AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -itrpR_mjan_opreg_300.orf -g0.314 -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 = 0.314 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MJ0233 71 M. jannaschii predicted coding region MJ0233 #2 MJ0918 70 indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase (trpC) #3 MJ0921 289 conserved hypothetical protein #4 MJ0922 191 conserved hypothetical protein #5 MJ1036 300 M. jannaschii predicted coding region MJ1036 #6 MJ1037 62 tryptophan synthase beta subunit (trpB) #7 MJ1038 176 tryptophan synthase alpha subunit (trpA) #8 MJ1076 33 M. jannaschii predicted coding region MJ1076 #9 MJ1077 89 seryl-tRNA synthetase (serS) #10 MJ1078 273 M. jannaschii predicted coding region MJ1078 #11 MJ1079 177 conserved hypothetical protein #12 MJ1080 130 M. jannaschii predicted coding region MJ1080 #13 MJ1392 300 2-isopropylmalate synthase (leuA) #14 MJ1393 247 conserved hypothetical protein Motif number 1 CCTAATAGATATTTTTAAATACTTTAATTA 1 18 1 ATTTTTAAAT 0.909681 -54 TTTAATTATGAATTTTTATAATAAACTTGG 1 40 1 AATTTTTATA 0.796439 -32 GCATTATTAATAAATATTAAAC 3 3 1 ATTATTAATA 0.8738 -287 CAAAGATGATATTATAAAAAACTACAGAAA 3 77 0 ATTATAAAAA 0.519779 -213 AAATTTTATTATTTTTTATTATCATTATTG 3 230 0 ATTTTTTATT 0.889857 -60 AATAGAAAATATTTTATATTACATTTGGAC 4 42 0 ATTTTATATT 0.523876 -150 AGTTTGGTTAAATATTAAATAGTAACACAT 4 89 0 AATATTAAAT 0.662384 -103 ACACCTAAAAAATTTTAAAAGTTTTGGATC 4 167 0 AATTTTAAAA 0.87527 -25 AATAGTTATTATTTTTTAATAACAAAAT 5 9 0 ATTTTTTAAT 0.835825 -292 ATATTCTACAAATATTAATTAATTATACAA 5 176 1 AATATTAATT 0.756931 -125 TACAATTTGAATTTTTAAATTAACAAAAAT 5 201 1 ATTTTTAAAT 0.909681 -100 TTGTTGGAATATTATTAATATAAGATAAAA 5 269 1 ATTATTAATA 0.8738 -32 CTAAATTTTATATTTTATCTTATA 5 287 0 ATTTTATATT 0.523876 -14 AGAGGGACAGATTTTAAATAAAAGAACAAT 10 20 1 ATTTTAAATA 0.842345 -254 ATCTAAATCAATTTTTGATAATATGTATAA 10 81 0 ATTTTTGATA 0.895527 -193 AATTAGTGTTAATTTTAAAAAAACAAACAT 10 112 1 AATTTTAAAA 0.87527 -162 AAAAACAAACATTTTTTATTATTTTTTGCA 10 130 1 ATTTTTTATT 0.889857 -144 TCCAACGATAACTTTTAATTAGGATTGAGA 10 176 0 ACTTTTAATT 0.653118 -98 CAATGTTGGTATTTTTAAAAAGATTTTCCA 10 202 0 ATTTTTAAAA 0.937766 -72 TAAAAGATGCATTTTTAATATATTTTTAAT 10 241 1 ATTTTTAATA 0.959221 -33 TTTTTAATATATTTTTAATATATTATCTTT 10 252 1 ATTTTTAATA 0.959221 -22 TATTACATTCATTTTTAATTTTAAAAAACT 11 141 1 ATTTTTAATT 0.945387 -37 ACCCAATTAAATTTTTGATATGTTTTTGAT 12 28 1 ATTTTTGATA 0.895527 -103 ACCTTAATTAAATTTTAAATATTAAACTTG 12 71 1 AATTTTAAAT 0.835924 -60 GTTCTAAATTATTAAATTATAACTATA 12 114 0 ATTATTAAAT 0.807124 -17 AATTTTTATTATTTTTGAAAGATACTATAC 13 45 0 ATTTTTGAAA 0.846109 -256 ATCTTTATAAAATTTTTATTATTTTTGAAA 13 55 0 AATTTTTATT 0.791104 -246 TTTTATAAAGATTATTAATAAAGTTAATGG 13 73 1 ATTATTAATA 0.8738 -228 TTAATTTATAAATTTAAATTTAAAGATGTA 13 137 1 AATTTAAATT 0.464215 -164 TTCCCACATAAATTTTAAATATACAATATC 13 195 1 AATTTTAAAT 0.835924 -106 AATTTAATGAAATTTAAATACTCATAATGA 13 261 0 AATTTAAATA 0.716249 -40 ATTTTTGCTTATTTTAAAATGTTTTATTAG 14 12 1 ATTTTAAAAT 0.478069 -236 AGGTATTGATAATTTTAATATCAAAAGGTT 14 40 1 AATTTTAATA 0.916331 -208 CTTTTTCTAAATTTTTGAAAAATCAAAAAT 14 122 1 ATTTTTGAAA 0.846109 -126 TTTTTTAGACATTTTTGATTTTTCAAAAAT 14 132 0 ATTTTTGATT 0.895381 -116 TGTTCCATAAATTATTTATACAAACGGAAG 14 162 1 ATTATTTATA 0.711745 -86 ********** Masking position 5 Map Score: 49.0592 Number of sites scoring better than the average of aligned sites = 1879 Number in coding regions = 1239 Number in noncoding regions = 640 Number of orfs with sites within 600 bp upstream = 465 Fraction of orfs with sites within 600 bp upstream = 0.0746868 Motif number 2 GAAAATAGTTTAATATTTATTAATAATGC 3 8 0 TAATTTTTTA 0.935443 -282 AAAAGTGACCTAATGTTTTAAACTACAAAAAA 3 144 1 TAATTTTAAA 0.770916 -146 TTCGCAGAGGTAAATTTTATTATTTTTTATTA 3 239 0 TAAATTTTTA 0.923548 -51 CTAAGTTATATAATAGTTCTTAAATAATGTAT 4 117 1 TAATGTTTTA 0.887768 -75 CCAAAACTTTTAAAATTTTTTAGGTGTTATAA 4 170 1 TAAATTTTTA 0.92111 -22 TAAATAAAAATAATAGTTATTATTTTTTAATA 5 18 0 TAATGTTTTA 0.843483 -283 TTATAGTCATTTATAGTTATTAGATTTTCTAA 5 59 0 TTATGTTTTA 0.849524 -242 TCACATTATTTTATTTTTGTTAATTTAAAAAT 5 211 0 TTATTTTTTA 0.933965 -90 AAACCGGATTTAAACGTTAATATCATTCACAT 5 237 0 TAAAGTTATA 0.673806 -64 TTAGTCCCTTTAATGTCTCTTAAGATTGTCTC 7 29 0 TAATTCTTTA 0.781046 -148 ATTTCTTTAATTTTTTAACCTTTTGGTG 8 7 1 TTAATTTTAA 0.882719 -27 AATTAGGTATTTATGTTTTTTATTGTGTTTTT 9 27 0 TTATTTTTTA 0.933945 -63 AATAACACTCTTATTGTTTTTATTGAATTGAT 9 59 0 TTATGTTTTA 0.880587 -31 TAAATTAGTGTTAATTTTAAAAAAACAAACAT 10 110 1 TTAATTTAAA 0.710974 -164 TTTGCAGTAGTAATGTTTTATATCTCAATCCT 10 154 1 TAATTTTATA 0.833256 -120 TCACTAACTTTAAACTTTATTATTACATTCAT 11 121 1 TAAATTTTTA 0.923548 -57 TCACTCTGTTTTAAGTTTTTTAAAATTAAAAA 11 152 0 TTAATTTTTA 0.917868 -26 TATTCAAGTTTAATATTTAAAATTTAATTAAG 12 73 0 TAATTTTAAA 0.770887 -58 TAGTTATAATTTATAGTTATAATTTAATAATT 12 103 1 TTATGTTTAA 0.805273 -28 ATTAAATCTTTAATGCGAGTATT 13 2 1 TTAATCTTAA 0.606616 -299 AAAATTTTTATTATTTTTGAAAGATACTATAC 13 45 0 TTATTTTAAA 0.756832 -256 ACTTTATTAATAATCTTTATAAAATTTTTATT 13 65 0 TAATTTTTAA 0.911456 -236 GAAAGCCCCATTAACTTTATTAATAATCTTTA 13 78 0 TTAATTTTTA 0.917863 -223 TTCGCAGGAATAAAATCTTTAAAAGAAATCTT 13 107 1 TAAATCTTAA 0.610883 -194 ATCTTTAAATTTAAATTTATAAATTAAGATTT 13 132 0 TTAATTTTAA 0.88087 -169 **** *** *** Masking position 8 Map Score: 33.8838 Number of sites scoring better than the average of aligned sites = 1090 Number in coding regions = 722 Number in noncoding regions = 368 Number of orfs with sites within 600 bp upstream = 298 Fraction of orfs with sites within 600 bp upstream = 0.0478638 Motif number 3 AAAATTCATAATTAAAGTATTTAAAAATATCTA 1 23 0 ATAATATTTA 0.935039 -49 AGCTTATACTATTATTTTATTTTATCCTACCTT 2 12 1 ATATTATTTT 0.894771 -59 ATTATCACATTTAATAAAAAGAA 2 58 0 ATATCATTTA 0.783232 -13 ATTAATAAATATTAAACTATTTTCATATCTTAT 3 16 1 ATAATATTTT 0.939995 -274 GCAGAGGTAAATTTTATTATTTTTTATTATCAT 3 235 0 ATTTTATTTT 0.654932 -55 GGTAATAGAAAATATTTTATATTACATTTGGAC 4 42 0 ATATTATATT 0.656845 -150 AATATTAAATAGTAACACATTTATATAGTCAGA 4 76 0 ATAACATTTA 0.869398 -116 ATTTAACCAAACTAAGTTATATAATAGTTCTTA 4 106 1 ATAATATATA 0.781839 -86 ATAGTTCTTAAATAATGTATTTAAACCTAAAAA 4 129 1 ATAATATTTA 0.935039 -63 AGAATATAGCCCTAACTCATTTATGCCCATGAA 5 150 0 CTAACATTTA 0.539414 -151 TATCATTCACATTATTTTATTTTTGTTAATTTA 5 216 0 ATATTATTTT 0.894771 -85 CTAAATTTTATATTTTATCTTATATT 5 285 0 ATTTTATTTT 0.654932 -16 TTGAATTGATAATTAGGTATTTATGTTTTTTAT 9 36 0 ATTATATTTA 0.762625 -54 TAAAATTAACACTAATTTATCTAAATCAATTTT 10 96 0 ATAATATCTA 0.748189 -178 AAGATGCATTTTTAATATATTTTTAATATATTA 10 244 1 TTAATATTTT 0.502613 -30 ATATATTTTTAATATATTATCTTTCA 10 258 1 ATATTATCTT 0.620339 -16 TGTACTAAACTATATTGAATACTTAA 11 4 1 ATAATATATT 0.795642 -174 TTTATAAAAGAATAATCCATATTTATAGTTTAA 11 33 0 ATAACATATT 0.643051 -145 TAACTATTCAAGTTTAATATTTAAAATTTAATT 12 76 0 ATTTTATTTA 0.635545 -55 CTTTCGCAGGAATAAAATCTTTAAAAGAAATCT 13 105 1 ATAATCTTTA 0.556082 -196 TTTAAATTTCATTAAATTATTTTTTATGAGGGA 13 273 1 ATAATATTTT 0.939995 -28 ATCAATACCTAATAAAACATTTTAAAATAAGCA 14 17 0 ATAACATTTT 0.878377 -231 AAAAATGTTCCATAAATTATTTATACAAACGGA 14 157 1 CTAATATTTA 0.716902 -91 * *** ****** Masking position 10 Map Score: 22.0412 Number of sites scoring better than the average of aligned sites = 569 Number in coding regions = 393 Number in noncoding regions = 176 Number of orfs with sites within 600 bp upstream = 180 Fraction of orfs with sites within 600 bp upstream = 0.028911 Motif number 4 TTTAAATACTTTAATTATGAATTTTTATAATAA 1 31 1 TAATTATATT 0.906335 -41 TAGGATAAAATAAAATAATAGTATAAGCTC 2 8 0 TAAATAAATA 0.761086 -63 CCTACCTTTTTTAAATAGCAATTCTTTTTATTA 2 37 1 TAAATAGATT 0.928763 -34 TTCATAAAATTCAAATAGGACTTTCTGTAGTTT 3 56 1 TAAATAGATT 0.928763 -234 TGTTAAAGTTCCAAATAGAACTTTTTTGTAGTT 3 164 0 CAAATAGATT 0.787506 -126 CCTGTGATATTTAAATAGGACTTTCGCAGAGGT 3 260 0 TAAATAGATT 0.928763 -30 CTTAGTTTGGTTAAATATTAAATAGTAACACAT 4 89 0 TAAATATAAT 0.604831 -103 CCAAACTAAGTTATATAATAGTTCTTAAATAAT 4 112 1 TATATAAATT 0.604831 -80 AATATATAACTTAAATAAAAATAATAGTTATTA 5 28 0 TAAATAAATA 0.76109 -273 AATTGTATAATTAATTAATATTTGTAGAATATA 5 175 0 TAATTAAATT 0.906335 -126 TTATTTTTGTTAATTTAAAAATTCAAATTGTAT 5 200 0 TATTTAAATT 0.536511 -101 TAATATAAGATAAAATATAAAATTTAG 5 284 1 TAAATATAAT 0.604831 -17 TTTTAGCTTCTGAAATAGTATTTGGTAGTAATA 6 27 0 TAAATAGATT 0.928763 -36 GATACCCATTTAAATTAAGATTTTGATCAACCT 7 116 1 TAATTAAATT 0.906335 -61 ACATAAATACCTAATTATCAATTCAATAAAAAC 9 43 1 CAATTATATT 0.733374 -47 TATCTCAATCCTAATTAAAAGTTATCGTTGGAA 10 174 1 CAATTAAATT 0.733374 -100 ATTATAACTATAAATTATAACTATTCAAGTTTA 12 93 0 TAATTATATA 0.706686 -38 TCTAAATTATTAAATTATAACTATAAATTATAA 12 106 0 TAATTATATA 0.706686 -25 TTTAAATTTATAAATTAAGATTTCTTTTAAAGA 13 122 0 TAATTAAATT 0.906335 -179 ATATACATCTTTAAATTTAAATTTATAAATTAA 13 137 0 TAAATTTATT 0.452129 -164 CAATCCCTCATAAAAAATAATTTAATGAAATTT 13 276 0 TAAAAATATT 0.452128 -25 * ****** * ** Masking position 10 Map Score: 18.1608 Number of sites scoring better than the average of aligned sites = 361 Number in coding regions = 232 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 5 TATAAAAATTCATAATTAAAGTATTTAAAAAT 1 28 0 CTAATTAAGT 0.846824 -44 TTTATCCTACCTTTTTTAAATAGCAATTCTTT 2 32 1 CTTTTTAATA 0.765096 -39 ATTTTCATATCTTATTACAATTTTCATAAAAT 3 34 1 CTATTAAATT 0.476366 -256 TACAGAAAGTCCTATTTGAATTTTATGAAAAT 3 53 0 CTATTTAATT 0.927089 -237 CCAAATAGAACTTTTTTGTAGTTTAAAACATT 3 155 0 CTTTTTTAGT 0.704556 -135 TTGTATAGGACGTAATTGTATATGGATGTACA 3 201 0 CTAATTTATA 0.803006 -89 TTTTTATTATCATTATTGTATAGGACGTAATT 3 216 0 CTTATTTATA 0.637463 -74 CTGCGAAAGTCCTATTTAAATATCACAGGTGA 3 264 1 CTATTTAATA 0.88305 -26 TAAATAGTAACACATTTATATAGTCAGAAGGT 4 72 0 CCATTTTATA 0.639042 -120 GGTTTAAATACATTATTTAAGAACTATTATAT 4 124 0 CTTATTAAGA 0.586113 -68 TGACTATTCTCATATTTATAGTCATTTATAGT 5 74 0 CTATTTTAGT 0.846822 -227 ATATCATTCACATTATTTTATTTTTGTTAATT 5 218 0 CTTATTTATT 0.747539 -83 TATTGGGATACCCATTTAAATTAAGATTTTGA 7 110 1 CCATTTAATT 0.80228 -67 TATCGTTGGGCATAATTTTATACATATTATCA 10 64 1 CTAATTTATA 0.803005 -210 ATTAAAAATGCATCTTTTAATTCTAAATCAAT 10 228 0 CTCTTTAATT 0.786818 -46 AAGAATAATCCATATTTATAGTTTAAGTATTC 11 27 0 CTATTTTAGT 0.846822 -151 ATCCGCAATACCCAATTAAATTTTTGATATGT 12 19 1 CCAATTAATT 0.748829 -112 GTGATAAGACCTTAATTAAATTTTAAATATTA 12 63 1 CTAATTAATT 0.903313 -68 TGGTAATATACATCTTTAAATTTAAATTTATA 13 143 0 CTCTTTAATT 0.786818 -158 * ***** **** Masking position 6 Map Score: 14.7141 Number of sites scoring better than the average of aligned sites = 519 Number in coding regions = 368 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 6 AAATATCTATTAGGTGATAAT 1 1 0 TAGGTGTAAT 0.976064 -71 TGGATGTACAAAGGTGTTAAAGTTCCAAATA 3 180 0 AAGGTGTAAA 0.753387 -110 TAAAATTTTTTAGGTGTTATAA 4 180 1 TAGGTGTATA 0.856437 -12 GAAATAGTATTTGGTAGTAATACTTATACGT 6 18 0 TTGGTATAAT 0.947485 -45 TTTTAACCTTTTGGTGATAAT 8 23 1 TTGGTGTAAT 0.971684 -11 AATTGATAATTAGGTATTTATGTTTTTTATT 9 35 0 TAGGTATTAT 0.751046 -55 AAGAGTGTTATTGGTGATAAA 9 79 1 TTGGTGTAAA 0.952903 -11 TTTAGATAAATTAGTGTTAATTTTAAAAAAA 10 104 1 TTAGTGTAAT 0.730012 -170 GACTAAAAAGTTGGTAATATACATCTTTAAA 13 155 0 TTGGTATATA 0.725233 -146 AATGTTTTATTAGGTATTGATAATTTTAATA 14 29 1 TAGGTATGAT 0.817227 -219 CATTCTTAAGTAGGTAGTAATAATGTAATGT 14 192 0 TAGGTATAAT 0.955437 -56 ****** **** Masking position 5 Map Score: 6.71171 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 150 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 7 TTCCAAATAGAACTTTTTTGTAGTTTAAAA 3 159 0 AACTTTTTTG 0.690462 -131 TTTGGATCAAAAATTTTTAGGTTTAAATAC 4 145 0 AAATTTTTAG 0.897956 -47 AAAAATTTTAAAAGTTTTGGATCAAAAATT 4 160 0 AAAGTTTTGG 0.791609 -32 AAACTTTTAAAATTTTTTAGGTGTTATAA 4 173 1 AATTTTTTAG 0.581097 -19 ATTAATAACCAAAGTTTTAGCTTTTGTATA 5 115 1 AAAGTTTTAG 0.702587 -186 TATACAATTTGAATTTTTAAATTAACAAAA 5 199 1 GAATTTTTAA 0.438029 -102 AGCTAAAATTATCTTTTTGGG 6 52 1 ATCTTTTTGG 0.797937 -11 TGCCCGAACAACCTTTTTAGAAAAGGTTGA 7 142 0 ACCTTTTTAG 0.791609 -35 TTAATTTTTTAACCTTTTGGTGATAAT 8 17 1 AACCTTTTGG 0.85932 -17 TCGTTGGAAAATCTTTTTAAAAATACCAAC 10 198 1 ATCTTTTTAA 0.482414 -76 ATACCCAATTAAATTTTTGATATGTTTTTG 12 26 1 AAATTTTTGA 0.843023 -105 AATCTTTATAAAATTTTTATTATTTTTGAA 13 56 0 AAATTTTTAT 0.409456 -245 GTATATTACCAACTTTTTAGTCCAGAACTA 13 164 1 AACTTTTTAG 0.933993 -137 CCGATATATAAACCTTTTGATATTAAAATT 14 50 0 AACCTTTTGA 0.69864 -198 GAAAACCTTGGACTTTTTGGGTTCTTTTTC 14 99 1 GACTTTTTGG 0.841531 -149 TTCTTTTTCTAAATTTTTGAAAAATCAAAA 14 120 1 AAATTTTTGA 0.843023 -128 CATTTTTTAGACATTTTTGATTTTTCAAAA 14 134 0 ACATTTTTGA 0.590451 -114 ********** Masking position 5 Map Score: 10.3978 Number of sites scoring better than the average of aligned sites = 678 Number in coding regions = 488 Number in noncoding regions = 190 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 8 TAAATTTTAGTCTACGAACGTTCTATCAAA 3 103 0 TCTACGAACG 0.96882 -187 AAAATTTACCTCTGCGAAAGTCCTATTTAA 3 253 1 TCTGCGAAAG 0.96882 -37 ATGAAGCAATTATACAAAAGCTAAAACTTT 5 125 0 TATACAAAAG 0.889572 -176 TGAAAGATACTATACGAAAGTCATAAAATA 13 30 0 TATACGAAAG 0.959737 -271 AGATTTTATTCCTGCGAAAGCCCCATTAAC 13 95 0 CCTGCGAAAG 0.918927 -206 ATAAATTATTTATACAAACGGAAGACATTA 14 168 1 TATACAAACG 0.869766 -80 ********** Masking position 7 Map Score: 1.56808 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 2 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 9 GGACTTATTTAGTCCAAATGTAATATAAAATATT 4 31 1 AGTCCAATAT 0.936384 -161 ACATTTATATAGTCAGAAGGTAATAGAAAATATT 4 59 0 AGTCAAATAT 0.97159 -133 ATATGAGAATAGTCAGAAATTAACATTAATAACC 5 91 1 AGTCAAATAC 0.877218 -210 AAGATAATATATTAAAAATATATTAAAAATGCAT 10 247 0 ATTAAAATAT 0.750882 -27 TAAAGAGTGTAGTAAAGAACTAATAAAAAAGGAA 11 71 1 AGTAAGATAT 0.925326 -107 TATAATTTATAGTTATAATTTAATAATTTAGAAC 12 107 1 AGTTAAATAT 0.841172 -24 AAATACTCGCATTAAAGATTTAAT 13 1 0 ATTAAGATAT 0.679564 -300 ACTATACGAAAGTCATAAAATACTCGCATTAAAG 13 18 0 AGTCAAATAT 0.971614 -283 CCAACTTTTTAGTCCAGAACTATTTCCCACATAA 13 172 1 AGTCCGATAT 0.912955 -129 TTAAGTAGGTAGTAATAATGTAATGTCTTCCGTT 14 184 0 AGTAAAATAT 0.944204 -64 ***** ** ** * Masking position 8 Map Score: 5.0349 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 30 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 10 AATACTTTAATTATGAATTTTTATAATAAA 1 35 1 TTATGAATTT 0.564851 -37 GAGCTTATACTATTATTTTATTTTATCCT 2 10 1 CTATTATTTT 0.532264 -61 GAGGTAAATTTTATTATTTTTTATTATCAT 3 235 0 TTATTATTTT 0.934418 -55 AAAATAATAGTTATTATTTTTTAATAACAA 5 14 0 TTATTATTTT 0.934418 -287 ATAATAACTATTATTTTTATTTAAGTTATA 5 27 1 TTATTTTTAT 0.363559 -274 TATTTTATTTTTGTTAATTTAAAAATTCAA 5 207 0 TTGTTAATTT 0.370553 -94 ATCATTCACATTATTTTATTTTTGTTAATT 5 218 0 TTATTTTATT 0.511893 -83 GAAGCTAAAATTATCTTTTTGGG 6 50 1 TTATCTTTTT 0.567816 -13 CCCATTTAAATTAAGATTTTGATCAACCTT 7 120 1 TTAAGATTTT 0.660252 -57 ATTTCTTTAATTTTTTAACCTTTTGG 8 7 1 TTAATTTTTT 0.620845 -27 ATGTTTTTTATTGTGTTTTTAGAAATACAG 9 17 0 TTGTGTTTTT 0.808807 -73 AATTAGGTATTTATGTTTTTTATTGTGTTT 9 29 0 TTATGTTTTT 0.910284 -61 AATAACACTCTTATTGTTTTTATTGAATTG 9 61 0 TTATTGTTTT 0.675158 -29 AAAGAAACTATTGTTCTTTTATTTAAAATC 10 29 0 TTGTTCTTTT 0.614609 -245 TAAAAAATGTTTGTTTTTTTAAAATTAACA 10 118 0 TTGTTTTTTT 0.821478 -156 CAAACATTTTTTATTATTTTTTGCAGTAGT 10 135 1 TTATTATTTT 0.934418 -139 TAAATCAATGTTGGTATTTTTAAAAAGATT 10 207 0 TTGGTATTTT 0.340798 -67 TAAATATGGATTATTCTTTTATAAAGTCGT 11 41 1 TTATTCTTTT 0.792746 -137 GACAGTGTGATTATGATATTCCTTTTTTAT 11 93 0 TTATGATATT 0.5545 -85 TCACTCTGTTTTAAGTTTTTTAAAATTAAA 11 154 0 TTAAGTTTTT 0.600853 -24 TAAATTTTTGATATGTTTTTGATTTGATGT 12 35 1 ATATGTTTTT 0.353486 -96 TGCGAGTATTTTATGACTTTCGTATAGTAT 13 24 1 TTATGACTTT 0.521768 -277 TATAAAATTTTTATTATTTTTGAAAGATAC 13 50 0 TTATTATTTT 0.934418 -251 TTTCATTAAATTATTTTTTATGAGGGATTG 13 279 1 TTATTTTTTA 0.363559 -22 ATATCGGCTGTTATTATTTTCAAATTGAAA 14 73 1 TTATTATTTT 0.934418 -175 TTTTAGACATTTTTGATTTTTCAAAAATTT 14 130 0 TTTTGATTTT 0.457955 -118 ********** Masking position 2 Map Score: 20.2213 Number of sites scoring better than the average of aligned sites = 787 Number in coding regions = 558 Number in noncoding regions = 229 Number of orfs with sites within 600 bp upstream = 205 Fraction of orfs with sites within 600 bp upstream = 0.0329264 Motif number 11 ********** No masking Map Score: -2.81842e-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: -2.81842e-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: -2.81842e-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