AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i255_heat_shock_aquae_reg_300.orf -o255_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 Input sequences: #1 RAA01295 19 Aquifex_aeolicus #2 RAA01298 139 Aquifex_aeolicus #3 RAA01691 70 Aquifex_aeolicus #4 RAA01489 30 Aquifex_aeolicus #5 RAA00424 48 Aquifex_aeolicus #6 RAA00426 37 Aquifex_aeolicus #7 RAA00427 68 Aquifex_aeolicus Motif number 1 TTAAACTAGGAGGAAGAAG 1 7 1 TAGGAGGAAG 0.989229 -13 ATGGTGTTTTAAGGAGGTTGAT 2 3 0 AAGGAGGTTG 0.984977 -137 CGGGCGTAGCTCAGAGGTAGAGCACCTGCT 2 55 1 TCAGAGGTAG 0.862666 -85 CCTGCTTGGGAAGCAGGTGCTCTACCTCTG 2 66 0 AAGCAGGTGC 0.975862 -74 CCTGCTTCCCAAGCAGGAGGTCGCCGGTTC 2 79 1 AAGCAGGAGG 0.993061 -61 ACTCTGGTAAACGGAGGAAAGTT 3 58 1 ACGGAGGAAA 0.974846 -13 AAGTTTTATCAAGGAGGTGGGAAT 6 24 1 AAGGAGGTGG 0.997086 -14 GTATAATAAAAGGCAGGAAAGATAGGAGGT 7 43 1 AGGCAGGAAA 0.915629 -26 GCAGGAAAGATAGGAGGTGATAAA 7 55 1 TAGGAGGTGA 0.985946 -14 ********** Masking position 5 Map Score: 15.7141 Number of sites scoring better than the average of aligned sites = 858 Number in coding regions = 697 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 170 Fraction of orfs with sites within 600 bp upstream = 0.0273049 Motif number 2 TTTTATTATTAAATTTTATAATGGTGTTTTA 2 22 0 AATTTTATAA 0.890177 -118 AGCTACGCCCGCTTTTTATTATTAAATTTTA 2 35 0 GCTTTTATTA 0.968527 -105 CGCCCGCTCCAAATTTTTGTACAATTTTGCT 2 118 1 AATTTTTGTA 0.895591 -22 AAGCCTTATTTTAAATTGATAAT 4 3 1 GCTTATTTTA 0.939651 -28 AATTTATATGATAAAGCTCAA 5 1 1 AATTATATGA 0.882195 -48 GGGAAATTATTTTACAATTTGCCT 5 35 0 AATTATTTTA 0.958131 -14 TCCTTGATAAAACTTCTATTAAATAAAT 6 8 0 AATTCTATTA 0.942982 -30 AAATTATGTCAATTTTTTTTAA 7 2 0 AATTTTTTTA 0.973484 -67 TATCTTTCCTGCCTTTTATTATACAACCTTA 7 36 0 GCTTTTATTA 0.968524 -33 ** ******** Masking position 5 Map Score: 9.1833 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 120 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 3 TAATAATAAAAAGCGGGCGTAGCTCAGAGG 2 42 1 AAGCGGGCGT 0.990725 -98 CCTGCTTGGGAAGCAGGTGCTCTACCTCTG 2 66 0 AAGCAGGTGC 0.959765 -74 CCTGCTTCCCAAGCAGGAGGTCGCCGGTTC 2 79 1 AAGCAGGAGG 0.960437 -61 GACGGGACTCGAACCGGCGACCTCCTGCTT 2 89 0 GAACCGGCGA 0.972678 -51 CAAAAATTTGGAGCGGGCGACGGGACTCGA 2 107 0 GAGCGGGCGA 0.996487 -33 TTACTCTGGTAAACGGAGGAAAGTT 3 56 1 AAACGGAGGA 0.878435 -15 ********** Masking position 2 Map Score: 3.71202 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 192 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 4 TTAAAACACCATTATAAAATTTAATAATAA 2 21 1 ATTATAAAAT 0.875795 -119 GCTCCAAATTTTTGTACAATTTTGCTT 2 123 1 TTTGTACAAT 0.755988 -17 TGAGTTTATTTTTGTCAAGTTTCAAAATCA 3 13 0 TTTGTCAAGT 0.97956 -58 ACACAAAATTATCAATTTAAAATAAGG 4 14 0 ATTATCAATT 0.923974 -17 TTTCTTGAGCTTTATCATATAAATT 5 6 0 TTTATCATAT 0.867278 -43 AGAAAGGCAAATTGTAAAATAATTTCCC 5 31 1 ATTGTAAAAT 0.816475 -18 TAATAGAAGTTTTATCAAGGAGGTGGGAAT 6 18 1 TTTATCAAGG 0.88925 -20 TTAGTGAAATTATGTCAATTTTTTTTAA 7 9 0 TATGTCAATT 0.847427 -60 ********** Masking position 5 Map Score: 4.33803 Number of sites scoring better than the average of aligned sites = 329 Number in coding regions = 294 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 5 TTAAACTAGGAGGAAGAAG 1 10 1 GAGGAAGAAG 0.962273 -10 ATAATAAAAAGCGGGCGTAGCTCAGAGGTA 2 44 1 GCGGGCGTAG 0.995892 -96 TCCCAAGCAGGAGGTCGCCGGTTCGAGTCC 2 85 1 GAGGTCGCCG 0.992463 -55 AAAATTTGGAGCGGGCGACGGGACTCGAAC 2 105 0 GCGGGCGACG 0.998489 -35 ********** Masking position 4 Map Score: 2.98048 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 42 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 ********** No masking Map Score: 1.09013e-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 7 ********** No masking Map Score: 1.09013e-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 8 ********** No masking Map Score: 1.09013e-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