AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00260_mjan_reg_300.orf -o00260_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 MJ0206 95 conserved hypothetical protein #2 MJ0571 300 aspartate kinase (lysC) #3 MJ0634 300 conserved hypothetical protein #4 MJ0635 219 M. jannaschii predicted coding region MJ0635 #5 MJ0636 239 dihydrolipoamide dehydrogenase #6 MJ0818 162 M. jannaschii predicted coding region MJ0818 #7 MJ0820 263 M. jannaschii predicted coding region MJ0820 #8 MJ0821 70 M. jannaschii predicted coding region MJ0821 #9 MJ0822 300 S-layer structural protein #10 MJ1018 132 phosphoglycerate dehydrogenase (serA) #11 MJ1077 89 seryl-tRNA synthetase (serS) #12 MJ1078 273 M. jannaschii predicted coding region MJ1078 #13 MJ1079 177 conserved hypothetical protein #14 MJ1080 130 M. jannaschii predicted coding region MJ1080 #15 MJ1105 251 TRK system potassium uptake protein (trkA) #16 MJ1107 86 M. jannaschii predicted coding region MJ1107 #17 MJ1108 300 phenylalanyl-tRNA synthetase, subunit beta (pheT) #18 MJ1197 85 threonyl-tRNA synthetase (thrS) #19 MJ1214 49 type I restriction-modification enzyme 1, R subunit #20 MJ1217 41 conserved hypothetical protein #21 MJ1219 69 M. jannaschii predicted coding region MJ1219 #22 MJ1220 69 type I restriction-modification enzyme 1, M subunit #23 MJ1465 300 threonine synthase (thrC) #24 MJ1486 109 phosphoribosylglycinamide formyltransferase 2 (purT) #25 MJ1592 300 phosphoribosylaminoimidazolesuccinocarboxamide synthase (purC) #26 MJ1594 65 phosphoserine phosphatase (serB) #27 MJ1597 226 serine hydroxymethyltransferase (glyA) #28 MJ1600 77 conserved hypothetical protein Motif number 1 AAAGGTATATAATATTTATAATCATATATA 1 53 0 AATATTTATA 0.62216 -43 CCCTCATAAAATTATTTAAAGGTATATAAT 1 70 0 ATTATTTAAA 0.401278 -26 GAAGTTTAATTATTTTTATTCTTTATACTA 2 68 0 TATTTTTATT 0.89173 -233 ATAATGTTCTATTTTTAAATTTGATTAAAA 2 124 0 ATTTTTAAAT 0.744878 -177 AATAAAGAAAAATTTTAAATATACATGGTC 2 227 1 AATTTTAAAT 0.837077 -74 ACACCAAAAATTATTTTATAATTGATAAGA 2 276 0 TTATTTTATA 0.386156 -25 ATAATAAAAAAATTTTTATATGATTATCAA 3 92 1 AATTTTTATA 0.850412 -209 AGAAAATGCTAATTTTTAAAAGCTCTAAGT 3 135 1 AATTTTTAAA 0.802873 -166 GAATTTTTCCTATTTTTATTTAAAGATTTG 3 177 1 TATTTTTATT 0.89173 -124 CTACACCATTTAATTTAAATAATTTGATAT 3 271 0 TAATTTAAAT 0.500268 -30 ACTTTCTACTTTTTTTATTCTAATTTATT 4 10 1 TTTTTTTATT 0.823927 -210 ATTGCGCACTCTTTTTTATTTATATTATTG 4 57 1 CTTTTTTATT 0.749888 -163 TTTTCGTCTATAAATTTATTTAACTATATA 4 91 0 TAAATTTATT 0.54557 -129 TTAAAATTTTTTAAATAATATCTAT 5 6 1 ATTTTTTAAA 0.698246 -234 TGTTGTTCTTATTTTTTATTTGATTAAAAA 5 156 1 ATTTTTTATT 0.923589 -84 TTACAATTAAATTTTTTAATCAAATAAAAA 5 168 0 ATTTTTTAAT 0.896488 -72 ACATTAAACCAATTTTTAATT 5 229 1 AATTTTTAAT 0.938428 -11 AACCTCAAAGCTTTTTAATTTGGAACGCTA 6 61 1 CTTTTTAATT 0.502688 -102 AAAGATTACTATAATTTATTAGGATAATCC 6 94 1 ATAATTTATT 0.63799 -69 GTAACTTGCTATTTTTTAATAAGGCAGGAT 6 120 0 ATTTTTTAAT 0.896488 -43 AGAAGTTATTAAATTTAATTGAGGAGTTGG 7 60 0 AAATTTAATT 0.783111 -204 CGTCGGATAGTTTATTTATTGAATATGTTT 7 203 1 TTTATTTATT 0.575439 -61 TTAACTTTTTCTTTTTTATTTTTTTAGATG 8 16 1 CTTTTTTATT 0.749888 -55 TTTAATTCATAAATTTAAATTAATTGGTGA 8 47 1 AAATTTAAAT 0.721185 -24 AACCCCCACATATTTTTATAAGTTTCTACT 9 40 1 TATTTTTATA 0.687541 -261 TGGATATATCAAAATTAATTTTTATCCATT 9 77 1 AAAATTAATT 0.511197 -224 TGTTTGCAACTTTTTTAAATGGATAAAAAT 9 94 0 TTTTTTAAAT 0.530558 -207 AACTTTTTTTATTTTTTAATAGAGCGATAT 9 129 1 ATTTTTTAAT 0.896488 -172 TTGTTATACAAAATTTAATTTATAATATCG 9 153 0 AAATTTAATT 0.783111 -148 TCTGAATGAAAAATTTTATTATATCTTTGT 9 179 0 AAATTTTATT 0.914601 -122 TCGTTGGGCATAATTTTATACATATTATCA 12 66 1 TAATTTTATA 0.525456 -208 AATTAGTGTTAATTTTAAAAAAACAAACAT 12 112 1 AATTTTAAAA 0.578608 -162 AAAAACAAACATTTTTTATTATTTTTTGCA 12 130 1 ATTTTTTATT 0.923589 -144 TCAATGTTGGTATTTTTAAAAAGATTTTCC 12 203 0 TATTTTTAAA 0.611853 -71 TTAAAAGATGCATTTTTAATATATTTTTAA 12 240 1 CATTTTTAAT 0.79082 -34 ATTTTTAATATATTTTTAATATATTATCTT 12 251 1 TATTTTTAAT 0.855084 -23 TATGATATTCCTTTTTTATTAGTTCTTTAC 13 82 0 CTTTTTTATT 0.749888 -96 TTATTACATTCATTTTTAATTTTAAAAAAC 13 140 1 CATTTTTAAT 0.79082 -38 AACATATCAAAAATTTAATTGGGTATTGCG 14 22 0 AAATTTAATT 0.783111 -109 ACCTTAATTAAATTTTAAATATTAAACTTG 14 71 1 AATTTTAAAT 0.837077 -60 ATTTATAGTTATAATTTAATAATTTAGAAC 14 111 1 ATAATTTAAT 0.558014 -20 AAATTTTTAAAAATTTTATTTTACTGAAGT 16 40 0 AAATTTTATT 0.914601 -47 TAGAGGTTTTAAATTTAATTTCTAAGGGTT 17 11 0 AAATTTAATT 0.783111 -290 GTATTTAGGAATTATTTATTTATTTAGAGG 17 35 0 ATTATTTATT 0.777825 -266 GTCTGTAGATAATTTTAATTATAGTTTGTT 17 179 0 AATTTTAATT 0.877565 -122 ACAAAGCAAAAATATTTAATATATCTTTTT 18 36 1 AATATTTAAT 0.815314 -50 TCCTCAATGGATTTTTTAATGTATGGATT 19 10 0 ATTTTTTAAT 0.896488 -40 AGGAAGATTTAATTTTTATTTCAG 19 36 1 AATTTTTATT 0.955086 -14 AATAAAATTTTTATTGTTAATAAAA 20 6 1 AATTTTTATT 0.955086 -36 TTCACCAGCAAAATTTTATTAACAATAAAA 20 19 0 AAATTTTATT 0.914601 -23 AGCTGGAAGTTAATTTAATTTGTTTGATTG 21 34 1 TAATTTAATT 0.582883 -36 ACTTAGATAGTTATTTTAATGTTTTCACTA 22 40 0 TTATTTTAAT 0.627831 -30 ATAGATTCTAAATTTTTAATGCTAAATATT 23 33 1 AATTTTTAAT 0.938428 -268 TATTGCTATAAATATTTAATGCATAAAGAT 23 66 1 AATATTTAAT 0.815314 -235 GTAACCATGTATTATTAAATCTTTATGCAT 23 84 0 ATTATTAAAT 0.458173 -217 TAATTCTTTAAAATTTTATTAAGTTTTTGA 23 146 0 AAATTTTATT 0.914601 -155 CTTTTAGGCTTATATTAATTCTTTAAAATT 23 161 0 TATATTAATT 0.445736 -140 TTTAGCATTAAAATTTTATTCTATACTTTA 24 84 0 AAATTTTATT 0.914601 -26 ATATATTTTTATTTTTTATTTCACTGTTTT 25 75 1 ATTTTTTATT 0.923589 -226 TTATTACAAAATATTTTAAAAAGAACTATA 25 108 0 ATATTTTAAA 0.537984 -193 AGAACTATAAATTTTTTATATTACATTGTA 25 212 1 ATTTTTTATA 0.763593 -89 ACTCTCATTTAATTTTTAATCTTTATACTT 25 241 0 AATTTTTAAT 0.938428 -60 CTATAACTTTAAATTTTAATTATTAAAACT 25 268 0 AAATTTTAAT 0.884689 -33 TTAATTTTATTAAACTTTTTT 26 2 1 TAATTTTATT 0.805633 -64 AAAATTAAGTAAATTTTAATAAAAAAGTTT 26 22 0 AAATTTTAAT 0.884689 -44 TTAATTTTAAAATTTTTAAAGTTGGTGATT 26 44 1 AATTTTTAAA 0.802873 -22 GCACCAAAAACTTTTTTATATAGTGTCTTT 27 16 1 CTTTTTTATA 0.444738 -211 AAGGCATTTAAATATTTATTGTCAAATATT 27 93 1 AATATTTATT 0.860326 -134 TTTATTGTCAAATATTTATTAATAAACTTT 27 107 1 AATATTTATT 0.860326 -120 TACTGTCTTCAAAATTAATTAAAGTTTATT 27 127 0 AAAATTAATT 0.511197 -100 ATTAATACGGTATATTTATTGTTTCTATTT 27 179 1 TATATTTATT 0.704628 -48 CACAGAATAATATTTTTATATATAAAGGAT 28 16 1 TATTTTTATA 0.687541 -62 ********** Masking position 5 Map Score: 68.8761 Number of sites scoring better than the average of aligned sites = 3390 Number in coding regions = 2235 Number in noncoding regions = 1155 Number of orfs with sites within 600 bp upstream = 644 Fraction of orfs with sites within 600 bp upstream = 0.103437 Motif number 2 GAGAAAGCTTTTCCTAAATAGTTTTAATCAAAT 2 103 1 TTCTAAAGTT 0.552308 -198 AGACCATGTATATTTAAAATTTTTCTTTATTGG 2 225 0 TATTAAATTT 0.891885 -76 TATGTTGTATTAGATAAAGATTTTATGAGAAAT 3 27 0 TAATAAATTT 0.870147 -274 TTCCTATTTTTATTTAAAGATTTGATGTAATTT 3 183 1 TATTAAATTT 0.891885 -118 TCCAAACATCTTCATAAACTTTTTTTGTTAGAA 3 225 0 TTATAAATTT 0.889144 -76 GAGTGCGCAATTGATAAAAATTAGATAAAATAA 4 35 0 TTATAAATTA 0.79109 -185 TATATTATTGTATTTATATAGTTAAATAAATTT 4 77 1 TATTATAGTT 0.583583 -143 GCGATTCTAATATATAAACTTTTCGTCTATAAA 4 107 0 TAATAAATTT 0.870147 -113 TGCAAAAACTTATCTAAAACTTTCGATACCATT 5 99 0 TACTAAATTT 0.79632 -141 GATGAAACTTTTTCTAAAAGTTTCTTTTAAAAC 6 31 1 TTCTAAATTT 0.823934 -132 TATAGTAATCTTTTTATAGCGTTCCAAATTAAA 6 74 0 TTTTATAGTT 0.62651 -89 TATAAAAAGATTACTATAATTTATTAGGATAAT 6 89 1 TTCTATATTA 0.587414 -74 CCCCCACATATTTTTATAAGTTTCTACTAAATA 9 42 1 TTTTATATTT 0.864186 -259 ATGAAAAATTTTATTATATCTTTGTTATACAAA 9 171 0 TTTTATATTT 0.864186 -130 GACAAACTACTATATAAATCTTACGATATGAAA 9 226 0 TAATAAATTA 0.759828 -75 ATAGTTTCTTTTGTTATATCGTTGGGCATAATT 12 48 1 TTTTATAGTT 0.62651 -226 ATCTCAATCCTAATTAAAAGTTATCGTTGGAAA 12 175 1 TATTAAATTA 0.795653 -99 AGATGCATTTTTAATATATTTTTAATATATTAT 12 245 1 TTATATATTT 0.83789 -29 GAATAATCCATATTTATAGTTTAAGTATTCAAT 13 24 0 TATTATATTA 0.715084 -154 TCAAGTTTAATATTTAAAATTTAATTAAGGTCT 14 69 0 TATTAAATTA 0.795699 -62 TAAACTTGAATAGTTATAATTTATAGTTATAAT 14 93 1 TATTATATTA 0.715083 -38 TTATAATTTATAGTTATAATTTAATAATTTAGA 14 106 1 TATTATATTA 0.715083 -25 CAACCCCACTTTAATAGAGATTTGAAGTAACCA 15 27 0 TTATAGATTT 0.622553 -225 AATAATCCTATAATTAAAGTTTTTTGGTGTCAA 15 226 1 TATTAAATTT 0.891885 -26 TAAAATAAAATTTTTAAAAATTTTTAAGGAATT 16 47 1 TTTTAAATTT 0.908039 -40 ATATTTAGAATTTAGGAAATTCCT 16 73 0 TATTAGATTA 0.444726 -14 ATTATTTATTTATTTAGAGGTTTTAAATTTAAT 17 22 0 TATTAGATTT 0.629137 -279 TACAGACTCGTATATAAACATTTTGTGATAATA 17 202 1 TAATAAATTT 0.870147 -99 GATAATTGACTTAATAAAGCTTTATTATCACAA 17 224 0 TTATAAATTT 0.889144 -77 GCAAAAATATTTAATATATCTTTTTCTTTTATA 18 41 1 TTATATATTT 0.83789 -45 TAATTATCTTTATCTAAAATTTAA 18 72 1 TACTAAATTA 0.648609 -14 ATTTTTATTGTTAATAAAATTTTGCTGGTGAAA 20 17 1 TTATAAATTT 0.889144 -25 TAACCATGTATTATTAAATCTTTATGCATTAAA 23 80 0 TTTTAAATTT 0.908039 -221 TTTCAAAAACTTAATAAAATTTTAAAGAATTAA 23 144 1 TTATAAATTT 0.889144 -157 AAAGGAATCATTAATATAGTTTTTTGTTAATTA 24 45 0 TTATATATTT 0.83789 -65 GGCAGTTTTTATAACGTTCTTACGATGT 25 6 1 TTTTATAGTT 0.62651 -295 ATCGAAATCTTTGATATATTTTTATTTTTTATT 25 62 1 TTATATATTT 0.83789 -239 TTTTCAAATGTTAATAAAGTTTATTAATTAAGT 25 180 0 TTATAAATTA 0.79109 -121 ACTTTCACCTTAGCTATAACTTTAAATTTTAAT 25 278 0 TACTATATTT 0.715863 -23 TTAATTTTATTAAACTTTTTTATTAAAAT 26 7 1 TTTTAAATTT 0.908039 -59 TTAAACTTTTTTATTAAAATTTACTTAATTTTA 26 20 1 TTTTAAATTA 0.823377 -46 TTAAAGTTTATTAATAAATATTTGACAATAAAT 27 106 0 TTATAAATTT 0.889144 -121 TCTTCAAAATTAATTAAAGTTTATTAATAAATA 27 119 0 TATTAAATTA 0.795699 -108 ATAGAAACAATAAATATACCGTATTAATACTTA 27 174 0 TAATATAGTA 0.349574 -53 ** ***** *** Masking position 6 Map Score: 57.78 Number of sites scoring better than the average of aligned sites = 1311 Number in coding regions = 802 Number in noncoding regions = 509 Number of orfs with sites within 600 bp upstream = 412 Fraction of orfs with sites within 600 bp upstream = 0.0661741 Motif number 3 TAAAAATATTTGAAAAAATAGTGAAATATAATTTTTCT 2 32 0 TAAAATAATA 0.568085 -269 CCTAAATAGTTTTAATCAAATTTAAAAATAGAACATTA 2 115 1 TATAATAAAA 0.346673 -186 CTTTTTAGCTTATGAACTAAAAATATAAAAGGTTAATA 2 159 1 TAATAATAAA 0.614749 -142 GTGGTTAATCTTATCAATTATAAAATAATTTTTGGTGT 2 268 1 TCATAAAAAA 0.312379 -33 TTATTAACAATCTCAAATAATAAAAAAATTTTTATATG 3 76 1 TAATAAAAAA 0.90417 -225 ATCAATAATGTTGATAATCATATAAAAATTTTTTTATT 3 94 0 TTATAAAAAA 0.35093 -207 ACTTTTCGTCTATAAATTTATTTAACTATATAAATACA 4 85 0 TAATATAATA 0.707416 -135 GAGGTGATAATATGAAGAGATAGAAAAAAGCAGTGGGT 4 163 1 TAAAAAAAAA 0.836915 -57 TTAAAATTTTTTAAATAATATCTATTTT 5 1 1 TAATTTAAAA 0.594976 -239 TAACTTTCTCTTAAAAAGAAAATAAAAAGAAAATAGAT 5 30 0 TAAGAAAAAA 0.561614 -210 ACAACAACAATAACAATTGAAATAAAACCATGCAAAAA 5 124 0 TAATAAAAAC 0.675905 -116 CAATTAAATTTTTTAATCAAATAAAAAATAAGAACAAC 5 157 0 TAACATAAAA 0.5626 -83 TATTAAAAAATAGCAAGTTACTAAAGAATTTCTAAAGT 6 129 1 TAATATAAAA 0.94579 -34 TCTCCAGTCTTATAAACATATTCAATAAATAAACTATC 7 208 0 TAAAATAAAA 0.904665 -56 TTAAATCATCTAAAAAAATAAAAAAGAAAAAGTTAAGG 8 14 0 TAAAAAAAAA 0.836908 -57 AAGAAAAAATTTCTAATTCATTATAAACCCCCACATAT 9 15 1 TAATATTAAC 0.394733 -286 AAATATTTAGTAGAAACTTATAAAAATATGTGGGGGTT 9 40 0 TAATAAAATA 0.566682 -261 AATATCGCTCTATTAAAAAATAAAAAAAGTTACAAATG 9 122 0 TAAAAAAAAA 0.836865 -179 ACTGTATTTCTAAAAACACAATAAAAAACATAAATACC 11 16 1 TAAAATAAAA 0.904665 -74 AATACCTAATTATCAATTCAATAAAAACAATAAGAGTG 11 48 1 TAATATAAAC 0.794085 -42 GAGGGACAGATTTTAAATAAAAGAACAATAGTTTCTTT 12 21 1 TAATAAAAAA 0.904074 -253 CATTACTACTGCAAAAAATAATAAAAAATGTTTGTTTT 12 131 0 GAAAATAAAA 0.463101 -143 AGATAATATATTAAAAATATATTAAAAATGCATCTTTT 12 242 0 TAATTTAAAA 0.594927 -32 TCATTTTTAATTTTAAAAAACTTAAAACAGAGTGAAAC 13 149 1 TAAAATAAAC 0.677037 -29 GTTCTAAATTATTAAATTATAACTATAAA 14 112 0 TAATATAATA 0.703857 -19 ATTTAGAATTTAGGAAATTCCTTAAAAATTTTTAAAAA 16 57 0 TAATCTAAAA 0.462852 -30 AACCCTTAGAAATTAAATTTAAAACCTCTAAATA 17 7 1 TAATATTAAA 0.746778 -294 AATTTAAAACCTCTAAATAAATAAATAATTCCTAAATA 17 26 1 CAATATAAAA 0.613277 -275 ATTTCTAAATTCCAAACTTATACAACAAGACAATCAAT 17 69 1 TAATAAAAAA 0.90417 -232 ACAAGACAATCAATAAATCAATTAACAAAATTGAAAAT 17 93 1 CAATATAAAA 0.61328 -208 AGAATAACGATAGAATATTATTAAACAAACTATAATTA 17 156 1 TATTATAAAA 0.493822 -145 TGTAATAATAGGATAATTGACTTAATAAAGCTTTATTA 17 230 0 GAATATAAAA 0.61328 -71 CAACTAATTATTACAACTAAGATAAAAAATACTGCTGG 17 266 1 TAATAAAAAA 0.90417 -35 ACTACACCCTTATAAATTGATTAAACAAAGCAAAAATA 18 12 1 TAATATAAAA 0.94579 -74 ATTTAGAATCTATAAATAGAGTAAACACGAGATGT 23 8 0 TAAAATAAAC 0.677156 -293 AAATATTTAATGCATAAAGATTTAATAATACATGGTTA 23 75 1 TTAAATAAAA 0.352244 -226 TTTAAAATTTTATTAAGTTTTTGAAAAATGCTACATAT 23 132 0 TAATTTAAAA 0.594987 -169 ACAATATTTATCTCAAATGAGATAATTAACAAAAAACT 24 23 1 TAATAAAATA 0.566682 -87 GCCTTAGTTATTACAAAATATTTTAAAAAGAACTATAG 25 107 0 TAAAATTAAA 0.609232 -194 AGGAAGGGAGTTCAAACTTAATTAATAAACTTTATTAA 25 165 1 TAATATAAAA 0.945777 -136 ATCTTTATACTTACAATGTAATATAAAAAATTTATAGT 25 215 0 TAAGATTAAA 0.285904 -86 CAAAATGTTTTTGAAAGACACTATATAAAAAAGTTTTT 27 21 0 TAAAATTAAA 0.616102 -206 TAACGTTTAATAGAAATAGAAACAATAAATATACCGTA 27 184 0 TAAAAAAAAA 0.836915 -43 * ** * * * ** ** Masking position 15 Map Score: 35.487 Number of sites scoring better than the average of aligned sites = 1089 Number in coding regions = 792 Number in noncoding regions = 297 Number of orfs with sites within 600 bp upstream = 245 Fraction of orfs with sites within 600 bp upstream = 0.0393511 Motif number 4 TTCAAATATTTTTAGTATAAAGAATAAAAAT 2 56 1 TTTAGATAAA 0.83973 -245 ATTAAACTTCTTTAAGAGAAAGCTTTTCCTA 2 88 1 TTTAAAGAAA 0.849822 -213 ATAAAATAATTTTTGGTGTAAGTT 2 287 1 TTTTGTGTAA 0.680933 -14 AGATAAAGATTTTATGAGAAATATACGATTA 3 18 0 TTTATAGAAA 0.359316 -283 TTTTTCCTATTTTTATTTAAAGATTTGATGT 3 180 1 TTTTATTAAA 0.402835 -121 TTATTTAAAGATTTGATGTAATTTTCGATGA 3 192 1 ATTTGTGTAA 0.317945 -109 TATCAAATTATTTAAATTAAATGGTGTAGAG 3 272 1 TTTAATTAAA 0.407538 -29 GATAAAATAAATTAGAATAAAAAAAGTAGAA 4 14 0 ATTAGATAAA 0.540421 -206 TTATTTTCTTTTTAAGAGAAAGTTATTCTCA 5 43 1 TTTAAAGAAA 0.849822 -197 TTATTCTCATTTTTGCAGAAAAATAGCTTAT 5 65 1 TTTTGAGAAA 0.850857 -175 GATTAAAAAATTTAATTGTAATTGTTATTAA 5 177 1 TTTAATGTAA 0.682047 -63 ATATATTCAATTTTGATGAAACTTTTTCTAA 6 17 1 TTTTGTGAAA 0.723375 -146 GCTTTGAGGTTTTAAAAGAAACTTTTAGAAA 6 41 0 TTTAAAGAAA 0.849822 -122 TAATATTAGGATTAGGAGAAAAAGAGGAAGA 7 95 0 ATTAGAGAAA 0.700055 -169 TATCCAAATATTTAGTAGAAACTTATAAAAA 9 52 0 TTTAGAGAAA 0.914358 -249 TTTATAGGTATTTTGGTGAAATAT 10 4 0 TTTTGTGAAA 0.723375 -129 GAGGGACAGATTTTAAATAAAAGAACAATAG 12 21 1 TTTTAATAAA 0.60506 -253 TGTTTGTTTTTTTAAAATTAACACTAATTTA 12 110 0 TTTAAATTAA 0.701381 -164 CCAACATTGATTTAGAATTAAAAGATGCATT 12 223 1 TTTAGATTAA 0.814561 -51 TTTTAAGTTTTTTAAAATTAAAAATGAATGT 13 145 0 TTTAAATTAA 0.701381 -33 TTTAATAGAGATTTGAAGTAACCAATATGGG 15 20 0 ATTTGAGTAA 0.504198 -232 ATTTAGAGGTTTTAAATTTAATTTCTAAGGG 17 13 0 TTTAATTTAA 0.512611 -288 AGTTGTAATAATTAGTTGTAATAATAGGATA 17 253 0 ATTAGTGTAA 0.466121 -48 TTAAATTTTAGATAAAGATAATTATA 18 70 0 TTTTAATAAA 0.60506 -16 ATACCTAATATTTAGCATTAAAAATTTAGAA 23 38 0 TTTAGATTAA 0.814561 -263 AAAATTTTTAGCATTAAAATTTTATTC 24 93 0 TTTAGATTAA 0.814561 -17 CTTTAAAAATTTTAAAATTAAGTAAATTTTA 26 34 0 TTTAAATTAA 0.701381 -32 TTCAAAAACATTTTGAAGTAACCAGTAGCTT 27 44 1 TTTTGAGTAA 0.823186 -183 CTTATTAACGTTTAATAGAAATAGAAACAAT 27 196 0 TTTAAAGAAA 0.849822 -31 ***** ***** Masking position 3 Map Score: 25.172 Number of sites scoring better than the average of aligned sites = 805 Number in coding regions = 657 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 5 TTTAAAAATTAGCATTTTCTCATATCAATAAT 3 123 0 AGCATTTCCA 0.912231 -178 TTAATAAGGCAGGATTATCCTAATAAATTATA 6 103 0 AGGATATCTA 0.924799 -60 CAGTAGATAGATGATTATCCCAATCATATATA 10 45 0 ATGATATCCA 0.786258 -88 CTAATAAAAAAGGAATATCATAATCACACTGT 13 90 1 AGGATATCTA 0.924799 -88 GGTATACCACAGGACTTTCACAGGAATAAATT 15 81 1 AGGATTTCCA 0.986213 -171 CTATTGGCACAGGACTTTCACAGTTTTATAAT 15 161 0 AGGATTTCCA 0.986213 -91 AAAATTTTTAAGGAATTTCCTAAATTCTAAAT 16 63 1 AGGATTTCTA 0.95909 -24 AGTGCCTAATAGGACTTTCGCAAGAATACAAT 23 189 1 AGGATTTCCA 0.986213 -112 AACATTGAATAGGACTTTTGCAGTTTATAGAT 23 266 0 AGGATTTTCA 0.875196 -35 **** **** ** Masking position 6 Map Score: 9.41852 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 26 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 6 TACCTTTAAATAATTTTATGAGGGATATTA 1 76 1 TAATTTTATG 0.76193 -20 GACCATTTCTTATTTTTATGTTGTATTAGA 3 46 0 TATTTTTATG 0.716673 -255 ATCATATAAAAATTTTTTTATTATTTGAGA 3 86 0 AATTTTTTTA 0.628926 -215 TTAAAAGCTCTAAGTTTTTAGCTAAAGGAA 3 150 1 TAAGTTTTTA 0.853402 -151 TCTAACAAAAAAAGTTTATGAAGATGTTTG 3 226 1 AAAGTTTATG 0.755028 -75 TTATAGACGAAAAGTTTATATATTAGAATC 4 108 1 AAAGTTTATA 0.638074 -112 TTAAAATTTTTTAAATAATATCT 5 4 1 AAATTTTTTA 0.681979 -236 AAGTTTTAGATAAGTTTTTGCATGGTTTTA 5 110 1 TAAGTTTTTG 0.910531 -130 AATTACAATTAAATTTTTTAATCAAATAAA 5 170 0 AAATTTTTTA 0.681979 -70 ATTTATTGAATATGTTTATAAGACTGGAGA 7 216 1 TATGTTTATA 0.700549 -48 TTTTCTTTTTTATTTTTTTAGATGATTTAA 8 22 1 TATTTTTTTA 0.739964 -49 AACCCCCACATATTTTTATAAGTTTCTACT 9 40 1 TATTTTTATA 0.591319 -261 CTTTATCACCTAAGTTTTTGTATTGTTATT 9 280 0 TAAGTTTTTG 0.910531 -21 ATTAGGTATTTATGTTTTTTATTGTGTTTT 11 28 0 TATGTTTTTT 0.463343 -62 TCGTTGGGCATAATTTTATACATATTATCA 12 66 1 TAATTTTATA 0.646729 -208 CACTCTGTTTTAAGTTTTTTAAAATTAAAA 13 153 0 TAAGTTTTTT 0.52208 -25 AATACCCAATTAAATTTTTGATATGTTTTT 14 25 1 TAAATTTTTG 0.382526 -106 AAATTTTTGATATGTTTTTGATTTGATGTG 14 36 1 TATGTTTTTG 0.889424 -95 CCTATAATTAAAGTTTTTTGGTGTCAAACT 15 232 1 AAGTTTTTTG 0.483498 -20 ATTATCACAAAATGTTTATATACGAGTCTG 17 204 0 AATGTTTATA 0.582184 -97 ATATTTTTTTGAGGGATTTTA 21 2 1 TATTTTTTTG 0.832629 -68 AAAATTTTATTAAGTTTTTGAAAAATGCTA 23 137 0 TAAGTTTTTG 0.910531 -164 ATCATTAATATAGTTTTTTGTTAATTATCT 24 42 0 TAGTTTTTTG 0.611148 -68 AAAGAACTATAAATTTTTTATATTACATTG 25 210 1 AAATTTTTTA 0.681979 -91 ACTATATAAAAAAGTTTTTGGTGCTGTCT 27 10 0 AAAGTTTTTG 0.858388 -217 GTTACTTCAAAATGTTTTTGAAAGACACTA 27 36 0 AATGTTTTTG 0.827312 -191 CACAGAATAATATTTTTATATATAAAGGAT 28 16 1 TATTTTTATA 0.591319 -62 ********** Masking position 5 Map Score: 21.3752 Number of sites scoring better than the average of aligned sites = 781 Number in coding regions = 582 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 206 Fraction of orfs with sites within 600 bp upstream = 0.0330871 Motif number 7 TATACTAAAAATATTTGAAAAAATAGTGAAATA 2 42 0 ATTTGAAAAA 0.638074 -259 AGTTTTAATCAAATTTAAAAATAGAACATTATA 2 122 1 AATTAAAAAA 0.628017 -179 AAAAATATAAAAGGTTAATAAAAAGATGCTCCA 2 177 1 AATTAATAAA 0.844579 -124 AAATTATTTTATAATTGATAAGATTAACCACAC 2 266 0 ATTTGATAAA 0.850177 -35 ATTATTTGAGATTGTTAATAAGACCATTTCTTA 3 64 0 ATTTAATAAA 0.922919 -237 ATTTGATGTAATTTTCGATGAAATTCTAACAAA 3 202 1 ATTCGATGAA 0.33773 -99 GCAGTGGGTTATAACTAATGATAACCTGTTAGG 4 192 1 ATCTAATGAA 0.429163 -28 TATAAAGTTAATGGTTAATAACAATTACAATTA 5 189 0 ATTTAATAAA 0.922919 -51 CATTAACTTTATATTCAATAACATTAAACCAAT 5 209 1 ATTCAATAAA 0.785818 -31 ATATATATTCAATTTTGATGAAACTTTTTCTAA 6 15 1 AATTGATGAA 0.4303 -148 ATGGTTGTTAATAATTGATGAAATGGTGAATAG 10 108 1 ATTTGATGAA 0.624656 -25 ATTAAACTGTATTTCTAAAAACACAATAAAAAA 11 11 1 ATCTAAAAAA 0.443342 -79 TTTATCACCAATAACACTCTTATTGT 11 74 0 ATCCAATAAA 0.439937 -16 AGAGGGACAGATTTTAAATAAAAGAACAATAGT 12 20 1 ATTAAATAAA 0.41282 -254 ATCTAAATCAATTTTTGATAATATGTATAAAAT 12 78 0 ATTTGATAAA 0.850177 -196 AATTAGTGTTAATTTTAAAAAAACAAACATTTT 12 112 1 AATTAAAAAA 0.628013 -162 CAATGTTGGTATTTTTAAAAAGATTTTCCAACG 12 199 0 ATTTAAAAAA 0.788133 -75 TAGCATCATTATGTTCAATAAGAAATTTATTCC 15 103 0 ATTCAATAAA 0.785818 -149 TAAAATTTTTATTGTTAATAAAATTTTGCTGGT 20 13 1 ATTTAATAAA 0.922919 -29 TAATGCATAAAGATTTAATAATACATGGTTACA 23 82 1 AGTTAATAAA 0.559403 -219 ACATAGTGGCATGTTTAATAATATGTAGCATTT 23 112 1 ATTTAATAAA 0.922919 -189 CATTTTTCAAAAACTTAATAAAATTTTAAAGAA 23 140 1 AATTAATAAA 0.844579 -161 CTCAAATGAGATAATTAACAAAAAACTATATTA 24 34 1 ATTTAACAAA 0.533717 -76 TTTAATAAAAAAGTTTAATAAAATTAA 26 5 0 AATTAATAAA 0.844579 -61 AAATTAAGTAAATTTTAATAAAAAAGTTTAATA 26 18 0 AATTAATAAA 0.844579 -48 TACCGTATTAATACTTAAAAATATCTTTAAACT 27 158 0 ATTTAAAAAA 0.788133 -69 ATTTCTATTAAACGTTAATAAGAGGGATAAAA 27 205 1 AATTAATAAA 0.844579 -22 ** ******* * Masking position 8 Map Score: 28.0038 Number of sites scoring better than the average of aligned sites = 545 Number in coding regions = 418 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 8 ATTTTTAGTATAAAGAATAAAAATAATTAA 2 63 1 TAAAGAATAA 0.811277 -238 AACTCCCCAATAAAGAAAAATTTTAAATAT 2 219 1 TAAAGAAAAA 0.811277 -82 GTTGGATTTAAATAGAATTACCTTCTACTC 7 35 0 AATAGAATTA 0.557147 -229 AAAAAAATAAAAAAGAAAAAGTTAAGGAAT 8 11 0 AAAAGAAAAA 0.849879 -60 TTTAAAGAAAAAATTTCTAATT 9 3 1 TAAAGAAAAA 0.811277 -298 GATTTTAAATAAAAGAACAATAGTTTCTTT 12 29 1 AAAAGAACAA 0.879352 -245 ACGACTTTATAAAAGAATAATCCATATTTA 13 41 0 AAAAGAATAA 0.849879 -137 AAGAGTGTAGTAAAGAACTAATAAAAAAGG 13 73 1 TAAAGAACTA 0.807782 -105 AGATAATTATAAAAGAAAAAGATATATTAA 18 51 0 AAAAGAAAAA 0.849879 -35 AATAAAATTTTAAAGAATTAATATAAGCCT 23 156 1 TAAAGAATTA 0.765488 -145 AAAGCTAAAGTATAGAATAAAATTTTAATG 24 79 1 TATAGAATAA 0.557147 -31 AAATATTTTAAAAAGAACTATAGTCAAAAC 25 100 0 AAAAGAACTA 0.846964 -201 TTAACATTTGAAAAGAACTATAAATTTTTT 25 199 1 AAAAGAACTA 0.846964 -102 ATTAACGTTTAATAGAAATAGAAACAATAA 27 194 0 AATAGAAATA 0.557147 -33 ********** Masking position 6 Map Score: 12.2725 Number of sites scoring better than the average of aligned sites = 640 Number in coding regions = 535 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 9 TACCACCCTGTAGTGTTTTTTATACAGATGT 1 13 1 TAGTTTTTTT 0.867584 -83 GAAGTTTAATTATTTTTATTCTTTATACTAA 2 67 0 TATTTTATTC 0.532532 -234 TAGAACATTATATTCTCTTTTTAGCTTATGA 2 143 1 TATTTCTTTT 0.917171 -158 GAATTTTTCCTATTTTTATTTAAAGATTTGA 3 177 1 TATTTTATTT 0.718406 -124 AAATAATATCTATTTTCTTTTTATTTTCTTT 5 23 1 TATTTCTTTT 0.917171 -217 ATTTTCTTTTTATTTTCTTTTTAAGAGAAAG 5 34 1 TATTTCTTTT 0.917171 -206 AAGAGAAAGTTATTCTCATTTTTGCAGAAAA 5 56 1 TATTTCATTT 0.804261 -184 CTTTTTCTAAAAGTTTCTTTTAAAACCTCAA 6 38 1 AAGTTCTTTT 0.430189 -125 ATAGTTCCTTTTTGTGGATTTA 7 2 1 TAGTCCTTTT 0.824926 -262 TAAGTTTTTGTATTGTTATTTGATTGACGGT 9 269 0 TATTTTATTT 0.718406 -32 TTATGTTTTTTATTGTGTTTTTAGAAATACA 11 18 0 TATTTGTTTT 0.589125 -72 AAAAGAACAATAGTTTCTTTTGTTATATCGT 12 39 1 TAGTTCTTTT 0.913437 -235 AAACATTTTTTATTATTTTTTGCAGTAGTAA 12 136 1 TATTTTTTTT 0.873021 -138 ATTTTTAATATATTATCTTTCA 12 262 1 TATTTCTTTC 0.831774 -12 GTGATTATGATATTCCTTTTTTATTAGTTCT 13 86 0 TATTCTTTTT 0.7543 -92 ATCTTTGATATATTTTTATTTTTTATTTCAC 25 68 1 TATTTTATTT 0.718406 -233 GTTTTGACTATAGTTCTTTTTAAAATATTTT 25 100 1 TAGTCTTTTT 0.745263 -201 AAAAAATTTATAGTTCTTTTCAAATGTTAAT 25 198 0 TAGTCTTTTC 0.566418 -103 CTTTTTTATATAGTGTCTTTCAAAAACATTT 27 26 1 TAGTTCTTTC 0.824926 -201 **** ****** Masking position 4 Map Score: 16.0568 Number of sites scoring better than the average of aligned sites = 390 Number in coding regions = 286 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 10 AACTTACACCAAAAATTATTT 2 290 0 ACTTACACCA 0.637442 -11 AATATCACCTCTACACCATT 3 291 0 AATATCACCT 0.876046 -10 ATCTCTTCATATTATCACCTCCATTTGTGA 4 154 0 ATTATCACCT 0.844424 -66 AATTTCACCAATTAATTTAA 8 61 0 AATTTCACCA 0.911872 -10 ACTTTATCACCTAAGTTTTTGT 9 289 0 TTTATCACCT 0.74007 -12 ATATTTCACCAAAATACCTAT 10 2 1 TATTTCACCA 0.844424 -131 TTTATCACCAATAACACTCT 11 80 0 TTTATCACCA 0.806516 -10 CCTATCACCAGCAGTATTTT 17 291 0 CCTATCACCA 0.793591 -10 AATTTCACCAGCAAAATTTT 20 32 0 AATTTCACCA 0.911872 -10 ACTTTCACCTTAGCTATAAC 25 291 0 ACTTTCACCT 0.89512 -10 ********** Masking position 7 Map Score: 2.78471 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 77 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 11 CTCATAAAATTATTTAAAGGTATATAATATT 1 67 0 TATTTAAAGT 0.707359 -29 AAATATTTTTAGTATAAAGAATAAAAATAAT 2 59 1 AGTATAAAGA 0.178576 -242 AAAAGCTCTAAGTTTTTAGCTAAAGGAATTT 3 152 1 AGTTTTTAGT 0.451248 -149 TTCCTATTTTTATTTAAAGATTTGATGTAAT 3 183 1 TATTTAAAGT 0.707359 -118 ATAGACGAAAAGTTTATATATTAGAATCGCA 4 110 1 AGTTTATATT 0.336596 -110 AATGTTATTGAATATAAAGTTAATGGTTAAT 5 203 0 AATATAAAGT 0.707358 -37 TATATGTGATAGTTTATAGGTATTTTGGTGA 10 16 0 AGTTTATAGT 0.923819 -117 CTCTAAAAGCAGTAGATAGATGATTATCCCA 10 55 0 AGTAGATAGT 0.264402 -78 TGCATTTTATAATTTATGGTTGTTAATAATT 10 93 1 AATTTATGGT 0.47909 -40 TCTCAATCCTAATTAAAAGTTATCGTTGGAA 12 176 1 AATTAAAAGT 0.549633 -98 ATTGATTTAGAATTAAAAGATGCATTTTTAA 12 228 1 AATTAAAAGT 0.549683 -46 GAATAATCCATATTTATAGTTTAAGTATTCA 13 26 0 TATTTATAGT 0.707359 -152 GTAATAATAAAGTTTAAAGTTAGTGACAGTG 13 116 0 AGTTTAAAGT 0.923733 -62 GAATAGTTATAATTTATAGTTATAATTTAAT 14 100 1 AATTTATAGT 0.901438 -31 GTGTTTACTCTATTTATAGATTCTAAATTTT 23 18 1 TATTTATAGT 0.707359 -283 GGACTTTTGCAGTTTATAGATTTGTTAAGGT 23 256 0 AGTTTATAGT 0.923819 -45 TAATATAAAAAATTTATAGTTCTTTTCAAAT 25 204 0 AATTTATAGT 0.901438 -97 TTACATTGTAAGTATAAAGATTAAAAATTAA 25 232 1 AGTATAAAGT 0.762162 -69 TAATAATTAAAATTTAAAGTTATAGCTAAGG 25 273 1 AATTTAAAGT 0.901365 -28 AAGACAGTATAGTTTAAAGATATTTTTAAGT 27 148 1 AGTTTAAAGT 0.923817 -79 ********* * Masking position 3 Map Score: 13.6995 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 179 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 12 ATAATATTTATAATCATATATATCTTCCTA 1 45 0 TAATCATATA 0.942712 -51 CTTTTCTTAATCGTATATTTCTCATAA 3 8 1 TAATCGTATA 0.813763 -293 ATAATGTTGATAATCATATAAAAATTTTTT 3 98 0 TAATCATATA 0.942712 -203 TATATAAATACAATAATATAAATAAAAAAG 4 67 0 CAATAATATA 0.570942 -153 TTAAATTTTTTAATCAAATAAAAAATAAGA 5 162 0 TAATCAAATA 0.838682 -78 TATATACCGTCAATCAAATAACAATACAAA 9 264 1 CAATCAAATA 0.81094 -37 ATGATTATCCCAATCATATATATATGTGAT 10 37 0 CAATCATATA 0.931383 -96 ATGATTGGGATAATCATCTATCTACTGCTT 10 50 1 TAATCATCTA 0.793595 -83 TATGAAAAAATAATCCTATAATTAAAGTTT 15 218 1 TAATCCTATA 0.813808 -34 ********** Masking position 4 Map Score: 3.26941 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 22 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 13 CCTCTAAGAGGATGAAAACTAAGAA 2 6 1 AAGAGGATGA 0.888225 -295 AAACTTCTTTAAGAGAAAGCTTTTCCTAAA 2 91 1 AAGAGAAAGC 0.89008 -210 TGATAATATGAAGAGATAGAAAAAAGCAGT 4 167 1 AAGAGATAGA 0.798738 -53 TTTTCTTTTTAAGAGAAAGTTATTCTCATT 5 46 1 AAGAGAAAGT 0.905962 -194 TTAGGAGAAAAAGAGGAAGATATTGAGAAG 7 85 0 AAGAGGAAGA 0.95596 -179 AAAAATAAAAAAGAAAAAGTTAAGGAAT 8 9 0 AAGAAAAAGT 0.687845 -62 TGATAAAAGAGGATGAAACTCTTTGA 16 7 1 AAGAGGATGA 0.888225 -80 ATAATTATAAAAGAAAAAGATATATTAAAT 18 49 0 AAGAAAAAGA 0.835127 -37 ********** Masking position 4 Map Score: 2.15567 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 222 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 14 ********** No masking Map Score: 6.43995e-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 15 ********** No masking Map Score: 6.43995e-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