AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00290_mjan_reg_100.orf -o00290_mjan_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MJ0161 300 acetolactate synthase small subunit (ilvN) #2 MJ0277 183 acetolactate synthase large subunit (ilvB) #3 MJ0499 300 3-isopropylmalate dehydratase (leuC) #4 MJ0502 160 3-phosphoshikimate-1-carboxyvinyltransferase (aroA) #5 MJ0503 84 2-isopropylmalate synthase (leuA) #6 MJ0633 137 leucyl-tRNA synthetase (leuS) #7 MJ0663 27 acetolactate synthase large subunit (ilvB) #8 MJ0948 25 M. jannaschii predicted coding region MJ0948 #9 MJ0949 43 conserved hypothetical protein #10 MJ0950 184 conserved hypothetical protein #11 MJ1003 101 3-isopropylmalate dehydratase (leuC) #12 MJ1007 101 valyl-tRNA synthetase (valS) #13 MJ1008 100 branched-chain amino acid aminotransferase (ilvE) #14 MJ1195 135 2-isopropylmalate synthase (leuA) #15 MJ1271 205 3-isopropylmalate dehydratase (leuD) #16 MJ1276 217 dihydroxy-acid dehydratase (ilvD) #17 MJ1277 123 3-isopropylmalate dehydratase (leuD) #18 MJ1392 300 2-isopropylmalate synthase (leuA) #19 MJ1543 193 ketol-acid reductoisomerase (ilvC) Motif number 1 GTAAGATTTAAAAATAATAAAATAGATATT 1 270 0 AAAATAATAA 0.866156 -31 TTAAAGACTAAAAATAAAAAATAGAATTAA 2 20 0 AAAATAAAAA 0.92755 -164 AAAAAGTTTGATATAAAAAAGTGTTGGTAT 2 70 0 ATATAAAAAA 0.713546 -114 GCATTTGAAGAACTTTAAAAAGTTTGATAT 2 86 0 AACTTTAAAA 0.851818 -98 AATTGAAATCATATATAAAAATTTTTATAC 2 126 0 ATATATAAAA 0.713576 -58 AGTGTAAGTGATATAAAAAAGTTTATAAAA 3 121 0 ATATAAAAAA 0.713546 -180 GTGCCTTTCAAAATTAATAAACTTATTATT 3 234 0 AAATTAATAA 0.927504 -67 TTTTGATTAAAAAATAATAAAAAAATTTAT 5 47 1 AAAATAATAA 0.866156 -38 CAAAAGGGTTAAATTAATAAATGGAGTTTT 6 34 1 AAATTAATAA 0.927504 -104 TAATTAAGGTATATTAATAAGGCGTTTAAA 6 61 0 ATATTAATAA 0.833074 -77 CTAAGTATTGAACATTAAAAATGAAAGGAT 6 118 1 AACATTAAAA 0.743964 -20 GAAAATTTAAAATTAATATTAA 9 3 1 AAATTTAAAA 0.962017 -41 TTTAAAATTAATATTAAAAAACACGTTTAG 9 16 1 ATATTAAAAA 0.911348 -28 GTTTCTATTGAAATTTATATCTAAAAAGTT 10 159 0 AAATTTATAT 0.694709 -26 CTTTTTTGCAAAAAATATAACCAAAC 11 7 0 AAAAATATAA 0.610501 -95 ACATATTTGTAAATTTATAAATC 12 4 0 AAATTTATAA 0.927539 -98 GTTGAGGTTTAAATAAATAACTCTCTAATA 12 33 0 AAATAAATAA 0.75611 -69 TATTTTTATTAAATTAAAAACTCTTCAAAA 12 63 1 AAATTAAAAA 0.962017 -39 CTATTTGCAAAAAATAAAAATAGAGTCTAT 13 19 0 AAAATAAAAA 0.92755 -82 TGAATATTTAATATATAAAATTGTCTATTT 13 43 0 ATATATAAAA 0.713576 -58 TTAAATTGTCAAAATAAAAATAAAATGAAT 13 68 0 AAAATAAAAA 0.92755 -33 AATCAGATATATCATTAAAACGCTATAACT 14 54 0 ATCATTAAAA 0.541307 -82 AAATAACAGAAAATTAAAAAGTTTTGGTGG 14 112 1 AAATTAAAAA 0.962017 -24 TATCTTTCAGAAATTAATAAAATTTATTAA 15 90 0 AAATTAATAA 0.927504 -116 GAAAATGTTCAAATAAAAATATTCTTTAGG 15 128 0 AAATAAAAAT 0.522929 -78 CTTAATTTTAAAAATTAAATTTCAAAAGAG 15 160 0 AAAATTAAAT 0.695852 -46 ATTACCACCAAAAAATAAAA 16 1 0 AAAAATAAAA 0.756148 -217 TGATAAAAATAAATTCAAAAAGGAGCTTGA 16 79 1 AAATTCAAAA 0.872234 -139 GATGTTGAAAAAATTGAAAAAGAATGTGAA 16 169 1 AAATTGAAAA 0.718045 -49 ATTTAGAAAAAAATTCAAATTCAGAAA 16 201 1 AAATTCAAAT 0.549543 -17 GATTATAACTAAAATAAAAAGTAAGTGAAT 17 75 0 AAAATAAAAA 0.92755 -49 TACATTAATCATATTCAAAAGGTGAAATA 17 105 1 ATATTCAAAA 0.734931 -19 GTATCTTTCAAAAATAATAAAAATTTTATA 18 50 1 AAAATAATAA 0.866156 -251 TTTATTAATAATCTTTATAAAATTTTTATT 18 65 0 ATCTTTATAA 0.541288 -236 CAGGAATAAAATCTTTAAAAGAAATCTTAA 18 111 1 ATCTTTAAAA 0.700119 -190 CTTTAAATTTAAATTTATAAATTAAGATTT 18 132 0 AAATTTATAA 0.927539 -169 TTATAAATTTAAATTTAAAGATGTATATTA 18 142 1 AAATTTAAAG 0.582062 -159 TTGATATTGTATATTTAAAATTTATGTGGG 18 197 0 ATATTTAAAA 0.911387 -104 TAATTTAATGAAATTTAAATACTCATAATG 18 262 0 AAATTTAAAT 0.819032 -39 GCATTATCCTAAAATTAAATAGT 19 4 0 AAAATTAAAT 0.695852 -190 ATAGTGAAATAAATTTAAAACATAAATGTT 19 67 0 AAATTTAAAA 0.962017 -127 TAAAAACCATATAATAATAACATAGAATTT 19 123 0 ATAATAATAA 0.724351 -71 ********** Masking position 7 Map Score: 47.206 Number of sites scoring better than the average of aligned sites = 3364 Number in coding regions = 2220 Number in noncoding regions = 1144 Number of orfs with sites within 600 bp upstream = 587 Fraction of orfs with sites within 600 bp upstream = 0.094282 Motif number 2 GAGGGTGTTCAATTTTTCATAACTAAATTTAACAACTTT 1 64 0 AATTTTAATT 0.817159 -237 GACAAGGCTTAATTTTTCTTTTGTTAATTAATTGGCATC 1 163 0 AATTTTTTTT 0.946841 -138 TGATACCTGAAATTTTTGATTTGCATATTTTTGATAGGA 1 205 0 AATTTTTTTT 0.946843 -96 TCTATTTTTTATTTTTAGTCTTTAAGATTAGTAATTAAA 2 25 1 ATTTTATTTT 0.819085 -159 CTTAGTATAAAAATTTTTATATATGATTTCAATTTTATC 2 122 1 AATTTTATTT 0.920516 -62 ATTTTATCATTACTTTACCCTTAACATTTTTTGGTGATT 2 153 1 TATTTATTTT 0.876915 -31 TGATATAAAAAAGTTTATAAAAAATCTTTCATGAATAAT 3 104 0 AATTTAAATT 0.881204 -197 CAAAATTAATAAACTTATTATTAAACTTTGAACGCCTTC 3 217 0 AACTTATTTT 0.747409 -84 ACTTACTTAATTTATAAATGTTAATTTTTCTCATTA 4 8 1 TATTTAATTT 0.823599 -153 TAATTATAACAACCTTAATATATCACATTTAAATTATAC 4 107 1 AACTTATATT 0.572983 -54 TACCTGTATAAATTTTTTTATTATTTTTTAATCAAAATA 5 45 0 AATTTTTTTT 0.946815 -40 GAAAATTTAAAATTAATATTAAAAAACACGT 9 3 1 AATTTATTTA 0.464415 -41 ATTAAATGAAAATTATAGGATTTCATATTCAAAGCATTA 10 111 0 AATATATTTT 0.694655 -74 TAGAAAGCGAAACTTTTTAGATATAAATTTCAATAGAAA 10 149 1 AATTTTATTT 0.869455 -36 GTTTGGTTATATTTTTTGCAAAAAAGTTATTAGGTTAT 11 10 1 TATTTTAATT 0.505978 -92 GATTTATAAATTTACAAATATGTATTAGAGAGTTAT 12 8 1 AATTTAATTT 0.952847 -94 GAAGAGTTTTTAATTTAATAAAAATAGTTGAGGTTTAAA 12 50 0 TATTTAAATT 0.620775 -52 AATAAAATGAATATTTAATATATAAAATTGTCTATTTGC 13 41 0 ATTTTATATT 0.554176 -60 ATATTCATTTTATTTTTATTTTGACAATTTAACAAAGGT 13 66 1 TATTTTTTTT 0.804425 -35 GAATTAAATGAACTTTAATCTATCATTTTGAAAGGTTAA 14 16 1 AATTTATATT 0.92022 -120 ATCCCACCAAAACTTTTTAATTTTCTGTTATTTATGATG 14 106 0 AATTTTTTTT 0.946834 -30 GAAATTAATAAAATTTATTAATGGGTATTATAGGAGTTT 15 72 0 AATTTAATTT 0.952847 -134 TTCCTAAAGAATATTTTTATTTGAACATTTTCAGCTCTT 15 126 1 ATTTTTTTTT 0.723693 -80 AGCTCTTTTGAAATTTAATTTTTAAAATTAAGATAAAAT 15 158 1 AATTTATTTT 0.50335 -48 CACAGACGATAACTTTAACTTTTGAAATTCCAGAATTTA 16 39 1 AATTTATTTT 0.964383 -179 TCTGAATTTGAATTTTTTTCTAAATTCTTCACATTCTTT 16 187 0 AATTTTTATT 0.869322 -31 CTATTTTCTTATATTTAGATTTTCATATTAAACAATACA 17 19 1 ATTTTATTTT 0.819309 -105 GTGAATAAATAAGTTTTGTTTTCTGTATTGTTTAATATG 17 42 0 AATTTTTTTT 0.946844 -82 AAGCCCCATTAACTTTATTAATAATCTTTATAAAATTTT 18 69 0 AATTTAATTT 0.949757 -232 CTTTAAATTTAAATTTATAAATTAAGATTTCTTTTAAAG 18 123 0 AATTTAATTT 0.611509 -178 TTATAAATTTAAATTTAAAGATGTATATTACCAACTTTT 18 142 1 AATTTAATTT 0.952808 -159 AACACAACTAAATTATAGTGAAATAAATTTAAAACATAA 19 72 0 AATATAAATT 0.362949 -122 AATACTATTTTAAGGTTTTCGGTTTAATTTGATA 19 170 0 TATTTATTTT 0.876916 -24 ** **** ** ** Masking position 6 Map Score: 48.5905 Number of sites scoring better than the average of aligned sites = 1164 Number in coding regions = 823 Number in noncoding regions = 341 Number of orfs with sites within 600 bp upstream = 276 Fraction of orfs with sites within 600 bp upstream = 0.0443302 Motif number 3 TATCTTTAGAATATTTGCAAAAACCAATAATTTAGATGC 1 129 1 ATTAACCATA 0.971994 -172 CTATTTTATTATTTTTAAATCTTACTATAAAAAGGA 1 275 1 ATTATACATA 0.939868 -26 TATCTCAATAAGTTTTGAAAGGCACTATACTTTTAGAGT 3 148 0 ATTAAACATA 0.985417 -153 TAAGTTTATTAATTTTGAAAGGCACTATATATCTACAGT 3 239 1 ATTAAACATA 0.985416 -62 CTTCATATTGATATTTTGATTAAAAAATAATAAAAAAAT 5 34 1 ATTATAAATA 0.806684 -51 TTAATTTAACCCTTTTGCAAAGGACTATAACTACAAAGT 6 12 0 CTTAAACATA 0.889429 -126 CTTAGTATATAAATAGGTAAATAACGATATATAGTTGCT 10 63 1 ATGAAACATA 0.889429 -122 CAAAGCATTAAGATTTATAAGCAACTATATATCGTTATT 10 82 0 ATTAAACATA 0.985417 -103 GATTTATAAATTTACAAATATGTATTAGAG 12 2 1 ATTATCAATA 0.681863 -100 ACCTTTGTTAAATTGTCAAAATAAAAATAAAATGAATAT 13 66 0 ATTAAAAATA 0.947385 -35 ATTAGGTAAAATTTTTATAACATCCCATCATAAATAACA 14 81 1 ATTAACCATC 0.805128 -55 TCTGAAGTAAATATATAGAAACTCCTATAATACCCATTA 15 54 1 ATTAACCATA 0.971994 -152 AATTTTATTAATTTCTGAAAGATACCATATTTCCTAAAG 15 96 1 ATTAAACATA 0.985417 -110 AAAGAGCTGAAAATGTTCAAATAAAAATATTCTTTAGGA 15 127 0 ATTAAAAATA 0.947479 -79 TTTGAAATTTAATTTTTAAAATTAAGATAAAATATTTTT 15 164 1 ATTAAAAATA 0.94748 -42 AATTTTTATTATTTTTGAAAGATACTATACGAAAGTCAT 18 36 0 ATTAAACATA 0.985417 -265 TTTCCCACATAAATTTTAAATATACAATATCAAATATCT 18 194 1 ATTAAACATA 0.98539 -107 * * * ** ** *** Masking position 9 Map Score: 29.5712 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 65 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 AAACTATGAAAATTTTCTTTTAATCTTAACT 1 28 0 AATTTCTTTT 0.69699 -273 CAAACTTTTTAAAGTTCTTCAAATGCTAAAT 2 90 1 AAGTTCTTCA 0.817316 -94 GAAAGGTTCATCATATTAAGTCA 3 3 1 AAGTTCATCA 0.947342 -298 CAGCCCCCGTAAGGTTCATCATCCTAAATTA 3 74 1 AAGTTCATCA 0.947342 -227 TTTCATTTTTAATGTTCAATACTTAGTTTTT 6 113 0 AAGTTCAATA 0.795033 -25 ATTGGTTAATTTTCATTAGTATTAG 8 8 1 AATTTCATTA 0.963528 -18 GAAAGTTTCATCAAAACGATGCA 10 3 1 AATTTCATCA 0.951876 -182 GAAATCCTATAATTTTCATTTAATAGAAAGC 10 126 1 AATTTCATTT 0.902428 -59 TTTTAGATATAAATTTCAATAGAAACTAAAT 10 163 1 AATTTCAATA 0.81005 -22 TTATATATTAAATATTCATTTTATTTTTATT 13 55 1 AAATTCATTT 0.696509 -46 ATGATAGATTAAAGTTCATTTAATTCATCAA 14 11 0 AAGTTCATTT 0.893762 -125 ACCCATTAATAAATTTTATTAATTTCTGAAA 15 85 1 AATTTTATTA 0.724962 -121 TTCAAATAAAAATATTCTTTAGGAAATATGG 15 120 0 AAATTCTTTA 0.619787 -86 AGGAGCTTGAAAATTTCATCAAGAAAAAAAT 16 99 1 AATTTCATCA 0.951876 -119 ATCTTTATAAAATTTTTATTATTTTTGAAAG 18 54 0 AATTTTATTA 0.724963 -247 ATGAGTATTTAAATTTCATTAAATTATTTTT 18 266 1 AATTTCATTA 0.963527 -35 ** ******** Masking position 6 Map Score: 18.2262 Number of sites scoring better than the average of aligned sites = 311 Number in coding regions = 242 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 5 AAAAATTAAGTTAAGATTAAAAGAAAATTTTC 1 20 1 TTAGATAAAA 0.874213 -281 ATCTATTTTATTATTTTTAAATCTTACTATAA 1 273 1 TTATTTAAAT 0.480352 -28 TTTTTAAATCTTACTATAAAAAGGA 1 286 1 TTATATAAAA 0.870016 -15 GATTAGTAATTAAATATTAAATACCAACACTT 2 50 1 TAATATAAAT 0.740343 -134 TTTAAAAAGTTTGATATAAAAAAGTGTTGGTA 2 71 0 TTGTATAAAA 0.447842 -113 TGCTAAATCCTTAGTATAAAAATTTTTATATA 2 113 1 TTATATAAAA 0.870016 -71 AAGGGTAAAGTAATGATAAAATTGAAATCATA 2 143 0 TAAGATAAAT 0.743991 -41 ATTAATAAACTTATTATTAAACTTTGAACGCC 3 220 0 TTATATAAAC 0.702683 -81 AATTATACTCTGTTGATTAAAAAATTAGTGGT 4 138 1 TGTGATAAAA 0.742843 -23 CATATTGATATTTTGATTAAAAAATAATAAAA 5 37 1 TTTGATAAAA 0.758187 -48 AACTAAGTATTGAACATTAAAAATGAAAGGAT 6 116 1 TGACATAAAA 0.348787 -22 AAATTTAAAATTAATATTAAAAAACACGTTTA 9 13 1 TTATATAAAA 0.87209 -31 TAATGCATCGTTTTGATGAAACTTTC 10 5 0 TTTGATAAAC 0.600205 -180 CTTAATGCTTTGAATATGAAATCCTATAATTT 10 109 1 TGATATAAAT 0.869812 -76 AAAGTTTCGCTTTCTATTAAATGAAAATTATA 10 133 0 TTTTATAAAT 0.864897 -52 GTGTTCAAATTTTCTATCAAATAACCTAATAA 11 37 0 TTTTATAAAT 0.864417 -65 TAAAAATAGTTGAGGTTTAAATAAATAACTCT 12 39 0 TGAGTTAAAT 0.38332 -63 ACCTCAACTATTTTTATTAAATTAAAAACTCT 12 55 1 TTTTATAAAT 0.864104 -47 TAGACAATTTTATATATTAAATATTCATTTTA 13 46 1 TATTATAAAT 0.643155 -55 ATTTTTAAAATTAAGATAAAATATTTTTGTGG 15 175 1 TTAGATAAAT 0.911669 -31 TTCCAGAATTTATTGATAAAAATAAATTCAAA 16 66 1 TATGATAAAA 0.529223 -152 AAGATTTTTTTCTTGATGAAATTTTCAAGCTC 16 101 0 TCTGATAAAT 0.603629 -117 TCTGTATTGTTTAATATGAAAATCTAAATATA 17 28 0 TTATATAAAA 0.871877 -96 TTATTAATAATCTTTATAAAATTTTTATTATT 18 62 0 TCTTATAAAT 0.598739 -239 ATAATGAATCTGATGATAAAATTGAATCATCT 18 236 0 TGAGATAAAT 0.871944 -65 AAATTCTATGTTATTATTATATGGTTTTTATA 19 123 1 TTATATATAT 0.33521 -71 TATCGATTTCTGAATATCAAATTAAACCGAAA 19 156 1 TGATATAAAT 0.869812 -38 *** *** **** Masking position 7 Map Score: 23.4295 Number of sites scoring better than the average of aligned sites = 1012 Number in coding regions = 779 Number in noncoding regions = 233 Number of orfs with sites within 600 bp upstream = 204 Fraction of orfs with sites within 600 bp upstream = 0.0327658 Motif number 6 TAGGAAACCAAAAATTAAGTTAAGATTAA 1 10 1 AAAAATTAAG 0.936702 -291 TGCAAAAACCAATAATTTAGATGCCAATTA 1 144 1 AATAATTTAG 0.897829 -157 TTAACAAAAGAAAAATTAAGCCTTGTCATA 1 175 1 AAAAATTAAG 0.936702 -126 CTCACCATATAATAATTATGATACCTGAAA 1 232 0 AATAATTATG 0.468943 -69 TTTTTATACTAAGGATTTAGCATTTGAAGA 2 105 0 AAGGATTTAG 0.533149 -79 TTTCATGAATAATAATTTAGGATGATGAAC 3 87 0 AATAATTTAG 0.897829 -214 ATTAACATTTATAAATTAAGTAAGT 4 6 0 ATAAATTAAG 0.651121 -155 CATTAGAGACAAGAATTAAGAATCGGGTAT 4 42 1 AAGAATTAAG 0.93782 -119 TCTGTTGATTAAAAAATTAGTGGTG 4 146 1 AAAAAATTAG 0.585943 -15 ACATTATTAAAATAATTAAGGTATATTAAT 6 73 0 AATAATTAAG 0.928656 -65 AATGTTTTGTAAAAACTAAGTATTGAACAT 6 103 1 AAAAACTAAG 0.637938 -35 TTCATATTCAAAGCATTAAGATTTATAAGC 10 99 0 AAGCATTAAG 0.62849 -86 TTTGTAAATAAAGTATTTAGGTGATAAA 11 84 1 AAGTATTTAG 0.435196 -18 ATTTAATTTTTAAAATTAAGATAAAATATT 15 170 1 TAAAATTAAG 0.651208 -36 AAAGAATGTGAAGAATTTAGAAAAAAATTC 16 187 1 AAGAATTTAG 0.910566 -31 AAAGTAAGTGAATAAATAAGTTTTGTTTTC 17 58 0 AATAAATAAG 0.648387 -66 TAACTAAAATAAAAAGTAAGTGAATAAATA 17 70 0 AAAAAGTAAG 0.637938 -54 ATTTAAATTTATAAATTAAGATTTCTTTTA 18 126 0 ATAAATTAAG 0.651121 -175 CCTCATAAAAAATAATTTAATGAAATTTAA 18 274 0 AATAATTTAA 0.268825 -27 TTTATTTCACTATAATTTAGTTGTGTTCTA 19 84 1 TATAATTTAG 0.525764 -110 ********** Masking position 7 Map Score: 15.3953 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 241 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 7 TTTAGTAGAACTCACCATATAATAATTATGAT 1 240 0 CTCACCATAA 0.976167 -61 CCAATCACCAAAAAATGTTAAGGGT 2 169 0 ATCACCAAAA 0.962719 -15 AATCTCACCATTTAATTAGTCTTTA 3 286 0 CTCACCATAA 0.976167 -15 AATCTCACCGTTTAAATCAATATTT 7 4 1 CTCACCGTAA 0.975695 -24 TATGAATCACCGTCAAATCTTTTGAAG 12 85 0 ATCACCGAAA 0.961993 -17 TTCTTATCACCACAAAAATATTTTATC 15 189 0 ATCACCAAAA 0.962719 -17 AGCCATAATTACCACCAAAAAATAAAA 16 6 0 ACCACCAAAA 0.872753 -212 TAGGATAATGCTCTCCGTGTAATTGCTAAATA 19 23 1 CTCTCCGTAA 0.877969 -171 ******* *** Masking position 11 Map Score: 6.90797 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 41 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 8 AAAAATAATAAAATAGATATTTAGTAGAACTCA 1 258 0 AAAATATTTA 0.650819 -43 AAAGTGTTGGTATTTAATATTTAATTACTAATC 2 50 0 TATATATTTA 0.517698 -134 CTAATGAGAAAAATTAACATTTATAAATTAAGT 4 15 0 AAAACATTTA 0.847351 -146 ACAACCTTAATATATCACATTTAAATTATACTC 4 115 1 TATACATTTA 0.760453 -46 TAAGGCGTTTAAAACTCCATTTATTAATTTAAC 6 41 0 AAACCATTTA 0.796881 -97 TTAAAATAATTAAGGTATATTAATAAGGCGTTT 6 64 0 TAAATATTAA 0.758127 -74 AAAAACTAAGTATTGAACATTAAAAATGAAAGG 6 113 1 TATACATTAA 0.676006 -25 GAAAATTTAAAATTAATATTAAAAAACACGTT 9 10 1 AAAATATTAA 0.548048 -34 TTAAGGGACTGAAAGTCCATTTAATGCATCGTT 10 25 0 GAACCATTTA 0.546931 -160 ATTTATATACTAAGAGACATTAAGGGACTGAAA 10 44 0 TAAACATTAA 0.903356 -141 TGAAATCCTATAATTTTCATTTAATAGAAAGCG 10 125 1 TAATCATTTA 0.766879 -60 AATAACTCTCTAATACATATTTGTAAATTTATA 12 15 0 TAAATATTTG 0.446847 -87 AATAAAAATAAAATGAATATTTAATATATAAAA 13 53 0 AAAATATTTA 0.650822 -48 AATGATAGATTAAAGTTCATTTAATTCATCAA 14 10 0 TAATCATTTA 0.766879 -126 GAAACTCCTATAATACCCATTAATAAATTTTAT 15 71 1 TAACCATTAA 0.868377 -135 ATTTTAGTTATAATCTACATTAATCATATTCAA 17 90 1 TAAACATTAA 0.903363 -34 TATTCCTGCGAAAGCCCCATTAACTTTATTAAT 18 86 0 AAACCATTAA 0.718502 -215 AGATATTTGATATTGTATATTTAAAATTTATGT 18 200 0 TATATATTTA 0.518147 -101 TATGAGTATTTAAATTTCATTAAATTATTTTTT 18 265 1 TAATCATTAA 0.682145 -36 ATGTTGGTTATAAACGATATTTAGCAATTACAC 19 39 0 TAAATATTTA 0.794764 -155 ATATCGTTTATAACCAACATTTATGTTTTAAAT 19 52 1 TAAACATTTA 0.934747 -142 ACATAGAATTTAAATACCATTAGAACACAACTA 19 101 0 TAACCATTAG 0.525205 -93 ATCGATACTATAAAAACCATATAATAATAACAT 19 130 0 TAACCATATA 0.373099 -64 *** ******* Masking position 10 Map Score: 19.7482 Number of sites scoring better than the average of aligned sites = 443 Number in coding regions = 356 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 9 CTTTCGATAGAGGGTGTTCAATTTTTCATA 1 82 0 AGGGTGTTCA 0.951373 -219 CTTCCTTTAGGAGGCGTTCATTAATACCTT 3 191 0 GAGGCGTTCA 0.977818 -110 CTCCTAAAGGAAGGCGTTCAAAGTTTAATA 3 208 1 AAGGCGTTCA 0.989884 -93 GTATATTAATAAGGCGTTTAAAACTCCATT 6 53 0 AAGGCGTTTA 0.94937 -85 ATCCCAAAGAAAGGTGTTCAAATTTTCTAT 11 52 0 AAGGTGTTCA 0.977493 -50 ********** Masking position 7 Map Score: 3.57408 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 5 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 10 TTCTTTCTTTAATTCTATTTTTTATTTTTA 2 12 1 AATTCTATTT 0.936399 -172 AAATTATGATAATTCTATATACCCGATTCT 4 60 0 AATTCTATAT 0.922792 -101 TTGAATATGAAATCCTATAATTTTCATTTA 10 118 1 AATCCTATAA 0.656053 -67 GCAAATAGACAATTTTATATATTAAATATT 13 41 1 AATTTTATAT 0.673859 -60 TTCTCGGGAGAATTCTATTATATTTAG 15 8 0 AATTCTATTA 0.909567 -198 CCCATTAATAAATTTTATTAATTTCTGAAA 15 86 1 AATTTTATTA 0.634867 -120 TTGGGAGAGAAATTCTATAAACTTATGGAA 16 131 1 AATTCTATAA 0.890875 -87 TGTTATTTCTATTTTCTTATATTT 17 5 1 ATTTCTATTT 0.674472 -119 ATGGTATTTAAATTCTATGTTATTATTATA 19 114 1 AATTCTATGT 0.843364 -80 AATACTATTTTAAGGTTTTC 19 184 0 AATACTATTT 0.698914 -10 ********** Masking position 6 Map Score: 4.07549 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 117 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 11 TTAAAAGAAAATTTTCATAGTTTTTCGTAAAGT 1 36 1 ATTTCAATTT 0.894441 -265 TTCATAACTAAATTTAACAACTTTACGAAAAAC 1 55 0 AATTAAACTT 0.293329 -246 GAAATTTTTGATTTGCATATTTTTGATAGGATA 1 203 0 ATTGCAATTT 0.572003 -98 TTAAATATTAAATACCAACACTTTTTTATATCA 2 59 1 AATCCACCTT 0.761128 -125 AACACTTTTTTATATCAAACTTTTTAAAGTTCT 2 75 1 TATTCAATTT 0.598222 -109 TAATAAACTTATTATTAAACTTTGAACGCCTTC 3 217 0 ATTTTAATTT 0.585094 -84 AATCTCACCATTTAATTAGTCTT 3 288 0 AATTCACTTT 0.931622 -13 GGTATATAGAATTATCATAATTTCATTTGTATT 4 67 1 ATTTCAATTT 0.894441 -94 TCCATTTATTAATTTAACCCTTTTGCAAAGGAC 6 26 0 AATTAACTTT 0.61278 -112 AATCTCACCGTTTAAATCAATAT 7 1 1 AATTCACTTT 0.931622 -27 TTTTAATATTAATTTTAAATTTTC 9 2 0 AATTTAATTT 0.63628 -42 TTGAATATGAAATCCTATAATTTTCATTTAATA 10 118 1 AATCTAATTT 0.546179 -67 TTTTATTTTTATTTTGACAATTTAACAAAGGTG 13 73 1 ATTTGAATTT 0.452711 -28 TTATTTGAACATTTTCAGCTCTTTTGAAATTTA 15 142 1 ATTTCACCTT 0.78874 -64 TAACTTTTGAAATTCCAGAATTTATTGATAAAA 16 54 1 AATCCAATTT 0.87851 -164 TATTTCACCTTTTGAATATGATT 17 111 0 TATTCACTTT 0.658678 -13 AAAGATGTATATTACCAACTTTTTAGTCCAGAA 18 158 1 ATTCCACTTT 0.883104 -143 AATATCGTTTATAACCAACATTTATGTTTTAAA 19 51 1 ATACCACTTT 0.363755 -143 *** *** * *** Masking position 12 Map Score: 7.01905 Number of sites scoring better than the average of aligned sites = 718 Number in coding regions = 632 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 12 TTGCATATTTTTGATAGGATATGACAAGGC 1 194 0 TTGATAGGAT 0.768081 -107 TAATTATTATATGGTGAGTTCTACTAAATA 1 244 1 ATGGTGAGTT 0.840924 -57 GACTAATTAAATGGTGAGATT 3 290 1 ATGGTGAGAT 0.921102 -11 AAATATCAATATGAAGAGATTGATTTATTC 5 20 0 ATGAAGAGAT 0.880388 -65 AACATTAAAAATGAAAGGAT 6 128 1 ATGAAAGGAT 0.768081 -10 ATTGATTTAAACGGTGAGATT 7 2 0 ACGGTGAGAT 0.708855 -26 GTCAAATCTTTTGAAGAGTTTTTAATTTAA 12 71 0 TTGAAGAGTT 0.694791 -31 ATCTATCATTTTGAAAGGTTAAGTTATAGC 14 33 1 TTGAAAGGTT 0.506003 -103 TCTGTTATTTATGATGGGATGTTATAAAAA 14 92 0 ATGATGGGAT 0.945007 -44 TTAAAAAGTTTTGGTGGGATT 14 125 1 TTGGTGGGAT 0.927096 -11 ********** Masking position 10 Map Score: 2.5144 Number of sites scoring better than the average of aligned sites = 466 Number in coding regions = 431 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 13 AACCAAAAATTAAGTTAAGATTAAAAGAAAATTTTC 1 16 1 TATAAGAAAA 0.664455 -285 TTTTAATTCCTCGATGATGAGCAATAAAAAGCTGAC 3 30 0 TCTATGAAAA 0.934764 -271 TTATAAAAAATCTTTCATGAATAATAATTTAGGATG 3 93 0 TCTATGAAAA 0.934651 -208 TTTTAGAGTGTAAGTGATATAAAAAAGTTTATAAAA 3 121 0 TATATATAAA 0.656903 -180 ATATATAGTGCCTTTCAAAATTAATAAACTTATTAT 3 235 0 CCTAAAAAAA 0.647355 -66 TTAATTCTTGTCTCTAATGAGAAAAATTAACATTTA 4 25 0 TCTATGAAAA 0.934758 -136 ATTTTTTTATTATTTTTTAATCAAAATATCAATATG 5 37 0 TATTTAAAAA 0.519997 -48 ATAAAATGAATATTTAATATATAAAATTGTCTATTT 13 43 0 TATATATAAA 0.6556 -58 TTTATAACATCCCATCATAAATAACAGAAAATTAAA 14 94 1 CCTATAAAAA 0.862496 -42 AAAGATACCATATTTCCTAAAGAATATTTTTATTTG 15 113 1 TATCTAAAAA 0.616416 -93 ATGATTAATGTAGATTATAACTAAAATAAAAAGTAA 17 81 0 TATATAAAAA 0.910749 -43 TCGTATAGTATCTTTCAAAAATAATAAAAATTTTAT 18 43 1 TCTAAAAAAA 0.863354 -258 AACAATCCCTCATAAAAAATAATTTAATGAA 18 280 0 TCTATAAAAA 0.95568 -21 TTGCTAAATATCGTTTATAACCAACATTTATGTTTT 19 45 1 TCTATAAAAA 0.955767 -149 ** * **** ** * Masking position 13 Map Score: 7.14587 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 124 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 14 TTTTTATAGTAAGATTTAAAAATAATAAAA 1 278 0 AAGATTTAAA 0.6066 -23 GTTGGTATTTAATATTTAATTACTAATCTT 2 48 0 AATATTTAAT 0.692864 -136 CTTTACCCTTAACATTTTTTGGTGATTGG 2 165 1 AACATTTTTT 0.684897 -19 TTATTCATGAAAGATTTTTTATAAACTTTT 3 105 1 AAGATTTTTT 0.900765 -196 TCAAAGCATTAAGATTTATAAGCAACTATA 10 92 0 AAGATTTATA 0.579177 -93 TGAAAATTATAGGATTTCATATTCAAAGCA 10 114 0 AGGATTTCAT 0.464149 -71 AAATCTTTTGAAGAGTTTTTAATTTAATAA 12 68 0 AAGAGTTTTT 0.520334 -34 AAATAAAATGAATATTTAATATATAAAATT 13 51 0 AATATTTAAT 0.692864 -50 GAATGATAAAAACATTTATTCTCGGGAGAA 15 26 0 AACATTTATT 0.684897 -180 AGAAATTAATAAAATTTATTAATGGGTATT 15 82 0 AAAATTTATT 0.667721 -124 TCACCACAAAAATATTTTATCTTAATTTTA 15 180 0 AATATTTTAT 0.692864 -26 AAGGAGCTTGAAAATTTCATCAAGAAAAAA 16 98 1 AAAATTTCAT 0.616273 -120 TTTCTCTCCCAAGATTTTTTTCTTGATGAA 16 113 0 AAGATTTTTT 0.900765 -105 ACTCGCATTAAAGATTTAAT 18 1 0 AAGATTTAAT 0.910861 -300 AAAAATAATAAAAATTTTATAAAGATTATT 18 59 1 AAAATTTTAT 0.692864 -242 ATTTCTTTTAAAGATTTTATTCCTGCGAAA 18 106 0 AAGATTTTAT 0.910861 -195 TTTATAAATTAAGATTTCTTTTAAAGATTT 18 119 0 AAGATTTCTT 0.864667 -182 ********** Masking position 6 Map Score: 11.3812 Number of sites scoring better than the average of aligned sites = 385 Number in coding regions = 324 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 15 TGATATAAAAAAGTTTATAAAAAATCTTTCA 3 112 0 AAGTTTATAA 0.829712 -189 GTGCCTTTCAAAATTAATAAACTTATTATTA 3 233 0 AAATTAATAA 0.884984 -68 TATAATTACACAGTTAATACAAATGAAATTA 4 84 0 CAGTTAATAA 0.790031 -77 AAAGTAAGTGAATAAATCAATCTCTT 5 6 1 AAGTGAATAA 0.9571 -79 CAAAAGGGTTAAATTAATAAATGGAGTTTTA 6 34 1 AAATTAATAA 0.884984 -104 AAGAGTTTTTAATTTAATAAAAATAGTTGAG 12 57 0 AATTTAATAA 0.700481 -45 ATAAGTGAATAGACTCTATTTTT 13 3 1 AAGTGAATAA 0.9571 -98 AATAAAAATAAAATGAATATTTAATATATAA 13 55 0 AAATGAATAT 0.433674 -46 TATCATTCTGAAGTAAATATATAGAAACTCC 15 48 1 AAGTAAATAA 0.882884 -158 TATCTTTCAGAAATTAATAAAATTTATTAAT 15 89 0 AAATTAATAA 0.884984 -117 CCTTTTCCATAAGTTTATAGAATTTCTCTCC 16 134 0 AAGTTTATAA 0.829712 -84 ATCTAAATATAAGAAAATAGAAATAACA 17 8 0 AAGAAAATAA 0.445133 -116 AATAAAAAGTAAGTGAATAAATAAGTTTTGT 17 62 0 AAGTGAATAA 0.9571 -62 ********* * Masking position 7 Map Score: 10.1889 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 79 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295