AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00251_mjan_reg_300.orf -o00251_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 Input sequences: #1 MJ0002 300 M. jannaschii predicted coding region MJ0002 #2 MJ0050 109 group II decarboxylase #3 MJ0202 56 conserved hypothetical protein #4 MJ0203 120 phosphoribosylformylglycinamidine cyclo-ligase (purM) #5 MJ0204 99 amidophosphoribosyltransferase (purF) #6 MJ0684 68 aspartate aminotransferase (aspB2) #7 MJ1019 132 carbamoyl-phosphate synthase, small (or glutamine) subunit (carA) #8 MJ1132 188 conserved hypothetical protein #9 MJ1345 300 O-linked GlnNAc transferase #10 MJ1346 87 glutamine synthetase (glnA) #11 MJ1351 300 glutamate synthase (gltB) #12 MJ1352 300 NH(3)-dependent NAD+ synthetase (nadE) #13 MJ1377_MJ1378 184 MJ1377: glutamyl-tRNA synthetase (gltX), MJ1378: carbamoyl-phosphate synthase, medium subunit (carB1) #14 MJ1379 196 conserved hypothetical protein #15 MJ1381 124 carbamoyl-phosphate synthase, large subunit (carB2) #16 MJ1420 100 glucosamine--fructose-6-phosphate aminotransferase (isomerizing) (glmS) #17 MJ1479 259 putative aminotransferase #18 MJ1575 300 GMP synthase (guaA) Motif number 1 CAGTAGCACTAAATATAATATATCCAATCA 1 64 1 AAATATAATA 0.896908 -237 TCAAAATACCAATTATAAAAAATTATATAA 1 203 1 AATTATAAAA 0.940077 -98 AATTATAAAAAATTATATAAAAAATTACAT 1 213 1 AATTATATAA 0.86523 -88 TAATATCTCCAAAATTATTAGAAATTCTAA 1 268 0 AAAATTATTA 0.433167 -33 TCTTAGGTATAAATATAATACAATATACTA 2 33 0 AAATATAATA 0.896908 -77 CATCATGATTAAATTTATAAGTATTTAATG 2 66 0 AAATTTATAA 0.781653 -44 AAGAATTAGTAAAATTAAAAAGATAATTTA 5 14 0 AAAATTAAAA 0.712197 -86 AACAACCATAAATTATAAAATGCATAATGT 7 37 1 AATTATAAAA 0.940077 -96 CTTTGCAAAAAACTATAAAAACTTTGGTGG 8 15 0 AACTATAAAA 0.785516 -174 TTCCTTAATAAATTTTATTACTTTGCAAAA 8 35 0 AATTTTATTA 0.785283 -154 TTTCTTAGCCAATTTTAATATTAATCTTAT 8 142 1 AATTTTAATA 0.899373 -47 ATAAAAATTTAATTATAAAAGTCCATAAAT 9 49 0 AATTATAAAA 0.940077 -252 ATATAATTATAAATATAAAAATTTAATTAT 9 63 0 AAATATAAAA 0.920581 -238 TTATATTTATAATTATATTATAGCGTATAA 9 75 1 AATTATATTA 0.828074 -226 ACACTAAAATAATTTTAATAAATAATATCA 9 218 1 AATTTTAATA 0.899373 -83 ATTTAAATTAAAATATAAAAAT 10 3 0 AAATATAAAA 0.920581 -85 TTAAAAGATTAAAAATAAAAACATGAGGAA 11 273 1 AAAAATAAAA 0.766284 -28 AATAATAGTTAAATATATAAATATTGTAAA 13 32 0 AAATATATAA 0.825874 -153 AGATAATCTGAATAATAATAGTTAAATATA 13 45 0 AATAATAATA 0.770091 -140 ATAGTTATGCAATTTTAAAAGCTCATCCTC 13 82 0 AATTTTAAAA 0.922141 -103 ACCTACCATTAACTTTAAAAACCTTAACTG 13 152 0 AACTTTAAAA 0.734337 -33 TGGGAAATTATGAAAAAAGAAACCA 14 6 1 AATTATGAAA 0.680629 -191 AAACCAAAATAAATATATTAATTTTGATGA 14 30 1 AAATATATTA 0.781317 -167 ATTCTCTTTTAAATATATTATATA 16 5 0 AAATATATTA 0.781317 -96 CATAAACAATAATATTAATACTAATTTTAA 16 38 0 AATATTAATA 0.716574 -63 AATTGCAGTTAATTTTGAAAAGCACGATAA 17 30 0 AATTTTGAAA 0.616637 -230 TAATAAAAGAAATTTTAAAATATAGTGTCT 18 42 1 AATTTTAAAA 0.922141 -259 TGTTAAAATTAATATTAATAATGGATATTT 18 80 1 AATATTAATA 0.716574 -221 ********** Masking position 6 Map Score: 31.8331 Number of sites scoring better than the average of aligned sites = 1021 Number in coding regions = 674 Number in noncoding regions = 347 Number of orfs with sites within 600 bp upstream = 327 Fraction of orfs with sites within 600 bp upstream = 0.0525217 Motif number 2 TGGTTTGTTGATAATGGTTTTCACCAATCCCAG 1 11 0 ATAATGGTTA 0.633866 -290 GTTGACGCATTGATTGGATATATTATATTTAGT 1 71 0 TGATTGGATT 0.654339 -230 GTTTAGTTAATTAAAGGTTTATTTGGATTGTTT 1 104 0 TTAAAGGTAT 0.528171 -197 TAATTTTTTATAATTGGTATTTTGATGCTCTAT 1 195 0 TAATTGGTTT 0.895382 -106 TAGTATTTTATAATAGGACTTATGTAATTTTTT 1 231 0 TAATAGGATT 0.726162 -70 TTAGAAATTCTAATTGGTAGTATTTTATAATAG 1 248 0 TAATTGGTTT 0.895386 -53 TCCATAATGCAAATTGGATGTTTAAAAAATTTT 4 48 1 AAATTGGATT 0.759901 -73 TTATAAACACTAAAAGGAATTATTATTAATTAA 6 35 0 TAAAAGGATT 0.862625 -34 TTAGTGTTTATAAATGGTGATGTC 6 55 1 TAAATGGTTT 0.95298 -14 ATGTGATAGTTTATAGGTATTTTGGTGAAATAT 7 110 1 TTATAGGTTT 0.690172 -23 ATTTTAGGATAAAAAGGTATTTATGAACGCCTT 8 87 0 AAAAAGGTTA 0.633248 -102 ATGCTAAATGGTCCTTTCGCAATAGCA 11 5 1 TAAATGGTTT 0.95298 -296 TTAATCTTTATGAATGGAGATATTGAGAAAGAC 11 56 1 TGAATGGATT 0.817605 -245 TCAGCTGCAATTAATGGTCTTAACTTAATTCTA 11 112 0 TTAATGGTTA 0.740058 -189 TTTATTTCAATAAATGGTTCATTAAT 12 4 0 TAAATGGTAT 0.811355 -297 TTAAAAATTGAGAATGGTGATTTAGTTAAGGTG 12 56 1 AGAATGGTTT 0.817605 -245 GAAGACATTAAAAAAGGAGTTGTATTTATGCCA 12 131 1 AAAAAGGATT 0.792467 -170 TAATGGTAGGTAAATGGTGATAAT 13 171 1 TAAATGGTTA 0.847869 -14 ATATGTGTAATTAATGGATTATTGGCATTAAAG 14 131 1 TTAATGGAAT 0.571924 -66 TGAAAATAAAAAATAGGTGATTAT 15 111 1 AAATAGGTTA 0.421701 -14 TACTACTGGGATAATGGTAAATTACACAAAAGT 17 201 1 ATAATGGTAT 0.571924 -59 TTTTCATCTCAAAATGGAACTCTATTTTGTATG 17 236 0 AAAATGGATT 0.882278 -24 ATTAATATTAATAATGGATATTTGAACGCTCTC 18 87 1 ATAATGGATT 0.792892 -214 AACCTTTTACTAAAAGGTTCTTTCAAAATGTTT 18 245 1 TAAAAGGTTT 0.91171 -56 ******** * * Masking position 3 Map Score: 19.113 Number of sites scoring better than the average of aligned sites = 559 Number in coding regions = 498 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 3 AAATAAATTATCTTTTTAATTTTACTAAT 5 7 1 ATTCTTTTAA 0.789233 -93 TAAAATGCATAATGTCCTCTAAAAGCAGTAGAT 7 52 1 ATTCCTTAAA 0.924214 -81 AAGTTTTTATAGTTTTTTGCAAAGTAATAAAAT 8 21 1 ATTTTTCAAA 0.918058 -168 TTTATCCTAAAATGTTTTGCAAAAAACTATATA 8 107 1 ATTTTTCAAA 0.918058 -82 GTCTTCTTTAACTATCTTCCAAAGAAGGATATA 15 34 0 ATTCTTCAAA 0.988833 -91 TTTTATTTTCAATATCTTTTAAAACTATCTCAA 15 89 0 ATTCTTTAAA 0.972366 -36 ATTTTAAATAATTCTCTTTTAAATATATTATAT 16 12 0 ATTCTTTAAA 0.972366 -89 GATAAACCTAAATATCTCCTAAAGTAATAAATA 16 77 0 ATTCTCTAAA 0.847327 -24 ATTACACAAAAGTGTCATACAAAATAGAGTTCC 17 221 1 ATTCATCAAA 0.918375 -39 TTTTATTATGATTATCCTCCAAATTTATTGAAG 18 17 0 ATTCCTCAAA 0.968443 -284 TTTAAAATATAGTGTCTTTCAAAGTTGTTAAAA 18 55 1 ATTCTTCAAA 0.988833 -246 TTTTACTAAAAGGTTCTTTCAAAATGTTTTTGA 18 249 1 AGTCTTCAAA 0.933184 -52 ATATTTTATTAGTATCTTTCAAAAACATTTTGA 18 267 0 ATTCTTCAAA 0.988833 -34 * * **** **** Masking position 12 Map Score: 16.3745 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 165 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 4 GGAACGCTGAAATATTTCCAGTAGCACTAA 1 46 1 AATATTTCCA 0.959388 -255 CACTAAATATAATATATCCAATCAATGCGT 1 70 1 AATATATCCA 0.914506 -231 TTGGATTTTTAATATCTCCAAAATTATTAG 1 277 0 AATATCTCCA 0.956696 -24 AATATCTCCTCATTATTTGT 4 111 0 AATATCTCCT 0.926474 -10 ATTAATTAATAATAATTCCTTTTAGTGTTT 6 34 1 AATAATTCCT 0.797703 -35 TTATTTCCATATTATTTCCACATTAGTTTA 9 146 0 ATTATTTCCA 0.90805 -155 GATATTTTCTTTTATTTCCATATTATTTCC 9 157 0 TTTATTTCCA 0.760221 -144 TGTCTTTCTCAATATCTCCATTCATAAAGA 11 60 0 AATATCTCCA 0.956696 -241 TTAATCTTTGTTTATTTCCAAGGTCTTGCT 11 247 0 TTTATTTCCA 0.760221 -54 CATTTATTGAAATAAATCCAGATGATGCCA 12 21 1 AATAAATCCA 0.7579 -280 TAATAGGAATCATATTTCCTA 12 290 1 CATATTTCCT 0.717304 -11 TAATTACACATATAATTCCAACTAAAGTTA 14 114 0 TATAATTCCA 0.689403 -83 TTTGGGATTGATTATATCCTTCTTTGGAAG 15 22 1 ATTATATCCT 0.718345 -103 GATAAACCTAAATATCTCCTAAAGTAATAA 16 80 0 AATATCTCCT 0.926474 -21 ********** Masking position 4 Map Score: 15.2095 Number of sites scoring better than the average of aligned sites = 378 Number in coding regions = 343 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 5 TCAATGCGTCAACAAACAATCCAAATAAACCTTTAATTA 1 91 1 AAAAAATAAA 0.962215 -210 ATTTTAAGATAAGTTATAAATAAATCTTCAAACT 3 33 0 AAAAAATAAA 0.962214 -24 GAAAATTAAGAAGAATTAGTAAAATTAAAAAGATAATTT 5 15 0 AAAAATTAAA 0.913005 -85 TTTATTTGCTAAAAGTCTAAAAAACTAAAAAAGGGTTTT 5 67 1 AAAAACTAAA 0.763562 -33 TGCCACCACGAAAAGTATTATTAATTAATAATAATTCCT 6 15 1 AAAAATTAAT 0.833643 -54 ACCATTTATAAACACTAAAAGGAATTATTATTAATTAAT 6 34 0 AAAAATTATT 0.60586 -35 ATGTGGAAATAATATGGAAATAAAAGAAAATATCCAGTA 9 153 1 AAAAAAGAAA 0.69881 -148 TTTACACTAAAATAATTTTAATAAATAATATCATAGTAA 9 215 1 AAAAAATAAT 0.905109 -86 ATTAATGAACCATTTATTGAAATAAATCCAGATGAT 12 8 1 AACAAATAAA 0.69881 -293 CCAAAGCAAGAATAACTGAAGACATTAAAAAAGGAGTTG 12 114 1 AAACATTAAA 0.738825 -187 CTATTATATAAACAATTCTATAAATTAAATTCGTTCAAT 12 257 0 AAAAATTAAA 0.913005 -44 TATCCACCACAATAATATTTTACAATATTTATATATTTA 13 14 1 AAACAATATT 0.489805 -171 TAATCTGAATAATAATAGTTAAATATATAAATATTGTAA 13 33 0 AAAATATATA 0.470312 -152 GAAATTATGAAAAAAGAAACCAAAATAAATATATTAATT 14 14 1 AAAAAATAAA 0.962215 -183 CTACAAATATAAGATTCATCAAAATTAATATATTTATTT 14 36 0 AAAAATTAAT 0.833635 -161 AAGAGGGTTAAAGAAGAATAAGAAATATAGTATATAGTG 14 161 1 AAAAAATATA 0.886514 -36 ATAGTTAAAGAAGACGTTCCTAAAATAAAGAAAGAAGTT 15 52 1 AAAAAATAAA 0.962215 -73 AGATAGTTTTAAAAGATATTGAAAATAAAAAATAGGTGA 15 92 1 AAAAAATAAA 0.962214 -33 CAATAATATTAATACTAATTTTAAATAATTCTCTTTTAA 16 23 0 AAAAAATAAT 0.923989 -78 ATAAATAGTTAAAACCCATAAACAATAATATTAATACTA 16 45 0 AAACAATAAT 0.766203 -56 TTCGATATATAACACTTCAAACATATAAAAAAATAGAAC 17 138 1 AAAATATAAA 0.743348 -122 ATGTTTTTGAAAGATACTAATAAAATATAAGGTGATAAA 18 272 1 AAAAAATATA 0.886513 -29 ** * ******* Masking position 17 Map Score: 23.6551 Number of sites scoring better than the average of aligned sites = 831 Number in coding regions = 636 Number in noncoding regions = 195 Number of orfs with sites within 600 bp upstream = 199 Fraction of orfs with sites within 600 bp upstream = 0.0319627 Motif number 6 ATTTTAAGATAAGTTATAAATAA 3 44 0 TTTAAGTAAG 0.953834 -13 TTTTTTAGACTTTTAGCAAATAAATAAAAAG 5 60 0 TTTTAGAAAT 0.436418 -40 AATAAAATTTATTAAGGAAAGTTTAAACGCC 8 46 1 ATTAAGAAAG 0.914634 -143 CACTTTAAATATTAAGCAAAGAATAAGATTA 8 163 0 ATTAAGAAAG 0.914483 -26 ATTAGTTTATTTAAAGTTAATAAGATTGGGG 9 124 0 TTAAAGTAAT 0.703113 -177 AACAGATAGAATTAAGTTAAGACCATTAATT 11 106 1 ATTAAGTAAG 0.949026 -195 GAGAATGGTGATTTAGTTAAGGTGATTTCAA 12 65 1 ATTTAGTAAG 0.820222 -236 CATCCTCAATATTAAGATAATCTGAATAATA 13 58 0 ATTAAGTAAT 0.867084 -127 AAAAGGATACTTAAAGTTAAGTAACATAAAT 13 112 0 TTAAAGTAAG 0.880192 -73 TTAACTGATTATTAGGAAAAGGATACTTAAA 13 128 0 ATTAGGAAAG 0.647865 -57 GTTAAGGTTTTTAAAGTTAATGGTAGGTAAA 13 154 1 TTAAAGTAAT 0.703113 -31 AACTGCAATTTTTAAGGTAAGAATATAAAAG 17 50 1 TTTAAGTAAG 0.953834 -210 ****** **** Masking position 9 Map Score: 8.03483 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 117 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 GCTATTGGATTTTTAATATCTCCAAAATTA 1 281 0 TTTTAATATC 0.822204 -20 CTTTCTGTAGTTTAAATATTCCATAATGCA 4 29 1 TTTAAATATT 0.933813 -92 ATAAAAATTTTTTAAACATCCAATTTGCAT 4 54 0 TTTAAACATC 0.754421 -67 TCATTATTTGTTTCAATAACTATACGATTT 4 92 0 TTTCAATAAC 0.553861 -29 TCTTAGCCAATTTTAATATTAATCTTATTC 8 144 1 TTTTAATATT 0.742376 -45 GTTATCACTTTAAATATTAAGCAAAGAA 8 171 0 TTTAAATATT 0.933813 -18 TAGTTAAATATATAAATATTGTAAAATATT 13 27 0 TATAAATATT 0.563617 -158 TATTTATATATTTAACTATTATTATTCAGA 13 39 1 TTTAACTATT 0.866536 -146 GTTACTTAACTTTAAGTATCCTTTTCCTAA 13 118 1 TTTAAGTATC 0.795369 -67 GAACGTCTTCTTTAACTATCTTCCAAAGAA 15 41 0 TTTAACTATC 0.912429 -84 TATTTTTTATTTTCAATATCTTTTAAAACT 15 96 0 TTTCAATATC 0.877348 -29 ATAATTCTCTTTTAAATATATTATATA 16 8 0 TTTAAATATA 0.716567 -93 TAATACTAATTTTAAATAATTCTCTTTTAA 16 23 0 TTTAAATAAT 0.710025 -78 GTTTATGGGTTTTAACTATTTATTACTTTA 16 61 1 TTTAACTATT 0.866536 -40 TAGGAGAGCGTTCAAATATCCATTATTAAT 18 93 0 TTCAAATATC 0.754421 -208 ********** Masking position 5 Map Score: 8.43418 Number of sites scoring better than the average of aligned sites = 541 Number in coding regions = 397 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 8 CCTTTAATTTTTTTAGTTGATAA 2 97 0 CTTTAATTTT 0.80395 -13 TTTGTAGGAATAAAAATTTTTTAAACATCCAA 4 61 0 TAAAAATTTT 0.604781 -60 AATATCTCCTCATTATTTGTTTCAATAACTAT 4 99 0 CATTATTTTT 0.774564 -22 ACTAATTCTTCTTAATTTTCTTCTTTCTTTTT 5 34 1 CTTAATTCTT 0.419089 -66 TCTTCTTTCTTTTTATTTATTTGCTAAAAGTC 5 52 1 TTTTATTTTT 0.563922 -48 TATTATTAATTAATAATACTTTTCGTGGTGGC 6 16 0 TAATAATTTT 0.750445 -53 TATTAATTAATAATAATTCCTTTTAGTGTTTA 6 33 1 TAATAATCTT 0.67083 -36 CCTTAATAAATTTTATTACTTTGCAAAAAACT 8 31 0 TTTTATTTTT 0.563922 -158 GGAAGGCGTTCATAAATACCTTTTTATCCTAA 8 85 1 CATAAATCTT 0.699563 -104 CCTTTTTATCCTAAAATGTTTTGCAAAAAACT 8 103 1 CTAAAATTTT 0.600849 -86 TTGTTTATCCCAATATTTGTTTATTTTGCATT 9 14 0 CAATATTTTT 0.712267 -287 TATAAAAGTCCATAAATTACTTGTTTATCCCA 9 34 0 CATAAATCTT 0.699563 -267 AAGATTGGGGTATTAATTGTTTTATGACATTA 9 102 0 TATTAATTTT 0.806719 -199 ATATTTTACACTAAAATAATTTTAATAAATAA 9 211 1 CTAAAATTTT 0.600849 -90 AATATCATAGTAATAATAATTTAACGAAATTC 9 241 1 TAATAATTTT 0.750436 -60 ATGTTTTTATTTTTAATCTTTTAATCTTTGTT 11 265 0 TTTTAATTTT 0.717362 -36 CATTCTCAATTTTTAATGATTTGGCATCATCT 12 40 0 TTTTAATTTT 0.717362 -261 ACAACTCCTTTTTTAATGTCTTCAGTTATTCT 12 122 0 TTTTAATCTT 0.632363 -179 ATATCCACCACAATAATATTTTACAATATTTA 13 13 1 CAATAATTTT 0.829304 -172 GTAGCATTAACATTATTGGCTTTAATAACTGG 14 71 1 CATTATTCTT 0.699563 -126 TTCATAAATATTTTGGGATTGATT 15 3 1 CATAAATTTT 0.774564 -122 CACTATATTTTAAAATTTCTTTTATTATGATT 18 37 0 TAAAATTTTT 0.438402 -264 TATCCATTATTAATATTAATTTTAACAACTTT 18 75 0 TAATATTTTT 0.605078 -226 GGGAGGTGTTCATTAATGCCTTAGTTATTCCA 18 125 1 CATTAATCTT 0.820471 -176 ******* *** Masking position 7 Map Score: 19.2505 Number of sites scoring better than the average of aligned sites = 1223 Number in coding regions = 991 Number in noncoding regions = 232 Number of orfs with sites within 600 bp upstream = 219 Fraction of orfs with sites within 600 bp upstream = 0.0351751 Motif number 9 CCTTCCTTTTGGAAGGCGTTTAAACTTTCC 8 61 0 GGAAGGCGTT 0.988383 -128 CCTTCCAAAAGGAAGGCGTTCATAAATACC 8 75 1 GGAAGGCGTT 0.988383 -114 AGATAGTTAAAGAAGACGTTCCTAAAATAA 15 50 1 AGAAGACGTT 0.878579 -75 CTCTCCTATAGGGAGGTGTTCATTAATGCC 18 115 1 GGGAGGTGTT 0.976055 -186 AGCGTAAGCGAGGAGGTGTTAGATTTTTGA 18 213 1 AGGAGGTGTT 0.947621 -88 ********** Masking position 4 Map Score: 2.40226 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 19 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 10 ATGTAATTTTTTATATAATTTTTTATAATTG 1 212 0 TTATATATTT 0.58582 -89 ATAATAGGACTTATGTAATTTTTTATATAAT 1 224 0 TTATGTATTT 0.941824 -77 GTATAAGACTTTCTGTAGTTTAAATATTCCA 4 21 1 TTCTGTATTT 0.887809 -100 CCAATTTGCATTATGGAATATTTAAACTACA 4 34 0 TTATGGATAT 0.78323 -87 TTAGAGGACATTATGCATTTTATAATTTATG 7 43 0 TTATGCATTT 0.930659 -90 AACAAGTAATTTATGGACTTTTATAATTAAA 9 41 1 TTATGGATTT 0.962517 -260 ACACCTTAAGCTCTGGAATTTTACACAACTC 12 215 0 CTCTGGATTT 0.723578 -86 ATAAATATAGTTATGCAATTTTAAAAGCTCA 13 87 0 TTATGCATTT 0.930659 -98 ATATTATTGTTTATGGGTTTTAACTATTTAT 16 53 1 TTATGGGTTT 0.842649 -48 TATGACACTTTTGTGTAATTTACCATTATCC 17 209 0 TTGTGTATTT 0.81132 -51 ******* *** Masking position 4 Map Score: 2.57888 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 190 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 11 CAGCGTTCCCATGGTTTGTTGATAATGGTTT 1 24 0 ATGGTTTTTG 0.897956 -277 AAAGGTTTATTTGGATTGTTTGTTGACGCAT 1 94 0 TTGGATTTTT 0.810966 -207 TTTTTTATAATTGGTATTTTGATGCTCTATT 1 194 0 TTGGTATTTG 0.897956 -107 GCTATTGGATTTTTAATATCTCCAA 1 286 0 TTGGATTTTA 0.575494 -15 AAATAAATGTTTAGTATATTGTATTATATTT 2 22 1 TTAGTATTTG 0.845498 -88 AATTTGCATTATGGAATATTTAAACTACAGA 4 32 0 ATGGAATTTT 0.405753 -89 AAACCCTTTTTTAGTTTTTTAGACTTTTAGC 5 74 0 TTAGTTTTTA 0.678791 -26 TGATAGTTTATAGGTATTTTGGTGAAATAT 7 113 1 TAGGTATTTG 0.554825 -20 CAAAGTTTTTATAGTTTTTTGCAAAGTAATA 8 19 1 ATAGTTTTTG 0.845498 -170 AGAAATATATATAGTTTTTTGCAAAACATTT 8 116 0 ATAGTTTTTG 0.845498 -73 TATCCCAATATTTGTTTATTTTGCATTTCC 9 10 0 TTTGTTTTTT 0.65022 -291 TATTTCCACATTAGTTTATTTAAAGTTAATA 9 133 0 TTAGTTTTTT 0.869916 -168 TCTTTTAATCTTTGTTTATTTCCAAGGTCTT 11 250 0 TTTGTTTTTT 0.65022 -51 TATATTTATTTTGGTTTCTTTTTTCATAATT 14 16 0 TTGGTTTTTT 0.914918 -181 TGTGTAATTAATGGATTATTGGCATTAAAGA 14 134 1 ATGGATTTTG 0.778301 -63 TTTTCTATAGTAAGTTTTTTGTAACGCACTA 17 101 1 TAAGTTTTTG 0.660182 -159 CGAGGAGGTGTTAGATTTTTGATGAACCTTT 18 221 1 TTAGATTTTG 0.845497 -80 TTATATTTTATTAGTATCTTTCAAAAACATT 18 271 0 TTAGTATTTT 0.727355 -30 ******* *** Masking position 7 Map Score: 13.6316 Number of sites scoring better than the average of aligned sites = 514 Number in coding regions = 430 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 12 CTTAAACAATACGGCGATAAAT 3 2 0 AGGCGATAAA 0.822383 -55 TACTTTTCGTGGTGGCATAAA 6 1 0 GTGGCATAAA 0.76651 -68 TATATATATGATTGGGATAATCATCTATCTA 7 80 0 ATGGGATAAT 0.922548 -53 ATAAACAAATATTGGGATAAACAAGTAATTT 9 22 1 ATGGGATAAA 0.967651 -279 TATAGCGTATAATGTCATAAAACAATTAATA 9 93 1 ATGTCATAAA 0.831041 -208 TTCGTAAAATAGGGGGATTAAAATCGCATAT 9 270 1 AGGGGATTAA 0.874074 -31 AACGAAGTGGAATGGCATAAATACAACTCCT 12 145 0 ATGGCATAAA 0.945747 -156 TGGTAGGTAAATGGTGATAAT 13 174 1 AGGTGATAAT 0.758667 -11 TTAATGGATTATTGGCATTAAAGAGGGTTAA 14 141 1 ATGGCATTAA 0.812217 -56 TTTATATACTACTGGGATAATGGTAAATTAC 17 195 1 ATGGGATAAT 0.92257 -65 AATAAAATATAAGGTGATAAA 18 290 1 AGGTGATAAA 0.887557 -11 * ********* Masking position 7 Map Score: 7.14046 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 164 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 13 CTAAACGCTAAATATTCTCCATAATCAGTT 1 131 1 AATATTCTCC 0.744004 -170 TTTAATTTTACTAATTCTTCTTAATTTTCT 5 25 1 CTAATTCTTC 0.805417 -75 AATTCTTCTTAATTTTCTTCTTTCTTTTTA 5 37 1 AATTTTCTTC 0.662267 -63 CTTCTTATAGCAGATTCTTCACTTGAAATA 11 163 0 CAGATTCTTC 0.967227 -138 TAAGTCAGGGCAGATTCTTCTTATAGCAGA 11 179 0 CAGATTCTTC 0.967227 -122 CTACAAATATAAGATTCATCAAAATTAATA 14 45 0 AAGATTCATC 0.703087 -152 TAAAGTTACCAATATTCTTCCAGTTATTAA 14 92 0 AATATTCTTC 0.92559 -105 TACTATATTTCTTATTCTTCTTTAACCCTC 14 163 0 CTTATTCTTC 0.88536 -34 TTGGTATACCCAAATCCTTCTGAGTTGCAC 18 178 1 CAAATCCTTC 0.753718 -123 ********** Masking position 5 Map Score: 1.9988 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 105 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 14 CCTTTAATTTTTTTAGTTGATA 2 98 0 TTTAATTTTT 0.537828 -12 AGTCTTATACTATTATCTTT 4 1 0 TATTATCTTT 0.769188 -120 CTTAATTTTCTTCTTTCTTTTTATTTATTT 5 44 1 TTCTTTCTTT 0.8786 -56 ATAATTAAATTTTTATATTTATAATTATAT 9 63 1 TTTTATATTT 0.715399 -238 GAATACTGGATATTTTCTTTTATTTCCATA 9 165 0 TATTTTCTTT 0.516884 -136 ATATAAATTTTTCTATCTGTGAATACTGGA 9 185 0 TTCTATCTGT 0.876876 -116 ATTTTTATATTTTAATTTAAAT 10 3 1 TTTTATATTT 0.715399 -85 CTCCTCAAGGTTTAATCTTTATGAATGGAG 11 45 1 TTTAATCTTT 0.88309 -256 CTTAACTTAATTCTATCTGTTAAACCAAAC 11 97 0 TTCTATCTGT 0.876876 -204 TGTTTTTATTTTTAATCTTTTAATCTTTGT 11 266 0 TTTAATCTTT 0.88309 -35 ATTAAATTCGTTCAATCTTTACAGCACACA 12 243 0 TTCAATCTTT 0.912557 -58 CTATCTCAACTTCTTTCTTTATTTTAGGAA 15 68 0 TTCTTTCTTT 0.8786 -57 TAAAATAGAGTTCTATTTTTTTATATGTTT 17 156 0 TTCTATTTTT 0.776432 -104 ********** Masking position 6 Map Score: 6.5769 Number of sites scoring better than the average of aligned sites = 794 Number in coding regions = 709 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 15 ATTTTTGTAGGAATAAAAATTTTTTAAACATCCA 4 62 0 GATAAAATTT 0.689818 -59 AAACTATCACATATATATATGATTGGGATAATCA 7 88 0 AATAATATTT 0.946637 -45 ATTGGCTAAGAAATATATATAGTTTTTTGCAAAA 8 121 0 AATAATATTT 0.725802 -68 ATATAATTATAAATATAAAAATTTAATTATAAAA 9 59 0 AATAAAAATT 0.5935 -242 TTTTAGTGTAAAATATAAATTTTTCTATCTGTGA 9 193 0 AATAAAATTT 0.918083 -108 TCCTACTTCCATATATATATAATTTACGGTATAT 10 36 0 AATAATATTT 0.93644 -52 TCTTCACTTGAAATAAATATCATATCATCCTTTT 11 144 0 AATAATATTA 0.863767 -157 GGAATGGCATAAATACAACTCCTTTTTTAATGTC 12 134 0 AATAAACTTT 0.70924 -167 ATAGTTAAATATATAAATATTGTAAAATATTATT 13 24 0 AATAATATTA 0.863775 -161 AAGTTAAGTAACATAAATATAGTTATGCAATTTT 13 96 0 AATAATATTT 0.946585 -89 AAAGAAACCAAAATAAATATATTAATTTTGATGA 14 26 1 AATAATATTA 0.851469 -171 TAAGGTAAGAATATAAAAGTCTTTGGTTTTATAA 17 62 1 AATAAAGTTT 0.709272 -198 * *** **** ** Masking position 7 Map Score: 7.11059 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 105 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617