AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00130_mjan_reg_100.orf -o00130_mjan_100.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 MJ0238 131 anthranilate synthase component II (trpG) #3 MJ0502 160 3-phosphoshikimate-1-carboxyvinyltransferase (aroA) #4 MJ0503 84 2-isopropylmalate synthase (leuA) #5 MJ0520 192 NADH-ubiquinone oxidoreductase, subunit 1 #6 MJ0669 59 ATP-dependent RNA helicase, DEAD-family (deaD) #7 MJ0671 56 riboflavin-specific deaminase (ribG) #8 MJ0672 263 membrane bound transport protein, putative #9 MJ0771 88 cobalamin biosynthesis precorrin-2 methyltransferase (cbiL) #10 MJ1027 125 formate hydrogenlyase, subunit 5 #11 MJ1028 60 DNA topoisomerase VI, subunit B (top6B) #12 MJ1029 47 dimethyladenosine transferase (ksgA) #13 MJ1077 89 seryl-tRNA synthetase (serS) #14 MJ1078 273 M. jannaschii predicted coding region MJ1078 #15 MJ1123 70 conserved hypothetical protein #16 MJ1195 135 2-isopropylmalate synthase (leuA) #17 MJ1309 37 carbon monoxide dehydrogenase, hydrogenase anchor subunit CooM (cooM) #18 MJ1310 83 conserved hypothetical protein #19 MJ1362 68 NADH ubiquinone oxidoreductase, subunit 1 isolog #20 MJ1363 300 formate hydrogenlyase, subunit 7 #21 MJ1392 300 2-isopropylmalate synthase (leuA) #22 MJ1522 146 cobalamin biosynthesis precorrin-6Y methylase (cbiE) #23 MJ1575 300 GMP synthase (guaA) #24 MJ1576 80 LemA protein #25 MJ1577 29 M. jannaschii predicted coding region MJ1577 #26 MJ1578 66 cobalamin biosynthesis precorrin-3 methylase (cbiF) #27 MJ1656 300 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase (hpcE) Motif number 1 TCGGCACCATTTTATTATTTTATTTTAGGTT 1 188 1 TTTATTATTT 0.854073 -113 AAATAAATACTATTTAAAAATAGTTAATCCA 1 243 0 TATTTAAAAT 0.733971 -58 TAGTATTTATTTTTTAAATCTTAACTTAACA 1 262 1 TTTTTAAATT 0.951075 -39 GATGTAAAATTATTTAATTATTTTTTGTACT 2 11 1 TATTTAATTT 0.8567 -121 AATTTTTAAGATTTTTATAGTAAAAGGTGAT 2 43 1 ATTTTTATAT 0.563119 -89 ATTATTATCCTTTATAATTATGTCTTATATT 2 72 1 TTTATAATTT 0.887134 -60 TTATGTCTTATATTTTAATGTTAGGATGGGA 2 89 1 TATTTTAATT 0.847336 -43 ACTTACTTAATTTATAAATGTTAATTTTTCT 3 11 1 TTTATAAATT 0.907423 -150 AACAGAGTATAATTTAAATGTGATATATTAA 3 121 0 AATTTAAATT 0.758991 -40 CTGTATAAATTTTTTTATTATTTTTTAATCA 4 50 0 TTTTTTATTT 0.920635 -35 CCCAGATTTTTATTTTAATATTT 5 3 0 TATTTTAATT 0.84726 -190 TAAAATTTAATTTTTAAAGATGCT 6 46 0 AATTTAATTT 0.716095 -14 TATCATTTAGAATATAAAACTTAAATTTTAT 7 19 1 AATATAAAAT 0.378209 -38 GTAATAATTGTTTTTAATATTTTTTAACTGG 8 21 1 TTTTTAATAT 0.856343 -243 TCTTTCTTATTATTTTATTATTTCCATGCCT 8 55 1 TATTTTATTT 0.81654 -209 CTTCATAAATTCTATAATTTTTACTTTAAGT 8 108 1 TCTATAATTT 0.523074 -156 GATAACTTACTATATAAATTTAGCTAAATTG 9 30 0 TATATAAATT 0.789888 -59 TCTAAAAAAGTTTTTAATTGTAATTTTATAA 9 59 1 TTTTTAATTT 0.939723 -30 CTTACGATTTTATAAAATTACAATTAAAA 9 70 0 TTTATAAAAT 0.789132 -19 TATTATCATGTTTATAATTGTTGG 10 112 1 TTTATAATTT 0.887158 -14 TAACTAAACTATTTTTAAACT 11 1 0 ATTTTTAAAT 0.688103 -60 ATTTTTATTTTCTTTTCTCTT 12 1 1 ATTTTTATTT 0.828765 -47 GGTATTTATGTTTTTTATTGTGTTTTTAGAA 13 23 0 TTTTTTATTT 0.920677 -67 AATGTTTGTTTTTTTAAAATTAACACTAATT 14 112 0 TTTTTAAAAT 0.87874 -162 AAAACAAACATTTTTTATTATTTTTTGCAGT 14 131 1 TTTTTTATTT 0.920635 -143 TTGGAAAATCTTTTTAAAAATACCAACATTG 14 201 1 TTTTTAAAAT 0.871573 -73 TAAAAGATGCATTTTTAATATATTTTTAATA 14 241 1 ATTTTTAATT 0.845141 -33 TTTTTAATATATTTTTAATATATTATCTTTC 14 252 1 ATTTTTAATT 0.845141 -22 ATGATAATATTTTATAATTTTGTAATATTAT 15 15 1 TTTATAATTT 0.887152 -56 AAATTCTAACATTTTTATAATATTACAAAAT 15 31 0 ATTTTTATAT 0.448154 -40 CCACCAAAACTTTTTAATTTTCTGTTATTTA 16 111 0 TTTTTAATTT 0.939714 -25 GGTTTTTATAAAATTTTATGAGTGA 19 5 1 TTTATAAAAT 0.789132 -64 CTAATTTTTCAATTTTAAAGTTTTATTTTTA 20 67 0 AATTTTAAAT 0.389023 -234 AGTAATACTTTTTATTAATTTTCCAATACCA 20 96 1 TTTATTAATT 0.879462 -205 GCATAATAGATTTTTTAATTTAATTTCTTGC 20 199 0 TTTTTTAATT 0.935332 -102 CTTTATTGAGAATTTTAATATGCATAATAGA 20 220 0 AATTTTAATT 0.690289 -81 TTATAAAATTTTTATTATTTTTGAAAGATAC 21 50 0 TTTATTATTT 0.854073 -251 ATTAATAATCTTTATAAAATTTTTATTATTT 21 61 0 TTTATAAAAT 0.789132 -240 GAAATCTTAATTTATAAATTTAAATTTAAAG 21 131 1 TTTATAAATT 0.90741 -170 GTAATATACATCTTTAAATTTAAATTTATAA 21 142 0 TCTTTAAATT 0.730569 -159 TCCCACATAAATTTTAAATATACAATATCAA 21 196 1 ATTTTAAATT 0.880321 -105 TCATTATGAGTATTTAAATTTCATTAAATTA 21 261 1 TATTTAAATT 0.881713 -40 TTTCAATTTTTAAATTTTTAATTCAAA 22 7 1 TTTTTAAATT 0.951047 -140 TTTAACTTATATTTTTATATTCTTATTTTAT 22 39 1 ATTTTTATAT 0.498495 -108 TTTATATTCTTATTTTATATTCTTATTCTGA 22 52 1 TATTTTATAT 0.63199 -95 TTACCTTATCTTTTTAATTTTATTGATATTT 22 88 1 TTTTTAATTT 0.939714 -59 TACTATTATGTTTTTAAATATCAATAAAATT 22 103 0 TTTTTAAATT 0.951001 -44 TTTTAAAATTTCTTTTATTATGATTATCCTC 23 31 0 TCTTTTATTT 0.618182 -270 AAGACACTATATTTTAAAATTTCTTTTATTA 23 42 0 ATTTTAAAAT 0.538526 -259 TCAAATATCCATTATTAATATTAATTTTAAC 23 81 0 ATTATTAATT 0.745724 -220 GATATCAACTTATATAAATTTTATTATTAG 24 10 0 TATATAAATT 0.789888 -71 TTATTAATTTTAATTTTTAGGGGATTT 25 7 1 ATTTTAATTT 0.866784 -23 ATAAGTAAATTTTATTAATTTTGAAAGACCT 26 16 1 TTTATTAATT 0.879462 -51 AAGAGATTGTTTTATAATTTTAGAGGACTAT 27 217 1 TTTATAATTT 0.887152 -84 ********* * Masking position 5 Map Score: 70.9391 Number of sites scoring better than the average of aligned sites = 3125 Number in coding regions = 2127 Number in noncoding regions = 998 Number of orfs with sites within 600 bp upstream = 572 Fraction of orfs with sites within 600 bp upstream = 0.0918728 Motif number 2 ATAACAACCTAAAATAAAATAATAAAATGGT 1 193 0 AAAAAAAATA 0.756881 -108 CATAAATCTAAAAAAATAAATATAACAACCT 1 214 0 AAAAATAAAT 0.891621 -87 GTTAAGATTTAAAAAATAAATACTATTTAAA 1 256 0 AAAAATAAAT 0.891621 -45 AATTTAGTACAAAAAATAATTAAATAATTTT 2 16 0 AAAAATAATT 0.837038 -116 CTCTAATGAGAAAAATTAACATTTATAAATT 3 19 0 AAAATTAACA 0.86562 -142 TATTTTGATTAAAAAATAATAAAAAAATTTA 4 45 1 AAAAATAATA 0.837038 -40 AAATATTAAAATAAAAATCTGGGTGAGG 5 8 1 AAAAAAAAAT 0.832954 -185 CCATTTCATCAAAAACTAACACCTCCTCGCT 5 134 1 AAAACTAACA 0.890311 -59 TAAAATTTAATTTTTAAAGATG 6 48 0 AAAATTAATT 0.745673 -12 TTTAGAATATAAAACTTAAATTTTATTAACT 7 24 1 AAAATTAAAT 0.82444 -33 TCTCTTTTACAAAACAAAACTTAAAGTAAAA 8 126 0 AAAAAAAACT 0.872446 -138 AAGAGATATAAAAACTTAACTATTAACATAC 8 201 1 AAAATTAACT 0.86562 -63 TAACTTTATTAAAACAAAACTATATAAAAGG 10 16 1 AAAAAAAACT 0.872446 -110 TAAAAAAGAGAAAAGAAAATAAAAAT 12 6 0 AAAAAAAATA 0.756881 -42 AACACAATAAAAAACATAAATACCTAATTAT 13 30 1 AAAAATAAAT 0.891621 -60 TTAATTTTAAAAAAACAAACATTTTTTATTA 14 120 1 AAAACAAACA 0.831069 -154 TTACTACTGCAAAAAATAATAAAAAATGTTT 14 136 0 AAAAATAATA 0.837038 -138 TAAATAACAGAAAATTAAAAAGTTTTGGTGG 16 111 1 AAAATAAAAA 0.74001 -25 AAAGCTATTAAAAACATAAATATTAAT 18 7 0 AAAAATAAAT 0.891621 -77 TTAGCAACCAAAAAGCTAAAAGCTATTAAAA 18 25 0 AAAACTAAAA 0.855434 -59 CATACAAAATAAAAACAAACTCATAAATTCT 20 34 1 AAAACAAACT 0.831069 -267 AATTCTCTTAAAAATAAAACTTTAAAATTGA 20 59 1 AAAAAAAACT 0.872446 -242 TTCCAATACCAAAATCAAACAACCTACTTAT 20 116 1 AAAACAAACA 0.831069 -185 AGTGATGTATAAAATATAAATAGATTATGCT 20 249 0 AAAAATAAAT 0.891621 -52 AATCCCTCATAAAAAATAATTTAATGAAATT 21 277 0 AAAAATAATT 0.837038 -24 TTTTGAATTAAAAATTTAAAAATTGAAA 22 8 0 AAAATTAAAA 0.82444 -139 TTTTTAATTCAAAATTTAACTTATATTTTTA 22 25 1 AAAATTAACT 0.86562 -122 AAATATCAATAAAATTAAAAAGATAAGGTAA 22 88 0 AAAATAAAAA 0.74001 -59 TTGATATTTAAAAACATAATAGTAATAAATT 22 110 1 AAAAATAATA 0.837038 -37 AGGTTCATCAAAAATCTAACACCTCCTCGCT 23 219 0 AAAACTAACA 0.890311 -82 AAAATCCCCTAAAAATTAAAATTAATAA 25 8 0 AAAATTAAAA 0.82444 -22 GACCTACTATAAAAACAAAAACAAGAGGAGA 26 42 1 AAAACAAAAA 0.781968 -25 **** ****** Masking position 4 Map Score: 46.1454 Number of sites scoring better than the average of aligned sites = 1169 Number in coding regions = 834 Number in noncoding regions = 335 Number of orfs with sites within 600 bp upstream = 273 Fraction of orfs with sites within 600 bp upstream = 0.0438484 Motif number 3 AAAGTTAAACAAAATCTTTCAGATTTTGTAGCC 1 127 0 AATCTTTAGA 0.850693 -174 ATTTTGTTTAACTTTTTCTAAAAGTTTCGTTTG 1 145 1 ATTTTCTAAA 0.687794 -156 TTATGGATTAACTATTTTTAAATAGTATTTATT 1 240 1 AATTTTTAAT 0.590194 -61 TTTTACTATAAAAATCTTAAAAATTTAGTACAA 2 35 0 AATCTTAAAA 0.883031 -97 AAATTTTTTTATTATTTTTTAATCAAAATATCA 4 42 0 AATTTTTAAT 0.590194 -43 TTTTCGTTCAACTTTTTCTAAAAGTTTCGTTTA 5 66 0 ATTTTCTAAA 0.687794 -127 ATCTCTTTTTAGCATCTTTAAAAATTAAATTTT 6 36 1 AATCTTTAAA 0.972659 -24 CTTACGATTTTATAAAATTACAATTA 9 73 0 AATTTTAAAA 0.663029 -16 TTATCGTTGGAAAATCTTTTTAAAAATACCAAC 14 195 1 AATCTTTTAA 0.786481 -79 TTCTATTTAACTTTCTCTAAAAGATTGGAGGG 17 10 1 ATTCTCTAAA 0.894207 -28 TCTCACTCATAAAATTTTATAAAAACC 19 5 0 AATTTTAAAA 0.663029 -64 ACAAACTCATAAATTCTCTTAAAAATAAAACTT 20 48 1 ATTCTCTAAA 0.894207 -253 CAACCTACTTATAATCTTAAAAATCCGAAAGAT 20 135 1 AATCTTAAAA 0.883031 -166 AAAAATCCGAAAGATTTCTAAAACCTGTTCGCT 20 153 1 AATTTCTAAA 0.883673 -148 ACTTTCGTATAGTATCTTTCAAAAATAATAAAA 21 39 1 AATCTTTAAA 0.972659 -262 AACTTTATTAATAATCTTTATAAAATTTTTATT 21 65 0 AATCTTTTAA 0.786481 -236 TCGCAGGAATAAAATCTTTAAAAGAAATCTTAA 21 108 1 AATCTTTAAA 0.972659 -193 TACAATATCAAATATCTTTGAGATGATTCAATT 21 216 1 AATCTTTAGA 0.850693 -85 TTTAAAATATAGTGTCTTTCAAAGTTGTTAAAA 23 55 1 AGTCTTTAAA 0.790457 -246 TTTTACTAAAAGGTTCTTTCAAAATGTTTTTGA 23 249 1 ATTCTTTAAA 0.911636 -52 ATATTTTATTAGTATCTTTCAAAAACATTTTGA 23 267 0 AATCTTTAAA 0.972659 -34 AGCTTATAGCCTCATCTCTAAAAGTGTCTAAAA 27 58 0 CATCTCTAAA 0.708257 -243 ATATTGAAGAACTATCTCTTAATATTGATTTTG 27 100 1 AATCTCTAAT 0.819074 -201 AAATTATAAAACAATCTCTTAAATAATAAGTTA 27 204 0 AATCTCTAAA 0.966828 -97 * ****** *** Masking position 7 Map Score: 27.6132 Number of sites scoring better than the average of aligned sites = 625 Number in coding regions = 523 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 4 ACTTTTTCTAAAAGTTTCGTTTGTATCCCT 1 155 1 AAAGTTTCGT 0.820822 -146 AAAAATCTTAAAAATTTAGTACAAAAAATA 2 29 0 AAAATTTAGT 0.809992 -103 ACTTTTTCTAAAAGTTTCGTTTATAGTCCC 5 59 0 AAAGTTTCGT 0.820822 -134 TGAGGATGCTAAAATCTCTTTTTAGCATCT 6 23 1 AAAATCTCTT 0.834343 -37 TATAAAACTTAAATTTTATTAACTAAACAT 7 31 1 AAATTTTATT 0.80426 -26 GTCACCAAAAATTTATTGTCAATTTAG 9 8 1 AAAATTTATT 0.878107 -81 AGTTTAAAAATAGTTTAGTTAATTTCTAT 11 10 1 ATAGTTTAGT 0.64766 -51 TAAAAGAACAATAGTTTCTTTTGTTATATC 14 38 1 ATAGTTTCTT 0.785872 -236 TTATGTTTGTAAAATTTCTTTAGTGAGGGA 19 43 1 AAAATTTCTT 0.894862 -26 ACAAACTCATAAATTCTCTTAAAAATAAAA 20 48 1 AAATTCTCTT 0.741779 -253 ATTAAATTAAAAAATCTATTATGCATATTA 20 206 1 AAAATCTATT 0.809991 -95 TCAATAAAGCATAATCTATTTATATTTTAT 20 242 1 ATAATCTATT 0.668981 -59 TCACATTCAAATAATTTATTACTATTATGT 22 123 0 ATAATTTATT 0.773513 -24 ACTATATTTTAAAATTTCTTTTATTATGAT 23 38 0 AAAATTTCTT 0.894862 -263 TTATCACCTTATATTTTATTAGTATCTTTC 23 280 0 ATATTTTATT 0.660777 -21 CAACTTATATAAATTTTATTATTAG 24 6 0 AAATTTTATT 0.80426 -75 AATTATTTGGATAGTTTAGTATGTTTGATA 24 37 0 ATAGTTTAGT 0.64766 -44 TTTCATAAGTAAATTTTATTAATTTTGAAA 26 12 1 AAATTTTATT 0.80426 -55 TGGGAACTTTAAAATCTCTTTTTTAACAGC 27 149 0 AAAATCTCTT 0.834343 -152 ********** Masking position 5 Map Score: 18.4786 Number of sites scoring better than the average of aligned sites = 580 Number in coding regions = 408 Number in noncoding regions = 172 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 5 TACAAATGAAATTATGATAATTCTATATACCC 3 66 0 ATTTGAAATT 0.75584 -95 CAATCTCTTCATATTGATATTTTGATTAAAAA 4 28 1 ATATGAATTT 0.908507 -57 AAATGTTTAGTTAATAAAATTTAAGTTTTATA 7 31 0 TTATAAATTT 0.643488 -26 CACCAAAAATTTATTGTCAATTTAGCTAAATT 9 13 1 TTATGTAATT 0.808181 -76 ATCATAATTAATAATGATAATTAGCTTAACCT 10 44 0 ATATGAAATT 0.916642 -82 ATCATTATTAATTATGATAAATTATCTATTCA 10 58 1 ATTTGAAAAT 0.534604 -68 ATTATTTATTTTACTGATATTTA 11 48 1 TTATGAATTT 0.931104 -13 TTTAGATAAATTAGTGTTAATTTTAAAAAAAC 14 104 1 TTATGTAATT 0.808181 -170 ATATTTTATAATTTTGTAATATTATAAAAATG 15 21 1 ATTTGTATAT 0.223661 -50 TTATAGCGTTTTAATGATATATCTGATTAGGT 16 56 1 TTATGAATAT 0.833745 -80 ACTTTTTAATTTTCTGTTATTTATGATGGGAT 16 102 0 TTTTGTATTT 0.517153 -34 AGATTATGCTTTATTGAGAATTTTAATATGCA 20 227 0 TTATGAAATT 0.937368 -74 ATCATTATCATTAATGACAAATAGTGATGTAT 20 270 0 TTATGAAAAT 0.84741 -31 GTCATTAATGATAATGATAAATTACTG 20 284 1 ATATGAAAAT 0.803167 -17 TCTTTCAAAAATAATAAAAATTTTATAAAGAT 21 53 1 ATATAAAATT 0.594916 -248 TTGATATTGTATATTTAAAATTTATGTGGGAA 21 195 0 ATATTAAATT 0.367264 -106 AAAAAATAATTTAATGAAATTTAAATACTCAT 21 266 0 TTATGAATTT 0.931104 -35 CTTTTTAATTTTATTGATATTTAAAAACATAA 22 97 1 TTATGAATTT 0.931104 -50 TCTTTCAAAATTAATAAAATTTACTTATGAAA 26 12 0 TTATAAATTT 0.643488 -55 *** *** **** Masking position 5 Map Score: 11.1393 Number of sites scoring better than the average of aligned sites = 549 Number in coding regions = 434 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 6 AACTTTTAGAAAAAGTTAAACAAAATCTTTCAG 1 138 0 AAATTAACAA 0.504018 -163 TTTATTTTTTAAATCTTAACTTAACAGTTTTTA 1 267 1 AAATTAATTA 0.948963 -34 AATTTAGTACAAAAAATAATTAAATAATTTTAC 2 14 0 AAAATAATAA 0.461638 -118 CTTAATTTATAAATGTTAATTTTTCTCATTAGA 3 16 1 AAATTAATTT 0.691413 -145 TTTAATCAACAGAGTATAATTTAAATGTGATAT 3 126 0 AGAATAATTA 0.685703 -35 ATCAATATGAAGAGATTGATTTATTCACTTACT 4 13 0 AGATTGATTA 0.633101 -72 AAATATTAAAATAAAAATCTGGG 5 1 1 AAATTAAATA 0.668483 -192 TAAAATTTAATTTTTAAAGATGCT 6 46 0 AAATTAATTT 0.606944 -14 TTTAGTTAATAAAATTTAAGTTTTATATTCTAA 7 25 0 AAATTAATTT 0.606944 -32 TTTTAAATGTTTAGTTAATAAAATTTA 7 40 0 AAATTTATTA 0.638651 -17 TTTACAAAACAAAACTTAAAGTAAAAATTATAG 8 119 0 AAATTAAGTA 0.757226 -145 AAACTATATAAAAGGTTAAGCTAATTATCATTA 10 32 1 AAATTAACTA 0.856476 -94 GTAACAAAATAGAAATTAACTAAACTATTTTTA 11 15 0 AGATTAATAA 0.578495 -46 TTAGAGGGACAGATTTTAAATAAAAGAACAATA 14 18 1 AGATTAATAA 0.578495 -256 ACATATTATCAAAAATTGATTTAGATAAATTAG 14 85 1 AAATTGATTA 0.799302 -189 TATCATTTTGAAAGGTTAAGTTATAGCGTTTTA 16 36 1 AAATTAATTA 0.948848 -100 GGATGTTATAAAAATTTTACCTAATCAGATATA 16 73 0 AAATTTACTA 0.361856 -63 AACAGTATATAAACATTACGTTAGCAACCAAAA 18 43 0 AAATTACTTA 0.560575 -41 ACAAGAAGCAAGAAATTAAATTAAAAAATCTAT 20 192 1 AGATTAATTA 0.889619 -109 AATTCTCAATAAAGCATAATCTATTTATATTTT 20 237 1 AAAATAACTA 0.61765 -64 TCTTTAAAAGAAATCTTAATTTATAAATTTAAA 21 122 1 AAATTAATTA 0.948963 -179 CTTAATTTATAAATTTAAATTTAAAGATGTATA 21 136 1 AAATAAATTA 0.597206 -165 AATCCCTCATAAAAAATAATTTAATGAAATTTA 21 275 0 AAAATAATTA 0.834312 -26 TTTTTAATTCAAAATTTAACTTATATTTTTATA 22 25 1 AAATTAATTA 0.947006 -122 AATAAAATTAAAAAGATAAGGTAAAGATATCAG 22 79 0 AAAATAAGTA 0.457797 -68 ATAATAAAAGAAATTTTAAAATATAGTGTCTTT 23 41 1 AAATTAAATA 0.668468 -260 ACCACAAAAAAGAATTTGAATTATTTGGATAGT 24 52 0 AGATTGATTA 0.633101 -29 AAATCCCCTAAAAATTAAAATTAATAA 25 5 0 AAATAAATTA 0.597206 -25 ACAATCTCTTAAATAATAAGTTAATGATTCATT 27 194 0 AAAATAATTA 0.834312 -107 *** **** *** Masking position 3 Map Score: 29.1571 Number of sites scoring better than the average of aligned sites = 661 Number in coding regions = 431 Number in noncoding regions = 230 Number of orfs with sites within 600 bp upstream = 218 Fraction of orfs with sites within 600 bp upstream = 0.0350145 Motif number 7 GCCTCGCTACGCTCGGCAATGCCTCTTA 1 8 0 GCTCGGCATG 0.966372 -293 GCCGAGCGTAGCGAGGCAATGCATCCTATTT 1 22 1 GCGAGGCATG 0.986843 -279 AAAAATCTGGGTGAGGATATGGATACTTCAC 5 23 1 GTGAGGAATG 0.895235 -170 TCCGAGCGAAGCGAGGAGGTGTTAGTTTTTG 5 143 0 GCGAGGAGTG 0.991828 -50 TCCTCGCTTCGCTCGGAAGTGTAAATTTACA 5 157 1 GCTCGGAGTG 0.978949 -36 GTCAGGCCATGCGAGTCTATGAATAATGAAT 8 162 1 GCGAGTCATG 0.893342 -102 CCTCGCTTACGCTCGGAGGTGCAACTCAGAA 23 195 0 GCTCGGAGTG 0.978949 -106 CCGAGCGTAAGCGAGGAGGTGTTAGATTTTT 23 210 1 GCGAGGAGTG 0.991828 -91 ******* *** Masking position 10 Map Score: 8.93461 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 2 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 TGCATTGCCTCGCTACGCTCGGCAATGCCT 1 15 0 CGCTACGCTC 0.979958 -286 TGAAATGGAAAGCTACGCTTTCCAGCTATG 1 56 1 AGCTACGCTT 0.951063 -245 CCGAAGCTAACGCTTCGGTTAAATGAAAAC 1 98 0 CGCTTCGGTT 0.949867 -203 CCGAAGCGTTAGCTTCGGGCTACAAAATCT 1 110 1 AGCTTCGGGC 0.83423 -191 TGAAATGGAGAGCTATGCTTTCCAGCTATG 5 112 0 AGCTATGCTT 0.883677 -81 AACACCTCCTCGCTTCGCTCGGAAGTGTAA 5 151 1 CGCTTCGCTC 0.979958 -42 AAAACCTGTTCGCTATGCTCACAAGAAGCA 20 172 1 CGCTATGCTC 0.95028 -129 TGAGGCTATAAGCTTTGGTTTTGATATTGA 27 77 1 AGCTTTGGTT 0.823611 -224 ********** Masking position 4 Map Score: 4.97393 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 7 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 9 AAAATGGTGCCGAGGGAGGGATACAAACGAAA 1 169 0 CGAGGGAGGT 0.869466 -132 GGGACAATTTTGGGGGATTGATTTAA 2 116 1 TGGGGGATGT 0.986289 -16 ATAAATCTGGTGGGGGAGGGAT 8 252 1 TGGGGGAGGT 0.985353 -12 ATTTCTTTAGTGAGGGATAGGTT 19 56 1 TGAGGGATGT 0.97424 -13 AAAATTTATGTGGGAAATAGTTCTGGACTAAA 21 179 0 TGGGAAATGT 0.675576 -122 TTATTTTTTATGAGGGATTGTT 21 289 1 TGAGGGATGT 0.97424 -12 CACCTCCCTATAGGAGAGCGTTCAAATATCCA 23 101 0 TAGGAGAGGT 0.928545 -200 TTTTAATTTTTAGGGGATTTTT 25 18 1 TAGGGGATTT 0.853514 -12 AAATCAATATTAAGAGATAGTTCTTCAATATC 27 99 0 TAAGAGATGT 0.879601 -202 ACTTATTATTTAAGAGATTGTTTTATAATTTT 27 206 1 TAAGAGATGT 0.879601 -95 ATGAATTCAGTAGGGGAGTTTTAGATGCATTT 27 273 1 TAGGGGAGTT 0.844938 -28 ******** * * Masking position 7 Map Score: 9.34681 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 98 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 10 TTTTTTAGATTTATGGATTAACTATTTTTAAAT 1 230 1 TTATATTAAT 0.910329 -71 TAAATAGTATTTATTTTTTAAATCTTAACTTAA 1 258 1 TTATTTTAAT 0.464853 -43 AAATTAACATTTATAAATTAAGTAAGT 3 5 0 TTATATTAAT 0.910329 -156 AATTTAAATGTGATATATTAAGGTTGTTATAAT 3 109 0 TGATATTAAG 0.873451 -52 ATGAAGAGATTGATTTATTCACTTACTTT 4 7 0 TGATATTCAT 0.900653 -78 TTTAGCATCTTTAAAAATTAAATTTTA 6 43 1 TTAAATTAAT 0.621036 -17 TTATGATAAATTATCTATTCATTACCTTAGTGA 10 69 1 TTATATTCAT 0.849348 -57 AAATACCTAATTATCAATTCAATAAAAACAATA 13 47 1 TTATATTCAT 0.849348 -43 TTGATGAATTAAATGAACTTTAAT 16 2 1 TGATATTAAT 0.942278 -134 CCTTTCAAAATGATAGATTAAAGTTCATTTAAT 16 18 0 TGATATTAAG 0.873451 -118 TGACAAATAGTGATGTATAAAATATAAATAGAT 20 255 0 TGATATAAAT 0.72491 -46 TTAATGATAATGATAAATTACTG 20 288 1 TGATATTACG 0.466753 -13 TTTATAAAGATTATTAATAAAGTTAATGGGGCT 21 74 1 TTATATAAAT 0.621036 -227 AAATTTAAATTTATAAATTAAGATTTCTTTTAA 21 125 0 TTATATTAAA 0.519308 -176 AGGTTGATAATGAATCATTAACTTATTATTTAA 27 186 1 TGAAATTAAT 0.72491 -115 TAGATGAGGGTGATGAATTCAGTAGGGGAGTTT 27 261 1 TGATATTCAT 0.900653 -40 **** ***** * Masking position 8 Map Score: 10.1201 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 131 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 11 AACTGTGTAATTATAACAACCTTAATATAT 3 100 1 TTATAACAAC 0.854539 -61 TAAAAAGAGATTTTAGCATCCTCAACAACT 6 17 0 TTTTAGCATC 0.950929 -43 TAAAATCTCTTTTTAGCATCTTTAAAAATT 6 32 1 TTTTAGCATC 0.950929 -28 AATTGTAATTTTATAAAATCGTAAG 9 74 1 TTATAAAATC 0.611378 -15 GGTAAAATTTTTATAACATCCCATCATAAA 16 85 1 TTATAACATC 0.94134 -51 GATGATTCAATTTTATCATCAGATTCATTA 21 237 1 TTTTATCATC 0.829859 -64 TTAATATTAATTTTAACAACTTTGAAAGAC 23 68 0 TTTTAACAAC 0.878607 -233 AAACCAAAGCTTATAGCCTCATCTCTAAAA 27 68 0 TTATAGCCTC 0.786098 -233 AAAATCTCTTTTTTAACAGCTCCATTAATT 27 139 0 TTTTAACAGC 0.858825 -162 ********** Masking position 5 Map Score: 3.07343 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 275 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 12 AAAGCTACGCTTTCCAGCTATGAAAACTCTTTTAG 1 64 1 TTCAATGAAA 0.870946 -237 TAAGACATAATTATAAAGGATAATAATCACCTTTT 2 64 0 TTAAATAATA 0.54839 -68 ATGAGAAAAATTAACATTTATAAATTAAGTAAGT 3 10 0 TTCAATAAAT 0.877586 -151 AGAGCTATGCTTTCCAGCTATGAAAACTCTAAGAG 5 99 0 TTCAATGAAA 0.870946 -94 CCAGATTTTATCAGTTGTAAATTTACACTTCC 5 171 0 TTCAGTAAAT 0.786423 -22 AAATCTCTTTTTAGCATCTTTAAAAATTAAATTTT 6 34 1 TTCATTAAAA 0.724095 -26 ATTAACACCTGTAATAATTGTTTTTA 8 2 1 TTCAGTAATA 0.731138 -262 TTTCTCTTTTTTAGAATAAATAAAAAGTGAAACA 12 24 1 TTAAATAAAA 0.776196 -24 TTTATCACCAATAACACTCTTATTGT 13 74 0 TTCAATAACA 0.864748 -16 TTAAAAAGATTTTCCAACGATAACTTTTAATTAGG 14 183 0 TTCAATAACT 0.751928 -91 TATAAAAATGTTAGAATTTGTAATAAGGGGGAATA 15 43 1 TTAAGTAATA 0.384121 -28 ACATAAATCATTCTCACTCATAAAATTTTATAAAA 19 14 0 TTCAATAAAA 0.93797 -55 CTAAAGAAATTTTACAAACATAAATCATTCTCACT 19 31 0 TTCAATAAAT 0.877586 -38 TAATTTATCATTATCATTAATGACAAATAGTGATG 20 273 0 TTCAATGACA 0.740591 -28 TAATGGGGCTTTCGCAGGAATAAAATCTTTAAAAG 21 97 1 TTCAATAAAA 0.937972 -204 CATCTTTAAATTTAAATTTATAAATTAAGATTTCT 21 130 0 TTAAATAAAT 0.621815 -171 TTTATTGATATTTAAAAACATAATAGTAATAAATT 22 106 1 TTAAATAATA 0.54839 -41 AATATTAATTTTAACAACTTTGAAAGACACTATAT 23 61 0 TTCATTGAAA 0.53957 -240 TTTTCATAAGTAAATTTTATTAATT 26 1 1 TTCAGTAAAT 0.786421 -66 ** ** ****** Masking position 11 Map Score: 14.2233 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 245 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 13 TTAGGATGGGACAATTTTGGGGGATTGATTTAA 2 109 1 AAATTTGGGG 0.988939 -23 TCTGTTGATTAAAAAATTAGTGGTG 3 146 1 AAAATTAGGG 0.882166 -15 ATATTAAAATAAAAATCTGGGTGAGGATATGGA 5 13 1 AAATCTGGTG 0.84971 -180 AAGTAAAGAAATAAATCTGGTGGGGGAGGGAT 8 242 1 AAATCTGGGG 0.980631 -22 AGAAAATTAAAAAGTTTTGGTGGGATT 16 119 1 AAGTTTGGGG 0.959592 -17 AACTTTCTCTAAAAGATTGGAGGGAGAAT 17 19 1 AAAATTGGGG 0.970354 -19 ACTGACTTCAATAAATTTGGAGGATAATCATAA 23 12 1 AAATTTGGGG 0.988939 -289 AGATTGTTTTATAATTTTAGAGGACTATGTTGA 27 220 1 AAATTTAGGG 0.95338 -81 * ** ***** ** Masking position 3 Map Score: 6.55822 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 48 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 14 AATGCATCCTATTTTGATGAAATGGAAAGC 1 39 1 ATTTTGATGA 0.924453 -262 TCATATTGATATTTTGATTAAAAAATAATA 4 36 1 ATTTTGATTA 0.467522 -49 GAGGTGTTAGTTTTTGATGAAATGGAGAGC 5 129 0 TTTTTGATGA 0.939704 -64 GCCCATAGTTGTTGAGGATGCTAAAATC 6 9 1 TTGTTGAGGA 0.792186 -51 TGACAATAAATTTTTGGTGAC 9 2 0 TTTTTGGTGA 0.795562 -87 TTAAAAACTTTTTTAGATAACTTACTATAT 9 46 0 TTTTAGATAA 0.713758 -43 TCTAAATCAATTTTTGATAATATGTATAAA 14 80 0 TTTTTGATAA 0.786282 -194 TCAAAAATTGATTTAGATAAATTAGTGTTA 14 93 1 ATTTAGATAA 0.66192 -181 CCCTCCAATCTTTTAGAGAAAGTTAAATAG 17 13 0 TTTTAGAGAA 0.709524 -25 ACTTCAATAAATTTGGAGGATAATCATAAT 23 16 1 ATTTGGAGGA 0.714273 -285 AGGTGTTAGATTTTTGATGAACCTTTTACT 23 226 1 TTTTTGATGA 0.939704 -75 TAATTTTAATTTTTAGGGGATTTTT 25 15 1 TTTTAGGGGA 0.720954 -15 CTTAATATTGATTTTGAGGAGGAATTAATG 27 117 1 ATTTTGAGGA 0.922999 -184 TGTTTTATAATTTTAGAGGACTATGTTGAT 27 224 1 TTTTAGAGGA 0.911872 -77 TTAGAGGACTATGTTGATGATTATTTAGAT 27 236 1 ATGTTGATGA 0.75342 -65 GTTGATGATTATTTAGATGAGGGTGATGAA 27 248 1 ATTTAGATGA 0.8924 -53 ********** Masking position 4 Map Score: 14.8451 Number of sites scoring better than the average of aligned sites = 532 Number in coding regions = 462 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 15 GGAAAGCGTAGCTTTCCATTTCATCAAAATA 1 48 0 GCTTTCCATT 0.976529 -253 GGAAAGCTACGCTTTCCAGCTATGAAAACTC 1 62 1 GCTTTCCACT 0.984699 -239 GGAGAGCTATGCTTTCCAGCTATGAAAACTC 5 105 0 GCTTTCCACT 0.984699 -88 GGAAAGCATAGCTCTCCATTTCATCAAAAAC 5 119 1 GCTCTCCATT 0.960637 -74 ******** ** Masking position 5 Map Score: 0.169835 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 14 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185