AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00280_aful_reg_100.orf -o00280_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: AF0033 36 acyl carrier protein synthase (acaA-1) AF0672 27 medium-chain acyl-CoA ligase (alkK-3) Input sequences: #1 AF0006 104 corrinoid methyltransferase protein (mtaC-1) #2 AF0008 73 oxalate/formate antiporter (oxlT-1) #3 AF0014 95 A. fulgidus predicted coding region AF0014 #4 AF0016 54 A. fulgidus predicted coding region AF0016 #5 AF0018 22 3-ketoacyl-CoA thiolase (acaB-1) #6 AF0135 59 conserved hypothetical protein #7 AF0136 103 A. fulgidus predicted coding region AF0136 #8 AF0196 131 medium-chain acyl-CoA ligase (alkK-1) #9 AF0197 86 acetyl-CoA synthetase (acs-1) #10 AF0283 168 3-ketoacyl-CoA thiolase (acaB-7) #11 AF0438 79 3-ketoacyl-CoA thiolase (acaB-8) #12 AF0439 82 transcriptional regulatory protein, AsnC family #13 AF0442 300 succinoglycan biosynthesis regulator (exsB) #14 AF0498 197 acyl-coA dehydrogenase (acd-3) #15 AF0673 155 mercuric resistance operon regulatory protein (merR) #16 AF0685 140 enoyl-CoA hydratase (fad-2) #17 AF0845 73 acyl-CoA dehydrogenase (acd-5) #18 AF0846 112 Na+/H+ antiporter (nhe2) #19 AF0932 41 conserved hypothetical protein #20 AF0933 22 branched-chain amino acid aminotransferase (ilvE) #21 AF0968 205 3-ketoacyl-CoA thiolase (acaB-10) #22 AF1025_AF1026 150 AF1025: 3-hydroxyacyl-CoA dehydrogenase (hbd-4), AF1026: acyl-CoA dehydrogenase (acd-7) #23 AF1029 193 long-chain-fatty-acid--CoA ligase (fadD-5) #24 AF1122 111 3-hydroxyacyl-CoA dehydrogenase (hbd-5) #25 AF1141 35 acyl-CoA dehydrogenase (acd-8) #26 AF1142 221 glucose-1-phosphate cytidylyltransferase (rfbF) #27 AF1173 180 A. fulgidus predicted coding region AF1173 #28 AF1174 61 A. fulgidus predicted coding region AF1174 #29 AF1177 103 3-hydroxyacyl-CoA dehydrogenase (hbd-6) #30 AF1191 32 dihydroxynaphthoic acid synthase (menB) #31 AF1192 50 conserved hypothetical protein #32 AF1195 27 activator 1, replication factor C, 53 KD subunit #33 AF1196 65 N5,N10-methylenetetrahydromethanopterin reductase (mer-2) #34 AF1197 300 3-ketoacyl-CoA thiolase (fadA-2) #35 AF1208 165 conserved hypothetical protein #36 AF1289 300 conserved hypothetical protein #37 AF1641 31 enoyl-CoA hydratase (fad-4) #38 AF1642 50 histidyl-tRNA synthetase (hisS) #39 AF2013 275 coenzyme F390 synthetase (ftsA-3) #40 AF2014 63 sugar transporter, putative #41 AF2057 35 acyl-CoA dehydrogenase (acd-10) #42 AF2216 131 methylmalonyl-CoA decarboxylase, biotin carboxyl carrier subunit (mmdC) #43 AF2219 137 methylmalonyl-CoA mutase, subunit alpha, C-terminus (mcmA2) #44 AF2243 38 3-ketoacyl-CoA thiolase (fadA-3) #45 AF2244 300 acyl-CoA dehydrogenase (acd-11) #46 AF2271 177 A. fulgidus predicted coding region AF2271 #47 AF2272 87 A. fulgidus predicted coding region AF2272 #48 AF2273 57 3-hydroxyacyl-CoA dehydrogenase (hbd-10) #49 AF2275 63 acyl-CoA dehydrogenase (acd-12) #50 AF2277 49 DNA polymerase, bacteriophage-type #51 AF2416 115 3-ketoacyl-CoA thiolase (acaB-12) #52 AF2426 85 conserved hypothetical protein #53 AF2429 30 enoyl-CoA hydratase (fad-5) Motif number 1 GTTAATTAAAAAAAATTTTATAAAATGATTTG 3 17 0 AAAATTTATA 0.684299 -79 AATTAACAACAAAAAGTTAATTAAAAAAAATT 3 32 0 AAAATTAATT 0.840569 -64 ATTGACAAAGAAAAGTTAAAAA 4 1 0 AAAATAAAAA 0.79543 -54 TAAATTCCTTAAAAATTTAATATTTGCTCATT 6 26 1 AAAATTAATA 0.912372 -34 GGGAAAACAGGAAGTTACCGTTTTC 8 4 1 AAAAGGAAGT 0.480121 -128 TATCATCTTAAAAAATTGAATTATGCTCAAAG 9 19 0 AAAATGAATT 0.734909 -68 AGTTTGCTGCAAAATCTTTAATGGTCGTTCTG 10 51 1 AAAATTTAAT 0.555753 -118 TATATATCCAAAAAATTTAAGTTTGCTCTGCC 10 90 0 AAAATTAAGT 0.78818 -79 ATATTTCACGAAAACATTAAATATTACACGAC 11 47 1 AAAATTAAAT 0.85733 -33 AAGTAAACTAAAAATATAAAAATTTTATGTTT 12 54 0 AAAATAAAAA 0.79543 -29 TTTTATCTTTAAAATTTTAAGAATCAGATATA 14 123 0 AAAATTAAGA 0.880215 -75 CCTAAATGCAAAAAAATTTATATAGTCCTTAG 15 48 0 AAAATTTATA 0.684299 -108 GTTAAAAACAAAAATATAAAAATAAAAAT 21 8 0 AAAATAAAAA 0.79543 -198 CTAAACGCGTAAAAATTGAATATATCAAGTAT 21 107 1 AAAATGAATA 0.845554 -99 ACTCCTACCGAAAAGTTTTAAATCTTTCGCAA 22 17 1 AAAATTTAAA 0.711857 -134 ATGTCAAATCAAAATCTTAAATTGAGATAAAA 22 49 0 AAAATTAAAT 0.85733 -102 AAATTTCGTAAAAATAGTAAGAATTATAAAGG 22 101 1 AAAAGTAAGA 0.77621 -50 AATATAATCCAAAAAAGTAATTCACTAAAAGC 23 64 0 AAAAGTAATT 0.71335 -130 ATATTTTCGCAAAATCTGAAAAATTTGAATGG 23 91 1 AAAATGAAAA 0.861877 -103 GTAAAAAGCGAAAAGTTTTAAAAGGCTGAAAA 23 158 1 AAAATTTAAA 0.711857 -36 AAAGGCTGAAAAAATAGTTAAAGACA 23 178 1 AAAAGTTAAA 0.538341 -16 TTTTTTACTAAAAATGGTAATAGAGGCGTAAT 24 11 0 AAAAGTAATA 0.830924 -101 AGATTTCAACAAAAGTGGAATTTTTTACTAAA 24 31 0 AAAAGGAATT 0.566827 -81 GAAAAATGTTAAAAGGAGAGTTAT 26 208 0 AAAATTAAAA 0.922282 -14 ATAATTATGGAAAAGCTTAAATGGTTTGAATT 27 33 0 AAAATTAAAT 0.85733 -148 TTGTAATCTCAAAAGATTAAAATACTCTTCAA 28 26 1 AAAATTAAAA 0.922282 -36 AAATTACAGCAAAATAGTAATATATATGTTAA 31 16 1 AAAAGTAATA 0.830924 -35 TATCTGTTGGAAAAAATAAAAATTAAAA 33 7 0 AAAATAAAAA 0.79543 -59 TCTGTTAAAGAAAAGGTAAATACTACAAATAG 35 16 0 AAAATAAATA 0.77332 -150 TTTAGCTTCAAAAAAGTTAATTTAAGTATGTT 35 142 0 AAAATTAATT 0.840569 -24 AAGCTGCCAGAAAAGAGGAAGAAAGA 36 285 1 AAAAGGAAGA 0.645866 -16 TAAAGAATTAAAAAGCTAAAAATTTTATGCAA 40 35 0 AAAATAAAAA 0.79543 -29 TGCACCGTTGAAAACTTGAAGTGGTGAAGGTG 45 166 0 AAAATGAAGT 0.661771 -135 TTAACTTGGCAAAATTTAAATAATCACAAAAA 45 271 1 AAAATAAATA 0.77332 -30 ACAAAAAAGAAAAAGGTTAAAACTTAGTCAAC 46 143 1 AAAATTAAAA 0.922282 -35 AATAAAATGGAAAAACTTAATACAT 48 43 1 AAAATTAATA 0.912372 -15 **** ****** Masking position 4 Map Score: 35.9591 Number of sites scoring better than the average of aligned sites = 417 Number in coding regions = 173 Number in noncoding regions = 244 Number of orfs with sites within 600 bp upstream = 245 Fraction of orfs with sites within 600 bp upstream = 0.0393511 Motif number 2 TAGGGTGTTCCTTCAACCCCTACTCAATCT 7 26 0 CTTCAACCCC 0.677255 -78 ACCACCACCCCTTTTTTATTG 8 121 0 CCACCACCCC 0.914611 -11 GGTTCGAATCCCTCCCCCCGCATTTAGTTC 13 135 0 CCTCCCCCCG 0.791828 -166 TTTGTCCGCTCGGCAACCCCCGCTCAGATG 13 203 1 CGGCAACCCC 0.908928 -98 AATTTTTCCACGTCGCCCCCGTGGGGTAGC 16 44 1 CGTCGCCCCC 0.965267 -97 CTCAGGATATCCGCTACCCCACGGGGGCGA 16 56 0 CCGCTACCCC 0.960226 -85 GTCGAGGAGTCCGCAGCCCCTCAGGATATC 16 75 0 CCGCAGCCCC 0.97387 -66 GCTGCGGACTCCTCGACCCGGGTTCAACTC 16 88 1 CCTCGACCCG 0.769634 -53 ATTAAAAATTCCATGCCCCCGCCGGGAGTT 16 113 0 CCATGCCCCC 0.682003 -28 GCAATGACCGCTGCTGCCCCCAATCCGACG 26 33 1 CTGCTGCCCC 0.901396 -189 ACCATTGCCGCCTCTGCCTCTTTTGAGCAT 29 19 0 CCTCTGCCTC 0.82136 -85 TGTTTATTCCCGGCACCCCCATTTCGGAAA 36 235 1 CGGCACCCCC 0.956614 -66 GTTCAAATCTCGGCGGCCCCATCATTGAAC 39 87 0 CGGCGGCCCC 0.978008 -189 CCAGGCTACCCTACGGCCCCTCTGTAATGA 39 150 1 CTACGGCCCC 0.887262 -126 CTGAGCTCAACCACTCCCTCCTTCTCTCTC 42 70 0 CCACTCCCTC 0.817992 -62 TCTCTCAACCTCGCCGCCATCTTCCAGT 42 114 0 CCTCGCCGCC 0.790677 -18 AAGACCTTCTCCACCGCCTCAGCCTGAGGC 45 62 1 CCACCGCCTC 0.79134 -239 CCCAAACCTTCGGCTCCCTCGGATAATTTT 51 29 0 CGGCTCCCTC 0.834902 -87 ********** Masking position 7 Map Score: 17.5649 Number of sites scoring better than the average of aligned sites = 680 Number in coding regions = 625 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 3 TCAGTTCATAACAAAATTATCTGACTTTTGATT 1 28 0 AAAATTATTG 0.77302 -77 TGAGCAAATATTAAATTTTTAAGGAATTTACAT 6 23 0 TAAATTTTAG 0.884274 -37 CAGAGCAAACTTAAATTTTTTGGATATATAGGC 10 92 1 TAAATTTTGG 0.83718 -77 ACTAAAAATATAAAAATTTTATGTTTGCCATTA 12 47 0 TAAATTTTTG 0.930541 -36 AAGGTGGATTTCAAAGTTATATGAAGTCATCGC 13 274 0 TAAATTATTG 0.92365 -27 TGATGGAAGTTCAAAGTTATGCGAATATTCCAG 14 41 0 TAAATTATCG 0.871186 -157 AATTTTATCTTTAAAATTTTAAGAATCAGATAT 14 124 0 TAAATTTTAG 0.884273 -74 TAAGGACTATATAAATTTTTTTGCATTTAGGTA 15 49 1 AAAATTTTTG 0.790421 -107 TACGAAATTATTAAAGTTATTTGTCTGCAATTT 18 75 0 TAAATTATTG 0.92365 -38 GCGAAAGATTTAAAACTTTTCGGTAGGAGTTCA 22 14 0 TAAATTTTGG 0.83718 -137 TGACATACTTTGAAATTTATTTGAAAAAATTTC 22 75 1 TAAATTATTG 0.92365 -76 CTGAAGCCATTCAAATTTTTCAGATTTTGCGAA 23 96 0 TAAATTTTAG 0.884274 -98 GTCAGGTGGGAAAAAATTTTGAGGTGGGCATAG 27 83 1 AAAATTTTAG 0.682648 -98 GGTAAAATAATAACAATTATATGGCTTTAAACG 27 148 1 TACATTATTG 0.561946 -33 CTGAGGCCCGAGAAAGTTATGAGGGA 29 88 1 AAAATTATAG 0.660146 -16 ATTAAAAAGCTAAAAATTTTATGCAAATAAATA 40 28 0 TAAATTTTTG 0.930541 -36 GCCAACTTATTTAAAATTATTTGGAATGAACTT 43 25 1 TAAATTATTG 0.92365 -113 GTCATATAGGTAAAAATTTTTCGGATTAATTCC 43 98 0 TAAATTTTCG 0.882171 -40 CCGATGCGATTGAAAATTATCCGAGGGAGCCGA 51 17 1 TAAATTATCG 0.871186 -99 * *** **** ** Masking position 7 Map Score: 23.9367 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 56 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 4 AGTCAGATAATTTTGTTATGAACTGATTCATA 1 35 1 TTTTTATGAA 0.791951 -70 TCATAACAGCTTTTATCTTTAGAAGGCCTATT 1 62 1 TTTTTTTTAG 0.798971 -43 AGAAGGCCTATTTTCTAATTTGGAGGTGTTTA 1 82 1 TTTTTATTTG 0.739718 -23 TTTTTTCTTATTTATGAACCAGTT 2 3 1 TTTTTATTTA 0.817087 -71 TTATAAAATTTTTTTTAATTAACTTTTTGTTG 3 26 1 TTTTTATTAA 0.918013 -70 TTAATTAACTTTTTGTTGTTAATTAATTATTT 3 40 1 TTTTTGTTAA 0.657793 -56 AAATTTAATATTTGCTCATTAATAATTGTTAC 6 38 1 TTTGTATTAA 0.791951 -22 ATGAGCACGATTTGTTTATTTATGATGATAAA 8 57 1 TTTGTATTTA 0.602957 -75 CCACCACCCCTTTTTTATTGAATAATAATTTC 8 109 0 TTTTTTTGAA 0.679869 -23 TGAATTTAAATTTGCTCATTAAATGTTATAAA 9 52 1 TTTGTATTAA 0.791951 -35 AAAGAAAGGCTTTTATGTTGAGTAAATAAAGG 10 142 1 TTTTTTTGAG 0.574672 -27 TCAAAACAAATTTTATCTTTAAAATTTTAAGA 14 133 0 TTTTTTTTAA 0.862013 -65 ATTTTTATATTTTTGTTTTTAACACGCTGTTT 21 17 1 TTTTTTTTAA 0.862013 -189 TCCTTCACTTTTTTCTTATTAAAATACCATCC 34 271 0 TTTTTATTAA 0.918014 -30 GTTTTTTAATTAATCATAACCTT 37 2 1 TTTTTATTAA 0.918013 -30 ATTTTTTATTATTTGAAAAACGTTT 44 4 1 TTTTTATTTG 0.739718 -35 ATATAAAAAATTTTTTTATTTGTTTTGATTAA 46 31 1 TTTTTATTTG 0.739718 -147 AACCTTTTTCTTTTTTGTTTAACCATTAAAGT 46 129 0 TTTTTTTTAA 0.862013 -49 **** * ***** Masking position 6 Map Score: 11.4218 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 13 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 5 ACTGATTCATAACAGCTTTTATCTTTAGAAG 1 56 1 AACAGTTTTA 0.853186 -49 ACCAGTTCATAACAGCCTTTATTTAGCACTC 2 28 1 AACAGCTTTA 0.649657 -46 AGTTAATTAAAAAAAATTTTATAAAATGATT 3 19 0 AAAAATTTTA 0.642669 -77 CAAACTATGCAACAGTTTTTAAAATCGGAGT 10 26 0 AACAGTTTTA 0.853186 -143 TACTCAACATAAAAGCCTTTCTTTATTTTGA 10 135 0 AAAAGCTTTC 0.771769 -34 TGAACATCAAAAAAGCTTTTAATTCACCTGA 18 34 0 AAAAGTTTTA 0.950629 -79 AGCTGATTTAAAACGTTTTTCCGTT 19 5 0 AAACGTTTTC 0.817541 -37 ACTCCTACCGAAAAGTTTTAAATCTTTCGCA 22 17 1 AAAAGTTTAA 0.709165 -134 GCTTTGAAGACAAAGATTTTATTTTGTTTCG 23 24 0 CAAAGTTTTA 0.660129 -170 GTAAAAAGCGAAAAGTTTTAAAAGGCTGAAA 23 158 1 AAAAGTTTAA 0.709165 -36 TGCCCACCTCAAAATTTTTTCCCACCTGACT 27 82 0 AAAATTTTTC 0.588064 -99 AAGGGTGTTTAAAAGGTTTTAGAGTTGAGCG 38 16 0 AAAAGTTTTA 0.950629 -35 CAGTATTAAAAAACGGTTTTCCCGCCAGTTC 39 60 1 AAACGTTTTC 0.817541 -216 CGTTTGCAGCAAAAGGCTTTAAAAGCCACTG 39 187 0 AAAAGCTTTA 0.858768 -89 AATTAATCCGAAAAATTTTTACCTATATGAC 43 100 1 AAAAATTTTA 0.642669 -38 ATCACCCTGCAAACGTTTTTCAAATAATAAA 44 15 0 AAACGTTTTC 0.817541 -24 AAACAATTGAAAAAGGATTTAAATAGAACAC 45 242 0 AAAAGATTTA 0.608046 -59 AACAAATAAAAAAATTTTTTATATGCCACCA 46 24 0 AAAATTTTTA 0.72074 -154 AATACAAAAGATTTTATTAATTTTAC 49 48 0 AAAAGTTTTA 0.950629 -16 TCTTATCAGCAAACTATTTTAATTTGCCTTA 50 17 1 AAACTTTTTA 0.519683 -33 ***** ***** Masking position 8 Map Score: 15.7785 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 82 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 6 TCCAGAATTCGAATTGGAAAATTCGTTCGTGAGAG 14 11 0 GATTGGATCG 0.5625 -187 TAGTTCTACTGCAGTGGCAATGTTGGAGAATGAAA 14 82 0 GCGTGGATTG 0.932406 -116 CCACGGGGGCGACGTGGAAAAATTGGACTCTTGCA 16 33 0 GAGTGGATTG 0.905756 -108 ATCCTGAGGGGCTGCGGACTCCTCGACCCGGGTTC 16 78 1 GCGCGGTTCG 0.673447 -63 ATTGGGGGCAGCAGCGGTCATTGCAGCTGGAGAAA 26 22 0 GCGCGGAGCA 0.858244 -200 AAAAAATTTTGAGGTGGGCATAGTGCTCATAACAA 27 93 1 GAGTGGAGTG 0.972971 -88 AAAAGAGGCAGAGGCGGCAATGGTTAGGTTCTGAT 29 25 1 GAGCGGAGTT 0.906272 -79 CGTCCTTCATGAAGCGCTAAGAGCTTCATTCTCTT 34 122 0 GAGCGCAGCT 0.666763 -179 CACACCGCAGGAGGTGGCGATGGCTGCAGTGGATG 36 23 1 GAGTGGAGCT 0.924225 -278 AGTGGATGAAGACGTGGATGTTGTGGGCATAAGTC 36 50 1 GAGTGGGGTG 0.899884 -251 AGTCTTCACAGCGGTGCTCATCTTGCTTTAGTGCC 36 81 1 GCGTGCATTG 0.665414 -220 GCTCAAGCTTCGGCAAGGGTGTTTAAAAGGT 38 30 0 GCTCGGAGTG 0.845667 -21 AGAGTTTCTGGCTGCGGTAGCTGCGATAAATCGCT 42 31 1 GCGCGGGGCG 0.954688 -101 TTTACCCGCCGCTGTGGGCATTGCGAGGAGCAGAT 45 16 1 GCGTGGAGCG 0.986695 -285 TCAGGCTGAGGCGGTGGAGAAGGTCTTTTCCGGCA 45 54 0 GCGTGGAGTC 0.846025 -247 GCCTCAGCCTGAGGCGGAAACAGCTCTTCTATACC 45 77 1 GAGCGGAGCT 0.932787 -224 TTGAAAACTTGAAGTGGTGAAGGTGGAGGAGCTTG 45 156 0 GAGTGGAGTG 0.972971 -145 ** **** * *** Masking position 6 Map Score: 14.7842 Number of sites scoring better than the average of aligned sites = 684 Number in coding regions = 644 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 TGATAATGAATTTAAATTTGCTCATTAAATG 9 46 1 TTAAATTTGC 0.889173 -41 TTAATTGCAATTAAAATTGCCATTTAATGGC 12 23 1 TTAAATTGCC 0.879313 -60 TTATTGACATTAAAAATTCCATGCCCCCGC 16 121 0 TTAAAATTCC 0.755155 -20 CAAAAAAGCTTTTAATTCACCTGAAGACCAA 18 27 0 TTAATTCACC 0.645405 -86 TTCATGAAATTTCAAAATTGCAGACAAATAA 18 61 1 TTAAAATTGC 0.775825 -52 GGAAAAACGTTTTAAATCAGCTGATTAACTC 19 14 1 TTAAATCAGC 0.825624 -28 ATTATCTATTTTTAAATCGGCACATTACGTA 21 166 1 TTAAATCGGC 0.902935 -40 TCCACTTTTGTTGAAATCTGCAAGGCAATGC 24 44 1 TTAAATCTGC 0.901273 -68 ATAACGGTGATTAAATTCGGCGAAACACCTG 26 72 1 TTAATTCGGC 0.800504 -150 TCCCATTTGATTTAAATCACCTCCTTATGGG 26 168 1 TTAAATCACC 0.808412 -54 GGAGAGTTATTTAAAATTACCCATAAGGAGG 26 187 0 TTAAATTACC 0.787613 -35 AAAACCGTTTTTTAATACTGCCAGATACTGT 39 49 0 TTAATACTGC 0.629438 -227 TTTTTAATTCTTTAAATTTCC 40 53 1 TTAAATTTCC 0.877301 -11 ACCCTCCTCCTTTAAAATGCCAACAGCATAA 45 109 1 TTAAAATGCC 0.758619 -192 CAACGGTGCATTAAAAATTGCTCCTCGTTAA 45 188 1 TTAAAATTGC 0.775825 -113 TTGTGATTATTTAAATTTTGCCAAGTTAAAC 45 269 0 TTAATTTTGC 0.775825 -32 AGCAAACTATTTTAATTTGCCTTAAACATTA 50 24 1 TTAATTTGCC 0.758619 -26 ** ******** Masking position 5 Map Score: 13.2289 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 105 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 8 GTAACAATTATTAATGAGCAA 6 49 0 TAACAATTAT 0.786617 -11 TTATTGAACATAACAATTAATCAAAAAT 7 86 1 TAACAATTAA 0.936936 -18 CTCCAATTTATAACATTTAATGAGCAAATT 9 60 0 TAACATTTAA 0.925874 -27 AGTAGTCGTGTAATATTTAATGTTTTCGTG 11 53 0 TAATATTTAA 0.582626 -27 GCACATTACGTAAAATTTAAGTATTAACGA 21 185 1 TAAAATTTAA 0.777087 -21 GGTAAAATAATAACAATTATATGGCTTTAA 27 148 1 TAACAATTAT 0.786617 -33 GCTAACATTTAAACATTGTAAT 28 3 1 TAACATTTAA 0.925874 -59 TTGGAAAAAATAAAAATTAAAA 33 3 0 TAAAAATTAA 0.807335 -63 TTGTTTTGATTAAAATTTAATATCTCAGGT 46 50 1 TAAAATTTAA 0.777087 -128 CCTTTCAAGTTAACAATTAACTGCAGAAGT 46 89 0 TAACAATTAA 0.936936 -89 CTTTTTTGTTTAACCATTAAAGTCAAAAAT 46 122 0 TAACCATTAA 0.736699 -56 ********** Masking position 3 Map Score: 6.80232 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 3 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 GTAGAAGGTGGATTTCAAAGTTA 13 288 0 AAAGGTGGAT 0.611553 -13 GTAAGAATTATAAAGGAGGATTCCAAATATG 22 117 1 TAAGGAGGAT 0.921552 -34 AAAATTACCCATAAGGAGGTGATTTAAATCA 26 175 0 AAAGGAGGTG 0.921386 -47 AAGAAAAAAGTGAAGGAGGTGTATT 34 286 1 TAAGGAGGTG 0.969711 -15 GAAGCTCGTTTAAACGAGGTGTGGCTGATAT 35 67 1 TAACGAGGTG 0.918877 -99 GTTGGCATTTTAAAGGAGGAGGGTATAGAAG 45 102 0 TAAGGAGGAG 0.980901 -199 CTTGAAGTGGTGAAGGTGGAGGAGCTTGCTG 45 153 0 TAAGGTGGAG 0.9495 -148 TATCATGAGTTTAACGAGGAGCAATTTTTAA 45 198 0 TAACGAGGAG 0.947838 -103 * ********* Masking position 4 Map Score: 4.6082 Number of sites scoring better than the average of aligned sites = 372 Number in coding regions = 350 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 10 TCTCTCCCAATTTTACGAAACATTTATTGA 7 63 1 TTTTACGAAA 0.954145 -41 AAAATTCATATTTCACGAAAACATTAAATA 11 40 1 TTTCACGAAA 0.863809 -40 AATACTTAAATTTTACGTAATGTGCCGATT 21 180 0 TTTTACGTAA 0.837107 -26 TTCTTACTATTTTTACGAAATTTTTTCAAA 22 94 0 TTTTACGAAA 0.954145 -57 ATTTTTCAGATTTTGCGAAAATATAATCCA 23 85 0 TTTTGCGAAA 0.658277 -109 ACTTTTCGCTTTTTACGAAATTAAATAAGT 23 144 0 TTTTACGAAA 0.954145 -50 AAGTGGAATTTTTTACTAAAAATGGTAATA 24 21 0 TTTTACTAAA 0.787728 -91 CATAACAATCTTTCACAAAAAATAGCGTAA 49 22 1 TTTCACAAAA 0.595095 -42 ********** Masking position 9 Map Score: 5.4787 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 = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 11 AATCGGAGTACCACTACTGGGTGG 10 5 0 CCACTACTGG 0.829592 -164 AACCCTCGAACCCCTACGGGACAGGACCCT 13 161 1 CCCCTACGGG 0.868081 -140 GATATCCGCTACCCCACGGGGGCGACGTGG 16 51 0 ACCCCACGGG 0.960837 -90 AATTCCATGCCCCCGCCGGGAGTTGAACCC 16 107 0 CCCCGCCGGG 0.947284 -34 AAGGCACTGGCCCCTACAGGGTGATAACGC 34 60 1 CCCCTACAGG 0.969441 -241 TCACCAGGCTACCCTACGGCCCCTCTGTAA 39 147 1 ACCCTACGGC 0.928318 -129 GACAACTACTCCCCTACGGG 43 128 1 CCCCTACGGG 0.868081 -10 ********** Masking position 4 Map Score: 5.98525 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 41 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 12 AACATTGCCACTGCAGTAGAACTATGTGGCTA 14 93 1 CTGCATAAAC 0.968282 -105 CACTATTTAACTGCCCTACAACAAAGTGGCAA 17 20 1 CTGCCTAAAC 0.973591 -54 GGGGACATACATGCAGTACAACATGGGCCTGA 29 60 1 ATGCATAAAC 0.857375 -44 AAACACCAATCTGCGTTATCACCCTGTAGGGG 34 70 0 CTGCGTACAC 0.925212 -231 TTAAAAGCCACTGCCTTTAATCATTACAGAGG 39 168 0 CTGCCTTATC 0.752996 -108 TCTGCCTTAACACGCAGAAAATA 41 2 1 CTGCCTACAC 0.947424 -34 GCTGCGGTAGCTGCGATAAATCGCTATCTGAG 42 41 1 CTGCGTAATC 0.929953 -91 TACGACATCTCTGCATTAAAACGATTATGTCT 47 30 0 CTGCATAAAC 0.968282 -58 TATGTGGATTATGCAATATATCTGAAGCACAG 51 79 1 ATGCATAATC 0.759231 -37 ***** ** *** Masking position 7 Map Score: 3.69554 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 31 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 13 ATGAATCAGTTCATAACAAAATTATCTGAC 1 36 0 TCATAACAAA 0.914714 -69 AAATACTTTATCATCATAAATAAACAAATC 8 65 0 TCATCATAAA 0.624617 -67 TTCAAACCACTCAAAATAAAGAAAGGCTTT 10 125 1 TCAAAATAAA 0.869619 -44 CTTTATTTACTCAACATAAAAGCCTTTCTT 10 143 0 TCAACATAAA 0.806855 -26 CTTAATGTTGTCAAAACAAATTTTATCTTT 14 145 0 TCAAAACAAA 0.964192 -53 AACAGCGTGTTAAAAACAAAAATATAAAAA 21 18 0 TAAAAACAAA 0.679653 -188 TCAAAGTATGTCAAATCAAAATCTTAAATT 22 58 0 TCAAATCAAA 0.773822 -93 GGCATAGTGCTCATAACAAACATCAACACA 27 109 1 TCATAACAAA 0.914714 -72 ATAACAAACATCAACACAAAAGTTAACGGT 27 121 1 TCAACACAAA 0.944023 -60 GTTGAGTTTATCAAAACCAAGCTGCCAGAA 36 267 1 TCAAAACCAA 0.835277 -34 TAAATTTTAATCAAAACAAATAAAAAAATT 46 39 0 TCAAAACAAA 0.964192 -139 ********** Masking position 3 Map Score: 8.25532 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 13 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 14 ACTGTTGCATAGTTTGCTGCAAAATCTTTAAT 10 41 1 AGTTCTGCAA 0.681466 -128 GATACTTACACTTTAATTGCAATTAAAATTGC 12 11 1 CTTTTTGCAA 0.884517 -72 TAAAATTGCCATTTAATGGCAAACATAAAATT 12 34 1 ATTTTGGCAA 0.638007 -49 TATTAAAGTTATTTGTCTGCAATTTTGAAATT 18 68 0 ATTTCTGCAA 0.919096 -45 CTGTATTTAGCTTTAATGTCAATAATTAATTA 21 57 1 CTTTTGTCAA 0.638007 -149 AAAATAAAATCTTTGTCTTCAAAGCCCCAATT 23 30 1 CTTTCTTCAA 0.919096 -164 AAGTCCAGAACTTTCTCTGCTACCGTCGAGGT 34 24 0 CTTTCTGCTA 0.813113 -277 GATTTAGCTTCAAAAAAGTTAAT 35 153 0 ATTTCTTCAA 0.806718 -13 CTTTTAAAGCCTTTTGCTGCAAACGCATTCGT 39 193 1 CTTTCTGCAA 0.968672 -83 TGGAGAAGGTCTTTTCCGGCAAAAATCTGCTC 45 43 0 CTTTCGGCAA 0.950899 -258 ACCCTTTCACTTCCAGCAACTGCTT 47 73 0 CTTTCTTCCA 0.703191 -15 **** ****** Masking position 12 Map Score: 2.27252 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 288 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 15 CTCCGGGCAGGGAAAAATGTACTGGA 30 17 0 GGCAGGGAAA 0.979804 -16 CGAAATGGGGGTGCCGGGAATAAACACTTCAT 36 229 0 GGCCGGGAAA 0.987171 -72 CATCATTGAACTGGCGGGAAAACCGTTTTTTA 39 66 0 CGGCGGGAAA 0.927198 -210 GAGTGGTTGAGCTCAGGGAATATCCAAGAAAC 42 84 1 GTCAGGGAAA 0.844176 -48 AATGCCCACAGCGGCGGGTAAAACCCT 45 6 0 GGGCGGGTAA 0.979578 -295 GCCTCAGCCTGAGGCGGAAACAGCTCTTCTAT 45 77 1 GGGCGGAAAA 0.895757 -224 CATTTTAAAGGAGGAGGGTATAGAAGAGCTGT 45 96 0 GGGAGGGTAA 0.967991 -205 GAGCAGGGTAGAATGGGGAGGT 53 19 0 GGCAGGGTAA 0.967991 -12 * ******** * Masking position 10 Map Score: 4.78878 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 65 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432