AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00130_mjan_reg_300.orf -o00130_mjan_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: MJ1076 33 M. jannaschii predicted coding region MJ1076 Input sequences: #1 MJ0102 300 Phenylacrylic acid decarboxylase #2 MJ0237 300 arginyl-tRNA synthetase (argS) #3 MJ0238 131 anthranilate synthase component II (trpG) #4 MJ0502 160 3-phosphoshikimate-1-carboxyvinyltransferase (aroA) #5 MJ0503 84 2-isopropylmalate synthase (leuA) #6 MJ0520 192 NADH-ubiquinone oxidoreductase, subunit 1 #7 MJ0522 108 NADH dehydrogenase I #8 MJ0524 123 conserved hypothetical protein #9 MJ0525 122 conserved hypothetical protein #10 MJ0528 74 conserved hypothetical protein #11 MJ0529 132 repressor protein, putative #12 MJ0669 59 ATP-dependent RNA helicase, DEAD-family (deaD) #13 MJ0671 56 riboflavin-specific deaminase (ribG) #14 MJ0672 263 membrane bound transport protein, putative #15 MJ0771 88 cobalamin biosynthesis precorrin-2 methyltransferase (cbiL) #16 MJ1027 125 formate hydrogenlyase, subunit 5 #17 MJ1028 60 DNA topoisomerase VI, subunit B (top6B) #18 MJ1029 47 dimethyladenosine transferase (ksgA) #19 MJ1077 89 seryl-tRNA synthetase (serS) #20 MJ1078 273 M. jannaschii predicted coding region MJ1078 #21 MJ1079 177 conserved hypothetical protein #22 MJ1080 130 M. jannaschii predicted coding region MJ1080 #23 MJ1123 70 conserved hypothetical protein #24 MJ1195 135 2-isopropylmalate synthase (leuA) #25 MJ1196 85 asoB protein #26 MJ1309 37 carbon monoxide dehydrogenase, hydrogenase anchor subunit CooM (cooM) #27 MJ1310 83 conserved hypothetical protein #28 MJ1362 68 NADH ubiquinone oxidoreductase, subunit 1 isolog #29 MJ1363 300 formate hydrogenlyase, subunit 7 #30 MJ1392 300 2-isopropylmalate synthase (leuA) #31 MJ1521 88 Na+/H+ antiporter #32 MJ1522 146 cobalamin biosynthesis precorrin-6Y methylase (cbiE) #33 MJ1575 300 GMP synthase (guaA) #34 MJ1576 80 LemA protein #35 MJ1577 29 M. jannaschii predicted coding region MJ1577 #36 MJ1578 66 cobalamin biosynthesis precorrin-3 methylase (cbiF) #37 MJ1656 300 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase (hpcE) Motif number 1 AACCTAAAATAAAATAATAAAATGGTGCCG 1 189 0 AAAATAATAA 0.76674 -112 TAAATCTAAAAAAATAAATATAACAACCTA 1 213 0 AAAATAAATA 0.817664 -88 TAAGATTTAAAAAATAAATACTATTTAAAA 1 255 0 AAAATAAATA 0.817664 -46 TTTTTAAATAAATTTAATTACATACCTAAA 2 94 0 AATTTAATTA 0.663757 -207 TACTATGGAAAATATAAAAACCCAATGGGT 2 123 0 AATATAAAAA 0.911547 -178 TTAATTTATTAATTTAAATAAATGATAGAA 2 217 0 AATTTAAATA 0.878072 -84 TTAAATTAATAAATTAAAAAGAAGGTATTT 2 230 1 AAATTAAAAA 0.957409 -71 TTTTTTATTTAATTTAAAAATTGGGGATTT 2 265 0 AATTTAAAAA 0.950658 -36 TTTAGTACAAAAAATAATTAAATAATTTTA 3 15 0 AAAATAATTA 0.551131 -117 ACTTACTTAATTTATAAATGTTAATTTT 4 9 1 AATTTATAAA 0.855009 -152 TGATTAAAAAATAATAAAAAAATTTATACA 5 50 1 ATAATAAAAA 0.864976 -35 AAATATTAAAATAAAAATCTGGGTGAG 6 8 1 AAAATAAAAA 0.923106 -185 ATCTCACCTAATTTTATTAAATAATGGACA 7 86 0 ATTTTATTAA 0.462847 -23 TAATCAATCTAATATATAAACTTTTCGTCT 11 32 1 AATATATAAA 0.758937 -101 TCCTCTGGGAAATATATAAAAGTTACCCAC 11 70 0 AATATATAAA 0.758937 -63 TAAAACTTAAATTTTATTAACTAAACATTT 13 33 1 ATTTTATTAA 0.462847 -24 CAGTTAAAAAATATTAAAAACAATTATTAC 14 21 0 ATATTAAAAA 0.923025 -243 TGGAAATAATAAAATAATAAGAAAGAAATC 14 51 0 AAAATAATAA 0.76674 -213 AATTTAGCTAAATTTATATAGTAAGTTATC 15 31 1 AATTTATATA 0.687779 -58 CTTACGATTTTATAAAATTACAATTA 15 73 0 ATTTTATAAA 0.758807 -16 AAATATCAGTAAAATAAATAATGTAACAAA 17 40 0 AAAATAAATA 0.817664 -21 AAGAGAAAAGAAAATAAAAAT 18 2 0 AAAATAAAAA 0.923106 -46 AGAGGGACAGATTTTAAATAAAAGAACAAT 20 20 1 ATTTTAAATA 0.793328 -254 ATTAGTGTTAATTTTAAAAAAACAAACATT 20 113 1 ATTTTAAAAA 0.911255 -161 ACTGCAAAAAATAATAAAAAATGTTTGTTT 20 132 0 ATAATAAAAA 0.864976 -142 TATTAAAAATATATTAAAAATGCATCTTTT 20 242 0 ATATTAAAAA 0.923025 -32 GAAAGATAATATATTAAAAATATATTAAAA 20 253 0 ATATTAAAAA 0.923025 -21 AAGTTTTTTAAAATTAAAAATGAATGTAAT 21 142 0 AAATTAAAAA 0.957409 -36 CCTTAATTAAATTTTAAATATTAAACTTGA 22 72 1 ATTTTAAATA 0.793328 -59 TTATAGTTATAATTTAATAATTTAGAAC 22 113 1 AATTTAATAA 0.840871 -18 TAATATTACAAAATTATAAAATATTATCAT 23 15 0 AAATTATAAA 0.87293 -56 ATTTTGTAATATTATAAAAATGTTAGAATT 23 31 1 ATTATAAAAA 0.846113 -40 AAATAACAGAAAATTAAAAAGTTTTGGTGG 24 112 1 AAATTAAAAA 0.957409 -24 AGAAAAAGATATATTAAATATTTTTGCTTT 25 39 1 ATATTAAATA 0.817529 -47 CACTCATAAAATTTTATAAAAACC 28 5 0 ATTTTATAAA 0.758807 -64 TAAAACATACAAAATAAAAACAAACTCATA 29 29 1 AAAATAAAAA 0.923106 -272 TGGTATTGGAAAATTAATAAAAAGTATTAC 29 97 0 AAATTAATAA 0.860294 -204 GCAAGAAATTAAATTAAAAAATCTATTATG 29 199 1 AAATTAAAAA 0.957409 -102 TGATGTATAAAATATAAATAGATTATGCTT 29 248 0 AATATAAATA 0.793804 -53 TCTTTCAAAAATAATAAAAATTTTATAAAG 30 53 1 ATAATAAAAA 0.864976 -248 AAGAAATCTTAATTTATAAATTTAAATTTA 30 129 1 AATTTATAAA 0.855009 -172 TCCCACATAAATTTTAAATATACAATATCA 30 196 1 ATTTTAAATA 0.793328 -105 AATTTAATGAAATTTAAATACTCATAATGA 30 261 0 AATTTAAATA 0.878072 -40 GTATATCCAGATATTAAAAACTAAAAGATT 31 60 1 ATATTAAAAA 0.923025 -29 TTGAATTAAAAATTTAAAAATTGAAA 32 7 0 AATTTAAAAA 0.950658 -140 ATAAAATAAGAATATAAAAATATAAGTTAA 32 40 0 AATATAAAAA 0.911547 -107 AATATCAATAAAATTAAAAAGATAAGGTAA 32 88 0 AAATTAAAAA 0.957409 -59 GTTAAAATTAATATTAATAATGGATATTTG 33 81 1 ATATTAATAA 0.766661 -220 CTAATAATAAAATTTATATAAGTTGATATC 34 11 1 AATTTATATA 0.687779 -70 CTAAAAATTAAAATTAATAA 35 1 0 AAATTAATAA 0.860294 -29 AGGTCTTTCAAAATTAATAAAATTTACTTA 36 17 0 AAATTAATAA 0.860294 -50 TAGTCCTCTAAAATTATAAAACAATCTCTT 37 217 0 AAATTATAAA 0.87293 -84 ********** Masking position 5 Map Score: 70.5753 Number of sites scoring better than the average of aligned sites = 2080 Number in coding regions = 1338 Number in noncoding regions = 742 Number of orfs with sites within 600 bp upstream = 506 Fraction of orfs with sites within 600 bp upstream = 0.0812721 Motif number 2 CAAACGAAACTTTTAGAAAAAGTTAAACAAAATC 1 144 0 TTTTAGAATT 0.86908 -157 GATTAACTATTTTTAAATAGTATTTATTTTTTAA 1 245 1 TTTTAAAATT 0.92361 -56 ATAGTATTTATTTTTTAAATCTTAACTTAACAGT 1 261 1 TTTTTTAATA 0.658404 -40 CCCAATGGGTTTTTAAATAAATTTAATTACATAC 2 99 0 TTTTAAAATT 0.92361 -202 CTCTCTCATTTTTTATTTAATTTAAAAATTGGGG 2 269 0 TTTTATTATA 0.610401 -32 TTGTACTAAATTTTTAAGATTTTTATAGTAAAAG 3 35 1 TTTTTAAATT 0.834513 -97 TTTTATTATTTTTTAATCAAAATATCAATATGAA 5 35 0 TTTTAATATA 0.776579 -50 TAAACGAAACTTTTAGAAAAAGTTGAACGAAAAC 6 66 1 TTTTAGAATT 0.86908 -127 CTATGGGAACTTTTAATCAATCTAATATATAAAC 11 19 1 TTTTAATATA 0.776579 -114 AAAATTTAATTTTTAAAGATGCTAAAAAGAGATT 12 35 0 TTTTAAAATA 0.911131 -25 GTAATAATTGTTTTTAATATTTTTTAACTGGATT 14 21 1 TTTTTAAATT 0.834513 -243 TTAAAAACTTTTTTAGATAACTTACTATATAAAT 15 42 0 TTTTAGAATA 0.849148 -47 TATAGTTTTGTTTTAATAAAGTTATCGAG 16 6 0 TTTTAATATA 0.776579 -120 TAGCTTAACCTTTTATATAGTTTTGTTTTAATAA 16 21 0 TTTTATAATT 0.844959 -105 CCAACAATTATAAACATGATAATAGGTATAT 16 105 0 TTATAAAATA 0.678826 -21 TAATTTCTATTTTGTTACATTATTTATTTTACTG 17 30 1 TTTGTTAATT 0.392278 -31 TGTTTCACTTTTTATTTATTCTAAAAAAGAGAA 18 25 0 TTTTATTATA 0.610402 -23 TATTGTGTTTTTAGAAATACAGTTTAAT 19 5 0 TTAGAAAATT 0.414457 -85 AATAGTTTCTTTTGTTATATCGTTGGGCATAATT 20 47 1 TTTGTTAATT 0.392278 -227 TTGGGCATAATTTTATACATATTATCAAAAATTG 20 69 1 TTTTATAATA 0.822106 -205 AAAATGTTTGTTTTTTTAAAATTAACACTAATTT 20 111 0 TTTTTTTATA 0.395204 -163 AAACAAACATTTTTTATTATTTTTTGCAGTAGTA 20 132 1 TTTTTATATT 0.630946 -142 CAACGATAACTTTTAATTAGGATTGAGATATAAA 20 170 0 TTTTAATATT 0.803885 -104 ATGTTGGTATTTTTAAAAAGATTTTCCAACGATA 20 196 0 TTTTAAAATT 0.92361 -78 TTTTAATATATTTTTAATATATTATCTTTCA 20 253 1 TTTTTAAATA 0.810466 -21 TCATTTTTAATTTTAAAAAACTTAAAACAGAGTG 21 149 1 TTTTAAAATA 0.911131 -29 CCCAATTAAATTTTTGATATGTTTTTGATTTGAT 22 29 1 TTTTTGAATT 0.734655 -102 TAGTTATAATTTATAGTTATAATTTAATAATTTA 22 103 1 TTATAGTATT 0.316918 -28 TTTTGTAATATTATAAAAATGTTAGAATTTGTAA 23 32 1 TTATAAAATA 0.678826 -39 TGATGGGATGTTATAAAAATTTTACCTAATCAGA 24 77 0 TTATAAAATA 0.678826 -59 TCTTTTTCTTTTATAATTATCTTTATCTAAAATT 25 14 0 TTATAATATT 0.458003 -72 CCCTCCAATCTTTTAGAGAAAGTTAAATAGAA 26 9 0 TTTTAGAATT 0.86908 -29 AATATTTATGTTTTTAATAGCTTTTAGCTTTTTG 27 14 1 TTTTTAAATT 0.834513 -70 GGTTTTTATAAAATTTTATGAGTGAGA 28 4 1 TTTTATAATT 0.844959 -65 TAAAGTTTTATTTTTAAGAGAATTTATGAGTTTG 29 49 0 TTTTTAAATT 0.834513 -252 TTAGTAATACTTTTTATTAATTTTCCAATACCAA 29 94 1 TTTTTATATT 0.630946 -207 ATCTTTCGGATTTTTAAGATTATAAGTAGGTTGT 29 134 0 TTTTTAAATA 0.810467 -167 AGCGAACAGGTTTTAGAAATCTTTCGGATTTTTA 29 152 0 TTTTAGAATT 0.86908 -149 AGATTATGCTTTATTGAGAATTTTAATATGCATA 29 225 0 TTATTGAATT 0.363369 -76 TTTTATTATTTTTGAAAGATACTATACGAAAGTC 30 38 0 TTTGAAAATA 0.744341 -263 ATAATAAAAATTTTATAAAGATTATTAATAAAGT 30 63 1 TTTTATAATA 0.822106 -238 TTAAGATTTCTTTTAAAGATTTTATTCCTGCGAA 30 107 0 TTTTAAAATA 0.911131 -194 ATCTTTTTAATTTTATTGATATTTAAAAACATAA 32 95 1 TTTTATTATT 0.648833 -52 TTTTAACAACTTTGAAAGACACTATATTTTAAAA 33 54 0 TTTGAAAATA 0.744341 -247 TCAAAAACATTTTGAAAGAACCTTTTAGTAAAAG 33 248 0 TTTGAAAATT 0.774443 -53 TCAAAATGTTTTTGAAAGATACTAATAAAATATA 33 267 1 TTTGAAAATA 0.744341 -34 TGATATCAACTTATATAAATTTTATTATTAG 34 8 0 TTATATAATA 0.487888 -73 TTGTGTATTATTTTAGACACTTTTAGAGATGAGG 37 48 1 TTTTAGAATT 0.86908 -253 ******* * ** Masking position 9 Map Score: 58.3212 Number of sites scoring better than the average of aligned sites = 1492 Number in coding regions = 1075 Number in noncoding regions = 417 Number of orfs with sites within 600 bp upstream = 337 Fraction of orfs with sites within 600 bp upstream = 0.0541279 Motif number 3 TGAAAACTCTTTTAGTTTTCATTTAACCGAAGCG 1 84 1 TTTATTATTT 0.905745 -217 TTATTTTATTTTAGGTTGTTATATTTATTTTTTT 1 202 1 TTAGTTATAT 0.690322 -99 TGTAAAATTATTTAATTATTTTTTGTACTAAATT 3 13 1 TTTATTTTTT 0.894729 -119 CAGAGTATAATTTAAATGTGATATATTAAGGTTG 4 116 0 TTTATTATAT 0.816204 -45 AATTTAGCTATCATTTAGAATATAAA 13 3 1 TTTATTATTT 0.905745 -54 GTTAATAAAATTTAAGTTTTATATTCTAAATGAT 13 20 0 TTTATTATAT 0.816204 -37 AATTTTTACTTTAAGTTTTGTTTTGTAAAAGAGA 14 123 1 TTAATTTTTT 0.932248 -141 ATGTTAATAGTTAAGTTTTTATATCTCTTGTATG 14 196 0 TTAATTATAT 0.87789 -68 TAAAAAAGTTTTTAATTGTAATTTTATAAAATCG 15 61 1 TTTATTATTT 0.905745 -28 GATAATTAGCTTAACCTTTTATATAGTTTTGTTT 16 27 0 TTAATTATAT 0.87789 -99 AATAGTTTAGTTAATTTCTATTTTGTTACATTAT 17 19 1 TTAATTTTTT 0.932248 -42 TGTTTCACTTTTTATTTATTCTAAAAA 18 31 0 TTCATTATTT 0.815573 -17 TAATTAGGTATTTATGTTTTTTATTGTGTTTTTA 19 26 0 TTTATTTTAT 0.797066 -64 GTCACTAACTTTAAACTTTATTATTACATTCATT 21 120 1 TTAATTTTAT 0.864106 -58 TATTATTACATTCATTTTTAATTTTAAAAAACTT 21 138 1 TTCATTATTT 0.815573 -40 ATTATAACTATTCAAGTTTAATATTTAAAATTTA 22 79 0 TTCATTATAT 0.671443 -52 TAAATGAACTTTAATCTATCATTTTGAAAGGTTA 24 20 1 TTAATTATTT 0.939603 -116 GCAAAAATATTTAATATATCTTTTTCTTTTATAA 25 32 0 TTAATTTTTT 0.932242 -54 AATTTATGAGTTTGTTTTTATTTTGTATGTTTTA 29 29 0 TTTGTTTTTT 0.724922 -272 TTTTTCAATTTTAAAGTTTTATTTTTAAGAGAAT 29 60 0 TTAATTATTT 0.939603 -241 TAAAGCATAATCTATTTATATTTTATACATCACT 29 246 1 TCTATTTTTT 0.601476 -55 AATTTATAAATTAAGATTTCTTTTAAAGATTTTA 30 117 0 TTAATTTTTT 0.932248 -184 TTAAATTTCATTAAATTATTTTTTATGAGGGATT 30 274 1 TTAATTTTTT 0.932248 -27 CACCAATCTTTTAGTTTTTAATATCTGGATATAC 31 60 0 TTAGTTATAT 0.690322 -29 AATTCAAAATTTAACTTATATTTTTATATTCTTA 32 30 1 TTAATTTTTT 0.932248 -117 ACACTATATTTTAAAATTTCTTTTATTATGATTA 33 36 0 TTAATTTTTT 0.932248 -265 TCCAAATAATTCAAATTCTTTTTTGTGGTGAAAT 34 56 1 TCAATTTTTT 0.709587 -25 TGGACTTTTATTTGTGTATTATTTTAGACACTTT 37 37 1 TTTGTTATTT 0.748718 -264 GGCTATAAGCTTTGGTTTTGATATTGAAGAACTA 37 80 1 TTTGTTATAT 0.579291 -221 TTTGGGAACTTTAAAATCTCTTTTTTAACAGCTC 37 147 0 TTAATTTTTT 0.932248 -154 TGATTCATTATCAACCTCTGTTTTTGGGAACTTT 37 169 0 TCAATTTTTT 0.709587 -132 TAATGAATCATTAACTTATTATTTAAGAGATTGT 37 193 1 TTAATTATTT 0.939603 -108 **** * * **** Masking position 7 Map Score: 45.8118 Number of sites scoring better than the average of aligned sites = 787 Number in coding regions = 527 Number in noncoding regions = 260 Number of orfs with sites within 600 bp upstream = 218 Fraction of orfs with sites within 600 bp upstream = 0.0350145 Motif number 4 AGCGAAGCGAGGAGGTGTTAGTTTTTGATG 6 140 0 GGAGGTGTTA 0.993715 -53 CGCTTCGCTCGGAAGTGTAAATTTACAACT 6 161 1 GGAAGTGTAA 0.9423 -32 GCGTAAGCGAGGAGGTGTTAGGGTGTATCC 8 62 0 GGAGGTGTTA 0.993715 -62 GCTTACGCTCGGAGGTGTAAATTAATTTTG 8 84 1 GGAGGTGTAA 0.988086 -40 TGGAACTCTTGGAACTGTTATAGGGCCGAA 9 82 1 GGAACTGTTA 0.904604 -41 TCTCCTATAGGGAGGTGTTCATTAATGCCT 33 116 1 GGAGGTGTTC 0.973642 -185 GCTTACGCTCGGAGGTGCAACTCAGAAGGA 33 192 0 GGAGGTGCAA 0.950925 -109 GCGTAAGCGAGGAGGTGTTAGATTTTTGAT 33 214 1 GGAGGTGTTA 0.993715 -87 AGGAATTAATGGAGCTGTTAAAAAAGAGAT 37 136 1 GGAGCTGTTA 0.979657 -165 ********** Masking position 6 Map Score: 16.7461 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 1 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 5 ATGGATTAACTATTTTTAAATAGTATTTAT 1 242 1 TATTTTTAAA 0.776628 -59 TTAACTTAACAGTTTTTAATGGTGAATTT 1 282 1 AGTTTTTAAT 0.874408 -19 AAACCCAATGGGTTTTTAAATAAATTTAAT 2 106 0 GGTTTTTAAA 0.539219 -195 TTAAATACCTTCTTTTTAATTTATTAATTT 2 232 0 TCTTTTTAAT 0.693457 -69 GAAAATCCCCAATTTTTAAATTAAATAAAA 2 263 1 AATTTTTAAA 0.753117 -38 TTTTGTACTAAATTTTTAAGATTTTTATAG 3 33 1 AATTTTTAAG 0.606294 -99 CACCACTAATTTTTTAATCAACAGAGTA 4 143 0 ATTTTTTAAT 0.621726 -18 TTTTTTTATTATTTTTTAATCAAAATATCA 5 42 0 ATTTTTTAAT 0.621726 -43 AGGAGGTGTTAGTTTTTGATGAAATGGAGA 6 131 0 AGTTTTTGAT 0.756356 -62 TAAAATTTAATTTTTAAAGATGCTAAAA 12 42 0 AATTTTTAAA 0.753117 -18 CTGTAATAATTGTTTTTAATATTTTTTAAC 14 19 1 TGTTTTTAAT 0.888085 -245 TATCTAAAAAAGTTTTTAATTGTAATTTTA 15 57 1 AGTTTTTAAT 0.874408 -32 TTAACTAAACTATTTTTAAACT 17 3 0 TATTTTTAAA 0.776628 -58 TAGGTATTTATGTTTTTTATTGTGTTTTTA 19 26 0 TGTTTTTTAT 0.410628 -64 TATCTAAATCAATTTTTGATAATATGTATA 20 82 0 AATTTTTGAT 0.746403 -192 AAAATGTTTGTTTTTTTAAAATTAACACTA 20 115 0 TTTTTTTAAA 0.464007 -159 TCAATGTTGGTATTTTTAAAAAGATTTTCC 20 203 0 TATTTTTAAA 0.776628 -71 TTAAAAGATGCATTTTTAATATATTTTTAA 20 240 1 CATTTTTAAT 0.622393 -34 ATTTTTAATATATTTTTAATATATTATCTT 20 251 1 TATTTTTAAT 0.882679 -23 TTATTACATTCATTTTTAATTTTAAAAAAC 21 140 1 CATTTTTAAT 0.622393 -38 TACCCAATTAAATTTTTGATATGTTTTTGA 22 27 1 AATTTTTGAT 0.746403 -104 ATTTTTGATATGTTTTTGATTTGATGTGAT 22 38 1 TGTTTTTGAT 0.779649 -93 TCCCACCAAAACTTTTTAATTTTCTGTTAT 24 114 0 ACTTTTTAAT 0.664968 -22 TTAATATTTATGTTTTTAATAGCTTTTAGC 27 12 1 TGTTTTTAAT 0.888085 -72 TTTAAAGTTTTATTTTTAAGAGAATTTATG 29 55 0 TATTTTTAAG 0.637049 -246 AAATCTTTCGGATTTTTAAGATTATAAGTA 29 140 0 GATTTTTAAG 0.359018 -161 TGCATAATAGATTTTTTAATTTAATTTCTT 29 201 0 ATTTTTTAAT 0.621726 -100 AAATTTTTATTATTTTTGAAAGATACTATA 30 46 0 TATTTTTGAA 0.607882 -255 TTCATTAAATTATTTTTTATGAGGGATTGT 30 280 1 TATTTTTTAT 0.397796 -21 CCAATCTTTTAGTTTTTAATATCTGGATAT 31 62 0 AGTTTTTAAT 0.874408 -27 TCAATTTTTAAATTTTTAATTCAAAATTTA 32 13 1 AATTTTTAAT 0.868439 -134 CTTTACCTTATCTTTTTAATTTTATTGATA 32 86 1 TCTTTTTAAT 0.693457 -61 ATTACTATTATGTTTTTAAATATCAATAAA 32 106 0 TGTTTTTAAA 0.785736 -41 GGAGGTGTTAGATTTTTGATGAACCTTTTA 33 224 1 GATTTTTGAT 0.517025 -77 TCTTTCAAAATGTTTTTGAAAGATACTAAT 33 263 1 TGTTTTTGAA 0.620507 -38 ********** Masking position 5 Map Score: 34.2499 Number of sites scoring better than the average of aligned sites = 1186 Number in coding regions = 906 Number in noncoding regions = 280 Number of orfs with sites within 600 bp upstream = 272 Fraction of orfs with sites within 600 bp upstream = 0.0436878 Motif number 6 ACAACCTAAAATAAAATAATAAAATGGTGCCGAGG 1 186 0 ATAAAAAAAT 0.867987 -115 AGAAAAGTTTATATATGAAGATGATATTATAAGAA 2 186 0 ATATAAAAAT 0.72429 -115 AGACATAATTATAAAGGATAATAATCACCTTTTAC 3 62 0 ATAAAATAAT 0.937186 -70 AGAATCGGGTATATAGAATTATCATAATTTCATTT 4 60 1 ATATAATAAT 0.855753 -101 AACGAGTTCCATAAATATTCACCATACTTTTTC 9 9 0 ATAAATTAAT 0.894924 -114 TTTTCATAATCAATCATTATATTATCGCCA 11 113 0 ATAATATAAT 0.509447 -20 GAGTCTATGAATAATGAATAAACATACAAGAGATA 14 174 1 ATAATATAAT 0.860686 -90 ATAATTTATCATAATTAATAATGATAATTAGCTTA 16 48 0 ATAATATAAT 0.837815 -78 AGTAAAATAAATAATGTAACAAAATAGAAATTAAC 17 28 0 ATAATAAAAT 0.752997 -33 TGCATTTTTAATATATTTTTAATATATTATCTTTC 20 248 1 ATATATTAAT 0.761242 -26 TACTTAAACTATAAATATGGATTATTCTTTTATAA 21 30 1 ATAAATGAAT 0.773076 -148 TAAAGAACTAATAAAAAAGGAATATCATAATCACA 21 83 1 ATAAAAGAAT 0.881044 -95 AATTATAACTATAAATTATAACTATTCAAGTTTAA 22 92 0 ATAAAATAAT 0.936848 -39 TTACAAAATTATAAAATATTATCATTGAG 23 5 0 ATAAAATAAT 0.936945 -66 TAACATTTTTATAATATTACAAAATTATAAAATAT 23 21 0 ATAATTAAAT 0.633709 -50 AAAGATAATTATAAAAGAAAAAGATATATTAAATA 25 24 1 ATAAAAAAAT 0.868076 -62 TCTCTTAAAAATAAAACTTTAAAATTGAAAAATTA 29 62 1 ATAAATTAAT 0.894713 -239 GATGTATAAAATATAAATAGATTATGCTTTATTGA 29 242 0 ATATATAAAT 0.557277 -59 TATTTCCCACATAAATTTTAAATATACAATATCAA 30 192 1 ATAAATTAAT 0.881554 -109 GAATCTGATGATAAAATTGAATCATCTCAAAGATA 30 228 0 ATAAATGAAT 0.834062 -73 CAGAATAAGAATATAAAATAAGAATATAAAAATAT 32 47 0 ATATAATAAT 0.856269 -100 TCACATTCAAATAATTTATTACTATTATGTTTTTA 32 118 0 ATAATATAAT 0.852366 -29 ACTGACTTCAATAAATTTGGAGGATAATCATAATA 33 12 1 ATAAATGAAT 0.834451 -289 TTATCACCTTATATTTTATTAGTATCTTTCAAAAA 33 275 0 ATATTATAAT 0.719839 -26 TTTGGTTTTGATATTGAAGAACTATCTCTTAATAT 37 90 1 ATATTAGAAT 0.591697 -211 ***** ** * ** Masking position 2 Map Score: 27.9009 Number of sites scoring better than the average of aligned sites = 480 Number in coding regions = 337 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 7 CTTCCGAGCGAAGCGAGGAGGTGTTAGTTTT 6 145 0 AAGCGGGAGG 0.992409 -48 CTCCGAGCGTAAGCGAGGAGGTGTTAGGGTG 8 67 0 AAGCGGGAGG 0.992409 -57 CTCCTCGCTTACGCTCGGAGGTGTAAATTAA 8 78 1 ACGCTGGAGG 0.986459 -46 CTTTCTCTAAAAGATTGGAGGGAGAAT 26 21 1 AAGATGGAGG 0.967248 -17 TAAAAACTAAAAGATTGGTGGGATT 31 74 1 AAGATGGTGG 0.859772 -15 CTCCTCGCTTACGCTCGGAGGTGCAACTCAG 33 197 0 ACGCTGGAGG 0.986459 -104 CTCCGAGCGTAAGCGAGGAGGTGTTAGATTT 33 208 1 AAGCGGGAGG 0.992409 -93 ***** ***** Masking position 1 Map Score: 10.8038 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 5 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 8 ACTTTTTCTAAAAGTTTCGTTTGTATCCCT 1 155 1 AAAGTTTCGT 0.920623 -146 ATCAATCATCAAAGTTTAGGTATGTAATTA 2 80 1 AAAGTTTAGG 0.903366 -221 AAAAATCTTAAAAATTTAGTACAAAAAATA 3 29 0 AAAATTTAGT 0.659331 -103 ACTTTTTCTAAAAGTTTCGTTTATAGTCCC 6 59 0 AAAGTTTCGT 0.920623 -134 TTTTAAATGTTTAGTTAATAAAATT 13 42 0 AATGTTTAGT 0.757532 -15 AGGTATGTTAATAGTTAAGTTTTTATATCT 14 204 0 ATAGTTAAGT 0.69414 -60 AACCTTTTATATAGTTTTGTTTTAATAAAG 16 19 0 ATAGTTTTGT 0.84488 -107 AGTTTAAAAATAGTTTAGTTAATTTCTAT 17 10 1 ATAGTTTAGT 0.951441 -51 AGTATTCAATATAGTTTAGTACA 21 4 0 ATAGTTTAGT 0.951441 -174 AGAAAATTAAAAAGTTTTGGTGGGATT 24 119 1 AAAGTTTTGG 0.722116 -17 TTCTAAATGTAAAGTTTAGTGTCTGTATAT 31 36 1 AAAGTTTAGT 0.964252 -53 AATTATTTGGATAGTTTAGTATGTTTGATA 34 37 0 ATAGTTTAGT 0.951441 -44 ********** Masking position 1 Map Score: 11.9161 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 19 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 9 GAACCCGCGGCCTCCGCACAGCCAATGCGG 2 15 1 CCTCCGCACA 0.86887 -286 AAAACTAACACCTCCTCGCTTCGCTCGGAA 6 145 1 CCTCCTCGCT 0.984251 -48 TAAATTTACACTTCCGAGCGAAGCGAGGAG 6 156 0 CTTCCGAGCG 0.927253 -37 CACCCTAACACCTCCTCGCTTACGCTCGGA 8 67 1 CCTCCTCGCT 0.984251 -57 TTAATTTACACCTCCGAGCGTAAGCGAGGA 8 79 0 CCTCCGAGCG 0.989925 -45 CTGAGTTGCACCTCCGAGCGTAAGCGAGGA 33 197 1 CCTCCGAGCG 0.989925 -104 AAATCTAACACCTCCTCGCTTACGCTCGGA 33 209 0 CCTCCTCGCT 0.984251 -92 ********** Masking position 3 Map Score: 8.48588 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 1 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 10 AAAATGGTGCCGAGGGAGGGATACAAACGAAA 1 169 0 CGAGGGAGGT 0.833464 -132 TAGCTCAGACTGGGAGAGCGCCGCATTGGCTG 2 33 0 TGGGAGAGGC 0.844894 -268 AAATAAAAAATGAGAGAGGGAAGACT 2 285 1 TGAGAGAGGA 0.664079 -16 GGGACAATTTTGGGGGATTGATTTAA 3 116 1 TGGGGGATGT 0.977116 -16 ATAAATCTGGTGGGGGAGGGAT 14 252 1 TGGGGGAGGT 0.983331 -12 ATTTCTTTAGTGAGGGATAGGTT 28 56 1 TGAGGGATGT 0.958276 -13 AAAATTTATGTGGGAAATAGTTCTGGACTAAA 30 179 0 TGGGAAATGT 0.602026 -122 TTATTTTTTATGAGGGATTGTT 30 289 1 TGAGGGATGT 0.958276 -12 CACCTCCCTATAGGAGAGCGTTCAAATATCCA 33 101 0 TAGGAGAGGT 0.92652 -200 TTTTAATTTTTAGGGGATTTTT 35 18 1 TAGGGGATTT 0.682213 -12 AAATCAATATTAAGAGATAGTTCTTCAATATC 37 99 0 TAAGAGATGT 0.830767 -202 ACTTATTATTTAAGAGATTGTTTTATAATTTT 37 206 1 TAAGAGATGT 0.830767 -95 ATGAATTCAGTAGGGGAGTTTTAGATGCATTT 37 273 1 TAGGGGAGTT 0.747855 -28 ******** * * Masking position 7 Map Score: 7.14404 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 139 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 11 ACCTAAAATAAAATAATAAAATGGTGCCGAG 1 187 0 AAATAAAAAA 0.899519 -114 TAATTTAAATAAATGATAGAAAAGTTTATAT 2 207 0 AAATGAAGAA 0.872541 -94 TTTTTAAATTAAATAAAAAATGAGAGAGGGA 2 275 1 AAATAAAAAT 0.711127 -26 TTCTTGTCTCTAATGAGAAAAATTAACATTT 4 26 0 TAATGAAAAA 0.870491 -135 GATTAAAAAATAATAAAAAAATTTATACAGG 5 51 1 TAATAAAAAA 0.878019 -34 AGGGGGAAATAATGAAAAAACTTGGAAACC 8 10 1 TAATGAAAAA 0.870491 -114 ATCAGGGAAATAAAAGAAAGTGGGGCTG 10 8 1 AAATAAAGAA 0.879966 -67 AATAATAAAATAATAAGAAAGAAATCCAGTT 14 46 0 TAATAAAAAG 0.659877 -218 AAAGGCATGGAAATAATAAAATAATAAGAAA 14 57 0 AAATAAAAAA 0.899519 -207 CTTAAAGTAAAAATTATAGAATTTATGAAGT 14 107 0 AAATTAAGAA 0.731205 -157 GACAGATTTTAAATAAAAGAACAATAGTTTC 20 25 1 AAATAAAGAA 0.879966 -249 CTACTGCAAAAAATAATAAAAAATGTTTGTT 20 133 0 AAATAAAAAA 0.899519 -141 AGTAAAGAACTAATAAAAAAGGAATATCATA 21 81 1 TAATAAAAAG 0.659877 -97 AAAATGAATGTAATAATAAAGTTTAAAGTTA 21 125 0 TAATAAAAAG 0.659877 -53 TAATATTACAAAATTATAAAATATTATCATT 23 14 0 AAATTAAAAA 0.768619 -57 AATATTATAAAAATGTTAGAATTTGTAATAA 23 38 1 AAATGTAGAA 0.254206 -33 TAACCTTTCAAAATGATAGATTAAAGTTCAT 24 23 0 AAATGAAGAT 0.653075 -113 ATCCCATCATAAATAACAGAAAATTAAAAAG 24 102 1 AAATAAAGAA 0.879966 -34 TAGATAAAGATAATTATAAAAGAAAAAGATA 25 19 1 TAATTAAAAA 0.727591 -67 TAATGACAGATTAGGTTTAAC 27 73 0 TAATGAAGAT 0.602164 -11 GCAAGAAATTAAATTAAAAAATCTATTATGC 29 199 1 AAATTAAAAA 0.768619 -102 TCATTATCATTAATGACAAATAGTGATGTAT 29 270 0 TAATGAAAAT 0.648915 -31 TCATTAATGATAATGATAAATTACTG 29 285 1 TAATGAAAAT 0.648915 -16 TATCTTTCAAAAATAATAAAAATTTTATAAA 30 51 1 AAATAAAAAA 0.899519 -250 AGGATAATCATAATAAAAGAAATTTTAAAAT 33 32 1 TAATAAAGAA 0.854957 -269 CTAATAATAAAATTTATATAAG 34 2 1 TAATAAAAAA 0.878019 -79 TAGTCCTCTAAAATTATAAAACAATCTCTTA 37 216 0 AAATTAAAAA 0.768619 -85 ****** **** Masking position 4 Map Score: 30.9862 Number of sites scoring better than the average of aligned sites = 888 Number in coding regions = 646 Number in noncoding regions = 242 Number of orfs with sites within 600 bp upstream = 225 Fraction of orfs with sites within 600 bp upstream = 0.0361388 Motif number 12 AGCTACCAGCCCACAAAACAATCAATCATC 2 60 1 CCACAAAACA 0.710555 -241 GCTCTCCATTTCATCAAAAACTAACACCTC 6 129 1 TCATCAAAAA 0.754766 -64 TAAAAGTTACCCACAAAAAATAAGACGAAA 11 54 0 CCACAAAAAA 0.9217 -79 GTCACCAAAAATTTATTGTCA 15 2 1 TCACCAAAAA 0.946819 -87 TTTATCACCAATAACACTCTTATT 19 76 0 TCACCAATAA 0.714706 -14 AATCCCACCAAAACTTTTTAATTT 24 122 0 CCACCAAAAC 0.896912 -14 ATTACGTTAGCAACCAAAAAGCTAAAAGCT 27 32 0 CAACCAAAAA 0.784709 -52 ATTACCACCAAAAAATTTATATGC 31 5 1 CCACCAAAAA 0.976591 -84 AGTAAAAGGTTCATCAAAAATCTAACACCT 33 226 0 TCATCAAAAA 0.754766 -75 AATTTCACCACAAAAAAGAATTTGAAT 34 64 0 CCACAAAAAA 0.9217 -17 ********** Masking position 6 Map Score: 6.87224 Number of sites scoring better than the average of aligned sites = 299 Number in coding regions = 235 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 13 TTCATAGCTGGAAAGCGTAGCTTTCCATTT 1 58 0 GAAAGCGTAG 0.964538 -243 TTCATAGCTGGAAAGCATAGCTCTCCATTT 6 110 1 GAAAGCATAG 0.986732 -83 TTGACAAAGCATAGGAGGAGACCT 7 5 1 CAAAGCATAG 0.944512 -104 AAAAAACTTGGAAACCATAGAGGGAAACCC 8 25 1 GAAACCATAG 0.974928 -99 TTTACATTTAGAAAGCATATAAATTTTTTG 31 19 0 GAAAGCATAT 0.920058 -70 AGTTATTCCAGAAACCATAGGGCTTCGCCT 33 147 1 GAAACCATAG 0.974928 -154 ********** Masking position 4 Map Score: 3.86307 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 8 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 14 TAAATCTAAAAAAATAAATATAACAACCTAA 1 212 0 AAAATAAAAT 0.589141 -89 AAATGATAGAAAAGTTTATATATGAAGATGA 2 197 0 AAAGTTTAAT 0.566118 -104 GTCCCATCCTAACATTAAAATATAAGACATA 3 90 0 AACATTAAAT 0.366865 -42 TCTAATGAGAAAAATTAACATTTATAAATTA 4 18 0 AAAATTAAAT 0.919569 -143 TCAACAGAGTATAATTTAAATGTGATATATT 4 123 0 ATAATTTAAT 0.281069 -38 AAATAATAAAAAAATTTATACAGGTAATAAC 5 58 1 AAAATTTAAC 0.558381 -27 AAATATTAAAATAAAAATCTGGGTGAGG 6 8 1 AAAATAAAAT 0.589527 -185 CAAATTAATCAAAATTAATTTACACCTCCGA 8 92 0 AAAATTAATT 0.762394 -32 AATAAGACGAAAAGTTTATATATTAGATTGA 11 35 0 AAAGTTTAAT 0.566118 -98 AGCATCTTTAAAAATTAAATTTTA 12 46 1 AAAATTAATT 0.764222 -14 TTAGTTAATAAAATTTAAGTTTTATATTCTA 13 26 0 AAATTTAATT 0.353509 -31 TCAATTTAGCTAAATTTATATAGTAAGTTAT 15 29 1 TAAATTTAAT 0.421084 -60 ACGATTTTATAAAATTACAATTAAAAACTTT 15 65 0 AAAATTACAT 0.37303 -24 AAGAGAAAAGAAAATAAAAAT 18 1 0 AAAATAAAAT 0.589527 -47 CATATTATCAAAAATTGATTTAGATAAATTA 20 86 1 AAAATTGATT 0.245808 -188 TTGTTTTTTTAAAATTAACACTAATTTATCT 20 107 0 AAAATTAAAC 0.558381 -167 TAAGTTTTTTAAAATTAAAAATGAATGTAAT 21 142 0 AAAATTAAAA 0.652656 -36 AAACATATCAAAAATTTAATTGGGTATTGCG 22 22 0 AAAATTTATT 0.764237 -109 TTTAATATTTAAAATTTAATTAAGGTCTTAT 22 66 0 AAAATTTATT 0.764237 -65 GATGTTATAAAAATTTTACCTAATCAGATAT 24 74 0 AAATTTTACT 0.191189 -62 TAAATAACAGAAAATTAAAAAGTTTTGGTGG 24 111 1 AAAATTAAAA 0.652656 -25 TTAAATTTTAGATAAAGATAATT 25 3 1 AAATTTTAAT 0.659748 -83 TTGGTATTGGAAAATTAATAAAAAGTATTAC 29 97 0 AAAATTAAAA 0.652653 -204 AGTGATGTATAAAATATAAATAGATTATGCT 29 249 0 AAAATATAAT 0.58953 -52 TAATCTTTATAAAATTTTTATTATTTTTGAA 30 56 0 AAAATTTTAT 0.286444 -245 TTTAAATTTATAAATTAAGATTTCTTTTAAA 30 124 0 TAAATTAAAT 0.421084 -177 ATACATCTTTAAATTTAAATTTATAAATTAA 30 137 0 AAATTTAATT 0.354536 -164 TTTCCCACATAAATTTTAAATATACAATATC 30 194 1 AAATTTTAAT 0.659749 -107 ATAATTTAATGAAATTTAAATACTCATAATG 30 262 0 GAAATTTAAT 0.379406 -39 TTACCACCAAAAAATTTATATGCTTTCTAAA 31 12 1 AAAATTTAAT 0.91957 -77 TACAGACACTAAACTTTACATTTAGAAAGCA 31 32 0 AAACTTTAAT 0.414859 -57 TTTTGAATTAAAAATTTAAAAATTGAAA 32 8 0 AAAATTTAAA 0.652656 -139 TTTTTAATTCAAAATTTAACTTATATTTTTA 32 25 1 AAAATTTACT 0.582256 -122 AAATATCAATAAAATTAAAAAGATAAGGTAA 32 88 0 AAAATTAAAA 0.652656 -59 CAAAGTTGTTAAAATTAATATTAATAATGGA 33 74 1 AAAATTAAAT 0.919494 -227 CTAATAATAAAATTTATATAAGTTGATAT 34 9 1 AAAATTTAAT 0.91957 -72 AAATCCCCTAAAAATTAAAATTAATAA 35 7 0 AAAATTAAAT 0.919569 -23 CAAAATTAATAAAATTTACTTATGAAAA 36 8 0 AAAATTTATT 0.764237 -59 ATTCCTCCTCAAAATCAATATTAAGAGATAG 37 111 0 AAAATCAAAT 0.392832 -190 ******** ** Masking position 5 Map Score: 23.8077 Number of sites scoring better than the average of aligned sites = 793 Number in coding regions = 462 Number in noncoding regions = 331 Number of orfs with sites within 600 bp upstream = 262 Fraction of orfs with sites within 600 bp upstream = 0.0420816 Motif number 15 ATTAAAAACTGTTAAGTTAAGATTTAAAAA 1 272 0 GTTAAGTTAA 0.922592 -29 AATCATCAAAGTTTAGGTATGTAATTAAAT 2 83 1 GTTTAGGTAT 0.840484 -218 TTTTAAATGTTTAGTTAATAAAATTTAA 13 39 0 GTTTAGTTAA 0.922592 -18 TATATAAAAGGTTAAGCTAATTATCATTAT 16 36 1 GTTAAGCTAA 0.842992 -90 TTTAAAAATAGTTTAGTTAATTTCTATTTT 17 13 1 GTTTAGTTAA 0.922592 -48 ATTTTGAAAGGTTAAGTTATAGCGTTTTAA 24 40 1 GTTAAGTTAT 0.813544 -96 TGATATATCTGATTAGGTAAAATTTTTATA 24 70 1 GATTAGGTAA 0.840484 -66 AAATTAAAAAGATAAGGTAAAGATATCAGA 32 78 0 GATAAGGTAA 0.840484 -69 ********** Masking position 5 Map Score: 1.66536 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 = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911