AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i255_heat_shock_aquae_reg_100.orf -o255_aquae_100.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 0.988868 -13 ATGGTGTTTTAAGGAGGTTGAT 2 3 0 AAGGAGGTTG 0.984476 -137 CGGGCGTAGCTCAGAGGTAGAGCACCTGCT 2 55 1 TCAGAGGTAG 0.858672 -85 CCTGCTTGGGAAGCAGGTGCTCTACCTCTG 2 66 0 AAGCAGGTGC 0.975065 -74 CCTGCTTCCCAAGCAGGAGGTCGCCGGTTC 2 79 1 AAGCAGGAGG 0.992828 -61 ACTCTGGTAAACGGAGGAAAGTT 3 58 1 ACGGAGGAAA 0.974016 -13 AAGTTTTATCAAGGAGGTGGGAAT 6 24 1 AAGGAGGTGG 0.996987 -14 GTATAATAAAAGGCAGGAAAGATAGGAGGT 7 43 1 AGGCAGGAAA 0.91302 -26 GCAGGAAAGATAGGAGGTGATAAA 7 55 1 TAGGAGGTGA 0.985477 -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 0.89398 -118 AGCTACGCCCGCTTTTTATTATTAAATTTTA 2 35 0 GCTTTTATTA 0.969709 -105 CGCCCGCTCCAAATTTTTGTACAATTTTGCT 2 118 1 AATTTTTGTA 0.899228 -22 AAGCCTTATTTTAAATTGATAAT 4 3 1 GCTTATTTTA 0.941853 -28 AATTTATATGATAAAGCTCAA 5 1 1 AATTATATGA 0.88624 -48 GGGAAATTATTTTACAATTTGCCT 5 35 0 AATTATTTTA 0.959687 -14 TCCTTGATAAAACTTCTATTAAATAAAT 6 8 0 AATTCTATTA 0.94507 -30 AAATTATGTCAATTTTTTTTAA 7 2 0 AATTTTTTTA 0.974485 -67 TATCTTTCCTGCCTTTTATTATACAACCTTA 7 36 0 GCTTTTATTA 0.969706 -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 CCTCTGAGCTACGCCCGCTTTTTATTATTA 2 42 0 ACGCCCGCTT 0.990842 -98 CAGAGGTAGAGCACCTGCTTCCCAAGCAGG 2 66 1 GCACCTGCTT 0.960818 -74 GAACCGGCGACCTCCTGCTTGGGAAGCAGG 2 79 0 CCTCCTGCTT 0.961511 -61 AAGCAGGAGGTCGCCGGTTCGAGTCCCGTC 2 89 1 TCGCCGGTTC 0.973308 -51 TCGAGTCCCGTCGCCCGCTCCAAATTTTTG 2 107 1 TCGCCCGCTC 0.99657 -33 AACTTTCCTCCGTTTACCAGAGTAA 3 56 0 TCCTCCGTTT 0.88146 -15 ********** Masking position 9 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 TTATTATTAAATTTTATAATGGTGTTTTAA 2 21 0 ATTTTATAAT 0.883909 -119 AAGCAAAATTGTACAAAAATTTGGAGC 2 123 0 ATTGTACAAA 0.75885 -17 TGATTTTGAAACTTGACAAAAATAAACTCA 3 13 1 ACTTGACAAA 0.982078 -58 CCTTATTTTAAATTGATAATTTTGTGT 4 14 1 AATTGATAAT 0.932837 -17 AATTTATATGATAAAGCTCAAGAAA 5 6 1 ATATGATAAA 0.881978 -43 GGGAAATTATTTTACAATTTGCCTTTCT 5 31 0 ATTTTACAAT 0.811051 -18 ATTCCCACCTCCTTGATAAAACTTCTATTA 6 18 0 CCTTGATAAA 0.901792 -20 TTAAAAAAAATTGACATAATTTCACTAA 7 9 1 AATTGACATA 0.863976 -60 ********** Masking position 6 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 CTTCTTCCTCCTAGTTTAA 1 10 0 CTTCTTCCTC 0.965437 -10 TACCTCTGAGCTACGCCCGCTTTTTATTAT 2 44 0 CTACGCCCGC 0.996247 -96 GGACTCGAACCGGCGACCTCCTGCTTGGGA 2 85 0 CGGCGACCTC 0.993112 -55 GTTCGAGTCCCGTCGCCCGCTCCAAATTTT 2 105 1 CGTCGCCCGC 0.99862 -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