AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00360_aful_reg_100.orf -o00360_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: AF2243 38 3-ketoacyl-CoA thiolase (fadA-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 AF0033 36 acyl carrier protein synthase (acaA-1) #7 AF0135 59 conserved hypothetical protein #8 AF0136 103 A. fulgidus predicted coding region AF0136 #9 AF0196 131 medium-chain acyl-CoA ligase (alkK-1) #10 AF0197 86 acetyl-CoA synthetase (acs-1) #11 AF0283 168 3-ketoacyl-CoA thiolase (acaB-7) #12 AF0438 79 3-ketoacyl-CoA thiolase (acaB-8) #13 AF0439 82 transcriptional regulatory protein, AsnC family #14 AF0442 300 succinoglycan biosynthesis regulator (exsB) #15 AF0818 102 acylphosphatase (acyP) #16 AF0968 205 3-ketoacyl-CoA thiolase (acaB-10) #17 AF1029 193 long-chain-fatty-acid--CoA ligase (fadD-5) #18 AF1197 300 3-ketoacyl-CoA thiolase (fadA-2) #19 AF1215 101 cell division protein, putative #20 AF1289 300 conserved hypothetical protein #21 AF1305 72 D-arabino 3-hexulose 6-phosphate formaldehyde lyase (hps-2) #22 AF1306 77 conserved hypothetical protein #23 AF1418 49 glycerol-3-phosphate cytidyltransferase (taqD) #24 AF1419 24 ribose-phosphate pyrophosphokinase (prsA-2) #25 AF1420 216 membrane protein #26 AF1975 99 glutamyl-tRNA reductase (hemA) #27 AF1976 93 26S protease regulatory subunit 4 #28 AF2099 106 muconate cycloisomerase II (clcB) #29 AF2244 300 acyl-CoA dehydrogenase (acd-11) #30 AF2416 115 3-ketoacyl-CoA thiolase (acaB-12) Motif number 1 TAAACACCTCCAAATTAGAAAATAGGCCTTC 1 83 0 CAAATAGAAA 0.490651 -22 GTTAATTAAAAAAAATTTTATAAAATGATTT 3 18 0 AAAATTTTAT 0.811299 -78 ATTGACAAAGAAAAGTTAAAAA 4 2 0 AAAATTAAAA 0.869322 -53 TAAATTCCTTAAAAATTTAATATTTGCTCAT 7 26 1 AAAATTTAAT 0.917449 -34 TATCATCTTAAAAAATTGAATTATGCTCAAA 10 20 0 AAAATTGAAT 0.912231 -67 ATTTAATGAGCAAATTTAAATTCATTATCAT 10 45 0 CAAATTAAAT 0.914145 -42 ATTGGCAGAGCAAACTTAAATTTTTTGGATA 11 87 1 CAAATTAAAT 0.914145 -82 CTAAAAATATAAAAATTTTATGTTTGCCATT 13 48 0 AAAATTTTAT 0.811299 -35 AGGTGGATTTCAAAGTTATATGAAGTCATCG 14 275 0 CAAATTATAT 0.804661 -26 CAAAAGAATTCAAACTTATATACCGCAGGCA 15 70 1 CAAATTATAT 0.804661 -33 ACAAAAATATAAAAATAAAAAT 16 2 0 AAAATAAAAA 0.720176 -204 CTAAACGCGTAAAAATTGAATATATCAAGTA 16 107 1 AAAATTGAAT 0.912231 -99 TTGAACGAAACAAAATAAAATCTTTGTCTTC 17 19 1 CAAATAAAAT 0.804661 -175 CAAAATCTGAAAAATTTGAATGGCTTCAGAA 17 100 1 AAAATTGAAT 0.912231 -94 GTAAAAAGCGAAAAGTTTTAAAAGGCTGAAA 17 158 1 AAAATTTTAA 0.624546 -36 TTAACGAAAAAAAATTTTAAAATGGCGGTTG 22 47 1 AAAATTTAAA 0.811308 -31 AAAACTTTTATGCCTACCTGA 23 1 1 AAAATTTTAT 0.811308 -49 CTGAAAAGCAAAAATTAAAATGATAAAATGG 26 29 0 AAAATAAAAT 0.869322 -71 TGCTGAATAAAAAACTTAAAAAGCACTTGTG 26 63 1 AAAATTAAAA 0.869322 -37 GAGGGAAGCAAAAAATAAAATTGAGGGATAA 27 70 1 AAAATAAAAT 0.869322 -24 CAAACTTTTTAAAATTATAATCATAAATCGA 28 13 0 AAAATATAAT 0.811308 -94 TTAACTTGGCAAAATTTAAATAATCACAAAA 29 271 1 AAAATTAAAT 0.94504 -30 **** ****** Masking position 6 Map Score: 22.0258 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 91 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 180 Fraction of orfs with sites within 600 bp upstream = 0.028911 Motif number 2 CTATTTTCTAATTTGGAGGTGTTTAG 1 89 1 ATTGGAGGGT 0.780799 -16 TTTTCTGAACAAATGGTGGTTGT 3 83 1 AAAGGTGGTT 0.845714 -13 AGAGCTAATAGAAGGAGATTGAGTAGGGG 8 7 1 AATGAAGGGT 0.839197 -97 TTCAATAAAAAAGGGGTGGTGGT 9 119 1 AAGGGTGGGT 0.988625 -13 AAATGTTATAAATTGGAGGTGAACT 10 72 1 AATGGAGGGA 0.86639 -15 GTAGAAGGTGGATTTCAAAGTTATA 14 286 0 AGAGGTGGTT 0.861821 -15 TACCGCAGGCAAAAGGTGGGGTT 15 90 1 AAAGGTGGGT 0.976215 -13 AATAAGAAAAAAGTGAAGGAGGTGTATT 18 283 1 AAGGAAGGGT 0.941794 -18 CGGTCAAGCTGAGGCGTTGCTGTTTTTA 19 6 1 AAGTGAGGGT 0.802357 -96 CGCACACCGCAGGAGGTGGCGATGGCTGCAGTG 20 21 1 AGGGGTGGGT 0.98999 -280 TGCTGATCCTCGTTGGTGGAGTTATTCCGACAG 20 163 1 CGTGGTGGGT 0.781556 -138 GTCGAGCTGAAAAAGATGGGGGTTGATGAAGTG 20 204 1 AAAGATGGGT 0.884266 -97 GAATCAAAAAAAGAGGAAGGGCTT 24 2 0 AAGGGAAGGT 0.802357 -23 TAAAATGATAAAATGGTGGAGACTCCCGGAACG 26 12 0 AAAGGTGGGC 0.847762 -88 CCTCAGGCTGAGGCGGTGGAGAAGGTCTTTTCC 29 58 0 AGGGGTGGGA 0.958116 -243 GGCATTTTAAAGGAGGAGGGTATAGAAGAGCTG 29 97 0 AGGGGAGGTT 0.929618 -204 GAAGTGGTGAAGGTGGAGGAGCTTGCTGAAAGC 29 148 0 AGGGGAGGGT 0.98999 -153 GAGAAGATTGAGAGGAAGGCGTATGTGGATTAT 30 58 1 AGAGAAGGGA 0.667873 -58 *** ***** * * Masking position 9 Map Score: 19.5214 Number of sites scoring better than the average of aligned sites = 1215 Number in coding regions = 1158 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 3 TATGAACTGGTTCATAAATAAGAAAAAA 2 4 0 TTAATAGAAA 0.853754 -70 TTAACAACAAAAAGTTAATTAAAAAAAATTTTATA 3 27 0 ATAATAAAAA 0.963462 -69 ATCCTGATAAATAATTAATTAACAACAAAAAGTTA 3 45 0 ATAATAACAA 0.93124 -51 GTAACAATTATTAATGAGCAAATATTAAATT 7 39 0 ATAATAGCAA 0.87424 -21 ATTGAACATAACAATTAATCAAAAAT 8 88 1 ATAATAAAAA 0.963462 -16 ATACTTTATCATCATAAATAAACAAATCGTGCTCA 9 58 0 ATAATAACAA 0.93124 -74 TACGAAATTATTATTCAATAAAAAAGGGGTGGTGG 9 106 1 TTAATAAAAA 0.91487 -26 CCAATTTATAACATTTAATGAGCAAATTTAAATTC 10 53 0 ATAATAGCAA 0.874313 -34 AGTATGAAAGTAAACTAAAAATATAAAAATT 13 62 0 ATAACAAAAA 0.868148 -21 ATTAATTACGAGAGCAAATGAAAAATCTAAACGCG 16 81 1 ACAATAAAAA 0.758398 -125 ACCCGGATGGTATTTTAATAAGAAAAAAGTGAAGG 18 267 1 TTAATAGAAA 0.850758 -34 GTTGGGAAAAAGGTTTAAATAAAAAGCGTATTAAA 19 64 1 ATAAAAAAAA 0.707083 -38 AACAGATATTAGCGTAAATCAAAAAGTCCTTC 22 8 0 ATAATAAAAA 0.963462 -70 AATATCTGTTTTGCTTAACGAAAAAAAATTTTAAA 22 33 1 TTAACAAAAA 0.738841 -45 CTTTTCAGCATTGCTGAATAAAAAACTTAAAAAGC 26 52 1 TTAATAAAAA 0.874776 -48 CCCATCGAATACGATTAATCAAAAAGAATAAATAA 28 80 1 ATAATAAAAA 0.963462 -27 CAAGTTTTCAACGGTGCATTAAAAATTGCTCCTCG 29 180 1 ATCATAAAAA 0.758398 -121 * * *** ***** Masking position 8 Map Score: 17.093 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 28 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 4 TATGAACTGATTCATAACAGCTTTTATCTTTAGAA 1 51 1 TTAAAGCTTT 0.970255 -54 AGCTTTTATCTTTAGAAGGCCTATTTTCTAATTTG 1 69 1 TTAAACCTTT 0.705673 -36 TATGAACCAGTTCATAACAGCCTTTATTTAGCACT 2 23 1 TTAAAGCCTT 0.966808 -51 GATTTTATTTAAGATTTGCCTTTTTTGATAGCA 6 14 0 TTAATGCCTT 0.937508 -23 CCTTAAAAATTTAATATTTGCTCATTAATAATTGT 7 32 1 TTAATGCTAT 0.730601 -28 TGATAATGAATTTAAATTTGCTCATTAAATGTTAT 10 46 1 TTAATGCTAT 0.730601 -41 CCACTCAAAATAAAGAAAGGCTTTTATGTTGAGTA 11 131 1 TAAAAGCTTT 0.831128 -38 TTTAATTGCAATTAAAATTGCCATTTAATGGCAAA 13 22 1 ATAAAGCCTT 0.713659 -61 ATATAAAAATTTTATGTTTGCCATTAAATGGCAAT 13 38 0 TTAGTGCCTT 0.655471 -45 ATATTTTTGTTTTTAACACGCTGTTTTTAGCGTAC 16 23 1 TTTACGCTTT 0.475891 -183 GGATGATAATTTCAAAAGAGCTGTTATTCAACACG 18 169 0 TTAAAGCTTT 0.970255 -132 CGTTGCTGTTTTTAAACTTGCCTTTATCGAGATTG 19 25 1 TTAACGCCTT 0.909869 -77 GCAGCCCTTACAACCGCCATTTTAAAATTTT 22 57 0 CTAAAGCCTT 0.78696 -21 TTTTATCATTTTAATTTTTGCTTTTCAGCATTGCT 26 32 1 TTATTGCTTT 0.589743 -68 TAGTTCAGAATTCACAAGTGCTTTTTAAGTTTTTT 26 71 0 TTAAAGCTTT 0.970255 -29 AGGAGGAGGGTATAGAAGAGCTGTTTCCGCCTCAG 29 85 0 TAAAAGCTTT 0.831128 -216 CAACGGTGCATTAAAAATTGCTCCTCGTTAAACTC 29 188 1 TTAAAGCTCT 0.815695 -113 ** * ** *** ** Masking position 15 Map Score: 11.2153 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 59 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 5 CTAAACACCTCCAAATTAGAAAATA 1 90 0 TAAACTCAAA 0.659846 -15 CAATGCTATCAAAAAAGGCAAATCTTAAATAAA 6 10 1 CAAAAGAAAT 0.496129 -27 TATGCTCATGTAAATTCCTTAAAAATTTAATATT 7 16 1 TAAATTAAAA 0.512055 -44 GATTTTGCAGCAAACTATGCAACAGTTTTTAAAA 11 33 0 CAAACGAACA 0.6341 -136 ATATAGGCTTCAAACCACTCAAAATAAAGAAAGG 11 117 1 CAAACTAAAA 0.949499 -52 GAAAGTAAACTAAAAATATAAAAATTTTATGTTT 13 54 0 TAAAATAAAA 0.891998 -29 AATATTCATACAAAAGAATTCAAACTTATATACC 15 60 1 CAAAATCAAA 0.773289 -43 GTGTTAAAAACAAAAATATAAAAATAAAAAT 16 8 0 CAAAATAAAA 0.942935 -198 ATGAAAAATCTAAACGCGTAAAAATTGAATATAT 16 98 1 TAAACTAAAA 0.903823 -108 TATATTTTCGCAAAATCTGAAAAATTTGAATGGC 17 90 1 CAAAAGAAAA 0.880645 -104 CGAAAAGTTTTAAAAGGCTGAAAAAATAGTTAAA 17 166 1 TAAAATAAAA 0.891998 -28 GTTTGCTCATCAAAACCGTAAACACCAATCTGCG 18 87 0 CAAAATAACA 0.773289 -214 ATCGAGATTGCAAAGTTGGGAAAAAGGTTTAAAT 19 50 1 CAAAGGAAAA 0.581502 -52 GCTTAACGAAAAAAAATTTTAAAATGGCGGTTGT 22 45 1 AAAAATAAAA 0.565591 -33 ATCTCAATATCAAACTCATGAAAAACCTTATTAG 25 172 1 CAAACTAAAA 0.949499 -45 AAGCAAAAATTAAAATGATAAAATGGTGGAGACT 26 21 0 TAAAATAAAT 0.524301 -79 CATTGCTGAATAAAAAACTTAAAAAGCACTTGTG 26 60 1 TAAAATAAAA 0.891998 -40 TCAACCTTAGCAAACTTTTTAAAATTATAATCAT 28 20 0 CAAACTAAAA 0.949499 -87 TTTGCCAAGTTAAACAATTGAAAAAGGATTTAAA 29 250 0 TAAACTAAAA 0.903823 -51 ***** * **** Masking position 4 Map Score: 16.2162 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 83 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 6 CCACCCAGTAGTGGTACTCCGATTTTAAAAAC 11 11 1 GTGGTTCCGA 0.663746 -158 AAATGCGGGGGGAGGGATTCGAACCCTCGAAC 14 140 1 GGAGGTTCGA 0.963203 -161 GTCCTGTCCCGTAGGGGTTCGAGGGTTCGAAT 14 156 0 GTAGGTTCGA 0.819006 -145 TCATCTGAGCGGGGGTTGCCGAGCGGACAAAG 14 202 0 GGGGGGCCGA 0.990596 -99 CTGCTACCGTCGAGGTATCCGGGAGTTGT 18 8 0 CGAGGTCCGG 0.952649 -293 TTATCATCCCGGAGGAAGTCGAGTACACCGAA 18 195 1 GGAGGGTCGA 0.976604 -106 ATTTCCGAAATGGGGGTGCCGGGAATAAACAC 20 234 0 TGGGGGCCGG 0.893324 -67 TAAATTTTTTGGAGTTCGCCGAATTGATTTGC 21 27 0 GGAGTGCCGA 0.962371 -46 ATATGTATTTGGAGGCTTCCGGAACGTAGAGG 27 42 1 GGAGGTCCGG 0.985086 -52 GAAAATTATCCGAGGGAGCCGAAGGTTTGGGA 30 28 1 CGAGGGCCGA 0.97829 -88 ***** ***** Masking position 10 Map Score: 9.62287 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 199 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 GATAATTTTGTTATGAACTGATTCATAACAGCT 1 40 1 TATAATGATT 0.767564 -65 ATAAAGGCTGTTATGAACTGGTTCATAAATAAG 2 17 0 TATAATGGTT 0.907174 -57 AAAAAAAATTTTATAAAATGATTTGTCGTGA 3 9 0 TATAATGATT 0.767564 -87 AAATTTTTTTTAATTAACTTTTTGTTGTTAATT 3 31 1 TATAATTTTT 0.688466 -65 TTTTTGTTGTTAATTAATTATTTATCAGGATAT 3 49 1 TATAATATTT 0.83552 -47 ATATTTTTTCTGAACAAATGGTGGTTGT 3 78 1 TAAAATGGTG 0.720122 -18 TATTTGCTCATTAATAATTGTTAC 7 46 1 TAAAATGTTA 0.708071 -14 ATTGTTATGTTCAATAAATGTTTCGTAAAATTG 8 70 0 TAAAATGTTT 0.900204 -34 ATTTTTGATTAATTGTTATGTTCAATAA 8 86 0 TATAATGTTA 0.8365 -18 TTATTTATGATGATAAAGTATTTATGAATACTC 9 72 1 TATAATATTT 0.835525 -60 TTAAATTTGCTCATTAAATGTTATAAATTGGAG 10 57 1 TATAATGTTA 0.8365 -30 TACTCCGATTTTAAAAACTGTTGCATAGTTTGC 11 25 1 TAAAATGTTG 0.833596 -144 TTTGCTCTCGTAATTAATTATTGACATTAAAGC 16 66 0 TATAATATTG 0.738294 -140 TTTACGAAATTAAATAAGTATTTATTCTCAGGT 17 130 0 TAAAATATTT 0.706599 -64 TTTAAAAGGCTGAAAAAATAGTTAAAGACA 17 174 1 TAAAATAGTT 0.552965 -20 AGATGGGGGTTGATGAAGTGTTTATTCCCGGCA 20 217 1 TATAATGTTT 0.950068 -84 TCCGGATATGTAATAAATTTTTTGGAGTTCGCC 21 39 0 TATAATTTTT 0.688351 -34 AAAATTAAAATGATAAAATGGTGGAGACTCCCG 26 17 0 TATAATGGTG 0.844414 -83 TTTAAATCCTTTTTCAATTGTTTAACTTGGCAA 29 250 1 TTTAATGTTT 0.576508 -51 * ** ** ***** Masking position 9 Map Score: 14.9945 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 45 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 8 CAAATCGTGCTCATTTCGTCAGTTGTTGTTC 9 40 0 TCTTTCGTCA 0.974056 -92 TAATATTTAATGTTTTCGTGAAATATGAATT 12 42 0 TGTTTCGTGA 0.923444 -38 GTGTAAATCTTCTTTTCGTCATCAGAGATAT 14 59 1 TCTTTCGTCA 0.974058 -242 AAGCCCTTCCTCTTTTTTTGATTC 24 11 1 TCTTTTTTGA 0.754329 -14 TCAGGGCTATTCGTTTTGTCAAGTTATTCTG 25 100 1 TCTTTTGTCA 0.96884 -117 TTGCTAAGGTTGATTTTGTCAGGCTGCAAGA 28 41 1 TGTTTTGTCA 0.929177 -66 GCAGGCTCTTTTTGTGATTATTTAAAT 29 284 0 TCTTTTGTGA 0.959468 -17 ** ******** Masking position 11 Map Score: 3.44264 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 25 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 AAACGGTAACTTCCTGTTTTCCC 9 4 0 TTCCTGTTTT 0.91914 -128 GATTTTTCATTTGCTCTCGTAATTAATTAT 16 78 0 TTGCTCTCGT 0.784713 -128 GTGTGTCGATTTCCTCTCTTGTTGGTGGTT 18 225 0 TTCCTCTCTT 0.947899 -76 AGCTGAGGCGTTGCTGTTTTTAAACTTGCC 19 17 1 TTGCTGTTTT 0.800861 -85 TCTTTCTTCCTCTTTTCTGGCAGCTT 20 285 0 TTCCTCTTTT 0.969815 -16 AAGCCCTTCCTCTTTTTTTGATTC 24 7 1 TTCCTCTTTT 0.969815 -18 CTTCTATACCCTCCTCCTTTAAAATGCCAA 29 102 1 CTCCTCCTTT 0.828541 -199 GCCTTTATCTTCCTCCTGTGCTTCAGATA 30 97 0 TTCCTCCTGT 0.911523 -19 ********** Masking position 5 Map Score: 3.40809 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 105 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 GTTGTTGTTCGGGGGAAAACGGTAACTTCCT 9 19 0 GGGGGAAACG 0.891605 -113 TGTTTATTTATGATGATAAAGTATTTATGAA 9 69 1 TGATGAAAAG 0.820648 -63 GGGGTTGCCGAGCGGACAAAGGCGCAGGATT 14 192 0 AGCGGAAAAG 0.871662 -109 ATTGGGGCTTTGAAGACAAAGATTTTATTTT 17 30 0 TGAAGAAAAG 0.793835 -164 AGTTTTAAAAGGCTGAAAAAATAGTTAAAGA 17 171 1 GGCTGAAAAA 0.639826 -23 CCTCGACGGTAGCAGAGAAAGTTCTGGACTT 18 25 1 AGCAGAAAAG 0.873885 -276 GGCCCCTACAGGGTGATAACGCAGATTGGTG 18 68 1 GGGTGAAACG 0.908861 -233 TGGCTGCAGTGGATGAAGACGTGGATGTTGT 20 43 1 GGATGAGACG 0.791676 -258 GATATTGTCGAGCTGAAAAAGATGGGGGTTG 20 198 1 AGCTGAAAAG 0.891707 -103 AAAAGATGGGGGTTGATGAAGTGTTTATTCC 20 214 1 GGTTGAGAAG 0.635298 -87 GAATTTGGATTGGAGATGAAGAAAAGGGTC 23 30 1 TGGAGAGAAG 0.681508 -20 ATTGAGATATTGCAGAAAACGAATCCACGAA 25 149 0 TGCAGAAACG 0.85679 -68 CTCAGCCTGAGGCGGAAACAGCTCTTCTATA 29 79 1 GGCGGAACAG 0.778338 -222 AAGCACAGGAGGAAGATAAAGGC 30 103 1 GGAAGAAAAG 0.912894 -13 ****** **** Masking position 6 Map Score: 3.69495 Number of sites scoring better than the average of aligned sites = 1024 Number in coding regions = 946 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 11 TGATTAAAATAACTTGATTTGG 1 1 0 ATTGATTTGG 0.845239 -104 TAACAAAATTATCTGACTTTTGATTAAAATAA 1 21 0 ATGACTTTTG 0.797861 -84 CATCTTAAAAAATTGAATTATGCTCAAAGTGT 10 16 0 ATGAATTATG 0.810636 -71 TTTTCGTGAAATATGAATTTTGCCTTGCAGCT 12 29 0 ATGAATTTTG 0.954462 -51 GTGGATGAAGACGTGGATGTTGTGGGCATAAG 20 51 1 ATGGATGTTG 0.792936 -250 CTTTTCTGGCAGCTTGGTTTTGATAAACTCAA 20 268 0 ATTGGTTTTG 0.650047 -33 AGGAAAATTGAGTTTGGCAAATCAATT 21 6 1 ATGAGTTTGG 0.88098 -67 TTTTATGCCTACCTGAATTTGGATTGGAGATG 23 16 1 ATGAATTTGG 0.955273 -34 CCGAGCCCGCAGTTGAATTTGGACAG 25 5 0 ATGAATTTGG 0.955273 -212 TGAGTGATATATATGTATTTGGAGGCTTCCGG 27 32 1 ATGTATTTGG 0.792851 -62 AAGTTTGCTAAGGTTGATTTTGTCAGGCTGCA 28 37 1 ATTGATTTTG 0.84276 -70 TTTTGTGATTATTTAAATTTTGCCAAGTTAAA 29 270 0 ATAAATTTTG 0.646789 -31 AGGAAGGCGTATGTGGATTATGCAATATATCT 30 70 1 ATGGATTATG 0.832184 -46 * ********* Masking position 1 Map Score: 5.37874 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 54 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 12 CAAAATTATCTGACTTTTGATTAAAATAAC 1 20 0 TGACTTTTGA 0.775233 -85 CTTAAAAAATTGAATTATGCTCAAAGTGTG 10 15 0 TGAATTATGC 0.724934 -72 TCGTGAAATATGAATTTTGCCTTGCAGCTC 12 28 0 TGAATTTTGC 0.943561 -52 TTCTGTTCGTTGAGTTTGGGAGGTTCAAGA 14 108 0 TGAGTTTGGG 0.787287 -193 AGGAAAATTGAGTTTGGCAAATCAATTC 21 9 1 TGAGTTTGGC 0.928734 -64 TATGCCTACCTGAATTTGGATTGGAGATGA 23 19 1 TGAATTTGGA 0.953934 -31 AGCCCGCAGTTGAATTTGGACAG 25 4 0 TGAATTTGGA 0.953934 -213 AAAGCACTTGTGAATTCTGAACTATAAG 26 82 1 TGAATTCTGA 0.752106 -18 GTGATATATATGTATTTGGAGGCTTCCGGA 27 35 1 TGTATTTGGA 0.744496 -59 TGTGATTATTTAAATTTTGCCAAGTTAAAC 29 269 0 TAAATTTTGC 0.593599 -32 ********** Masking position 5 Map Score: 2.94881 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 65 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 13 TCTAAAGATAAAAGCTGTTATGAATCAGTTCATA 1 51 0 AAGCTTTGAA 0.978622 -54 AAATTAGAAAATAGGCCTTCTAAAGATAAAAGCT 1 69 0 AAGGTTTAAA 0.80047 -36 GTGCTAAATAAAGGCTGTTATGAACTGGTTCATA 2 23 0 AGGCTTTGAA 0.905183 -51 TTATGATGATAAAGTATTTATGAATACTCATACG 9 76 1 AAGTTTTGAA 0.817775 -56 ACTCAACATAAAAGCCTTTCTTTATTTTGAGTGG 11 131 0 AAGCTTTTTA 0.72206 -38 AAAATTCTGCATAGGATTTATGAATATTGTGGTT 14 234 1 AAGGTTTGAA 0.924475 -67 GTGTTGAATAACAGCTCTTTTGAAATTATCATCC 18 170 1 AAGCTTTGAA 0.978622 -131 AGCCCTTACAACCGCCATTTTAAAATTTTTTTTC 22 52 0 ACGCTTTAAA 0.757801 -26 AAAAACTTAAAAAGCACTTGTGAATTCTGAACTA 26 72 1 AAGCTTTGAA 0.978622 -28 TGAGGCGGAAACAGCTCTTCTATACCCTCCTCCT 29 86 1 AAGCTTTATA 0.788249 -215 AGTTTAACGAGGAGCAATTTTTAATGCACCGTTG 29 188 0 GAGCTTTTAA 0.6635 -113 * *** ** **** Masking position 14 Map Score: 4.47616 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 95 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 14 ACCCTCGAACCCCTACGGGACAGGACCCTC 14 162 1 CCCTACGGGA 0.90657 -139 TACCGTCGAGGTATCCGGGAGTTGT 18 6 0 GTATCCGGGA 0.839456 -295 GGGGCCAGTGCCTTCCGGAAGTCCAGAACT 18 44 0 CCTTCCGGAA 0.948482 -257 GTACTCGACTTCCTCCGGGATGATAATTTC 18 191 0 TCCTCCGGGA 0.9185 -110 TATTAAAATACCATCCGGGTCCAATTCTTT 18 257 0 CCATCCGGGT 0.93517 -44 GTGAAATAGACTATCCGGGAAGCTTTGAAG 25 64 0 CTATCCGGGA 0.964537 -153 CCGTTCCGGGAGTCTCCACCA 26 2 1 CGTTCCGGGA 0.976783 -98 CTTCCCTCTACGTTCCGGAAGCCTCCAAAT 27 48 0 CGTTCCGGAA 0.905863 -46 ********** Masking position 4 Map Score: 4.20572 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 185 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 15 AACAACAACTGACGAAATGAGCACGATTTGT 9 41 1 GACGAATGAG 0.86759 -91 TATCTCTGATGACGAAAAGAAGATTTACACG 14 58 0 GACGAAAGAA 0.97096 -243 TCCCAAACTCAACGAACAGAACTAAATGCGG 14 117 1 AACGAAAGAA 0.975804 -184 AATATTTTCGAACGAATTGAAATCATATAAA 15 35 0 AACGAATGAA 0.955782 -68 TTGATGAGCAAACGAAGAGAATGAAGCTCTT 18 108 1 AACGAAAGAA 0.975804 -193 TGTTTTGCTTAACGAAAAAAAATTTTAAAAT 22 39 1 AACGAAAAAA 0.861861 -39 ****** **** Masking position 6 Map Score: 1.71409 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 25 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467