AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -icrp_rpxx_opreg_100.orf -g0.290 -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 = 0.29 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 RP053 300 ADP,ATP CARRIER PROTEIN (tlc1) #2 RP054 72 GLYCEROL-3-PHOSPHATE TRANSPORTER (glpT) #3 RP071 196 TRANSCRIPTIONAL ACTIVATOR PROTEIN CZCR (czcR) #4 RP095 300 ALANINE RACEMASE (alr) #5 RP322 300 unknown #6 RP332 300 unknown #7 RP333 32 CAPD PROTEIN (capD) #8 RP427 121 PETR PROTEIN (ompR) #9 RP449 99 THREONINE DEHYDRATASE (tdcB) #10 RP505 184 KPSF PROTEIN (kpsF) #11 RP581 114 unknown #12 RP600 195 unknown #13 RP707 194 unknown Motif number 1 CCTATAGTTAATAAAATGTTTATTGAGTTCTTTC 1 199 1 AAAAATGTAT 0.623904 -102 AATTTGTAAAAAAATATAAAAAAGCTTCTA 2 7 1 TAAAAAATAA 0.877506 -66 GAATTTAATAGTAAAAATTTTATAATTTGATTAA 3 59 1 GAAAAATTAA 0.910763 -138 ACGTTCATTAATAATATAAGTAAAGAATATTTAA 3 89 0 AAATATATAA 0.561464 -108 AAGCACTAGATAAAAAATTATAATTTAGTTAATA 3 126 1 TAAAAATTAT 0.816489 -71 TATCAATCAAATAAAATTAGTAAAAACAAGAGTA 4 34 1 AAAAATTTAA 0.940176 -267 TTGTCATCAATGAATATAACTATACCTAGTATTG 4 88 0 TAATATATAA 0.738288 -213 ATTAAAAGCAGAAAAATTTTTAAAAGAACATGTG 4 123 1 GAAAATTTAA 0.941218 -178 CTACCATTTATAAAAAATTGTAAATTTGGTAGTA 4 188 1 TAAAAATTAA 0.956637 -113 TATAATATTATGAAAATTTATAGATAAGTCAGAT 4 254 0 TAAAATTTAA 0.97176 -47 TTATAGTGTTATAAAATGAGTATATACT 4 283 1 AAAAATGTAA 0.891535 -18 TTATTACAAATCAAAAATAATAAATCTTGATTCA 5 53 0 TAAAAATTAA 0.956657 -248 TTGATTTGTAATAAAAATTCTAAATTTTTATTTT 5 73 1 AAAAAATTAA 0.90924 -228 TATTTCTAAGTCAAAAATAATAGTTATT 5 283 1 TAAAAATTAT 0.816687 -18 TAAAATAAAAGTACAACAATCATTG 6 2 1 AAATAAATAA 0.449397 -299 ATACTGAAATATAAAAAAATTAGATTTTAAAATA 6 64 1 AAAAAAATAA 0.766012 -237 TATACTTGAATAAAAATTGATACTGTAAGTTCTA 6 129 0 TAAAATTTAT 0.874818 -172 TCTAGAAATATTAAAATTTGTATAAAAAGTAATA 6 169 1 TAAAATTTAA 0.971923 -132 TGTATAAAAAGTAATAAGGATAAATTAATTAGTG 6 187 1 GAATAAGTAA 0.571032 -114 AAGGGTGCGATAAAAAATAATATAACC 6 284 1 TAAAAATTAA 0.956657 -17 GACCACGGGTTCAAAATTATTAATATCATAGTTG 8 71 0 TAAAATTTAT 0.874819 -51 ACCACGAGATGTAAAATGAGTATAA 8 107 1 GAAAATGTAA 0.893342 -15 AAAACCTTTTTAAAAATTTATATAGTTTATAGCA 9 16 1 TAAAATTTAA 0.97176 -84 ATTATATAATTAAAAATTGCTATAAACTATATAA 9 33 0 TAAAATTTAA 0.971931 -67 CCACACAGCTTAAAACTTCTTACAATAATGGTC 10 10 0 TAAACTTTAA 0.696368 -175 TAAACCACGGTGAAAATGAGTAAATTAA 10 167 1 TAAAATGTAA 0.947673 -18 CTAGAAACAATAAAAATGACTATAACGTAACTTA 11 45 1 TAAAATGTAA 0.947673 -70 TTTTTTTATAATAATATTATTAAAATAATAAGGT 12 29 1 AAATATTTAA 0.796666 -167 TTATTGATAATAAAAGTTAATAGAACTTTCCCAA 12 155 0 TAAAGTTTAA 0.696399 -41 ATCAATAATAGAAAAAAACGTAAAT 12 181 1 GAAAAAATAA 0.769374 -15 GTGAATTGAGTTAATATTATTATACCGTAAACTT 13 46 1 TAATATTTAA 0.896182 -149 * ****** ** * Masking position 4 Map Score: 40.7657 Number of sites scoring better than the average of aligned sites = 1200 Number in coding regions = 769 Number in noncoding regions = 431 Number of orfs with sites within 600 bp upstream = 205 Fraction of orfs with sites within 600 bp upstream = 0.0329264 Motif number 2 ATTGTATGGGATGAAATTTTAATATTTTACCTTCAAT 1 19 1 AAATATATTT 0.896659 -282 CAATATTCTTATGACAATACAAAATATTGAAGGTAAA 1 44 0 AAATAAATAT 0.859981 -257 GAAATATCAAATAAGCCTTTACAATTTAAAGTTCACT 1 88 1 AACTAAATTT 0.833463 -213 ATATATAGAAATCAAAATTAAGTAAAAATTGTTTTCT 1 153 1 AAATATAAAA 0.419883 -148 GAAGATAAACATTATACTAAAATATATGATAGAAGTC 1 253 0 AAATATATAT 0.757454 -48 GTTTATCTTCAAATAAATAGAAAATTTAATT 1 280 1 ATATAAATTT 0.910417 -21 AAAAACAACAATATTATTGGATAATTAGGTAATTTT 3 10 0 ATATAAATTA 0.903913 -187 AGAATATTTAATCAAATTATAAAATTTTTACTATTAA 3 63 0 AAATAAATTT 0.944643 -134 TTCATTAATAATATAAGTAAAGAATATTTAATCAAAT 3 83 0 ATATAAATAT 0.780528 -114 AAAAAATTATAATTTAGTTAATAATTATTAACTAAAT 3 137 1 ATATAAATTA 0.904044 -60 ACTGAATCACATGTTCTTTTAAAAATTTTTCTGCTTT 4 127 0 ATCTAAAATT 0.426194 -174 ATTTTTGTTAATGATACTCTAGAAGTATCTGACTTAT 4 228 1 AAATAAAGTA 0.59119 -73 TACTCATTTTATAACACTATAATATTATGAAAATTTA 4 268 0 AAATATATTA 0.889751 -33 CTACTATAAAATAAAAATTTAGAATTTTTATTACAAA 5 77 0 AAATAAATTT 0.944642 -224 CCAATAACGTAACTTACTATAAAATATGCTACTATAA 5 105 0 ATATAAATAT 0.785322 -196 ATAAATCAATAAGTAATTACAATATTAAAACTATATG 5 151 0 ATATATATTA 0.827788 -150 AATTTAAAGTACAATACTGGATAAATTTATAGCGTTT 5 193 0 AAATAAAATT 0.809601 -108 TAGTATAACAATAATACTGAAATATAAAAAAATTAGA 6 51 1 AAATATATAA 0.743899 -250 ATATAAAAAAATTAGATTTTAAAATATGCGATTAAGT 6 72 1 AAATAAATAT 0.859981 -229 GTTCTAAAACATTAGATTTAATTATTACTTAATCGCA 6 98 0 AAATATATTA 0.889749 -203 ATTCAAGTATAGAAAAATCTAGAAATATTAAAATTTG 6 152 1 AAATAAAATA 0.798183 -149 CAGTTAATTGTAAAATTAGGTATTTATA 7 2 1 ATATAAATTA 0.904339 -31 TCCAGTTGATACTATATTATATAATTAAAAATTGCTA 9 45 0 AAATAAATTA 0.94073 -55 ATTTTAAATCAAGAAACTTTACTATTTTAATAAGTTA 11 72 0 AAATATATTT 0.896659 -43 CTATAACATCTTGCAAAATTTTTTTATAATA 12 5 1 AACTAAATTT 0.833462 -191 TTTTATAATAATATTATTAAAATAATAAGGTTCTATG 12 32 1 ATATATAATA 0.54469 -164 AATCATTTTAAAATACTTGAATAATTAAGCACTCTAA 12 105 1 ATCTAAATTA 0.697057 -91 * * * * * ***** Masking position 8 Map Score: 30.7617 Number of sites scoring better than the average of aligned sites = 771 Number in coding regions = 462 Number in noncoding regions = 309 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 3 AATAAACATTTTATTAACTATAGGATGTGAAA 1 191 0 TTTTAACATA 0.960567 -110 TTATAAACTCTCCTCAACTATAAAAAGTAAGA 2 50 0 TCTCAACATA 0.74833 -23 ATATTGTTGTTTTTCAATTAAAGGTAGAATTT 3 33 1 TTTCAATAAA 0.811142 -164 CTTTATACGTTCATTAATAATATAAGTAAAGA 3 97 0 TCTTAATATA 0.787262 -100 TAGTTAATAATTATTAACTAAATTATAATTTT 3 139 0 TTTTAACAAA 0.888026 -58 TAGTTAATAATTATTAACTAAATTATTATCAA 3 151 1 TTTTAACAAA 0.888026 -46 ATTAACTAAATTATTATCAAAATTGAATTTTA 3 163 1 TTTTATCAAA 0.663818 -34 GATTGATAATTTCTTTTCAATAATGACAATT 4 10 0 TTTTTTCATA 0.601622 -291 TGAAAAGAAATTATCAATCAAATAAAATTAGT 4 23 1 TTTCAATAAA 0.811144 -278 GATCAGATTTTTGTTAATGATACTCTAGAAGT 4 222 1 TTTTAATATA 0.952378 -79 TCTCGTGGTATTTTTATCGATATTTCTAAGTC 5 263 1 TTTTATCATA 0.858462 -38 TAAAGATATATTATTTATGATAGAAAGGGTGC 6 260 1 TTTTTATATA 0.832761 -41 TTTATAGCAATTTTTAATTATATAATATAGTA 9 41 1 TTTTAATATA 0.952378 -59 CAAGCTACCATTATTAATTATATTT 9 85 1 TTTTAATATA 0.952378 -15 GCGTAATTTCTTTTCAATGATAATTTAGGTAT 10 92 1 TTTCAATATA 0.92954 -93 TCACCGTGGTTTATTAACTATATCTAGTACAT 10 148 0 TTTTAACATA 0.960567 -37 CTTGCAAAATTTTTTTATAATAATATTATTAA 12 20 1 TTTTTATATA 0.83275 -176 GAACCTTATTATTTTAATAATATTATTATAAA 12 33 0 ATTTAATATA 0.563305 -163 ATGAACATCATTTTCAATGATATAGAGCCTAG 12 66 1 TTTCAATATA 0.92954 -130 TTAACTTTTATTATCAATAATAGAAAAAAACG 12 169 1 TTTCAATATA 0.92954 -27 ACTATTATTTTCCATATCAACGTATT 13 5 1 TTTTTTCATA 0.601622 -190 ** ***** *** Masking position 4 Map Score: 30.8088 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 137 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 4 TTTGACTTCTATCATATATTTTAGTATAATGT 1 250 1 ATCTATATTT 0.604321 -51 TTACCTAATTATCCAATAATATTGTTGTTTTT 3 15 1 ATCAATATAT 0.703161 -182 ATAATTTTTTATCTAGTGCTTTATACGTTCAT 3 115 0 ATCAGTGTTT 0.972226 -82 CACTAACTGAATCACATGTTCTTTTAAAAATT 4 137 0 ATCCATGTCT 0.903603 -164 CTATAAATTTATCCAGTATTGTACTTTAAATT 5 198 1 ATCAGTATGT 0.787324 -103 CAAAAACCATATCTCGTGGTATTTTTATCGAT 5 252 1 ATCCGTGTAT 0.918469 -49 ATATTTTAAAATCTAATTTTTTTATATTTCAG 6 67 0 ATCAATTTTT 0.677683 -234 TTATTACTTAATCGCATATTTTAAAATCTAAT 6 82 0 ATCCATATTT 0.908019 -219 TAATAATTAAATCTAATGTTTTAGAACTTACA 6 108 1 ATCAATGTTT 0.949563 -193 TTAGAAACTCATCCCGTGGTTTGACCACGAAA 8 31 1 ATCCGTGTTT 0.975931 -91 CTCATTTTACATCTCGTGGTTTGACCACGGGT 8 95 0 ATCCGTGTTT 0.975931 -27 TGCTTAATTATTCAAGTATTTTAAAATGATTT 12 104 0 TTCAGTATTT 0.627719 -92 GTAAACTTTAATCGAGTGATCTATATAACTTA 13 72 1 ATCAGTGTCT 0.9377 -123 *** **** *** Masking position 7 Map Score: 9.54488 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 67 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 ATATTGAAGGTAAAATATTAAAATTTCATC 1 28 0 TAAAATATTA 0.685889 -273 TCAATATTCTTATGACAATACAAAATATTG 1 52 0 TATGACAATA 0.39965 -249 AATTTGTAAAAAAATATAAAAAAGCT 2 7 1 TAAAAAAATA 0.494781 -66 ATTCTTTACTTATATTATTAATGAACGTAT 3 95 1 TATATTATTA 0.790731 -102 AATTATTAACTAAATTATTATCAAAATTGA 3 159 1 TAAATTATTA 0.734927 -38 CAATTGAGATTATATCAATACTAGGTATAG 4 73 1 TATATCAATA 0.895757 -228 CATCAATGAATATAACTATACCTAGTATTG 4 88 0 TATAACTATA 0.732136 -213 TTTATAACACTATAATATTATGAAAATTTA 4 268 0 TATAATATTA 0.721836 -33 ATAAAAATTCTAAATTTTTATTTTATAGTA 5 83 1 TAAATTTTTA 0.485879 -218 ATATGACTAATATACCAATAACGTAACTTA 5 126 0 TATACCAATA 0.716286 -175 ATTACAATATTAAAACTATATGACTAATAT 5 143 0 TAAAACTATA 0.686932 -158 GTTTACTAAATAAATCAATAAGTAATTACA 5 167 0 TAAATCAATA 0.853588 -134 CAATACTGGATAAATTTATAGCGTTTACTA 5 189 0 TAAATTTATA 0.554243 -112 TTGCATTAGTTATACTTATAGTATAACAAT 6 33 1 TATACTTATA 0.485008 -268 ATACTTATAGTATAACAATAATACTGAAAT 6 44 1 TATAACAATA 0.884211 -257 CTGTAAGTTCTAAAACATTAGATTTAATTA 6 111 0 TAAAACATTA 0.752974 -190 TCATAAATAATATATCTTTACAATAAGGTT 6 250 0 TATATCTTTA 0.69392 -51 TATATATAAATACCTAATTTTA 7 21 0 TATATAAATA 0.627495 -12 TAAGTTATATTTATATTAGATTAGA 8 6 1 TATATTTATA 0.559309 -116 ATAAACTATATAAATTTTTAAAAAGGTTTT 9 16 0 TAAATTTTTA 0.485879 -84 GATACTATATTATATAATTAAAAATTGCTA 9 45 0 TATATAATTA 0.50644 -55 GAAACTTTACTATTTTAATAAGTTACGTTA 11 67 0 TATTTTAATA 0.281654 -48 AAAATTTTTTTATAATAATATTATTAAAAT 12 25 1 TATAATAATA 0.757466 -171 ATAATATTATTAAAATAATAAGGTTCTATG 12 39 1 TAAAATAATA 0.754159 -157 AAGTTTACGGTATAATAATATTAACTCAAT 13 50 0 TATAATAATA 0.757466 -145 ********** Masking position 9 Map Score: 21.5182 Number of sites scoring better than the average of aligned sites = 1048 Number in coding regions = 624 Number in noncoding regions = 424 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 6 TAACTAACTAAATGAAAATTTAGTGAACTTTA 1 114 0 AAGAAAATTA 0.842944 -187 AAAAGAAAACAATTTTTACTTAATTTTGATTT 1 161 0 AATTTTATTA 0.681635 -140 TAATATAAGTAAAGAATATTTAATCAAATTAT 3 80 0 AAGAATATTA 0.774243 -117 CTAGATAAAAAATTATAATTTAGTTAATAATT 3 131 1 AATATAATTA 0.942548 -66 TCTAAGTCAAAAATAATAGTTATT 5 287 1 AATAATATTA 0.770936 -14 GTTATACTATAAGTATAACTAATGCAATGATT 6 28 0 AATATAATAA 0.770158 -273 CATTAGATTTAATTATTACTTAATCGCATATT 6 94 0 AATATTATTA 0.912915 -207 AAAAAGTAATAAGGATAAATTAATTAGTGGAT 6 192 1 AAGATAATTA 0.943555 -109 ACCTTATTGTAAAGATATATTATTTATGATAG 6 251 1 AAGATATTTA 0.639561 -50 AATCTAATATAAATATAACTTA 8 1 0 AATATAATTA 0.942363 -121 AGTTTATAGCAATTTTTAATTATATAATATAG 9 39 1 AATTTTATTA 0.681635 -61 AAATATAATTAATAATGGTAGC 9 88 0 AATATAATAA 0.770158 -12 ATTTCTTTTCAATGATAATTTAGGTATCAACA 10 97 1 AAGATAATTA 0.943559 -88 ** ***** *** Masking position 2 Map Score: 9.49633 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 122 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 7 AAATTTTAATATTTTACCTTCAATATTTTGTATTG 1 32 1 ATTACCTAAA 0.903306 -269 TCTATCATATATTTTAGTATAATGTTTATCTTCAA 1 257 1 ATTAGTTATT 0.501669 -44 TAAAACCTGAATCTTACTTTTTATAGTTGAGGAGA 2 39 1 ATTACTTTAA 0.555985 -34 TTACTATTAAATTCTACCTTTAATTGAAAAACAAC 3 38 0 ATTACCTAAT 0.957167 -159 TTATAACACTATAATATTATGAAAATTTATAGATA 4 262 0 ATTATTTAAA 0.662163 -39 TTCATAGTGCATATTACTATCAAGTCTTTAATACT 5 22 0 ATTACTTAAT 0.968153 -279 ACTATAAAATATGCTACTATAAAATAAAAATTTAG 5 92 0 ATTACTTAAT 0.967841 -209 CCAATAACGTAACTTACTATAAAATATGCTACTAT 5 107 0 AATACTTAAT 0.838337 -194 TTTATCCAGTATTGTACTTTAAATTAGCTGTACTT 5 205 1 ATTACTTAAT 0.967813 -96 TAAATACCTAATTTTACAATTAACTG 7 2 0 ATTACATAAT 0.808626 -31 TTAATTATATAATATAGTATCAACTGGATTTCAAG 9 54 1 AATAGTTAAT 0.664672 -46 ATAATTAATAATGGTAGCTTGAAATCCAGTTGATA 9 71 0 ATTAGCTAAT 0.885807 -29 TATTTTAATAATATTATTATAAAAAAATTTTGCAA 12 21 0 ATTATTTAAA 0.661237 -175 AGTTAATATTATTATACCGTAAACTTTAATCGAGT 13 54 1 ATTACCTAAT 0.954777 -141 ** **** * ** * Masking position 6 Map Score: 9.54318 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 121 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 8 TTTATATTTTTTTACAAATT 2 1 0 TTTACAAATT 0.780024 -72 TACTCTTGTTTTTACTAATTTTATTTGATT 4 38 0 TTTACTAATT 0.871131 -263 TAGGTATAGTTATATTCATTGATGACAATA 4 94 1 TATATTCATT 0.786388 -207 AGTATATACTCATTTTATAACACT 4 287 0 TATACTCATT 0.97056 -14 TATTACTTTTTATACAAATTTTAATATTTC 6 173 0 TATACAAATT 0.87113 -128 TTATACTCATTTTACATCTCG 8 111 0 TATACTCATT 0.97056 -11 TTAATTTACTCATTTTCACCGTGG 10 171 0 TTTACTCATT 0.945336 -14 AATACATATACATATTGAACTTTATT 11 7 1 TATACATATT 0.727893 -108 TAAGTTACGTTATAGTCATTTTTATTGTTT 11 49 0 TATAGTCATT 0.845113 -66 ********** Masking position 4 Map Score: 6.57435 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 38 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 9 TTGAAGGTAAAATATTAAAATTTCATCCCATACA 1 21 0 AAATTATTTC 0.760337 -280 AGAAGTCAAACAAATTGATTTTTTCTAGAAAGAA 1 226 0 CAATTATTTT 0.935463 -75 TATAAAAAGTAAGATTCAGGTTTTAGAAGCTTTT 2 30 0 AAATTATTTT 0.941077 -43 ATTATCCAATAATATTGTTGTTTTTCAATTAAAG 3 22 1 AAATTTTTTT 0.734888 -175 CACTAGATAAAAAATTATAATTTAGTTAATAATT 3 129 1 AAATTTTTTA 0.52075 -68 AATTATTATCAAAATTGAATTTTATGGAGAAAAA 3 171 1 AAATTATTTA 0.879874 -26 GATCTACTACCAAATTTACAATTTTTTATAAATG 4 192 0 CAATTAATTT 0.880904 -109 ACTATGAATCAAGATTTATTATTTTTGATTTGTA 5 49 1 AAATTAATTT 0.891602 -252 CTATAAAATAAAAATTTAGAATTTTTATTACAAA 5 77 0 AAATTAATTT 0.885854 -224 TGAAATATAAAAAAATTAGATTTTAAAATATGCG 6 68 1 AAAATATTTT 0.491039 -233 AAAATCTAGAAATATTAAAATTTGTATAAAAAGT 6 165 1 AAATTATTTG 0.733966 -136 AAACAACTATGATATTAATAATTTTGAACCCGTG 8 68 1 GAATTAATTT 0.631748 -54 ATATCTAGTACATATTTAGTATTAGGAGTATTTG 10 127 0 CAATTAATTA 0.775976 -58 AATACATATACATATTGAACTTTATTACTTGTTG 11 11 1 CAATTATTTA 0.870556 -104 GATAAAAGCACATATTCAGTTTTTTTCGTCACCA 13 132 0 CAATTATTTT 0.935595 -63 ** *** * **** Masking position 4 Map Score: 10.5633 Number of sites scoring better than the average of aligned sites = 393 Number in coding regions = 238 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 10 TGTATGGGATGAAATTTTAATATTTTACCT 1 21 1 GAAATTTTAA 0.601521 -280 CTAACTAAATGAAAATTTAGTGAACTTTAA 1 113 0 GAAAATTTAG 0.830904 -188 CAAATAAATAGAAAATTTAATT 1 289 1 GAAAATTTAA 0.934062 -12 TATAAGTAAAGAATATTTAATCAAATTATA 3 79 0 GAATATTTAA 0.867852 -118 ATAATATTATGAAAATTTATAGATAAGTCA 4 257 0 GAAAATTTAT 0.643117 -44 TTTTATAGTAGCATATTTTATAGTAAGTTA 5 103 1 GCATATTTTA 0.69064 -198 TACAATACTGGATAAATTTATAGCGTTTAC 5 191 0 GATAAATTTA 0.57397 -110 AAAAAGTACAGCTAATTTAAAGTACAATAC 5 213 0 GCTAATTTAA 0.869388 -88 TTACTTAATCGCATATTTTAAAATCTAATT 6 81 0 GCATATTTTA 0.69064 -220 AAGTAATAAGGATAAATTAATTAGTGGATC 6 195 1 GATAAATTAA 0.744261 -106 TCTTTTCAATGATAATTTAGGTATCAACAA 10 100 1 GATAATTTAG 0.758547 -85 ATATTATCCCGCTAATTTTAAATCAAGAAA 11 93 0 GCTAATTTTA 0.754987 -22 TAAAATACTTGAATAATTAAGCACTCTAAT 12 113 1 GAATAATTAA 0.678296 -83 ********** Masking position 7 Map Score: 4.88275 Number of sites scoring better than the average of aligned sites = 552 Number in coding regions = 420 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 11 CAGTTAATATATAGAAATCAAAATTAAGTAA 1 147 1 ATAGAATCAA 0.912369 -154 AGGATGTGAAAAAGAAAACAATTTTTACTTA 1 171 0 AAAGAAACAA 0.76894 -130 TTTTTTCTAGAAAGAACTCAATAAACATTTT 1 211 0 AAAGAATCAA 0.942175 -90 GTTCTTTCTAGAAAAAATCAATTTGTTTGAC 1 225 1 GAAAAATCAA 0.733189 -76 AAAATATATGATAGAAGTCAAACAAATTGAT 1 241 0 ATAGAATCAA 0.912369 -60 CCTTTAATTGAAAAACAACAATATTATTGGA 3 26 0 AAAAACACAA 0.66548 -171 ATTTTTCTCCATAAAATTCAATTTTGATAAT 3 175 0 ATAAAATCAA 0.917579 -22 AGCGTTTACTAAATAAATCAATAAGTAATTA 5 169 0 AAATAATCAA 0.846288 -132 GTACTTTTTAAAAAACATCAAAAACCATATC 5 234 1 AAAAACTCAA 0.906891 -67 GCAACAAGTAATAAAGTTCAATATGTATATG 11 15 0 ATAAAGTCAA 0.698948 -100 AATCATTTTAAAATACTTGAATAATTAAGCA 12 105 1 AAATACTGAA 0.398133 -91 ATTATTGATAATAAAAGTTAATAGAACTTTC 12 159 0 ATAAAATTAA 0.467291 -37 GTGGTGACGAAAAAAACTGAATATGTGCTTT 13 131 1 AAAAAATGAA 0.789226 -64 ****** **** Masking position 5 Map Score: 4.64018 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 132 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 12 ATTGAAGGTAAAATATTAAAATTTCATCCCA 1 25 0 AATATTAAAA 0.953681 -276 TGACAATACAAAATATTGAAGGTAAAATATT 1 39 0 AATATTGAAG 0.758387 -262 ATTTGTAAAAAAATATAAAAAAGCTTCTAAA 2 12 1 AATATAAAAA 0.852859 -61 AACTCTCCTCAACTATAAAAAGTAAGATTCA 2 46 0 AATATAAAAA 0.852859 -27 AATTGTCATTATTGAAAAGAAATTATC 4 7 1 CATATTGAAA 0.862217 -294 AATCAAATAAAATTAGTAAAAACAAGAGTAT 4 38 1 AATAGTAAAA 0.685858 -263 TCATTGATGACAATATTAAAAGCAGAAAAAT 4 109 1 CATATTAAAA 0.929072 -192 AAAGCAGAAAAATTTTTAAAAGAACATGTGA 4 127 1 AATTTTAAAA 0.733164 -174 ATTATAAGATCAGTATTAAAGACTTGATAGT 5 11 1 CATATTAAAG 0.806952 -290 TAAGTAATTACAATATTAAAACTATATGACT 5 148 0 CATATTAAAA 0.929072 -153 AATAATACTGAAATATAAAAAAATTAGATTT 6 60 1 AATATAAAAA 0.852859 -241 ATTTTTATTCAAGTATAGAAAAATCTAGAAA 6 146 1 AATATAGAAA 0.734679 -155 AAAAATCTAGAAATATTAAAATTTGTATAAA 6 164 1 AATATTAAAA 0.953681 -137 ACGGGTTCAAAATTATTAATATCATAGTTGT 8 70 0 AATATTAATA 0.595617 -52 AAACTATATAAATTTTTAAAAAGGTTTTAAT 9 13 0 AATTTTAAAA 0.733164 -87 GACCATTATTGTAAGAAGTTTTAA 10 4 1 CATATTGTAA 0.309258 -181 CTATAACGTAACTTATTAAAATAGTAAAGTT 11 64 1 ACTATTAAAA 0.685858 -51 TTTATAATAATATTATTAAAATAATAAGGTT 12 33 1 TATATTAAAA 0.669552 -163 TAGAGTGCTTAATTATTCAAGTATTTTAAAA 12 110 0 AATATTCAAG 0.471308 -86 ** ******** Masking position 4 Map Score: 18.8249 Number of sites scoring better than the average of aligned sites = 504 Number in coding regions = 337 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 13 AAATCAAAATTAAGTAAAAATTGTTTTCTT 1 161 1 TAAGTAAAAA 0.819202 -140 AATATTTAATCAAATTATAAAATTTTTACT 3 68 0 CAAATTATAA 0.464308 -129 AATTATTAACTAAATTATAATTTTTTATCT 3 133 0 TAAATTATAA 0.732867 -64 AATAAATCAATAAGTAATTACAATATTAAA 5 159 0 TAAGTAATTA 0.685916 -142 AATATGCGATTAAGTAATAATTAAATCTAA 6 94 1 TAAGTAATAA 0.959688 -207 ATTGATACTGTAAGTTCTAAAACATTAGAT 6 118 0 TAAGTTCTAA 0.667684 -183 ATTTGTATAAAAAGTAATAAGGATAAATTA 6 184 1 AAAGTAATAA 0.736608 -117 TATTGTGAGCTATGTAAAAAACCTTATTGT 6 231 1 TATGTAAAAA 0.459678 -70 CTTTCTATCATAAATAATATATCTTTACAA 6 257 0 TAAATAATAT 0.584666 -44 TAAGTTATATTTATATTAGA 8 1 1 TAAGTTATAT 0.801307 -121 AAATATAATTAATAATGGTAGCTTG 9 85 0 TAATTAATAA 0.652978 -15 TTTCTAGCAACAAGTAATAAAGTTCAATAT 11 22 0 CAAGTAATAA 0.884152 -93 TCTGATACAATAAGTTATATAGATCACTCG 13 84 0 TAAGTTATAT 0.801307 -111 TAGGTGATTTTATGTAATAACACATGTATT 13 166 1 TATGTAATAA 0.819202 -29 ********** Masking position 2 Map Score: 5.1888 Number of sites scoring better than the average of aligned sites = 508 Number in coding regions = 321 Number in noncoding regions = 187 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 14 ********** No masking Map Score: 3.71914e-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 15 ********** No masking Map Score: 3.71914e-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