AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00010_bbur_reg_300.orf -o00010_bbur_300.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -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 = 0.28 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 BB0004 246 phosphoglucomutase (femD) #2 BB0057 72 glyceraldehyde 3-phosphate dehydrogenase (gap) #3 BB0060 83 conserved hypothetical protein #4 BB0061 73 thioredoxin (trxA) #5 BB0087 120 L-lactate dehydrogenase (ldh) #6 BB0088 159 GTP-binding membrane protein (lepA) #7 BB0089 71 B. burgdorferi predicted coding region BB0089 #8 BB0093 21 V-type ATPase, subunit B (atpB) #9 BB0094 85 V-type ATPase, subunit A (atpA) #10 BB0096 183 V-type ATPase, subunit E, putative #11 BB0100 156 glutamate racemase (murI) #12 BB0116 173 PTS system, maltose and glucose-specific IIABC component (malX) #13 BB0337 115 enolase (eno) #14 BB0347 183 fibronectin/fibrinogen-binding protein, putative #15 BB0348 97 pyruvate kinase (pyk) #16 BB0437 172 chromosomal replication initiator protein (dnaA) #17 BB0438 240 DNA polymerase III, subunit beta (dnaN) #18 BB0439 90 conserved hypothetical protein #19 BB0440 91 ribosomal protein L34 (rpmH) #20 BB0444 45 nucleotide sugar epimerase #21 BB0445 166 fructose-bisphosphate aldolase (fba) #22 BB0554 261 B. burgdorferi predicted coding region BB0554 #23 BB0557 138 phosphocarrier protein HPr (ptsH-2) #24 BB0644 154 conserved hypothetical protein #25 BB0645 45 PTS system, glucose-specific IIBC component (ptsG) #26 BB0658 133 phosphoglycerate mutase (gpmA) #27 BB0732 263 penicillin-binding protein (pbp-3) #28 BBB04_BBB05 276 BBB04: PTS system, cellobiose-specific IIC component (celB), BBB05: PTS system, cellobiose-specific IIA component (celC) #29 BBB29 300 PTS system, maltose and glucose-specific IIABC component (malX) Motif number 1 AAGAAAAGCTTATTAATATAAGCAAAAAAA 1 133 1 TATTAATATA 0.53267 -114 ATACTTAAAAATTTGTTTTTTTGCTTATAT 1 148 0 ATTTGTTTTT 0.888294 -99 TCCTCCAATTTTTTGATTTTATTCTTACTA 2 47 0 TTTTGATTTT 0.815165 -26 ATAGCAATTAAATTATTTTATTTTGCAAA 3 10 0 AATTATTTTA 0.735879 -74 AATTCCTTATTATTAATATTGTATTTGTGA 4 18 1 TATTAATATT 0.704086 -56 ATTTGTTTTTAATTTTTAAA 5 1 1 ATTTGTTTTT 0.888294 -120 TTGTATATAGTTTTAATTTAATGGAGTAAT 5 100 1 TTTTAATTTA 0.720992 -21 CACGATCAGATATTATTTTAGCTTTTTGAA 6 126 0 TATTATTTTA 0.790658 -34 TTTTGATTTATTATTTCTTTTAATA 7 6 1 ATTTATTATT 0.877678 -66 TTATTATTTCTTTTAATATTAAATTTTCTC 7 18 1 TTTTAATATT 0.799172 -54 AATTTAATATATTTATTATT 7 62 1 ATTTATTATT 0.877678 -10 TTGATATGTTTTTTAATATTGTAAAATTTT 10 75 1 TTTTAATATT 0.799172 -109 ATTGTAAAATTTTTGATATTAAAAATTTAT 10 92 1 TTTTGATATT 0.764892 -92 GATATTAAAAATTTATTTTATGCTTTTTTA 10 106 1 ATTTATTTTA 0.823303 -78 AGTGTTAGGTTATTATTTTTATCTTATATG 10 154 1 TATTATTTTT 0.887442 -30 ATACTTAACTTATTAATATTGTTAAATCAA 11 16 1 TATTAATATT 0.704086 -141 GTTAAATCAATTTTATTATAGCTTAAAACT 11 36 1 TTTTATTATA 0.823303 -121 ATTTAACAATTTTTATTATTTTAATTCTTG 11 81 1 TTTTATTATT 0.906774 -76 GGTATTATATATTTTTTATAAATAAGTGAT 12 28 0 ATTTTTTATA 0.546109 -146 ACACTATTTTATTATAAAGCTTTTTT 12 158 0 TTTTATTATA 0.823303 -16 TTTCCAAAAGAATTATTATTGTGAGCTTTG 13 21 0 AATTATTATT 0.810887 -95 AGCTTTAAATTTTTATTTTATGTATTAAAC 14 134 0 TTTTATTTTA 0.863318 -50 TTTTACAAAATATTGTTATTCAATGACAAA 15 43 1 TATTGTTATT 0.826239 -55 ATGTAATAGATATTATTTTTTTTTTAATGT 16 41 0 TATTATTTTT 0.887442 -132 AAGAATCAAAAATTATTTTAAACAATTGAA 17 20 1 AATTATTTTA 0.735879 -221 GATTTTGTATTTTTATTTTTTATAGATATA 17 172 0 TTTTATTTTT 0.929504 -69 GAAAAGCTTATTTTAATATTCAAAATAGCA 18 24 0 TTTTAATATT 0.799172 -67 GTTTATTCAATATTGTTTTTTGCATTGTGG 18 57 1 TATTGTTTTT 0.865697 -34 ATCAATTTTTTATACCACAATGCA 18 77 0 ATTTTTTATA 0.546109 -14 GGCAGCATAAAATTGTTTTTAATGGAGGAG 19 68 1 AATTGTTTTT 0.826239 -24 TTTATTAAAAATTTATTATTTTGCATAAAA 21 21 0 ATTTATTATT 0.877678 -146 TTATGTTTGGTTTTGATTTAATAATTATTT 21 53 1 TTTTGATTTA 0.678732 -114 TTTAATAATTATTTATTTTTTGATTTAAAT 21 69 1 ATTTATTTTT 0.906774 -98 TAGGTGTATAATTTATTATAGGCATTTGAT 21 113 1 ATTTATTATA 0.774631 -54 CTCCTTTCCATTTTATTTTTTCTTTTATCA 21 139 0 TTTTATTTTT 0.929504 -28 AGCCGGGGGCTATTTTTATTGACAAATAGT 22 92 1 TATTTTTATT 0.670595 -170 TTTTAAGTGAATTTTTTATTAATTTATTTT 22 138 1 ATTTTTTATT 0.715233 -124 TTTTTTATTAATTTATTTTAAGATTGTTGC 22 149 1 ATTTATTTTA 0.823303 -113 GTTTTTGAGGTTTTATTTTTTAATCCTTTT 22 200 1 TTTTATTTTT 0.929504 -62 TTTTTAATCCTTTTTATTTATGCAATGTTA 22 216 1 TTTTTATTTA 0.474945 -46 GTTTTTACTAATTTAATTTTTTTGT 22 247 1 ATTTAATTTT 0.799172 -15 GGAATATATAATTTATTTTTATGTATTATA 23 65 1 ATTTATTTTT 0.906774 -74 TCATTATGAATATTGTTTTTTTTGATTAAC 23 104 0 TATTGTTTTT 0.865697 -35 GATAAATTGTTTTTGTTTTTAGTTTATGTT 24 41 1 TTTTGTTTTT 0.915108 -114 TCTTTAAAAGAATTGTTTTTTTTTAAATAA 24 76 1 AATTGTTTTT 0.826239 -79 TACAGATTATATTTTTTATTTAAAAAAAAA 24 91 0 ATTTTTTATT 0.715233 -64 TGTATTTAAGTTTTTATATTTTTTAAGAAA 24 117 1 TTTTTATATT 0.582109 -38 CCTCCTGTAAAATTTATTTTCTTAAAAAAT 24 134 0 AATTTATTTT 0.454429 -21 TTAAGGGTTAATTTATTTTTTATTTTAGGA 25 19 1 ATTTATTTTT 0.906774 -27 ATTATTTTATTTACCAATACTAA 26 121 0 ATTTTATTTA 0.400222 -13 AGCTTCAAATTGTTTTAAACAGTTTTA 27 8 1 AATTGTTTTA 0.694921 -256 TTTATAGCTTAATTGTTTTAAACTTTTTTA 27 44 0 AATTGTTTTA 0.694921 -220 AGGGTAGATTTATTGATTTTTGGCTAAGCG 27 76 0 TATTGATTTT 0.72506 -188 GATGGTATGTTTTTGATTTTAAGGGTAGAT 27 97 0 TTTTGATTTT 0.815165 -167 AGTGTAAAATTATTGTTATAATTTTACACT 27 182 0 TATTGTTATA 0.69492 -82 AAAATTTCGATATTTTTATTGTTAATATCG 28 17 1 TATTTTTATT 0.670595 -260 TAAGATTGGTTTTTATTTTTTCTTTCTAAT 28 89 1 TTTTATTTTT 0.929504 -188 TTCTTTCTAATTTTATTATTTTATTATAAT 28 108 1 TTTTATTATT 0.906774 -169 TCATTTTGGCTATTTTTTTTAATTTGCTGT 28 203 1 TATTTTTTTT 0.734034 -74 ********** Masking position 4 Map Score: 68.6065 Number of sites scoring better than the average of aligned sites = 3854 Number in coding regions = 2480 Number in noncoding regions = 1374 Number of orfs with sites within 600 bp upstream = 229 Fraction of orfs with sites within 600 bp upstream = 0.0367812 Motif number 2 TAATGGATTCAAAAGTATTAGGACAAATCT 1 21 1 AAAAGTATTA 0.697669 -226 CTTGCCAGAATTAAGTTTTTCAAGTATCAT 1 49 1 TTAAGTTTTT 0.592285 -198 ACCCTTAAAGAAAAGCTTATTAATATAAGC 1 126 1 AAAAGCTTAT 0.54385 -121 AAACAAATTTTTAAGTATAATAACATAAGT 1 160 1 TTAAGTATAA 0.707221 -87 TAGTTTTGTATATAGTTTTAATTTAATGGA 5 95 1 TATAGTTTTA 0.762605 -26 GCAATAATGCAAAAGTTTTTCTTACGAATA 6 55 0 AAAAGTTTTT 0.726311 -105 CAGATATTATTTTAGCTTTTTGAATAAATC 6 120 0 TTTAGCTTTT 0.565099 -40 ATAGTTGAGAATAAGTATATTCTTTAAAGA 10 28 1 ATAAGTATAT 0.625404 -156 AAAACTTTAAAAAAGCATAAAATAAATTTT 10 113 0 AAAAGCATAA 0.822721 -71 TATTAATAAGTTAAGTATTTAGG 11 4 0 TTAAGTATTT 0.485869 -153 TCAATTTTATTATAGCTTAAAACTTTTTTT 11 42 1 TATAGCTTAA 0.85907 -115 CCCTAAAAAGTAAAGTATAAATATTAACAA 11 120 0 TAAAGTATAA 0.817082 -37 GTGTAGTAAGTAAAGTTTTTTTTTGCAAAA 12 131 1 TAAAGTTTTT 0.731187 -43 TTTTTGCAAAAAAAGCTTTATAATAAAATA 12 150 1 AAAAGCTTTA 0.493107 -24 TATAATGTTAAAAAGTTTAAATGTGTAGTA 13 53 0 AAAAGTTTAA 0.870221 -63 AATGTATATTTTTAGTATAATGTTAAAAAG 13 68 0 TTTAGTATAA 0.657499 -48 ACTCTTATTATTAAGCTTAAGCTATTAACA 14 18 1 TTAAGCTTAA 0.484852 -166 ATTGACAATAAATAGTTTAAATGTAGTTTT 14 47 0 AATAGTTTAA 0.850192 -137 ATTATGGAAATAAAGTTTATTGACAATAAA 14 65 0 TAAAGTTTAT 0.835183 -119 TACTATTAATAATAGTTTATTTCCATGATA 14 101 0 AATAGTTTAT 0.804154 -83 TTCAATGACAAAAAGCATAAAATTTATAAA 15 61 1 AAAAGCATAA 0.822721 -37 GTGAATTTTTAAAAGTTTTTGGTATTTCCT 16 71 0 AAAAGTTTTT 0.726311 -102 TTTAACATTATATAGTATAATGTTAAATTA 16 121 0 TATAGTATAA 0.780208 -52 ACTTGCATCATATAGTATTAAATACAATTA 17 107 1 TATAGTATTA 0.657499 -134 TAATATTCAAAATAGCATTAATAACTCACT 18 11 0 AATAGCATTA 0.682434 -80 ATAAACCTAGAAAAGCTTATTTTAATATTC 18 33 0 AAAAGCTTAT 0.54385 -58 ACTAACATGGTATAGCATATAAATGCAATT 19 22 0 TATAGCATAT 0.750606 -70 TTTTGCATAAAAAAGTTTAAAA 21 3 0 AAAAGTTTAA 0.870221 -164 CTGTTTTCAAATTAGTTTTAAGTGAATTTT 22 123 1 ATTAGTTTTA 0.623997 -139 TTGTTAGAATAAGTTTAATTACTATCTT 23 9 1 ATAAGTTTAA 0.782863 -130 ACATAAGAAATATAGCATAATAAAGATAGT 23 31 0 TATAGCATAA 0.806187 -108 GCCTAAATTATAGCTTAATGTGTATTGA 24 9 1 TATAGCTTAA 0.85907 -146 TGTTTTTGTTTTTAGTTTATGTTAGTTTTC 24 48 1 TTTAGTTTAT 0.699185 -107 TAATCTGTATTTAAGTTTTTATATTTTTTA 24 112 1 TTAAGTTTTT 0.592285 -43 AAATTAACCCTTAAGTTTAAAA 25 3 0 TTAAGTTTAA 0.785864 -43 TTGATAAACTTAAAGCTTAATGTATTTTAA 26 27 1 TAAAGCTTAA 0.539139 -107 TAATGTATTTTAAAGTATATCATTATTTAA 26 44 1 TAAAGTATAT 0.763699 -90 ATAATTATAAATTAGCATAAAATCTAGTCA 26 92 0 ATTAGCATAA 0.682434 -42 ACACAAATAAAAAAGTTTAAAACAATTAAG 27 37 1 AAAAGTTTAA 0.870221 -227 TAAGCGTGTTTATAGCTTAATTGTTTTAAA 27 52 0 TATAGCTTAA 0.85907 -212 TAATACATGAAATAGCATATGAAAACGATA 28 42 0 AATAGCATAT 0.741952 -235 TAAATGGCTTATTAGCTTTTCATTTTGGCT 28 184 1 ATTAGCTTTT 0.5621 -93 GTATTATTTCATTAGCTTTTGCGGAATTTA 28 231 1 ATTAGCTTTT 0.5621 -46 ********** Masking position 4 Map Score: 39.8386 Number of sites scoring better than the average of aligned sites = 1401 Number in coding regions = 885 Number in noncoding regions = 516 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 3 TTTTGAATCCATTAAATATTTTCC 1 5 0 ATTAAATATT 0.788304 -242 ATTTTATCAACTTTAACATTCATAAGTTAA 1 89 1 CTTTAACATT 0.887282 -158 TGTTATTATACTTAAAAATTTGTTTTTTTG 1 155 0 CTTAAAAATT 0.76976 -92 ATTGCTATAATTTTAATAATCAATAGTATA 1 193 0 TTTTAATAAT 0.732983 -54 TTAATTTGTGATTTAATAATTCTAGTAAGA 2 25 1 ATTTAATAAT 0.851389 -48 AATCACATACCTTTAAAAATTAAAAACAAA 5 12 0 CTTTAAAAAT 0.837703 -109 ATCATTACTTATTTAAAATTAGTTTTGTAT 5 76 1 ATTTAAAATT 0.899999 -45 ACAAGTCAAAATTTAAAAAT 6 1 0 ATTTAAAAAT 0.885855 -159 TTACGAGAAAATTTAATATTAAAAGAAATA 7 22 0 ATTTAATATT 0.868646 -50 TTGATATGTTTTTTAATATTGTAAAATTTT 10 75 1 TTTTAATATT 0.759479 -109 AATTTTTGATATTAAAAATTTATTTTATGC 10 99 1 ATTAAAAATT 0.8352 -85 AATAAAATTGATTTAACAATATTAATAAGT 11 23 0 ATTTAACAAT 0.912066 -134 TAAAAAAAACATTTAACAATTTTTATTATT 11 71 1 ATTTAACAAT 0.912066 -86 CATTTAAACTTTTTAACATTATACTAAAAA 13 60 1 TTTTAACATT 0.850691 -56 TACCAAAAACTTTTAAAAATTCACAAACAA 16 77 1 TTTTAAAAAT 0.788851 -96 TAGAATCCTAATTTAACATTATACTATATA 16 113 1 ATTTAACATT 0.922677 -60 AGCACTATACTTTTAACATTATATAGTATA 16 132 0 TTTTAACATT 0.850691 -41 CAAAAATTATTTTAAACAATTGAACCAAAT 17 26 1 TTTAAACAAT 0.736082 -215 ATTAAATACAATTAAACAATCAAACAGTAG 17 123 1 ATTAAACAAT 0.853821 -118 GAAAAGCTTATTTTAATATTCAAAATAGCA 18 24 0 TTTTAATATT 0.759479 -67 TATTATTCCTCTTTAAAATTCAATACAAAG 20 24 0 CTTTAAAATT 0.855856 -22 CATAAAATTTATTAAAAATTTATTATTTTG 21 28 0 ATTAAAAATT 0.8352 -139 TTTGGTTTTGATTTAATAATTATTTATTTT 21 58 1 ATTTAATAAT 0.851389 -109 AATAAAAAGGATTAAAAAATAAAACCTCAA 22 204 0 ATTAAAAAAT 0.814463 -58 AATTTATTTTCTTAAAAAATATAAAAACTT 24 124 0 CTTAAAAAAT 0.744014 -31 AACCTTAGTAATTAAATAATGATATACTTT 26 55 0 ATTAAATAAT 0.763709 -79 TTCTTTAAAATTTCGATATTTT 28 3 1 CTTTAAAATT 0.855856 -274 CTTTAATTGTATTAAACATTAACATAAGAA 29 248 1 ATTAAACATT 0.870452 -53 ********** Masking position 5 Map Score: 35.1294 Number of sites scoring better than the average of aligned sites = 838 Number in coding regions = 537 Number in noncoding regions = 301 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 4 TTTTCAAGTATCATTTCAGAAAAAATTTTATCAAC 1 65 1 TATTTAAAAA 0.718279 -182 AAGCTTATTAATATAAGCAAAAAAACAAATTTTTA 1 138 1 AATAAAAAAA 0.843884 -109 TTCTAGTAAGAATAAAATCAAAAAATTGGAGGATT 2 44 1 ATAAAAAAAA 0.703227 -29 CATTAAATTAAAACTATATACAAAACTAATTTTAA 5 88 0 AACTAAAAAA 0.541342 -33 AATTAACTCATAAATTACGAGAAAATTTAATATTA 7 31 0 TAATTAAAAA 0.70615 -41 AACAAAACTTTAAAAAAGCATAAAATAAATTTTTA 10 111 0 TAAAAAAAAA 0.81139 -73 AACTCCTTATCATATAAGATAAAAATAATAACCT 10 160 0 TATATAAAAA 0.706782 -24 AGCTTAAAACTTTTTTTAAAAAAAACATTTAACAA 11 55 1 TTTTTAAAAA 0.395421 -102 AATATCAAGAATTAAAATAATAAAAATTGTTAAAT 11 81 0 ATAAAAAAAA 0.703226 -76 TATTTTTTATAAATAAGTGATAAAACGGAGGCAAA 12 14 0 AATAAAAAAA 0.843884 -160 AGTAAAGTTTTTTTTTGCAAAAAAAGCTTTATAAT 12 139 1 TTTTTAAAAA 0.395421 -35 TTGAATAACAATATTTTGTAAAAAATTCAAAACTT 15 31 0 AATTTAAAAA 0.751148 -67 GACAAAAAGCATAAAATTTATAAAAGTGGAGGAAG 15 67 1 AAAAAAAAAA 0.835883 -31 GATAAATTCTACATTAAAAAAAAAATAATATCTAT 16 31 1 AATTAAAAAA 0.851141 -142 ATAATTTATCAAAAATACAACAAAAAAACAACCTA 17 54 1 AAAATAAAAA 0.728978 -187 CTATTACTACTATATATCTATAAAAAATAAAAATA 17 160 1 TTATAAAAAA 0.679185 -81 AAATAAAAATACAAAATCCACAAAATCTTATTAAG 17 184 1 AAAAAAAAAA 0.835883 -57 AACAATATTGAATAAACCTAGAAAAGCTTATTTTA 18 39 0 ATAAAAAAAA 0.703227 -52 TAAAAATTTATTATTTTGCATAAAAAAGTTTAAAA 21 11 0 TATTTAAAAA 0.711433 -156 GTTGAATTGAATTTAAATCAAAAAATAAATAATTA 21 74 0 ATTAAAAAAA 0.715428 -93 TATAGGCATTTGATAAAAGAAAAAATAAAATGGAA 21 129 1 TATAAAAAAA 0.820328 -38 AAGGTCCTTGTTTTTATTCAGAAAACATCTATAAT 22 11 1 TTTTAAAAAA 0.691889 -251 TGTCCATTTATCAAAAGAGATAAAAATAGCCGGGG 22 65 1 TAAAAAAAAA 0.81139 -197 AATCTTAAAATAAATTAATAAAAAATTCACTTAAA 22 139 0 TAATTAAAAA 0.70615 -123 ACTTTTTACATTATAATACATAAAAATAAATTATA 23 71 0 TATAAAAAAA 0.820257 -68 TAATGTAAAAAGTTAATCAAAAAAAACAATATTCA 23 93 1 ATTAAAAAAA 0.715493 -46 AAACTAACATAAACTAAAAACAAAAACAATTTATC 24 41 0 AACTAAAAAA 0.541342 -114 AAGAATTGTTTTTTTTTAAATAAAAAATATAATCT 24 83 1 TTTTTAAAAA 0.397341 -72 ATTTATTTTCTTAAAAAATATAAAAACTTAAATAC 24 118 0 TAAAAAAAAA 0.811389 -37 CTAATAATTATAAATTAGCATAAAATCTAGTCAAG 26 90 0 TAATTAAAAA 0.70615 -44 CTTTCAATTAACAAAACTTACAAAATGCTGTTTAC 27 145 1 AAAAAAAAAA 0.835883 -119 TATGAAAACGATATTAACAATAAAAATATCGAAAT 28 20 0 AATTAAAAAA 0.851141 -257 TAAAATAATAAAATTAGAAAGAAAAAATAAAAACC 28 96 0 AATTAAAAAA 0.851141 -181 TCCAATTTAGAATATTATAATAAAATAATAAAATT 28 116 0 ATATTAAAAA 0.569645 -161 TAAATGGTCAACAATAAAGAGAAAAAAAGGTGCTC 29 134 0 AAATAAAAAA 0.843443 -167 * **** * **** Masking position 10 Map Score: 37.9559 Number of sites scoring better than the average of aligned sites = 2003 Number in coding regions = 1283 Number in noncoding regions = 720 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 5 TTTTTTCTGAAATGATACTTGAAAAACTTAATTC 1 56 0 AATATACAAA 0.946439 -191 CCACTTATGTTATTATACTTAAAAATTTGTTTTT 1 158 0 TATATACAAA 0.608064 -89 TGATTATTAAAATTATAGCAATAATATGACTAGA 1 201 1 AATATAGTAA 0.579541 -46 TTTGTGATTTAATAATTCTAGTAAGAATAAAATC 2 29 1 AATATTCTAA 0.635588 -44 TATAGCAATTAATCATACTTGTAAGTTATATGTG 3 37 1 AATATACTAA 0.930249 -47 ATTAAATATACCCTAAAATAATCCACA 3 67 0 AAAATACAAA 0.930249 -17 ATCGACTTAAAATTATATCACAAATACAATATTA 4 31 0 AATATATAAA 0.401032 -43 AACTATATACAAAACTAATTTTAAATAAGTAATG 5 78 0 AAACTAATAA 0.452236 -43 TATTAAAAGAAATAATAAATCAAAA 7 2 0 AATATAAAAA 0.687776 -70 TTGGCACAATAATACTTCTTTAAAGAATATACTT 10 40 0 AATCTTCAAA 0.603239 -144 ACTTTTTTTAAAAAAAACATTTAACAATTTTTAT 11 63 1 AAAAAACTAA 0.469151 -94 ATCTTGAGAAAAAGCTACAATTAAAGTAAGGTAT 12 53 0 AAACTACTAA 0.868812 -121 ATTCTTTTGGAAAAATACTACACATTTAAACTTT 13 38 1 AAAATACACA 0.644286 -78 ATTATACTAAAAATATACATTAAAGTAAATAATA 13 77 1 AAAATACAAA 0.930249 -39 AGCTATTAACAAAACTACATTTAAACTATTTATT 14 37 1 AAACTACTAA 0.868812 -147 TTATTTCCATAATACTACATATCATGGAAATAAA 14 82 1 AATCTACTCA 0.54373 -102 GACACAGATAAATTCTACATTAAAAAAAAAATAA 16 25 1 AATCTACAAA 0.920797 -148 ATAATTTATCAAAAATACAACAAAAAAACAACCT 17 54 1 AAAATACAAA 0.930249 -187 GCCTATAATAAATTATACACCTAAGAAGTTGAAT 21 102 0 AATATACTAA 0.930249 -65 TAAATTAATAAAAAATTCACTTAAAACTAATTTG 22 130 0 AAAATTCTAA 0.568295 -132 AGGATTAAAAAATAAAACCTCAAAAACATCCGAC 22 193 0 AATAAACAAA 0.608064 -69 CTTTTTACATTATAATACATAAAAATAAATTATA 23 71 0 TATATACAAA 0.608064 -68 TCTTTTAAAGAAAACTAACATAAACTAAAAACAA 24 53 0 AAACTAAAAA 0.522416 -102 AAAAATCAATAAATCTACCCTTAAAATCAAAAAC 27 85 1 AAACTACTAA 0.868812 -179 CATAGTGTAAAATTATAACAATAATTTTACACTA 27 179 1 AATATAATAA 0.624426 -85 CATATAAATCATTAATACATGAAATAGCATATGA 28 50 0 ATTATACAAA 0.458758 -227 GCAAATTAAAAAAAATAGCCAAAATGAAAAGCTA 28 196 0 AAAATAGAAA 0.579541 -81 AAGCTAATGAAATAATACAGCAAATTAAAAAAAA 28 215 0 AATATACAAA 0.946439 -62 *** **** *** Masking position 14 Map Score: 19.966 Number of sites scoring better than the average of aligned sites = 417 Number in coding regions = 250 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 6 AATTAAGTTTTTCAAGTATCATTTCAGAAAAAAT 1 57 1 TTAGTATTTT 0.811658 -190 ATTTGTTTTTAATTTTTAAAGGTAT 5 2 1 TTTTTTTTTT 0.80806 -119 TAAAATTAGTTTTGTATATAGTTTTAATTTAATG 5 89 1 TTTATATTTT 0.573765 -32 TTTTGATTTATTATTTCTTTTAATAT 7 3 1 TTTTTATTTT 0.828842 -69 TGGTTGTATTATTTCTAATAGTTG 10 1 1 TGTGTATTTT 0.841258 -183 TATTAAAAATTTATTTTATGCTTTTTTAAAGTTT 10 108 1 TTTTTATTTT 0.828842 -76 TTATGCTTTTTTAAAGTTTTGTTTGCTAATAAGT 10 123 1 TTAGTTTTTT 0.789319 -61 TAAAAATTGTTAAATGTTTTTTTTAAAAAAAGTT 11 62 0 TATGTTTTTT 0.608884 -95 TATTGTGAGCTTTGTGTATAATCT 13 1 0 TTTGTATTCT 0.55148 -115 ATTATTTACTTTAATGTATATTTTTAGTATAATG 13 76 0 TTTGTATTTT 0.945339 -40 TATTTTTTTTTTAATGTAGAATTTATCTGTGTCT 16 24 0 TTTGTAGTTT 0.701385 -149 GTAGGTTGTTTTTTTGTTGTATTTTTGATAAATT 17 56 0 TTTGTTGTTT 0.671265 -185 CTATACCATGTTAGTGTTTAATTTGTAGCTTGGC 19 37 1 TTTGTTTTTT 0.937638 -55 TTTAATAAATTTTATGTTTGGTTTTGATTTAATA 21 42 1 TTTGTTTTTT 0.937638 -125 TAATAATTATTTATTTTTTGATTTAAATTCAATT 21 71 1 TTTTTTTTTT 0.80806 -96 TTCAACTTCTTAGGTGTATAATTTATTATAGGCA 21 103 1 TATGTATTTT 0.641669 -64 CCTTTCCATTTTATTTTTTCTTTTATCAAATGCC 21 133 0 TTTTTTTTTT 0.80806 -34 TAATTTATAATGTTAGCATAATTTGTCCATTTAT 22 42 1 TGAGCATTTT 0.0858244 -220 TCGGATGTTTTTGAGGTTTTATTTTTTAATCCTT 22 194 1 TTGGTTTTTT 0.715996 -68 CTCATTATGAATATTGTTTTTTTTGATTAACTTT 23 101 0 ATTGTTTTTT 0.419016 -38 ATAAATTGTTTTTGTTTTTAGTTTATGTTAGTTT 24 42 1 TTTTTTTTTT 0.80806 -113 TTTTAGTTTATGTTAGTTTTCTTTAAAAGAATTG 24 57 1 TGAGTTTTTT 0.534456 -98 TGTATTTAAGTTTTTATATTTTTTAAGAAAATAA 24 117 1 TTTATATTTT 0.573765 -38 AACTTAAGGGTTAATTTATTTTTTATTTTAGGAG 25 16 1 TTTTTATTTT 0.828842 -30 GAGAGGTGGATGATGGTATGTTTTTGATTTTAAG 27 104 0 TGGGTATTTT 0.470507 -160 TCTTATGCACTTATAGTATACTTTAGTAAAAAGT 27 240 1 TTAGTATTTT 0.811658 -24 CTTCATAAGATTGGTTTTTATTTTTTCTTTCTAA 28 84 1 TTTTTTTTTT 0.80806 -193 TTTTTTTAATTTGCTGTATTATTTCATTAGCTTT 28 216 1 TTTGTATTTT 0.945339 -61 ** ***** *** Masking position 12 Map Score: 28.7727 Number of sites scoring better than the average of aligned sites = 545 Number in coding regions = 327 Number in noncoding regions = 218 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 7 AATGTTAAAGTTGATAAAATTTTTTCTGAAAT 1 77 0 TTGATAAATT 0.769937 -170 TTGACACTTGTTGTTAATTTGTGATTTAATAA 2 12 1 TTGTTAATTT 0.870468 -61 TATTGTATTTGTGATATAATTTTAAGTCGATA 4 34 1 GTGATATATT 0.114754 -40 ATTTTTAAATTTTGACTTGTAGT 6 2 1 TTTTTAAATT 0.601052 -158 TTTTTTAATATTGTAAAATTTTTGATATTAAA 10 83 1 TTGTAAAATT 0.877437 -101 ATTTTATGCTTTTTTAAAGTTTTGTTTGCTAA 10 120 1 TTTTTAAATT 0.601052 -64 ATAATAAAAATTGTTAAATGTTTTTTTTAAAA 11 68 0 TTGTTAAAGT 0.725115 -89 GATATTAACTTTGTTAATATTTATACTTTACT 11 110 1 TTGTTAATTT 0.870468 -47 AAATGTAGTTTTGTTAATAGCTTAAGCTTAAT 14 27 0 TTGTTAATGT 0.541763 -157 TAACAATATTTTGTAAAAAATTCAAAACTTTA 15 29 0 TTGTAAAAAT 0.315893 -69 TCTAAATTGTTTGTGAATTTTTAAAAGTTTTT 16 81 0 TTGTGAATTT 0.46011 -92 TGTTGTATTTTTGATAAATTATTTGGTTCAAT 17 44 0 TTGATAAATT 0.769937 -197 AGTAAATATCTTGTTAAATTGTAGGTTGTTTT 17 78 0 TTGTTAAATT 0.937476 -163 TACTGTTTGATTGTTTAATTGTATTTAATACT 17 120 0 TTGTTTAATT 0.468201 -121 TGTGTATTGAATGATAAATTGTTTTTGTTTTT 24 29 1 ATGATAAATT 0.335524 -126 TTTTTTATTTGTGTAAAACTGTTTAAAACAAT 27 19 0 GTGTAAAATT 0.825253 -245 TAGCTTAATTGTTTTAAACTTTTTTATTTGTG 27 38 0 GTTTTAAATT 0.498457 -226 TGTTTACATAGTGTAAAATTATAACAATAATT 27 173 1 GTGTAAAATT 0.825253 -91 GATTGTTATAGTGTAAAATTATTGTTATAATT 27 189 0 GTGTAAAATT 0.825253 -75 GATATTTTTATTGTTAATATCGTTTTCATATG 28 25 1 TTGTTAATTG 0.369019 -252 CTTATTAGCTTTGTAAAAATTTTATTACGCTT 29 94 1 TTGTAAAATT 0.877437 -207 ATTGTTGGAGGTGTAAATGTCTGGTCACAGTA 29 167 0 GTGTAAATTT 0.679139 -134 TACGGTTCTTATGTTAATGTTTAATACAATTA 29 251 0 ATGTTAATTT 0.503461 -50 ******** * * Masking position 2 Map Score: 10.5031 Number of sites scoring better than the average of aligned sites = 520 Number in coding regions = 352 Number in noncoding regions = 168 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 8 TTAAAAATTTGTTTTTTTGCTTATATTAAT 1 144 0 GTTTTTTTGC 0.718122 -103 ATTAAATTATTTTATTTTGCAAA 3 4 0 TTTATTTTGC 0.95145 -80 TTAAAGAAGTATTATTGTGCCAACTTGATA 10 51 1 ATTATTGTGC 0.81432 -133 AGGGGTGATTATTATTTTGTA 11 146 1 ATTATTTTGT 0.837157 -11 ATCTAACCTTATTATTTGGCTTGTGTAGTA 12 109 1 ATTATTTGGC 0.889759 -65 TAAGTAAAGTTTTTTTTTGCAAAAAAAGCT 12 137 1 TTTTTTTTGC 0.87449 -37 AATTCAAAACTTTACTTTGCTATAAGCAGT 15 13 0 TTTACTTTGC 0.786807 -85 TTTTTGATAAATTATTTGGTTCAATTGTTT 17 39 0 ATTATTTGGT 0.640506 -202 TTAAAAATTTATTATTTTGCATAAAAAAGT 21 17 0 ATTATTTTGC 0.958828 -150 TACTAATTTAATTTTTTTGT 22 252 1 ATTTTTTTGT 0.646362 -10 AATTACTATCTTTATTATGCTATATTTCTT 23 27 1 TTTATTATGC 0.713473 -112 GGCTATTTTTTTTAATTTGCTGTATTATTT 28 210 1 TTTAATTTGC 0.713473 -67 ********** Masking position 6 Map Score: 3.40625 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 211 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 9 TTATTATTAATATTGTATTTGTGATATAATT 4 24 1 TATTGATTTG 0.433405 -50 ATTTGTTTTTAATTTTTAAAG 5 1 1 ATTTGTTTTA 0.390735 -120 AAAAGGAATTTAAATGAATACA 9 2 1 AAAGGATTTA 0.119711 -84 GCTATAATAAAATTGATTTAACAATATTAAT 11 27 0 AATTGTTTAA 0.76885 -130 TTGATTGTTTAATTGTATTTAATACTATATG 17 115 0 AATTGATTTA 0.937869 -126 GATAAAATGTAATAGAATATATAAGGAGGCA 17 218 1 AATAGATATA 0.139263 -23 TAATATTCAAAATAGCATTAATAACTCACT 18 10 0 AATAGATTAA 0.442374 -81 TATTATTGACAATTGCATTTATATGCTATAC 19 12 1 AATTGATTTA 0.937869 -80 GGCAGCATAAAATTGTTTTTAATGGAGGAGC 19 68 1 AATTGTTTTA 0.899637 -24 GCTTGCTTTGTATTGAATTTTAAAGAGGAAT 20 19 1 TATTGATTTT 0.414723 -27 TAAGAAGTTGAATTGAATTTAAATCAAAAAA 21 84 0 AATTGATTTA 0.937869 -83 AATTAGTTTTAAGTGAATTTTTTATTAATTT 22 132 1 AAGTGATTTT 0.28142 -130 TTGAATGATAAATTGTTTTTGTTTTTAGTTT 24 35 1 AATTGTTTTG 0.69119 -120 TCTTTAAAAGAATTGTTTTTTTTTAAATAAA 24 76 1 AATTGTTTTT 0.674627 -79 AGCTTCAAATTGTTTTAAACAGTTTTAC 27 8 1 AATTGTTTAA 0.76885 -256 TTTATAGCTTAATTGTTTTAAACTTTTTTAT 27 43 0 AATTGTTTAA 0.76885 -221 TAATATTCTAAATTGGATTTATCTTCATCAA 28 134 1 AATTGATTTA 0.937869 -143 GGGGTGGGGATATTGAATCTAATCCGAGACT 29 37 0 TATTGATCTA 0.255737 -264 AATGAGCTTTAATTGTATTAAACATTAACAT 29 242 1 AATTGATTAA 0.848515 -59 ***** ***** Masking position 8 Map Score: 5.55037 Number of sites scoring better than the average of aligned sites = 537 Number in coding regions = 354 Number in noncoding regions = 183 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 10 TGCTATAGCAATTAATCATACTTGTAAGTTATATGT 3 34 1 ATATATATTA 0.940924 -50 ATTTTAAATAAGTAATGATAAAAATATTCTATCGCA 5 59 0 ATATATAATA 0.863833 -62 TTTTCTTACGAATACTAATACTACTTCCCCCCTGAA 6 33 0 ATATATATTT 0.798056 -127 AAATACTTAACTTATTAATATTGTTAAATCAATTTT 11 14 1 CTATATATTA 0.749963 -143 GAAATAAACTATTATTAATAGTACTAGTTTAATACA 14 108 1 ATATATATTA 0.940924 -76 ATAGATATATAGTAGTAATAGTAGTAAGCTACTGTT 17 145 0 ATATATATTA 0.940924 -96 AATGCCTATAATAAATTATACACCTAAGAAGTTGAA 21 103 0 AAATATAATA 0.716468 -64 GAAAACATCTATAATTTATAATGTTAGCATAATTTG 22 31 1 AAATATATTA 0.863823 -231 TTAGTAATTAAATAATGATATACTTTAAAATACATT 26 45 0 ATATATAATT 0.611493 -89 TTTATTTACCAATACTAATAATTATAAATTAGCATA 26 103 0 ATATATATTA 0.940809 -31 TAAGTGCATAAGAATTAATAATGTTATGGGTTGATT 27 217 0 AAATATATTA 0.863835 -47 * ** * *** * ** Masking position 8 Map Score: 4.6734 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 47 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 11 TCTAAGGGCTTTGCCAATCACATACCTTTA 5 27 0 TTGCCAATCA 0.590842 -94 AAAGTTTTGTTTGCTAATAAGTGTTAGGTT 10 135 1 TTGCTAATAA 0.864464 -49 GATATTAACTTTGTTAATATTTATACTTTA 11 110 1 TTGTTAATAT 0.824217 -47 AAATGTAGTTTTGTTAATAGCTTAAGCTTA 14 29 0 TTGTTAATAG 0.796364 -155 AAACTATTTATTGTCAATAAACTTTATTTC 14 59 1 TTGTCAATAA 0.941271 -125 ATAAATGCAATTGTCAATAATAA 19 4 0 TTGTCAATAA 0.941271 -88 AAATAATAAATTTTTAATAAATTTTATGTT 21 30 1 TTTTTAATAA 0.559865 -137 ACAGCACTATTTGTCAATAAAAATAGCCCC 22 97 0 TTGTCAATAA 0.941271 -165 GATATTTTTATTGTTAATATCGTTTTCATA 28 25 1 TTGTTAATAT 0.824217 -252 CTAAGGGTAGCTGTTAATAAGGCTAAGG 29 9 0 CTGTTAATAA 0.754242 -292 ********** Masking position 6 Map Score: 3.94798 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 124 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 12 ********** No masking Map Score: 1.13569e-11 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 13 TGTTAAAGTTGATAAAATTTTTTCTGAAAT 1 77 0 GATAAAATTT 0.90379 -170 TTGTATTTGTGATATAATTTTAAGTCGATA 4 36 1 GATATAATTT 0.516542 -38 CATAAATTACGAGAAAATTTAATATTAAAA 7 28 0 GAGAAAATTT 0.461174 -44 AAAAGCATAAAATAAATTTTTAATATCAAA 10 103 0 AATAAATTTT 0.704813 -81 TTTAAGCTATAATAAAATTGATTTAACAAT 11 33 0 AATAAAATTG 0.651739 -124 GAATTAAAATAATAAAAATTGTTAAATGTT 11 78 0 AATAAAAATT 0.521689 -79 TTTTTCTCAAGATCAAATTAAATCTTGCTT 12 74 1 GATCAAATTA 0.17253 -100 GTATTATGGAAATAAAGTTTATTGACAATA 14 67 0 AATAAAGTTT 0.518218 -117 TAATACATAAAATAAAAATTTAAAGCTTAG 14 137 1 AATAAAAATT 0.521689 -47 TGACAAAAAGCATAAAATTTATAAAAGTGG 15 66 1 CATAAAATTT 0.88734 -32 ATTTTATCTTAATAAGATTTTGTGGATTTT 17 196 0 AATAAGATTT 0.466305 -45 ATCTTATTAAGATAAAATGTAATAGAATAT 17 208 1 GATAAAATGT 0.634805 -33 AGCTTGGCAGCATAAAATTGTTTTTAATGG 19 63 1 CATAAAATTG 0.60584 -29 TATGCAAAATAATAAATTTTTAATAAATTT 21 24 1 AATAAATTTT 0.704813 -143 CAAAACCAAACATAAAATTTATTAAAAATT 21 38 0 CATAAAATTT 0.88734 -129 GTAAAGGGAATATATAATTTATTTTTATGT 23 59 1 TATATAATTT 0.121718 -80 TGTATTGAATGATAAATTGTTTTTGTTTTT 24 31 1 GATAAATTGT 0.30207 -124 TTTTTAAGAAAATAAATTTTACAGGAGGT 24 136 1 AATAAATTTT 0.704813 -19 TATAAATTAGCATAAAATCTAGTCAAGATT 26 87 0 CATAAAATCT 0.441947 -47 ATAATAAAATAATAAAATTAGAAAGAAAAA 28 105 0 AATAAAATTA 0.547479 -172 GATTTATCTTCATCAAATTTGTTTAGAGTG 28 149 1 CATCAAATTT 0.580833 -128 TGCAAAGCGTAATAAAATTTTTACAAAGCT 29 100 0 AATAAAATTT 0.905569 -201 ********** Masking position 2 Map Score: 3.17963 Number of sites scoring better than the average of aligned sites = 775 Number in coding regions = 529 Number in noncoding regions = 246 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 14 ACAAAATCCTCCAATTTTTTGATTTTAT 2 55 0 ACCCAATTTT 0.915393 -18 AAAGTTCTTCCTCCACTTTTATAAATTTTA 15 78 0 CCCCACTTTT 0.962367 -20 AACAAAAAAACAACCTACAATTTAACAAGATATT 17 72 1 CCCCAATTTA 0.945217 -169 ATAAAAATAGCCCCCGGCTATTTTTATCTCTTTT 22 77 0 CCCCTATTTT 0.974015 -185 TTCAATATCCCCACCCCCTATTTTAGCTGCAATA 29 51 1 CCCCTATTTT 0.974015 -250 GACATTTACACCTCCAACAATTTTTCCAACCGAT 29 178 1 CCCCAATTTT 0.985903 -123 * ** ******* Masking position 11 Map Score: 0.0692928 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 6 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 15 TACTCCATTAAATTAAAACTATATACAAAAC 5 97 0 AATTAAACTA 0.639554 -24 AAATATATTAAATTAACTCATAAATTACGAG 7 45 0 AATTAACCAT 0.696737 -27 CTCAAGATCAAATTAAATCTTGCTTGATTTA 12 79 1 AATTAAACTT 0.933175 -95 TAAAATAAAAATTTAAAGCTTAGATATAAAC 14 144 1 ATTTAAACTT 0.87868 -40 TTTGTAAAAAATTCAAAACTTTACTTTGCTA 15 21 0 ATTCAAACTT 0.69588 -77 GCCTAAATTATAGCTTAATGTGTATT 24 6 1 AATTATACTT 0.597757 -149 ATAAAAAATAAATTAACCCTTAAGTTTAAAA 25 11 0 AATTAACCTT 0.911143 -35 TGCTTGATAAACTTAAAGCTTAATGTATTTT 26 24 1 ACTTAAACTT 0.765407 -110 TCTAGTCAAGATTTAAACCTTAGTAATTAAA 26 69 0 ATTTAAACTT 0.87868 -65 ACACTATAACAATCAACCCATAACATTATTA 27 207 1 AATCAACCAT 0.420571 -57 TAAGCCATTTAATTAACACTCTAAACAAATT 28 164 0 AATTAACCTC 0.780402 -113 TTTCCAACCGATTTAAAACGTCAAACATCCT 29 200 1 ATTTAAACGT 0.576978 -101 TGTTTAATACAATTAAAGCTCATTTGATTAA 29 235 0 AATTAAACTC 0.828758 -66 ******* *** Masking position 5 Map Score: 2.32211 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 216 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419