AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -icrp_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 BB0151 76 N-acetylglucosamine-6-phosphate deacetylase (nagA) #2 BB0152 26 glucosamine-6-phosphate isomerase (nagB) #3 BB0155 61 B. burgdorferi predicted coding region BB0155 #4 BB0156 28 B. burgdorferi predicted coding region BB0156 #5 BB0158 153 antigen, S2, putative #6 BB0159 23 B. burgdorferi predicted coding region BB0159 #7 BB0160 47 alanine racemase (alr) #8 BB0240 300 glycerol uptake facilitator (glpF) #9 BB0241 42 glycerol kinase (glpK) #10 BB0242 53 B. burgdorferi predicted coding region BB0242 #11 BB0243 71 glycerol-3-phosphate dehydrogenase, anaerobic (glpA) #12 BB0351 106 B. burgdorferi predicted coding region BB0351 #13 BB0404 165 B. burgdorferi predicted coding region BB0404 #14 BB0554 261 B. burgdorferi predicted coding region BB0554 #15 BB0557 138 phosphocarrier protein HPr (ptsH-2) #16 BB0564 207 B. burgdorferi predicted coding region BB0564 #17 BB0618 87 cytidine deaminase (cdd) #18 BB0642 78 spermidine/putrescine ABC transporter, ATP-binding protein (potA) #19 BB0643 154 conserved hypothetical protein #20 BB0665 42 B. burgdorferi predicted coding region BB0665 #21 BB0668 70 flagellar filament outer layer protein (flaA) #22 BB0683 93 3-hydroxy-3-methylglutaryl-CoA synthase Motif number 1 TTTAAAATAAAAAATATAAGCT 1 3 1 TAAAATAAAA 0.933509 -74 ATGCTTATAGTAAAATAAAATAAATAAAAG 1 46 1 TAAAATAAAA 0.933509 -31 AAATAAAAGGAAAATAAAAA 1 67 1 AAAATAAAAA 0.722375 -10 AAAGTCATTTTAAATAATAATATAAAAAT 3 43 1 TAAATAATAA 0.91788 -19 ATTGAAAGATTAAAAATAAAAATGCAATTT 5 14 1 TAAAAATAAA 0.927231 -140 AAATGCAATTTTAAATAAAACCAAAAGCGA 5 33 1 TTAAATAAAA 0.882468 -121 TGATTTAATGTAAATTTTAATTACCGCCTA 5 98 1 TAAATTTTAA 0.793746 -56 ATAAAAACAAAAGGAAATATC 6 2 1 TAAAAACAAA 0.907212 -22 ACTACAAATTAATAGAAAAAAGATTTTT 7 9 1 TTAATAGAAA 0.532182 -39 ATTCATAATTTAAAAATTAAAATTCTTAAA 8 47 1 TAAAAATTAA 0.920192 -254 TTAATCTTAATTAAAAATAAGATATTAAAT 8 86 1 TTAAAAATAA 0.909827 -215 AAATAAGATATTAAATATAATTTTAATAAG 8 100 1 TTAAATATAA 0.866551 -201 GTCTCTTTTATTAAAAAAAATTAATTTTTC 8 140 0 TTAAAAAAAA 0.915552 -161 TAAAAGAGACTAAAATAAAAAAATTCTAAC 8 160 1 TAAAATAAAA 0.933509 -141 ACCATCTTGCAAAAAACAAAATAAAATTTA 8 188 1 AAAAAACAAA 0.719443 -113 AAAAACAAAATAAAATTTAATTAAAAGATT 8 199 1 TAAAATTTAA 0.880388 -102 TTTAATCTGAATAATATTAAATCTTTTAAT 8 218 0 ATAATATTAA 0.486683 -83 TTAAAAAATCAAAAATTAAAACTTCTTAAT 8 243 1 AAAAATTAAA 0.698707 -58 AACTTCTTAATAAAAAATAAAATAGTTATA 8 262 1 TAAAAAATAA 0.958006 -39 AATTAAAACAAATGGTCTTTTC 11 3 1 TTAAAACAAA 0.83961 -69 AGTATTTAACTAAAAAGAAAAGAAATTAAC 11 48 1 TAAAAAGAAA 0.812661 -24 TAATTTATTGTAAAATAAAAGAAAAAAC 12 9 0 TAAAATAAAA 0.933509 -98 TAAGGCTAAATTAATTATAAATAAGATTTA 13 48 0 TTAATTATAA 0.77082 -118 CCCAAAAATTTAAATATTAAGTTTTTAATC 13 138 0 TAAATATTAA 0.856013 -28 AAAAATTCACTTAAAACTAATTTGAAAACA 14 124 0 TTAAAACTAA 0.841739 -138 TTAAAATAAATTAATAAAAAATTCACTTAA 14 140 0 TTAATAAAAA 0.841523 -122 TGCAACAATCTTAAAATAAATTAATAAAAA 14 150 0 TTAAAATAAA 0.85852 -112 TAAAAAGGATTAAAAAATAAAACCTCAAAA 14 202 0 TAAAAAATAA 0.958006 -60 TAACATTGCATAAATAAAAAGGATTAAAAA 14 216 0 TAAATAAAAA 0.908431 -46 ACAAAAAAATTAAATTAGTAAAA 14 249 0 AAAAAATTAA 0.790599 -13 TTATAATACATAAAAATAAATTATATATTC 15 66 0 TAAAAATAAA 0.927231 -73 CATATATTGATAAATACAAATTAGAAGTTA 16 75 1 TAAATACAAA 0.82721 -133 TAGAAGTTAATAAAATTTAATTTACCAAAA 16 96 1 TAAAATTTAA 0.880388 -112 AATAAAAAACATAATTTTAACAGAATTCTA 16 128 1 ATAATTTTAA 0.390191 -80 CTTTCTACCTTAAATTATAAGATAGAATTC 16 150 0 TAAATTATAA 0.885565 -58 GTAGGTTAAATTAAATTTAATATAAAAAAG 16 182 1 TTAAATTTAA 0.487587 -26 CAATATTTCAATAAAATAAACCACAATGGC 17 42 1 ATAAAATAAA 0.641893 -46 CAATGGCTAATAAAATATAACAGGTGGGAA 17 65 1 TAAAATATAA 0.940443 -23 GGCATTTACATAAATAATAATATTAAGTAT 18 15 1 TAAATAATAA 0.91788 -64 TATGGCTGTATTAATACAAATCAAGATTAT 18 43 0 TTAATACAAA 0.719375 -36 TATTTTCTTAAAAAATATAAAAACTTAAAT 19 26 1 AAAAATATAA 0.806058 -129 TTTTTAAATAAAAAATATAATCTGTATTTA 19 51 0 AAAAATATAA 0.806058 -104 ATTTTTTATTTAAAAAAAAACAATTCTTTT 19 65 1 TAAAAAAAAA 0.952966 -90 TAACATAAACTAAAAACAAAAACAATTTAT 19 104 1 TAAAAACAAA 0.907212 -51 TCCTTATAATTAAATTATAATAATCAT 20 8 0 TAAATTATAA 0.885565 -35 TATAAGGATTTTAAAAGTAATTT 20 30 1 TTAAAAGTAA 0.712529 -13 TTTTTATTAGTAAAATTTAATTTA 21 5 0 TAAAATTTAA 0.880388 -66 AATTTTACTAATAAAAATAATTAAAAAACG 21 18 1 ATAAAAATAA 0.762582 -53 CTAATTTTTGTAAATTATAATATAATACTT 22 48 1 TAAATTATAA 0.885565 -46 ********** Masking position 4 Map Score: 73.8012 Number of sites scoring better than the average of aligned sites = 3270 Number in coding regions = 1951 Number in noncoding regions = 1319 Number of orfs with sites within 600 bp upstream = 236 Fraction of orfs with sites within 600 bp upstream = 0.0379056 Motif number 2 TTTAAAATAAAAAATATAAGCTTTAAAA 1 7 1 ATAAAAAATA 0.924859 -70 TATAAGCTTTAAAAAAGATTAATGCTTATAGT 1 25 1 AAAAAAATAA 0.938751 -52 TTATAGTAAAATAAAATAAATAAAAGGAAAAT 1 50 1 ATAAAAAATA 0.924859 -27 GCAATTTTAAATAAAACCAAAAGCGACTTGAC 5 37 1 ATAAAACAAA 0.876502 -117 TTACCGCCTAAAAAAGGCTTTAAATGGTATAA 5 118 1 AAAAAGCTTA 0.699433 -36 ATAAAAACAAAAGGAAATATCT 6 1 1 ATAAAACAAA 0.876502 -23 ATTAATAGAAAAAAGATTTTTACTTCTCTAAG 7 18 1 AAAAGATTTA 0.558112 -30 AAAACAAAAAATCCTTAAACAAATTTT 8 6 1 AAAAAACTTA 0.916653 -295 TTAATTAAAAATAAGATATTAAATATAATTTT 8 92 1 ATAAGAATAA 0.831255 -209 AATTTTTCTAATAAAAGCCTTATTAAAATTAT 8 116 0 ATAAAACTTA 0.898293 -185 CTCTTTTATTAAAAAAAATTAATTTTTCTAAT 8 136 0 AAAAAAATAA 0.938751 -165 TTTTTTTAATAAAAGAGACTAAAATAAAAAAA 8 151 1 AAAAGAATAA 0.859835 -150 GACTAAAATAAAAAAATTCTAACCATCTTGCA 8 167 1 AAAAAATTAA 0.73917 -134 GCAAAAAACAAAATAAAATTTAATTAAAAGAT 8 196 1 AAATAAATTA 0.695193 -105 TATTCAGATTAAAAAATCAAAAATTAAAACTT 8 235 1 AAAAAACAAA 0.898353 -66 TTAATAAAAAATAAAATAGTTATAAAGATAAG 8 268 1 ATAAAAATTA 0.932113 -33 AAGAAAAAATATTTATCTTTATTAA 9 4 1 AAAAAAATTA 0.944742 -39 TTATTAAAGGAAAAAGGAAAAACT 9 29 1 AAAAAGAAAA 0.744053 -14 AACTAAAAAGAAAAGAAATTAACCAAA 11 55 1 AAAAGAATAA 0.859835 -17 TTATTGTAAAATAAAAGAAAAAAC 12 3 0 ATAAAAAAAA 0.916899 -104 TAATATAACTATAAAAATTATACATAATTTAT 12 31 0 ATAAAATATA 0.694731 -76 AATTAATTATAAATAAGATTTAGTAGATAATT 13 38 0 AAATAAATTA 0.695193 -128 TCCATTTATCAAAAGAGATAAAAATAGCCGGG 14 67 1 AAAAGAAAAA 0.846132 -195 TTGCATAAATAAAAAGGATTAAAAAATAAAAC 14 209 0 AAAAAGATAA 0.764315 -53 ACAAAAAAATTAAATTAGTAAAAA 14 248 0 AAAAAATAAA 0.717547 -14 TTCCCTTTACATAAGAAATATAGCATAATAAA 15 37 0 ATAAGAAATA 0.83126 -102 AAGTTAATCAAAAAAAACAATATTCATAATGA 15 102 1 AAAAAACATA 0.907911 -37 ACCAAAAACAATAAAAAACATAATTTTAACAG 16 119 1 ATAAAAAATA 0.924859 -89 TAAATTTAATATAAAAAAGTTAACA 16 193 1 ATAAAAATTA 0.932113 -15 AGTCAATGTAAAATAAGCTAAAAAC 17 4 0 AAATAACAAA 0.541061 -84 AAAAGGCATTTACATAAATAAT 18 1 1 AAAAGGATTA 0.59149 -78 TTATTTTCTTAAAAAATATAAAAACTTAAATA 19 25 1 AAAAAAAAAA 0.932155 -130 TTTTTTTTAAATAAAAAATATAATCTGTATTT 19 52 0 ATAAAAAATA 0.924859 -103 CGAAAATTTTATAAAAGATTTATATATATAAG 21 46 1 ATAAAAATTA 0.932113 -25 ATCTTATATAATAAAACCTAAAAATGGAAGTT 22 12 0 ATAAAACAAA 0.876502 -82 GTAAATTATAATATAATACTTAAGGCCATTAA 22 57 1 ATATAAATTA 0.646839 -37 ****** * *** Masking position 3 Map Score: 50.4669 Number of sites scoring better than the average of aligned sites = 2464 Number in coding regions = 1558 Number in noncoding regions = 906 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 3 TTTTATTTTCCTTTTATTTATTTTATTTTA 1 56 0 CTTTTATTTA 0.808415 -21 GACTTTAAGTCAATTATTTAGGAGAATTAA 3 19 0 CAATTATTTA 0.778909 -43 TATATTATTACTATGATTTAATGTAAATTT 5 85 1 CTATGATTTA 0.806832 -69 TTTAATGTAAATTTTAATTACCGCCTAAAA 5 101 1 ATTTTAATTA 0.64668 -53 AGATTAATGTCAATAATTTAAGAATTTTAA 8 63 0 CAATAATTTA 0.930244 -238 AATATTAAATCTTTTAATTAAATTTTATTT 8 206 0 CTTTTAATTA 0.746932 -95 TTTTATTTTACAATAAATTATGTATAATTT 12 19 1 CAATAAATTA 0.903117 -88 AGTTTAATAACAATAAATTATCTACTAAAT 13 23 1 CAATAAATTA 0.903117 -143 TCTTATTTATAATTAATTTAGCCTTACTTA 13 52 1 AATTAATTTA 0.873837 -114 CAGAAAACATCTATAATTTATAATGTTAGC 14 29 1 CTATAATTTA 0.950163 -233 AACAATCTTAAAATAAATTAATAAAAAATT 14 147 0 AAATAAATTA 0.85255 -115 ACAAAAAAATTAAATTAGTAAAAACCT 14 245 0 AATTAAATTA 0.828905 -17 TAAAGGGAATATATAATTTATTTTTATGTA 15 60 1 ATATAATTTA 0.922015 -79 TCTATTTGCGATTTAAATTACATTCAAAGG 16 18 0 ATTTAAATTA 0.873837 -190 AGTTAATAAAATTTAATTTACCAAAAACAA 16 100 1 ATTTAATTTA 0.908274 -108 GAATTCTATCTTATAATTTAAGGTAGAAAG 16 150 1 TTATAATTTA 0.725951 -58 TTTATATTAAATTTAATTTAACCTACAACT 16 178 0 ATTTAATTTA 0.908274 -30 ACACATTAAGCTATAATTTAGGC 19 142 1 CTATAATTTA 0.950163 -13 AAATCCTTATAATTAAATTATAATAATCAT 20 11 0 AATTAAATTA 0.828905 -32 TATTAGTAAAATTTAATTTA 21 1 0 ATTTAATTTA 0.908274 -70 AAGTATTATATTATAATTTACAAAAATTAG 22 48 0 TTATAATTTA 0.725951 -46 ATACTCCTCAATGAATTAATGGCCTTAA 22 76 0 CAATGAATTA 0.671395 -18 ********** Masking position 4 Map Score: 27.9065 Number of sites scoring better than the average of aligned sites = 476 Number in coding regions = 230 Number in noncoding regions = 246 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 4 TAATCTTTTTTAAAGCTTATATTTTTTATTT 1 15 0 TAAACTTATA 0.880801 -62 TAAAAAAGATTAATGCTTATAGTAAAATAAA 1 34 1 TAATCTTATA 0.706378 -43 AAAACAAAAAATCCTTAAACAAATTTTAG 8 9 1 AAATCTTAAA 0.902145 -292 TTAAAAATTAAAATTCTTAAATTATTGACAT 8 56 1 AAATCTTAAA 0.902145 -245 ATTATTGACATTAATCTTAATTAAAAATAAG 8 76 1 TTAACTTAAT 0.721175 -225 TATTTTTGTTATAATCTTAAAGCTTTGTTTT 10 17 0 ATAACTTAAA 0.939585 -37 TTTATTGTTATTAAACTTATACAAAGCTT 13 9 0 TTAACTTATA 0.802282 -157 AATTATCTACTAAATCTTATTTATAATTAAT 13 38 1 TAAACTTATT 0.706378 -128 TTTATAGATTAAAAACTTAATATTTAAATTT 13 132 1 AAAACTTAAT 0.90214 -34 AATTTATCCCAAAAATTTAAATATTAAGTTT 13 144 0 AAAATTTAAA 0.542283 -22 AATACATGCAACAATCTTAAAATAAATTAAT 14 155 0 ACAACTTAAA 0.805097 -107 ATTAAAAAATAAAACCTCAAAAACATCCGAC 14 193 0 AAAACTCAAA 0.760549 -69 ACAAAAAAATTAAATTAGTAAAAA 14 248 0 AAAAATTAAA 0.542283 -14 AAGATAGTAATTAAACTTATTCTAACAA 15 8 0 TTAACTTATT 0.569165 -131 TCAATGTAAAATAAGCTAAAAAC 17 3 0 ATAACTAAAA 0.748356 -85 CAAATCAAGATTATACTTAATATTATTATTT 18 26 0 TTATCTTAAT 0.457131 -53 TAAAAAATATAAAAACTTAAATACAGATTAT 19 34 1 AAAACTTAAA 0.965888 -121 GAAAACTAACATAAACTAAAAACAAAAACAA 19 98 1 ATAACTAAAA 0.748355 -57 ATTACTTTTAAAATCCTTATAATTAAATTAT 20 20 0 AAATCTTATA 0.824852 -23 CTTATATAATAAAACCTAAAAATGGAAGTTT 22 11 0 AAAACTAAAA 0.844111 -83 AAAAATTAGCAAAATCTTATATAATAAAACC 22 26 0 AAAACTTATA 0.935339 -68 **** ****** Masking position 7 Map Score: 18.2505 Number of sites scoring better than the average of aligned sites = 1233 Number in coding regions = 775 Number in noncoding regions = 458 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 5 AGTCATTTTAAATAATAATATAAAAAT 3 45 1 AATAATAATA 0.783467 -17 AAAGATTAAAAATAAAAATGCAATTTTAAA 5 18 1 AATAAAAATG 0.731633 -136 TGCAATTTTAAATAAAACCAAAAGCGACTT 5 36 1 AATAAAACCA 0.674123 -118 ATTAATCTTAATTAAAAATAAGATATTAAA 8 85 1 ATTAAAAATA 0.647815 -216 AAGAGACTAAAATAAAAAAATTCTAACCAT 8 163 1 AATAAAAAAA 0.727417 -138 ATAAAATAGTTATAAAGATAAGGAGATATA 8 278 1 TATAAAGATA 0.381561 -23 TTTTTCCTTTAATAAAGATAAATATTTTTT 9 14 0 AATAAAGATA 0.890741 -29 TTAAGATTATAACAAAAATATACTGGTAAC 10 28 1 AACAAAAATA 0.855909 -26 AATTAAAACAAATGGTCTTT 11 1 1 AATTAAAACA 0.582591 -71 GTATAAGTTTAATAACAATAAATTATCTAC 13 18 1 AATAACAATA 0.752551 -148 ATGTTTTCTGAATAAAAACAAGGACCTT 14 9 0 AATAAAAACA 0.953647 -253 TATCAAAAGAGATAAAAATAGCCGGGGGCT 14 73 1 GATAAAAATA 0.752551 -189 ACTATTTGTCAATAAAAATAGCCCCCGGCT 14 92 0 AATAAAAATA 0.96443 -170 AATATAGCATAATAAAGATAGTAATTAAAC 15 23 0 AATAAAGATA 0.890741 -116 CATTATAATACATAAAAATAAATTATATAT 15 68 0 CATAAAAATA 0.75255 -71 AAAGTTAATCAAAAAAAACAATATTCATAA 15 101 1 AAAAAAAACA 0.744498 -38 CATTTACATAAATAATAATATTAAGTATAA 18 17 1 AATAATAATA 0.783467 -62 TTTTTATTTAAAAAAAAACAATTCTTTTAA 19 67 1 AAAAAAAACA 0.744498 -88 ATAAACTAAAAACAAAAACAATTTATCATT 19 108 1 AACAAAAACA 0.818421 -47 AAATTTTACTAATAAAAATAATTAAAAAAC 21 17 1 AATAAAAATA 0.96443 -54 ********** Masking position 5 Map Score: 21.2661 Number of sites scoring better than the average of aligned sites = 1113 Number in coding regions = 715 Number in noncoding regions = 398 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 6 GGTAGGTATTAATTCTCCTAAATAATTGACT 3 11 1 AATTCTCTAA 0.82088 -51 TCTTTTCTAAAATTTGTTTAAGGATTTTTTG 8 15 0 AATTTGTTAA 0.426007 -286 AGATATTAAATATAATTTTAATAAGGCTTTT 8 105 1 TATAATTTAA 0.50522 -196 AAAAAAAATTAATTTTTCTAATAAAAGCCTT 8 127 0 AATTTTTTAA 0.925098 -174 TAGAAAAATTAATTTTTTTTAATAAAAGAGA 8 138 1 AATTTTTTTA 0.461353 -163 AGATGGTTAGAATTTTTTTATTTTAGTCTCT 8 164 0 AATTTTTTAT 0.326927 -137 GAATAATATTAAATCTTTTAATTAAATTTTA 8 209 0 AAATCTTTAA 0.5416 -92 TAAAAAATAAAATAGTTATAAAGATAAGGAG 8 272 1 AATAGTTTAA 0.346099 -29 ATATTTTTGTTATAATCTTAAAGCTTTGTTT 10 18 0 TATAATCTAA 0.288637 -36 ATAACAAAAATATACTGGTAACAAAATT 10 36 1 TATACTGTAA 0.305772 -18 ATTATACATAATTTATTGTAAAATAAAAGAA 12 16 0 ATTTATTTAA 0.60973 -91 AATTATGTATAATTTTTATAGTTATATTAAT 12 34 1 AATTTTTTAG 0.418571 -73 TAAGCATGGAAATTAATATAACTATAAAAAT 12 45 0 AATTAATTAA 0.431689 -62 GCTGTTTTGATATTATTTTAAGTAAGGCTAA 13 69 0 TATTATTTAA 0.763754 -97 TAAATGGACAAATTATGCTAACATTATAAAT 14 44 0 AATTATGTAA 0.808497 -218 TATTTTTATCTCTTTTGATAAATGGACAAAT 14 62 0 TCTTTTGTAA 0.154015 -200 ATTAATAAAAAATTCACTTAAAACTAATTTG 14 130 0 AATTCACTAA 0.24679 -132 TTTTTTATTAATTTATTTTAAGATTGTTGCA 14 149 1 ATTTATTTAA 0.609729 -113 TAGTAATTAAACTTATTCTAACAA 15 4 0 ACTTATTTAA 0.564314 -135 CAAAAAAAACAATATTCATAATGAGGGGTTT 15 110 1 AATATTCTAA 0.607861 -29 TATTACCTCATATATTGATAAATACAAATTA 16 67 1 TATATTGTAA 0.320502 -141 TGGTAAATTAAATTTTATTAACTTCTAATTT 16 92 0 AATTTTATAA 0.714119 -116 TATAAGATAGAATTCTGTTAAAATTATGTTT 16 134 0 AATTCTGTAA 0.82088 -74 TATTTTATTGAAATATTGTAATATAGTCAAT 17 29 0 AAATATTTAA 0.521172 -59 TTACATAAATAATAATATTAAGTATAATCTT 18 20 1 AATAATATAA 0.404305 -59 CTGTAAAATTTATTTTCTTAAAAAATATAAA 19 16 1 TATTTTCTAA 0.598934 -139 AAAAGAATTGTTTTTTTTTAAATAAAAAATA 19 64 0 TTTTTTTTAA 0.35593 -91 AAAAAAAAACAATTCTTTTAAAGAAAACTAA 19 76 1 AATTCTTTAA 0.920211 -79 CTTATAATTAAATTATAATAATCAT 20 5 0 AATTATATAA 0.682423 -38 TTACTTTTAAAATCCTTATAATTAAATTATA 20 19 0 AATCCTTTAA 0.459779 -24 AAATTACTTTTAAAATCCTTATA 20 30 0 ATTACTTTAA 0.348812 -13 TAAATTAAATTTTACTAATAAAAATAAT 21 8 1 AATTTTATAA 0.714119 -63 TTCGTTTTTTAATTATTTTTATTAGTAAAAT 21 19 0 AATTATTTTA 0.424227 -52 TAAAAAACGAAAATTTTATAAAAGATTTATA 21 39 1 AAATTTTTAA 0.55855 -32 AGATTTTGCTAATTTTTGTAAATTATAATAT 22 40 1 AATTTTTTAA 0.925098 -54 ******* *** Masking position 9 Map Score: 10.9583 Number of sites scoring better than the average of aligned sites = 2329 Number in coding regions = 1499 Number in noncoding regions = 830 Number of orfs with sites within 600 bp upstream = 177 Fraction of orfs with sites within 600 bp upstream = 0.0284292 Motif number 7 CTTTGACATTAGCATTCTATATTATTACTA 5 68 1 AGCATTCTAT 0.957675 -86 ATAATCTTAAAGCTTTGTTTTGAACTT 10 8 0 AGCTTTGTTT 0.88002 -46 AAGCTTTGTATAAGTTTAATA 13 2 1 AGCTTTGTAT 0.933255 -164 TCTTGATATTAGCATTCTATTTGCGATTTA 16 33 0 AGCATTCTAT 0.957675 -175 TAATTTTAACAGAATTCTATCTTATAATTT 16 139 1 AGAATTCTAT 0.916356 -69 TTTCTTTAAAAGAATTGTTTTTTTTTAAAT 19 72 0 AGAATTGTTT 0.813963 -83 AGTTTATGTTAGTTTTCTTTAAAAGAATTG 19 85 0 AGTTTTCTTT 0.765001 -70 ATTTTATAAAAGATTTATATATATAAGGAG 21 51 1 AGATTTATAT 0.750291 -20 AATGGCCTTAAGTATTATATTATAATTTAC 22 57 0 AGTATTATAT 0.720941 -37 ********** Masking position 5 Map Score: 4.7703 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 88 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 CGACTTGACTTTGACATTAGCATTCTATAT 5 60 1 TTGACATTAG 0.947436 -94 GTAATTAAAATTTACATTAAATCATAGTAA 5 92 0 TTTACATTAA 0.593591 -62 ACTACAAATTAATAGAAAAAAG 7 3 1 TACAAATTAA 0.797828 -45 TCTTAAATTATTGACATTAATCTTAATTAA 8 70 1 TTGACATTAA 0.918405 -231 TTTAATATTATTCAGATTAAAAAATCAAAA 8 227 1 TTCAGATTAA 0.728354 -74 CAATTAAGCATGGAAATTAATATAACTATA 12 50 0 TGGAAATTAA 0.835549 -57 CATGCTTAATTGGAAATTAGAGTAAGGTGG 12 68 1 TGGAAATTAG 0.890497 -39 TAGTGCTGTTTTCAAATTAGTTTTAAGTGA 14 118 1 TTCAAATTAG 0.933106 -144 AATATTAATCTTGATATTAGCATTCTATTT 16 41 0 TTGATATTAG 0.775447 -167 TATTGATAAATACAAATTAGAAGTTAATAA 16 79 1 TACAAATTAG 0.863318 -129 CATAAGGAGGTTGGAATTAG 18 69 1 TTGGAATTAG 0.740667 -10 TATCATTCAATACACATTAAGCTATAATTT 19 131 1 TACACATTAA 0.810443 -24 ********** Masking position 6 Map Score: 5.3546 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 135 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 TGCAATTTTAAATAAAACCAAAAGCGACTTGA 5 36 1 AATAAACCAA 0.442149 -118 ACTACAAATTAATAGAAAAAAGATTTT 7 6 1 AAATTATAAA 0.742448 -42 AAGCTTTAAGATTATAACAAAAATATACTGGT 10 23 1 ATTATACAAA 0.422951 -31 AAAAGAAAAGAAATTAACCAAA 11 60 1 AAATTACCAA 0.911617 -12 TTAAGCATGGAAATTAATATAACTATAAAAAT 12 45 0 AAATTATAAA 0.742448 -62 ATTTATAATTAATTTAGCCTTACTTAAAATAA 13 56 1 AATTTACCTA 0.720964 -110 AAATTTATCCCAAAAATTTAAAT 13 153 0 AATTTACCAA 0.940666 -13 ATAAATGGACAAATTATGCTAACATTATAAAT 14 44 0 AAATTAGCAA 0.431214 -218 ATAATTTGTCCATTTATCAAAAGAGATAAAAA 14 59 1 CATTTACAAA 0.667583 -203 ATCTTAAAATAAATTAATAAAAAATTCACTTA 14 141 0 AAATTATAAA 0.742448 -121 CAAAAAAATTAAATTAGTAAAAACCTAACATT 14 239 0 AAATTATAAA 0.742448 -23 TTACATAAGAAATATAGCATAATAAAGATAGT 15 31 0 AATATACAAA 0.87116 -108 TTCTAATTTGTATTTATCAATATATGAGGTAA 16 69 0 TATTTACATA 0.180855 -139 AATAAAATTTAATTTACCAAAAACAATAAAAA 16 104 1 AATTTACAAA 0.956601 -104 AAAAAACATAATTTTAACAGAATTCTATCTTA 16 131 1 ATTTTACAAA 0.704958 -77 TATTAAATTTAATTTAACCTACAACTTTCTAC 16 172 0 AATTTACCAC 0.726649 -36 GGTTAAATTAAATTTAATATAAAAAAGTTAAC 16 185 1 AATTTATAAA 0.815868 -23 ATTTCAATAAAATAAACCACAATGGCTAATAA 17 46 1 AATAAACAAA 0.524254 -42 CTTTTAAAGAAAACTAACATAAACTAAAAACA 19 90 1 AAACTACAAA 0.616637 -65 AAACAAAAACAATTTATCATTCAATACACATT 19 117 1 AATTTACATC 0.375911 -38 CCTTATAATTAAATTATAATAATCAT 20 5 0 AAATTAAAAA 0.415602 -38 AATCTTATATAATAAAACCTAAAAATGGAAGT 22 13 0 AATAAACCAA 0.442149 -81 TAATTTACAAAAATTAGCAAAATCTTATATAA 22 33 0 AAATTACAAA 0.934813 -61 ****** ** ** Masking position 6 Map Score: 12.9325 Number of sites scoring better than the average of aligned sites = 1191 Number in coding regions = 772 Number in noncoding regions = 419 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 10 AATCAATTTTAAGGAGATCTCA 2 15 1 AAGGAGATCT 0.921272 -12 GGTATAAAGGAAGAAGATCTA 5 143 1 AAGAAGATCT 0.900886 -11 ATAAAAACAAAAGGAAATATCTT 6 11 1 AAGGAAATAT 0.948967 -13 CTTAATTAAAAATAAGATATTAAATATAAT 8 91 1 AATAAGATAT 0.785482 -210 TTATAAAGATAAGGAGATATAATT 8 287 1 AAGGAGATAT 0.959904 -14 AAGAAAAAATATTTATCTTT 9 1 1 AAGAAAAAAT 0.694832 -42 TTCTTATGTAAAGGGAATATATAATTTATT 15 52 1 AAGGGAATAT 0.812896 -87 CACAATGGCTAATAAAATATAACAGGTGGG 17 63 1 AATAAAATAT 0.739862 -25 TATATTTTTTAAGAAAATAAATTTTACAGG 19 15 0 AAGAAAATAA 0.694832 -140 ********** Masking position 7 Map Score: 3.12068 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 165 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 11 ********** No masking Map Score: 6.56785e-12 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 12 ********** No masking Map Score: 6.56785e-12 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: 6.56785e-12 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