AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i199_trans1_mjan_reg_300.orf -o199_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: RMJ01689 25 M_jannaschii_chromosome RMJ13823 22 M_jannaschii_chromosome RMJ00466 27 M_jannaschii_chromosome RMJ00175 32 M_jannaschii_chromosome RMJ01164 22 M_jannaschii_chromosome Input sequences: #1 RMJ08301 300 M_jannaschii_chromosome #2 RMJ10183 41 M_jannaschii_chromosome #3 RMJ02887 33 M_jannaschii_chromosome #4 RMJ13792 59 M_jannaschii_chromosome #5 RMJ07518 85 M_jannaschii_chromosome #6 RMJ13714 300 M_jannaschii_chromosome #7 RMJ06988 57 M_jannaschii_chromosome #8 RMJ04045 82 M_jannaschii_chromosome #9 RMJ15889 300 M_jannaschii_chromosome #10 RMJ00474 155 M_jannaschii_chromosome #11 RMJ07853 273 M_jannaschii_chromosome #12 RMJ03993 155 M_jannaschii_chromosome #13 RMJ09839 97 M_jannaschii_chromosome #14 RMJ15198 300 M_jannaschii_chromosome #15 RMJ06275 300 M_jannaschii_chromosome #16 RMJ03510 25 M_jannaschii_chromosome #17 RMJ07702 84 M_jannaschii_chromosome #18 RMJ14130 96 M_jannaschii_chromosome #19 RMJ15668 198 M_jannaschii_chromosome #20 RMJ00821 42 M_jannaschii_chromosome #21 RMJ12447 38 M_jannaschii_chromosome #22 RMJ13379 57 M_jannaschii_chromosome #23 RMJ14726 32 M_jannaschii_chromosome #24 RMJ06762 126 M_jannaschii_chromosome #25 RMJ14744 37 M_jannaschii_chromosome #26 RMJ05778 300 M_jannaschii_chromosome #27 RMJ04788 300 M_jannaschii_chromosome #28 RMJ09060 71 M_jannaschii_chromosome #29 RMJ14877 185 M_jannaschii_chromosome #30 RMJ12218 174 M_jannaschii_chromosome #31 RMJ06687 85 M_jannaschii_chromosome #32 RMJ04756 147 M_jannaschii_chromosome #33 RMJ08379 300 M_jannaschii_chromosome #34 RMJ09467 141 M_jannaschii_chromosome #35 RMJ07626 57 M_jannaschii_chromosome #36 RMJ12537 110 M_jannaschii_chromosome #37 RMJ08709 49 M_jannaschii_chromosome #38 RMJ15425 296 M_jannaschii_chromosome #39 RMJ09366 300 M_jannaschii_chromosome #40 RMJ09720 283 M_jannaschii_chromosome #41 RMJ03708 300 M_jannaschii_chromosome #42 RMJ07630 116 M_jannaschii_chromosome Motif number 1 CTTAAATTAATTTTATTGATTTTGGAAGAC 1 129 0 TTTTATTGAT 0.768512 -172 TAAATAGCTTTTTTATAGTGTCTTTCAAAA 1 210 0 TTTTATAGTG 0.469092 -91 ATGGATACCATATTATATATTATTTTCGGT 6 54 0 TATTATATAT 0.550432 -247 TATATATTCTTTTTATATATTCCCACAATA 6 100 0 TTTTATATAT 0.929624 -201 GTGTTTCATTTTTTATATATTCTTTTTATA 6 113 0 TTTTATATAT 0.929624 -188 CGCCACTTCTTTTTATTTTTTAATATCTAT 6 235 1 TTTTATTTTT 0.962019 -66 TTAAATCCCATTTTATATTTTTTTAATATT 8 39 1 TTTTATATTT 0.957055 -44 TTTATATTTTTTTAATATTTTAAAGCATTT 8 50 1 TTTAATATTT 0.622267 -33 ATTGTGCTATTTTTATAGTTCTGTTCTTTT 9 52 0 TTTTATAGTT 0.831262 -249 ATTATCACAATTATATTTATGAAATGTTGA 9 103 1 TTATATTTAT 0.743223 -198 TTTATTTTTATTATATTTATTCTAAAATGG 9 247 0 TTATATTTAT 0.743223 -54 TTTTTATCTTTTTTATTTTTATTATATTTA 9 258 0 TTTTATTTTT 0.962019 -43 CCTTATTATTTTATATTAATTGAAGATTTT 10 63 0 TTATATTAAT 0.593308 -93 CCAAGTAATTTTTTATAATTTTTTAATGTT 11 20 1 TTTTATAATT 0.918245 -254 ACCTAAATTATTTTATTATGCAAACCCATA 11 61 1 TTTTATTATG 0.696032 -213 TGGTGTTGCATATTATTATTATTCAATTTT 11 117 0 TATTATTATT 0.541896 -157 TATATGAATATTTTATATAGTATTCCCTTA 11 168 0 TTTTATATAG 0.703271 -106 AAATCTATTATTGTATTTATAGATTCAAAT 11 227 1 TTGTATTTAT 0.724721 -47 ATGACCTCCGTATTATTATTCTGAATTTGA 11 251 0 TATTATTATT 0.541896 -23 TTCAAATATGTTGTATAAATATCTTATCTA 12 43 0 TTGTATAAAT 0.538667 -113 ATAAAAAAAGTTTTATATTTTTAGGGATTA 12 81 0 TTTTATATTT 0.957055 -75 TAAACCTCTATTTTATTTTTTAAAATTTAT 12 123 1 TTTTATTTTT 0.962019 -33 GATAGCCTAATTATATTTATGAAACAATAT 15 79 1 TTATATTTAT 0.743223 -222 GTTTATATACTTTTATTGTTGTTTAACTCA 15 126 0 TTTTATTGTT 0.848454 -175 CCTTCATAAATTTTATTAATTTTGAAAGGC 15 177 0 TTTTATTAAT 0.88331 -124 AATTAGTTATTTATATTTTTCGG 24 4 0 TTATATTTTT 0.829968 -123 CTCCTTTGTGTTTTATTTATTTGTTTTAAC 24 87 0 TTTTATTTAT 0.937574 -40 CAACCGAAAATTTTATATATGGTTTCTGAT 26 103 1 TTTTATATAT 0.929624 -198 TTTTGAAAAATTTTATATTGCTAAGATATC 26 130 0 TTTTATATTG 0.799892 -171 GATGAGGCTATTTTATAAATCTTTAATAGC 26 173 0 TTTTATAAAT 0.869318 -128 CTCCTTTCTTTTTTATATTTAACAAAAAGC 26 247 0 TTTTATATTT 0.957055 -54 AAATAATAGTTATTATTTTTTAA 27 4 0 TATTATTTTT 0.701211 -297 AAATAATAACTATTATTTTTATTTAAGTTA 27 16 1 TATTATTTTT 0.701211 -285 GTTTTAGCTTTTGTATAATTGCTTCATGGG 27 119 1 TTGTATAATT 0.663199 -182 AAAATTCAAATTGTATAATTAATTAATATT 27 177 0 TTGTATAATT 0.663199 -124 ATTCACATTATTTTATTTTTGTTAATTTAA 27 206 0 TTTTATTTTT 0.962019 -95 ATATTTTATCTTATATTAATAATATTCCAA 27 263 0 TTATATTAAT 0.593308 -38 GACACCTAAATTTTATATTTTATCTTATAT 27 277 0 TTTTATATTT 0.957055 -24 TAAGAGAGATTTTTATTGATTTTGAAAAGA 31 65 0 TTTTATTGAT 0.768512 -21 TATTTTTACTTTTTATTTTTCTAAAAATAT 32 59 0 TTTTATTTTT 0.962019 -89 AAGGATTTGCTTTTATTTTTACTTTTTATT 32 72 0 TTTTATTTTT 0.962019 -76 CAAAAATTGATTTAATTTTTTGATGTTTTT 33 74 1 TTTAATTTTT 0.651836 -227 GGAGTAAATGTTTTATATTGAATATTGACA 33 187 1 TTTTATATTG 0.799892 -114 AGATAAATACTTTTATAAATACTT 34 5 0 TTTTATAAAT 0.869318 -137 TTTTGAGTAATTTAATAATTCAAGTAATAA 34 83 0 TTTAATAATT 0.45365 -59 TTCTTTAATTTTTTACTTTTTTA 37 4 1 TTTAATTTTT 0.651836 -46 AATAACTACTTTTTATATATCTTTATTTTT 38 17 1 TTTTATATAT 0.929624 -280 TTTAACGGTATTTTATTATTAATAAAATAA 38 202 0 TTTTATTATT 0.927362 -95 ACTCTTTATCTTATATAAATTTAACGGTAT 38 221 0 TTATATAAAT 0.561922 -76 TTAAGGGCATTTTTATAAATATCTTTATTT 39 197 0 TTTTATAAAT 0.869318 -104 TCCCTCCTATTTTTATTTTTGTTATTTGTT 39 276 0 TTTTATTTTT 0.962019 -25 TAGCTCCTAATTTTATTTTTATTTTATTTA 40 19 1 TTTTATTTTT 0.962019 -265 TTTATTTTTATTTTATTTATCTGTGTTTAA 40 30 1 TTTTATTTAT 0.937574 -254 ATTTTCACATTTTTATAATTTTAGCTTATA 40 118 0 TTTTATAATT 0.918245 -166 CCCTACGGGCTTTTATATTTATTCCTTAAT 40 177 0 TTTTATATTT 0.957055 -107 CCCGTAGGGCTTTTATAAATGCATTTTTCA 40 198 1 TTTTATAAAT 0.869318 -86 TTTTCAAAAATTATATATTTGAAAAACACT 40 222 1 TTATATATTT 0.811141 -62 AACTTATTTTTATTTTTGTTTAAGTAT 41 8 1 TTTTATTTTT 0.962019 -293 TCACTGAATCTTATATTTTTCAAATACTAT 41 101 1 TTATATTTTT 0.829968 -200 TATATGACTTTTTTATTATTTTTAAGGTTC 42 33 0 TTTTATTATT 0.927362 -84 ATAAATAGTTTTTTATTTTGTAAATTTGAA 42 60 1 TTTTATTTTG 0.819589 -57 TAATTCATATTTGTATATTTTCAAATTTAC 42 79 0 TTGTATATTT 0.796193 -38 ********** Masking position 5 Map Score: 78.1166 Number of sites scoring better than the average of aligned sites = 1497 Number in coding regions = 997 Number in noncoding regions = 500 Number of orfs with sites within 600 bp upstream = 410 Fraction of orfs with sites within 600 bp upstream = 0.0658529 Motif number 2 CAAAATCAATAAAATTAATTTAAGGAACATTG 1 135 1 AAATTATTTA 0.859439 -166 ATAAAATACTTTAAAATAATTGAG 2 3 1 AAATATTTAA 0.713431 -39 AATTATTTAAAAATTTATTTAAT 4 2 0 AAATTTTTAA 0.874739 -58 TTTTATTCAAAAACTTAATAAATAAGAGAGGA 5 13 0 AAATTATAAA 0.920765 -73 TTTTTGAATAAAATTAGATAAAATAAACACAA 5 32 1 AAATAATAAA 0.805552 -54 GTTCTTTTTAAAAGTTAATAAAAGTTATTAAG 9 28 0 AAATTATAAA 0.920765 -273 TAAAAATATAAAACTTTTTTTATATCACGTTT 12 88 1 AAATTTTTTA 0.835428 -68 TTATTTTTTAAAATTTATTTAAGGTGAGATT 12 135 1 AAATTTTTAA 0.874739 -21 ATGTGTAGATAAAATTAATATATTTGGTATAT 13 34 0 AAATTATATA 0.894145 -64 TATGAAACGAAAAGTATATATATGAGAAAATT 14 125 0 AAATAATATA 0.750715 -176 TAACCATACAAAAATTGTTATAAGTTATGAAA 14 150 0 AAATTTTATA 0.874739 -151 TGAATCAGTTAAATTTAATAAAAAAAGAGTAA 14 265 0 AAATTATAAA 0.920765 -36 AACAACAATAAAAGTATATAAACTTCTTACAG 15 133 1 AAATAATAAA 0.805552 -168 AGTGCCTTTCAAAATTAATAAAATTTATGAAG 15 174 1 AAATTATAAA 0.920765 -127 AGTGTCTTTCAAACTTCTTAAATAACTAAGGC 15 245 0 AAATTTTAAA 0.90572 -56 CTTTAACTTTAAATTTATTTTAACTTTCTGAA 18 13 1 AAATTTTTTA 0.835428 -84 CTCAAAATTTAAATTTAATTTAGAACGTGT 21 9 0 AAATTATTTA 0.85995 -30 CTTCCTGATAAAAATTGTTTAA 23 1 0 AAATTTTTAA 0.874739 -32 ACTCAACCGAAAATTTTATATATGGTTTCTGA 26 100 1 AAATTATATA 0.89415 -201 TTTTTTAAGTAAAATATTTATATCAGATACCA 26 203 1 AAATATTATA 0.713431 -98 AAGAAACTTTATTTATTATGTTTTT 31 4 1 AAATTATTTA 0.859954 -82 ATTTTTGTTTAAATTTTTTAAAGGTCAGAGAA 33 49 0 AAATTTTAAA 0.90572 -252 AATTTAAACAAAAATTGATTTAATTTTTTGAT 33 66 1 AAATTATTTA 0.859949 -235 TCCTATCCAAAAAGTATATAAATATAGAGAAA 33 105 1 AAATAATAAA 0.805552 -196 CTCTATATTTAAATTTATTAAAAATTTTGAAA 35 14 1 AAATTTTAAA 0.90572 -44 TTTTAGTAATAAACTATTTAAATAGTAAGGCA 38 71 0 AAATATTAAA 0.774 -226 TTTAAAACCAAAAATTATTTAAAATATTATGT 39 39 1 AAATTTTTAA 0.874739 -262 TCAAAACTTAAAAGTTAATTTAAAAATTAGAA 39 240 1 AAATTATTTA 0.85995 -61 AGTGTTTTTCAAAGTTAATAAAAATTAAGGAA 40 154 1 AAATTATAAA 0.920765 -130 TTTTTTGTTTAAAGTTTATTAAAAATGTCTTG 41 211 0 AAATTATTAA 0.89415 -90 ACAAAATAAAAAACTATTTATATGACTTTTTT 42 49 0 AAATATTATA 0.713431 -68 *** ** ***** Masking position 5 Map Score: 45.7979 Number of sites scoring better than the average of aligned sites = 820 Number in coding regions = 521 Number in noncoding regions = 299 Number of orfs with sites within 600 bp upstream = 269 Fraction of orfs with sites within 600 bp upstream = 0.0432059 Motif number 3 ATAAAATAAAAATGCAGAAACA 3 3 1 AAAATAAAAA 0.906633 -31 TAGATATTAAAAAATAAAAAGAAGTGGCGC 6 234 0 AAAATAAAAA 0.906633 -67 AAATATTAAAAAAATATAAAATGGGATTTA 8 40 0 AAAATATAAA 0.906633 -43 AAATATAATAAAAATAAAAAAGATAAAAAA 9 259 1 AAAATAAAAA 0.906633 -42 GAAATTATTGAACATTAAAAAATTATAAAA 11 30 0 AACATTAAAA 0.716162 -244 TTAATCCCTAAAAATATAAAACTTTTTTTA 12 80 1 AAAATATAAA 0.906633 -76 TTAGGCTATCAACATTTAAATTGTAGAGCA 15 59 0 AACATTTAAA 0.716162 -242 TAACAAAAAATTTAAATACCCTATCT 17 7 1 AAAATTTAAA 0.906633 -78 TTTATTTCAGAAAGTTAAAATAAATTTAAA 18 20 0 AAAGTTAAAA 0.888255 -77 TGTGAGATTTAAAGTATAAATATGGGTTTT 19 102 1 AAAGTATAAA 0.888255 -97 AACTCACCTCAAAATTTAAATTTAATTTAG 21 18 0 AAAATTTAAA 0.906633 -21 CCGAAAAATATAAATAACTAATTA 24 5 1 AAAATATAAA 0.906633 -122 GAATGATATTAACGTTTAAATCCGGTTTTT 27 232 1 AACGTTTAAA 0.673783 -69 AATATAAGATAAAATATAAAATTTAGGTGT 27 276 1 AAAATATAAA 0.906633 -25 TAGGACAATAAAAGTAAAAAATAAATATGA 30 40 1 AAAGTAAAAA 0.888255 -135 AGAGAAACATTAAAAGACCTTGCTT 32 6 1 AACATTAAAA 0.716162 -142 AGAAAAATAAAAAGTAAAAATAAAAGCAAA 32 67 1 AAAGTAAAAA 0.888255 -81 TGACCTTTAAAAAATTTAAACAAAAATTGA 33 54 1 AAAATTTAAA 0.906633 -247 TCTAAGTTCCAAAGTTAAAATATATTTGCC 33 228 1 AAAGTTAAAA 0.888255 -73 TAATTTGTTAAAAGTTTAAAAGCTTATTGG 36 57 0 AAAGTTTAAA 0.888255 -54 AAAATTTAAAAAAGTAAAAAATTAAAGAA 37 10 0 AAAGTAAAAA 0.888255 -40 TTTAAATTTTAAAATTTAAAAAAGTAAAAA 37 20 0 AAAATTTAAA 0.906633 -30 TTTAAATTTTAAAATTTAAAGGTGGGTTTT 37 30 1 AAAATTTAAA 0.906633 -20 AATAGCATTGAAAGTTTAAAACCAAAAATT 39 25 1 AAAGTTTAAA 0.888255 -276 ACAAATAACAAAAATAAAAATAGGAGGGAA 39 277 1 AAAATAAAAA 0.906633 -24 ACAGATAAATAAAATAAAAATAAAATTAGG 40 24 0 AAAATAAAAA 0.906633 -260 TACTTAAACAAAAATAAAAATAAGTT 41 7 0 AAAATAAAAA 0.906633 -294 AATGTTACATAAAATTAAAATTGACAAAAT 41 167 0 AAAATTAAAA 0.906633 -134 TTTAAACAAAAAAGTTTAAATAGTATTATC 41 230 1 AAAGTTTAAA 0.888255 -71 TCAAATTTACAAAATAAAAAACTATTTATA 42 59 0 AAAATAAAAA 0.906633 -58 ********** Masking position 5 Map Score: 58.0236 Number of sites scoring better than the average of aligned sites = 1186 Number in coding regions = 752 Number in noncoding regions = 434 Number of orfs with sites within 600 bp upstream = 348 Fraction of orfs with sites within 600 bp upstream = 0.0558946 Motif number 4 AATACCTTAGTTATTTCAAAAGTTTTGAAAGACAC 1 188 1 TTATTTATTT 0.878488 -113 TAAATAGCTTTTTTATAGTGTCTTTCAAAACTTTT 1 205 0 TTTTATTTTT 0.750037 -96 TTTAAAATCTTTTATTTGAGTGTTTTGTTTGGTTT 1 246 0 TTTATTTTTT 0.873621 -55 CTCCAGCATATTTATTGATATCTTTAAAATCTTTT 1 268 0 TTTATTTTTT 0.873621 -33 TTTCCTCTCTTATTTATTAAGTTTTTGAATAAAA 5 10 1 TTATTTATTT 0.878488 -76 CCTTAAATTATTATGTGTTTTGTTTGTGTTTATTT 5 52 0 TTATGTTTTT 0.760617 -34 ATATTATATATTATTTTCGGTTTTTAGTAAGGTTA 6 40 0 TTATTTTTTT 0.907838 -261 GTGTTTCATTTTTTATATATTCTTTTTATATATTC 6 108 0 TTTTATTTTT 0.750037 -193 TCCGCGCCACTTCTTTTTATTTTTTAATATCTATT 6 231 1 TTCTTTTTTT 0.634102 -70 CCATTTTATATTTTTTTAATATTTTAAAGCATTTG 8 46 1 TTTTTTATTT 0.892445 -37 ATTTACCTTCTTTTTTATCTTTTTTATTTTTATTA 9 264 0 TTTTTTTTTT 0.918735 -37 TTATTTTATATTAATTGAAGATTTTATAAAACATT 10 53 0 TTAATTATTT 0.815517 -103 CACCAAGTAATTTTTTATAATTTTTTAATGTTCAA 11 18 1 TTTTTTTTTT 0.918735 -256 ATTACATTAATTATTTATTGTTTTTTATAATCTCA 14 214 1 TTATTTTTTT 0.907838 -87 TAGTTACTCTTTTTTTATTAAATTTAACTGATTCA 14 262 1 TTTTTTATTT 0.892445 -39 AGTGCCTTAGTTATTTAAGAAGTTTGAAAGACACT 15 242 1 TTATTTATTT 0.878488 -59 ACGTTCTAAATTAAATTTAAATTTTGAGGTGAGTT 21 13 1 TTAAATATTT 0.539861 -26 TCCTTTGTGTTTTATTTATTTGTTTTAACCGTAAT 24 81 0 TTTATTTTTT 0.873621 -46 ATTTTGAGACTTTATTCTACTATTTAATTCTCATT 26 62 1 TTTATTTTTT 0.873621 -239 TTTATAAATCTTTAATAGCAAATTTCAGGAAATTT 26 157 0 TTTAATATTT 0.573844 -144 CTCATCTTTTTTAAGTAAAATATTTATATCAGATA 26 197 1 TTAAGTTTTT 0.660188 -104 TCATCCTCCTTTCTTTTTTATATTTAACAAAAAGC 26 247 0 TTCTTTTTTT 0.634102 -54 CAAATATTAATTAATTATACAATTTGAATTTTTAA 27 175 1 TTAATTATTT 0.815517 -126 ATATTAACGTTTAAATCCGGTTTTTGTTGGAATAT 27 237 1 TTAAATTTTT 0.615173 -64 GGATACCCATTTAAATTAAGATTTTGATCAACCTT 29 115 1 TTAAATATTT 0.539861 -71 TTACAAATATTTTTTTCTCATATTTATTTTTTACT 30 52 0 TTTTTTTTTT 0.918735 -123 AAGAAACTTTATTTATTATGTTTTTTCTGAGTT 31 9 1 TTATTTTTTT 0.907838 -77 TTGTTGATGTTTAATTTTAATCTTTTCAAAATCAA 31 45 1 TTAATTTTTT 0.857611 -41 GGATTTGCTTTTATTTTTACTTTTTATTTTTCTAA 32 65 0 TTATTTTTTT 0.907838 -83 TTAAATCAATTTTTGTTTAAATTTTTTAAAGGTCA 33 54 0 TTTTGTATTT 0.728002 -247 ATTGATTTAATTTTTTGATGTTTTTATCCTATCCA 33 79 1 TTTTTTTTTT 0.918735 -222 TTATGTTATGTTTTGTTTTGATTTTGAGTAATTTA 34 99 0 TTTTGTATTT 0.728002 -43 TATATTTAAATTTATTAAAAATTTTGAAAGAGTTG 35 17 1 TTTATTATTT 0.83535 -41 TTCTTTAATTTTTTACTTTTTTAAATTTT 37 5 1 TTAATTATTT 0.815517 -45 TTAATAATGATTAATTTTTCTTTTTTAGTAATAAA 38 90 0 TTAATTTTTT 0.857611 -207 GTTATTTTGTTTTTTTCATATTTTTTATTACTTAT 38 142 0 TTTTTTTTTT 0.918735 -155 CCTCCTATTTTTATTTTTGTTATTTGTTTGGTTTC 39 269 0 TTATTTTTTT 0.907838 -32 TAGCTCCTAATTTTATTTTTATTTTATTTATCTGT 40 19 1 TTTTATATTT 0.68772 -265 ATTTCTGTAGTTTTTTGACTATTTTGATACTCCGA 40 74 1 TTTTTTATTT 0.892445 -210 GGCTTTTATATTTATTCCTTAATTTTTATTAACTT 40 165 0 TTTATTATTT 0.83535 -119 TAAATATTATTTTAATGGAATTTTTAATATAGTAT 41 124 0 TTTAATTTTT 0.647229 -177 AATTTTAATTTTATGTAACATTTTTTTATATTAGC 41 175 1 TTATGTTTTT 0.760617 -126 ATTTAAACTTTTTTGTTTAAAGTTTATTAAAAATG 41 216 0 TTTTGTATTT 0.728002 -85 TTTATATGACTTTTTTATTATTTTTAAGGTTCCAC 42 30 0 TTTTTTTTTT 0.918735 -87 AAATAGTTTTTTATTTTGTAAATTTGAAAATATAC 42 62 1 TTATTTATTT 0.878488 -55 ****** * *** Masking position 6 Map Score: 68.3867 Number of sites scoring better than the average of aligned sites = 1441 Number in coding regions = 1010 Number in noncoding regions = 431 Number of orfs with sites within 600 bp upstream = 303 Fraction of orfs with sites within 600 bp upstream = 0.0486669 Motif number 5 TTAAATAAATTTTTAAATAATTGAAACACT 4 12 1 TTTTAAATAA 0.726973 -48 TTTATTAAGTTTTTGAATAAAATTAGATAA 5 23 1 TTTTGAATAA 0.861006 -63 TTATTTTCGGTTTTTAGTAAGGTTAAAGGA 6 35 0 TTTTTAGTAA 0.936329 -266 TTCTTTTTATTTTTTAATATCTATTTACTA 6 241 1 TTTTTAATAT 0.632982 -60 AATTTCGTGTTTTATAGTAAATAGATATTA 6 255 0 TTTATAGTAA 0.640318 -46 ATTTTATATTTTTTTAATATTTTAAAGCAT 8 48 1 TTTTTAATAT 0.632982 -35 AGTTCTGTTCTTTTTAAAAGTTAATAAAAG 9 36 0 TTTTTAAAAG 0.472183 -265 TTAACACCATTTTAGAATAAATATAATAAA 9 241 1 TTTAGAATAA 0.423489 -60 ACCATAATATTTTTTAGTAGCCCAATTATT 10 130 0 TTTTTAGTAG 0.758068 -26 CTTAAATAAATTTTAAAAAATAAAATAGAG 12 128 0 TTTTAAAAAA 0.468799 -28 AGTTACTCTTTTTTTATTAAATTTAACTGA 14 263 1 TTTTTATTAA 0.624591 -38 ATAAATATGGGTTTTAGTAAATATTGATGC 19 117 1 GTTTTAGTAA 0.493953 -82 CCATTAAGAATTTTTAGTAAAGAGTGTTTT 20 14 0 TTTTTAGTAA 0.936329 -29 TTTCAGGAAATTTTGAAAAATTTTATATTG 26 140 0 TTTTGAAAAA 0.662394 -161 GCCTCATCTTTTTTAAGTAAAATATTTATA 26 195 1 TTTTAAGTAA 0.75501 -106 CCGAACAACCTTTTTAGAAAAGGTTGATCA 29 139 0 TTTTTAGAAA 0.805258 -47 CCACTCCAACTTTTTAGTAAAAGCTGCCCG 29 166 0 TTTTTAGTAA 0.936329 -20 TTTTTATTGATTTTGAAAAGATTAAAATTA 31 56 0 TTTTGAAAAG 0.315294 -30 TATTACAATATTTTTAGAAAAATAAAAAGT 32 52 1 TTTTTAGAAA 0.805258 -96 TTTGTTTTGATTTTGAGTAATTTAATAATT 34 93 0 TTTTGAGTAA 0.878357 -49 TCTTTCAAAATTTTTAATAAATTTAAATAT 35 18 0 TTTTTAATAA 0.796454 -40 TATATCTTTATTTTTAGTAATACTTAATAT 38 32 1 TTTTTAGTAA 0.936329 -265 TAATTTTTCTTTTTTAGTAATAAACTATTT 38 84 0 TTTTTAGTAA 0.936329 -213 ATTAAAGACATTTTTAATAATGATTAATTT 38 108 0 TTTTTAATAA 0.796454 -189 AAAGTTTATTTTATTAATAATAAAATACCG 38 197 1 TTATTAATAA 0.297981 -100 AGACATAATATTTTAAATAATTTTTGGTTT 39 43 0 TTTTAAATAA 0.726973 -258 AATAAAGATATTTATAAAAATGCCCTTAAA 39 198 1 TTTATAAAAA 0.290005 -103 TATTCCTTAATTTTTATTAACTTTGAAAAA 40 158 0 TTTTTATTAA 0.624591 -126 AATATATAATTTTTGAAAAATGCATTTATA 40 211 0 TTTTGAAAAA 0.662394 -73 TTTAATGGAATTTTTAATATAGTATTTGAA 41 119 0 TTTTTAATAT 0.632982 -182 GCTCAAGACATTTTTAATAAACTTTAAACA 41 208 1 TTTTTAATAA 0.796454 -93 ********** Masking position 6 Map Score: 28.0202 Number of sites scoring better than the average of aligned sites = 642 Number in coding regions = 458 Number in noncoding regions = 184 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 6 TTTTATTGATTTTGGAAGACACTATATTTTGCA 1 116 0 TTTGAACACT 0.989093 -185 TTTCAAAAGTTTTGAAAGACACTATAAAAAAGC 1 201 1 TTTGAACACT 0.989093 -100 AATTGAAGATTTTATAAAACATTAGATTACATA 10 43 0 TTTAAACATT 0.69093 -113 TTTTATTAATTTTGAAAGGCACTATAATCTTAC 15 164 0 TTTGAACACT 0.989093 -137 AACGCCCTCCTTTGGAAGGCGTTCATTAGTGCC 15 215 1 TTTGAACGTT 0.842177 -86 ATTTAAGAAGTTTGAAAGACACTATATAGTTAA 15 254 1 TTTGAACACT 0.989093 -47 TTGGCATTATTTTGAAAGACATTATAGATTAAA 19 151 0 TTTGAACATT 0.962388 -48 TGAAGTAGAGTTTGCAATTCACTATTTATAATT 24 30 0 TTTGAACACT 0.989091 -97 TTTTATTAACTTTGAAAAACACTTATGGTATTT 40 144 0 TTTGAACACT 0.989093 -140 AAATTATATATTTGAAAAACACTTATATTTTAC 40 229 1 TTTGAACACT 0.989093 -55 **** ** **** Masking position 7 Map Score: 17.5012 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 = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 TGTTTATACACTCCTTTTCTTTTATTACACTAATCC 1 18 1 CCCTTTTTAT 0.831894 -283 TATTCACCTTCTCTCTCAATTATTTTAAAGTATTTT 2 13 0 CCTCTTTTTT 0.70384 -29 ATTTAGTCACCTTAAATTATTATGTGTTTTGTT 5 63 0 CCCTTTTTTT 0.965412 -23 CCCTCCGCGCCACTTCTTTTTATTTTTTAATATCTA 6 228 1 CCTTCTTTTT 0.8182 -73 CTAATCACCTTCAATAATTTTTTGTTGAATG 7 37 0 CCCTTTATTT 0.905435 -21 GATATATATACCCCCTATTTAATACTTATATCACCA 9 163 1 CCCCTTATAT 0.352572 -138 AATCACCCCTCCATTTGTTATAATGGTTTAT 10 6 1 CCCTCTTTTT 0.944311 -150 TTAATCACCATAATATTTTTTAGTAGCCCAA 10 135 0 CCCATATTTT 0.765929 -21 TTCACTAAACCTCTATTTTATTTTTTAAAATTTATT 12 118 1 CCTATATTTT 0.464805 -38 GGATTTCCACCTTTATATCTTATTT 16 3 0 CCCTTATTTT 0.954683 -23 CACTGCACCTCTGTATTTTATATGCCATCTG 17 64 0 CCCTCATTTT 0.927527 -21 GTTTTTACCCCCTATAACTTATTATTTGGCATTAT 19 174 0 CCTATTTTTT 0.535031 -25 AATTTACACCTCCAAATGTTCTCCTTTGTGTT 24 105 0 CCCTCATTTT 0.927527 -22 CCATTTCTATCCCCTTCACTTATTATTAT 25 4 0 CCCTTTTTTT 0.965412 -34 CATAGTCATCCTCCTTTCTTTTTTATATTTAACAAA 26 251 0 CCCTTTTTTT 0.965412 -50 TAATATCATTCACATTATTTTATTTTTGTTAATTTA 27 207 0 CCATTTTTTT 0.538709 -94 GGTTACTCCTCCCTACCATTTTGTTTAAATATAA 30 151 0 CCCCTATTTT 0.871105 -24 ATTCTCCCTCCTTCTCATTTTTTACTCCGGAGG 33 278 0 CCCTTATTTT 0.954683 -23 AATCTTCACCTTTCATAATTATGTTATGTTTT 34 120 0 CCCTTTATTT 0.905435 -22 TCATTTCCAACTCTTTCAAAATTTTTAATAAATTTA 35 23 0 CCTTTAATTT 0.657299 -35 GTCCCTTCACCTTATTTTTAGTTGTTGA 36 93 0 CCTTCTTTTT 0.8182 -18 AAAACCCACCTTTAAATTTTAAAATTTAAAAA 37 28 0 CCCTTATTTA 0.502617 -22 TGCAAGTTATCACCCCTGAATATAATTCAAAAAAAC 38 267 0 CCCCCATTAT 0.421268 -30 AGTATTCCCTCCTATTTTTATTTTTGTTATTTGT 39 277 0 CCCTATTTTT 0.769534 -24 TAAAATATAGCTCCTAATTTTATTTTTATTTTATTT 40 12 1 CCCTATTTTT 0.769534 -272 AATTATCCCCTTTATAAATTTCTTATTTATCTG 40 261 0 CCTTTAATTT 0.657299 -23 AGTTTCACCCTTTTGGTATTATTTAATTGTGTT 41 278 0 CCTTTTATAT 0.310603 -23 CATTTCACCTCAAAAATTTGTGGAACCTTAA 42 6 1 CCCTCAATTT 0.814478 -111 * **** ** ** * Masking position 13 Map Score: 29.5785 Number of sites scoring better than the average of aligned sites = 405 Number in coding regions = 331 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 8 TCCGTTATTAATTTATACCTCAAATAATGCAAAC 1 51 1 ATTTACCTAA 0.743862 -250 ATTTAGTCACCTTAAATTATTATGTG 5 70 0 TTACACCTAA 0.800333 -16 CTAATCACCTTCAATAATTTTTTG 7 44 0 CTACACCTAA 0.694171 -14 AATCACCCCTCCATTTGTTATAAT 10 1 1 AATCCCCTAT 0.784865 -155 TGAATCTATATTTAATCCCTAAAAATATAAAACT 12 69 1 TTTTCCCTAA 0.593205 -87 AATCTCACCTTAAATAAATTTTAA 12 142 0 AATCACCTAA 0.91767 -14 GGATTTCCACCTTTATATCTTATTT 16 10 0 ATTCACCTAT 0.896642 -16 GTTTTTACCCCCTATAACTTATTATTT 19 182 0 TTTCCCCTAA 0.916098 -17 AAACTCACCTCAAAATTTAAATTT 21 25 0 AAACACCTAA 0.77049 -14 AATTATCACCTATAACAAAAGCAGA 22 43 0 ATTCACCTAA 0.956034 -15 AATTTACACCTCCAAATGTTCTCCT 24 112 0 ATTCACCTAA 0.956034 -15 GTTTGACACCTAAATTTTATATTTT 27 286 0 TTTCACCTAT 0.841505 -15 TTAAAGGGCTTTTAGTCCCTTTAATGTCTCTTAA 29 38 0 TTTTCCCTAA 0.593205 -148 AAAACCCACCTTTAAATTTTAAAAT 37 35 0 AAACACCTAA 0.77049 -15 ATGTGCAAGTTATCACCCCTGAATATAATTCAAA 38 272 0 TATCCCCTAT 0.690673 -25 AATTATCCCCTTTATAAATTTCTTA 40 269 0 ATTCCCCTAT 0.876806 -15 CATTTCACCTCAAAAATTTGTGGA 42 1 1 CATCACCTAA 0.794364 -116 AAATTACCACCTTAAAATTAATTCAT 42 101 0 ATTCACCTAA 0.956034 -16 *** ***** ** Masking position 10 Map Score: 12.7863 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 135 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 9 ATTAATTTAAGGAACATTGAACGCCTTTAAGGCGT 1 148 1 GATTGAACCC 0.992219 -153 AATAACTAAGGTATTAATGAACGCCTTAAAGGCGT 1 168 0 GAATGAACCC 0.982293 -133 GCGCGGAGGGGGGGATTTGAACCCCCGCGGGGCAA 6 203 0 GGTTGAACCC 0.988245 -98 AAGTTATTAAGGAAATTTGAACTCCTTC 9 4 0 GATTGAACCC 0.99221 -297 GCGGACCCGAGGGGATTTGAACCCCCGACCCCCGG 14 15 1 GGTTGAACCC 0.988245 -286 ATTTATGAAGGAATGTTTGAACGCCCTCCTTTGGA 15 196 1 GATTGAACCC 0.992219 -105 AATAACTAAGGCACTAATGAACGCCTTCCAAAGGA 15 222 0 GAATGAACCC 0.982293 -79 * * ****** ** Masking position 10 Map Score: 9.88774 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 2 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 10 AAGTGTTTCAATTATTTAAAAATTTATTTAAT 4 10 0 ATATAAAAAT 0.428033 -50 TTTTATTATATTTATTCTAAAATGGTGTTAAGT 9 239 0 TTATTAAAAT 0.609238 -62 TTATTATTATTCAATTTTAAAATGAGGTATAAA 11 102 0 TAATTAAAAT 0.552033 -172 ACCAAATAATTATATATGAATATTTTATATAGT 11 177 0 TTATGAATAT 0.501365 -97 TTGGAGTGTTTCAATAAGAAAATTAATGTGTAG 13 58 0 TAATGAAAAT 0.889124 -40 GAAAAGTATATATATGAGAAAATTCATTTTAAA 14 116 0 TTATGAAAAT 0.910283 -185 ACTGTAATGGATAATTGGAAAATAGAAACTCCC 15 22 1 AAATGAAAAT 0.793793 -279 ATTTTATAAGATTATAGGAAAATAATTCTATTC 26 23 0 ATATGAAAAT 0.829566 -278 ATTTAAGTTATATATTAGAAAATCTAATAACTA 27 36 1 TTATGAAAAT 0.910282 -265 TAAATGACTATAAATATGAGAATAGTCAGAAAT 27 69 1 TAATGAGAAT 0.400458 -232 TTTATTTTTGTTAATTTAAAAATTCAAATTGTA 27 192 0 TAATAAAAAT 0.552032 -109 AAAATATTTCTTTATTTGAATATTCTG 30 5 0 TTATGAATAT 0.501358 -170 AAGAAATATTTTTATAGGACAATAAAAGTAAAA 30 26 1 TTATGACAAT 0.45802 -149 GTAAAAAATAAATATGAGAAAAAAATATTTGTA 30 53 1 ATATGAAAAA 0.419502 -122 TGCTATATGCTGTATGGGAAAATCATTGTGTAA 34 40 1 TTATGAAAAT 0.910283 -102 AACCCACCTTTAAATTTTAAAATTTAAAAAAGT 37 25 0 TAATTAAAAT 0.552033 -25 GTTTATTTTATTAATAATAAAATACCGTTAAAT 38 200 1 TAATTAAAAT 0.552032 -97 AACTTAAAAGTTAATTTAAAAATTAGAAACCAA 39 244 1 TAATAAAAAT 0.552032 -57 TAAAATTATAAAAATGTGAAAATACCATAAGTG 40 125 1 AAATGAAAAT 0.793802 -159 TCAAAAATTATATATTTGAAAAACACTTATATT 40 225 1 TTATGAAAAA 0.600849 -59 ATTTTACAGATAAATAAGAAATTTATAAAGGGG 40 255 1 TAATGAAATT 0.301738 -29 TGGATTGAAAAATATCTGAAAATATTACAATGT 41 58 0 ATATGAAAAT 0.829632 -243 TTTTTAATATAGTATTTGAAAAATATAAGATTC 41 106 0 ATATGAAAAA 0.419501 -195 GTCTTGAGCTAATATAAAAAAATGTTACATAAA 41 184 0 ATATAAAAAT 0.428083 -117 TTTTATTTTGTAAATTTGAAAATATACAAATAT 42 70 1 TAATGAAAAT 0.889124 -47 * *** ****** Masking position 5 Map Score: 17.6814 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 227 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 11 ATTTGAGGTATAAATTAATAACGGATTAGT 1 46 0 TAAATTAATA 0.511826 -255 TATTTATTGATATCTTTAAAATCTTTTATT 1 265 0 TATCTTTAAA 0.770743 -36 AGTATTGTGCTATTTTTATAGTTCTGTTCT 9 55 0 TATTTTTATA 0.564438 -246 TTATTTTTATTATATTTATTCTAAAATGGT 9 246 0 TATATTTATT 0.762375 -55 CTTATTATTTTATATTAATTGAAGATTTTA 10 62 0 TATATTAATT 0.561585 -94 TATTTGAATCTATATTTAATCCCTAAAAAT 12 65 1 TATATTTAAT 0.561586 -91 ATTAGAGGCATAACTTTATATACCAAATAT 13 17 1 TAACTTTATA 0.733456 -81 ATATACCAAATATATTAATTTTATCTACAC 13 34 1 TATATTAATT 0.561585 -64 GCCACAAACCTATATTTATAATTAACCATA 14 174 0 TATATTTATA 0.88827 -127 TTAAATACCCTATCTTAATATTATTTACTA 17 22 1 TATCTTAATA 0.77074 -63 AACTTTAACTTTAAATTTATTTTAA 18 6 1 TAACTTTAAA 0.523489 -91 CGTTCTAAATTAAATTTAAATTTTGAGGTG 21 14 1 TAAATTTAAA 0.511827 -25 TATTTTATCTTATATTAATAATATTCCAAC 27 262 0 TATATTAATA 0.762238 -39 AATAAAGAAATATTTTTATAGGACAATAAA 30 22 1 TATTTTTATA 0.564438 -153 TGTCATTAATTATATTTAAACAAAATGGTA 30 142 1 TATATTTAAA 0.762375 -33 ATAGTTTCTCTATATTTATATACTTTTTGG 33 111 0 TATATTTATA 0.88827 -190 TAAAAGTATTTATCTTTATATGCTATATGC 34 20 1 TATCTTTATA 0.893835 -122 ATTCTCTATATTTAAATTTATTAAAA 35 7 1 TATATTTAAA 0.762375 -51 ATCCAAACTTTATCTTAATAACCCAATAAG 36 35 1 TATCTTAATA 0.77074 -76 ACTTTTTATATATCTTTATTTTTAGTAATA 38 24 1 TATCTTTATT 0.770743 -273 AAAATACCGTTAAATTTATATAAGATAAAG 38 218 1 TAAATTTATA 0.724215 -79 TTTTTATAAATATCTTTATTTCACCCTATG 39 188 0 TATCTTTATT 0.770743 -113 ACTCCGAGTATAACTTTATAAGCTAAAATT 40 102 1 TAACTTTATA 0.733456 -182 TACGGGCTTTTATATTTATTCCTTAATTTT 40 174 0 TATATTTATT 0.762375 -110 TTTCAAATACTATATTAAAAATTCCATTAA 41 118 1 TATATTAAAA 0.561585 -183 ********** Masking position 5 Map Score: 20.8186 Number of sites scoring better than the average of aligned sites = 800 Number in coding regions = 563 Number in noncoding regions = 237 Number of orfs with sites within 600 bp upstream = 227 Fraction of orfs with sites within 600 bp upstream = 0.03646 Motif number 12 GATATAAGTATTAAATAGGGGGTATATATA 9 165 0 TTAAATAGGG 0.595171 -136 TAGTTAGCTCTTAAATAGTTAATTCTTTAG 10 96 1 TTAAATAGTT 0.599028 -60 ACAACCTGAGATAAAGAGGACCCGTAGCCT 14 78 0 ATAAAGAGGA 0.665923 -223 AAAATTCATTTTAAAGAGTGCTTACAACCT 14 101 0 TTAAAGAGTG 0.883262 -200 GGAAGATACGATAAAGAGTATATAATAATA 19 68 0 ATAAAGAGTA 0.881307 -131 AGAATTTTTAGTAAAGAGTGTTTTGGT 20 8 0 GTAAAGAGTG 0.667733 -35 CAGATTTATCTTAAAGAGTGAGGGATTGAA 22 17 0 TTAAAGAGTG 0.883262 -41 ATAACTAATTATAAATAGTGAATTGCAAAC 24 24 1 ATAAATAGTG 0.845594 -103 AAAATGAGAATTAAATAGTAGAATAAAGTC 26 69 0 TTAAATAGTA 0.84312 -232 TTTTAGAAAAATAAAAAGTAAAAATAAAAG 32 63 1 ATAAAAAGTA 0.629397 -85 ATAAAGATATATAAAAAGTAGTTATTATGG 38 13 0 ATAAAAAGTA 0.629397 -284 AATAAACTATTTAAATAGTAAGGCAACTTA 38 66 0 TTAAATAGTA 0.84312 -231 TTTATATAAGATAAAGAGTACTATAAATGT 38 232 1 ATAAAGAGTA 0.881307 -65 ACAAAAAAGTTTAAATAGTATTATCAACAT 41 235 1 TTAAATAGTA 0.84312 -66 AAAAAGTCATATAAATAGTTTTTTATTTTG 42 50 1 ATAAATAGTT 0.599028 -67 ********** Masking position 5 Map Score: 9.22627 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 93 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 13 TGTTTGGTTTAATATCTAAATAGCTTTTTTAT 1 224 0 ATATCAAATA 0.778158 -77 GAACTATAAAAATAGCACAATACTAAAATATT 9 61 1 ATAGCCAATA 0.832243 -240 ATATAGTATCATTATCACAATTATATTTATGA 9 93 1 ATATCCAATT 0.814055 -208 GAATCTTATGATTAACTCAACATTTCATAAAT 9 117 0 ATAACCAACA 0.807559 -184 AATATTTTTTAGTAGCCCAATTATTCTCTCTA 10 123 0 ATAGCCAATT 0.681523 -33 CGCTAATACTATTAACCAAATAATTATATATG 11 192 0 ATAACAAATA 0.799502 -82 GAAAAATATAAATAACTAATTATAAATAGTGA 24 13 1 ATAACAATTA 0.375645 -114 TTTTAACCGTAATATCTAAACAATATTAATTT 24 62 0 ATATCAAACA 0.560595 -65 AATTTAAATGGGTATCCCAATAGGGCGAAGTC 29 100 0 GTATCCAATA 0.70315 -86 ACTTTATCTTAATAACCCAATAAGCTTTTAAA 36 41 1 ATAACCAATA 0.92024 -70 TAACAAATTAATTAACTCAACAACTAAAAATA 36 77 1 ATAACCAACA 0.807559 -34 AAAAAAACAAAATAACTCATTAATAGTAACAA 38 161 1 ATAACCATTA 0.635146 -136 ACTCATTAATAGTAACAAAATTAAAGTTTATT 38 175 1 ATAACAAATT 0.632362 -122 TATTATATTATCACAATAGCATTGAAAG 39 7 1 ATATCCAATA 0.910308 -294 TTATACTCGGAGTATCAAAATAGTCAAAAAAC 40 83 0 ATATCAAATA 0.778158 -201 AATAATATTTAGTATCTCAATTTTGTCAATTT 41 148 1 ATATCCAATT 0.814055 -153 TAGATATGATGATAACACAATTAAATAATACC 41 265 1 GTAACCAATT 0.537365 -36 * **** ***** Masking position 4 Map Score: 8.76442 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 103 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 14 ACCTGTCATTGCCCTACCCGGGCTTTTCAG 1 85 0 GCCCTACCCG 0.956412 -216 GCGGGGCAAAGCCCCATGGGATCTCCAGTC 6 182 0 GCCCCATGGG 0.947473 -119 ATGGGGCTTTGCCCCGCGGGGGTTCAAATC 6 195 1 GCCCCGCGGG 0.954432 -106 GGGGTTCAAATCCCCTCGGGTCCGCCAAT 14 10 0 TCCCCTCGGG 0.70958 -291 GACGGGGTGTGCCCTCCTGGGGCATCCGCG 18 55 0 GCCCTCCTGG 0.81613 -42 GATGCCCCAACCGTTTTACGGGG 18 84 0 GCCCCAACCG 0.888931 -13 GCTATTTTAGCCCCAACCGTTTGAGAATA 19 10 1 GCCCCAACCG 0.888931 -189 ATAGGACTTCGCCCTATTGGGATACCCATT 29 96 1 GCCCTATTGG 0.792629 -90 AAGTCCTAACTCCCTACCGGTAAGAATATT 33 152 0 TCCCTACCGG 0.895282 -149 ATTTATAAAAGCCCTACGGGCTTTTATATT 40 188 0 GCCCTACGGG 0.980169 -96 ********** Masking position 4 Map Score: 4.97436 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 16 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 15 GATTTTGGAAGACACTATATTTTGCAAACC 1 112 0 GACACTATAT 0.929972 -189 AGTTTTGAAAGACACTATAAAAAAGCTATT 1 208 1 GACACTATAA 0.585616 -93 ATGATTAATGGATACCATATTATATATTAT 6 61 0 GATACCATAT 0.900007 -240 TTGTGATAATGATACTATATAATATTTTAG 9 83 0 GATACTATAT 0.924571 -218 CATGTAAGGGAATACTATATAAAATATTCA 11 164 1 AATACTATAT 0.587399 -110 CAACATATTTGAATCTATATTTAATCCCTA 12 60 1 GAATCTATAT 0.451764 -96 TTATATTTATGAAACAATATAGCATTCTGG 15 89 1 GAAACAATAT 0.540879 -212 AAGTTTGAAAGACACTATATAGTTAAATCA 15 261 1 GACACTATAT 0.929972 -40 TAAGATATCAGAAACCATATATAAAATTTT 26 109 0 GAAACCATAT 0.860098 -192 ATTTATATCAGATACCATATAATATGGATG 26 218 1 GATACCATAT 0.900007 -83 TTCTGGTCAAGACACCATAGGACTTCGCCC 29 80 1 GACACCATAG 0.605994 -106 AAGAAACTTTATTTATTATGTT 31 3 1 GAAACTTTAT 0.451764 -83 ATATTTTTCAAATACTATATTAAAAATTCC 41 113 1 AATACTATAT 0.587399 -188 ACAAAATTGAGATACTAAATATTATTTTAA 41 144 0 GATACTAAAT 0.546776 -157 ********** Masking position 2 Map Score: 5.24145 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 46 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357