AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i294_mixed1_aquae_reg_300.orf -o294_aquae_300.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RAA01117 16 Aquifex_aeolicus RAA01265 27 Aquifex_aeolicus RAA01155 17 Aquifex_aeolicus RAA01268 16 Aquifex_aeolicus RAA00291 18 Aquifex_aeolicus RAA01105 38 Aquifex_aeolicus RAA01569 24 Aquifex_aeolicus RAA00301 25 Aquifex_aeolicus RAA00343 36 Aquifex_aeolicus Input sequences: #1 RAA01012 41 Aquifex_aeolicus #2 RAA01250 300 Aquifex_aeolicus #3 RAA01252 96 Aquifex_aeolicus #4 RAA01254 19 Aquifex_aeolicus #5 RAA01255 126 Aquifex_aeolicus #6 RAA01256 58 Aquifex_aeolicus #7 RAA01257 174 Aquifex_aeolicus #8 RAA01258 57 Aquifex_aeolicus #9 RAA01264 77 Aquifex_aeolicus #10 RAA01266 42 Aquifex_aeolicus #11 RAA01362 126 Aquifex_aeolicus #12 RAA01371 29 Aquifex_aeolicus #13 RAA01457 117 Aquifex_aeolicus #14 RAA01459 211 Aquifex_aeolicus #15 RAA01460 33 Aquifex_aeolicus #16 RAA01499 76 Aquifex_aeolicus #17 RAA01500 110 Aquifex_aeolicus #18 RAA00451 300 Aquifex_aeolicus #19 RAA00455 72 Aquifex_aeolicus #20 RAA00466 48 Aquifex_aeolicus #21 RAA00049 45 Aquifex_aeolicus #22 RAA00179 62 Aquifex_aeolicus #23 RAA00181 41 Aquifex_aeolicus #24 RAA00197 66 Aquifex_aeolicus #25 RAA00199 271 Aquifex_aeolicus #26 RAA00232 68 Aquifex_aeolicus #27 RAA00236 96 Aquifex_aeolicus #28 RAA00237 37 Aquifex_aeolicus #29 RAA00669 250 Aquifex_aeolicus #30 RAA00757 300 Aquifex_aeolicus #31 RAA01104 62 Aquifex_aeolicus #32 RAA01116 91 Aquifex_aeolicus #33 RAA01118 74 Aquifex_aeolicus Motif number 1 AAAAAATAACGCTTTATCAATAACTTATTA 2 35 1 GCTTTATCAA 0.914156 -266 CTTGAGTATACCTTTATAAAATTTTTACCC 2 121 1 CCTTTATAAA 0.978916 -180 CTTTTTAGCCCCTTTTTAAAAGTATATCAC 2 265 1 CCTTTTTAAA 0.975575 -36 CACTTTAATACCTTTATAAAGAAATTCTTA 3 13 1 CCTTTATAAA 0.978916 -84 TTTTTTGCCCCCTTTATAAGAATATTTTTA 5 24 1 CCTTTATAAG 0.890927 -103 TCAGGTTTCTTCTTTTTAAGTTACACGAGT 5 91 0 TCTTTTTAAG 0.566755 -36 TTGGTGCCCCGCTCTTAAAATTAAAACTTT 6 25 1 GCTCTTAAAA 0.509561 -34 CTTTTGGCGGGCTTTAAAAATAAAAAAAAT 9 25 1 GCTTTAAAAA 0.838112 -53 CCTTCTCTCTCCTTTTAAAACCTTTTGAGG 10 15 1 CCTTTTAAAA 0.885272 -28 TAAAAATTTGGCTTTTAAAAGACTTGACAT 13 70 0 GCTTTTAAAA 0.816635 -48 TTAATCTCTTCCTCTTTAAAGAGTTCCTTG 14 56 0 CCTCTTTAAA 0.903084 -156 GTCTTCCTTTCCTTTTTAATCTCTTCCTCT 14 71 0 CCTTTTTAAT 0.894472 -141 ACTTTAAACACCTATTTAAAGGAGCAGGGA 15 14 1 CCTATTTAAA 0.701076 -20 ATTGAGTATGCCTTTATAAAATTTTTACCC 18 27 0 CCTTTATAAA 0.978916 -274 CTAAAAAAACGCTTTATAAATAACTTATTA 18 113 0 GCTTTATAAA 0.964027 -188 AATATTATGACCTTTATCAAAGTAAATCAA 19 45 0 CCTTTATCAA 0.948587 -28 CTTTATACCTTTTTATAATCTTTAAGT 20 8 1 CCTTTTTATA 0.673985 -41 TACAATTTGTTCTTTATAATAAATCCTTCA 24 22 0 TCTTTATAAT 0.647178 -45 GTGTTATATATCTTTATAATGTCTTT 27 7 0 TCTTTATAAT 0.647178 -90 AAAAACCTAAGCTTTTTCAAGGCTATGACA 27 43 0 GCTTTTTCAA 0.901581 -54 TTCCTTCTTTCCTTTATAATACTTTCCTT 28 19 1 CCTTTATAAT 0.907862 -19 CAAGGGGAAGCCTTTTTAAAAGCCCGCAAA 29 60 0 CCTTTTTAAA 0.975575 -191 CTTGAGTATACCTTTATAAAATTTCCAT 30 9 0 CCTTTATAAA 0.978916 -292 AAAAAATAACGCTTTATCAATAACTTATTA 30 95 0 GCTTTATCAA 0.914156 -206 GGTTGCTTTAGCTCTTTCAACTTTCAACTC 30 161 0 GCTCTTTCAA 0.681234 -140 TATGATATATTCTTTATAAAGAAAATTAAG 31 23 1 TCTTTATAAA 0.896298 -40 ********** Masking position 5 Map Score: 39.441 Number of sites scoring better than the average of aligned sites = 467 Number in coding regions = 400 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 2 CAGAGGAGGAAGCTTCATCCTG 1 2 1 AGAGGAGAAG 0.592089 -40 TACTTTTAAAAAGGGGCTAAAAAGCCCCTCC 2 258 0 AAGGGGCAAA 0.782683 -43 AAATACAGGGAGGTAAGAA 4 7 1 AGGGAGGAAG 0.967098 -13 GCAAAAAAGAAAGAAGGAAAA 5 1 0 AAGAAGGAAA 0.92521 -126 TATTCTTATAAAGGGGGCAAAAAAGAAAGAA 5 17 0 AAGGGGGAAA 0.97643 -110 GGATTTATAGAAGGGGGCAAGAGCCCCCATG 8 20 0 AAGGGGGAAG 0.976867 -38 AAATCCTTTTAGGAGGGAAAATA 8 45 1 AGGAGGGAAA 0.867715 -13 GCCCGCCAAAAGGCGGGCAAAAGACA 9 6 0 AGGCGGGAAA 0.823643 -72 GGAGATATAAATAGAGGTAAAGGAAAATG 9 59 1 ATAGAGGAAA 0.615287 -19 CTATAACCTGAAGGAGGTTAGCAA 11 113 1 AAGGAGGTAG 0.70666 -14 GATGTCATTAAAAAAGTAAATTTTAAATT 12 10 1 AAAAAAGAAA 0.41174 -20 GGAAGAGATTAAAAAGGAAAGGAAGACGATA 14 74 1 AAAAAGGAAG 0.862325 -138 CGTTTTGACCAAGCAGGTAAAAGTTCTTCTT 14 165 0 AAGCAGGAAA 0.898042 -47 GGAACTTTTGCGGGAGGAAAGTGTGAACTAT 16 17 0 CGGGAGGAAG 0.805809 -60 TTAACTCTACAAAGAGGTAAAAGCC 21 31 1 AAAGAGGAAA 0.959308 -15 TTGCCTACAAAAGGTGGGAACTAAATTCTTT 25 235 1 AAGGTGGAAC 0.613991 -37 TAAAAAACTGAGAGAGGTAAGAGAC 27 82 1 AGAGAGGAAG 0.935895 -15 TTATAAAGGAAAGAAGGAAAAAGGGGC 28 7 0 AAGAAGGAAA 0.92521 -31 CAAAACCTACAAGGAAGAAAAGCCTACAAGG 29 85 0 AAGGAAGAAA 0.843912 -166 AGGTTTTGGGAAAGGAGTAAGTATACTTTTT 29 108 1 AAAGGAGAAG 0.704952 -143 CTGTTCCACAAAAGTGGAAAGTAAGAAAAAG 29 133 0 AAAGTGGAAG 0.871221 -118 TTGAAAGTTGAAAGAGCTAAAGCAACCGCAC 30 164 1 AAAGAGCAAA 0.672088 -137 TGTGGAGTTGAAAGTGGAAAATGCTGCAAAA 30 222 1 AAAGTGGAAA 0.869054 -79 CTGCAAAAACAAAAAGGAAAAAGCTGAGGTT 30 245 1 AAAAAGGAAA 0.860032 -56 CCAAAAGGAAAATATGATATAT 31 2 1 CAAAAGGAAA 0.464511 -61 GGGGCAACCCAAGCGGGGAAGGTGCGGTTTA 32 22 0 AAGCGGGAAG 0.886833 -70 GTGATGGGGAAGGGTGGCAAAACCCAAGGAG 32 62 1 AGGGTGGAAA 0.89032 -30 ******* *** Masking position 10 Map Score: 29.0764 Number of sites scoring better than the average of aligned sites = 1749 Number in coding regions = 1567 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 180 Fraction of orfs with sites within 600 bp upstream = 0.028911 Motif number 3 AATTTCCGCTAACCTGAGGTTCTGCAAACTTGA 2 93 1 AACGAGGTTT 0.991545 -208 AATTTTCCTTAATATTAGGTTATATTTATCGCC 3 54 0 AAATAGGTTT 0.893044 -43 CTTGAAAAATTCTCCGAGGTTTTCAAATTTAAC 14 27 0 TCCGAGGTTT 0.818528 -185 AATTTCCGCTAACCCGAGGTTCTGCAAAATTGA 18 52 0 AACGAGGTTT 0.991545 -249 GCCCTAAGTAAATAAGAGGTTTTTCTTTCTCAT 18 232 1 AAAGAGGTTT 0.974242 -69 CTAACCTCCTAAAAAGAAGTTTTATTCTTAAAC 22 14 1 AAAGAAGTTT 0.730701 -49 TTAAACTTAATACCGTAGGTTTTTTATTCAAC 22 41 1 TACTAGGTTT 0.852943 -22 GCTTTGGGAGAAAATGAGGTATTTTATTTCTCA 25 129 1 AAAGAGGTAT 0.814156 -143 AGCCTTGAAAAAGCTTAGGTTTTTTTTATTTTA 27 49 1 AACTAGGTTT 0.962807 -48 AATTTCCGCTAACCCGAGGTTCTGCAAACTTGA 30 34 0 AACGAGGTTT 0.991545 -267 AAAAAGGAAAAAGCTGAGGTTCCTAATGTACCG 30 255 1 AACGAGGTTC 0.952677 -46 TAAGTTTAGTAAACGGAGGTTTTT 31 49 1 AACGAGGTTT 0.991544 -14 ** * ****** * Masking position 7 Map Score: 18.6665 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 97 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 4 AAACTTCTGACCCTCACGAAACGAACGTTAA 2 64 1 CCCTCACGAA 0.863692 -237 GCTAAAAAGCCCCTCCTGGCTCCTTGGCAAT 2 243 0 CCCTCCTGGT 0.744684 -58 CACACAACCTCCTTAAATTTAATTTTC 3 80 0 ACCTCCTTAA 0.97635 -17 TTCTTACCTCCCTGTATTT 4 4 0 ACCTCCCTGA 0.90524 -16 ACCTAAACCCTCCTGATCAGGTTTCTTC 5 109 0 CCCTCCTGAC 0.943839 -18 GCACCAACCCCCCTCATTAGC 6 1 0 CCCTCATTAC 0.8681 -58 AACAACACCTCCTTAAAGTTTTAATTT 6 42 0 ACCTCCTTAA 0.97635 -17 TATTTTCCCTCCTAAAAGGATTTATAG 8 41 0 CCCTCCTAAA 0.934534 -17 TTGCTAACCTCCTTCAGGTTATAGAGT 11 110 0 ACCTCCTTCG 0.734844 -17 GGTTCCCACCTCCTTTTAAGTTTTTTCT 13 8 1 ACCTCCTTTA 0.877526 -110 CTTTTGTATTCCCTGCTTACAGTCCTTATGG 14 124 0 CCCTGCTTAA 0.761393 -88 TTGAGTGACCTCACAAGATTCATTTTAA 17 93 0 ACCTCACAAA 0.677037 -18 TAGTCGCAATCCCTCATTATTAGGGCGTAAC 18 158 0 CCCTCATTAT 0.744965 -143 ACGCTAACCTCCTAAAAAGAAGTTTTA 22 7 1 ACCTCCTAAA 0.92356 -56 GCGTGACCTCCTGAAGGATTTATTAT 24 6 1 ACCTCCTGAG 0.934315 -61 AACCTACCTCCCGACATTATTATCTT 24 51 0 ACCTCCCGAA 0.948162 -16 GAAATAAAATACCTCATTTTCTCCCAAAGCT 25 128 0 ACCTCATTTC 0.491555 -144 ATAGCATAGCCCCTCACTAAAAATATAGCAA 29 195 1 CCCTCACTAA 0.894325 -56 ACTTCACACCTCCTTGGGTTTTGCCACC 32 74 0 ACCTCCTTGG 0.881364 -18 ********* * Masking position 4 Map Score: 17.3668 Number of sites scoring better than the average of aligned sites = 512 Number in coding regions = 420 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 5 TCAGGTTAGCGGAAATTAACGTTCGTTTCGTGA 2 77 0 GAAATTAACT 0.951679 -224 TGAAGGGATTGAAAATCAAGGGTAAAAATTTTA 2 137 0 GAAATCAAGT 0.908613 -164 ATTAAATTAAAAATATGTGATATA 2 287 0 TAAATTAAAT 0.844482 -14 TAATATTAAGGAAAATTAAATTTAAGGAGGTTG 3 70 1 GAAATTAAAT 0.94445 -27 AGTAGATGAGGGAAATCAAAAAAATTTTTTTAT 5 61 0 GAAATCAAAA 0.561084 -66 GCCCCGCTCTTAAAATTAAAACTTTAAGGAGGT 6 30 1 TAAATTAAAT 0.844482 -29 AGTGATTGAAAATCAAGGGTAAAAATTTTA 18 8 1 GAAATCAAGT 0.908613 -293 TCGGGTTAGCGGAAATTAACATTCGTTTCATTA 18 68 1 GAAATTAACT 0.951679 -233 CTTTATCAAAGTAAATCAACACTTACTTATCAT 19 31 0 GAAATCAACT 0.941779 -42 AGTTAAATTAAATTTAATACTTAAC 21 3 1 TAAATTAAAT 0.844482 -43 AATTCTTTTTTTAAATCAACTTTT 25 258 1 TAAATCAACT 0.83783 -14 ACCAATTTAAATTATAGTTATTGATATAT 26 50 0 TAAATTATAT 0.485178 -19 TTGTGGAACAGGAAATTATAAATATCAAGGCGA 29 153 1 GAAATTATAT 0.746883 -98 TCGGGTTAGCGGAAATTAACATTCGTTTCGTGA 30 50 1 GAAATTAACT 0.951679 -251 TCTTTATAAAGAAAATTAAGTTTAGTAAACGGA 31 33 1 GAAATTAAGT 0.923696 -30 * ******** * Masking position 8 Map Score: 16.0915 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 31 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 6 GAACGTTAATTTCCGCTAACCTGAGGTTCT 2 86 1 TTCCGCTAAC 0.968475 -215 TAACCTGAGGTTCTGCAAACTTGAGTATAC 2 102 1 TTCTGCAAAC 0.965653 -199 TACCGCTCCCTCAAAAGGTTTTAAAA 10 27 0 TCCCTCAAAA 0.810322 -16 ATTTAACTTTTTCCTCAAAATCT 14 4 0 TTCCTCAAAA 0.908549 -208 CACACTTTCCTCCCGCAAAAGTTCCCTTTT 16 23 1 TCCCGCAAAA 0.961099 -54 TAACCCGAGGTTCTGCAAAATTGAGTATGC 18 46 0 TTCTGCAAAA 0.945586 -255 GAATGTTAATTTCCGCTAACCCGAGGTTCT 18 62 0 TTCCGCTAAC 0.968475 -239 TAATTTCCTGTTCCACAAAAGTGGAAAGTA 29 141 0 TTCCACAAAA 0.849265 -110 TAACCCGAGGTTCTGCAAACTTGAGTATAC 30 28 0 TTCTGCAAAC 0.965653 -273 GAATGTTAATTTCCGCTAACCCGAGGTTCT 30 44 0 TTCCGCTAAC 0.968475 -257 AAGTGGAAAATGCTGCAAAAACAAAAAGGA 30 233 1 TGCTGCAAAA 0.831244 -68 ********** Masking position 8 Map Score: 14.1284 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 106 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 CGTTTCGTGAGGGTCAGAAGTTTAATAAGT 2 57 0 GGGTCAGAAG 0.965283 -244 AATTGCCAAGGAGCCAGGAGGGGCTTTTTA 2 242 1 GAGCCAGGAG 0.812297 -59 GGGGGCAAAAAAGAAAGAAGGAAAA 5 6 0 AAGAAAGAAG 0.860413 -121 GTTTTAAAAGGAGAGAGAAGGGGAA 10 6 0 GAGAGAGAAG 0.837724 -37 TTCGCATGGTGGGACAGGAGAAGGATTGTA 11 28 0 GGGACAGGAG 0.982884 -99 GAGATTAAAAAGGAAAGGAAGACGATACCC 14 78 1 AGGAAAGGAA 0.685967 -134 CTATGATACGGGGACAGAAGCCGCCTGTGT 17 53 1 GGGACAGAAG 0.985877 -58 CGTTTCATTAAGGTCAGAAGTCTAATAAGT 18 91 1 AGGTCAGAAG 0.910836 -210 TTTATGAAATGAGAAAGAAAAACCTCTTAT 18 243 0 GAGAAAGAAA 0.699794 -58 ATAAAGATTTCGGTAAGAAGATAACAAGAA 25 46 0 CGGTAAGAAG 0.774221 -226 AGTATTATAAAGGAAAGAAGGAAAAAGGGG 28 12 0 AGGAAAGAAG 0.950275 -26 TGTAGGTTTTGGGAAAGGAGTAAGTATACT 29 105 1 GGGAAAGGAG 0.977165 -146 ********** Masking position 6 Map Score: 10.5392 Number of sites scoring better than the average of aligned sites = 428 Number in coding regions = 402 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 TAGGAACCCTGCACGCCTGTGTCTAA 2 5 1 AACCTCACGC 0.915682 -296 ATTTTTAACTAATTTTTCAAGGTAAATTTATA 13 93 1 AATTTCAAGG 0.89262 -25 AACCTCGGAGAATTTTTCAAGGAACTCTTTAA 14 39 1 AATTTCAAGG 0.89262 -173 TATGGTTTCAAACTTCTCAAGGGGTATCGTCT 14 97 0 AATTCCAAGG 0.905922 -115 ATTAGGGCGTAACCCTGCACGCCTGTGTCTAA 18 139 0 AACCTCACGC 0.915682 -162 TTTAATACTTAACTCTACAAAGAGGTAAAAGC 21 23 1 AATCTCAAAG 0.839539 -23 GCCTTTTTAAAAGCCCGCAAAGTGCCTACCTC 29 49 0 AACCCCAAAG 0.875324 -202 CAAGGAAGAAAAGCCTACAAGGGGAAGCCTTT 29 75 0 AACCTCAAGG 0.977589 -176 TCCTTTCCCAAAACCTACAAGGAAGAAAAGCC 29 92 0 AACCTCAAGG 0.977589 -159 TTCAACTTTCAACTCCACACGGTACATTAGAA 30 144 0 AATCCCACGG 0.980594 -157 TTCCACTTTCAACTCCACACGGTACATTAGAA 30 209 0 AATCCCACGG 0.980594 -92 TTATGAATATACATCCACACGGTACATTAGGA 30 275 0 ACTCCCACGG 0.896636 -26 ** *** ***** Masking position 9 Map Score: 13.5366 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 167 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 9 GAAGTTTAATAAGTTATTGATAAAGCGTTAT 2 40 0 AAGTTTTGAT 0.872473 -261 CTGGCTTAAGAATTTCTTTATAAAGGTATTA 3 18 0 AATTTTTTAT 0.915827 -79 CCTTTATAAGAATATTTTTATATGACTATAA 5 34 1 AATATTTTAT 0.637201 -93 AAATCAAAAAAATTTTTTTATAGTCATATAA 5 51 0 AATTTTTTAT 0.915827 -76 ATCTCCATTAATTTTTTTTATTTTTAAAGCC 9 34 0 ATTTTTTTAT 0.805683 -44 CCCATCAAATTAATTTATACAATCCTTC 11 8 1 AATTATTTAT 0.482125 -119 ACCTCCTTTTAAGTTTTTTCTGACATTTATC 13 18 1 AAGTTTTTCT 0.813732 -100 GAAGTCTAATAAGTTATTTATAAAGCGTTTT 18 107 1 AAGTTTTTAT 0.945933 -194 TTAATACCGTAGGTTTTTTATTCAAC 22 47 1 AGGTTTTTAT 0.750216 -16 ATCTTACAATTTGTTCTTTATAATAAATCCT 24 25 0 TTGTTTTTAT 0.536419 -42 AAAATGAGGTATTTTATTTCTCACCTTTAGT 25 139 1 ATTTTTTTCT 0.508672 -133 ATTTAAATTATAGTTATTGATATATTAGAGA 26 44 0 TAGTTTTGAT 0.542829 -25 TTACCTCTCTCAGTTTTTTATAAAATAAAAA 27 71 0 CAGTTTTTAT 0.718481 -26 GGTGTCTAATAAGTTATTGATAAAGCGTTAT 30 89 1 AAGTTTTGAT 0.872473 -212 ACTAAACTTAATTTTCTTTATAAAGAATATA 31 28 0 ATTTTTTTAT 0.805683 -35 TTAAGTCTTTAATATGTTTATCTTAA 33 59 1 AATATTTTAT 0.637201 -16 ***** ***** Masking position 7 Map Score: 7.36565 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 162 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 10 ATTGATAAAGCGTTATTTTTTAGACACAGGCGTGC 2 21 0 CGTTATTTAC 0.914887 -280 CGGAAATTAACGTTCGTTTCGTGAGGGTCAGAAGT 2 66 0 CGTTCTTGAG 0.795283 -235 GTATAGCAACCCTTACGTTGGAAACAT 7 3 0 CCTTATTGAC 0.943269 -172 GCTTCTGTCCCCGTATCATAGATACGCGGTTTTAG 17 39 0 CCGTAATGAC 0.788625 -72 ATTTATAAAGCGTTTTTTTAGACACAGGCGTGCAG 18 122 1 CGTTTTTGAC 0.907426 -179 AGAGAAGTATCGGTAGCTTTGGGAGAAAATGAGGT 25 114 1 CGGTATTGAG 0.963656 -158 ATTGATAAAGCGTTATTTTTTGGACACAGGCACAC 30 104 1 CGTTATTTAC 0.914887 -197 CAACTCCACACGGTACATTAGAAACCCTGTGTGCC 30 132 0 CGGTATTGAC 0.990015 -169 CAACTCCACACGGTACATTAGAAACTCATAACCAT 30 197 0 CGGTATTGAC 0.990015 -104 TACATCCACACGGTACATTAGGAACCTCAGCTTTT 30 263 0 CGGTATTGAC 0.990016 -38 ***** ** * ** Masking position 9 Map Score: 7.7834 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 17 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 ACCTCAGGTTAGCGGAAATTAACGTTCGTT 2 83 0 AGCGGAAATT 0.973198 -218 GGAATACAAAAGGGGAATTTTTAAGAAGAA 14 143 1 AGGGGAATTT 0.797147 -69 ACCTCGGGTTAGCGGAAATTAACATTCGTT 18 65 1 AGCGGAAATT 0.973198 -236 TGGATACTTCAGGGGAAAGCCCGTGGCAGT 23 21 1 AGGGGAAAGC 0.88233 -21 GTTCCACAAAAGTGGAAAGTAAGAAAAAGT 29 132 0 AGTGGAAAGT 0.974818 -119 ACCTCGGGTTAGCGGAAATTAACATTCGTT 30 47 1 AGCGGAAATT 0.973198 -254 TACCGTGTGGAGTTGAAAGTTGAAAGAGCT 30 152 1 AGTTGAAAGT 0.884024 -149 TACCGTGTGGAGTTGAAAGTGGAAAATGCT 30 217 1 AGTTGAAAGT 0.884024 -84 AGTGGAAATTTTAACTCAGT 33 1 1 AGTGGAAATT 0.967813 -74 ********** Masking position 6 Map Score: 10.5678 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 79 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 12 TTATTTTTTAGACACAGGCGTGCAGGGTTC 2 14 0 GACACAGGCG 0.996527 -287 AAAAACTGCTTACACAGGCGGCTTCTGTCC 17 64 0 TACACAGGCG 0.986344 -47 CGTTTTTTTAGACACAGGCGTGCAGGGTTA 18 132 1 GACACAGGCG 0.996527 -169 TTATTTTTTGGACACAGGCACACAGGGTTT 30 116 1 GACACAGGCA 0.986344 -185 ********** Masking position 6 Map Score: 5.82576 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 0 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 ATGTTTCCAACGTAAGGGTTGCTATACACAA 7 7 1 CCCAAGGTTG 0.82739 -168 TTTTTAAAGCCCGCCAAAAGGCGGGCAAAAGACA 9 10 0 CCCAAGGGGG 0.989816 -68 AGTGTCATAGCCTTCGCATGGTGGGACAGGAGAAG 11 35 0 CCCATGGGGG 0.985654 -92 CAGGGTTACGCCCTAATAATGAGGGATTGCGACTA 18 154 1 CCAAATGGGG 0.695698 -147 CTTTATTTTGCCTACAAAAGGTGGGAACTAAATTC 25 228 1 CCCAAGGGGG 0.989816 -44 CTCGGTAAGGGCTTCAGAAGTTGGGGACGTAAT 29 9 0 GCCAAGTGGG 0.95583 -242 CGAAGCTGGGGCAACCCAAGCGGGGAAGGTGCGGT 32 25 0 GCCAAGCGGG 0.9833 -67 CCTTCCCCATCACCCCGAAGCTGGGGCAACCCAAG 32 40 0 CACAAGCGGG 0.947317 -52 ** * **** *** Masking position 8 Map Score: 4.43898 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 49 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 14 GTCAGAAGTTTAATAAGTTATTGATAAAGC 2 45 0 TAATAAGTTA 0.926634 -256 TTTTCCTTAATATTAGGTTATATTTATCGC 3 55 0 TATTAGGTTA 0.82902 -42 GGTTTCTTCTTTTTAAGTTACACGAGTAGA 5 88 0 TTTTAAGTTA 0.738941 -39 TCCCACCTCCTTTTAAGTTTTTTCTGACAT 13 14 1 TTTTAAGTTT 0.738942 -104 GTCAGAAGTCTAATAAGTTATTTATAAAGC 18 103 1 TAATAAGTTA 0.926634 -198 AGTGTTTATTTATTAAGTTTATGAAATGAG 18 260 0 TATTAAGTTT 0.92665 -41 AAACCTACGGTATTAAGTTTAAGAATAAAA 22 33 0 TATTAAGTTT 0.92665 -30 ATCGGCAAAGTAATAAGTCAATAAAACTAA 25 165 0 TAATAAGTCA 0.684419 -107 GTCTTTCCGTTAATAGGTTTACTGTCTCTT 25 201 1 TAATAGGTTT 0.829019 -71 GTTAGGTGTCTAATAAGTTATTGATAAAGC 30 85 1 TAATAAGTTA 0.926634 -216 TTATAAAGAAAATTAAGTTTAGTAAACGGA 31 36 1 AATTAAGTTT 0.594037 -27 TTTAAGTCTTTAATATGTTTATCTTAA 33 58 1 TAATATGTTT 0.639929 -17 ********** Masking position 5 Map Score: 8.24078 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 22 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 15 ATTTTATAAAGGTATACTCAAGTTTGCAGAA 2 112 0 GGATACTCAA 0.973254 -189 CGTAAGGGTTGCTATACACAACGCTTGCCAC 7 21 1 GCATACACAA 0.965162 -154 CTGTAAGCAGGGAATACAAAAGGGGAATTTT 14 133 1 GGATACAAAA 0.825177 -79 ATTTTATAAAGGCATACTCAATTTTGCAGAA 18 35 1 GGATACTCAA 0.973254 -266 TCTAGATATGGCAAAACACAAGAACAAAATC 25 86 0 GCAAACACAA 0.923385 -186 ATTTTATAAAGGTATACTCAAGTTTGCAGAA 30 17 1 GGATACTCAA 0.973254 -284 GGGAAGGGTGGCAAAACCCAAGGAGGTGTGA 32 68 1 GCAAACCCAA 0.876079 -24 ** ******** Masking position 6 Map Score: 3.88677 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 55 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234