AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -iargR_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 MJ0069 145 acetylglutamate kinase (argB) #2 MJ0429 167 argininosuccinate synthetase (argG) #3 MJ0721 194 acetylornithine aminotransferase (argD) #4 MJ0791 300 argininosuccinate lyase (argH) #5 MJ0881 300 ornithine carbamoyltransferase (argF) #6 MJ1019 132 carbamoyl-phosphate synthase, small (or glutamine) subunit (carA) #7 MJ1096 221 N-acetyl-gamma-glutamyl-phosphate reductase (argC) #8 MJ1097 108 diaminopimelate decarboxylase (lysA) #9 MJ1098 227 RNA maturase isolog #10 MJ1099 205 conserved hypothetical protein #11 MJ1378 184 carbamoyl-phosphate synthase, medium subunit (carB1) #12 MJ1379 196 conserved hypothetical protein #13 MJ1381 124 carbamoyl-phosphate synthase, large subunit (carB2) #14 MJ1495 151 conserved hypothetical protein Motif number 1 AGGTAATTAATAAAAATTAAGATTTTAGATAAAA 1 39 0 TAAATTAAAT 0.889094 -107 TTATTGTTTGATAAATTTTAAATAATTCCTTTAT 1 98 1 AAATTTTAAA 0.700386 -48 TATAGCAATATTAATAAAAATACTTTCACATAAA 3 33 1 TAAAAAAAAT 0.796829 -162 AAAACAACACAAAATATAAATACTTATAATGCAT 3 120 1 AAAATAAAAT 0.878416 -75 CAAAATGATTTTAAAATTAAAAATAAAACTTTTA 3 163 0 TAAATTAAAT 0.889094 -32 GCACCATACAAAAAATTAAAGAATAGTTGGCGAT 4 34 0 AAATTAAAAT 0.848696 -267 ACTTTAAATCATAATATATATAGAGGTTTTGTAT 4 103 0 AAAATATAAA 0.678205 -198 TATTATGATTTAAAGTTAAATAGTAAATTATATA 4 121 1 TAATTAAAAT 0.813155 -180 TAATAAGTTAAAAATTTTAACATATATAATTTAC 4 143 0 AAATTTAAAA 0.911755 -158 ATTAGAATTTTTAATAATAAAACAATTATAACTT 4 173 1 TAAAATAAAA 0.878485 -128 TAAAACAATTATAACTTTAAAAAAGTAAATTATT 4 190 1 AAATTTAAAA 0.911756 -111 TTTTTGATATAAAATTATAAAATAGTTAAAAATA 4 220 0 AAATATAAAA 0.878483 -81 TATCAAAAAATGAAATATAACATAATCAATATTA 4 245 1 TAATATAAAA 0.848696 -56 TATAAAAAATACAATAATAAAACAGTTCTTAAAA 5 31 1 AAAAATAAAA 0.903079 -270 TATAGCACTGAAAAATATAACACAAAGTTAATAA 5 69 1 AAATATAAAA 0.878485 -232 ACAAAGTTAATAAATAAAAAGAATTACAAAAACA 5 90 1 TAAAAAAAAT 0.796944 -211 GGTTATTGAATGAAATTAAATAAATAAGGGCAAT 5 163 0 TAATTAAAAA 0.848694 -138 AGAAACTACAACAATATAAATAATGGCTCATGAT 5 239 1 AAAATAAAAT 0.878416 -62 ATTAACAACCATAAATTATAAAATGCATAATGTC 6 34 1 AAATTATAAT 0.55929 -99 AGAATAGATAAAAAATTAAAGATTGGA 7 4 0 AAATTAAAAT 0.848696 -218 ATTTTCAGTTTAAAAAATAAAAGAATAGATAAAA 7 25 0 TAAAATAAAA 0.878485 -197 AAGTTTATTAAAAACTAATAAAATCTAAACGCCT 7 120 1 AAATAATAAT 0.470329 -102 TCTTTATATGATAAAATAAAAATAACGCCCGGGA 8 80 0 AAAATAAAAA 0.903079 -29 TAAAAAGAAAACAAAATTAAAAATTATAAAAAT 9 10 0 AAAATTAAAT 0.911756 -218 TCAATAGAAAAGAAGTATAAAAGAACAAAAATTG 9 80 1 AAATATAAAA 0.878485 -148 CATCCATATAAGAAGAATAAAAAAAGAATGGGTT 9 189 1 AAAAATAAAA 0.903079 -39 CATTAATACCTCAATTATTACAAAATGTTTTGAT 10 45 0 TAATATTAAA 0.559288 -161 GTGTTCCTTATTAATTTTAATACTTTTGAAAGAC 10 105 1 TAATTTAAAT 0.861225 -101 GAAAGACATTAAAATTTTAAAACATTAAGTTTTT 10 132 1 AAATTTAAAA 0.911755 -74 ATGATTAATGACAATATATATAAAAACTTAATGT 10 153 0 AAAATATAAA 0.678205 -53 AAGCTCATCCTCAATATTAAGATAATCTGAATAA 11 112 1 TAAATTAAAA 0.911756 -73 TAAGATAATCTGAATAATAATAGTTAAATATATA 11 129 1 TAAAATAAAT 0.84861 -56 ATAATATTTTACAATATTTATATATTTAACTATT 11 147 0 AAAATTTAAA 0.750759 -38 ATAAGATTCATCAAAATTAATATATTTATTTTGG 12 33 0 TAAATTAAAA 0.911756 -164 TGTTAATGCTACAAATATAAGATTCATCAAAATT 12 49 0 AAATATAAAT 0.848696 -148 AGAGGGTTAAAGAAGAATAAGAAATATAGTATAT 12 162 1 AAAAATAAAA 0.903079 -35 TAAAAGATATTGAAAATAAAAAATAGGTGATTAT 13 101 1 TAAATAAAAT 0.848696 -24 GTGTCAATATTCAATAAAAATATTTTTCCTGCGA 14 89 1 TAAAAAAAAT 0.796829 -63 TTCATGAATATAAATATAGTTGCCTTAT 14 134 0 TAAATAAAAA 0.878416 -18 * ** ***** * * Masking position 10 Map Score: 51.0184 Number of sites scoring better than the average of aligned sites = 2664 Number in coding regions = 1758 Number in noncoding regions = 906 Number of orfs with sites within 600 bp upstream = 554 Fraction of orfs with sites within 600 bp upstream = 0.0889817 Motif number 2 ACTAAGGTAATTAATAAAAATTAAGATTTTAG 1 45 0 TTAATAAATT 0.860413 -101 AAAGGAATTATTTAAAATTTATCAAACAATAA 1 98 0 TTTAAAATAT 0.749706 -48 AGTTTAAGGATTTATAATTTTATGTAAGATAT 2 122 1 TTTATAATTA 0.777437 -46 TATGTAAGATATAAAAATATTTTGTGAGGGAT 2 142 1 ATAAAAATTT 0.776385 -26 TATAGCAATATTAATAAAAATACTTTCACATA 3 33 1 TTAATAAATA 0.777437 -162 ATACTTTCACATAAAAATGTTTTGTTGGTGAC 3 52 1 ATAAAAATTT 0.776385 -143 GTTGAGTATTTTAATCATTTTTGATATGGTTT 3 86 0 TTAATCATTT 0.830224 -109 GAAGTAATGCATTATAAGTATTTATATTTTGT 3 128 0 ATTATAAATT 0.6996 -67 GATTTTAAAATTAAAAATAAAACTTTTAAGGG 3 159 0 TTAAAAAAAA 0.629319 -36 TATTTTTAATTTTAAAATCATTTTGGTGATTA 3 172 1 TTTAAAAATT 0.779334 -23 TTCTAATAAGTTAAAAATTTTAACATATATAA 4 148 0 TTAAAAATTA 0.791066 -153 ATTAGAATTTTTAATAATAAAACAATTATAAC 4 173 1 TTAATAAAAA 0.682975 -128 TAATAAAACAATTATAACTTTAAAAAAGTAAA 4 187 1 ATTATAATTA 0.644791 -114 TATAAAATAGTTAAAAATAATTTACTTTTTTA 4 207 0 TTAAAAAATT 0.829281 -94 TTTTAACTATTTTATAATTTTATATCAAAAAA 4 223 1 TTTATAATTA 0.777437 -78 GAAATATAACATAATCAATATTATTTAAACAC 4 256 1 ATAATCAATT 0.648828 -45 TCAATATTATTTAAACACGATTAAAATGCATT 4 270 1 TTAAACAATT 0.736972 -31 TATTGTATTTTTTATAATAAATTAACTGTTTA 5 15 0 TTTATAAAAT 0.73432 -286 AAAACAGTTCTTAAAAAACTTATAGCACTGAA 5 49 1 TTAAAAATTA 0.791066 -252 AAGTTAATAAATAAAAAGAATTACAAAAACAT 5 93 1 ATAAAAAATT 0.716257 -208 CAATTAACTATTAATAATATTTGATGTTTTTG 5 116 0 TTAATAATTT 0.894492 -185 ATTTATGGGAATTAACAATTAACTATTAATAA 5 131 0 ATTAACATAA 0.337194 -170 TTTTATACTATTAAAAACTATTTTATATTATC 5 270 0 TTAAAAAATT 0.829281 -31 TTTATCACCTTTTATACTATTA 5 289 0 TTTATCATTT 0.78048 -12 CATTATGCATTTTATAATTTATGGTTGTTAAT 6 34 0 TTTATAATAT 0.791698 -99 TATGATTGGGATAATCATCTATCTACTGCTTT 6 73 0 ATAATCATAT 0.61048 -60 AAAAGAATAGATAAAAAATTAAAGATTGGA 7 9 0 ATAAAAATAA 0.548072 -213 TATTTTCAGTTTAAAAAATAAAAGAATAGATA 7 28 0 TTAAAAAAAA 0.62925 -194 ATAGATGCTCTTTATAATATTTTCAGTTTAAA 7 45 0 TTTATAATTT 0.860413 -177 ATCTATTAGATTTAAAAGGAATCCATCTAAAA 7 71 1 TTTAAAAAAT 0.685351 -151 TTATTAGTTTTTAATAAACTTTTTGTAAAAAA 7 109 0 TTAATAATTT 0.894492 -113 GTTCAAAGGTTTTATAAAAAATCTTAAATTAT 7 197 1 TTTATAAAAT 0.73432 -25 TTATTTTTATTTTATCATATAAAGAATTGG 8 89 1 TTTATCATAA 0.554093 -20 ATTTTTATAATTTTTAATTTTGTTT 9 4 1 TTTATAATTT 0.860412 -224 TTGTTTTCTTTTTATAATGTTAGGGAAATTTT 9 30 1 TTTATAATTA 0.777437 -198 TCAATCATACTTAATAAAATTTCCCTAACATT 9 45 0 TTAATAATTT 0.894492 -183 TCTACGCCTATTAATAAGCAATTTTTGTTCTT 9 100 0 TTAATAAAAT 0.791734 -128 TTAATCACCTTTGCTATAATCA 10 1 1 TTAATCATTT 0.830225 -205 CACCTTTGCTATAATCATTAAAGATAATAATC 10 16 1 ATAATCAAAA 0.392313 -190 ATCATTAAAGATAATAATCAAAACATTTTGTA 10 29 1 ATAATAAAAA 0.528196 -177 TTTCAAAAGTATTAAAATTAATAAGGAACACT 10 104 0 ATTAAAAAAT 0.530905 -102 AACTTAATGTTTTAAAATTTTAATGTCTTTCA 10 131 0 TTTAAAATTA 0.733531 -75 GACAATATATATAAAAACTTAATGTTTTAAAA 10 146 0 ATAAAAATAA 0.548217 -60 TATATTGTCATTAATCATTTTTGAAATCAATA 10 169 1 TTAATCATTT 0.830224 -37 ATTATCACCATTTACCTACCAT 11 1 1 ATTATCAATT 0.573255 -184 ACCATTAACTTTAAAAACCTTAACTGATTATT 11 28 1 TTAAAAATTA 0.791066 -157 TATTTGTAGCATTAACATTATTGGCTTTAATA 12 66 1 ATTAACAATT 0.514236 -131 TTGAGATAGTTTTAAAAGATATTGAAAATAAA 13 89 1 TTTAAAATAT 0.74974 -36 ATAATCACCTATTTTTTATTTT 13 113 0 ATAATCATAT 0.61048 -12 TCAATATTCAATAAAAATATTTTTCCTGCGAA 14 92 1 ATAAAAATTT 0.776385 -60 ******* *** Masking position 7 Map Score: 52.1457 Number of sites scoring better than the average of aligned sites = 3458 Number in coding regions = 2402 Number in noncoding regions = 1056 Number of orfs with sites within 600 bp upstream = 639 Fraction of orfs with sites within 600 bp upstream = 0.102634 Motif number 3 TTTAGATTGATTATTGACAGTTATTATTAGCAGTT 2 31 1 TTATTGGATT 0.710913 -137 ATCCTTAAACTTTTTGTATTTTATTGCTTATAGTT 2 98 0 TTTTTGTATT 0.921744 -70 ATATAAAAATATTTTGTGAGGGATTGTC 2 150 1 ATTTTGGATT 0.775555 -18 ATTTTTATTAATATTGCTATAATTAATCTTTTTGG 3 19 0 ATATTGTTTA 0.778696 -176 ATTTTAATCATTTTTGATATGGTTTAAGTCACCAA 3 76 0 TTTTTGTTTT 0.927641 -119 AAGTATTTATATTTTGTGTTGTTTTTTGTTGAGTA 3 110 0 ATTTTGTTTT 0.933126 -85 TATATTTCATTTTTTGATATAAAATTATAAAATAG 4 229 0 TTTTTGTAAT 0.560576 -72 AACTGTTTTATTATTGTATTTTTTATAATAAATTA 5 23 0 TTATTGTTTA 0.763761 -278 TTATTTATTAACTTTGTGTTATATTTTTCAGTGCT 5 72 0 ACTTTGTATT 0.52734 -229 ATATTTGATGTTTTTGTAATTCTTTTTATTTATTA 5 97 0 TTTTTGTTTT 0.927641 -204 ATTCCCATAAATATTGCCCTTATTTATTTAATTTC 5 151 1 ATATTGTTTT 0.915314 -150 GTTTATGTGGTTATTGAATGAAATTAAATAAATAA 5 170 0 TTATTGGATT 0.710909 -131 GCCATTATTTATATTGTTGTAGTTTCTTACGTAAT 5 231 0 ATATTGTTTT 0.915314 -70 ATAATTTTTAATTTTGTTTTCTTTTTATAATGTTA 9 17 1 ATTTTGTTTT 0.933126 -211 TAATAAGCAATTTTTGTTCTTTTATACTTCTTTTC 9 86 0 TTTTTGTTAT 0.581534 -142 TAATCAAAACATTTTGTAATAATTGAGGTATTAAT 10 43 1 ATTTTGTTTG 0.624208 -163 GTTTTTATATATATTGTCATTAATCATTTTTGAAA 10 160 1 ATATTGTATC 0.541733 -46 TCATTAATCATTTTTGAAATCAATATCATGGGTGT 10 176 1 TTTTTGTATA 0.793162 -30 TTGTAAAATATTATTGTGGTGGATATTG 11 167 1 TTATTGTATA 0.748135 -18 TAATATATTTATTTTGGTTTCTTTTTTCATAATTT 12 15 0 ATTTTGTTTT 0.933126 -182 AGCATTAACATTATTGGCTTTAATAACTGGAAGAA 12 73 1 TTATTGTATA 0.748135 -124 TTCATAAATATTTTGGGATTGATTATATCCTTCT 13 10 1 ATTTTGTATT 0.927641 -115 TTTTTATTGAATATTGACACTCTTTGAGTGTCTAA 14 74 0 ATATTGCTTT 0.520789 -78 ****** * *** Masking position 5 Map Score: 20.7008 Number of sites scoring better than the average of aligned sites = 474 Number in coding regions = 383 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 4 CTTATCTCACCAACTACCAAAAA 1 3 1 TATTCACCAA 0.984674 -143 TTTATCCCCAAAAATTTCTAT 2 1 1 TTTTCCCCAA 0.90154 -167 GGAGTATATATAACTCACCTATTATATATAA 2 65 0 TAATCACCTA 0.803758 -103 ACTTATCACCAAAAAGATTAAT 3 2 1 CTTTCACCAA 0.949691 -193 TGATATGGTTTAAGTCACCAACAAAACATTT 3 66 0 TAATCACCAA 0.966689 -129 TTAATCACCAAAATGATTTTA 3 184 0 TTATCACCAA 0.952053 -11 ATTTTCCACATTTTTCACAAATGTAATAATA 4 75 1 TTTTCACAAA 0.792058 -226 TATTTCACCAATGCATTTTAA 4 290 0 TATTCACCAA 0.984674 -11 GTCTATTCACCATTTCATCAATTATTAACAA 6 11 1 CATTCATCAA 0.707169 -122 ATATTTCACCAAAATACCTATA 6 121 0 TATTCACCAA 0.984674 -12 *** ******* Masking position 5 Map Score: 11.3401 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 82 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 5 TACTGCTTTTAGAGGACATTATGCATTTTAT 6 51 0 AGAGGACTTA 0.926117 -82 GCCTTCCTATAGAAGCCATTCATTATATTCC 7 150 1 AGAAGCCTTC 0.96695 -72 GTCTTCTTATAGAAGGCGTTCATTAATACCT 10 68 0 AGAAGGCTTC 0.96695 -138 GCCTTCTATAAGAAGACGTTCAAGTGTTCCT 10 82 1 AGAAGACTTC 0.987658 -124 AGATAGTTAAAGAAGACGTTCCTAAAATAAA 13 50 1 AGAAGACTTC 0.987658 -75 GTGATGATAAATAGGACTTTCGCAGTTTATG 14 29 1 ATAGGACTTC 0.963445 -123 TGCCTTATTAATAGGACTTTCGCAGGAAAAA 14 111 0 ATAGGACTTC 0.963445 -41 ******* *** Masking position 3 Map Score: 7.69091 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 12 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 TATCAAACAATAACTTTAAATAATAGAAGC 1 81 0 TAACTTTAAA 0.946632 -65 TATTGTTTGATAAATTTTAAATAATTCCTT 1 99 1 TAAATTTTAA 0.628826 -47 GTTTTATTTTTAATTTTAAAATCATTTTGG 3 168 1 TAATTTTAAA 0.951224 -27 ATTTACTATTTAACTTTAAATCATAATATA 4 119 0 TAACTTTAAA 0.946632 -182 AAAACAATTATAACTTTAAAAAAGTAAATT 4 191 1 TAACTTTAAA 0.946632 -110 AACTATTTTATAATTTTATATCAAAAAATG 4 227 1 TAATTTTATA 0.625281 -74 TAATATAAAATAGTTTTTAATAGTATAAAA 5 272 1 TAGTTTTTAA 0.791314 -29 GAGCATCTATTAGATTTAAAAGGAATCCAT 7 67 1 TAGATTTAAA 0.728791 -155 TAGATTTTATTAGTTTTTAATAAACTTTTT 7 117 0 TAGTTTTTAA 0.791314 -105 ATTTTTATAATTTTTAATTTTGTTTTC 9 8 1 TAATTTTTAA 0.872253 -220 TGTTCCTTATTAATTTTAATACTTTTGAAA 10 106 1 TAATTTTAAT 0.640969 -100 AAAGACATTAAAATTTTAAAACATTAAGTT 10 133 1 AAATTTTAAA 0.640969 -73 TACCTACCATTAACTTTAAAAACCTTAACT 11 23 1 TAACTTTAAA 0.946632 -162 TTATGTTACTTAACTTTAAGTATCCTTTTC 11 62 0 TAACTTTAAG 0.706457 -123 TATAGTTATGCAATTTTAAAAGCTCATCCT 11 93 1 CAATTTTAAA 0.725726 -92 GAAGTTGAGATAGTTTTAAAAGATATTGAA 13 85 1 TAGTTTTAAA 0.915471 -40 ********** Masking position 5 Map Score: 17.3872 Number of sites scoring better than the average of aligned sites = 573 Number in coding regions = 399 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 7 CCATTCATTATATTCCTCTTACTATAAGGT 7 165 1 TATTCCTCTT 0.968443 -57 TTTGTTCTTTTATACTTCTTTTCTATTGAT 9 79 0 TATACTTCTT 0.936104 -149 ATTCTTTTTTTATTCTTCTTATATGGATGC 9 188 0 TATTCTTCTT 0.973696 -40 TATTCTTCTTTAACCCTCTTTAATGCCAAT 12 151 0 TAACCCTCTT 0.890985 -46 CTATATTTCTTATTCTTCTTTAACCCTCTT 12 161 0 TATTCTTCTT 0.973696 -36 GGATTGATTATATCCTTCTTTGGAAGATAG 13 26 1 TATCCTTCTT 0.975586 -99 ********** Masking position 7 Map Score: 4.89456 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 86 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 TTAGTTACGGCTTCTATTATTTAAAGTTATT 1 72 1 CTCTATTATT 0.961297 -74 ATATATAACTCACCTATTATATATAAACTGC 2 60 0 CCCTATTATA 0.847869 -108 GGAGCGTCATCGCCAACTATTCTTTAATTTT 4 26 1 CCCAACTATT 0.863408 -275 TTGTATGGTGCCCCTATTATTTTCCACATTT 4 57 1 CCCTATTATT 0.975375 -244 ATTACAAAAACATCAAATATTATTAATAGTT 5 112 1 CTCAAATATT 0.727847 -189 TTGCAAATATCGTCTATCATTACGTAAGAAA 5 213 1 CTCTATCATT 0.838183 -88 TTCACCATTTCATCAATTATTAACAACCATA 6 16 1 CTCAATTATT 0.944336 -117 ATCATTTCTACGCCTATTAATAAGCAATTTT 9 107 0 CCCTATTAAT 0.847869 -121 TTCATTAATACCTCAATTATTACAAAATGTT 10 50 0 CTCAATTATT 0.944337 -156 ATAATCACCTATTTTTTATTTTCAAT 13 109 0 CCCTATTTTT 0.847869 -16 * ********* Masking position 6 Map Score: 7.2431 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 101 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 TTTATCCACTCATAAACTTAAAAGGTTTT 1 127 1 CATAAACTAA 0.95491 -19 ACCTATTATATATAAACTGCTAATAATAACTGT 2 47 0 TATAAACGAA 0.926302 -121 TTATATCTTACATAAAATTATAAATCCTTAAAC 2 123 0 CATAAAATAA 0.871208 -45 CCAAAATGATTTTAAAATTAAAAATAAAACTTT 3 165 0 TTTAAAATAA 0.649356 -30 CATTTTTTGATATAAAATTATAAAATAGTTAAA 4 224 0 TATAAAATAA 0.78724 -77 TTCTTAAACAGTTAATTTATTATAA 5 3 1 CTTAAACGAA 0.922077 -298 AAAAGAATTACAAAAACATCAAATATTATTAAT 5 106 1 CAAAAACTAA 0.659735 -195 TCAATAACCACATAAACGTGTAATTTTGCAAAT 5 188 1 CATAAACTAA 0.954914 -113 TCTTTTATTTTTTAAACTGAAAATATTATAAAG 7 35 1 TTTAAACGAA 0.866013 -187 TCCCTAACATTATAAAAAGAAAACAAAATTAAA 9 23 0 TATAAAAGAA 0.800569 -205 TCACCTTTGCTATAATCATTAAAGATAATAATC 10 15 1 TATAATCTAA 0.514606 -191 AACTTAATGTTTTAAAATTTTAATGTCTTTCAA 10 130 0 TTTAAAATAA 0.649356 -76 ATTTACCTACCATTAACTTTAAAAACCTTAACT 11 20 1 CATTAACTAA 0.659703 -165 TTTATCATCACTTAAACTGGTGATTGACT 14 7 0 CTTAAACGGA 0.616202 -145 CAAATTTATACATAAACTGCGAAAGTCCTATTT 14 37 0 CATAAACGAA 0.958291 -115 ******* * ** Masking position 5 Map Score: 10.5724 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 191 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 10 TTTCTATTTAGATTGATTATTGACAGTTAT 2 25 1 GATTGATTAT 0.957781 -143 TTTTGTATTTTATTGCTTATAGTTTTGGAG 2 92 0 TATTGCTTAT 0.825601 -76 TCACCAAAAAGATTAATTATAGCAATATTA 3 16 1 GATTAATTAT 0.759151 -179 TGTTGTTTTTTGTTGAGTATTTTAATCATT 3 99 0 TGTTGAGTAT 0.829253 -96 GTTTAAATAATATTGATTATGTTATATTTC 4 256 0 TATTGATTAT 0.965006 -45 AGGGAAATTTTATTAAGTATGATTGAGTAT 9 51 1 TATTAAGTAT 0.78181 -177 TATTAAGTATGATTGAGTATCAATAGAAAA 9 61 1 GATTGAGTAT 0.954987 -167 TTATTATCTTTAATGATTATAGCAAAGGTG 10 16 0 TAATGATTAT 0.761567 -190 TTACAAAATGTTTTGATTATTATCTTTAAT 10 32 0 TTTTGATTAT 0.777968 -174 ATTATCTTAATATTGAGGATGAGCTTTTAA 11 108 0 TATTGAGGAT 0.815743 -77 AATATTTTGGGATTGATTATATCCTTCTTT 13 17 1 GATTGATTAT 0.957781 -108 AAAATATTTTTATTGAATATTGACACTCTT 14 85 0 TATTGAATAT 0.831701 -67 ********** Masking position 9 Map Score: 9.18843 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 119 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 11 AGCCCGGGTCGCCTAGCCAGG 8 2 1 GCCCGGGTCG 0.997796 -107 TAAAAATAACGCCCGGGAGGGGATTTGAAC 8 68 0 GCCCGGGAGG 0.992862 -41 AAATGATAAAGCCCGGGTCGCCTAGCCAGA 9 131 1 GCCCGGGTCG 0.997796 -97 ********** Masking position 5 Map Score: 2.40908 Number of sites scoring better than the average of aligned sites = 2 Number in coding regions = 0 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 12 TCTCACCAACTACCAAAAATCTCGTTTTATC 1 15 1 TACCAAAAAC 0.867154 -131 AATCTCGTTTTATCTAAAATCTTAATTTTTA 1 32 1 TATCTAAAAC 0.31365 -114 ACTTATCACCAAAAAGATTAATTATAG 3 7 1 CACCAAAAAA 0.96568 -188 TGGTTTAAGTCACCAACAAAACATTTTTATG 3 61 0 CACCAACAAA 0.84124 -134 TTAAAATACTCAACAAAAAACAACACAAAAT 3 104 1 CAACAAAAAC 0.808304 -91 TTAATCACCAAAATGATTTTAAAATT 3 179 0 CACCAAAATA 0.959478 -16 ATATTTCACCAAAATACCTATAAACTA 6 116 0 CACCAAAATC 0.969489 -17 AAAAGGAATCCATCTAAAATCCTGTTTTTTT 7 84 1 CATCTAAAAC 0.725539 -138 CAATATCCACCACAATAATATTTTACAA 11 167 0 CACCACAATA 0.816818 -18 TGAAAAAAGAAACCAAAATAAATATATTAAT 12 21 1 AACCAAAATA 0.69891 -176 ATATAAGATTCATCAAAATTAATATATTTAT 12 38 0 CATCAAAATA 0.869808 -159 ********* * Masking position 8 Map Score: 2.6214 Number of sites scoring better than the average of aligned sites = 405 Number in coding regions = 322 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 13 AGCCCGGGTCGCCTAGCCAGGATAGGGCGC 8 11 1 GCCTAGCCAG 0.994314 -98 GCGCTGGCCTGCGGAGCCAGTTTTTTCAGG 8 37 1 GCGGAGCCAG 0.987625 -72 AGCCCGGGTCGCCTAGCCAGATAGCATGGG 9 140 1 GCCTAGCCAG 0.994314 -88 ********** Masking position 5 Map Score: 0.749726 Number of sites scoring better than the average of aligned sites = 2 Number in coding regions = 0 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 14 TTAATTTTTATTAATTACCTTAGTTACGGCTT 1 53 1 TTATTCCTTA 0.962845 -93 TAAATTTTAAATAATTCCTTTATCCACTCATA 1 109 1 ATATTCTTTA 0.678189 -37 TTATAATGCATTACTTCCCTTAAAAGTTTTAT 3 143 1 TTATTCCTTA 0.962846 -52 GGTGCCCCTATTATTTTCCACATTTTTCACAA 4 63 1 TTATTCCACA 0.697649 -238 TAGTTAATTGTTAATTCCCATAAATATTGCCC 5 138 1 TTATTCCATA 0.930753 -163 ATTCCCATAAATATTGCCCTTATTTATTTAAT 5 151 1 ATATGCCTTA 0.883447 -150 CCTTATTTATTTAATTTCATTCAATAACCACA 5 168 1 TTATTCATTC 0.655003 -133 TCAAAAATGATTAATGACAATATATATAAAAA 10 161 0 TTATGCAATA 0.825139 -45 AGCATTAACATTATTGGCTTTAATAACTGGAA 12 73 1 TTATGCTTTA 0.829825 -124 AATTAATGGATTATTGGCATTAAAGAGGGTTA 12 139 1 TTATGCATTA 0.900973 -58 CACCTATTTTTTATTTTCAATATCTTTTAAAA 13 98 0 TTATTCAATA 0.851545 -27 GAATATAAATATAGTTGCCTTATTAATAGGAC 14 125 0 ATATTCCTTA 0.902093 -27 *** ** ***** Masking position 3 Map Score: 7.15842 Number of sites scoring better than the average of aligned sites = 287 Number in coding regions = 246 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 15 ********** No masking Map Score: 4.32964e-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