AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -ipurR_mjan_opreg_100.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 MJ0059 215 nitrogen regulatory protein P-II (glnB) #2 MJ0102 300 Phenylacrylic acid decarboxylase #3 MJ0203 120 phosphoribosylformylglycinamidine cyclo-ligase (purM) #4 MJ0204 99 amidophosphoribosyltransferase (purF) #5 MJ0561 281 adenylosuccinate synthetase (purA) #6 MJ0616 108 phosphoribosylaminoimidazole carboxylase, (purE) #7 MJ0929 300 adenylosuccinate lyase (purB) #8 MJ0934 300 polyferredoxin (mvhB) #9 MJ0936 94 conserved hypothetical protein #10 MJ0937 63 phosphoribosylamine--glycine ligase (purD) #11 MJ1019 132 carbamoyl-phosphate synthase, small (or glutamine) subunit (carA) #12 MJ1132 188 conserved hypothetical protein #13 MJ1264 76 phosphoribosylformylglycinamidine synthase II (purL) #14 MJ1265 189 nucleoside diphosphate kinase, (ndk) #15 MJ1344 300 nitrogen regulatory protein P-II (glnB) #16 MJ1368 122 sulfate transport system permease protein (cysT) #17 MJ1378 184 carbamoyl-phosphate synthase, medium subunit (carB1) #18 MJ1381 124 carbamoyl-phosphate synthase, large subunit (carB2) #19 MJ1486 109 phosphoribosylglycinamide formyltransferase 2 (purT) #20 MJ1592 300 phosphoribosylaminoimidazolesuccinocarboxamide synthase (purC) #21 MJ1597 226 serine hydroxymethyltransferase (glyA) #22 MJ1616 228 inosine-5'-monophosphate dehydrogenase, (guaB) Motif number 1 CCTTTTAGATAAAAATAAAAATGATTACTAC 1 134 1 AAAATAAAAA 0.899222 -82 AAATTTGTAAAATTATAAAAATGAGGTTGAG 1 192 1 AATATAAAAA 0.95409 -24 ACCTAAAATAAAATAATAAAATGGTGCCGAG 2 187 0 AATAATAAAA 0.792657 -114 ATAAATCTAAAAAAATAAATATAACAACCTA 2 213 0 AAAATAAATA 0.82131 -88 TTAAGATTTAAAAAATAAATACTATTTAAAA 2 255 0 AAAATAAATA 0.82131 -46 AGACTTTCTGTAGTTTAAATATTCCATAATG 3 26 1 TATTTAAATA 0.627015 -95 TAGGAATAAAAATTTTTTAAACATCCAATTT 3 58 0 AATTTTTAAA 0.583148 -63 AAGAATTAGTAAAATTAAAAAGATAATTTAT 4 13 0 AAATTAAAAA 0.804148 -87 GACTTTTAGCAAATAAATAAAAAGAAAGAAG 4 53 0 AATAAATAAA 0.725337 -47 CAAAATGATAAATAATTTAAACCTTCAAATA 5 43 0 AAAATTTAAA 0.566187 -239 TTCTTTTCAAAACTAATAAAATCTATTTATG 5 87 1 AATAATAAAA 0.792657 -195 ATCTATGTTATACTATTTATATTCCAAAATA 5 153 1 TATATTTATA 0.349692 -129 AAATATATAGAACTATAAAAAACTTATAATA 5 179 1 AATATAAAAA 0.954096 -103 AATATTAATTAACTTTAAATATTACAATTAC 5 238 1 AATTTAAATA 0.831262 -44 TTACAATTACAAAAAAATATAAGGTTTTGAA 5 259 1 AAAAAATATA 0.368683 -23 TTTTAAAACTAATTATAAATAAATTATGGTT 6 51 0 AATATAAATA 0.913269 -58 TTTGAAAATAAAAATTAAATAATTATCTAA 7 10 0 AAATTAAATA 0.678974 -291 AACCCTTAGAAATTAAATAAAAATCCTTTGA 7 90 1 AATAAATAAA 0.725332 -211 ACCAAACAACAAAATTAAAAATCCTAAAACC 7 188 1 AAATTAAAAA 0.804148 -113 CCAAATAATAAATTATAAACAGACTTCTATA 7 218 1 AATATAAACA 0.631641 -83 GTTTGATGTTTATTTAAAAAAGCATTTTCAG 7 258 0 TATTAAAAAA 0.563757 -43 ATAAACATCAAACTATAAAAATCATTAGCAA 7 276 1 AATATAAAAA 0.954096 -25 GAGAATTTAAAATAATAAAAAGTGGCCGGCG 8 108 0 AAAATAAAAA 0.89922 -193 TTAATTGTTCTAAAATAAAAAGAAGCCCGGC 8 243 0 TAAATAAAAA 0.7543 -58 ATTAATCGATAAATTTAAATATTTTTAAAAT 8 269 1 AATTTAAATA 0.831262 -32 TTACTTAAGATATTTTAAAAATATTTAAATT 8 280 0 TATTTAAAAA 0.764564 -21 GGATTAATGTAATAATAAAAAAGTAAAAAAG 10 24 0 AAAATAAAAA 0.89922 -40 CCATTTCATCAATTATTAACAACCATAAATT 11 20 1 AATATTAACA 0.441044 -113 TAACAACCATAAATTATAAAATGCATAATGT 11 36 1 AATTATAAAA 0.63757 -97 CTTTGCAAAAAACTATAAAAACTTTGGTGGT 12 14 0 AATATAAAAA 0.954096 -175 GTTTTTTGCAAAGTAATAAAATTTATTAAGG 12 32 1 AATAATAAAA 0.792657 -157 TTTTGCAAAAAACTATATATATTTCTTAGCC 12 121 1 AATATATATA 0.772898 -68 AGAATAAGATTAATATTAAAATTGGCTAAGA 12 144 0 TATATTAAAA 0.766929 -45 ATTCTTTGCTTAATATTTAAAGTGATAAC 12 170 1 TATATTTAAA 0.511246 -19 ATATTGCTCATATATAAAAAATGAAATTGCC 14 45 0 TAATAAAAAA 0.360001 -145 CTATCTCGAAAAATTTAAATATTGCTCATAT 14 63 0 AATTTAAATA 0.831262 -127 ATACGGAAGTTATTAAAAATAATGATAATAT 14 106 0 TATAAAAATA 0.445197 -84 TTTAAAGTATTAGTAATAATAATAGTAATTA 14 145 1 TATAATAATA 0.400828 -45 CAATCTTATTAACTTTAAATAAACTAATGTG 15 32 0 AATTTAAATA 0.831262 -269 AATGTCATAAAACAATTAATACCCCAATCTT 15 56 0 AAAATTAATA 0.678974 -245 ATATAATTATAAATATAAAAATTTAATTATA 15 97 1 AATATAAAAA 0.954096 -204 TATAAAAATTTAATTATAAAAGTCCATAAAT 15 110 1 TATTATAAAA 0.377022 -191 TTATAGAGCCAAGTATAAAAATGTAGGAAAT 15 173 0 AATATAAAAA 0.954096 -128 ACTCTAAAAATAGTATAAAAACTTTTCGGTA 15 206 0 TATATAAAAA 0.877314 -95 TTCCGTTTCCAAGTATATATATGGAGGCTGA 15 275 1 AATATATATA 0.772898 -26 TTTCATTAAAAATTTATTAAA 16 1 0 AATTATTAAA 0.358628 -122 TAAATTACCTAATTATATAAAATTTGTGTTA 16 64 0 AATATATAAA 0.868537 -59 ACCTACCATTAACTTTAAAAACCTTAACTGA 17 24 1 AATTTAAAAA 0.905341 -161 AATAATAGTTAAATATATAAATATTGTAAAA 17 144 1 AATATATAAA 0.86854 -41 GAAGTTGAGATAGTTTTAAAAGATATTGAAA 18 85 1 TATTTTAAAA 0.602251 -40 AGATATTGAAAATAAAAAATAGGTGATTAT 18 105 1 AAAAAAAATA 0.646802 -20 CAGTGAAATAAAAAATAAAAATATATCAAAG 20 70 0 AAAATAAAAA 0.899222 -231 TATTACAAAATATTTTAAAAAGAACTATAGT 20 106 0 TATTTAAAAA 0.764564 -195 ACTTACAATGTAATATAAAAAATTTATAGTT 20 214 0 TATATAAAAA 0.877314 -87 TGTAAGTATAAAGATTAAAAATTAAATGAGA 20 238 1 AAATTAAAAA 0.804148 -63 TTTAAATTTTAATTATTAAAACTCTCATTTA 20 260 0 AATATTAAAA 0.905328 -41 TGAAAGACACTATATAAAAAAGTTTTTGGTG 21 17 0 TAATAAAAAA 0.360001 -210 ATTTGACAATAAATATTTAAATGCCTTCCTT 21 89 0 AATATTTAAA 0.752488 -138 CTGTCTTCAAAATTAATTAAAGTTTATTAAT 21 124 0 AATAATTAAA 0.548565 -103 AGATATTTTTAAGTATTAATACGGTATATTT 21 165 1 AATATTAATA 0.831262 -62 TAGAAATAGAAACAATAAATATACCGTATTA 21 181 0 AAAATAAATA 0.82131 -46 ATTGATTGACAAAAAATAAAATAATTATCTA 22 45 0 AAAAATAAAA 0.62138 -184 GGGGCATCAATAATATAAAAATTGATTGACA 22 65 0 TATATAAAAA 0.877314 -164 AAATAAAATAAAGTTAATATATGGGGGCATC 22 88 0 AATTAATATA 0.38498 -141 ACATTAATTCAATAAAAAATAAAATAAAGTT 22 104 0 AAAAAAAATA 0.646802 -125 TAAGTTCATAAACTATTTAAATAATCATATA 22 135 1 AATATTTAAA 0.752488 -94 ATCATATAAAAAGTATAAATACCCCTCTTCT 22 175 1 AATATAAATA 0.914572 -54 ** ******** Masking position 9 Map Score: 73.4281 Number of sites scoring better than the average of aligned sites = 4008 Number in coding regions = 2666 Number in noncoding regions = 1342 Number of orfs with sites within 600 bp upstream = 658 Fraction of orfs with sites within 600 bp upstream = 0.105686 Motif number 2 GGTTTTTAGATTAATTTGAATTTGGTAGTAATC 1 156 0 TTATTTATTT 0.934554 -60 TCTCAACCTCATTTTTATAATTTTACAAATTTG 1 191 0 ATTTTAATTT 0.642573 -25 GAAAACTCTTTTAGTTTTCATTTAACCGAAGCG 2 85 1 TTATTTATTT 0.934554 -216 GTTATATTTATTTTTTTAGATTTATGGATTAAC 2 219 1 TTTTTTATTT 0.918606 -82 TAAATAGTATTTATTTTTTAAATCTTAACTTAA 2 258 1 TTATTTAAAT 0.786688 -43 AATTTTCTTCTTTCTTTTTATTTATTTGCTAAA 4 47 1 TTTTTTATTT 0.918607 -53 AAGGTTTAAATTATTTATCATTTTGTGAAATTA 5 49 1 TTATTAATTT 0.850769 -233 AAACCTTATATTTTTTTGTAATTGTAATATTTA 5 253 0 TTTTTTAATT 0.78669 -29 TTATTTATAATTAGTTTTAAAATCTCTTACATA 6 60 1 TTATTTAAAT 0.786688 -49 AGATAATTATTTAATTTTTATTTTCAAAAATCT 7 13 1 TTATTTATTT 0.934554 -288 GCTGGTTTGATTATTTAGAATATTTAAGTTTAT 7 56 0 TTATTAATAT 0.817822 -245 CTAAATGCTCTTATTTTCAAAATCCAAACATAT 7 136 1 TTATTTAAAT 0.786522 -165 GCCACTTTTTATTATTTTAAATTCTCAAGGTAA 8 113 1 ATTTTTAATT 0.595532 -188 TTACTTAAGATATTTTAAAAATA 8 288 0 TTATTAATAT 0.818367 -13 CACATCCTTCATTTTTTGTATATCCACAAATAA 13 28 1 ATTTTTATAT 0.780691 -49 TGGCAATTTCATTTTTTATATATGAGCAATATT 14 44 1 ATTTTTATAT 0.775229 -146 CTTTTATTTCCATATTATTTCCACA 15 3 1 TTTTTTATAT 0.899194 -298 CAATATTTGTTTATTTTGCATTTCCTACATTTT 15 154 1 TTATTTATTT 0.934554 -147 CACCTATTTTTTATTTTCAATATCTTTTAAAAC 18 97 0 TTATTTATAT 0.91836 -28 TGATATATTTTTATTTTTTATTTCACTGTTTTG 20 73 1 TTATTTATTT 0.934554 -228 ATTAATAAACTTTATTAACATTTGAAAAGAACT 20 185 1 TTTTTAATTT 0.818374 -116 GAGAGTTTTAATAATTAAAATTTAAAGTTATAG 20 265 1 ATATTAATTT 0.694285 -36 TTAATTAAAGTTTATTAATAAATATTTGACAAT 21 110 0 TTTTTAAAAT 0.537829 -117 CGGTATATTTATTGTTTCTATTTCTATTAAACG 21 186 1 ATTTTTATTT 0.818374 -41 AGGGGTATTTATACTTTTTATATGATGCCCTTG 22 168 0 ATATTTATAT 0.818371 -61 *** *** **** Masking position 6 Map Score: 27.1187 Number of sites scoring better than the average of aligned sites = 787 Number in coding regions = 549 Number in noncoding regions = 238 Number of orfs with sites within 600 bp upstream = 216 Fraction of orfs with sites within 600 bp upstream = 0.0346932 Motif number 3 TAGGAAGGAAAATTCTTTCCTTAGTAAGTTA 1 77 0 AATCTTTCCT 0.885387 -139 AATGGAAAGCTACGCTTTCCAGCTATGAAAA 2 59 1 TACCTTTCCA 0.793916 -242 AGTAAATTTGAACTCCTTCCTAATGGAAGGA 5 118 1 AACCCTTCCT 0.993726 -164 AACATAGATAAACTCCTTCCATTAGGAAGGA 5 131 0 AACCCTTCCA 0.993726 -151 GGAAAGTTTAAACGCCTTCCAAAAGGAAGGC 12 61 1 AACCCTTCCA 0.993726 -128 GGTATTTATGAACGCCTTCCTTTTGGAAGGC 12 74 0 AACCCTTCCT 0.993726 -115 GGCACTGATGAACTCCTTCCATTAGGAAGGG 20 142 1 AACCCTTCCA 0.993726 -159 TTAAGTTTGAACTCCCTTCCTAATGGAAGGA 20 155 0 ACTCCTTCCT 0.903095 -146 GTAGCTTATGAACACCTTCCAAAGGAAGGCA 21 68 1 AACCCTTCCA 0.993726 -159 TAAATATTTAAATGCCTTCCTTTGGAAGGTG 21 80 0 AATCCTTCCT 0.978112 -147 *** ******* Masking position 7 Map Score: 20.0867 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 31 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 4 TCTTTTTTCCTTTTAGATAAAAATAAAAATGATTAC 1 126 1 TTTAAAATAA 0.837736 -90 AAATAAATACTATTTAAAAATAGTTAATCCATAAAT 2 238 0 TTTAAAATTA 0.84993 -63 TAAATATTACAATTACAAAAAAATATAAGGTTTTGA 5 253 1 ATTAAAATAT 0.822953 -29 TTTTAAAATCTCTTACATAAAAATTTAGACCTTTTT 6 74 1 TTTAAAATTT 0.932165 -35 GGCTTCTTTTTATTTTAGAACAATTAATCGATAAAT 8 247 1 TTTAAAATTA 0.84993 -54 TACTTAAGATATTTTAAAAATATTTAAATTTATCGA 8 274 0 ATTAAAATTA 0.677583 -27 TGTCATTATCTCTTATATAACAATTTTTTAATGAGA 9 17 0 TTTAAAATTT 0.932165 -78 TAATGGAGAATATTTTATAACACTATCTATGTCATT 9 46 0 TTTAAAATAT 0.926071 -49 TATCTACTGCTTTTAGAGGACATTATGCATTTTATA 11 50 0 TTTAGAATAT 0.938492 -83 AATTTTATTACTTTGCAAAAAACTATAAAAACTTTG 12 19 0 CTTAAAATAT 0.757742 -170 ATATATAGTTTTTTGCAAAACATTTTAGGATAAAAA 12 105 0 TTTAAAATTT 0.932165 -84 GGGTATTAATTGTTTTATGACATTATACGCTATAAT 15 63 1 TTTAGAATAT 0.938492 -238 TTTAATAAATTTTTAATGAAAATATTATACTATCA 16 10 1 TTTAGAATAT 0.938492 -113 AATATATAAATATTGTAAAATATTATTGTGGTGGAT 17 155 1 TTTAAAATAT 0.926071 -30 TTATATCCTTCTTTGGAAGATAGTTAAAGAAGACGT 18 33 1 CTTAGAATTA 0.632695 -92 GTGCCTTAGTTATTACAAAATATTTTAAAAAGAACT 20 111 0 TTTAAAATTT 0.932165 -190 AAAGATTAAAAATTAAATGAGAGTTTTAATAATTAA 20 247 1 ATTAGAATTT 0.861321 -54 TTCAAAATGTTTTTGAAAGACACTATATAAAAAAGT 21 25 0 TTTAGAATAT 0.938492 -202 ACTTTAATTAATTTTGAAGACAGTATAGTTTAAAGA 21 132 1 ATTAGAATAT 0.84989 -95 AAGACAGTATAGTTTAAAGATATTTTTAAGTATTAA 21 148 1 ATTAGAATTT 0.861321 -79 AGTTCTGCAATATTCTATGAAAGTTAGGTGATGGG 22 10 0 TTTAGAATTA 0.873394 -219 * ** * ** * *** Masking position 4 Map Score: 24.8536 Number of sites scoring better than the average of aligned sites = 437 Number in coding regions = 316 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 5 TATTTGTTTCAATAACTATACGATTTTTGT 3 88 0 AATAACTATA 0.922922 -33 CCTTCAAATAATAAACCATAACAACCCCCC 5 23 0 ATAAACCATA 0.747814 -259 TAGTTTTGAAAAGAACCATATAATTTCACA 5 72 0 AAGAACCATA 0.737603 -210 CCAAAATATATAGAACTATAAAAAACTTAT 5 176 1 TAGAACTATA 0.690899 -106 CTTAATATTAATTAACTTTAAATATTACAA 5 235 1 ATTAACTTTA 0.857846 -47 TGTTCAAAACCTTATATTTTTTTG 5 268 0 CAAAACCTTA 0.526541 -14 ACTCTATAATCAAAACCATAATTTATTTAT 6 38 1 CAAAACCATA 0.630912 -71 ATTTCACCAAAATACCTATAAACTATCACA 11 111 0 AATACCTATA 0.51031 -22 TTACTTTGCAAAAAACTATAAAAACTTTGG 12 18 0 AAAAACTATA 0.915346 -171 ATGTTTTGCAAAAAACTATATATATTTCTT 12 118 1 AAAAACTATA 0.915346 -71 CCCCAATCTTATTAACTTTAAATAAACTAA 15 36 0 ATTAACTTTA 0.857846 -265 TTTACCTACCATTAACTTTAAAAACCTTAA 17 21 1 ATTAACTTTA 0.857846 -164 ATTTATGTTACTTAACTTTAAGTATCCTTT 17 64 0 CTTAACTTTA 0.729337 -121 TTTAAAATTGCATAACTATATTTATGTTAC 17 83 0 CATAACTATA 0.84244 -102 ATAATTAACAAAAAACTATATTAATGATTC 19 44 1 AAAAACTATA 0.915346 -66 ATATTTTAAAAAGAACTATAGTCAAAACAG 20 98 0 AAGAACTATA 0.888144 -203 AACTTAATTAATAAACTTTATTAACATTTG 20 179 1 ATAAACTTTA 0.844945 -122 AACATTTGAAAAGAACTATAAATTTTTTAT 20 201 1 AAGAACTATA 0.888144 -100 TCACCTTAGCTATAACTTTAAATTTTAATT 20 277 0 TATAACTTTA 0.686594 -24 ATATTTATTAATAAACTTTAATTAATTTTG 21 118 1 ATAAACTTTA 0.844945 -109 AAAAATATCTTTAAACTATACTGTCTTCAA 21 145 0 TTAAACTATA 0.702197 -82 GCCCCCATATATTAACTTTATTTTATTTTT 22 91 1 ATTAACTTTA 0.857846 -138 TTATAACCTTTTTAACTATATTTAGAAGAG 22 199 0 TTTAACTATA 0.723082 -30 ********** Masking position 9 Map Score: 21.5264 Number of sites scoring better than the average of aligned sites = 469 Number in coding regions = 369 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 6 TGTAGGAATAAAAATTTTTTAAACATCCAA 3 61 0 AAAATTTTTT 0.704715 -60 AGATATTTTAAAAATATTTAAATTTATCGA 8 274 0 AAAATATTTA 0.711475 -27 TTACTTAAGATATTTTAAAAATATTT 8 285 0 AAGATATTTT 0.693382 -16 CTCTTATATAACAATTTTTTAATGAGAGAA 9 14 0 ACAATTTTTT 0.676632 -81 ATAGTGTTATAAAATATTCTCCATTATAAA 9 56 1 AAAATATTCT 0.556462 -39 TATCGCCTCGAAGATATTTTATAATGGAGA 9 73 0 AAGATATTTT 0.693382 -22 TTTTTATCCTAAAATGTTTTGCAAAAAACT 12 105 1 AAAATGTTTT 0.725724 -84 GTATCACCTCAAAATGTTATGGCAATTTCA 14 25 1 AAAATGTTAT 0.6933 -165 GATTTAACCAACAATATTATCATTATTTTT 14 93 1 ACAATATTAT 0.703292 -97 ATTTTTAATGAAAATATTATACTATCAAAT 16 19 1 AAAATATTAT 0.699181 -104 ATAATATTTTACAATATTTATATATTTAAC 17 151 0 ACAATATTTA 0.689078 -34 TAAATATTGTAAAATATTATTGTGGTGGAT 17 161 1 AAAATATTAT 0.699181 -24 AATCAATCCCAAAATATTTATGAA 18 5 0 AAAATATTTA 0.711475 -120 TGCTCCCTAAACAATATTTATCTCAAATGA 19 13 1 ACAATATTTA 0.689078 -97 TTTTAGCATTAAAATTTTATTCTATACTTT 19 85 0 AAAATTTTAT 0.652188 -25 AAAATTTTTAGCATTAAAAT 19 100 0 AAAATTTTTA 0.636286 -10 TAGTTATTACAAAATATTTTAAAAAGAACT 20 111 0 AAAATATTTT 0.497653 -190 TGGTTACTTCAAAATGTTTTTGAAAGACAC 21 38 0 AAAATGTTTT 0.725724 -189 GTATAGTTTAAAGATATTTTTAAGTATTAA 21 154 1 AAGATATTTT 0.693382 -73 ********** Masking position 5 Map Score: 17.6822 Number of sites scoring better than the average of aligned sites = 681 Number in coding regions = 477 Number in noncoding regions = 204 Number of orfs with sites within 600 bp upstream = 177 Fraction of orfs with sites within 600 bp upstream = 0.0284292 Motif number 7 CCCCTAATGGAAAAGCTTAAATATATAACTTACT 1 52 1 AAAACTAAAT 0.966842 -164 TTCGGGCTACAAAATCTGAAAGATTTTGTTTAAC 2 123 1 AAAACTAAAT 0.966842 -178 TAAAAGTCTAAAAAACTAAAAAAGGGTTTTTAAT 4 76 1 AAAACTAAAG 0.787138 -24 AGCTTACTCTATAATCAAAACCATAATTTATTTA 6 33 1 ATAACAAAAT 0.637194 -76 TTTTGAAAATAAAAATTAAATAATTATCTAA 7 8 0 AAAATTAAAT 0.872939 -293 TTTATTTTCAAAAATCTGAATAATTCAATAAACT 7 29 1 AAAACTAAAT 0.966779 -272 GAATAATTCAATAAACTTAAATATTCTAAATAAT 7 46 1 ATAACTAAAT 0.946936 -255 TAAAAATCCTAAAACCCAAATAATAAATTATAAA 7 203 1 AAAACCAAAT 0.886719 -98 CAATTAATCGATAAATTTAAATATTTTTAAAATA 8 267 1 ATAATTAAAT 0.808048 -34 TAGATAGATGATTATCCCAATCATATATATATGT 11 80 1 ATTACCAAAT 0.436086 -53 GTGGATATACAAAAAATGAAGGATGTGTTATTAA 13 21 0 AAAAATAAAT 0.676607 -56 ATCTATCTCGAAAAATTTAAATATTGCTCATATA 14 62 0 AAAATTAAAT 0.873151 -128 TTATAAATATAAAAATTTAATTATAAAAGTCCAT 15 103 1 AAAATTAAAT 0.873023 -198 AGGTAATTTAATTACCTTAAAAATGATTAAGATT 16 85 1 ATTACTAAAT 0.742322 -38 CAATATTAAGATAATCTGAATAATAATAGTTAAA 17 123 1 ATAACTAAAT 0.943676 -62 TGATTCCTTTAAAAGCTAAAGTATAGAATAAAAT 19 68 1 AAAACTAAAT 0.966842 -42 **** ** ** ** Masking position 9 Map Score: 16.3932 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 183 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 8 TATATAACTTACTAAGGAAAGAATTTTCCTTCC 1 73 1 ACTAAGAAAA 0.322135 -143 CCTTCCTATTATTTAGGAATAAAGAATCTTTTT 1 100 1 ATTTAGATAA 0.65385 -116 CCAAATTCAAATTAATCTAAAAACCACCAAATT 1 164 1 ATTAACAAAA 0.86903 -52 AACAACCTAAAATAAAATAATAAAATGGTGCCG 2 189 0 AATAAAAAAA 0.747271 -112 ATTTTTTTAGATTTATGGATTAACTATTTTTAA 2 228 1 ATTTAGATAA 0.65385 -73 TTAAGTTAAGATTTAAAAAATAAATACTATTTA 2 258 0 ATTTAAAAAA 0.750062 -43 TTTTTTAGACTTTTAGCAAATAAATAAAAAGAA 4 58 0 TTTTACAAAA 0.200361 -42 AGGAGTTCAAATTTACTCATAAATAGATTTTAT 5 102 0 ATTTATATAA 0.619863 -180 TAAATATTACAATTACAAAAAAATATAAGGTTT 5 253 1 AATTAAAAAA 0.706998 -29 TTGATTATAGAGTAAGCTATAAAATATCAGGAG 6 18 0 AGTAACATAA 0.342009 -91 TTTTAAAACTAATTATAAATAAATTATGGTTTT 6 49 0 AATTAAATAA 0.598469 -60 CAAAAATCTGAATAATTCAATAAACTTAAATAT 7 37 1 AATAATAAAA 0.722299 -264 AACCCTTAGAAATTAAATAAAAATCCTTTGAAC 7 90 1 AATTAAAAAA 0.706998 -211 AAGACAATCCATTAACCAAACAACAAAATTAAA 7 174 1 ATTAACAAAA 0.86903 -127 AAACCCAAATAATAAATTATAAACAGACTTCTA 7 214 1 AATAATATAA 0.616362 -87 TTTTAGAACAATTAATCGATAAATTTAAATATT 8 259 1 ATTAACATAA 0.803868 -42 TTGCTTTTGGATTAATGTAATAATAAAAAAGTA 10 30 0 ATTAAGAAAA 0.789353 -34 TATGGTTGTTAATAATTGATGAAATGGTGAATA 11 14 0 AATAATATAA 0.616362 -119 CACTTTAAATATTAAGCAAAGAATAAGATTAAT 12 161 0 ATTAACAAAA 0.86903 -28 AAATAATATTAATTAACTAATAAGGTGTAATT 13 55 1 AATTACAAAA 0.813217 -22 AGGTGATACCATTAAAAGAATAA 14 1 0 ATTAAAAAAA 0.786206 -189 TTCGAGATAGATTTAACCAACAATATTATCATT 14 84 1 ATTTACAAAA 0.844112 -106 AAATATAAAAATTTAATTATAAAAGTCCATAAA 15 107 1 ATTTATATAA 0.619863 -194 ACGTTCCTAAAATAAAGAAAGAAGTTGAGATAG 18 65 1 AATAAGAAAA 0.750809 -60 CAAATGAGATAATTAACAAAAAACTATATTAAT 19 36 1 AATTACAAAA 0.813217 -74 AAAACAGTGAAATAAAAAATAAAAATATATCAA 20 72 0 AATAAAATAA 0.646194 -229 ATTGTCAAATATTTATTAATAAACTTTAATTAA 21 110 1 ATTTATATAA 0.619863 -117 TGGGGGCATCAATAATATAAAAATTGATTGACA 22 65 0 AATAAAAAAA 0.747271 -164 TGAACTTAACATTAATTCAATAAAAAATAAAAT 22 110 0 ATTAATAAAA 0.763865 -119 ***** * ** ** Masking position 5 Map Score: 22.1198 Number of sites scoring better than the average of aligned sites = 1302 Number in coding regions = 1000 Number in noncoding regions = 302 Number of orfs with sites within 600 bp upstream = 243 Fraction of orfs with sites within 600 bp upstream = 0.0390299 Motif number 9 GGGAATTAGGAAGATGGGTAGTAGGTAAGA 1 25 0 AAGATGGGTA 0.841265 -191 CCTAAATAATAGGAAGGAAAATTCTTTCCT 1 87 0 AGGAAGGAAA 0.743518 -129 ATGGTGCCGAGGGAGGGATACAAACGAAAC 2 168 0 GGGAGGGATA 0.940299 -133 ATAAAATATCAGGAGGGATATT 6 3 0 AGGAGGGATA 0.983416 -106 ATAATATCAAAAGCGGGATAGTT 14 177 1 AAGCGGGATA 0.941413 -13 CTATCTTCCAAAGAAGGATATAATCAATCC 18 26 0 AAGAAGGATA 0.942869 -99 AAACGTTAATAAGAGGGATAAAA 21 214 1 AAGAGGGATA 0.983739 -13 CTATATTTAGAAGAGGGGTATTTATACTTT 22 184 0 AAGAGGGGTA 0.971638 -45 ********** Masking position 10 Map Score: 4.92033 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 32 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 10 AATTATCTTTTTAATTTTACTAATTCTTCTTAATT 4 16 1 TTAATTTTTT 0.954853 -84 CTAATTCTTCTTAATTTTCTTCTTTCTTTTTATTT 4 35 1 TTAATTTTTT 0.954853 -65 TTAAAGTTAATTAATATTAAGAATTTCCAATGTAT 5 221 0 TTAATTTGTT 0.870954 -61 AGATAATTATTTAATTTTTATTTTCAAAAATCTGA 7 13 1 TTAATTTTTC 0.728421 -288 TTTAGGATTTTTAATTTTGTTGTTTGGTTAATGGA 7 181 0 TTAATTTTTT 0.954853 -120 TGTTTATAATTTATTATTTGGGTTTTAGGATTTTT 7 204 0 TTATTTTGTT 0.459892 -97 CTTTCCTTAATAAATTTTATTACTTTGCAAAAAAC 12 32 0 TAAATTTTTT 0.811043 -157 AATTTTAATATTAATCTTATTCTTTGCTTAATATT 12 152 1 TTAATTTTTT 0.954853 -37 TATTCTTTGCTTAATATTTAAAGTGATAAC 12 169 1 TTAATTTATG 0.431342 -20 TATTAGTTAATTAATATTATTTGTGGATATACAAA 13 42 0 TTAATTTTTG 0.904251 -35 AAAAATAATGATAATATTGTTGGTTAAATCTATCT 14 88 0 ATAATTTTTT 0.589291 -102 CTTTTATAATTAAATTTTTATATTTATAATTATAT 15 97 0 TAAATTTTTT 0.811043 -204 CTATCCCTAATCAATCTTAATCATTTTTAAGGTAA 16 96 0 TCAATTTTTT 0.715725 -27 TCAGATTATCTTAATATTGAGGATGAGCTTTTAAA 17 107 0 TTAATTTGTG 0.750853 -78 AAAGGAATCATTAATATAGTTTTTTGTTAATTATC 19 43 0 TTAATTATTT 0.589291 -67 CATTTAATTTTTAATCTTTATACTTACAATGTAAT 20 231 0 TTAATTTTTT 0.954853 -70 GCTATAACTTTAAATTTTAATTATTAAAACTCTCA 20 264 0 TAAATTTTTT 0.811043 -37 TACGGTATATTTATTGTTTCTATTTCTATTAAACG 21 184 1 TTATTTTTTT 0.727392 -43 TCAATCAATTTTTATATTATTGATGCCCCCATATA 22 67 1 TTTATTTTTG 0.543682 -162 ATATATTAACTTTATTTTATTTTTTATTGAATTAA 22 97 1 TTTATTTTTT 0.727392 -132 ***** ** * ** Masking position 7 Map Score: 17.4553 Number of sites scoring better than the average of aligned sites = 281 Number in coding regions = 191 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 11 CCATTAGGAAGGAGTTCAAATTTACTCATA 5 114 0 GGAGTTCAAA 0.967521 -168 CCTAATGGAAGGAGTTTATCTATGTTATAC 5 136 1 GGAGTTTATC 0.876852 -146 CCTTTTGGAAGGCGTTTAAACTTTCCTTAA 12 57 0 GGCGTTTAAA 0.870751 -132 CCAAAAGGAAGGCGTTCATAAATACCTTTT 12 79 1 GGCGTTCATA 0.969841 -110 CCTAATGGAAGGAGTTCATCAGTGCCTTAG 20 138 0 GGAGTTCATC 0.9631 -163 CATTAGGAAGGGAGTTCAAACTTAATTAAT 20 161 1 GGAGTTCAAA 0.967521 -140 TCCTTTGGAAGGTGTTCATAAGCTACTGGT 21 64 0 GGTGTTCATA 0.921811 -163 ********** Masking position 8 Map Score: 4.71517 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 29 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 12 GGTAAGATAATTCCTATAAAA 1 1 0 TTCCTTAAAA 0.860809 -215 ATAAAAATGATTACTACCAAATTCAAATTAA 1 148 1 TTACTCCAAA 0.775489 -68 AAAATTTTTATTCCTACAAAAATCGTATAGT 3 73 1 TTCCTCAAAA 0.797346 -48 AATTATATGGTTCTTTTCAAAACTAATAAAA 5 77 1 TTCTTTCAAA 0.871535 -205 TATACTATTTATATTCCAAAATATATAGAAC 5 161 1 ATATTCAAAA 0.558006 -121 TATTTAATTTTTATTTTCAAAAATCTGAATA 7 20 1 TTATTTCAAA 0.839599 -281 CTAAATGCTCTTATTTTCAAAATCCAAACAT 7 136 1 TTATTTCAAA 0.839599 -165 TTACTTAAGATATTTTAAAAATATTTAAAT 8 281 0 ATATTTAAAA 0.664922 -20 AATGCATAATGTCCTCTAAAAGCAGTAGATA 11 55 1 GTCCTTAAAA 0.493779 -78 TGAAAATATTATACTATCAAATGTCATCAAT 16 27 1 ATACTTCAAA 0.700773 -96 AAATATATAAATATTGTAAAATATTATTGTG 17 154 1 ATATTTAAAA 0.664922 -31 TATTTTCAATATCTTTTAAAACTATCTCAAC 18 88 0 ATCTTTAAAA 0.720039 -37 ATATTAATGATTCCTTTAAAAGCTAAAGTAT 19 61 1 TTCCTTAAAA 0.860809 -49 TTGACTATAGTTCTTTTTAAAATATTTTGTA 20 103 1 TTCTTTTAAA 0.431039 -198 AGTGCCTTAGTTATTACAAAATATTTTAAAA 20 117 0 TTATTCAAAA 0.745336 -184 AAATTTATAGTTCTTTTCAAATGTTAATAAA 20 195 0 TTCTTTCAAA 0.871535 -106 AAGCTACTGGTTACTTCAAAATGTTTTTGAA 21 44 0 TTACTCAAAA 0.752212 -183 ATTTAAATATTTATTGTCAAATATTTATTAA 21 98 1 TTATTTCAAA 0.839599 -129 ***** ***** Masking position 5 Map Score: 13.6111 Number of sites scoring better than the average of aligned sites = 469 Number in coding regions = 358 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 13 TATAGAACTATAAAAAACTTATAATAACTT 5 184 1 TAAAAAACTT 0.765047 -98 TTCTTAATATTAATTAACTTTAAATATTAC 5 233 1 TAATTAACTT 0.887002 -49 TTTGAACTAATTAATAACTTCTAAATGCTC 7 116 1 TTAATAACTT 0.746216 -185 AAGGCGTTCATAAATACCTTTTTATCCTAA 12 87 1 TAAATACCTT 0.824751 -102 ATCATTATTTTTAATAACTTCCGTATCAAA 14 111 1 TTAATAACTT 0.746216 -79 TACCCCAATCTTATTAACTTTAAATAAACT 15 38 0 TTATTAACTT 0.827713 -263 TAAAAGTCCATAAATTACTTGTTTATCCCA 15 126 1 TAAATTACTT 0.544368 -175 GTTAGGAATGTAATTTCCTTTTCCCTAAGA 15 238 1 TAATTTCCTT 0.656625 -63 TTAGGTAATTTAATTACCTTAAAAATGATT 16 83 1 TAATTACCTT 0.884919 -40 CCATTAACTTTAAAAACCTTAACTGATTAT 17 29 1 TAAAAACCTT 0.761319 -156 ATATTTATGTTACTTAACTTTAAGTATCCT 17 66 0 TACTTAACTT 0.49887 -119 TTGGGATTGATTATATCCTTCTTTGGAAGA 18 23 1 TTATATCCTT 0.442347 -102 CAAACTTAATTAATAAACTTTATTAACATT 20 177 1 TAATAAACTT 0.84178 -124 AAATATTTATTAATAAACTTTAATTAATTT 21 116 1 TAATAAACTT 0.84178 -111 TTTAAATAGTTTATGAACTTAACATTAATT 22 126 0 TTATGAACTT 0.50048 -103 AGTCTCACCTTTATAACCTTTTTAACTATA 22 209 0 TTATAACCTT 0.761319 -20 ********** Masking position 9 Map Score: 11.3447 Number of sites scoring better than the average of aligned sites = 475 Number in coding regions = 391 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 14 GTAGCTTTCCATTTCATCAAAATAGGATGC 2 42 0 ATTTCATCAA 0.957023 -259 GAACCATATAATTTCACAAAATGATAAATA 5 60 0 ATTTCACAAA 0.889852 -222 CTTTTCACCAAAAAGGTCTAA 6 98 0 TTTTCACCAA 0.863567 -11 TCTATTCACCATTTCATCAATTATTAACAA 11 12 1 ATTTCATCAA 0.957023 -121 ATATTTCACCAAAATACCTATA 11 121 0 ATTTCACCAA 0.972467 -12 TTCGAGATAGATTTAACCAACAATATTATC 14 84 1 ATTTAACCAA 0.797744 -106 ATAGCGTATAATGTCATAAAACAATTAATA 15 66 0 ATGTCATAAA 0.742544 -235 ATACTATCAAATGTCATCAATTTTGTTTAA 16 37 1 ATGTCATCAA 0.926523 -86 ********** Masking position 6 Map Score: 4.79657 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 102 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 15 TCTTTCAGATTTTGTAGCCCGAAGCTAACGC 2 115 0 TTTGTGCCCG 0.769905 -186 GATGGGTTCGGGTGTGGCCCCCCCGCTAT 8 9 0 GGTGTGCCCC 0.99108 -292 CGAACTCGGAAGTTAAGCCCCCCAGCGATGC 8 41 1 AGTTAGCCCC 0.879755 -260 TAAGCCCCCCAGCGATGCCCCGAGTACTGCC 8 54 1 AGCGAGCCCC 0.974318 -247 AGTGGCCGGCGGCGTCGCCCCTTTCCCGCCA 8 88 0 GGCGTGCCCC 0.986962 -213 ATGCCCTGGTGGTGTAGCCCGGCCTATCATA 8 160 1 GGTGTGCCCG 0.979873 -141 TTTTTATATTATTGATGCCCCCATATATTAA 22 75 1 ATTGAGCCCC 0.938977 -154 ***** ***** Masking position 7 Map Score: 2.23637 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 7 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049