AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i199_trans1_mjan_reg_100.orf -o199_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: 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 RMJ03993 155 M_jannaschii_chromosome #12 RMJ09839 97 M_jannaschii_chromosome #13 RMJ15198 300 M_jannaschii_chromosome #14 RMJ06275 300 M_jannaschii_chromosome #15 RMJ03510 25 M_jannaschii_chromosome #16 RMJ15668 198 M_jannaschii_chromosome #17 RMJ00821 42 M_jannaschii_chromosome #18 RMJ12447 38 M_jannaschii_chromosome #19 RMJ13379 57 M_jannaschii_chromosome #20 RMJ14726 32 M_jannaschii_chromosome #21 RMJ06762 126 M_jannaschii_chromosome #22 RMJ14744 37 M_jannaschii_chromosome #23 RMJ05778 300 M_jannaschii_chromosome #24 RMJ12218 174 M_jannaschii_chromosome #25 RMJ06687 85 M_jannaschii_chromosome #26 RMJ04756 147 M_jannaschii_chromosome #27 RMJ09467 141 M_jannaschii_chromosome #28 RMJ07626 57 M_jannaschii_chromosome #29 RMJ12537 110 M_jannaschii_chromosome #30 RMJ08709 49 M_jannaschii_chromosome #31 RMJ15425 296 M_jannaschii_chromosome #32 RMJ09720 283 M_jannaschii_chromosome #33 RMJ03708 300 M_jannaschii_chromosome #34 RMJ07630 116 M_jannaschii_chromosome Motif number 1 CTTAAATTAATTTTATTGATTTTGGAAGAC 1 129 0 TTTTATTGAT 0.853159 -172 GTTTCTGCATTTTTATTTTAT 3 2 0 TTTTATTTTA 0.88695 -32 GGATACCATATTATATATTATTTTCGGTTT 6 52 0 TTATATATTA 0.584209 -249 TATATATTCTTTTTATATATTCCCACAATA 6 100 0 TTTTATATAT 0.940413 -201 GTGTTTCATTTTTTATATATTCTTTTTATA 6 113 0 TTTTATATAT 0.940413 -188 CGCCACTTCTTTTTATTTTTTAATATCTAT 6 235 1 TTTTATTTTT 0.971407 -66 TAATTTCGTGTTTTATAGTAAATAGATATT 6 256 0 TTTTATAGTA 0.572964 -45 TTAAATCCCATTTTATATTTTTTTAATATT 8 39 1 TTTTATATTT 0.959241 -44 ATTGTGCTATTTTTATAGTTCTGTTCTTTT 9 52 0 TTTTATAGTT 0.853159 -249 ATTATCACAATTATATTTATGAAATGTTGA 9 103 1 TTATATTTAT 0.860578 -198 TTTATTTTTATTATATTTATTCTAAAATGG 9 247 0 TTATATTTAT 0.860578 -54 TTTTTATCTTTTTTATTTTTATTATATTTA 9 258 0 TTTTATTTTT 0.971407 -43 TAATCTAATGTTTTATAAAATCTTCAATTA 10 47 1 TTTTATAAAA 0.390013 -109 AACCTTATTATTTTATATTAATTGAAGATT 10 65 0 TTTTATATTA 0.84308 -91 ATAAAAAAAGTTTTATATTTTTAGGGATTA 11 81 0 TTTTATATTT 0.959241 -75 TAAACCTCTATTTTATTTTTTAAAATTTAT 11 123 1 TTTTATTTTT 0.971407 -33 GTTACTCTTTTTTTATTAAATTTAACTGAT 13 264 1 TTTTATTAAA 0.615989 -37 GATAGCCTAATTATATTTATGAAACAATAT 14 79 1 TTATATTTAT 0.860578 -222 GTTTATATACTTTTATTGTTGTTTAACTCA 14 126 0 TTTTATTGTT 0.893444 -175 CCTTCATAAATTTTATTAATTTTGAAAGGC 14 177 0 TTTTATTAAT 0.876105 -124 AATTAGTTATTTATATTTTTCGG 21 4 0 TTATATTTTT 0.899094 -123 CTCCTTTGTGTTTTATTTATTTGTTTTAAC 21 87 0 TTTTATTTAT 0.959241 -40 CAACCGAAAATTTTATATATGGTTTCTGAT 23 103 1 TTTTATATAT 0.940413 -198 GATGAGGCTATTTTATAAATCTTTAATAGC 23 173 0 TTTTATAAAT 0.8245 -128 CTCCTTTCTTTTTTATATTTAACAAAAAGC 23 247 0 TTTTATATTT 0.959241 -54 CATATTTATTTTTTACTTTTATTGTCCTAT 24 39 0 TTTTACTTTT 0.719563 -136 TTGTCATTAATTATATTTAAACAAAATGGT 24 141 1 TTATATTTAA 0.584209 -34 AAGAAACTTTATTTATTATGTTTTTT 25 7 1 CTTTATTTAT 0.640027 -79 TAAGAGAGATTTTTATTGATTTTGAAAAGA 25 65 0 TTTTATTGAT 0.853159 -21 TATTTTTACTTTTTATTTTTCTAAAAATAT 26 59 0 TTTTATTTTT 0.971407 -89 AAGGATTTGCTTTTATTTTTACTTTTTATT 26 72 0 TTTTATTTTT 0.971407 -76 AGATAAATACTTTTATAAATACTT 27 5 0 TTTTATAAAT 0.8245 -137 TTCTTTAATTTTTTACTTTTTTAAATTTTA 30 11 1 TTTTACTTTT 0.719563 -39 AATAACTACTTTTTATATATCTTTATTTTT 31 17 1 TTTTATATAT 0.940413 -280 TTTTATATATCTTTATTTTTAGTAATACTT 31 27 1 CTTTATTTTT 0.719563 -270 TAATGAGTTATTTTGTTTTTTTCATATTTT 31 153 0 TTTTGTTTTT 0.577235 -144 TTTAACGGTATTTTATTATTAATAAAATAA 31 202 0 TTTTATTATT 0.910784 -95 ACTCTTTATCTTATATAAATTTAACGGTAT 31 221 0 TTATATAAAT 0.549489 -76 TAGCTCCTAATTTTATTTTTATTTTATTTA 32 19 1 TTTTATTTTT 0.971407 -265 TTTATTTTTATTTTATTTATCTGTGTTTAA 32 30 1 TTTTATTTAT 0.959241 -254 ATTTTCACATTTTTATAATTTTAGCTTATA 32 118 0 TTTTATAATT 0.876105 -166 CCCTACGGGCTTTTATATTTATTCCTTAAT 32 177 0 TTTTATATTT 0.959241 -107 CCCGTAGGGCTTTTATAAATGCATTTTTCA 32 198 1 TTTTATAAAT 0.8245 -86 TTTTCAAAAATTATATATTTGAAAAACACT 32 222 1 TTATATATTT 0.860578 -62 TGAAAAACACTTATATTTTACAGATAAATA 32 241 1 TTATATTTTA 0.672954 -43 AACTTATTTTTATTTTTGTTTAAGTAT 33 8 1 TTTTATTTTT 0.971407 -293 TCACTGAATCTTATATTTTTCAAATACTAT 33 101 1 TTATATTTTT 0.899094 -200 TGTAACATTTTTTTATATTAGCTCAAGACA 33 188 1 TTTTATATTA 0.84308 -113 TATATGACTTTTTTATTATTTTTAAGGTTC 34 33 0 TTTTATTATT 0.910784 -84 ********** Masking position 4 Map Score: 70.048 Number of sites scoring better than the average of aligned sites = 1664 Number in coding regions = 1122 Number in noncoding regions = 542 Number of orfs with sites within 600 bp upstream = 408 Fraction of orfs with sites within 600 bp upstream = 0.0655316 Motif number 2 AAAATTTATCACAAGTGGTGGTGAAG 4 44 1 AAATGTGGTG 0.950552 -16 AAAACACATAATAATTTAAGGTGACTAAAT 5 66 1 AAATAAGGTG 0.973807 -20 TAAAACACGAAATTATGGAGGTGCAACCTTGAC 6 271 1 ATTTGAGGTG 0.979669 -30 TCAACAAAAAATTATTGAAGGTGATTAG 7 40 1 ATATAAGGTG 0.960046 -18 ATAAGAATACAGAATTTGTGGTGATATAAGTAT 9 184 0 AAATGTGGTG 0.950552 -117 AACCATTATAACAAATGGAGGGGTGATT 10 6 0 AAATGAGGGG 0.942466 -150 GGCTACTAAAAAATATTATGGTGATTAA 10 138 1 AATTATGGTG 0.958243 -18 TTTTTTAAAATTTATTTAAGGTGAGATT 11 138 1 TTATAAGGTG 0.838581 -18 AAATAAGATATAAAGGTGGAAATCC 15 6 1 AATTAAGGTG 0.982912 -20 AATTAAATTTAAATTTTGAGGTGAGTTT 18 21 1 AATTGAGGTG 0.986764 -18 ACAAAGGAGAACATTTGGAGGTGTAAATT 21 108 1 AATTGAGGTG 0.986764 -19 ATAATAATAAGTGAAGGGGATAGAAATGG 22 7 1 AAATAAGGGG 0.92668 -31 TTAAATTTTAAAATTTAAAGGTGGGTTTT 30 31 1 AATTAAGGTG 0.982912 -19 TATAAAAAGTAGTTATTATGGTG 31 1 0 ATTTATGGTG 0.936837 -296 TGTGTTTAAATATTGTAGTGGTGATTTCTGTAG 32 51 1 TTTTGTGGTG 0.806054 -233 TAAATAAGAAATTTATAAAGGGGATAATT 32 265 1 ATTTAAGGGG 0.92668 -19 AGGTTCCACAAATTTTTGAGGTGAAATG 34 6 0 ATTTGAGGTG 0.979669 -111 AAATATGAATTAATTTTAAGGTGGTAATTT 34 97 1 TATTAAGGTG 0.925573 -20 * ** * ****** Masking position 6 Map Score: 26.872 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 36 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 3 TTCAAAAGTTTTGAAAGACACTATAAAAAAGCTATT 1 202 1 TTAACAATAA 0.777825 -99 ATAAAATACTTTAAAATAATTGAGAG 2 1 1 ATAACTAAAA 0.654986 -41 TTTTAAGTGTTTCAATTATTTAAAAATTTATTTAAT 4 11 0 TTAATTAAAA 0.90726 -49 TCTAATTTTATTCAAAAACTTAATAAATAAGAGAGG 5 14 0 TTAACTATAA 0.583099 -72 ATAACTATCCTTTAACCTTACTAAAAACCGAAAATA 6 28 1 TTAATAAAAA 0.960763 -273 AAAATGGGATTTAAAAGCTATTAAAAGGGAAATTTA 8 17 0 TTAATAAAAA 0.960765 -66 CTCAAATGCTTTAAAATATTAAAAAAATATAAAATG 8 47 0 TTAATTAAAA 0.907231 -36 TCTGTTCTTTTTAAAAGTTAATAAAAGTTATTAAGG 9 27 0 TTAATAAAAA 0.960765 -274 TGAATCTATATTTAATCCCTAAAAATATAAAACTTT 11 69 1 TTAACTAAAT 0.5831 -87 CTCACCTTAAATAAATTTTAAAAAATAAAATAGAGG 11 127 0 ATAATAAAAT 0.629866 -29 TATATTTATAATTAACCATACAAAAATTGTTATAAG 13 158 0 ATAATAAAAA 0.882651 -143 TAGTGAGATTATAAAAAACAATAAATAATTAATGTA 13 216 0 ATAACAAAAT 0.518149 -85 TCTGAATCAGTTAAATTTAATAAAAAAAGAGTAACT 13 263 0 TTAAAAAAAA 0.754942 -38 TTGTTATGAGTTAAACAACAATAAAAGTATATAAAC 14 120 1 TTAACAAAAA 0.93917 -181 TATAGTGCCTTTCAAAATTAATAAAATTTATGAAGG 14 171 1 TTAATAAAAA 0.960764 -130 TTTAAGAAGTTTGAAAGACACTATATAGTTAAATCA 14 255 1 TTAACAATAT 0.441989 -46 AAAATGAGAATTAAATAGTAGAATAAAGTCTCAAAA 23 63 0 TTAATAATAA 0.847093 -238 TCTTAGCAATATAAAATTTTTCAAAATTTCCTGAAA 23 134 1 ATAATTAAAA 0.750306 -167 AAATTTGCTATTAAAGATTTATAAAATAGCCTCATC 23 167 1 TTAATTAAAA 0.907245 -134 TCCTTTCTTTTTTATATTTAACAAAAAGCATCCATA 23 240 0 TTATTAAAAA 0.696548 -61 AAGATTAAAATTAAACATCAACAAAAACTCAGAAAA 25 33 0 TTAACAAAAA 0.939298 -53 TTTTAATCTTTTCAAAATCAATAAAAATCTCTCTTA 25 59 1 TTAACAAAAA 0.939298 -27 GCATATAAAGATAAATACTTTTATAAATACTT 27 7 0 ATAATTATAA 0.404708 -135 ACTTGAATTATTAAATTACTCAAAATCAAAACAAAA 27 88 1 TTAACTAAAT 0.583094 -54 ATTCTCTATATTTAAATTTATTAAAAATTTTGAAAG 28 11 1 TTAATAAAAA 0.960581 -47 ACCTTTAAATTTTAAAATTTAAAAAAGTAAAAAATT 30 17 0 TTAATTAAAA 0.907254 -33 TTAGGTAATATTAAGTATTACTAAAAATAAAGATAT 31 33 0 TTAGTAAAAA 0.573822 -264 AAAAGAAAAATTAATCATTATTAAAAATGTCTTTAA 31 101 1 TTATTAAAAA 0.696543 -196 TAAATAAGTAATAAAAAATATGAAAAAAACAAAATA 31 139 1 ATAATAAAAA 0.882651 -158 AAAATAACTCATTAATAGTAACAAAATTAAAGTTTA 31 169 1 ATAATAAAAA 0.882647 -128 TAAAGTTTATTTTATTAATAATAAAATACCGTTAAA 31 196 1 TTATTAAAAA 0.696132 -101 TTTATATAAGATAAAGAGTACTATAAATGTGTTAAG 31 232 1 ATAATAATAA 0.629854 -65 ATAAGTGTTTTTCAAAGTTAATAAAAATTAAGGAAT 32 151 1 TTAATAAAAA 0.960765 -133 AAATGCATTTTTCAAAAATTATATATTTGAAAAACA 32 214 1 TTAATTATAT 0.33367 -70 AGATTTATACTTAAACAAAAATAAAAATAAGTT 33 8 0 TTAAAAAAAA 0.754842 -293 ACTTTTTTGTTTAAAGTTTATTAAAAATGTCTTGAG 33 209 0 TTAATAAAAA 0.960724 -92 GATAACACAATTAAATAATACCAAAAGGGTGAAACT 33 275 1 TTAATAAAAA 0.960758 -26 TTGTGGAACCTTAAAAATAATAAAAAAGTCATATAA 34 28 1 TTAAAAAAAA 0.754944 -89 TTTGTATATTTTCAAATTTACAAAATAAAAAACTAT 34 64 0 TTAATAAAAT 0.8471 -53 ** ** ** **** Masking position 4 Map Score: 54.3256 Number of sites scoring better than the average of aligned sites = 1107 Number in coding regions = 760 Number in noncoding regions = 347 Number of orfs with sites within 600 bp upstream = 292 Fraction of orfs with sites within 600 bp upstream = 0.0469001 Motif number 4 ATAAAATAAAAATGCAGAAACAA 3 4 1 AAATAAAAAT 0.845597 -30 CCTTTAACCTTACTAAAAACCGAAAATAAT 6 36 1 TACTAAAAAC 0.474831 -265 AGTAAATAGATATTAAAAAATAAAAAGAAG 6 240 0 TATTAAAAAA 0.825048 -61 AATATCTATTTACTATAAAACACGAAATTA 6 256 1 TACTATAAAA 0.8259 -45 TGCTTTAAAATATTAAAAAAATATAAAATG 8 47 0 TATTAAAAAA 0.825048 -36 AAAAGAACAGAACTATAAAAATAGCACAAT 9 52 1 AACTATAAAA 0.747662 -249 AGAATAAATATAATAAAAATAAAAAAGATA 9 254 1 TAATAAAAAT 0.897627 -47 AATCTTCAATTAATATAAAATAATAAGGTT 10 65 1 TAATATAAAA 0.837665 -91 ATAATTGGGCTACTAAAAAATATTATGGTG 10 131 1 TACTAAAAAA 0.883656 -25 TAATCCCTAAAAATATAAAACTTTTTTTAT 11 81 1 AAATATAAAA 0.763199 -75 GTTATGCCTCTAATATAAAT 12 1 0 TAATATAAAT 0.845596 -97 TTGTATGGTTAATTATAAATATAGGTTTGT 13 171 1 AATTATAAAT 0.661202 -130 CAGTTAAATTTAATAAAAAAAGAGTAACTA 13 262 0 TAATAAAAAA 0.892028 -39 AAACACTCTTTACTAAAAATTCTTAATGGA 17 15 1 TACTAAAAAT 0.889635 -28 CCGAAAAATATAAATAACTAATTAT 21 6 1 AAATATAAAT 0.773785 -121 ATAAATAACTAATTATAAATAGTGAATTGC 21 20 1 AATTATAAAT 0.661202 -107 GCTTTTTGTTAAATATAAAAAAGAAAGGAG 23 247 1 AAATATAAAA 0.763199 -54 TATTTAAATTTATTAAAAATTTTGAAAGAG 28 19 1 TATTAAAAAT 0.833472 -39 TTAACTCAACAACTAAAAATAAGGTGAAGG 29 88 1 AACTAAAAAT 0.834293 -23 TATTAAGTATTACTAAAAATAAAGATATAT 31 31 0 TACTAAAAAT 0.889635 -266 AATAGTTTATTACTAAAAAAGAAAAATTAA 31 85 1 TACTAAAAAA 0.883656 -212 AATTAATCATTATTAAAAATGTCTTTAATT 31 109 1 TATTAAAAAT 0.833472 -188 TTTAAATAAGTAATAAAAAATATGAAAAAA 31 137 1 TAATAAAAAA 0.892028 -160 AGATAAAGAGTACTATAAATGTGTTAAGTT 31 240 1 TACTATAAAT 0.834291 -57 CAGATAAATAAAATAAAAATAAAATTAGGA 32 23 0 AAATAAAAAT 0.845597 -261 TATAAGCTAAAATTATAAAAATGTGAAAAT 32 118 1 AATTATAAAA 0.647688 -166 TTTTCAAAGTTAATAAAAATTAAGGAATAA 32 159 1 TAATAAAAAT 0.897627 -125 ATTAAGGAATAAATATAAAAGCCCGTAGGG 32 177 1 AAATATAAAA 0.763199 -107 ACTTAAACAAAAATAAAAATAAGTT 33 6 0 AAATAAAAAT 0.845597 -295 TCAAATACTATATTAAAAATTCCATTAAAA 33 120 1 TATTAAAAAT 0.833472 -181 TGTCTTGAGCTAATATAAAAAAATGTTACA 33 188 0 TAATATAAAA 0.837665 -113 GTTTAAAGTTTATTAAAAATGTCTTGAGCT 33 207 0 TATTAAAAAT 0.833472 -94 ACCTTAAAAATAATAAAAAAGTCATATAAA 34 35 1 TAATAAAAAA 0.892028 -82 CAAATTTACAAAATAAAAAACTATTTATAT 34 58 0 AAATAAAAAA 0.837667 -59 ********** Masking position 5 Map Score: 50.9573 Number of sites scoring better than the average of aligned sites = 1282 Number in coding regions = 803 Number in noncoding regions = 479 Number of orfs with sites within 600 bp upstream = 369 Fraction of orfs with sites within 600 bp upstream = 0.0592676 Motif number 5 TTAATACCTTAGTTATTTCAAAAGTTTTGAAAGACAC 1 186 1 ATTTTAGTTT 0.717475 -115 CTTTAAAATCTTTTATTTGAGTGTTTTGTTTGGTTTA 1 245 0 TTTTTGTTTT 0.706162 -56 TTTTATCCCCTTGTTTCTGCATTTTTATTTTAT 3 9 0 CTTTTATTTT 0.542253 -25 TTTCCTCTCTTATTTATTAAGTTTTTGAATAAAA 5 8 1 TTTTTAGTTT 0.878858 -78 ATTATGTGTTTTGTTTGTGTTTATTTTATCTAATTTT 5 41 0 TTTGTATTTT 0.878858 -45 CCATATTATATATTATTTTCGGTTTTTAGTAAGGTTA 6 40 0 TTTTTTTTTT 0.899518 -261 ATTTTTTATATATTCTTTTTATATATTCCCACAATAC 6 99 0 TTTTTATATT 0.818566 -202 CCTCCGCGCCACTTCTTTTTATTTTTTAATATCTATT 6 229 1 ATTTTTTTTT 0.758082 -72 TCCCATTTTATATTTTTTTAATATTTTAAAGCATTTG 8 44 1 TTTTTATTTT 0.951722 -39 TATAATATTTTAGTATTGTGCTATTTTTATAGTTCTG 9 59 0 TTTTGATTTT 0.809397 -242 ACCTTCTTTTTTATCTTTTTTATTTTTATTATATTTA 9 258 0 TTTTTTTTTT 0.899518 -43 ACCTCTATTTTATTTTTTAAAATTTATTTAAGGTGAG 11 126 1 TTTTTTTTAT 0.547355 -30 AATATTCACCTCATGTTTGGAGTGTTTCAATAAGAAA 12 70 0 TTTTTTGTTT 0.767143 -28 TAATTACATTAATTATTTATTGTTTTTTATAATCTCA 13 212 1 ATTTTTTTTT 0.758082 -89 TTCTGGGAGTTTCTATTTTCCAATTATCCATTACAGT 14 22 0 TTTTTATTAT 0.72699 -279 TTAGTGCCTTAGTTATTTAAGAAGTTTGAAAGACACT 14 240 1 ATTTTAGTTT 0.717475 -61 CTATAACTTATTATTTGGCATTATTTTGAAAGACATT 16 161 0 TTTGGATTTT 0.609798 -38 CTCCTTTGTGTTTTATTTATTTGTTTTAACCGTAATA 21 80 0 TTTTTGTTTT 0.706162 -47 AAATTTCAGGAAATTTTGAAAAATTTTATATTGCTAA 23 136 0 ATTTGATTTT 0.597578 -165 AGATACCATATAATATGGATGCTTTTTGTTAAATATA 23 227 1 TTTGGTTTTT 0.415093 -74 TTCTCATATTTATTTTTTACTTTTATTGTCCTATAAA 24 36 0 TTTTTTTATT 0.672 -139 TCCTTACAAATATTTTTTTCTCATATTTATTTTTTAC 24 53 0 TTTTTATATT 0.818566 -122 CTCCCTACCATTTTGTTTAAATATAATTAATGACAAA 24 140 0 TTTTTATAAT 0.378663 -35 TTTATTTATTATGTTTTTTCTGAGTTTTTGTTGATGT 25 18 1 ATTTTAGTTT 0.717475 -68 CTAAGAGAGATTTTTATTGATTTTGAAAAGATTA 25 62 0 ATTTTATTTT 0.873427 -24 AAGGATTTGCTTTTATTTTTACTTTTTATTTTTCTAA 26 65 0 TTTTTTTTTT 0.899518 -83 AGCAAATCCTTAATCTTTGGTGATATTGATGGAGAGG 26 91 1 TTTTTATATT 0.818566 -57 AATCATTGTGTAATCTTTCCAAATTATTACTTGAATT 27 60 1 TTTTTATTAT 0.72699 -82 AATTATGTTATGTTTTGTTTTGATTTTGAGTAATTTA 27 99 0 TTTGTATTTT 0.878858 -43 CCTCATTTCCAACTCTTTCAAAATTTTTAATAAATTT 28 24 0 ATTTTATTTT 0.873426 -34 TTGAGTTAATTAATTTGTTAAAAGTTTAAAAGCTTAT 29 60 0 TTTGTAGTTT 0.727509 -51 TTCTTTAATTTTTTACTTTTTTAAATTTTAAA 30 6 1 TTTTTTTTTT 0.899518 -44 TAAGTTGCCTTACTATTTAAATAGTTTATTACTAAAA 31 66 1 TTTTTAGTTT 0.878858 -231 TGAGTTATTTTGTTTTTTTCATATTTTTTATTACTTA 31 143 0 TTTTTATTTT 0.951722 -154 ATGTGTTAAGTTTTTTTGAATTATATTCAGGGGTGAT 31 258 1 TTTTGATATT 0.492866 -39 TAGCTCCTAATTTTATTTTTATTTTATTTATCTGTGT 32 19 1 TTTTTTTTAT 0.547356 -265 TATTTTATTTATCTGTGTTTAAATATTGTAGTGGTGA 32 38 1 ATTGTATATT 0.367569 -246 TGATTTCTGTAGTTTTTTGACTATTTTGATACTCCGA 32 72 1 ATTTTATTTT 0.873427 -212 AAAACACTTATGGTATTTTCACATTTTTATAATTTTA 32 125 0 TTTTTATTTT 0.951722 -159 ATGGACATTGTAATATTTTCAGATATTTTTCAATCCA 33 54 1 TTTTTATATT 0.818566 -247 TCAATTTTAATTTTATGTAACATTTTTTTATATTAGC 33 173 1 TTTGTTTTTT 0.767143 -128 CTATTTAAACTTTTTTGTTTAAAGTTTATTAAAAATG 33 216 0 TTTGTAGTTT 0.727511 -85 TATTTATATGACTTTTTTATTATTTTTAAGGTTCCAC 34 30 0 ATTTTTTTTT 0.758082 -87 TAAAATTAATTCATATTTGTATATTTTCAAATTTACA 34 78 0 TTTTTATTTT 0.951722 -39 * * *** ***** Masking position 6 Map Score: 58.3543 Number of sites scoring better than the average of aligned sites = 1708 Number in coding regions = 1254 Number in noncoding regions = 454 Number of orfs with sites within 600 bp upstream = 345 Fraction of orfs with sites within 600 bp upstream = 0.0554128 Motif number 6 TATTATTCACCTTCTCTCTCAAT 2 29 0 TTATCACCTT 0.831807 -13 TTTTATCCCCTTGTTTCTGCAT 3 22 0 TTTTCCCCTT 0.777511 -12 ATTTAGTCACCTTAAATTATTAT 5 73 0 TTATCACCTT 0.831807 -13 GGGGGTTCAAATCCCCCCCTCCGCGCCACTT 6 212 1 ATCCCCCCTC 0.741983 -89 CTAATCACCTTCAATAATTTT 7 47 0 CTATCACCTT 0.856574 -11 AATCACCCCTCCATTTGTTAT 10 1 1 AATACCCCTC 0.505784 -155 AATCTCACCTTAAATAAATTT 11 145 0 AATTCACCTT 0.902063 -11 AAATATTCACCTCATGTTTGGAG 12 85 0 ATATCACCTC 0.956081 -13 GTCGGGGGTTCAAATCCCCTCGGGTCCGCCA 13 13 0 CAATCCCCTC 0.628837 -288 AAGATATTCACCTCTGAATCAGTT 13 287 0 ATATCACCTC 0.956081 -14 GGATTTCCACCTTTATATCTTAT 15 13 0 ATTCCACCTT 0.929698 -13 AAACTCACCTCAAAATTTAAA 18 28 0 AAATCACCTC 0.89972 -11 AATTATCACCTATAACAAAAGC 19 46 0 ATTTCACCTA 0.721332 -12 AATTTCTCACCTTCCTGATAAAA 20 20 0 TTTTCACCTT 0.87065 -13 AATTTACACCTCCAAATGTTCT 21 115 0 ATTACACCTC 0.82707 -12 AATCTTCACCTTTCATAATTAT 27 130 0 ATCTCACCTT 0.875936 -12 ATTACCACCTCATTTCCAACT 28 47 0 ATTCCACCTC 0.94604 -11 AAAACCCACCTTTAAATTTTAA 30 38 0 AAACCACCTT 0.800187 -12 AATTATCCCCTTTATAAATTTC 32 272 0 ATTTCCCCTT 0.920652 -12 CATTTCACCTCAAAAATTTGT 34 1 1 CATTCACCTC 0.816221 -116 AAATTACCACCTTAAAATTAATT 34 104 0 ATTCCACCTT 0.929698 -13 *** ******* Masking position 10 Map Score: 19.4277 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 116 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 7 ATTAATTTAAGGAACATTGAACGCCTTTAAGGCGT 1 148 1 GATTGAACCC 0.994041 -153 AATAACTAAGGTATTAATGAACGCCTTAAAGGCGT 1 168 0 GAATGAACCC 0.986407 -133 GCGCGGAGGGGGGGATTTGAACCCCCGCGGGGCAA 6 203 0 GGTTGAACCC 0.990862 -98 AAGTTATTAAGGAAATTTGAACTCCTTC 9 4 0 GATTGAACCC 0.994029 -297 GCGGACCCGAGGGGATTTGAACCCCCGACCCCCGG 13 15 1 GGTTGAACCC 0.990862 -286 ATTTATGAAGGAATGTTTGAACGCCCTCCTTTGGA 14 196 1 GATTGAACCC 0.994041 -105 AATAACTAAGGCACTAATGAACGCCTTCCAAAGGA 14 222 0 GAATGAACCC 0.986407 -79 * * ****** ** Masking position 10 Map Score: 11.9408 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 8 GTTTAATATCTAAATAGCTTTTTTATAGTGTC 1 218 0 TAAATAGTTT 0.938051 -83 ATTAAATAAATTTTTAAATAATTG 4 3 1 TAAATAATTT 0.880693 -57 TGTTTTATAGTAAATAGATATTAAAAAATAAA 6 246 0 TAAATAGTTT 0.938055 -55 ATATAAGTATTAAATAGGGGGTATATATATCT 9 162 0 TAAATAGGGT 0.721658 -139 AGTTAGCTCTTAAATAGTTAATTCTTTAGAGA 10 97 1 TAAATAGTAT 0.899925 -59 ATATGTTGTATAAATATCTTATCTATGTTGAA 11 36 0 TAAATATTAT 0.721045 -120 TTTTAGGGATTAAATATAGATTCAAATATGTT 11 61 0 TAAATATGTT 0.82533 -95 AATCTCACCTTAAATAAATTTTAAAAAATAAA 11 134 0 TAAATAATTT 0.880693 -22 AAATTCATTTTAAAGAGTGCTTACAACCTGAG 13 98 0 TAAAGAGGTT 0.831724 -203 TGGTTAATTATAAATATAGGTTTGTGGCAAAA 13 176 1 TAAATATGTT 0.82533 -125 TAAAAAACAATAAATAATTAATGTAATTATTA 13 209 0 TAAATAATAT 0.814266 -92 ATTTAAAGTATAAATATGGGTTTTAGTAAATA 16 108 1 TAAATATGTT 0.82533 -91 GAATTTTTAGTAAAGAGTGTTTTGGT 17 5 0 TAAAGAGGTT 0.831724 -38 CCGAAAAATATAAATAACTAATTATAAATAGT 21 11 1 TAAATAATAT 0.814266 -116 TAACTAATTATAAATAGTGAATTGCAAACTCT 21 25 1 TAAATAGGAT 0.907076 -102 AATATTCAAATAAAGAAATATTTTTATAGGAC 24 14 1 TAAAGAATTT 0.689423 -161 AAAAACATAATAAATAAAGTTTCTT 25 4 0 TAAATAAGTT 0.889061 -82 CCTTACTATTTAAATAGTTTATTACTAAAAAA 31 73 1 TAAATAGTAT 0.899925 -224 GTCTTTAATTTAAATAAGTAATAAAAAATATG 31 129 1 TAAATAATAT 0.814266 -168 AAAAGTCATATAAATAGTTTTTTATTTTGTAA 34 51 1 TAAATAGTTT 0.938055 -66 ******* * ** Masking position 1 Map Score: 22.7087 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 124 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 9 AGGTTTGCAAAATATAGTGTCTTCCAAAATCA 1 111 1 AATATGTTCT 0.9503 -190 AAATAGCTTTTTTATAGTGTCTTTCAAAACTT 1 207 0 TTTATGTTCT 0.936642 -94 TTTGTTTGTGTTTATTTTATCTAATTTTATTC 5 37 0 TTTATTTTCT 0.57946 -49 AATAATATATAATATGGTATCCATTAATCATA 6 60 1 AATATGTTCC 0.736091 -241 ACTAAAATATTATATAGTATCATTATCACAAT 9 82 1 TATATGTTCA 0.894989 -219 ATGTTGTATAAATATCTTATCTATGTTGAACT 11 34 0 AATATTTTCT 0.640567 -122 ACATTAATTATTTATTGTTTTTTATAATCTCA 13 217 1 TTTATGTTTT 0.57946 -84 CCCAGAATGCTATATTGTTTCATAAATATAAT 14 88 0 TATATGTTCA 0.894989 -213 ATGATTTAACTATATAGTGTCTTTCAAACTTC 14 260 0 TATATGTTCT 0.971649 -41 TTATATACTCTTTATCGTATCTTCCAGTCTGT 16 73 1 TTTATGTTCT 0.936642 -126 TAAATAGTAGAATAAAGTCTCAAAATCCGTAG 23 56 0 AATAAGTTCA 0.523779 -245 GAAAATTTTATATATGGTTTCTGATATCTTAG 23 108 1 TATATGTTCT 0.971649 -193 GCATCCATATTATATGGTATCTGATATAAATA 23 217 0 TATATGTTCT 0.971649 -84 AAACATAATAAATAAAGTTTCTT 25 2 0 AATAAGTTCT 0.81559 -84 AGCAAGGTCTTTTAATGTTTCTCT 26 3 0 TTTAAGTTCT 0.773729 -145 TGGAATTTTTAATATAGTATTTGAAAAATATA 33 112 0 AATATGTTTT 0.640567 -189 ATTAAAATAATATTTAGTATCTCAATTTTGTC 33 143 1 TATTTGTTCT 0.733522 -158 ***** ** *** Masking position 8 Map Score: 14.2759 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 138 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 10 TAAACCAAACAAAACACTCAAATAAAAGAT 1 245 1 AAAACACTCA 0.95984 -56 TTAAATAATTGAAACACTTAAAAATTTATC 4 24 1 GAAACACTTA 0.959839 -36 AAACACAAACAAAACACATAATAATTTAAG 5 56 1 AAAACACATA 0.825274 -30 ATTATTAAATGAAACACTTAGCATAACATT 7 11 1 GAAACACTTA 0.959839 -47 AAAAAGCACTTACAGTTGTTAA 11 3 1 AAAGCACTTA 0.874981 -153 TTTTCTTATTGAAACACTCCAAACATGAGG 12 69 1 GAAACACTCC 0.799031 -29 ACCAAAACACTCTTTACTAAAAA 17 4 1 AAAACACTCT 0.790253 -39 ATATAATTCAAAAAAACTTAACACATTTAT 31 254 0 AAAAAACTTA 0.745721 -43 TTAACTTTGAAAAACACTTATGGTATTTTC 32 142 0 AAAACACTTA 0.971071 -142 ATATATTTGAAAAACACTTATATTTTACAG 32 234 1 AAAACACTTA 0.971071 -50 ********** Masking position 6 Map Score: 7.78589 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 28 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 11 TTTGAGGTATAAATTAATAACGGATTAGTG 1 45 0 AAATTAATAA 0.821123 -256 AAAATCAATAAAATTAATTTAAGGAACATT 1 136 1 AAATTAATTT 0.451604 -165 ATAAAATAAAAATGCAGAAACAA 3 4 1 AAATAAAAAT 0.736623 -30 ATTAAATAAATTTTTAAATAATT 4 4 1 AAATAAATTT 0.520593 -56 CTTCAACATCAAATTAATAACTATCCTTTA 6 12 1 AAATTAATAA 0.821123 -289 AATATAATAAAAATAAAAAAGATAAAAAAG 9 260 1 AAATAAAAAA 0.668348 -41 ATCTCACCTTAAATAAATTTTAAAAAATAA 11 135 0 AAATAAATTT 0.520593 -21 TGTGTAGATAAAATTAATATATTTGGTATA 12 35 0 AAATTAATAT 0.841565 -63 TTCAATAAGAAAATTAATGTGTAGATAAAA 12 52 0 AAATTAATGT 0.720706 -46 GTTTGTGGCAAAATTAATAATTACATTAAT 13 195 1 AAATTAATAA 0.821123 -106 GTGCCTTTCAAAATTAATAAAATTTATGAA 14 175 1 AAATTAATAA 0.821123 -126 ACACGTTCTAAATTAAATTTAAATTTTGA 18 10 1 AAATTAAATT 0.598532 -29 ACTCTACTTCAAATTAATATTGTTTAGATA 21 52 1 AAATTAATAT 0.841565 -75 CGGTTAAAACAAATAAATAAAACACAAAGG 21 85 1 AAATAAATAA 0.736623 -42 TAAAAGTAAAAAATAAATATGAGAAAAAAA 24 48 1 AAATAAATAT 0.793919 -127 AACTTTTAACAAATTAATTAACTCAACAAC 29 71 1 AAATTAATTA 0.598532 -40 AAAAAGTAAAAAATTAAAGAA 30 2 0 AAATTAAAGA 0.596733 -48 TTACTTATTTAAATTAAAGACATTTTTAAT 31 120 0 AAATTAAAGA 0.596733 -177 AATAGTAACAAAATTAAAGTTTATTTTATT 31 182 1 AAATTAAAGT 0.672305 -115 AAATACCGTTAAATTTATATAAGATAAAGA 31 219 1 AAATTTATAT 0.25986 -78 CAGATAAATAAAATAAAAATAAAATTAGGA 32 23 0 AAATAAAAAT 0.736623 -261 ACTTAAACAAAAATAAAAATAAGTT 33 6 0 AAATAAAAAT 0.736623 -295 ATGTTACATAAAATTAAAATTGACAAAATT 33 166 0 AAATTAAAAT 0.821123 -135 CAAATTTACAAAATAAAAAACTATTTATAT 34 58 0 AAATAAAAAA 0.668348 -59 ********** Masking position 4 Map Score: 26.2548 Number of sites scoring better than the average of aligned sites = 625 Number in coding regions = 394 Number in noncoding regions = 231 Number of orfs with sites within 600 bp upstream = 214 Fraction of orfs with sites within 600 bp upstream = 0.034372 Motif number 12 CAATAAAATTAATTTAAGGAACATTGAACGC 1 141 1 AATTTAGGAA 0.939475 -160 ATTCAACAAAAAATTATTGAAGGTGATTAG 7 38 1 AAATTTTGAA 0.607862 -20 TTAAAAGGGAAATTTAAGGAAT 8 2 0 AATTTAGGAA 0.939475 -81 AAAATTAATAAAATTTATGAAGGAATGTTTG 14 184 1 AAATTATGAA 0.808953 -117 TTTAATAGCAAATTTCAGGAAATTTTGAAAA 23 151 0 AATTTAGGAA 0.939475 -150 AAAAAGTAAAAAATTAAAGAA 30 1 0 AAATTAAGAA 0.705993 -49 AAGTTAATAAAAATTAAGGAATAAATATAAA 32 165 1 AAATTAGGAA 0.939475 -119 TCACCTCAAAAATTTGTGGAACCTTAAAAAT 34 15 1 AATTTTGGAA 0.850353 -102 ***** ***** Masking position 2 Map Score: 3.11441 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 63 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 13 AGACACTATAAAAAAGCTATTTAGATATTAAA 1 217 1 AAAACTATTT 0.775191 -84 TCAATTATTTAAAAATTTATTTAAT 4 4 0 AAAATTATTT 0.701478 -56 TTTTATTTTTTAATATCTATTTACTATAAAAC 6 245 1 TAAACTATTT 0.474922 -56 CTCTCTAAAGAATTAACTATTTAAGAGCTAAC 10 98 0 AATACTATTT 0.836031 -58 ACGTTTCACTAAACCTCTATTTTATTTTTTAA 11 114 1 AAACCTATTT 0.874195 -42 ATTTTGCCACAAACCTATATTTATAATTAACC 13 177 0 AAACATATTT 0.760277 -124 ATATTTACTAAAACCCATATTTATACTTTAAA 16 109 0 AAACATATTT 0.761826 -90 CACTATTTATAATTAGTTATTTATATTTTTCG 21 12 0 AATATTATTT 0.587443 -115 TAGAGTTTGCAATTCACTATTTATAATTAGTT 21 26 0 AATCCTATTT 0.826231 -101 ATATTCAAATAAAGAAATATTTTTATAGGACA 24 15 1 AAAAATATTT 0.792096 -160 TAAATATGAGAAAAAAATATTTGTAAGGATGC 24 61 1 AAAAATATTT 0.792096 -114 CTTTTTTAGTAATAAACTATTTAAATAGTAAG 31 74 0 AATACTATTT 0.886793 -223 TGTTACTATTAATGAGTTATTTTGTTTTTTTC 31 160 0 AATATTATTT 0.687786 -137 ATTTTTCAAAAATTATATATTTGAAAAACACT 32 220 1 AATAATATTT 0.714682 -64 TTTACAAAATAAAAAACTATTTATATGACTTT 34 52 0 AAAACTATTT 0.867208 -65 *** * ****** Masking position 9 Map Score: 14.1569 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 162 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 14 AATCTTATGATTAACTCAACATTTCATAAA 9 118 0 TTAACTCAAC 0.969952 -183 CTGTTAAGTTTTAACTTAACACCATTTTAG 9 226 1 TTAACTTAAC 0.890408 -75 TATATCACGTTTCACTAAACCTCTATTTTA 11 108 1 TTCACTAAAC 0.897653 -48 AATTCTCATTTTCACTCAACCGAAAATTTT 23 87 1 TTCACTCAAC 0.972103 -214 AACAAATTAATTAACTCAACAACTAAAAAT 29 78 1 TTAACTCAAC 0.969952 -33 ********** Masking position 6 Map Score: 1.28538 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 14 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 15 ATAGTATCATTATCACAATTATATTTATGAA 9 95 1 TACACAATTA 0.936243 -206 GAGCTAACTATAACCTTATTATTTTATATTA 10 75 0 TACCTTATTA 0.626436 -81 TATTTTTTAGTAGCCCAATTATTCTCTCTAA 10 122 0 TACCCAATTA 0.959046 -34 TAAATGTTGATAGCCTAATTATATTTATGAA 14 71 1 TACCTAATTA 0.922595 -230 GTCTCTCTTTTAACCTAATTTTTGTCATTAA 24 120 1 TACCTAATTT 0.626466 -55 AAACAAAACATAACATAATTATGAAAGGTGA 27 116 1 TACATAATTA 0.881984 -26 TTTATCTTAATAACCCAATAAGCTTTTAAAC 29 43 1 TACCCAATAA 0.767175 -68 TCATTAATAGTAACAAAATTAAAGTTTATTT 31 177 1 TACAAAATTA 0.694326 -120 CAAAAAAACTTAACACATTTATAGTACTCTT 31 245 0 TACACATTTA 0.673867 -52 GATATGATGATAACACAATTAAATAATACCA 33 267 1 TACACAATTA 0.936241 -34 ** ******** Masking position 9 Map Score: 2.81153 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 22 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432