AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i033_Pyruvate_Synthase_1_mjan_reg_300.orf -o033_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: RMJ12055 24 M_jannaschii_chromosome Input sequences: #1 RMJ04092 288 M_jannaschii_chromosome #2 RMJ00836 18 M_jannaschii_chromosome #3 RMJ05016 29 M_jannaschii_chromosome #4 RMJ11171 119 M_jannaschii_chromosome #5 RMJ13440 183 M_jannaschii_chromosome #6 RMJ13199 103 M_jannaschii_chromosome #7 RMJ01908 43 M_jannaschii_chromosome #8 RMJ08206 98 M_jannaschii_chromosome #9 RMJ10471 175 M_jannaschii_chromosome #10 RMJ03238 201 M_jannaschii_chromosome #11 RMJ02105 108 M_jannaschii_chromosome #12 RMJ11183 138 M_jannaschii_chromosome #13 RMJ11456 35 M_jannaschii_chromosome #14 RMJ00462 107 M_jannaschii_chromosome #15 RMJ11437 192 M_jannaschii_chromosome #16 RMJ10373 276 M_jannaschii_chromosome #17 RMJ02093 255 M_jannaschii_chromosome #18 RMJ11918 20 M_jannaschii_chromosome #19 RMJ12466 89 M_jannaschii_chromosome #20 RMJ01547 160 M_jannaschii_chromosome #21 RMJ02758 132 M_jannaschii_chromosome #22 RMJ14018 103 M_jannaschii_chromosome #23 RMJ02345 177 M_jannaschii_chromosome #24 RMJ12182 111 M_jannaschii_chromosome Motif number 1 AATTTAGAAGCCCAAAGGGCTTCTATATGT 1 67 1 CCCAAAGGGC 0.973625 -222 TTATTCAGAAACCATAGGGCTTCGCCCTAT 8 25 1 ACCATAGGGC 0.981325 -74 CCTGGGTATCCCAATAGGGCGAAGCCCTAT 8 38 0 CCAATAGGGC 0.991576 -61 CTACATTGTATCCATAGGGGAAACCCCCTA 9 20 1 TCCATAGGGG 0.957388 -156 AAGGTTCATCCCAATAGGGGGTTTCCCCTA 9 34 0 CCAATAGGGG 0.991075 -142 GGGGAGTATCCCAATAGAGGGGCGAAGCCC 9 132 1 CCAATAGAGG 0.962309 -44 CTGTATAAGACCCATAGAGGGGCTTCGCCC 9 151 0 CCCATAGAGG 0.969017 -25 AAACTTGGAAACCATAGAGGGAAACCCTCT 12 28 1 ACCATAGAGG 0.919318 -111 AGGGTGTATCCCAATAGAGGGTTTCCCTCT 12 43 0 CCAATAGAGG 0.962309 -96 TCTGGGTATCCCAATAGGGCGAAGCCCTAT 14 57 1 CCAATAGGGC 0.991576 -51 ATTATTATACACCATAGGGCTTCGCCCTAT 14 70 0 ACCATAGGGC 0.981325 -38 ATTAAAAGTTCCCATAGGTGATAAA 15 6 0 CCCATAGGTG 0.885458 -187 AATAGGTATCCCAATAGGGCGAAGCTATGG 16 69 0 CCAATAGGGC 0.991576 -208 TCGTTTGATTAAAATAGGGCTTAACTCTAT 16 208 1 AAAATAGGGC 0.688107 -69 TTATAGAAGCTCAAAAGGGCTTCTATACCA 17 48 0 TCAAAAGGGC 0.818695 -208 TATCCAAAATACAAAAGGGGATAGC 20 146 1 ACAAAAGGGG 0.912126 -15 ********** Masking position 6 Map Score: 39.5894 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 44 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 2 AATAATATCCTTTGATAATTGGTTATAAGTTGGG 1 25 0 TTGTAATTTT 0.663683 -264 TGTGCCTTATTTAATTAAAAACTTTGATAATTGG 1 94 1 TTATAAAATT 0.857839 -195 TTGTTCAACTTTTACTAAAAGTTTCTTTTAAAAC 1 192 1 TTATAAAATT 0.857839 -97 CTACATTTGTTATATAAATCTTTGACTGT 3 7 0 TTTTAAATTT 0.880764 -23 ATGCTTCTATTTTTTTAAATTGTTATTTTCTTCT 4 23 1 TTTTAAATTT 0.880764 -97 TGTTATTTTCTTCTCTATTATATTATAGTCGTTA 4 43 1 TTTTATTATT 0.85365 -77 TAATATAACCTTGTGTTAATATTTAACGACTATA 4 66 0 TTTTTAATTT 0.617366 -54 TTTCTTTCTTTAATTCTATTTTTTA 5 2 1 TTTTCTTTTT 0.530654 -182 AGTGTTGGTATTTAATATTTAATTACTAATCTTA 5 47 0 TTATATTTTT 0.693616 -137 CAACACTTTTTTATATCAAACTTTTTAAAGTTCT 5 74 1 TTTTCAAATT 0.75085 -110 GTATAAAAATTTTTATATATGATTTCAATTTTAT 5 126 1 TTTTATATTT 0.874371 -58 ATGATTTCAATTTTATCATTACTTTACCCTTAAC 5 144 1 TTTTCATTTT 0.545444 -40 TAAATAGTTTTTTGTTATTATTTTTTATGGACAA 6 34 0 TTGTATTATT 0.729552 -70 TGGTGAAGCTTTTACTAAAAGGTTCATCCCAATA 9 48 0 TTATAAAATT 0.857839 -128 ACCCAGATTTTTATTTTAATATTT 10 1 0 TTTTTAATTT 0.617366 -201 TCGTTCAACTTTTTCTAAAAGTTTCGTTTATAGT 10 62 0 TTTTAAAATT 0.914651 -140 GGTTTCCAAGTTTTTTCATTATTTCCCCCT 12 7 0 TTTTCATTTT 0.545444 -132 TAAATTAATTTTGATTAATTTGTTTGGAAAAATT 12 101 1 TTATAATTTT 0.706114 -38 GACGAAAAGTTTATATATTAGATTGATTAAAAGT 15 27 0 TTTTATTATT 0.85365 -166 TTGATCAACCTTTTCTAAAAGGTTGTTCGAGTAA 16 109 1 TTTTAAAATT 0.914651 -168 CGAGTAACCTTTTACTAAAAGGTTGGGAGCAATG 16 136 1 TTATAAAATT 0.857839 -141 TAAAACTAAGTTATTTATATCATTTTGGTAGTTA 17 135 1 TTTTATATTT 0.874371 -121 TACATAATAATTTGTTAAAATATTAACTACCAAA 17 158 0 TTGTAAAATT 0.832105 -98 TTTGGATTTTTTGATTTTTATATTTTAAATAATA 17 203 1 TTATTTTATT 0.417727 -53 TTCTATTTTATTGTCTATATTATTTAAAATATAA 17 220 0 TTTTATATTT 0.874371 -36 TTACCTTTAACTTTTAAGTTTTGTTTTTAT 19 7 1 TTATTTTATT 0.417727 -83 CTTTTTTTAATTTTTTATAACATTTTCACTTGTA 20 19 1 TTTTATAATT 0.909889 -142 CTCTACTATTTTATTTATAATATTATCATTCAAA 20 57 1 TTTTATAATT 0.909889 -104 ATATAGGGGATTATATATAGCTTTTATTTTAAAA 20 103 0 TTTTATAGTT 0.50379 -58 ACAGTAAGCTTTAAATATTAAGTTAAAAATATTA 21 18 1 TTATATTATT 0.766595 -115 ATTTTAAAATTTTGTTAAAAATTTACTAGCATCC 22 60 1 TTGTAAAATT 0.832105 -44 ATATATACTCTTCGGTTTAATATTAGGACACGCT 23 90 0 TTGTTTAATT 0.504955 -88 TATATTTAACTTAACTATAACTTTAGTGTTGTAA 23 119 1 TTATATAATT 0.850426 -59 ** * ***** ** Masking position 6 Map Score: 33.522 Number of sites scoring better than the average of aligned sites = 1692 Number in coding regions = 1218 Number in noncoding regions = 474 Number of orfs with sites within 600 bp upstream = 373 Fraction of orfs with sites within 600 bp upstream = 0.0599101 Motif number 3 GAAGCCCTTTGGGCTTCTAAATTCCATAGTA 1 59 0 GGGCTTCAAA 0.914882 -230 GAAGCCCAAAGGGCTTCTATATGTGCCTTAT 1 73 1 GGGCTTCATA 0.929786 -216 CGTTAGCTTCGGGCTACAAAAACTCGAAGAG 1 158 1 GGGCTACAAA 0.879299 -131 AGAAACCATAGGGCTTCGCCCTATTGGGATA 8 31 1 GGGCTTCCCC 0.842706 -68 TCGCCCTATTGGGATACCCAGGATGCATTGC 8 46 1 GGGATACCAG 0.880294 -53 GTATCCATAGGGGAAACCCCCTATTGGGATG 9 27 1 GGGAAACCCC 0.853688 -149 CCCCTCTATTGGGATACTCCCCAAATCTTAC 9 123 0 GGGATACCCC 0.891785 -53 ACCCATAGAGGGGCTTCGCCCCTCTATTGGG 9 141 0 GGGCTTCCCC 0.842706 -35 TCCCAATAGAGGGTTTCCCTCTATGGTTTCC 12 34 0 GGGTTTCCTC 0.924945 -105 ACCCTCTATTGGGATACACCCTAACACCTCC 12 51 1 GGGATACCCC 0.957957 -88 ACCCAGAGCGGGGCTTCACTACGTTCAGCCC 14 33 0 GGGCTTCCTA 0.982482 -75 TCGCCCTATTGGGATACCCAGAGCGGGGCTT 14 48 0 GGGATACCAG 0.880294 -60 ATACACCATAGGGCTTCGCCCTATTGGGATA 14 63 0 GGGCTTCCCC 0.842706 -45 GATTAAAATAGGGCTTAACTCTATCTCTATT 16 214 1 GGGCTTACTC 0.878966 -63 AAGCTCAAAAGGGCTTCTATACCAATAACCT 17 41 0 GGGCTTCATA 0.929786 -215 ******* *** Masking position 3 Map Score: 24.8407 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 22 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 4 AATGGACGAGTTTTGATGAAACCGAAGCGT 1 131 1 TTTTGATGAA 0.984265 -158 CTCGAAGAGTTTTTGTTCAACTTTTACTAA 1 180 1 TTTTGTTCAA 0.786793 -109 CCTTAACATTTTTTGGTGATTGG 5 171 1 TTTTGGTGAT 0.946673 -13 TTCCAAATACTTTTTGTGAAGGGTATATAA 6 65 0 TTTTTGTGAA 0.814524 -39 CTATTATGACTTTTTATGAAATAGTATTTC 7 11 0 TTTTTATGAA 0.87901 -33 AGGTGTTAGGTTTTGGTGAAGCTTTTACTA 9 65 0 TTTTGGTGAA 0.974234 -111 AGGTGTTAGTTTTTGATGAAATGGAGAGCT 10 128 0 TTTTGATGAA 0.984265 -74 TGTAAATTAATTTTGATTAATTTGTTTGGA 12 99 1 TTTTGATTAA 0.831334 -40 CTATGGGAACTTTTAATCAATCTAATATAT 15 19 1 TTTTAATCAA 0.787253 -174 AATGCATCTGTTTTGATCAACGCACCATAG 16 45 1 TTTTGATCAA 0.969568 -232 TTTAACTAAGTTTTGATCAACCTTTTCTAA 16 97 1 TTTTGATCAA 0.969568 -180 TTAAGCCCTATTTTAATCAAACGAACTCAT 16 202 0 TTTTAATCAA 0.787253 -75 TGTTATCTATTTTTGATGATTGA 17 4 0 TTTTGATGAT 0.967072 -252 CTATAAAAACTTTTGATGATTGACTATAAT 17 91 1 TTTTGATGAT 0.967072 -165 TCTTCACTATTTTTGGTGATACA 19 77 1 TTTTGGTGAT 0.946673 -13 GATGTAATGTTTTTGAAGATAAGCGTGTCC 23 69 1 TTTTGAAGAT 0.71534 -109 ********** Masking position 4 Map Score: 24.6806 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 181 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 5 TATTATCCCTCCAAGTAGTTTTTGAT 1 273 0 TATCCTCCGT 0.953167 -16 CACCAAAACCTAACACCTCCTCGCTTACGCTCGG 9 77 1 TACCCTCCGC 0.998747 -99 TCTTACTAATTTACACCTCCGAGCGTAAGCGAGG 9 95 0 TACCCTCCGC 0.998747 -81 CATCAAAAACTAACACCTCCTCGCTTCGCTCGGA 10 140 1 TACCCTCCGC 0.998747 -62 AGTTGTAAATTTACACTTCCGAGCGAAGCGAGGA 10 157 0 TACCTTCCGC 0.988887 -45 GGATACACCCTAACACCTCCTCGCTTACGCTCGG 12 62 1 TACCCTCCGC 0.998747 -77 CAAAATTAATTTACACCTCCGAGCGTAAGCGAGG 12 80 0 TACCCTCCGC 0.998747 -59 CTACGCTCGGTAATGCCTCTTAGCATAG 16 5 0 TATCCTCTGC 0.953167 -272 * ** ***** ** Masking position 3 Map Score: 21.5784 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 0 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 6 ATTTGGAAAGGTTAGGAGTTGATTAAC 6 87 1 GTTAGGAGTG 0.978357 -17 CCGAGCGTAAGCGAGGAGGTGTTAGGTTTTG 9 80 0 GCGAGGAGTG 0.997127 -96 CCTCGCTTACGCTCGGAGGTGTAAATTAGTA 9 95 1 GCTCGGAGTG 0.994175 -81 AAAAATCTGGGTGAGGATATGGATACTTCAC 10 23 1 GTGAGGATTG 0.905671 -179 TCCGAGCGAAGCGAGGAGGTGTTAGTTTTTG 10 143 0 GCGAGGAGTG 0.997127 -59 TCCTCGCTTCGCTCGGAAGTGTAAATTTACA 10 157 1 GCTCGGAATG 0.979656 -45 CCGAGCGTAAGCGAGGAGGTGTTAGGGTGTA 12 65 0 GCGAGGAGTG 0.997127 -74 CCTCGCTTACGCTCGGAGGTGTAAATTAATT 12 80 1 GCTCGGAGTG 0.994175 -59 ACCTCGCTACGCTCGGTAATGCCTCTTAGCA 16 14 0 GCTCGGTATG 0.92277 -263 ACCGAGCGTAGCGAGGTAATGCATCTGTTTT 16 28 1 GCGAGGTATG 0.960475 -249 TGCGGTAGTTATGAGGAGATGAGTTCGTTTG 16 184 1 ATGAGGAGTG 0.871375 -93 ******** ** Masking position 10 Map Score: 21.8832 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 9 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 TATTTAATTAAAAACTTTGATAATTGGTTAAATG 1 101 1 AAATTTGAAT 0.820262 -188 CCCATGCTTCTATTTTTTTAAATTGTTATTTTCT 4 20 1 TATTTTTAAT 0.613214 -100 CCTTCTAAGCTACTTTTATATAATATAACCTTGT 4 86 0 TACTTATAAT 0.745422 -34 TTTTAGTCTTTAAGATTAGTAATTAAATATTAAA 5 37 1 TAATTAGTAT 0.788112 -147 TTTTTATATCAAACTTTTTAAAGTTCTTCAAATG 5 81 1 AAATTTTAAT 0.897855 -103 ATCATATATAAAAATTTTTATACTAAGGATTTAG 5 115 0 AAATTTTAAT 0.897855 -69 TTATCTCACCTAATTTTATTAAATAATGGACATT 11 84 0 TAATTATTAT 0.877512 -25 AATAAGACGAAAAGTTTATATATTAGATTGATTA 15 32 0 AAATTATAAT 0.912988 -161 TTTTGTGGGTAACTTTTATATATTTCCCAGAGGA 15 66 1 AACTTATAAT 0.671914 -127 TCTATACCAATAACCTTAGAAAATGTTATCTATT 17 23 0 TAATTAGAAT 0.886235 -233 TCAATCATCAAAAGTTTTTATAGTTATATAATAA 17 80 0 AAATTTTAAT 0.897855 -176 ATGACTATTTTATCATTATATATTTTAACAATTC 19 39 1 TATTTATAAT 0.654327 -51 TTATGAAACTTTTTTTAATTTTTTATAAC 20 6 1 AAATTTTTAT 0.807579 -155 TATTTTAAAATAAATTTAAATATTTGAATGATAA 20 79 0 TAATTAAAAT 0.546502 -82 ATTGTGATGCTAATATTTTTAACTTAATATTTAA 21 28 0 TAATTTTTAT 0.857146 -105 GCATCACAATAAATTTTATATATTGGGAATTGAA 21 52 1 AAATTATAAT 0.912988 -81 CTTATTACCATAAAATTTTAAAATTTTGTTAAAA 22 46 1 TAATTTTAAT 0.92629 -58 TGTTGTTAGATAACCTTATTCAATTAATTAATGA 23 37 1 TAATTATTAT 0.877512 -141 TAGGTAATATAAAGATTTTAGAATGGTGACATTA 23 154 1 AAATTTTAAT 0.897855 -24 TATTAAATAGTAATATTTGTTAGTTTGAAAATAA 24 23 0 TAATTTGTAT 0.756997 -89 TTATTATCGTTAATCTTATATATTAGTTATTAAA 24 50 0 TAATTATAAT 0.937517 -62 CTTAGACTAATAATATTAGTTAGTATTATTATTA 24 78 0 TAATTAGTAT 0.788112 -34 *** ***** * * Masking position 7 Map Score: 22.3084 Number of sites scoring better than the average of aligned sites = 834 Number in coding regions = 560 Number in noncoding regions = 274 Number of orfs with sites within 600 bp upstream = 249 Fraction of orfs with sites within 600 bp upstream = 0.0399936 Motif number 8 GGCTACAAAAACTCGAAGAGTTTTTGTTCAA 1 169 1 ATCGAAGAGT 0.855545 -120 TCACCAAAAAATGTTAAGGGTAAAGTAATGA 5 159 0 AGTTAAGGGT 0.569623 -25 GTATTTGGAAAGGTTAGGAGTTGATTAAC 6 85 1 AGTTAGGAGT 0.889957 -19 TAAATTTTAAGAGGCATTGCTTCT 8 85 0 ATTTAAGAGG 0.874315 -14 CTCCGAGCGTAAGCGAGGAGGTGTTAGGTTT 9 82 0 AGCGAGGAGG 0.990746 -94 CTCCTCGCTTACGCTCGGAGGTGTAAATTAG 9 93 1 AGCTCGGAGG 0.962361 -83 AGCTATGAAAACTCTAAGAGTTTTCGTTCAA 10 88 0 ATCTAAGAGT 0.752225 -114 CTTCCGAGCGAAGCGAGGAGGTGTTAGTTTT 10 145 0 AGCGAGGAGG 0.990746 -57 CTCCGAGCGTAAGCGAGGAGGTGTTAGGGTG 12 67 0 AGCGAGGAGG 0.990746 -72 CTCCTCGCTTACGCTCGGAGGTGTAAATTAA 12 78 1 AGCTCGGAGG 0.962361 -61 GTTTGGAAAAATTTGAGGTGGGTAATA 12 122 1 ATTGAGGTGG 0.800457 -17 CTATGCTAAGAGGCATTACCGAG 16 3 1 AGCTAAGAGG 0.976524 -274 ATTAAAAATTATTTGAGGTGGTAAA 16 262 1 ATTGAGGTGG 0.800457 -15 TAATATTATTAGTCTAAGGGGTGAGAGA 24 94 1 ATCTAAGGGG 0.871922 -18 * ********* Masking position 1 Map Score: 15.7456 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 101 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 9 TTTATCTCACCTAATTTTATTAAATAA 11 92 0 TCCCTAATTT 0.757042 -17 CGGAATATGTTTTCCTAATTTATTTGGTAGA 15 147 1 TTCCTAATTT 0.809285 -46 CCCTATTGGGATACCTATTTAACTAAGTTTT 16 80 1 ATCCTATTTA 0.834031 -197 GATAGAGTTAAGCCCTATTTTAATCAAACGA 16 208 0 AGCCTATTTT 0.781704 -69 TTAGAAAATGTTATCTATTTTTGATGATTGA 17 11 0 TTTCTATTTT 0.816609 -245 AATTTTTGTTTCTTCTATTTTATTGTCTATA 17 235 0 TCTCTATTTT 0.765792 -21 AATATCACTATTTTTATTTT 18 7 0 ATACTATTTT 0.886004 -14 TTTTGTTTTTATGACTATTTTATCATTATAT 19 29 1 ATACTATTTT 0.886004 -61 ATTCCAAATCTTCACTATTTTTGGTGATACA 19 69 1 TTACTATTTT 0.910998 -21 TTGTAATAACTCTACTATTTTATTTATAATA 20 48 1 TCACTATTTT 0.882575 -113 ATCATCACCTATTTTGGCTGTTTCG 21 118 0 TCCCTATTTT 0.943197 -15 AAAAACACCAATTCCTATTTTTCTACTTTTT 22 15 1 ATCCTATTTT 0.944967 -89 AATCTTTATATTACCTATTTACAACACTAAA 23 140 0 TTCCTATTTA 0.868732 -38 ACTAACAAATATTACTATTTAATAACTAATA 24 33 1 ATACTATTTA 0.694623 -79 ** ******** Masking position 7 Map Score: 12.1947 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 126 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 10 TCCGAGCGTAAGCGAGGAGGTGTTAGGTTT 9 82 0 AGCGAGGAGG 0.991885 -94 TCCTCGCTTACGCTCGGAGGTGTAAATTAG 9 94 1 CGCTCGGAGG 0.994823 -82 TTCCGAGCGAAGCGAGGAGGTGTTAGTTTT 10 145 0 AGCGAGGAGG 0.991885 -57 CTCCTCGCTTCGCTCGGAAGTGTAAATTTA 10 156 1 CGCTCGGAAG 0.967461 -46 TCCGAGCGTAAGCGAGGAGGTGTTAGGGTG 12 67 0 AGCGAGGAGG 0.991885 -72 TCCTCGCTTACGCTCGGAGGTGTAAATTAA 12 79 1 CGCTCGGAGG 0.994823 -60 ********** Masking position 8 Map Score: 11.3115 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 1 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 11 TTAACCAATTATCAAAGTTTTTAATTAAATA 1 101 0 ACAAAGTTTT 0.806421 -188 GTGGTTTTAAAAGAAACTTTTAGTAAAAGTT 1 198 0 AGAAACTTTT 0.954103 -91 ACTTTTTTATATCAAACTTTTTAAAGTTCTT 5 78 1 ACAAACTTTT 0.972731 -106 CCCTATTGGGATGAACCTTTTAGTAAAAGCT 9 45 1 AGAACCTTTT 0.960129 -131 GGGACTATAAACGAAACTTTTAGAAAAAGTT 10 59 1 AGAAACTTTT 0.954104 -143 ATAAATATTCACCATACTTTTTC 13 3 0 ACATACTTTT 0.805137 -33 CTAAGTTTTGATCAACCTTTTCTAAAAGGTT 16 102 1 ACAACCTTTT 0.976372 -175 AGGTTACTCGAACAACCTTTTAGAAAAGGTT 16 115 0 ACAACCTTTT 0.976372 -162 AGGTTGTTCGAGTAACCTTTTACTAAAAGGT 16 128 1 ATAACCTTTT 0.821889 -149 AAACATTGCTCCCAACCTTTTAGTAAAAGGT 16 142 0 CCAACCTTTT 0.876449 -135 TTATGAAACTTTTTTTAATTTTT 20 3 1 AGAAACTTTT 0.954104 -158 GTAAATTTTTAACAAAATTTTAAAATTTTAT 22 55 0 ACAAAATTTT 0.737582 -49 * ********* Masking position 4 Map Score: 17.1259 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 70 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 12 ACAATTTAAAAAAATAGAAGCATGGGCTAA 4 16 0 AAAATAGAAG 0.915042 -104 AATAGAGAAGAAAATAACAATTTAAAAAAA 4 32 0 AAAATAACAA 0.788281 -88 TTAAAGACTAAAAATAAAAAATAGAATTAA 5 20 0 AAAATAAAAA 0.932746 -164 AAGTAATGATAAAATTGAAATCATATATAA 5 138 0 AAAATTGAAA 0.595253 -46 TTGTCCATAAAAAATAATAACAAAAAACTA 6 34 1 AAAATAATAA 0.706489 -70 AAATATTAAAATAAAAATCTGGGTGAG 10 8 1 AAAATAAAAA 0.932746 -194 ATCAGGGAAATAAAAGAAAGTGGGGC 14 7 1 GAAATAAAAG 0.617377 -101 TATCCATTATAAATTAAAAATTATTTGAGG 16 250 1 AAATTAAAAA 0.512099 -27 TATATTATTTAAAATATAAAAATCAAAAAA 17 209 0 AAAATATAAA 0.616331 -47 TATAGACAATAAAATAGAAGAAACAAAAAT 17 235 1 AAAATAGAAG 0.915042 -21 AAAATAAAAATAGTGATATT 18 1 1 AAAATAAAAA 0.932746 -20 AATGTTATAAAAAATTAAAAAAAGTTTCAT 20 13 0 AAAATTAAAA 0.662651 -148 TATTATAAATAAAATAGTAGAGTTATTACA 20 49 0 AAAATAGTAG 0.651478 -112 AATTTATTTTAAAATAAAAGCTATATATAA 20 97 1 AAAATAAAAG 0.935003 -64 TTAATTATCCAAAATACAAAAGGGGATAGC 20 141 1 AAAATACAAA 0.70422 -20 CAAAATAACAGTAAGCTTTAA 21 2 1 AAAATAACAG 0.794317 -131 AAAAAGTAGAAAAATAGGAATTGGTGTTTT 22 16 0 AAAATAGGAA 0.602344 -88 TGTTAGTTTGAAAATAAACGGGGGAGATT 24 10 0 AAAATAAACG 0.617377 -102 ********** Masking position 5 Map Score: 16.13 Number of sites scoring better than the average of aligned sites = 570 Number in coding regions = 340 Number in noncoding regions = 230 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 13 TGGGGCTGAAAGCCCCAACTTATAACCAATTAT 1 12 1 ACCCCATTAT 0.975091 -277 ATAAATTAGCCCATGCTTCTATTTTTTTAA 4 8 1 ACCCAGTTCT 0.859374 -112 TAAACCCCCTCCTTCTAAGCTACTTT 4 104 0 ACCCCCTTCT 0.97249 -16 AAAAACCCCCAAATATGACGCTTTTG 6 4 1 ACCCCAATAT 0.963949 -100 CTATTGGGATACTCCCCAAATCTTACTAATTTA 9 116 0 ATCCCAATCT 0.923262 -60 CACTACGTTCAGCCCCACTTTCTTTTATTTCCC 14 15 0 ACCCCCTTCT 0.97249 -93 AAAATCAAAAAATCCAAATTTCTTTAGGTTACA 17 188 0 ATCCAATTCT 0.752781 -68 GCTATATATAATCCCCTATATATTGTTAATTAT 20 116 1 ACCCCAATAT 0.963949 -45 TGTGTTTTCAATTCCCAATATATAAAATTTATT 21 59 0 ATCCCAATAT 0.882966 -74 AATCTCCCCCGTTTATTTTCAAACTA 24 4 1 CCCCCGTTAT 0.822159 -108 * **** * **** Masking position 11 Map Score: 4.88384 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 117 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 14 TAAGTTGGGGCTTTCAGCCCCAA 1 4 0 CTTTCAGCCC 0.994081 -285 TAAGTTAGGGCTTTCAGCCCTAATTAATGT 11 59 1 CTTTCAGCCC 0.994081 -50 GGCTTCACTACGTTCAGCCCCACTTTCTTT 14 23 0 CGTTCAGCCC 0.989951 -85 TCTCTCACCCCTTAGACTAAT 24 101 0 CTCTCACCCC 0.97351 -11 ********** Masking position 6 Map Score: 3.05899 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 14 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 15 TCTCTATTATATTATAGTCGTTAAATATTAACAC 4 54 1 ATTGTGTTAA 0.939791 -66 CTATTTTTTATTTTTAGTCTTTAAGATTAGTAAT 5 26 1 TTTGTTTTAA 0.869176 -158 CACCCAGATTTTATCAGTTGTAAATTTACACTTC 10 172 0 TTAGTGTAAA 0.639245 -30 TTTGGAAAAATTTGAGGTGGGTAATA 12 123 1 TTTGTGGTAA 0.912432 -16 TTTCGTCTTATTTTTTGTGGGTAACTTTTATATA 15 54 1 TTTGTGGTAA 0.912513 -139 TTAAAAATTATTTGAGGTGGTAAA 16 263 1 TTTGTGTAAA 0.939008 -14 TATTTATATCATTTTGGTAGTTAATATTTTAACA 17 146 1 ATTGTGTTAA 0.939797 -110 ATTTTTTGATTTTTATATTTTAAATAATATAGAC 17 208 1 TTTATTTAAA 0.510365 -48 ATAGTGAAGATTTGGAATTGTTAAAATATATAAT 19 53 0 TTTATGTTAA 0.906284 -37 TAATATTATCATTCAAATATTTAAATTTATTTTA 20 74 1 ATTATTTTAA 0.525814 -87 TAACTATAACTTTAGTGTTGTAAATAGGTAATAT 23 130 1 TTTGTGTAAA 0.937347 -48 AGTTAGTATTATTATTATCGTTAATCTTATATAT 24 61 0 ATTATGTTAA 0.834049 -51 *** ** ***** Masking position 13 Map Score: 4.48181 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 186 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775