AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i146_NADH-formate_Dehydrogenase_aquae_reg_300.orf -o146_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: RAA01416 19 Aquifex_aeolicus Input sequences: #1 RAA01311 139 Aquifex_aeolicus #2 RAA01386 43 Aquifex_aeolicus #3 RAA01389 44 Aquifex_aeolicus #4 RAA01390 25 Aquifex_aeolicus #5 RAA01418 30 Aquifex_aeolicus #6 RAA00245 300 Aquifex_aeolicus #7 RAA00361 75 Aquifex_aeolicus #8 RAA00309 299 Aquifex_aeolicus Motif number 1 TACTATAAAGACAAAAACAAAATAATGAGTGCTTC 6 39 0 ACAAAACAAA 0.992915 -262 AAAGTAAACAACAAAAGCTAAATAAATAAGACTTA 6 72 0 ACAAAACAAA 0.992915 -229 AAAAACTTAATCAAAAACAATAAAACAGAGCTGTT 6 162 1 TCAAAACAAA 0.966771 -139 TAAATGGTGAAGAAAGGCTAAAAAACAAAGGGGAA 6 202 0 AGAAAGCAAA 0.972453 -99 AATTGTGTCAAGAAAAACGAGCCAACTTAAATGGT 6 229 0 AGAAAACAAA 0.986343 -72 AGTGCCCTCCGCAAAAACTATGTAAAGATATACCA 6 273 0 GCAAAACAAA 0.987556 -28 AGGGTAAATAAGAAAAGCCATAAAAACTGC 7 6 0 AGAAAACAAA 0.986343 -70 GAAGAACGCCGCAAAGACTACCAAGAAGGCTAAAG 8 40 0 GCAAAGCAAG 0.911527 -260 TATAAACGGAACAAAACCTACCAATAGAACAGGAA 8 196 0 ACAAAACAAT 0.961707 -104 ****** * * ** Masking position 10 Map Score: 13.338 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 22 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 2 CCGCTCCAAATTTTTGTACAATTTTGCTT 1 6 0 TTTTGTAAAT 0.928732 -134 CGCCCGCTTTTTATTATTAAATTTTATAATGGTG 1 100 1 TTTTATTAAT 0.960736 -40 AGTCGTTATTATTAATAAAGGTTTAATTTCAG 2 9 1 TTTTAATAAT 0.935172 -35 AATTTTTAATATACAATCAAGTTTT 4 9 0 TTTAATAACT 0.723775 -17 AGGCTTTTTAATTTAAAATGTTTCTAACT 5 12 0 TTTAATTAAT 0.858495 -19 TATTTAGCTTTTGTTGTTTACTTTATATACTGGC 6 83 1 TTTTGTTACT 0.97266 -218 TGTTTTATTGTTTTTGATTAAGTTTTTCCAATTC 6 155 0 TTTTGATAAT 0.950609 -146 TTTATGGCTTTTCTTATTTACCCTCAATTAAATT 7 17 1 TTTTATTACT 0.963651 -59 CTCAATTAAATTTTTGTTAAACTTAAAAATCACT 7 39 1 TTTTGTTAAT 0.970444 -37 CGTACTTTACTTCTTAAAAACTCTTTATTTGGAC 8 86 1 TTTTAAAACT 0.861621 -214 CTTGGTGGCATTTTTGATGATCGTTATTCCTGTT 8 170 1 TTTTGATATT 0.800793 -130 ** ***** ** * Masking position 10 Map Score: 10.2267 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 91 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 3 TATAAAATTTAATAATAAAAAGCGGGCGTAGC 1 96 0 AAAAAAAAAG 0.897057 -44 AACCTTTATTAATAATAACGACT 2 2 0 AAAAAACGAC 0.91097 -42 GAAACATTTTAAATTAAAAAGCCT 5 17 1 AATTAAAAGC 0.602458 -14 AGCTACAGAAAAAGCTAGATCGTTT 6 4 1 TAAGAAAAGC 0.64861 -297 GACTTACTATAAAGACAAAAACAAAATAATGA 6 46 0 AAGAAAAAAC 0.851995 -255 ACAAAAGCTAAATAAATAAGACTTACTATAAA 6 65 0 AAAATAAGAC 0.666099 -236 ATATAAAGTAAACAACAAAAGCTAAATAAATA 6 79 0 AAAAAAAAGC 0.973788 -222 ATAAAGAAGGAATTGGAAAAACTTAATCAAAA 6 146 1 AATGAAAAAC 0.832051 -155 ACAAAGGGGAAAATACAACAGCTCTGTTTTAT 6 181 0 AATAAACAGC 0.857571 -120 AGAAAGGCTAAAAAACAAAGGGGAAAATACAA 6 195 0 AAAAAAAGGG 0.875349 -106 AAATTGTGTCAAGAAAAACGAGCCAACTTAAA 6 233 0 AAAAAACGAG 0.744699 -68 ATTGAGGGTAAATAAGAAAAGCCATAAAAACT 7 13 0 AAAAAAAAGC 0.973788 -63 CTACCAATAGAACAGGAATAACGATCATCAAA 8 182 0 AAAGAATAAC 0.662245 -118 GTAGAAGGCAAAGAATATAAACGGAACAAAAC 8 214 0 AAAAATAAAC 0.750533 -86 ** ** ****** Masking position 2 Map Score: 7.62116 Number of sites scoring better than the average of aligned sites = 638 Number in coding regions = 584 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 4 TGTACAAAAATTTGGAGCGGGCGACGGGACTCGA 1 20 1 TTTGGGGGGA 0.985871 -120 ATAATGGTGTTTTAAGGAGGTTGAT 1 125 1 TTTAAGGGGA 0.984093 -15 AAGGTTTAATTTCAGGGAGGAAGAGA 2 28 1 TTCAGGGGGA 0.994709 -16 AAATAACATTTTTAGTCTGGGGGATAAATTTTTC 3 21 0 TTTAGCGGGA 0.977577 -24 ACGAGCCAACTTAAATGGTGAAGAAAGGCTAAAA 6 214 0 TTAAAGTGGA 0.836853 -87 TGCGGCGTTCTTCAGTGCGGCTTACGTACTTTAC 8 62 1 TTCAGGGGTA 0.980874 -238 AAATTGCCGTTTTAGAGGTGAGTAAAAG 8 282 1 TTTAGGTGTA 0.944059 -18 ***** * ** ** Masking position 14 Map Score: 3.69127 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 98 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 GTCCCGTCGCCCGCTCCAAATTTTTGTACA 1 20 0 CCGCTCCAAA 0.962155 -120 ATCAACCTCCTTAAAACACCATTAT 1 125 0 CCTCCTTAAA 0.926243 -15 TCTCTTCCTCCCTGAAATTAAACCTT 2 28 0 CCTCCCTGAA 0.978709 -16 ATAATGAGTGCTTCACCAAACGATCTAGCT 6 23 0 CTTCACCAAA 0.836263 -278 AAAAGTGCCCTCCGCAAAAACTATGTAA 6 283 0 CCTCCGCAAA 0.986049 -18 ACCTTCCTCCCGAAGTGATTTTTAA 7 61 0 CCTCCCGAAG 0.925974 -15 GCACTGAAGAACGCCGCAAAGACTACCAAG 8 50 0 ACGCCGCAAA 0.885633 -250 AGTACGTAAGCCGCACTGAAGAACGCCGCA 8 62 0 CCGCACTGAA 0.924765 -238 ********** Masking position 9 Map Score: 3.48676 Number of sites scoring better than the average of aligned sites = 410 Number in coding regions = 380 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 CTTAAAACACCATTATAAAATTTAATAATA 1 111 0 CATTATAAAA 0.823145 -29 AATTCCGTTTGAAAAATTTATCCCC 3 6 1 CGTTTGAAAA 0.964936 -39 GAGTTAGAAACATTTTAAATTAAAAAGCCT 5 11 1 CATTTTAAAT 0.697734 -20 GATATACCAGTGTTTTAAAATTGTGTCAAG 6 252 0 TGTTTTAAAA 0.846344 -49 ACGTACTTTACTTCTTAAAAACTCTTTATT 8 85 1 CTTCTTAAAA 0.781146 -215 TTTATTTGGACGTCAGAGAAGAGAGTGTAC 8 109 1 CGTCAGAGAA 0.802503 -191 ACAAGGAACTCGTTGTAGAAGGCAAAGAAT 8 230 0 CGTTGTAGAA 0.934613 -70 TGTTAAAGTACGTTTTAAAATTGCCGTTTT 8 265 1 CGTTTTAAAA 0.982458 -35 TTAAAATTGCCGTTTTAGAGGTGAGTAAAA 8 279 1 CGTTTTAGAG 0.925 -21 ********** Masking position 7 Map Score: 3.28381 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 168 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 7 CTCGAACCGGCGACCTCCTGCTTGGGAAGC 1 49 1 CGACCTCCTG 0.985544 -91 ATCAACCTCCTTAAAACACCAT 1 128 0 CAACCTCCTT 0.967473 -12 TCTCTTCCTCCCTGAAATTAAAC 2 31 0 CTTCCTCCCT 0.987824 -13 ACCTTCCTCCCGAAGTGATTTT 7 64 0 CTTCCTCCCG 0.992094 -12 ********** Masking position 6 Map Score: 1.78196 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 57 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 AAAATTTAATAATAAAAAGCGGGCGTAGCT 1 95 0 AATAAAAAGC 0.909027 -45 TATCCCCCAGACTAAAAATGTTATTT 3 29 1 ACTAAAAATG 0.817463 -16 TTGATTGTATATTAAAAATT 4 16 1 ATTAAAAATT 0.88787 -10 AACATTTTAAATTAAAAAGCCT 5 19 1 ATTAAAAAGC 0.95828 -12 TTTGCCTTACATCAATAAGCCAGTATATAA 6 105 0 ATCAATAAGC 0.801377 -196 TTTTAAGTTTAACAAAAATTTAATTGAGGG 7 37 0 AACAAAAATT 0.771502 -39 TTTTGTTAAACTTAAAAATCACTTCGGGAG 7 50 1 CTTAAAAATC 0.861576 -26 AATAACGATCATCAAAAATGCCACCAAGGG 8 168 0 ATCAAAAATG 0.923109 -132 ********** Masking position 5 Map Score: 1.25498 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 122 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 9 ACAAAAATTTGGAGCGGGCGACGGGACTCG 1 23 1 GGAGCGGGCG 0.992344 -117 ACCTGCTTCCCAAGCAGGAGGTCGCCGGTT 1 53 0 CAAGCAGGAG 0.945882 -87 TCCTGCTTGGGAAGCAGGTGCTCTACCTCT 1 64 1 GAAGCAGGTG 0.988041 -76 TTAATAATAAAAAGCGGGCGTAGCTCAGAG 1 90 0 AAAGCGGGCG 0.986386 -50 GGACGTCAGAGAAGAGAGTGTACTTATTCA 8 116 1 GAAGAGAGTG 0.872376 -184 ********** Masking position 3 Map Score: 1.21976 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 125 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 TGGGAAGCAGGTGCTCTACCTCTGAGCTAC 1 71 1 GTGCTCTACC 0.987286 -69 AAAATAATGAGTGCTTCACCAAACGATCTA 6 26 0 GTGCTTCACC 0.976849 -275 CTGCAAGGGAGTACTCAACACCTTTAGCCT 8 19 1 GTACTCAACA 0.877533 -281 TGCGGCTTACGTACTTTACTTCTTAAAAAC 8 77 1 GTACTTTACT 0.943731 -223 ATTTTAAAACGTACTTTAACAAGTGCACAA 8 256 0 GTACTTTAAC 0.927371 -44 ********** Masking position 5 Map Score: 0.0300727 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 104 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 11 ********** No masking Map Score: 6.56131e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 12 ********** No masking Map Score: 6.56131e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 13 ********** No masking Map Score: 6.56131e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0