AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00252_mjan_reg_300.orf -o00252_mjan_300.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 Purged sequences: MJ1553 21 transcriptional regulatory protein, arsR family Input sequences: #1 MJ0002 300 M. jannaschii predicted coding region MJ0002 #2 MJ0020 300 asparaginase (ansA) #3 MJ0050 109 group II decarboxylase #4 MJ0429 167 argininosuccinate synthetase (argG) #5 MJ0561 281 adenylosuccinate synthetase (purA) #6 MJ0564 300 alanyl-tRNA synthetase (alaS) #7 MJ0684 68 aspartate aminotransferase (aspB2) #8 MJ0791 300 argininosuccinate lyase (argH) #9 MJ0929 300 adenylosuccinate lyase (purB) #10 MJ1054 300 UDP-glucose dehydrogenase, putative #11 MJ1116 136 asparagine synthetase (asnB) #12 MJ1404 300 M. jannaschii predicted coding region MJ1404 #13 MJ1405 47 M. jannaschii predicted coding region MJ1405 #14 MJ1406 89 aspartate carbamoyltransferase regulatory chain (pyrI) #15 MJ1479 259 putative aminotransferase #16 MJ1545 77 conserved hypothetical protein #17 MJ1548 53 conserved hypothetical protein #18 MJ1550 243 M. jannaschii predicted coding region MJ1550 #19 MJ1552 103 conserved hypothetical protein #20 MJ1554 82 conserved hypothetical protein #21 MJ1555 150 aspartyl-tRNA synthetase (aspS) #22 MJ1581 260 aspartate carbamoyltransferase catalytic chain (pyrB) Motif number 1 CCAGTAGCACTAAATATAATATATCCAATC 1 63 1 TAAATATAAT 0.612136 -238 ACCAATTATAAAAAATTATATAAAAAATTA 1 210 1 AAAAATTATA 0.907362 -91 GAATGCAATTTAAATATATTAAGGAACTT 2 10 0 TAAATATATT 0.612067 -291 TCATCCGCCATAAATATATTAAGTAGCTTT 2 107 0 TAAATATATT 0.612067 -194 TTTATTTTGCAAATATTAATTTATATATTT 2 190 1 AAATATTAAT 0.78846 -111 TTTTTATATTTAAATATATAAATTAATATT 2 201 0 TAAATATATA 0.701901 -100 TTTAAATATAAAAATTTATATGATAGCTAT 2 217 1 AAAATTTATA 0.777726 -84 ATTAGGGTATAAAAATTATAAAAAGATAGC 2 242 0 AAAAATTATA 0.907362 -59 TTCTTAGGTATAAATATAATACAATATACT 3 34 0 TAAATATAAT 0.612136 -76 ACATCATGATTAAATTTATAAGTATTTAAT 3 67 0 TAAATTTATA 0.733821 -43 TATCAACTAAAAAAATTAAAGG 3 98 1 AAAAATTAAA 0.907539 -12 ATATCTTACATAAAATTATAAATCCTTAAA 4 124 0 TAAAATTATA 0.885261 -44 ATGTAAGATATAAAAATATTTTGTGAGGGA 4 143 1 TAAAAATATT 0.815527 -25 TTAAACCTTCAAATAATAAACCATAACAAC 5 28 0 AAATAATAAA 0.826018 -254 TTTATATTCCAAAATATATAGAACTATAAA 5 168 1 AAAATATATA 0.749249 -114 TGGAAATTCTTAATATTAATTAACTTTAAA 5 227 1 TAATATTAAT 0.746019 -55 TACAATTACAAAAAAATATAAGGTTTTGAA 5 260 1 AAAAAATATA 0.893303 -22 AGTTATATTTAAATATTAATTTTCATAAGA 6 156 0 AAATATTAAT 0.78846 -145 ATATAACTTATAAAATTATAGCTACTTACC 6 178 1 TAAAATTATA 0.885261 -123 ACAAATTAATAAAATTTATTTATGAACCAC 6 221 1 AAAATTTATT 0.701016 -80 TATTATTAATTAATAATAATTCCTTTTAGT 7 30 1 TAATAATAAT 0.714863 -39 GCACCATACAAAAAATTAAAGAATAGTTGG 8 38 0 AAAAATTAAA 0.907539 -263 GTTAAATAGTAAATTATATATGTTAAAATT 8 135 1 AAATTATATA 0.628764 -166 TTAGAATTTTTAATAATAAAACAATTATAA 8 174 1 TAATAATAAA 0.789096 -127 ATAAAATAGTTAAAAATAATTTACTTTTTT 8 208 0 TAAAAATAAT 0.815634 -93 TTTTTTGATATAAAATTATAAAATAGTTAA 8 225 0 TAAAATTATA 0.885261 -76 AATCGTGTTTAAATAATATTGATTATGTTA 8 262 0 AAATAATATT 0.760841 -39 TTTTGAAAATAAAAATTAAATAATTATCTA 9 12 0 AAAAATTAAA 0.907539 -289 CCTAAAACCCAAATAATAAATTATAAACAG 9 210 1 AAATAATAAA 0.826018 -91 AGAAATATAATAATATTATACAATTATTAA 10 259 1 TAATATTATA 0.814247 -42 AATATTTGCAAAATTTTAATTTAAATATCT 11 59 0 AAATTTTAAT 0.570753 -78 TTGTGTTAGCTAATATTAAAAAATAAGGTA 11 106 1 TAATATTAAA 0.814248 -31 AAAAAATATATAAAATTATT 12 1 0 TAAAATTATT 0.837959 -300 ACAAATTAATAAAAAATATATAAAATTATT 12 11 0 AAAAAATATA 0.893303 -290 TATCATGCCAAAATAATATATAAATCTTAC 12 77 1 AAATAATATA 0.826018 -224 ACGATTTTTTAAAAAATATTATTACTCAAA 12 105 1 AAAAAATATT 0.848726 -196 TTATTTGTTTAAAAATTAATATTTGAGTAA 12 126 0 AAAAATTAAT 0.868023 -175 GTTAAACTTTAAATATTAAATGTGATATAA 12 253 1 AAATATTAAA 0.847617 -48 AATATATTATTAAAATTAAAAGGAA 13 6 0 TAAAATTAAA 0.885519 -42 ATAAAATAATAAAAAATATATTATTAAAAT 13 20 0 AAAAAATATA 0.893303 -28 AAATAATAATAAAATAATAAAAA 13 35 0 TAATAATAAA 0.789096 -13 ATAAAAATGCTAAAAATATTAGAGAAAATT 14 48 1 TAAAAATATT 0.815527 -42 TTAAAATTTAAAGCTTTTGTTC 14 78 0 AAAATTTAAA 0.777856 -12 TATTTATGGATAAAATTAAAAAGGAAGTGC 18 19 1 TAAAATTAAA 0.885519 -225 AGATAATACCAAATAATAAAATCCAATACC 18 80 0 AAATAATAAA 0.826018 -164 ACAAACAAGCAAATATTATTGCAGAAATCA 18 136 0 AAATATTATT 0.788459 -108 AAAATAATTAAAAAATTAAAT 21 2 0 AAAAATTAAA 0.907539 -149 TGTCAAAAATAAAAAATAATTAAAAAATTA 21 14 0 AAAAAATAAT 0.848801 -137 TTTTAACCTATAAAATTAAATATATAGATA 21 45 1 TAAAATTAAA 0.885519 -106 TTCAATCATAAAATTTTATTTCTGTGAAAG 22 86 1 AAATTTTATT 0.570752 -175 ********** Masking position 7 Map Score: 57.5573 Number of sites scoring better than the average of aligned sites = 2522 Number in coding regions = 1746 Number in noncoding regions = 776 Number of orfs with sites within 600 bp upstream = 532 Fraction of orfs with sites within 600 bp upstream = 0.0854481 Motif number 2 TTTATATAATTTTTTATAATTGGTATTTTGA 1 203 0 TTTTTAAATT 0.837826 -98 ACATAAGTCCTATTATAAAATACTACCAATT 1 239 1 TATTATAAAT 0.571621 -62 TCTCCAAAATTATTAGAAATTCTAATTGGTA 1 262 0 TATTAGAATT 0.602419 -39 ATCATATAAATTTTTATATTTAAATATATAA 2 210 0 TTTTTAATTT 0.831816 -91 GATAGCTATCTTTTTATAATTTTTATACCCT 2 238 1 TTTTTAAATT 0.837826 -63 CCTTTAATTTTTTTAGTTGATAAACATC 3 92 0 TTTTTTAGTT 0.704476 -18 TGACAGTTATTATTAGCAGTTTATATATAAT 4 45 1 TATTAGAGTT 0.519398 -123 ATCCTTAAACTTTTTGTATTTTATTGCTTAT 4 102 0 TTTTTGATTT 0.723723 -66 CCTCACAAAATATTTTTATATCTTACATAAA 4 140 0 TATTTTATAT 0.587339 -28 CATAAATAGATTTTATTAGTTTTGAAAAGAA 5 87 0 TTTTATAGTT 0.681511 -195 TATTATAAGTTTTTTATAGTTCTATATATTT 5 179 0 TTTTTAAGTT 0.786587 -103 AGTTAATTAATATTAAGAATTTCCAATGTAT 5 221 0 TATTAAAATT 0.740987 -61 GTAATTGTAATATTTAAAGTTAATTAATATT 5 238 0 TATTTAAGTT 0.694482 -44 ACCTTATATTTTTTTGTAATTGTAATATTTA 5 253 0 TTTTTGAATT 0.732403 -29 TAAATGCTCTTATTTTCAAATTCTAAACTTA 6 28 1 TATTTTAAAT 0.597924 -273 AAGACAAAAATGTTTGTATATGAATTTGCCT 6 122 0 TGTTTGATAT 0.33824 -179 TGAAAATTAATATTTAAATATAACTTATAAA 6 161 1 TATTTAATAT 0.687561 -140 GTAGCTATAATTTTATAAGTTATATTTAAAT 6 172 0 TTTTATAGTT 0.681511 -129 CATAAATAAATTTTATTAATTTGTGAGATAC 6 214 0 TTTTATAATT 0.749959 -87 CCACGAAAAGTATTATTAATTAATAATAATT 7 20 1 TATTATAATT 0.6491 -49 TTCCTTTTAGTGTTTATAAATGGTGATGTC 7 49 1 TGTTTAAAAT 0.502062 -20 CCTCTATATATATTATGATTTAAAGTTAAAT 8 111 1 TATTATATTT 0.639107 -190 AAGTTAAAAATTTTAACATATATAATTTACT 8 142 0 TTTTAAATAT 0.762073 -159 ATTGTTTTATTATTAAAAATTCTAATAAGTT 8 168 0 TATTAAAATT 0.74094 -133 ATAATTTACTTTTTTAAAGTTATAATTGTTT 8 192 0 TTTTTAAGTT 0.786587 -109 TTTTTAACTATTTTATAATTTTATATCAAAA 8 222 1 TTTTATATTT 0.741697 -79 TTATATTTCATTTTTTGATATAAAATTATAA 8 234 0 TTTTTTATAT 0.697684 -67 ATTATTCAGATTTTTGAAAATAAAAATTAAA 9 22 0 TTTTTGAAAT 0.663817 -279 TTGTTGAATATGTTTGGATTTTGAAAATAAG 9 145 0 TGTTTGATTT 0.41468 -156 ATTATTTGGGTTTTAGGATTTTTAATTTTGT 9 196 0 TTTTAGATTT 0.70162 -105 TATAGAAGTCTGTTTATAATTTATTATTTGG 9 218 0 TGTTTAAATT 0.582913 -83 TTGCTAATGATTTTTATAGTTTGATGTTTAT 9 276 0 TTTTTAAGTT 0.786587 -25 AGTAATGCTATATTTACAATTAATTGTTGGA 10 166 1 TATTTAAATT 0.761166 -135 AATTGTATAATATTATTATATTTCTCTTACA 10 253 0 TATTATATAT 0.560945 -48 TGAGTTTATTTATTAATAATTGTATAATATT 10 270 0 TATTAAAATT 0.740944 -31 ATTTAATCTTTATTAAGATATTTAAATTAAA 11 44 1 TATTAAATAT 0.66391 -93 TGTTAGCTAATATTAAAAAATAAGGTATATT 11 109 1 TATTAAAAAT 0.673551 -28 ATTTTTAAATATACCTTATTTT 11 125 0 TTTTTAATAT 0.781095 -12 TTTATATATTTTTTATTAATTTGTGTAGGTT 12 17 1 TTTTATAATT 0.749959 -284 TAATAATATTTTTTAAAAAATCGTAAGATTT 12 98 0 TTTTAAAAAT 0.769874 -203 TATCATTATTTGTTTAAAAATTAATATTTGA 12 130 0 TGTTTAAAAT 0.502062 -171 CTTTAAAATATTTTAAAATATCTTTTATCAT 12 155 0 TTTTAAATAT 0.762073 -146 AGCAGTTACGTATTAAGAAATGTGAATGTTT 12 222 0 TATTAAAAAT 0.673621 -79 TCACATTTAATATTTAAAGTTTAACAGCAGT 12 247 0 TATTTAAGTT 0.694482 -54 ATAATATATTTTTTATTATTTTATTATTATT 13 26 1 TTTTATATTT 0.741697 -22 TTTATTATTTTATTATTATTT 13 37 1 TATTATATTT 0.639107 -11 TCTCTAATATTTTTAGCATTTTTATTTGTGT 14 42 0 TTTTAGATTT 0.70162 -48 TAGAGTTCTATTTTTTTATATGTTTGAAGTG 15 150 0 TTTTTTATAT 0.697683 -110 TGGTATTGGATTTTATTATTTGGTATTATCT 18 79 1 TTTTATATTT 0.741697 -165 TCCTTCCTATTTTTATTAAATGGTAGGTAGA 18 215 0 TTTTATAAAT 0.683916 -29 TATAGTATCTTTTTTAGATATATAAATGAAT 20 33 1 TTTTTAATAT 0.781095 -50 ATGAATTAGCTTTTTAAATATTCTTAGGTGA 20 58 1 TTTTTAATAT 0.781095 -25 GTGTAAATGGTTTTTATAGTTTCCTAAGCTT 21 80 0 TTTTTAAGTT 0.786587 -71 TTCTCCAAAATTTTTATAAATCTTTTTTATA 22 196 1 TTTTTAAAAT 0.788446 -65 TTATAAATCTTTTTTATAAATACTCTATCAA 22 209 1 TTTTTAAAAT 0.788446 -52 ****** **** Masking position 4 Map Score: 55.6746 Number of sites scoring better than the average of aligned sites = 3118 Number in coding regions = 2191 Number in noncoding regions = 927 Number of orfs with sites within 600 bp upstream = 525 Fraction of orfs with sites within 600 bp upstream = 0.0843238 Motif number 3 GATTGGATATATTATATTTAGTGCTACTGG 1 63 0 ATTATATTTA 0.515396 -238 CTGATTATGGAGAATATTTAGCGTTTAGTT 1 129 0 AGAATATTTA 0.837515 -172 AAGTTCCTTAATATATTTAAATTGCATTC 2 10 1 AATATATTTA 0.603775 -291 AGTAGCTTTAAGTATATATACTTACCTCAA 2 86 0 AGTATATATA 0.878408 -215 AAAGCTACTTAATATATTTATGGCGGATGA 2 107 1 AATATATTTA 0.603775 -194 AGTATATTGTATTATATTTATACCTAAGAA 3 34 1 ATTATATTTA 0.515396 -76 TATTATTAGCAGTTTATATATAATAGGTGA 4 52 1 AGTTTATATA 0.691783 -116 ATAGTTTTGGAGTATATATAACTCACCTAT 4 74 0 AGTATATATA 0.878408 -94 AAAAAGTTTAAGGATTTATAATTTTATGTA 4 118 1 AGGATTTATA 0.706779 -50 TTAACTTATTAGAATTTTTAATAATAAAAC 8 166 1 AGAATTTTTA 0.661162 -135 TTGATTATTTAGAATATTTAAGTTTATTGA 9 53 0 AGAATATTTA 0.837515 -248 ATTAGTTCAAAGGATTTTTATTTAATTTCT 9 97 0 AGGATTTTTA 0.841546 -204 TTTGGGTTTTAGGATTTTTAATTTTGTTGT 9 193 0 AGGATTTTTA 0.841546 -108 TTTATTTTGGAGTTTATTTAGCTGTAATTT 10 204 1 AGTTTATTTA 0.831803 -97 AAATCCCCTGAGTTTATTTATTAATAATTG 10 279 0 AGTTTATTTA 0.831803 -22 AAAACCTCTAAGGTTATTTATAATAAATTG 11 14 1 AGGTTATTTA 0.813389 -123 AATCTTTATTAAGATATTTAAATTAAAATT 11 48 1 AAGATATTTA 0.573226 -89 TAAAAAATAAGGTATATTTAAAAAT 11 122 1 GGTATATTTA 0.780421 -15 TAATATTTTTAGCATTTTTATTTGTGTTTC 14 39 0 AGCATTTTTA 0.617982 -51 TTAAGAGTAAAGTTTATATACTACTGGGAT 15 183 1 AGTTTATATA 0.691783 -77 TTAGAGGATATTTATGGATAAAAT 18 5 1 AGGATATTTA 0.933464 -239 AGGTAGATAAGGGATATTTAGTTTAGTTTT 18 192 0 GGGATATTTA 0.758018 -52 ATATCACCTAAGAATATTTAAAAAGCTAAT 20 62 0 AGAATATTTA 0.837515 -21 TTGTGTAAATGGTTTTTATAGTTTCCTAAG 21 83 0 GGTTTTTATA 0.159464 -68 GGTTTGATAGAGTATTTATAAAAAAGATTT 22 213 0 AGTATTTATA 0.73225 -48 TCCCTATTAAAGCATATATATGAGGTTTGA 22 236 0 AGCATATATA 0.659795 -25 ********** Masking position 5 Map Score: 24.9598 Number of sites scoring better than the average of aligned sites = 510 Number in coding regions = 381 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 4 ATTAAAGGTTTATTTGGATTGTTTGTTGACG 1 97 0 TATTGGATTG 0.72509 -204 GCTGCTGAGCTATGATGATTGATGGGCGAAC 2 148 1 TATATGATTG 0.661116 -153 TAAACATTTATTTGAGGTTTAATT 3 4 0 TTTAGGTTTA 0.784775 -106 AATTTCTATTTAGATTGATTATTGACAGTTA 4 23 1 TAGTTGATTA 0.252559 -145 ATACAAAAAGTTTAAGGATTTATAATTTTAT 4 114 1 TTTAGGATTT 0.571708 -54 GGTTTATTATTTGAAGGTTTAAATTATTTAT 5 36 1 TTGAGGTTTA 0.73452 -246 TGTTGTTTGGTTTATGGATTGTCTTGTTGGA 6 59 0 TTTTGGATTG 0.918067 -242 AATTTCTGATTTTGTTGTTTGGTTTATGGAT 6 71 0 TTTTTGTTTG 0.874075 -230 CTATAATCTATTGTAGGTTTGGAATTTCTGA 6 93 0 TTGAGGTTTG 0.910327 -208 CCCATCACCTTTAATGATTGCAGTTTTTAG 6 281 0 TTTATGATTG 0.892331 -20 TTCTAAGGGTTTGCTGGTTTGATTATTTAGA 9 70 0 TTGTGGTTTG 0.894762 -231 TGTTGTTTGGTTAATGGATTGTCTTGTTGAA 9 168 0 TTATGGATTG 0.735906 -133 GATTTTTAATTTTGTTGTTTGGTTAATGGAT 9 180 0 TTTTTGTTTG 0.874075 -121 ATTATTTGGGTTTTAGGATTTTTAATTTTGT 9 196 0 TTTAGGATTT 0.571708 -105 ATTTTTATAGTTTGATGTTTATTTAAAAAAG 9 267 0 TTTATGTTTA 0.693138 -34 TCTTTTATCATTATTTGTTTAAAAATTAATA 12 135 0 TTATTGTTTA 0.319943 -166 TAACAGAAATTTTGATGATTGATATTATATC 12 276 0 TTTATGATTG 0.892331 -25 TTCTATTTTTTTATATGTTTGAAGTGTTATA 15 145 0 TTAATGTTTG 0.673314 -115 TATTATCTATTTGATGGATTAACTGTATTTT 18 102 1 TTGTGGATTA 0.698545 -142 TAATATTTGCTTGTTTGTTTGTAATAGGGTT 18 148 1 TTGTTGTTTG 0.840432 -96 AGAAATAAAATTTTATGATTGAATAAAGATG 22 78 0 TTTATGATTG 0.892331 -183 AAAGCATATATATGAGGTTTGATAGAGTATT 22 227 0 TATAGGTTTG 0.75899 -34 *** ******* Masking position 9 Map Score: 15.5991 Number of sites scoring better than the average of aligned sites = 380 Number in coding regions = 308 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 5 TGGATTTTTAATATCTCCAAAATTATTAGAAAT 1 273 0 ATTCCAAAAT 0.882936 -28 ATATAAATTAATATTTGCAAAATAAAAAGTGGC 2 183 0 ATTTCAAAAT 0.907054 -118 ATAAAATCTATTTATGAGTAAATTTGAACTCCT 5 102 1 TTATGTAAAT 0.438716 -180 AATAAAGAAATAATTCCTAAATGCTCTTATTT 6 10 1 ATATCTAAAT 0.787963 -291 TTTGTCTTCTTTCTTATGAAAATTAATATTTAA 6 145 1 TTTTGAAAAT 0.67952 -156 GAACTAATTAATAACTTCTAAATGCTCTTATTT 9 119 1 ATACCTAAAT 0.735613 -182 CTAAATGCTCTTATTTTCAAAATCCAAACATAT 9 136 1 TTTTCAAAAT 0.860476 -165 TCTATAAGTAATTTTCTGAAAATGCTTTTTTAA 9 243 1 ATTTGAAAAT 0.47492 -58 CAGACATAAAATTACAGCTAAATAAACTCCAAA 10 209 0 ATACCTAAAT 0.735612 -92 TTTATGCTAAATATTTGCAAAATTTTAATTTAA 11 65 0 ATTTCAAAAT 0.907054 -72 TATGCAGTATATCATGCCAAAATAATATATAAA 12 68 1 ATATCAAAAT 0.884624 -233 TTCTTTAATATTGTTAGGAAAATAGAGCCAAAT 12 188 1 TTTTGAAAAT 0.67952 -113 GTTTTCATCTCAAAATGGAACTCTAT 15 244 0 TTATCAAAAT 0.828875 -16 AACATAATGCATTTCAACAAAATCAAAAACTTT 16 47 1 ATTCCAAAAT 0.87924 -31 ATACTATATAATGATTTCTAAATCGTTCGG 20 8 0 ATATCTAAAT 0.787963 -75 ACACACAATATTTTCTCCAAAATTTTTATAAAT 22 184 1 TTTCCAAAAT 0.821976 -77 ** ** ****** Masking position 10 Map Score: 11.6477 Number of sites scoring better than the average of aligned sites = 392 Number in coding regions = 308 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 6 AAAAAATTATATAAAAAATTACATAAGTCCTATTAT 1 219 1 ATAAAACAAA 0.94725 -82 GAAAAGAACCATATAATTTCACAAAATGATAAATAA 5 59 0 ATAAAACAAA 0.94725 -223 TCCAAAATATATAGAACTATAAAAAACTTATAATAA 5 175 1 ATAAAAAAAA 0.641793 -107 TAATTTTCATAAGAAAGAAGACAAAAATGTTTGTAT 6 134 0 AAGAAACAAA 0.507675 -167 TTTTTCACAAATGTAATAATACAAAACCTCTATATA 8 85 1 ATGAAACAAA 0.931627 -216 TCATTTTTTGATATAAAATTATAAAATAGTTAAAAA 8 222 0 ATAAAATAAA 0.719676 -79 ATATCAAAAAATGAAATATAACATAATCAATATTAT 8 244 1 ATGAAACAAA 0.931627 -57 TTATTTTTTAATATTAGCTAACACAACTTAACATTT 11 96 0 ATATAACAAA 0.914262 -41 TATAATATACATAATAACCTACACAAATTAATAAAA 12 27 0 ATATAACAAA 0.914262 -274 TTATTTTGGCATGATATACTGCATAAGTAATATAAT 12 57 0 ATGTAGCAAA 0.461786 -244 AAATAATAATAAAATAATAAAAAATATATTATTA 13 24 0 ATAAAAAAAA 0.641793 -24 AAAATATTAGAGAAAATTGAACAAAAGCTTTAAATT 14 60 1 AGAAAACAAA 0.668234 -30 TCGAATACTTATAGTGCGTTACAAAAAACTTACTAT 15 107 0 ATATGACAAA 0.700252 -153 CACTTCAAACATATAAAAAAATAGAACTCTATTTTA 15 150 1 ATAAAATAAA 0.719676 -110 TACTGGGATAATGGTAAATTACACAAAAGTGTCATA 15 204 1 ATGTAACAAA 0.890005 -56 AATAAACATAATGCATTTCAACAAAATCAAAAACTT 16 43 1 ATGATACAAA 0.522537 -35 TTGGGGAAGAATATTACTTCATAAAAGAACATGAAA 17 22 1 ATATAATAAA 0.603887 -32 AATAGGGTTTATAATATATGACAAAACTAAACTAAA 18 170 1 ATATAACAAA 0.914262 -74 AAAATTAAATATATAGATACACAAAAGCTTAGGAAA 21 56 1 ATAAGACAAA 0.797326 -95 *** ** *** ** Masking position 13 Map Score: 15.4682 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 100 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 7 TAACAGGTTGAATGCAATTTAAATATATTAA 2 18 0 AATCAATTTA 0.700908 -283 GTATAAATATAATACAATATACTAAACATTT 3 26 0 AATCAATATA 0.572028 -84 AAAACTAATAAAATCTATTTATGAGTAAATT 5 95 1 AAACTATTTA 0.88898 -187 TGTTCAAAACCTTATATTTTTTTGTA 5 266 0 AAACCTTATA 0.721152 -16 AAGACCTCTTAAAACATTTTAAGTGGTTCAT 6 242 0 AAACATTTTA 0.888978 -59 TAATAATACAAAACCTCTATATATATTATGA 8 98 1 AAACTCTATA 0.721152 -203 TATTTCACCAATGCATTTTAATCGTGTTTA 8 281 0 AATCATTTTA 0.700908 -20 AATCTATTTAAAACCTCTTTAATCTTGTGAT 10 20 0 AAACTCTTTA 0.81931 -281 TATTACTTGGAAATCTATTTAAAACCTCTTT 10 31 0 AAACTATTTA 0.88898 -270 AATAAAGATTAAATCAATTTATTATAAATAA 11 27 0 AAACAATTTA 0.88898 -110 AACAAAATCAAAAACTTTATATAATA 16 62 1 AAACTTTATA 0.820371 -16 AACGATTTAGAAATCATTATATAGTATCTTT 20 14 1 AAACATTATA 0.820372 -69 GGAAACTATAAAAACCATTTACACAATTATT 21 87 1 AAACCATTTA 0.81931 -64 CAAATCACTAAAAACTTTTTAAGGTTAATAA 21 113 0 AAACTTTTTA 0.888978 -38 *** ******* Masking position 2 Map Score: 8.31354 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 221 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 8 AATACCAATTATAAAAAATTATATAAAAAA 1 207 1 ATAAAAAATT 0.779971 -94 AAAAAATTATATAAAAAATTACATAAGTCC 1 219 1 ATAAAAAATT 0.779971 -82 TATTTTGCAAATATTAATTTATATATTTAA 2 192 1 ATATTAATTT 0.669651 -109 ATATTTAAATATAAAAATTTATATGATAGC 2 214 1 ATAAAAATTT 0.673041 -87 ATCAATCTAAATAGAAATTTTTGGGGATAA 4 12 0 ATAGAAATTT 0.662358 -156 TAAAAAACTTATAATAACTTACTTGCCATA 5 194 1 ATAATAACTT 0.532444 -88 TTATATTTAAATATTAATTTTCATAAGAAA 6 154 0 ATATTAATTT 0.669651 -147 TTAAAGTTAAATAGTAAATTATATATGTTA 8 130 1 ATAGTAAATT 0.888879 -171 TAACTTTAAAAAAGTAAATTATTTTTAACT 8 201 1 AAAGTAAATT 0.310128 -100 TCATTTTTTGATATAAAATTATAAAATAGT 8 228 0 ATATAAAATT 0.6046 -73 TAAAACCCAAATAATAAATTATAAACAGAC 9 212 1 ATAATAAATT 0.893543 -89 TAATCTTGTGATAATAAATTC 10 2 0 ATAATAAATT 0.893543 -299 TTTCCAAGTAATAGTAAATTCGATACGGTT 10 49 1 ATAGTAAATT 0.888879 -252 AAGGTTATTTATAATAAATTGATTTAATCT 11 23 1 ATAATAAATT 0.893543 -114 AATAAAAAATATATAAAATTATT 12 4 0 ATATAAAATT 0.6046 -297 TATTACTCAAATATTAATTTTTAAACAAAT 12 124 1 ATATTAATTT 0.669651 -177 TTTAATTTTAATAATATATTTTTTATTATT 13 16 1 ATAATATATT 0.320527 -32 AAATAATAATAAAATAATAAAAAAT 13 33 0 ATAATAAAAT 0.464919 -15 TGCCTTTTCTATAGTAAGTTTTTTGTAACG 15 97 1 ATAGTAAGTT 0.520464 -163 TACTGGGATAATGGTAAATTACACAAAAGT 15 204 1 ATGGTAAATT 0.399868 -56 AGTGCTTACTATAGTAATTGGAAGCATTGG 18 44 1 ATAGTAATTG 0.278982 -200 ATAATACCAAATAATAAAATCCAATACCAC 18 78 0 ATAATAAAAT 0.464919 -166 GTCTTTCAAGATAATAATTTGCTAATTTAC 22 156 0 ATAATAATTT 0.829206 -105 AAAAAGATTTATAAAAATTTTGGAGAAAAT 22 193 0 ATAAAAATTT 0.673041 -68 ********** Masking position 6 Map Score: 19.3092 Number of sites scoring better than the average of aligned sites = 452 Number in coding regions = 274 Number in noncoding regions = 178 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 9 AAACCATTATCAACAAACCATGGGAACGCT 1 24 1 CAACAAACCA 0.66893 -277 ATCAATGCGTCAACAAACAATCCAAATAAA 1 90 1 CAACAAACAA 0.775006 -211 ATTAATAGAGCATCAAAATACCAATTATAA 1 191 1 CATCAAAATA 0.805243 -110 AAACTATAAGCAATAAAATACAAAAAGTTT 4 97 1 CAATAAAATA 0.68355 -71 ATTACAATTACAAAAAAATATAAGGTTTTG 5 258 1 CAAAAAAATA 0.601192 -24 ATAAACCAAACAACAAAATCAGAAATTCCA 6 75 1 CAACAAAATC 0.86002 -226 CTGAATAATTCAATAAACTTAAATATTCTA 9 44 1 CAATAAACTT 0.73079 -257 ATTAACCAAACAACAAAATTAAAAATCCTA 9 184 1 CAACAAAATT 0.926304 -117 TTTAAATAAACATCAAACTATAAAAATCAT 9 271 1 CATCAAACTA 0.817692 -30 TAATATCAATCATCAAAATTTCTGTTAAAA 12 280 1 CATCAAAATT 0.827284 -21 TAGTGCGTTACAAAAAACTTACTATAGAAA 15 102 0 CAAAAAACTT 0.654513 -158 CAATATCCGACAATAAACATAATGCATTTC 16 32 1 CAATAAACAT 0.442727 -46 TAATGCATTTCAACAAAATCAAAAACTTTA 16 51 1 CAACAAAATC 0.86002 -27 TTGCAGAAATCAACAAAAATACAGTTAATC 18 118 0 CAACAAAAAT 0.786257 -126 ATGCCTTTGGCATCAAAATTCCTTATATGG 22 51 0 CATCAAAATT 0.827284 -210 ********** Masking position 5 Map Score: 8.65633 Number of sites scoring better than the average of aligned sites = 401 Number in coding regions = 348 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 10 GAACGCATTAAATACTTATAAATTTAATCA 3 61 1 AATACTTATA 0.914282 -49 TTTGTATTTTATTGCTTATAGTTTTGGAGT 4 91 0 ATTGCTTATA 0.795925 -77 TAAAATTATAAATCCTTAAACTTTTTGTAT 4 114 0 AATCCTTAAA 0.53605 -54 AGAACTATAAAAAACTTATAATAACTTACT 5 187 1 AAAACTTATA 0.79133 -95 TGTTCAAAACCTTATATTTTTTTGTA 5 266 0 AAACCTTATA 0.780052 -16 ATATTTAAATATAACTTATAAAATTATAGC 6 170 1 ATAACTTATA 0.839244 -131 ATTAATAATAATTCCTTTTAGTGTTTATAA 7 38 1 ATTCCTTTTA 0.613987 -31 TTTTCAGAAAATTACTTATAGAAGTCTGTT 9 235 0 ATTACTTATA 0.93624 -66 TAAATATAGCATTACTTATAATTTTCGTTA 10 152 0 ATTACTTATA 0.93624 -149 TGTATATTATATTACTTATGCAGTATATCA 12 52 1 ATTACTTATG 0.715972 -249 TTATATATCGAATACTTATAGTGCGTTACA 15 120 0 AATACTTATA 0.914282 -140 TGGCATCAAAATTCCTTATATGGTATAAAA 22 44 0 ATTCCTTATA 0.932123 -217 ********** Masking position 1 Map Score: 8.44127 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 55 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 11 GAGCATCAAAATACCAATTATAAAAAATTA 1 198 1 ATACCAATTA 0.872067 -103 TTATAAAATACTACCAATTAGAATTTCTAA 1 251 1 CTACCAATTA 0.82916 -50 TATAAATATAATACAATATACTAAACATTT 3 26 0 ATACAATATA 0.577078 -84 TATCTATGTTATACTATTTATATTCCAAAA 5 152 1 ATACTATTTA 0.747753 -130 AGCTACTTACCTACCATGTATCTCACAAAT 6 197 1 CTACCATGTA 0.796715 -104 CAAATAGATAATACCAAATAATAAAATCCA 18 85 0 ATACCAAATA 0.846928 -159 CCTTATCTACCTACCATTTAATAAAAATAG 18 210 1 CTACCATTTA 0.914666 -34 TCTAAAAAAGATACTATATAATGATTTCTA 20 21 0 ATACTATATA 0.706409 -62 GAAACTATAAAAACCATTTACACAATTATT 21 88 1 AAACCATTTA 0.679308 -63 ACAGCTTTTTATACCATATAAGGAATTTTG 22 38 1 ATACCATATA 0.924352 -223 ********** Masking position 6 Map Score: 2.47817 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 62 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 12 TAAGAATCAGTTTTTAAGGTGGAACG 2 285 1 TTTTTAAGGT 0.942181 -16 CACTGGGGGGTTGTTATGGTTTATTATTTG 5 19 1 TTGTTATGGT 0.824274 -263 TATTATAAGTTTTTTATAGTTCTATATATT 5 180 0 TTTTTATAGT 0.910861 -102 TCTTTAATTTTTTGTATGGTGCCCCTATTA 8 46 1 TTTGTATGGT 0.824274 -255 ATAATTTACTTTTTTAAAGTTATAATTGTT 8 193 0 TTTTTAAAGT 0.892398 -108 TTGCTAATGATTTTTATAGTTTGATGTTTA 9 277 0 TTTTTATAGT 0.910861 -24 TTAACTGCAATTTTTAAGGTAAGAATATAA 15 48 1 TTTTTAAGGT 0.942181 -212 GTGTAAATGGTTTTTATAGTTTCCTAAGCT 21 81 0 TTTTTATAGT 0.910861 -70 CACTAAAAACTTTTTAAGGTTAATAATTGT 21 109 0 TTTTTAAGGT 0.942181 -42 ********** Masking position 5 Map Score: 10.2091 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 36 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 13 GTAGGTAAGTAGCTATAATTTTATAAGTTAT 6 180 0 ACTATAATTT 0.795529 -121 GAGTTTATTTAGCTGTAATTTTATGTCTGAG 10 213 1 ACTGTAATTT 0.939239 -88 TGTTTAATTTGGCTCTATTTTCCTAACAATA 12 196 0 GCTCTATTTT 0.843574 -105 CTCATTCAATACCTCTAATTTT 14 2 0 ACTCTAATTT 0.95306 -88 TTTCAAAATTAACTGCAATTTTTAAGGTAAG 15 40 1 ACTGCAATTT 0.80414 -220 AAAAAAATAGAACTCTATTTTAAGAGTAAAG 15 164 1 ACTCTATTTT 0.95306 -96 CTCAAAATGGAACTCTATTTTGTATGACACT 15 231 0 ACTCTATTTT 0.95306 -29 TTGATGGATTAACTGTATTTTTGTTGATTTC 18 112 1 ACTGTATTTT 0.939239 -132 * ********* Masking position 7 Map Score: 2.27263 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 93 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 14 ********** No masking Map Score: -1.39676e-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: -1.39676e-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