AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00252_pyro_reg_300.orf -o00252_pyro_300.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -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 = 0.42 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 PH0016 300 475aa long hypothetical protein #2 PH0066 227 328aa long hypothetical L-asparaginase #3 PH0067 59 184aa long hypothetical protein #4 PH0134 300 300aa long hypothetical protein #5 PH0136 24 375aa long hypothetical Na(+)/H(+) antiporter #6 PH0137 274 378aa long hypothetical protein #7 PH0231 95 303aa long hypothetical protein #8 PH0232 53 305aa long hypothetical L-asparaginase #9 PH0241 284 434aa long hypothetical asparaginyl-tRNA synthetase #10 PH0243 69 601aa long hypothetical glutamine--fructose-6-phosphate aminotransferase #11 PHS005 138 92aa long hypothetical protein #12 PH0297 36 915aa long hypothetical alanyl-tRNA synthetase #13 PH0434 185 336aa long hypothetical protein #14 PH0437 263 367aa long hypothetical protein #15 PH0438 58 339aa long hypothetical adenylosuccinate synthetase #16 PH0770 167 154aa long hypothetical protein #17 PH0771 46 391aa long hypothetical aspartate aminotransferase #18 PH0935 40 246aa long hypothetical protein #19 PH1102 121 480aa long hypothetical asparagine synthetase #20 PH1103 23 127aa long hypothetical 30S ribosomal protein S8 #21 PH1308 38 386aa long hypothetical serine aminotransferase #22 PH1371 191 389aa long hypothetical aspartate aminotransferase #23 PH1463 40 438aa long hypothetical L-asparaginase Motif number 1 CAGCGTAGCAAAGATTTCCAATTTTCTTTAGAAA 1 71 0 AAGTTTCAAT 0.873761 -230 CGCTGATGGTATGTTTTTCAATATCTCTCTGGGG 1 100 1 ATGTTTTAAT 0.921755 -201 GAGAAAATATAAATTTTTGAAGTAGCTCTCCTCA 1 140 0 AAATTTTAAA 0.691389 -161 ATTTATCCCAATACTTTTAAATATGACTAATTTG 1 276 1 ATATTTTAAT 0.77434 -25 TTAAAGTGTCAAGATTTTGAAGTTATTTCGAACA 2 125 0 AAGTTTTAAT 0.980788 -103 TCTAATAAGTAAGATTTAGAATTTTTGGCAAATA 2 186 0 AAGTTTAAAT 0.891063 -42 AAGTCAAACCAAGGTTTTTAATCTAAACTAGCGA 4 144 0 AAGTTTTAAT 0.980787 -157 AGATGAGGGAAAAGTTTTTAATTTGAAAAAGTCG 4 209 1 AAATTTTAAT 0.936811 -92 TCGCCCAGGAAATTTTTTTAATATGCCCCAATAT 10 35 1 AATTTTTAAT 0.785403 -35 TGCCCCAAGAATGAATTTAAAAATCAAGGAACAT 11 21 0 ATGATTTAAT 0.640512 -118 ATTTAACGAGAAACTTTTAAAAGAGGGATTTTAA 13 73 0 AAATTTTAAA 0.691389 -113 TCAAAAGGGTAAGCATTTTAAGGTACCCCTTTAC 15 16 1 AAGATTTAAT 0.885096 -43 ATAAATTTAAAAGTTTTTTAAGTTCATAATATCA 16 94 0 AAGTTTTAAT 0.980742 -74 GTGTTGCTAAAAATTTTTAAATTTTGACCGGTAT 16 126 0 AAATTTTAAT 0.897893 -42 AAAGTTTTATAAATTTTTCATGTAA 17 2 1 AAGTTTAAAT 0.882553 -45 AGAAATTGGGAAGGTTTTTACATTCCATTAGGTA 19 88 1 AAGTTTTACT 0.858685 -34 CATAGGCTATAAGTTTGTCAAGCTTTATAAAGGT 22 41 1 AAGTTGTAAT 0.858705 -151 *** **** ** * Masking position 6 Map Score: 17.6072 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 157 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 2 CCATAAACCTTCTAACGAGGGGATTTGGATA 2 94 0 TCTAAGAGGG 0.799009 -134 TTGGACCTACTATAGCAAGGGTACCCTCGCT 4 27 1 TATAGAAGGG 0.821375 -274 TAGTTTTTCATTTAGCGAGGGTACCCTTGCT 4 40 0 TTTAGGAGGG 0.985096 -261 TCGTTCCCAAATTAGCGAGGGATTAAGTCGA 4 240 1 ATTAGGAGGG 0.983091 -61 TATTTGAGAATTTGAAGAGGGTA 5 3 0 TTTGAGAGGG 0.945468 -22 AATATGAAAGATAAGGGAGGAAAAAATGTAA 6 27 0 ATAAGGAGGA 0.754806 -248 TAGCGAAAAATAAAAAGAGGGATGATGAGTT 9 17 0 TAAAAGAGGG 0.770794 -268 TTTAGCTTACAATAGGGAGGGCACTTC 13 7 0 AATAGGAGGG 0.960483 -179 CGAGAAACTTTTAAAAGAGGGATTTTAAGAT 13 70 0 TTAAAGAGGG 0.889434 -116 TTACTTACCCTTTGGTAAGGAGT 15 46 1 TTTGGAAGGA 0.556589 -13 TAGCAACACAATTGGTGAGGGGGAGAA 16 151 1 ATTGGGAGGG 0.979488 -17 TCATTTAGAAATTGGGAAGGTTTTTACATTC 19 82 1 ATTGGAAGGT 0.612733 -40 TGCCCAATAGCGAGGTGGGTTAA 20 6 1 AATAGGAGGT 0.828735 -18 TTTGTCCTCGATTGAGGAGGTGAC 22 4 0 ATTGAGAGGT 0.752254 -188 CAGAAAAATGTTAAGAGAGGGGATATAAACC 23 11 0 TTAAGGAGGG 0.961813 -30 ***** ***** Masking position 8 Map Score: 13.1364 Number of sites scoring better than the average of aligned sites = 584 Number in coding regions = 534 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 3 CCTCACGATTCCCCCAGAGAGATATTGAAAAA 1 113 0 CCCCCAGAGA 0.985938 -188 TGATCTACCTCGCCCTGAAGGGTGATGTTTTC 1 177 0 CGCCCTGAGG 0.816462 -124 TTGCTCCAAGCTTCCAGAGAGCACTCCAAGTG 1 207 0 CTTCCAGAGC 0.687667 -94 TCCCACTTAATTCCCTGAGGAACTTCGGTTTT 2 58 0 TTCCCTGAAA 0.53826 -170 CCCCCAGAAAGCGTTAATAACC 3 48 0 CCCCCAGAGC 0.987837 -12 GGTTCACGATTCCCCGGAGAGGGCGGGAACCG 9 85 0 TCCCCGGAGG 0.939759 -200 CCGGTCGGAACCCCCGGTTCACGATTCCCCGG 9 100 0 CCCCCGGTAC 0.708601 -185 AAGCTCTTCATCCCCTGTCGGCCCGGTCGGAA 9 122 0 TCCCCTGTGC 0.909092 -163 ATGCCCTATGCCCCAAGAATGAATTTAAAAAT 11 31 0 CCCCAAGAGA 0.867286 -108 GAATCTGGAGCCCCCTGATCGGTGATGATCAG 11 100 1 CCCCCTGAGG 0.976652 -39 GTTATCAGCTCCGCAGACTGATCATCACCGA 11 118 0 TCCGCAGAGA 0.848537 -21 ACCCCTAAAGCTCCAAGTGTGAGTAACATAA 12 10 0 CTCCAAGTGA 0.450506 -27 TCTACAGAAATCTCCAGTTTGATTTAACGAGA 13 96 0 TCTCCAGTGA 0.609724 -90 GATTTAGTGCTTCCCAGTACGGTATCTTCATG 14 166 0 TTCCCAGTGG 0.849559 -98 AATAGGGAATTCCGCTGAAGGGTGTTGTAGGG 16 11 0 TCCGCTGAGG 0.769712 -157 CTTTCGATAGTTCCCAGATAACCTTTATAAAG 22 63 0 TTCCCAGAAC 0.723902 -129 GAATACCCCCAGAAAAATGTTAAGAGA 23 24 0 CCCCCAGAAA 0.933519 -17 ******** ** Masking position 7 Map Score: 12.1121 Number of sites scoring better than the average of aligned sites = 424 Number in coding regions = 376 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 4 TTTTCTTCAAAATTTATCCCAATACTTTTAAA 1 265 1 AATTTATCAA 0.918018 -36 TAAGATTTAGAATTTTTGGCAAATACTATGAA 2 179 0 AATTTTTCAA 0.965651 -49 ATCATCAGAGAACTTTTCGCTAGTTTAGATTA 4 128 1 AACTTTTCTA 0.728049 -173 TTTTTCTCAAAATTTTTGCCAATTTATCTTAT 6 197 0 AATTTTTCAA 0.965651 -78 AGATATATTAAATTTTTCTCAAAATTTTTGCC 6 209 0 AATTTTTCAA 0.965651 -66 CTACCTCCACAACATATATCAACTCATCAAAT 6 249 0 AACATATCAA 0.631245 -26 TTTTCCAAGAAATTTTGAACAAAGTATCACAA 9 209 1 AATTTTGCAA 0.854288 -76 TAAGCCAAAAAATATTTAACTAGATAAACTCA 16 51 0 AATATTTCTA 0.735337 -117 TCACAAAAATAATTTAAGCCAAAAAATATTTA 16 65 0 AATTTAACAA 0.611745 -103 AAAATTTAAAAATTTTTAGCAACACAATTGGT 16 135 1 AATTTTTCAA 0.965651 -33 CCTCGATACGAATATTTTACAAACAAGTAAAA 22 120 0 AATATTTCAA 0.918018 -72 ******* *** Masking position 2 Map Score: 8.36894 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 27 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 TATCCCAATACTTTTAAATATGACTAATTT 1 279 1 CTTTTAAATA 0.538805 -22 TTATAAATCTCTTTCATAGTATTTGCCAAA 2 167 1 CTTTCATAGT 0.561492 -61 GTGCTGAAGTCTATTAGTTTTTCATTTAGC 4 55 0 CTATTAGTTT 0.304755 -246 GGGAACGACTTTTTCAAATTAAAAACTTTT 4 218 0 TTTTCAAATT 0.650034 -83 CCCTTTCCCACTTTTAGAATAGTGAGTTAT 4 273 0 CTTTTAGAAT 0.73122 -28 CCTCCCTTATCTTTCATATTCACTATATCG 6 38 1 CTTTCATATT 0.90419 -237 CTATATCGGCCTTTTATTTTTAGAATAATC 6 60 1 CTTTTATTTT 0.773872 -215 TAATGCTTTCCTTTTATATTGGGGGAATTT 6 136 1 CTTTTATATT 0.913559 -139 TTTCGATATCCTTTCAATTTTGGGATGGGC 8 33 1 CTTTCAATTT 0.807951 -21 TGTTCCTTGATTTTTAAATTCATTCTTGGG 11 22 1 TTTTTAAATT 0.6753 -117 CGCTTATTCACTTTTAAATTATGCCCTATG 11 53 0 CTTTTAAATT 0.935678 -86 ACTCCTCATACTTTTCGATTGGAGTCTCCT 14 85 0 CTTTTCGATT 0.797302 -179 ACTTAAAAAACTTTTAAATTTATACCGGTC 16 105 1 CTTTTAAATT 0.935678 -63 TTGCTAAAAATTTTTAAATTTTGACCGGTA 16 127 0 TTTTTAAATT 0.6753 -41 ATACTTTTCTTTTACATCCTTTC 19 4 1 CTTTTCTTTT 0.444047 -118 CTTTTACATCCTTTCAGAATTGCCCACTTT 19 19 1 CTTTCAGAAT 0.708406 -103 ATCCCGTTTGCTTTCAGATTGCATACTAAT 19 52 1 CTTTCAGATT 0.937694 -70 ********** Masking position 4 Map Score: 9.46995 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 201 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 6 ATCATCCTGCGGCAATGGGGCAAGTAGCTCT 1 17 0 GGCAAGGGGC 0.871412 -284 AACTTTCTAAAGAAAATTGGAAATCTTTGCT 1 68 1 AGAAATTGGA 0.816374 -233 ATCTCTCTGGGGGAATCGTGAGGAGAGCTAC 1 122 1 GGGAACGTGA 0.859642 -179 AGTGCTCTCTGGAAGCTTGGAGCAATTGAAA 1 214 1 GGAAGTTGGA 0.784666 -87 TAGATCCCAGGGAAGGTGGGCTCTATGGTGA 2 23 1 GGAAGTGGGC 0.903463 -205 CTTCTAACGAGGGGATTTGGATAGAGCTCCC 2 86 0 GGGGATTGGA 0.679629 -142 TTCTAAAAGTGGGAAAGGGGAAGGAAT 4 284 1 GGGAAGGGGA 0.946401 -17 CGGAGAGGGCGGGAACCGGGCCGGTTAAAAA 9 72 0 GGGAACGGGC 0.968481 -213 GCCCTCTCCGGGGAATCGTGAACCGGGGGTT 9 93 1 GGGAACGTGA 0.859642 -192 AATTTTTCCAAGAAATTTTGAACAAAGTATC 9 206 1 AGAAATTTGA 0.446295 -79 GAATGCATATGGAAATTTGGCTCAGTGATGG 9 261 1 GGAAATTGGC 0.919308 -24 AAACGGGATGAGAAAGTGGGCAATTCTGAAA 19 30 0 AGAAATGGGC 0.919475 -92 GCAATCTGAAAGCAAACGGGATGAGAAAGTG 19 43 0 AGCAACGGGA 0.834662 -79 TAATTCATTTAGAAATTGGGAAGGTTTTTAC 19 78 1 AGAAATGGGA 0.926221 -44 ***** ***** Masking position 2 Map Score: 8.47974 Number of sites scoring better than the average of aligned sites = 541 Number in coding regions = 505 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 7 TAAAAGTGGGAAAGGGGAAGGAAT 4 287 1 AAAGGGGAAG 0.975443 -14 AAGGATATCGAAAGGTTAAAAGAATTATGG 8 16 0 AAAGGTTAAA 0.863771 -38 AAAGGGATAAAAAGGTTTAGTTGACTTTAT 13 148 0 AAAGGTTTAG 0.910301 -38 CCCTGTCAAAAGGGTAAGCATTTTAAGG 15 9 1 AAAGGGTAAG 0.983342 -50 ACTCCTTACCAAAGGGTAAGTAAAGGGGTA 15 39 0 AAAGGGTAAG 0.983342 -20 GAAAGGTGAAGCTCTAATAAT 18 30 0 AAAGGTGAAG 0.970496 -11 ACCCCCAGAAAAATGTTAAGAGAGGGGATA 23 17 0 AAATGTTAAG 0.863771 -24 ********** Masking position 3 Map Score: 7.07846 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 77 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 TTTCTCTTCGAAAACATCACCCTTCAGGGCG 1 168 1 AAACATCACC 0.799462 -133 GGGAAAAACTCATCATCCCTCTTTTTA 9 7 1 AATCATCATC 0.945293 -278 GCAAAGCAAAAGCTCTTCATCCCCTGTCGGC 9 132 0 AGTCTTCATC 0.96498 -153 GCGAAGGGCGTGGTCATCATCTGCTCAGCAA 9 159 0 TGTCATCATC 0.925529 -126 GCTCGGATCCAGTTCTTCATCGCCCAGGAAA 10 16 1 AGTCTTCATC 0.964979 -54 GGGGGCTCCAGATTCATCATCTTAATAGGAT 11 84 0 GATCATCATC 0.841677 -55 CTCCGCAGACTGATCATCACCGATCAGGGGG 11 110 0 TGTCATCACC 0.941178 -29 TCTCTTCTCAAACTCTTCACCTAATATTTTG 14 50 0 AATCTTCACC 0.947524 -214 AGTAATTATTAGAGCTTCACCTTTC 18 26 1 AGGCTTCACC 0.904052 -15 ** ******** Masking position 7 Map Score: 5.44708 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 72 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 9 CTTACTTATTAGAATTTGAGTTGGTGGTCA 2 207 1 AGAATTTGAG 0.93491 -21 TTGATCCTCAAGAATTGGAGATGAGGGAAA 4 191 1 AGAATTGGAG 0.977691 -110 ATATTTGAGAATTTGAAGAGGGTA 5 8 0 AGAATTTGAA 0.650723 -17 TGGGCGATGAAGAACTGGATCCGAGCTGAT 10 12 0 AGAACTGGAT 0.907623 -58 AGAGAGTAGTATAACTGGAGGTAATTTTAG 13 33 0 ATAACTGGAG 0.808107 -153 TATTAGGTGAAGAGTTTGAGAAGAGAATTA 14 55 1 AGAGTTTGAG 0.770426 -209 TGAAGGCTAGAGAAGCGGAGTGGAAGCGCC 14 121 1 AGAAGCGGAG 0.886786 -143 TTGAACACCCAGAACCGGATTACATGAAAA 17 25 0 AGAACCGGAT 0.827664 -22 AGATTAGGATTGAATTGGAGTGATATCTTT 22 93 1 TGAATTGGAG 0.873557 -99 ********** Masking position 3 Map Score: 2.24984 Number of sites scoring better than the average of aligned sites = 344 Number in coding regions = 318 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 10 CTGGAAGCTTGGAGCAATTGAAAGCTAACACTA 1 222 1 GGACAATGAA 0.844056 -79 AAAAGTATTGGGATAAATTTTGAAGAAAAGGCA 1 261 0 GGAAAATTTA 0.898355 -40 ATAAAAGGGTGGTTAAAGTGTCAAGATTTTGAA 2 138 0 GGTAAATGTA 0.959257 -90 TGCTATAGTAGGTCCAAATGGTAGCGGAAAAAC 4 11 0 GGTCAATGGA 0.91857 -290 AGATAAGGGAGGAAAAAATGTAACGTTGGACGA 6 17 0 GGAAAATGTA 0.978206 -258 AAAAATAATAAGATAAATTGGCAAAAATTTTGA 6 190 1 AGAAAATGGA 0.81178 -85 AAAATTTCTTGGAAAAATTGTCAAATAGCAGGT 9 192 0 GGAAAATGTA 0.977984 -93 AATTTATACCGGTCAAAATTTAAAAATTTTTAG 16 121 1 GGTAAATTTA 0.822576 -47 CCTCAATCGAGGACAAAGTGGGACATAGGCTAT 22 18 1 GGAAAATGGA 0.977775 -174 *** *** *** * Masking position 7 Map Score: 5.2179 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 44 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 ATAAATTTTGAAGAAAAGGCAAAATACTAG 1 252 0 AAGAAAAGGC 0.881597 -49 GAAAGAGATTTATAAAAGGGTGGTTAAAGT 2 152 0 TATAAAAGGG 0.899659 -76 TTCCCACTTTTAGAATAGTGAGTTATCATC 4 269 0 TAGAATAGTG 0.679503 -32 GTGAATATGAAAGATAAGGGAGGAAAAAAT 6 31 0 AAGATAAGGG 0.909347 -244 TTATTCTAAAAATAAAAGGCCGATATAGTG 6 58 0 AATAAAAGGC 0.648425 -217 TAACATTACTAAGCAAAGTGTTATAATGAT 6 96 0 AAGCAAAGTG 0.578073 -179 ATTCCCCCAATATAAAAGGAAAGCATTATA 6 134 0 TATAAAAGGA 0.580062 -141 AATTTTAGCTTACAATAGGGAGGGCACTTC 13 11 0 TACAATAGGG 0.817544 -175 ACCAAAGGGTAAGTAAAGGGGTACCTTAAA 15 32 0 AAGTAAAGGG 0.798793 -27 ACTCCTTACCAAAGGGTAAGTAAAGG 15 43 0 TACCAAAGGG 0.770349 -16 ACTCAAGCCTTAGAATAGGGAATTCCGCTG 16 26 0 TAGAATAGGG 0.943684 -142 TTCCATTAGGTAGATAAGGGCG 19 110 1 TAGATAAGGG 0.920766 -12 GAACTATCGAAAGATTAGGATTGAATTGGA 22 82 1 AAGATTAGGA 0.417053 -110 ********** Masking position 7 Map Score: 3.39156 Number of sites scoring better than the average of aligned sites = 702 Number in coding regions = 630 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 12 TCTGGGGGAATCGTGAGGAGAGCTACTTCAA 1 127 1 TCGGAGGAGA 0.912608 -174 AGGGTGATGTTTTCGAAGAGAAAATATAAAT 1 160 0 TTTGAAGAGA 0.964102 -141 TTGGGATAAATTTTGAAGAAAAGGCAAAATA 1 256 0 TTTGAAGAAA 0.7502 -45 TTGGGAAGAGCCTAGATCCCA 2 1 1 TTGGAAGAGC 0.838265 -227 TGGCAAATACTATGAAAGAGATTTATAAAAG 2 164 0 TATAAAGAGA 0.621712 -64 CACCAGATCATATAGAGGAGAACAGTAAATA 7 68 0 TATGAGGAGA 0.955719 -28 TCACCTAATATTTTGAGGAGATCCCTGGTAG 14 34 0 TTTGAGGAGA 0.971928 -230 GGTGAAGAGTTTGAGAAGAGAATTAAGGAGA 14 60 1 TTGGAAGAGA 0.956865 -204 AAAATATTCGTATCGAGGACAGATTGGGTTT 22 134 1 TATGAGGACA 0.781285 -58 *** ******* Masking position 6 Map Score: 2.65855 Number of sites scoring better than the average of aligned sites = 269 Number in coding regions = 243 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 13 CCACCTTCCCTGGGATCTAGGCTCTTCCCAA 2 11 0 TGGGTCTAGG 0.97948 -217 CCAGGGAAGGTGGGCTCTATGGTGAAGTGAA 2 29 1 TGGGTCTATG 0.954926 -199 GACTTAATATTGGGGCATATTAAAAAAATTT 10 44 0 TGGGCATATT 0.89444 -26 AATTCATTCTTGGGGCATAGGGCATAATTTA 11 38 1 TGGGCATAGG 0.990063 -101 GAGGACAAAGTGGGACATAGGCTATAAGTTT 22 26 1 TGGGCATAGG 0.990063 -166 **** ****** Masking position 8 Map Score: 0.648527 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 16 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 14 CCCCCAGAAAGCGTTAATAACCAATTACT 3 41 0 AAGCGTTATA 0.918406 -19 TATGTATAATTAGCCTTGATATTTAAAAATA 6 166 1 TAGCCTTATA 0.980177 -109 ATCGATATCATAGCGTTTATAAGATTATCTA 7 19 1 TAGCGTTATA 0.962786 -77 CTGAAGACTTAATATTGGGGCATA 10 56 0 AAGACTTATA 0.736378 -14 TCCGCTTCTCTAGCCTTCACATAATACTCCT 14 109 0 TAGCCTTACA 0.938393 -155 ATTACTGGAATAGCATTGATA 18 1 0 TAGCATTATA 0.90416 -40 AGTTCCCAGATAACCTTTATAAAGCTTGACA 22 56 0 TAACCTTATA 0.865244 -136 ******* *** Masking position 9 Map Score: 0.702203 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 72 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 15 ACTAATAGACTTCAGCACGGTTTTACCTTC 4 67 1 TTCAGCACGG 0.894376 -234 TTTTAGAATAATCAGCTCAATCATTATAAC 6 77 1 ATCAGCTCAA 0.864652 -198 CGTGGTCATCATCTGCTCAGCAAAGCAAAA 9 152 0 ATCTGCTCAG 0.910786 -133 GATCAGCTCGGATCCAGTTCT 10 2 1 ATCAGCTCGG 0.984621 -68 CCGCAGACTGATCATCACCGATCAGGGGGC 11 109 0 ATCATCACCG 0.841522 -30 GTTATCAGCTCCGCAGACTGATC 11 126 0 ATCAGCTCCG 0.984621 -13 ********** Masking position 2 Map Score: 0.836004 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 22 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185