AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i033_mjan_pyro_300.orf -o033_mjan_pyro_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.37 -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 = 0.37 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 #25 RPH00878 130 Pyrococcus_OT3 #26 RPH01532 194 Pyrococcus_OT3 Motif number 1 AATTTAGAAGCCCAAAGGGCTTCTATATGT 1 67 1 CCCAAAGGGC 0.984046 -222 TTATTCAGAAACCATAGGGCTTCGCCCTAT 8 25 1 ACCATAGGGC 0.988732 -74 CCTGGGTATCCCAATAGGGCGAAGCCCTAT 8 38 0 CCAATAGGGC 0.994934 -61 CTACATTGTATCCATAGGGGAAACCCCCTA 9 20 1 TCCATAGGGG 0.973281 -156 AAGGTTCATCCCAATAGGGGGTTTCCCCTA 9 34 0 CCAATAGGGG 0.994094 -142 GGGGAGTATCCCAATAGAGGGGCGAAGCCC 9 132 1 CCAATAGAGG 0.977101 -44 CTGTATAAGACCCATAGAGGGGCTTCGCCC 9 151 0 CCCATAGAGG 0.980325 -25 AAACTTGGAAACCATAGAGGGAAACCCTCT 12 28 1 ACCATAGAGG 0.950116 -111 AGGGTGTATCCCAATAGAGGGTTTCCCTCT 12 43 0 CCAATAGAGG 0.977101 -96 TCTGGGTATCCCAATAGGGCGAAGCCCTAT 14 57 1 CCAATAGGGC 0.994934 -51 ATTATTATACACCATAGGGCTTCGCCCTAT 14 70 0 ACCATAGGGC 0.988732 -38 ATTAAAAGTTCCCATAGGTGATAAA 15 6 0 CCCATAGGTG 0.926512 -187 AATAGGTATCCCAATAGGGCGAAGCTATGG 16 69 0 CCAATAGGGC 0.994934 -208 TCGTTTGATTAAAATAGGGCTTAACTCTAT 16 208 1 AAAATAGGGC 0.786757 -69 TTATAGAAGCTCAAAAGGGCTTCTATACCA 17 48 0 TCAAAAGGGC 0.88306 -208 TATCCAAAATACAAAAGGGGATAGC 20 146 1 ACAAAAGGGG 0.945529 -15 ********** Masking position 6 Map Score: 38.0022 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 TGTGCCTTATTTAATTAAAAACTTTGATAATTG 1 94 1 TTATAAAACT 0.837783 -195 ACGCTTCGGTTTCATCAAAACTCGTCCATTTAA 1 128 0 TTACAAAATC 0.87292 -161 TTAGTAAAAGTTGAACAAAAACTCTTCGAGTTT 1 177 0 TTACAAAACT 0.942125 -112 TTGTTCAACTTTTACTAAAAGTTTCTTTTAAAA 1 192 1 TTATAAAATT 0.917813 -97 CTAAATCCTTAGTATAAAAATTTTTATATATGA 5 115 1 AGAAAAAATT 0.598451 -69 ATAAAAAATAATAACAAAAAACTATTTATATAC 6 40 1 ATAAAAAACT 0.755315 -64 TTATATACCCTTCACAAAAAGTATTTGGAAAGG 6 65 1 TTAAAAAATA 0.835209 -39 GAAATACTATTTCATAAAAAGTCATAATAGTTT 7 11 1 TTAAAAAATC 0.741603 -33 TGGTGAAGCTTTTACTAAAAGGTTCATCCCAAT 9 49 0 TTATAAAAGT 0.760444 -127 TAGTAAAAGCTTCACCAAAACCTAACACCTCCT 9 65 1 TTACAAAACT 0.942125 -111 AAACGAAACTTTTAGAAAAAGTTGAACGAAAAC 10 67 1 TTAAAAAATT 0.936334 -135 AGCTCTCCATTTCATCAAAAACTAACACCTCCT 10 128 1 TTACAAAACT 0.942125 -74 ATGTCCATTATTTAATAAAATTAGGTGAGATAA 11 85 1 TTATAAAATA 0.79375 -24 TCCAAACAAATTAATCAAAATTAATTTACACCT 12 96 0 TTACAAAATA 0.92384 -43 ATATATTAGATTGATTAAAAGTTCCCATAGGTG 15 16 0 TTATAAAATT 0.917813 -177 TTAGAAAAGGTTGATCAAAACTTAGTTAAATAG 16 94 0 TTACAAAATT 0.972375 -183 CTCCCAACCTTTTAGTAAAAGGTTACTCGAACA 16 132 0 TTATAAAAGT 0.760444 -145 TCAATCATCAAAAATAGATAACATTT 17 4 1 ATACAAAATA 0.846281 -252 ATTATAGTCAATCATCAAAAGTTTTTATAGTTA 17 88 0 ATACAAAATT 0.94109 -168 ATAAAATAGAAGAAACAAAAATT 17 243 1 AGACAAAATT 0.781037 -13 TGTATCACCAAAAATAGTGAAGATTT 19 74 0 ATACAAAATA 0.846281 -16 GTTATAAAAAATTAAAAAAAGTTTCATAA 20 7 0 ATAAAAAATT 0.869702 -154 TTTTATGGTAATAAGAAAAAGTAGAAAAATAGG 22 28 0 ATAAAAAATA 0.696993 -76 CTAGTAAATTTTTAACAAAATTTTAAAATTTTA 22 56 0 TTACAAAATT 0.972375 -48 GAAGATGATTTGGATAAAAAGGTTAATTAACGA 26 38 0 TGAAAAAAGT 0.482788 -157 TATTTGAAAGTTTATCAAAATTTTCGAGCATTT 26 74 0 TTACAAAATT 0.972375 -121 ** * ***** ** Masking position 7 Map Score: 28.5846 Number of sites scoring better than the average of aligned sites = 649 Number in coding regions = 426 Number in noncoding regions = 223 Number of orfs with sites within 600 bp upstream = 184 Fraction of orfs with sites within 600 bp upstream = 0.0295535 Motif number 3 TACTATGGAATTTAGAAGCCCAAAGGGCTTC 1 59 1 TTTGAAGCCC 0.915361 -230 ATAAGGCACATATAGAAGCCCTTTGGGCTTC 1 73 0 TATGAAGCCC 0.971608 -216 CTCTTCGAGTTTTTGTAGCCCGAAGCTAACG 1 158 0 TTTGTAGCCC 0.714412 -131 TATCCCAATAGGGCGAAGCCCTATGGTTTCT 8 31 0 GGGGAAGCCC 0.868884 -68 TTGTATCCATAGGGGAAACCCCCTATTGGGA 9 25 1 AGGGAAACCC 0.768184 -151 GTAAGATTTGGGGAGTATCCCAATAGAGGGG 9 123 1 GGGGTATCCC 0.827633 -53 CCCAATAGAGGGGCGAAGCCCCTCTATGGGT 9 141 1 GGGGAAGCCC 0.868884 -35 GGAAACCATAGAGGGAAACCCTCTATTGGGA 12 34 1 GAGGAAACCC 0.948338 -105 GGAGGTGTTAGGGTGTATCCCAATAGAGGGT 12 51 0 GGGGTATCCC 0.85077 -88 GGGCTGAACGTAGTGAAGCCCCGCTCTGGGT 14 33 1 TAGGAAGCCC 0.989862 -75 TATCCCAATAGGGCGAAGCCCTATGGTGTAT 14 63 1 GGGGAAGCCC 0.868884 -45 TATCCCAATAGGGCGAAGCTATGGTGCGTTG 16 62 0 GGGGAAGCTA 0.639123 -215 AACTACCGCATGGCTAAGCTCAAACATTGCT 16 163 0 TGGTAAGCTC 0.658167 -114 AATAGAGATAGAGTTAAGCCCTATTTTAATC 16 214 0 GAGTAAGCCC 0.842515 -63 AGGTTATTGGTATAGAAGCCCTTTTGAGCTT 17 41 1 TATGAAGCCC 0.971608 -215 ATAATAAACTTATAGAAGCTCAAAAGGGCTT 17 56 0 TATGAAGCTC 0.830303 -200 ATAAAAGCTATATATAATCCCCTATATATTG 20 110 1 TATTAATCCC 0.448765 -51 *** ******* Masking position 7 Map Score: 23.1739 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 51 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 4 CTTCTAAGCTACTTTTATATAATATAACCTTGT 4 86 0 ATTATATAAT 0.92694 -34 TAGTATAAAAATTTTTATATATGATTTCAATTT 5 124 1 ATTATATATG 0.864904 -60 ATAAGACGAAAAGTTTATATATTAGATTGATTA 15 32 0 ATTATATATT 0.979245 -161 TTTGTGGGTAACTTTTATATATTTCCCAGAGGA 15 67 1 ATTATATATT 0.979245 -126 TTCATAATCAATCATTATATTATCGCCATGGAA 15 108 0 ATTATATTAT 0.68768 -85 AACCTTAGAAAATGTTATCTATTTTTGATGATT 17 13 0 ATTATCTATT 0.864897 -243 AAAAGTTTTTATAGTTATATAATAAACTTATAG 17 72 0 ATTATATAAT 0.926939 -184 GGATTTTTTGATTTTTATATTTTAAATAATATA 17 206 1 ATTATATTTT 0.891161 -50 TGACTATTTTATCATTATATATTTTAACAATTC 19 40 1 ATTATATATT 0.979226 -50 ATTTTAAAATAAATTTAAATATTTGAATGATAA 20 79 0 ATTAAATATT 0.890659 -82 AATAACAGTAAGCTTTAAATATTAAGTTAAAAA 21 14 1 ATTAAATATT 0.891176 -119 CATCACAATAAATTTTATATATTGGGAATTGAA 21 53 1 ATTATATATT 0.97918 -80 TATTAAACCGAAGAGTATATATTTAACTTAACT 23 102 1 AGTATATATT 0.864895 -76 TATTATCGTTAATCTTATATATTAGTTATTAAA 24 50 0 ATTATATATT 0.97918 -62 GTGTGGCGCAAAGCTTATATATTGTGCATTCAA 25 89 0 ATTATATATT 0.979245 -42 * ********* Masking position 7 Map Score: 22.2396 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 48 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 5 ATCAAAAACTACTTGGAGGGATAATA 1 273 1 ACGGAGGATA 0.946864 -16 CCGAGCGTAAGCGAGGAGGTGTTAGGTTTTGGTG 9 77 0 GCGGAGGGTA 0.998569 -99 CCTCGCTTACGCTCGGAGGTGTAAATTAGTAAGA 9 95 1 GCGGAGGGTA 0.998569 -81 TCCGAGCGAAGCGAGGAGGTGTTAGTTTTTGATG 10 140 0 GCGGAGGGTA 0.998569 -62 TCCTCGCTTCGCTCGGAAGTGTAAATTTACAACT 10 157 1 GCGGAAGGTA 0.987327 -45 CCGAGCGTAAGCGAGGAGGTGTTAGGGTGTATCC 12 62 0 GCGGAGGGTA 0.998569 -77 CCTCGCTTACGCTCGGAGGTGTAAATTAATTTTG 12 80 1 GCGGAGGGTA 0.998569 -59 CTATGCTAAGAGGCATTACCGAGCGTAG 16 5 1 GCAGAGGATA 0.946864 -272 ** ***** ** * Masking position 7 Map Score: 20.7799 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 GGGCTTCTAAATTCCATAGTAAATAATATCCTTTG 1 45 0 ATTAGAAATA 0.711485 -244 AATTATCAAAGTTTTTAATTAAATAAGGCACATAT 1 91 0 GTTATAAATA 0.691773 -198 TTTTTATAGCATTCCAGATTAAAAAACTCTGTGGT 1 224 0 ATTATAAAAA 0.946624 -65 AAAGAGTGTTATAACACATCAAAAACTACTTGGAG 1 256 1 ATAATAAAAA 0.876245 -33 AGAGAAGAAAATAACAATTTAAAAAAATAGAAGCA 4 24 0 ATATTAAAAA 0.772681 -96 AATCTTAAAGACTAAAAATAAAAAATAGAATTAAA 5 19 0 ACTATAAAAA 0.73108 -165 AGTCTTTAAGATTAGTAATTAAATATTAAATACCA 5 41 1 ATTATAAATA 0.933409 -143 ACTTTAAAAAGTTTGATATAAAAAAGTGTTGGTAT 5 70 0 GTTATAAAAA 0.739604 -114 ATATGACGCTTTTGTCCATAAAAAATAATAACAAA 6 23 1 TTTATAAAAA 0.509585 -81 AACTATTATGACTTTTTATGAAATAGTATTTC 7 8 0 ACTATAAATA 0.682403 -36 AAATATTAAAATAAAAATCTGGGTGAG 10 3 1 ATAAAAAAAA 0.535692 -199 ATTTTGATTAATTTGTTTGGAAAAATTTGAGGTGG 12 108 1 ATTTGAAAAA 0.599646 -31 TAATATAATGATTGATTATGAAAAATGGCGGAATA 15 119 1 ATTATAAAAA 0.946623 -74 TGGGGTATCCATTATAAATTAAAAATTATTTGAGG 16 245 1 ATTATAAAAA 0.946553 -32 TAAGTTTATTATATAACTATAAAAACTTTTGATGA 17 75 1 ATATAAAAAA 0.356485 -181 TGTCTATATTATTTAAAATATAAAAATCAAAAAAT 17 208 0 ATTATTAAAA 0.488511 -48 TTTAAATAATATAGACAATAAAATAGAAGAAACAA 17 226 1 ATAATAAATA 0.848395 -30 TGAAAATGTTATAAAAAATTAAAAAAAGTTTCATA 20 12 0 ATAATAAAAA 0.876245 -149 GAATGATAATATTATAAATAAAATAGTAGAGTTAT 20 53 0 ATTATAAATA 0.933408 -108 TATTTATAATATTATCATTCAAATATTTAAATTTA 20 68 1 ATTTTAAATA 0.870618 -93 AAATATTTAAATTTATTTTAAAATAAAAGCTATAT 20 88 1 ATTTTAAATA 0.870618 -73 AGCTTTAAATATTAAGTTAAAAATATTAGCATCAC 21 24 1 ATTTAAAATA 0.523054 -109 AATCTTATATATTAGTTATTAAATAGTAATATTTG 24 38 0 ATTATAAATA 0.933409 -74 GAAAATTTTGATAAACTTTCAAATATCCTCCCATT 26 82 1 ATATTAAATA 0.728741 -113 GTAGATGGACATTAATGTTCAAAAAAGAAACAACG 26 122 0 ATTTTAAAAA 0.894892 -73 *** ** ***** Masking position 12 Map Score: 22.5388 Number of sites scoring better than the average of aligned sites = 813 Number in coding regions = 579 Number in noncoding regions = 234 Number of orfs with sites within 600 bp upstream = 227 Fraction of orfs with sites within 600 bp upstream = 0.03646 Motif number 7 ACTTTTAGTAAAAGTTGAACAAAAACTCTT 1 184 0 AAAGTTGAAC 0.836496 -105 ACTTTTACTAAAAGTTTCTTTTAAAACCAC 1 199 1 AAAGTTTCTT 0.703438 -90 AGAACTTTAAAAAGTTTGATATAAAAAAGT 5 78 0 AAAGTTTGAT 0.870401 -106 GCTTTTACTAAAAGGTTCATCCCAATAGGG 9 45 0 AAAGGTTCAT 0.889179 -131 CCTTTTAGTAAAAGCTTCACCAAAACCTAA 9 60 1 AAAGCTTCAC 0.716954 -116 ACTTTTAGAAAAAGTTGAACGAAAACTCTT 10 74 1 AAAGTTGAAC 0.836496 -128 ACCTTTTAGAAAAGGTTGATCAAAACTTAG 16 102 0 AAAGGTTGAT 0.859326 -175 ACCTTTTCTAAAAGGTTGTTCGAGTAACCT 16 116 1 AAAGGTTGTT 0.621575 -161 CCTTTTAGTAAAAGGTTACTCGAACAACCT 16 128 0 AAAGGTTACT 0.778386 -149 TTTAGACAAAAAAGCTGAATTATAGTCAAT 17 109 0 AAAGCTGAAT 0.847759 -147 AAAATTAAAAAAAGTTTCATAA 20 3 0 AAAGTTTCAT 0.898182 -158 CTTAATATTTAAAGCTTACTGTTATTTTG 21 10 0 AAAGCTTACT 0.683428 -123 CATAGTCCTAAAGTTCAATAAGCAAATGT 23 10 1 AAAGTTCAAT 0.695481 -168 TATCAAACTTAAAGTTGAATTAAACTCAGG 25 45 1 AAAGTTGAAT 0.908765 -86 TTTCCAACCGAAAGTTGAATGCACAATATA 25 75 1 AAAGTTGAAT 0.908765 -56 ATTTGGATAAAAAGGTTAATTAACGAACCC 26 34 0 AAAGGTTAAT 0.923667 -161 AGGATATTTGAAAGTTTATCAAAATTTTCG 26 81 0 AAAGTTTATC 0.647558 -114 ********** Masking position 6 Map Score: 12.515 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 201 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 8 ATTTACACCTCCGAGCGTAAGCGAGGAGGT 9 91 0 CCGAGCGTAA 0.991618 -85 ATTTACACTTCCGAGCGAAGCGAGGAGGTG 10 153 0 CCGAGCGAAG 0.987792 -49 ATTTACACCTCCGAGCGTAAGCGAGGAGGT 12 76 0 CCGAGCGTAA 0.991618 -63 GAAAGTGGGGCTGAACGTAGTGAAGCCCCG 14 26 1 CTGAACGTAG 0.9073 -82 AGAGGCATTACCGAGCGTAGCGAGGTAATG 16 19 1 CCGAGCGTAG 0.996246 -258 ********** Masking position 4 Map Score: 5.75683 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 1 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 9 AGTTGAACAAAAACTCTTCGAGTTTTTGTA 1 172 0 AAACTCTTCG 0.881715 -117 GTTTTAAAAGAAACTTTTAGTAAAAGTTGA 1 196 0 AAACTTTTAG 0.980622 -93 TATTGGGATGAACCTTTTAGTAAAAGCTTC 9 48 1 AACCTTTTAG 0.969414 -128 ACTATAAACGAAACTTTTAGAAAAAGTTGA 10 62 1 AAACTTTTAG 0.980622 -140 AGTTGAACGAAAACTCTTAGAGTTTTCATA 10 86 1 AAACTCTTAG 0.951033 -116 TCTAATATATAAACTTTTCGTCTTATTTTT 15 39 1 AAACTTTTCG 0.951033 -154 TTACTCGAACAACCTTTTAGAAAAGGTTGA 16 113 0 AACCTTTTAG 0.969414 -164 CATTGCTCCCAACCTTTTAGTAAAAGGTTA 16 140 0 AACCTTTTAG 0.969414 -137 GTTATATAATAAACTTATAGAAGCTCAAAA 17 62 0 AAACTTATAG 0.926232 -194 TGAACATTATAAACGTTTAGTGGGGGGATA 25 14 0 AAACGTTTAG 0.905032 -117 GTTCATTATCAAACTTAAAGTTGAATTAAA 25 39 1 AAACTTAAAG 0.614701 -92 ********** Masking position 2 Map Score: 17.4285 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 45 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 10 CTATAAAAAGAGTGTTATAACACATCAAAAA 1 250 1 AGTGTATAAC 0.645873 -39 ACAGTCAAAGATTTATATAACAAATGTAG 3 11 1 ATTTTATAAC 0.681322 -19 ATATATAAAAATTTTTATACTAAGGATTTAG 5 115 0 ATTTTATACT 0.59872 -69 ACAAAAAACTATTTATATACCCTTCACAAAA 6 53 1 ATTTTATACC 0.90641 -51 GCTTCGCCCTATTGGGATACCCAGGATGCAT 8 43 1 ATTGGATACC 0.985959 -56 TCGCCCCTCTATTGGGATACTCCCCAAATCT 9 126 0 ATTGGATACT 0.915384 -50 GAGACCTCCTATTGCTATACCACCCGTCCAT 11 28 1 ATTGTATACC 0.977715 -81 GAAACCCTCTATTGGGATACACCCTAACACC 12 48 1 ATTGGATACA 0.859844 -91 GCTTCGCCCTATTGGGATACCCAGAGCGGGG 14 51 0 ATTGGATACC 0.985959 -57 CCCAGAGGATAATGTTATTCCATGGCGATAA 15 91 1 AATGTATTCC 0.555355 -102 GCTTCGCCCTATTGGGATACCTATTTAACTA 16 74 1 ATTGGATACC 0.985959 -203 TCCAATTTATATTGTGATTACCT 22 91 1 ATTGGATTAC 0.776442 -13 **** ****** Masking position 7 Map Score: 8.5444 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 90 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 11 AATATAACCTTGTGTTAATATTTAACGACTA 4 68 0 TTGTTAATAT 0.711045 -52 AGGGTAAAGTAATGATAAAATTGAAATCATA 5 143 0 ATGATAAAAT 0.930287 -41 AAATATTAAAATAAAAATCTGG 10 2 1 ATATTAAAAT 0.790118 -200 TAAATTTACAACTGATAAAATCTGGGTGATG 10 178 1 ATGATAAAAT 0.930287 -24 ATGTCCATTATTTAATAAAATTAGGTGAGAT 11 85 1 TTAATAAAAT 0.661349 -24 TACATAATAATTTGTTAAAATATTAACTACC 17 161 0 TTGTTAAAAT 0.873722 -95 TAAAATATATAATGATAAAATAGTCATAAAA 19 35 0 ATGATAAAAT 0.930287 -55 AAGATTTGGAATTGTTAAAATATATAATGAT 19 50 0 ATGTTAAAAT 0.928743 -40 TAAATATTTGAATGATAATATTATAAATAAA 20 66 0 ATGATAATAT 0.82592 -95 ATATAGCTTTTATTTTAAAATAAATTTAAAT 20 92 0 TTTTTAAAAT 0.576767 -69 ATTACCATAAAATTTTAAAATTTTGTTAAAA 22 49 1 ATTTTAAAAT 0.723146 -55 CACCCCTTAGACTAATAATATTAGTTAGTAT 24 86 0 ATAATAATAT 0.572411 -26 * ********* Masking position 7 Map Score: 6.97 Number of sites scoring better than the average of aligned sites = 291 Number in coding regions = 225 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 12 AAGTAGCTTAGAAGGAGGGGGTTTA 4 105 1 GAAGGAGGGG 0.777033 -15 ACCTCCGAGCGTAAGCGAGGAGGTGTTAGG 9 85 0 GTAAGCGAGG 0.92072 -91 GTATAAGACCCATAGAGGGGCTTCGCCCCT 9 149 0 CATAGAGGGG 0.838939 -27 AAATAAAAATCTGGGTGAGGATATGGATAC 10 19 1 CTGGGTGAGG 0.738664 -183 CACTTCCGAGCGAAGCGAGGAGGTGTTAGT 10 148 0 CGAAGCGAGG 0.948773 -54 ACCTCCGAGCGTAAGCGAGGAGGTGTTAGG 12 70 0 GTAAGCGAGG 0.92072 -69 GGAAATAAAAGAAAGTGGGGCTGAACGTAG 14 16 1 GAAAGTGGGG 0.92072 -92 TTGGGATACCCAGAGCGGGGCTTCACTACG 14 41 0 CAGAGCGGGG 0.977284 -67 CATTACCGAGCGTAGCGAGGTAATGCATCT 16 24 1 CGTAGCGAGG 0.889582 -253 ATGTAAACATCAGAGTGGGGATGATAA 26 178 1 CAGAGTGGGG 0.943873 -17 ********** Masking position 5 Map Score: 4.53412 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 19 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 CTTATAACCAATTATCAAAGGATATTATTTACTA 1 30 1 ATTAAAGGTA 0.76774 -259 TTTTGTTATTATTTTTTATGGACAAAAGCGTCAT 6 25 0 ATTTATGGCA 0.830485 -79 TCCAAATACTTTTTGTGAAGGGTATATAAATAGT 6 60 0 TTTTAAGGTA 0.750826 -44 CACAAAAAGTATTTGGAAAGGTTAGGAGTTGATT 6 77 1 ATTTAAGGTA 0.962984 -27 GTTTGGAAAAATTTGAGGTGGGTAATA 12 122 1 ATTTGTGGTA 0.942176 -17 TTTTCGTCTTATTTTTTGTGGGTAACTTTTATAT 15 53 1 ATTTGTGGTA 0.942176 -140 ATAATTTTTAATTTATAATGGATACCCCAAATAG 16 240 0 ATTTATGGTA 0.962984 -37 ATTAAAAATTATTTGAGGTGGTAAA 16 262 1 ATTTGTGGAA 0.674301 -15 AATAGATAACATTTTCTAAGGTTATTGGTATAGA 17 23 1 ATTTAAGGTA 0.962984 -233 AAAAATCCAAATTTCTTTAGGTTACATAATAATT 17 180 0 ATTTTAGGTA 0.803963 -76 AATAGTGAAGATTTGGAATTGTTAAAATATATAA 19 54 0 ATTTATTGTA 0.651159 -36 TCATTAATTAATTGAATAAGGTTATCTAACAACA 23 37 0 ATTGAAGGTA 0.830485 -141 **** **** ** Masking position 14 Map Score: 6.40271 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 62 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 14 GATACCCAGGATGCATTGCTTCTGCAAAGAAG 8 58 1 AGCATTGCTC 0.985731 -41 AAATTTTAAGAGGCATTGCTTCTTTGCAGAAG 8 76 0 AGCATTGCTC 0.985731 -23 TCTAATATATAAACTTTTCGTCTTATTTTTTG 15 39 1 AACTTTTCTC 0.736029 -154 ATCAAAACAGATGCATTACCTCGCTACGCTCG 16 30 0 AGCATTACTC 0.95892 -247 GGCTAAGCTCAAACATTGCTCCCAACCTTTTA 16 151 0 AACATTGCCC 0.957461 -126 TTATCTTCAAAAACATTACATCATTAATTAAT 23 59 0 AACATTACTC 0.918714 -119 CACAATATATAAGCTTTGCGCCACACATCTGG 25 96 1 AGCTTTGCCC 0.952881 -35 * ******* ** Masking position 1 Map Score: 2.65632 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 11 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 15 ACCAATTATCAAAGGATATTATTTACTATGGAATT 1 36 1 AAAGTATATA 0.393064 -253 TACTAATCTTAAAGACTAAAAATAAAAAATAGAAT 5 23 0 AAAATAAAAA 0.848788 -161 AATCACCAAAAAATGTTAAGGGTAAAGTAATGATA 5 157 0 AAAGTAAGAA 0.907574 -27 TGTCCATAAAAAATAATAACAAAAAACTATTTATA 6 35 1 AAAATAAAAA 0.848788 -69 TACCCTTCACAAAAAGTATTTGGAAAGGTTAGGAG 6 70 1 AAAATATTAA 0.619385 -34 AAATATTAAAATAAAAATCTGGGTG 10 1 1 AAAATAAAAA 0.848788 -201 GAAAAAGTATGGTGAATATTTATGGA 13 2 1 AAAATATGAA 0.832364 -34 AGTTACCCACAAAAAATAAGACGAAAAGTTTATAT 15 45 0 AAAATAAAAA 0.848788 -148 TTAACTACCAAAATGATATAAATAACTTAGTTTTA 17 135 0 AAAGTATAAA 0.900516 -121 TTTATATTTTAAATAATATAGACAATAAAATAGAA 17 219 1 AAAATATGAA 0.832364 -37 AACAAAACTTAAAAGTTAAAGGTAA 19 1 0 AAAGTAAGAA 0.907574 -89 TTACAAGTGAAAATGTTATAAAAAATTAAAAAAAG 20 19 0 AAAGTATAAA 0.900516 -142 ATTTGAATGATAATATTATAAATAAAATAGTAGAG 20 57 0 TAAATATAAA 0.587959 -104 ATTTTAAAATAAAAGCTATATATAATCCCCTATAT 20 102 1 AAAGTATTAA 0.743989 -59 AGTAAGCTTTAAATATTAAGTTAAAAATATTAGCA 21 20 1 AAAATAATAA 0.643127 -113 TGTTTCGTTTTATAGATAAAGAGAAGGACTATGTG 21 90 0 TATGTAAGAA 0.269484 -43 TTTACAACACTAAAGTTATAGTTAAGTTAAATATA 23 119 0 TAAGTATGAA 0.713975 -59 TAGTGTTGTAAATAGGTAATATAAAGATTTTAGAA 23 142 1 AATGTAAAAA 0.572231 -36 TATATAAGATTAACGATAATAATAATACTAACTAA 24 62 1 TAAGTAAAAA 0.738353 -50 *** * *** * ** Masking position 7 Map Score: 13.4803 Number of sites scoring better than the average of aligned sites = 859 Number in coding regions = 676 Number in noncoding regions = 183 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809