AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -ifruR_bbur_opreg_300.orf -g0.282 -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 = 0.282 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 BB0057 72 glyceraldehyde 3-phosphate dehydrogenase (gap) #2 BB0060 83 conserved hypothetical protein #3 BB0061 73 thioredoxin (trxA) #4 BB0347 183 fibronectin/fibrinogen-binding protein, putative #5 BB0348 97 pyruvate kinase (pyk) #6 BB0408 173 PTS system, fructose-specific IIABC component (fruA-1) #7 BB0437 172 chromosomal replication initiator protein (dnaA) #8 BB0438 240 DNA polymerase III, subunit beta (dnaN) #9 BB0439 90 conserved hypothetical protein #10 BB0440 91 ribosomal protein L34 (rpmH) #11 BB0444 45 nucleotide sugar epimerase #12 BB0445 166 fructose-bisphosphate aldolase (fba) #13 BB0554 261 B. burgdorferi predicted coding region BB0554 #14 BB0557 138 phosphocarrier protein HPr (ptsH-2) #15 BB0629_BB0630 81 BB0629: PTS system, fructose-specific IIABC component (fruA-2), BB0630: 1-phosphofructokinase (fruK) #16 BB0724 87 K+ transport protein (ntpJ) #17 BB0727 27 pyrophosphate--fructose 6-phosphate 1-phosphotransferase (pfk) Motif number 1 AAATTATTTTATTTTGCAAA 2 1 0 ATTTTGCAAA 0.884924 -83 TGCTATAGCAATTAATCATACTTGTAAGTT 2 34 1 ATTAATCATA 0.785927 -50 ATAATTCCTTATTATTAATATTGTATTTGT 3 16 1 ATTATTAATA 0.869606 -58 GAAATAAACTATTATTAATAGTACTAGTTT 4 108 1 ATTATTAATA 0.869606 -76 GAATAACAATATTTTGTAAAAAATTCAAAA 5 34 0 ATTTTGTAAA 0.903665 -64 AAAGCATAAAATTTATAAAAGTGGAGGAAG 5 72 1 ATTTATAAAA 0.880205 -26 CAATTTTTATATTATTTAAAATAATCAGTT 6 12 0 ATTATTTAAA 0.817462 -162 ACATATCGCAATATTGAAAAGGTAAAACAA 6 39 0 ATATTGAAAA 0.813578 -135 TATAAAAAATATTTTTTAAACTAAACAGGG 6 84 0 ATTTTTTAAA 0.916622 -90 TTTAAAAAATATTTTTTATATTAGGTGGCT 6 94 1 ATTTTTTATA 0.942436 -80 GTAATTAAACATATTGTATAATATACAATA 6 139 0 ATATTGTATA 0.866649 -35 TTGTTTGTGAATTTTTAAAAGTTTTTGGTA 7 77 0 ATTTTTAAAA 0.916618 -96 TTTTAACATTATATAGTATAATGTTAAATT 7 122 0 ATATAGTATA 0.813578 -51 GAACCAAATAATTTATCAAAAATACAACAA 8 47 1 ATTTATCAAA 0.858193 -194 TTGTATTTTTATTTTTTATAGATATATAGT 8 168 0 ATTTTTTATA 0.942436 -73 TATTAATGCTATTTTGAATATTAAAATAAG 9 18 1 ATTTTGAATA 0.933196 -73 GCAAAAAACAATATTGAATAAACCTAGAAA 9 50 0 ATATTGAATA 0.866649 -41 ATCAATTTTTTATACCACAATGCA 9 77 0 ATTTTTTATA 0.942436 -14 AAAATTTATTATTTTGCATAAAAAAGTTTA 12 14 0 ATTTTGCATA 0.919689 -153 AAAATAATAAATTTTTAATAAATTTTATGT 12 29 1 ATTTTTAATA 0.942436 -138 TAGGTGTATAATTTATTATAGGCATTTGAT 12 113 1 ATTTATTATA 0.916623 -54 GAAAACATCTATAATTTATAATGTTAGCAT 13 31 1 ATAATTTATA 0.75626 -231 TAATTTGTCCATTTATCAAAAGAGATAAAA 13 60 1 ATTTATCAAA 0.858193 -202 CTTAAAATAAATTAATAAAAAATTCACTTA 13 141 0 ATTAATAAAA 0.75003 -121 CTAACATTGCATAAATAAAAAGGATTAAAA 13 217 0 ATAAATAAAA 0.583179 -45 TACATAAGAAATATAGCATAATAAAGATAG 14 32 0 ATATAGCATA 0.781548 -107 ATACATAAAAATAAATTATATATTCCCTTT 14 61 0 ATAAATTATA 0.675697 -78 TTTATGTATTATAATGTAAAAAGTTAATCA 14 82 1 ATAATGTAAA 0.639996 -57 GAAACCCCTCATTATGAATATTGTTTTTTT 14 112 0 ATTATGAATA 0.85053 -27 ATCTCCTTTGATTTATAAAATCAATTAAAT 15 15 1 ATTTATAAAA 0.880205 -67 GTGTATATACATTTATTAAATTTTACTATT 15 46 0 ATTTATTAAA 0.880502 -36 CTTTATATATTATATAGTGTATAT 15 68 0 ATATATTATA 0.836464 -14 TAATTACATTATTTTTAATAT 16 2 0 ATTTTTAATA 0.942436 -86 AATTTATCTTATATAGCATAATATTTTAAC 16 47 0 ATATAGCATA 0.781548 -41 TATAAGATAAATTTTTAATAATTTAAACAA 16 64 1 ATTTTTAATA 0.942436 -24 ********** Masking position 8 Map Score: 49.6583 Number of sites scoring better than the average of aligned sites = 2158 Number in coding regions = 1386 Number in noncoding regions = 772 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 2 CTCCAATTTTTTGATTTTATTCTTACTAGAA 1 44 0 TTGTTTTATT 0.900685 -29 TAGCAATTAAATTATTTTATTTTGCAAA 2 8 0 ATTTTTTATT 0.607115 -76 TAAATTTTTATTTTATGTATTAAACTAGTAC 4 128 0 TTTATGTATT 0.910124 -56 AAGTAAAGTTTTGAATTTTTTACAAAATATT 5 26 1 TTGATTTTTT 0.915206 -72 GGTATGCTATTTTTATTGTATATTATACAAT 6 126 1 TTTATTGTAT 0.674846 -48 AGATATTATTTTTTTTTTAATGTAGAATTTA 7 33 0 TTTTTTTAAT 0.800992 -140 AGGTTGTTTTTTTGTTGTATTTTTGATAAAT 8 57 0 TTTTTGTATT 0.76841 -184 GATTGTTTAATTGTATTTAATACTATATGAT 8 113 0 TTGATTTAAT 0.900684 -128 TAAGCTACTGTTTGATTGTTTAATTGTATTT 8 126 0 TTTATTGTTT 0.863654 -115 GATTTTGTATTTTTATTTTTTATAGATATAT 8 171 0 TTTATTTTTT 0.935979 -70 TTATTGACAATTGCATTTATATGCTATACCA 10 14 1 TTGATTTATA 0.708456 -78 CAGCATAAAATTGTTTTTAATGGAGGAGCGT 10 70 1 TTGTTTTAAT 0.748205 -22 TGGGCTTGCTTTGTATTGAATTTTAAAGAGG 11 16 1 TTGATTGAAT 0.79713 -30 TATGTTTGGTTTTGATTTAATAATTATTTAT 12 54 1 TTTATTTAAT 0.924645 -113 TTTAATAATTATTTATTTTTTGATTTAAATT 12 69 1 ATTATTTTTT 0.647799 -98 ACCTAAGAAGTTGAATTGAATTTAAATCAAA 12 87 0 TTGATTGAAT 0.797058 -80 TTCTTAGGTGTATAATTTATTATAGGCATTT 12 109 1 TATATTTATT 0.633785 -58 CTCCTTTCCATTTTATTTTTTCTTTTATCAA 12 138 0 TTTATTTTTT 0.935979 -29 AAGGTCCTTGTTTTTATTCAGAAAACAT 13 8 1 TTGTTTTATT 0.900685 -254 TGAATTTTTTATTAATTTATTTTAAGATTGT 13 145 1 ATTATTTATT 0.822362 -117 TTTAAGATTGTTGCATGTATTGGGTAGGGTC 13 165 1 TTGATGTATT 0.88202 -97 GTTTTTGAGGTTTTATTTTTTAATCCTTTTT 13 200 1 TTTATTTTTT 0.935979 -62 TTTTAATCCTTTTTATTTATGCAATGTTAGG 13 217 1 TTTATTTATG 0.734514 -45 TTTTTACTAATTTAATTTTTTTGT 13 248 1 TTTATTTTTT 0.935975 -14 TATAATTTATTTTTATGTATTATAATGTAAA 14 71 1 TTTATGTATT 0.910124 -68 TGAATATTGTTTTTTTTGATTAACTTTTTAC 14 97 0 TTTTTTGATT 0.84183 -42 GATAATCTCCTTTGATTTATAAAATCAATTA 15 11 1 TTTATTTATA 0.766967 -71 TTACTATTTATTTAATTGATTTTATAAATCA 15 23 0 TTTATTGATT 0.941734 -59 AAAGTTGTTTAAATTATTAAAAATTTAT 16 70 0 TTTAATTATT 0.630427 -18 *** ******* Masking position 6 Map Score: 33.1763 Number of sites scoring better than the average of aligned sites = 2421 Number in coding regions = 1551 Number in noncoding regions = 870 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 3 CTATAGCAATTAAATTATTTTATTTTGCAA 2 12 0 TAAATTATTT 0.916189 -72 CCTTATTATTAATATTGTATTTGTGATATA 3 22 1 AATATTGTAT 0.472001 -52 CTATCGACTTAAAATTATATCACAAATACA 3 37 0 AAAATTATAT 0.633284 -37 AAACTACATTTAAACTATTTATTGTCAATA 4 48 1 TAAACTATTT 0.835168 -136 TTATTGTCAATAAACTTTATTTCCATAATA 4 66 1 TAAACTTTAT 0.70622 -118 ATCATGGAAATAAACTATTATTAATAGTAC 4 102 1 TAAACTATTA 0.594054 -82 ATCTAAGCTTTAAATTTTTATTTTATGTAT 4 139 0 TAAATTTTTA 0.813786 -45 AGTAAAGTTTTGAATTTTTTACAAAATATT 5 27 1 TGAATTTTTT 0.665012 -71 TTTTTTACAAAATATTGTTATTCAATGACA 5 41 1 AATATTGTTA 0.430296 -57 TCCACTTTTATAAATTTTATGCTTTTTGTC 5 67 0 TAAATTTTAT 0.838353 -31 AAACAATTTTTATATTATTTAAAATAATCA 6 15 0 TATATTATTT 0.813647 -159 AAATAATATAAAAATTGTTTTACCTTTTCA 6 25 1 AAAATTGTTT 0.867502 -149 TAGTTTAAAAAATATTTTTTATATTAGGTG 6 91 1 AATATTTTTT 0.736873 -83 GGAAATACCAAAAACTTTTAAAAATTCACA 7 72 1 AAAACTTTTA 0.483318 -101 GGATTCTATCTAAATTGTTTGTGAATTTTT 7 91 0 TAAATTGTTT 0.934072 -82 AATTTAACATTATACTATATAATGTTAAAA 7 122 1 TATACTATAT 0.408903 -51 GTTTTAGCACTATACTTTTAACATTATATA 7 137 0 TATACTTTTA 0.447891 -36 TGAAGAATCAAAAATTATTTTAAACAATTG 8 18 1 AAAATTATTT 0.834755 -223 ATTATTTGGTTCAATTGTTTAAAATAATTT 8 29 0 TCAATTGTTT 0.649587 -212 GTATTTTTGATAAATTATTTGGTTCAATTG 8 42 0 TAAATTATTT 0.916189 -199 AGGTTTATTCAATATTGTTTTTTGCATTGT 9 55 1 AATATTGTTT 0.723385 -36 ATCAATTTTTTATACCACAAT 9 80 0 TCAATTTTTT 0.665012 -11 TTGGCAGCATAAAATTGTTTTTAATGGAGG 10 66 1 AAAATTGTTT 0.867502 -26 TTTTAAACTTTTTTATGCAAAAT 12 4 1 TAAACTTTTT 0.8753 -163 TGCAAAATAATAAATTTTTAATAAATTTTA 12 26 1 TAAATTTTTA 0.813786 -141 AAATTTTTAATAAATTTTATGTTTGGTTTT 12 37 1 TAAATTTTAT 0.838353 -130 TAGTTTTAAGTGAATTTTTTATTAATTTAT 13 135 1 TGAATTTTTT 0.665012 -127 TTTTACTAATTTAATTTTTTTGT 13 249 1 TTAATTTTTT 0.421202 -13 TACATAAAAATAAATTATATATTCCCTTTA 14 60 0 TAAATTATAT 0.788891 -79 CCTCATTATGAATATTGTTTTTTTTGATTA 14 106 0 AATATTGTTT 0.723385 -33 CTTTATATATTATATAGTGTATATA 15 67 0 TATATTATAT 0.598798 -15 CTATATAAGATAAATTTTTAATAATTTAAA 16 61 1 TAAATTTTTA 0.813786 -27 ********** Masking position 6 Map Score: 33.5153 Number of sites scoring better than the average of aligned sites = 2247 Number in coding regions = 1484 Number in noncoding regions = 763 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 4 ATTATTTTAGGGTATATTTAAT 2 72 1 GGTATATTTA 0.880854 -12 AAAAGGTAAAACAATTTTTATATTATTTAA 6 23 0 ACAATTTTTA 0.650452 -151 AATACATATCGCAATATTGAAAAGGTAAAA 6 42 0 GCAATATTGA 0.686511 -132 GCTGTGGTATGCTATTTTTATTGTATATTA 6 121 1 GCTATTTTTA 0.973544 -53 AAATTGTTTGTGAATTTTTAAAAGTTTTTG 7 80 0 TGAATTTTTA 0.592792 -93 TTGTGGATTTTGTATTTTTATTTTTTATAG 8 177 0 TGTATTTTTA 0.762768 -64 AGTTATTAATGCTATTTTGAATATTAAAAT 9 15 1 GCTATTTTGA 0.94045 -76 ATAGCCCCCGGCTATTTTTATCTCTTTTGA 13 75 0 GCTATTTTTA 0.973544 -187 ATAGCCGGGGGCTATTTTTATTGACAAATA 13 90 1 GCTATTTTTA 0.973544 -172 TCTTTATTATGCTATATTTCTTATGTAAAG 14 35 1 GCTATATTTC 0.776138 -104 ********** Masking position 5 Map Score: 7.08134 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 196 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 ATAAAATAATTTAATTGCTATAGCAATTAA 2 19 1 TTAATTGCTA 0.539827 -65 ACAAGTATGATTAATTGCTATAGCAATTAA 2 29 0 TTAATTGCTA 0.539827 -55 CAATAAATAGTTTAAATGTAGTTTTGTTAA 4 42 0 TTTAAATGTA 0.400918 -142 ATAAACTATTATTAATAGTACTAGTTTAAT 4 111 1 ATTAATAGTA 0.461306 -73 TTTCAAGGTGTTTATATCTAAGCTTTAAAT 4 154 0 TTTATATCTA 0.212425 -30 TTGAATAACAATATTTTGTAAAAAATTCAA 5 36 0 ATATTTTGTA 0.457284 -62 CTCCACTTTTATAAATTTTATGCTTTTTGT 5 68 0 ATAAATTTTA 0.455867 -30 GGTATGCTATTTTTATTGTATATTATACAA 6 126 1 TTTTATTGTA 0.447066 -48 TACAATATGTTTAATTACTAGGAGACCACA 6 151 1 TTAATTACTA 0.556419 -23 TTAATTAAAATCTAGACACAGATA 7 5 1 TTAAAATCTA 0.697799 -168 CTAGACACAGATAAATTCTACATTAAAAAA 7 22 1 ATAAATTCTA 0.886429 -151 TAAAAAAAAAATAATATCTATTACATAGGA 7 45 1 ATAATATCTA 0.430074 -128 ACTTTTAACATTATATAGTATAATGTTAAA 7 124 0 TTATATAGTA 0.493934 -49 AAATATCTTGTTAAATTGTAGGTTGTTTTT 8 77 0 TTAAATTGTA 0.891553 -164 TTTAATTGTATTTAATACTATATGATGCAA 8 109 0 TTTAATACTA 0.51364 -132 TGTTTGATTGTTTAATTGTATTTAATACTA 8 119 0 TTTAATTGTA 0.720528 -122 TTTTTTATAGATATATAGTAGTAATAGTAG 8 157 0 ATATATAGTA 0.461306 -84 TCTTATTAAGATAAAATGTAATAGAATATA 8 209 1 ATAAAATGTA 0.65185 -32 ATGCCTCCTTATATATTCTATTACATTTTA 8 220 0 ATATATTCTA 0.709949 -21 AGTGAGTTATTAATGCTATTTTGAATAT 9 9 1 ATTAATGCTA 0.464252 -82 ACAATTGCATTTATATGCTATACCATGTTA 10 20 1 TTATATGCTA 0.496896 -72 ATGTTAGTGTTTAATTTGTAGCTTGGCAGC 10 44 1 TTAATTTGTA 0.753835 -48 TAAATTTTTAATAAATTTTATGTTTGGTTT 12 36 1 ATAAATTTTA 0.455867 -131 ATTTTTTGATTTAAATTCAATTCAACTTCT 12 83 1 TTAAATTCAA 0.284327 -84 AATGCCTATAATAAATTATACACCTAAGAA 12 109 0 ATAAATTATA 0.545552 -58 TGCTAACATTATAAATTATAGATGTTTTCT 13 30 0 ATAAATTATA 0.545552 -232 TAGAATAAGTTTAATTACTATCTTTATTAT 14 15 1 TTAATTACTA 0.556419 -124 ATACATAAAAATAAATTATATATTCCCTTT 14 61 0 ATAAATTATA 0.545552 -78 TTTTTATGTATTATAATGTAAAAAGTTAAT 14 80 1 TTATAATGTA 0.400919 -59 AATCAATTAAATAAATAGTAAAATTTAATA 15 33 1 ATAAATAGTA 0.731953 -49 ********** Masking position 2 Map Score: 17.946 Number of sites scoring better than the average of aligned sites = 1138 Number in coding regions = 680 Number in noncoding regions = 458 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 6 ATCCTCCAATTTTTTGATTTTATTCTTACTA 1 47 0 TTTTGATTTT 0.736987 -26 AATCAAAAAATTGGAGGATTTTGT 1 59 1 TTGAGGATTT 0.881889 -14 TAAATTTTTATTTTATGTATTAAACTAGTAC 4 128 0 TTTATGTATT 0.584334 -56 TTTTTAAAAGTTTTTGGTATTTCCTATGTAA 7 65 0 TTTTGGTATT 0.90138 -108 ATCTAAATTGTTTGTGAATTTTTAAAAGTTT 7 83 0 TTGTGAATTT 0.444895 -90 TTTTTTGTCCTTGTTGGTTTTAGCACTATAC 7 152 0 TTTTGGTTTT 0.963106 -21 GGTTGTTTTTTTGTTGTATTTTTGATAAATT 8 56 0 TTTTGTATTT 0.450072 -185 TCTTGTTAAATTGTAGGTTGTTTTTTTGTTG 8 71 0 TTTAGGTTGT 0.768012 -170 TTAATAAGATTTTGTGGATTTTGTATTTTTA 8 187 0 TTGTGGATTT 0.881889 -54 AAATAAGCTTTTCTAGGTTTATTCAATATTG 9 41 1 TTTAGGTTTA 0.690754 -50 ATAAATTTTATGTTTGGTTTTGATTTAATAA 12 46 1 TGTTGGTTTT 0.866991 -121 TAATTATTTATTTTTTGATTTAAATTCAATT 12 74 1 TTTTTGATTT 0.674046 -93 GTATAATTTATTATAGGCATTTGATAAAAGA 12 118 1 TTTAGGCATT 0.632519 -49 GTCGGATGTTTTTGAGGTTTTATTTTTTAAT 13 193 1 TTGAGGTTTT 0.935473 -69 ATTTATGCAATGTTAGGTTTTTACTAATTTA 13 231 1 TGTAGGTTTT 0.866991 -31 TATAATTTATTTTTATGTATTATAATGTAAA 14 71 1 TTTATGTATT 0.584334 -68 ** ******** Masking position 1 Map Score: 7.07825 Number of sites scoring better than the average of aligned sites = 880 Number in coding regions = 617 Number in noncoding regions = 263 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 7 AAACTATTTATTGTCAATAAACTTTATTTC 4 59 1 TTGTCAATAA 0.976461 -125 TAACAATATTTTGTAAAAAATTCAAAACTT 5 31 0 TTGTAAAAAA 0.781019 -67 TTTATGCTTTTTGTCATTGAATAACAATAT 5 52 0 TTGTCATTGA 0.795243 -46 ACCAAATAATTTATCAAAAATACAACAAAA 8 49 1 TTATCAAAAA 0.778978 -192 ATAAATGCAATTGTCAATAATAA 10 4 0 TTGTCAATAA 0.976461 -88 ACAGCACTATTTGTCAATAAAAATAGCCCC 13 97 0 TTGTCAATAA 0.976461 -165 ********** Masking position 6 Map Score: 2.6901 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 84 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 TTAAATGTAGTTTTGTTAATAGCTTAAGCTT 4 30 0 TTTTGTAATA 0.775512 -154 ATATGTAGTATTATGGAAATAAAGTTTATTG 4 73 0 TTATGAAATA 0.872201 -111 CAGGGAAATTTTATCTAAATACATATCGCAA 6 58 0 TTATCAAATA 0.781046 -116 CTATTACATTTTATCTTAATAAGATTTTGTG 8 202 0 TTATCTAATA 0.927708 -39 CTAGAAAAGCTTATTTTAATATTCAAAATAG 9 26 0 TTATTTAATA 0.939315 -65 AATGGACAAATTATGCTAACATTATAAATTA 13 42 0 TTATGTAACA 0.952944 -220 TTTTATTAATTTATTTTAAGATTGTTGCATG 13 151 1 TTATTTAAGA 0.826474 -111 GTAATTAAACTTATTCTAACAA 14 2 0 TTATTTAACA 0.927365 -137 AATAATGTAATTATGATAATATTTCAATGTT 16 19 1 TTATGTAATA 0.960864 -69 ATATAGCATAATATTTTAACATTGAAATATT 16 36 0 ATATTTAACA 0.642415 -52 ***** ***** Masking position 4 Map Score: 4.61357 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 114 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 9 ********** No masking Map Score: 9.82981e-13 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 10 ********** No masking Map Score: 9.82981e-13 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 11 TCCTCCAATTTTTTGATTTTATTCTTACTA 1 47 0 TTTTGATTTT 0.81367 -26 ATCAAAAAATTGGAGGATTTTGT 1 60 1 TGGAGGATTT 0.839376 -13 CAAAGTAAAGTTTTGAATTTTTTACAAAAT 5 24 1 TTTTGAATTT 0.81367 -74 TTTTTTTTAATGTAGAATTTATCTGTGTCT 7 24 0 TGTAGAATTT 0.693755 -149 TTTTAAAAGTTTTTGGTATTTCCTATGTAA 7 65 0 TTTTGGTATT 0.599234 -108 TCTAAATTGTTTGTGAATTTTTAAAAGTTT 7 83 0 TTGTGAATTT 0.743296 -90 TTTTTGTCCTTGTTGGTTTTAGCACTATAC 7 152 0 TGTTGGTTTT 0.932514 -21 GTTGTTTTTTTGTTGTATTTTTGATAAATT 8 56 0 TGTTGTATTT 0.546941 -185 CTTGTTAAATTGTAGGTTGTTTTTTTGTTG 8 71 0 TGTAGGTTGT 0.534805 -170 TAATAAGATTTTGTGGATTTTGTATTTTTA 8 187 0 TTGTGGATTT 0.909694 -54 TAAATTTTATGTTTGGTTTTGATTTAATAA 12 47 1 GTTTGGTTTT 0.815146 -120 AATTATTTATTTTTTGATTTAAATTCAATT 12 75 1 TTTTTGATTT 0.480456 -92 TCGGATGTTTTTGAGGTTTTATTTTTTAAT 13 194 1 TTGAGGTTTT 0.851751 -68 TTTATGCAATGTTAGGTTTTTACTAATTTA 13 232 1 GTTAGGTTTT 0.715512 -30 ********** Masking position 10 Map Score: 5.79672 Number of sites scoring better than the average of aligned sites = 1118 Number in coding regions = 776 Number in noncoding regions = 342 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 12 ********** No masking Map Score: 9.82981e-13 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 ********** No masking Map Score: 9.82981e-13 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 14 ********** No masking Map Score: 9.82981e-13 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