -76 CCTACCGAAAAGTTTTAAATCTTTCGCAATTTTA 15 118 0 ATTTAAATTT 0.902065 -33 ATTGTTCTGAAAACTTAAAACTTTTCATTTAATT 18 506 1 AATTAAATTT 0.467659 -95 GTTACTATTTAAATTTTTTGGAAAAGA 19 4 1 ATTTTAATTT 0.943026 -140 TCAATTTTTCAATATAAAAAATTTTCGGAATTTC 19 36 0 ATTAAAATTT 0.90189 -108 AATTCGCTCAACTCTAAAACCTTTTAAACACCCT 20 12 1 ATTAAAATTT 0.902067 -39 CATTTAAAATATTTTTTTAGCTTTCAAAACCTTT 21 38 1 ATTTTTATTT 0.815899 -65 TAACACGCAGAAAATATAAGGTTTTGGT 22 18 1 AATATAATTT 0.761734 -18 TCTTTTTGTGATTATTTAAATTTTGCCAAGTTAA 27 271 0 ATTTTAATTT 0.943026 -30 AATACAAAAGATTTTATTAATTTTACGCTATTTT 28 40 0 ATTATTATTT 0.815899 -24 * * ***** *** Masking position 5 Map Score: 28.2442 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 57 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 2 CTTGATAAGGTCTCGACGTCTTTCACCATC 18 4 0 TCTCCGCTCC 0.9691 -597 ACTTTGAGATTCTCTTCGACGGCATCCCGCTTGATAA 18 33 0 TCTCCGCCCC 0.994732 -568 TCGAAGAGAATCTCAAAGTCCTTAAGCGTGTCAACGG 18 51 1 TCTCAGCTGC 0.577753 -550 ACTTTGCCCACCTCTCCGTCTGCAAGCGGGTCATCGC 18 96 1 CCTCCGCCGC 0.968681 -505 CTCAAGCCCGTCTCACCCTCTTCGAGCAGCATCTTCC 18 171 1 TCTCCCCCGC 0.975536 -430 CCGAGAACTGCCTCATAGTCCACAGCCTTCCGCGGTA 18 241 1 CCTCAGCCCC 0.951646 -360 TAGCGATTTATCGCAGCTACCGCAGCCAGAAACTCTT 25 30 0 TCGCCTCCCC 0.916197 -102 TATTCCCTGAGCTCAACCACTCCCTCCTTCTCTCTCA 25 69 0 GCTCCCCCCC 0.99238 -63 TCTCTCAACCTCGCCGCCATCTTCCAGTTTCTTGG 25 107 0 CCTCCGCCCC 0.991615 -25 GAAAAGACCTTCTCCACCGCCTCAGCCTGAGGCGGAA 27 59 1 TCTCCCCCCC 0.993723 -242 GGCGGAAACAGCTCTTCTATACCCTCCTCCTTTAAAA 27 89 1 GCTCCTTCCC 0.876776 -212 CTTTCAGCAAGCTCCTCCACCTTCACCACTTCAAGTT 27 149 1 GCTCCCCTCC 0.955897 -152 TTAATCCTAATCTCCCCTCTAACTCCCTTAATCACCA 30 183 0 TCTCCTTCCC 0.896363 -118 ATGCTCTCTCAGCTCCTCCTTCAGCTCGTCCGA 30 278 0 TCTCCTCCCA 0.820119 -23 GTTTCCCATAGCTCTAACCCTCCTACCATTCTTCCAA 31 30 0 GCTCACCCCC 0.955897 -56 **** ** * * ** Masking position 4 Map Score: 22.5393 Number of sites scoring better than the average of aligned sites = 716 Number in coding regions = 685 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 3 CTAAACTCCCCCCTTAAAGTCCGTCATC 3 201 0 CTCCCCCTTA 0.93876 -18 ACCCTCAATCCTGCGCCTTTGTCCGCTCGGCAA 6 186 1 CTGCCCTTTC 0.931884 -115 TAACTTTGAAATCCACCTTCTAC 6 288 1 ATCCCCTTCC 0.970009 -13 AAAATAGATAATCCGCCTGTACCGAATTTGTTC 13 145 0 ATCCCCTGTC 0.748156 -61 CATATTTGGAATCCTCCTTTATAATTCTTACTA 15 24 1 ATCCCCTTTA 0.887858 -127 TCAACGGCAACTCCTACTTTGCCCACCTCTCCG 18 81 1 CTCCACTTTC 0.833769 -520 CGGGCTTGAGCACAGCCTTCGACTTTCCAACTC 18 148 0 CACACCTTCC 0.820571 -453 CCTCATAGTCCACAGCCTTCCGCGGTACATGTT 18 251 1 CACACCTTCC 0.820571 -350 AACAACCTCCCTTACCTACATTTTTA 18 585 0 AACCCCCTTC 0.826273 -16 CTGCACATCCAACCACCTTTTAAGTTCGATTTA 19 76 0 AACCCCTTTA 0.759534 -68 ACCACCCCATTTTCAACGAAACCAA 19 129 0 CACCCATTTA 0.528181 -15 GCAGAACCTTCTGCCCCCTCTACAACTTAATAG 24 87 1 CTGCCCCTCC 0.894414 -88 AGCTCAACCACTCCCTCCTTCTCTCTCAGATAG 25 64 0 CTCCTCCTTC 0.70555 -68 CTTCTATACCCTCCTCCTTTAAAATGCCAACAG 27 102 1 CTCCCCTTTA 0.969777 -199 CAGCAAGCTCCTCCACCTTCACCACTTCAAGTT 27 153 1 CTCCCCTTCC 0.992429 -148 AGGCTTACGCCTCCTCCTACATAACTTTTGCGG 30 73 1 CTCCCCTACA 0.769601 -228 GCTCTCTCAGCTCCTCCTTCAGCTCGTCCGACG 30 276 0 CTCCCCTTCC 0.992429 -25 AGGTTTATACCTCCCCATTCTACCCTGCTC 32 11 1 CTCCCATTCC 0.919764 -20 **** ***** * Masking position 7 Map Score: 16.3292 Number of sites scoring better than the average of aligned sites = 1797 Number in coding regions = 1720 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 4 TGAGCAAATTTGCGCAAAAGTGTTTTAATTTTC 3 90 1 TCGAAAATGT 0.693468 -129 TGTTTTAATTTTCGCAAAAATTTTCATTTTTAA 3 110 1 TCGAAAATTT 0.955226 -109 TTTAATGGCAAACATAAAATTTTTATATTTTTA 5 45 1 ACAAAAATTT 0.703137 -38 GGGCGATGACTTCATATAACTTTGAAATCCACC 6 272 1 TCAATAATTT 0.766659 -29 TTCTGGAATATTCGCATAACTTTGAACTTCCAT 7 39 1 TCGATAATTT 0.857266 -159 CTATATCTGATTCTTAAAATTTTAAAGATAAAA 7 122 1 TCTAAAATTT 0.786695 -76 AATACCTAAATGCAAAAAAATTTATATAGTCCT 8 51 0 TCAAAAATTT 0.92108 -105 ATCGGCACATTACGTAAAATTTAAGTATTAACG 13 181 1 TCGAAAATTA 0.910026 -25 AAAGTTTGAAATCGAAAAACTTATACATTTGAA 14 28 1 ACGAAAATTA 0.672413 -81 ACGAAATTTTTTCAAATAAATTTCAAAGTATGT 15 62 1 TCAATAATTT 0.766659 -89 GAGATAAAATTGCGAAAGATTTAAAACTTTTCG 15 114 1 TCGAAGATTA 0.676146 -37 CATGAACTCCTACCGAAAAGTTTTAAATCTTTC 15 127 0 TCCAAAATTT 0.850854 -24 TATGTCATTGTTCTGAAAACTTAAAACTTTTCA 18 500 1 TCTAAAATTA 0.63616 -101 GAATTTCTTTTCCAAAAAATTTAAATAGTAAC 19 10 0 TCAAAAATTA 0.846931 -134 GGAAAAGAAATTCCGAAAATTTTTTATATTGAA 19 30 1 TCCAAAATTT 0.850854 -114 AGAAGTTCATTCCAAATAATTTTAAATAAGTTG 26 27 0 TCAATAATTT 0.766659 -111 GCGGAATTAATCCGAAAAATTTTTACCTATATG 26 96 1 TCGAAAATTT 0.955226 -42 AATACAAAAGATTTTATTAATTTTA 28 49 0 TCAAAGATTT 0.706672 -15 CCAATCAAAAACCGCAAAAGTTATGTAGGAGGA 30 84 0 ACGAAAATTA 0.672413 -217 * ** **** *** Masking position 11 Map Score: 17.3639 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 98 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 5 TGATAATGAATTTAAATTTGCTCATTAAATG 2 46 1 TTTAAATTGC 0.895267 -41 TGTTCCTTTTTAATATCGCTGATTAATTA 3 9 1 TTTAATATGC 0.716607 -210 TTAATTGCAATTAAAATTGCCATTTAATGGC 5 23 1 TTAAAATTCC 0.895516 -60 TTATTGACATTAAAAATTCCATGCCCCCGC 10 121 0 TTAAAAATCC 0.798703 -20 CAAAAAAGCTTTTAATTCACCTGAAGACCAA 12 27 0 TTTAATTCCC 0.823285 -86 ATTATCTATTTTTAAATCGGCACATTACGTA 13 166 1 TTTAAATCGC 0.862579 -40 ATAACGGTGATTAAATTCGGCGAAACACCTG 17 72 1 TTAAATTCGC 0.775894 -150 TCCCATTTGATTTAAATCACCTCCTTATGGG 17 168 1 TTTAAATCCC 0.879386 -54 GGAGAGTTATTTAAAATTACCCATAAGGAGG 17 187 0 TTAAAATTCC 0.895514 -35 ACCCTCCTCCTTTAAAATGCCAACAGCATAA 27 109 1 TTTAAAATCC 0.82132 -192 CAACGGTGCATTAAAAATTGCTCCTCGTTAA 27 188 1 TTAAAAATGC 0.773548 -113 TTGTGATTATTTAAATTTTGCCAAGTTAAAC 27 269 0 TTAAATTTGC 0.825019 -32 AGCAAACTATTTTAATTTGCCTTAAACATTA 29 24 1 TTTAATTTCC 0.863845 -26 ******** ** Masking position 5 Map Score: 8.70134 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 52 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 6 TAAGTTGAAATCAGACCAAAATGGGATTGAAAGTG 6 21 1 TCAACAAGGG 0.634853 -280 ATTCGAACCCTCGAACCCCTACGGGACAGGACCCT 6 156 1 TCGACCAGGG 0.900005 -145 GCGGACAAAGGCGCAGGATTGAGGGTCCTGTCCCG 6 177 0 GCGAGAGGGG 0.826141 -124 GCAGAATTTTTCATCTGAGCGGGGGTTGCCGAGCG 6 209 0 TCACGAGGGG 0.971225 -92 TTTTTCCACGTCGCCCCCGTGGGGTAGCGGATATC 10 46 1 TCGCCCGGGT 0.920369 -95 CGACCCGGGTTCAACTCCCGGCGGGGGCATGGAAT 10 101 1 TCACCCGGGG 0.98174 -40 ATTGCCACAATCGTCGGATTGGGGGCAGCAGCGGT 17 39 0 TCGCGAGGGG 0.989245 -183 TTGATTTAAATCACCTCCTTATGGGTAATTTTAAA 17 174 1 TCACCCAGGG 0.930312 -48 GCCCACCTCTCCGTCTGCAAGCGGGTCATCGCTGT 18 101 1 CCGCGCGGGG 0.973307 -500 GTCGTTTGGGTCGACTGCAAGCGGGATCTGCATTG 30 25 1 TCGCGCGGGG 0.994316 -276 CTCCTTCAGCTCGTCCGACGGCTGGTATCCCTTCC 30 261 0 TCGCGAGTGG 0.87863 -40 *** * ** * *** Masking position 2 Map Score: 8.36461 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 158 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 7 ATTGTGAGCAAATTTGCGCAAAAGTGTTTTAAT 3 86 1 AATTCGAAAA 0.970659 -133 AAAGTGTTTTAATTTTCGCAAAAATTTTCATTT 3 106 1 AATTCGAAAA 0.970659 -113 TATTTTAAAAAACTTGCGAAAGCGTGCTGAGAT 9 102 0 AATTCGAAGC 0.768703 -64 TTAAATCGGCACATTACGTAAAATTTAAGTATT 13 177 1 ACTTCGAAAA 0.873403 -29 TTATTTGAAAAAATTTCGTAAAAATAGTAAGAA 15 48 0 AATTCGAAAA 0.970659 -103 AATTGAGATAAAATTGCGAAAGATTTAAAACTT 15 110 1 AATTCGAAGA 0.934316 -41 TTTGGAAAAGAAATTCCGAAAATTTTTTATATT 19 27 1 AATTCGAAAT 0.839096 -117 AAGAATAAAAAATTAACGGAAAAGGTTTTGAAA 21 59 0 AATACGAAAA 0.937419 -44 CTTTCACAAAAAATAGCGTAAAATTAATAAAAT 28 31 1 AATACGAAAA 0.937419 -33 TAAACCAATCAAAAACCGCAAAAGTTATGTAGG 30 88 0 AAAACGAAAA 0.678223 -213 ** ** ** **** Masking position 10 Map Score: 6.97148 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 26 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 8 CTAAACTCCCCCCTTAAAGTCCGTCATCT 3 200 0 CCCCTTAAAG 0.752665 -19 CGCTCGGCAACCCCCGCTCAGATGAAAAATT 6 209 1 CCCCGCTCAG 0.860632 -92 TTCCACGTCGCCCCCGTGGGGTAGCGGATAT 10 49 1 CCCCGTGGGG 0.969022 -92 GGGAGTTGAACCCGGGTCGAGGAGTCCGCAG 10 89 0 CCCGGTCGAG 0.906408 -52 AAATTCCATGCCCCCGCCGGGAGTTGAACCC 10 107 0 CCCCGCCGGG 0.927437 -34 ACAGCGATGACCCGCTTGCAGACGGAGAGGT 18 105 0 CCCCTTGCAG 0.979165 -496 GCCCGTCTCACCCTCTTCGAGCAGCATCTTC 18 176 1 CCCCTTCGAG 0.979163 -425 GGATAAACTCCCCTCGTGAAGGGAAACTCTC 18 285 1 CCCCGTGAAG 0.962013 -316 AACCTCGCCGCCATCTTCCAGTTTCTTGGAT 25 105 0 CCACTTCCAG 0.804155 -27 CAATGCAGATCCCGCTTGCAGTCGACCCAAA 30 29 0 CCCCTTGCAG 0.979165 -272 *** ******* Masking position 2 Map Score: 5.3512 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 190 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 9 GGTACATTGTTGTGCACTGCAGTGCAATTGTGA 3 60 1 TGGCCTGCGT 0.96616 -159 AAATATGAATTTTGCCTTGCAGCTCTATGCGTA 4 20 0 TTGCTTGCGC 0.848994 -60 TTCTCCAACATTGCCACTGCAGTAGAACTATGT 7 87 1 TTCCCTGCGT 0.976233 -111 CCCCAGTATATTTCTCCAGCTGCAATGACCGCT 17 12 1 TTCTCAGCGC 0.833934 -210 CCAGCTGCAATGACCGCTGCTGCCCCCAATCCG 17 27 1 TGCCCTGCGC 0.993733 -195 CTTCTGTTGGTGTCCTCTGCGGTGCCAAAGCCC 18 210 1 TGCCCTGCGT 0.98776 -391 GATCGTTCTCTTTTCTCTGCTGTGTTT 24 5 0 TTTCCTGCGT 0.84197 -170 GCATAATCGATGGCTATTGCTGCTATATCTGGC 24 145 0 TGCTTTGCGC 0.8601 -30 CTCCTCGCAATGCCCACAGCGGCGGGTAAAACC 27 13 0 TGCCCAGCGC 0.980432 -288 ** ** **** ** Masking position 1 Map Score: 4.93049 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 171 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 ACGAAAAGAAGATTTACACGTCCACTTTCAATCCC 6 43 0 GTTTACTCCC 0.967067 -258 AGCCCCTCAGGATATCCGCTACCCCACGGGGGCGA 10 56 0 GTATCCACCC 0.821091 -85 GTTTATCGGAGGTTTTCCCGACCTCTGGCAAAGAT 17 114 0 GTTTTCACCC 0.97586 -108 ACTCCCATTTGATTTAAATCACCTCCTTATGGGTA 17 166 1 GTTTATACCC 0.72697 -56 CGGCAACTCCTACTTTGCCCACCTCTCCGTCTGCA 18 85 1 TCTTTCACCC 0.680498 -516 TCTCTGCCCAGCTTTTTGCAACCACGGTTTGAGAC 18 416 1 GTTTTCACCC 0.97586 -185 ATTTTTTATTCTTTTAAGCATCCTCAGTTAAGAG 21 79 1 CTTTACTCCC 0.757445 -24 AGGGTTTTACCCGCCGCTGTGGGCATT 27 3 1 GTTTTCGCCC 0.9148 -298 TGCCGGAAAAGACCTTCTCCACCGCCTCAGCCTGA 27 54 1 GCCTTCACCC 0.835952 -247 AACTTGAGATGCTTTCAGCAAGCTCCTCCACCTTC 27 138 1 GTTTCCAGCC 0.794577 -163 ACCCAGAGGAGGCTTACGCCTCCTCCTACATAACT 30 64 1 GCTTACTCCC 0.955678 -237 TTATATAGTTGCCTTCGTCATCCTCAGGAAGGGAT 30 235 1 GCTTCCTCCC 0.954822 -66 AGGTTTATACCTCCCCATTCTACCCT 32 2 1 GTTTACTCCC 0.967067 -29 * **** * *** * Masking position 5 Map Score: 7.69532 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 243 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 11 TCCCATCTAATGATTTATCTGACAAAATAG 8 101 0 TGATTTATCT 0.948752 -55 TAGTTAAAAATGTTTTGTCTAATACTCTAA 9 30 1 TGTTTTGTCT 0.87892 -136 ATATCAGGTATGATTTATCTCAGCACGCTT 9 86 1 TGATTTATCT 0.948752 -80 TTTAAAGGAAAGATTTATCTTGCAAGAGTC 10 13 1 AGATTTATCT 0.813015 -128 ATTATTAAAGTTATTTGTCTGCAATTTTGA 12 72 0 TTATTTGTCT 0.819884 -41 TTCTGCCTATTGATTTGTCTTTGAGTCTTG 24 63 0 TGATTTGTCT 0.967106 -112 ********** Masking position 5 Map Score: 1.45038 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 3 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 CATAAAATTTTTATATTTTTAGTTTACTTTCATACT 5 57 1 TTATTTATTC 0.685883 -26 CTTTTCGTCATCAGAGATATCTTTTACTTGGACATGC 6 70 1 TGAGATCTTC 0.899022 -231 GTTCTAGATTTGGTATATAACCTTTACTTAATGTTGT 7 164 0 TTATATCTTC 0.875128 -34 TTTTACGCGTTTAGATTTTTCATTTGCTCTCGTAATT 13 84 0 TGATTTCTTC 0.965035 -122 TATCTCAATTTAAGATTTTGATTTGACATACTTTGAA 15 83 0 TGATTTATTC 0.846032 -68 TAAAAAATGGGTCTATATTTCTTTTTC 16 1 0 GTATATCTTC 0.837295 -35 GTGGGCAAAGTAGGAGTTGCCGTTGACACGCTTAAGG 18 70 0 TGAGTTCTTC 0.933035 -531 CGGCTATCCGGGAGAGTTTCCCTTCACGAGGGGAGTT 18 290 0 GGAGTTCTTC 0.910961 -311 ACCTTTTAAGTTCGATTTAACATTCTCAATTTTTCAA 19 58 0 TGATTTCTTC 0.965034 -86 GCTATATCTGGCTGATATAGCCTTTTCTCGTCGAATT 24 120 0 GGATATCTTC 0.928316 -55 TTCCAGTTTCTTGGATATTCCCTGAGCTCAACCACTC 25 84 0 TGATATCTGC 0.735564 -48 CTCTTTTTGTGATTATTTAAATTTTGCCAAGTTAAAC 27 269 0 GTATTTATTC 0.615837 -32 TTCAGCAATCTGCTATTTGACGTTTCCCATAGCTCTA 31 51 0 TTATTTCTTC 0.916441 -35 * ***** * ** * Masking position 5 Map Score: 5.59031 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 89 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 13 TATAACATTTAATGAGCAAATTTAAATTCAT 2 51 0 AAGAGCAAAT 0.573515 -36 CTCTGATGACGAAAAGAAGATTTACACGTCC 6 55 0 GAAAGAAGAT 0.761259 -246 CCCCCGCTCAGATGAAAAATTCTGCATAGGA 6 219 1 GAGAAAAATT 0.381665 -82 ATATTTTGAAAATGAGAAGTTAAAATC 11 57 1 AAGAGAAGTT 0.693548 -17 GCTGGGCAGAGAGAAGAAAAGTTCGAGACAC 18 397 0 GAAAGAAAAG 0.712552 -204 GAAAGAATGGGAAGAGAAATGTCTCAAACCG 18 440 0 GAGAGAAATG 0.919608 -161 GACGAATATAAATGAGAAAAGGAAAGAATGG 18 461 0 AAGAGAAAAG 0.637604 -140 AAATTTTTTGGAAAAGAAATTCCGAAAATTT 19 21 1 GAAAGAAATT 0.716759 -123 AAACACAGCAGAGAAAAGAGAACGATCG 24 8 1 GCGAGAAAAG 0.59195 -167 AATAGAATTCGACGAGAAAAGGCTATATCAG 24 115 1 GAGAGAAAAG 0.919608 -60 AATTTTGGGCGATGAGAAGTTCATTCCAAAT 26 43 0 GAGAGAAGTT 0.936364 -95 TGGGCATTGCGAGGAGCAGATTTTTGCCGGA 27 30 1 GAGAGCAGAT 0.916783 -271 GGAGGGTATAGAAGAGCTGTTTCCGCCTCAG 27 85 0 GAGAGCTGTT 0.640078 -216 TGAGTTTAACGAGGAGCAATTTTTAATGCAC 27 193 0 GAGAGCAATT 0.897363 -108 ATAGTTTGCTGATAAGAAGTTTT 29 3 0 GAAAGAAGTT 0.761259 -47 CGAGCTGAAGGAGGAGCTGAGAGAGCAT 30 283 1 GAGAGCTGAG 0.635312 -18 ** ******** Masking position 5 Map Score: 5.20412 Number of sites scoring better than the average of aligned sites = 1420 Number in coding regions = 1349 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 14 TTTTTAATCGTTAATCCCAAATAAAGTTAAATA 3 136 1 TTAATCAAAA 0.955184 -83 CAAATAAAGTTAAATATCAATAATTTAACCTAT 3 153 1 TAAATCAATA 0.671819 -66 TACTTACACTTTAATTGCAATTAAAATTGCCAT 5 13 1 TTAATCAATA 0.935699 -70 AAATTGCCATTTAATGGCAAACATAAAATTTTT 5 36 1 TTAATCAAAA 0.955178 -47 CATGGAATTTTTAATGTCAATAA 10 128 1 TTAATCAATA 0.923744 -13 AAACAGCGTGTTAAAAACAAAAATATAAAAATA 13 16 0 TTAAACAAAA 0.74997 -190 GTATTTAGCTTTAATGTCAATAATTAATTACGA 13 59 1 TTAATCAATA 0.923744 -147 CGATGAGAAGTTCATTCCAAATAATTTTAAATA 26 32 0 TTCATCAAAA 0.816367 -106 TTTAGCGGAATTAATCCGAAAAATTTTTACCTA 26 92 1 TTAATGAAAA 0.734024 -46 CAAAATTTAAATAATCACAAAAAGAGCCTGC 27 280 1 ATAATCAAAA 0.749969 -21 ***** **** * Masking position 9 Map Score: 3.08482 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 10 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 15 AGGGTCCTGTCCCGTAGGGGTTCGAGGGTT 6 161 0 CCCGTAGGGG 0.952176 -140 CCACGTCGCCCCCGTGGGGTAGCGGATATC 10 51 1 CCCGTGGGGT 0.92021 -90 TAGCGGATATCCTGAGGGGCTGCGGACTCC 10 70 1 CCTGAGGGGC 0.920969 -71 GAAGATGCTGCTCGAAGAGGGTGAGACGGG 18 177 0 CTCGAAGAGG 0.751523 -424 TAAAATGACGCCTGAAGAGTTTCTGGCTGC 25 16 1 CCTGAAGAGT 0.816476 -116 CCCGTAGGGGAGTAGTTGTC 26 128 0 CCCGTAGGGG 0.952176 -10 ACCGCCTCAGCCTGAGGCGGAAACAGCTCT 27 74 1 CCTGAGGCGG 0.945101 -227 ATTGTTTCACCCAGAGGAGGCTTACGCCTC 30 56 1 CCAGAGGAGG 0.920732 -245 GGTATCCCTTCCTGAGGATGACGAAGGCAA 30 243 0 CCTGAGGATG 0.78932 -58 ********** Masking position 1 Map Score: 1.8964 Number of sites scoring better than the average of aligned sites = 383 Number in coding regions = 353 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