AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i193_dna_polymerase_aquae_reg_100.orf -o193_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 RAA00570 168 Aquifex_aeolicus #2 RAA00572 63 Aquifex_aeolicus #3 RAA00573 58 Aquifex_aeolicus #4 RAA01159 17 Aquifex_aeolicus #5 RAA01092 22 Aquifex_aeolicus Motif number 1 CCTCTTCTGGTTTTACATTACTGAGAATT 1 10 0 TTTTACATTA 0.97893 -159 TAAAAAAATGTTTTAATTTATTTTAAAGAT 1 132 0 TTTTAATTTA 0.977696 -37 TAAAACATTTTTTTACTTTCGGAGGTGGAT 1 147 1 TTTTACTTTC 0.964666 -22 AATAGAAAAATATTAATATAATC 2 4 0 TATTAATATA 0.735114 -60 TATATTAATATTTTTCTATTCGCATTATTT 2 14 1 TTTTTCTATT 0.909457 -50 TCCTTTAGGGTTTTTCATAAAAATAATGCG 2 34 0 TTTTTCATAA 0.895054 -30 CCTTCCCCTCTTTTTCATAAATCTTTTTTC 3 17 1 TTTTTCATAA 0.895054 -42 TCATAAATCTTTTTTCTTTTTCAAAGGAGG 3 31 1 TTTTTCTTTT 0.956871 -28 AGCTTTTAATTTATATT 4 5 0 TTTTAATTTA 0.977696 -13 CAAGTTTTAATATAAAGACTTA 5 5 1 TTTTAATATA 0.951573 -18 ********** Masking position 4 Map Score: 14.4722 Number of sites scoring better than the average of aligned sites = 886 Number in coding regions = 801 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 2 AGAATAAAAGCCTCTTCTGGTTTTACATTA 1 20 0 CCTCTTCTGG 0.993456 -149 TTCCAAACTTCTTCCTTTGGGTGTTGTAAA 1 92 1 CTTCCTTTGG 0.988275 -77 ACATCCACCTCCGAAAGTAAAAAA 1 155 0 CCACCTCCGA 0.947626 -14 AGCACTTACCTCCTTTAGGGTTTTTCAT 2 46 0 CCTCCTTTAG 0.990513 -18 TTTTCCTTCCCCTCTTTTTCATAAATCTTT 3 13 1 CCTCTTTTTC 0.929421 -46 GGCTCAGACCTCCTTTGAAAAAGAAAAA 3 41 0 CCTCCTTTGA 0.995883 -18 ********** Masking position 6 Map Score: 7.75792 Number of sites scoring better than the average of aligned sites = 357 Number in coding regions = 320 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 3 AATTCTCAGTAATGTAAAACCAG 1 4 1 TCTCAGTAAT 0.982878 -165 GTCCGATAGCTCCCAGTATTAGAAGAATAA 1 43 0 TCCCAGTATT 0.993379 -126 ATTTTTCTATTCGCATTATTTTTATGAAAA 2 23 1 TCGCATTATT 0.982144 -41 ********** Masking position 5 Map Score: 0.630999 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 17 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 4 TAGAAGAATAAAAGCCTCTTCTGGTTTTAC 1 24 0 AAAGCCTCTT 0.875443 -145 GAAGTTTGGAATAACCTTTTGTGACGTAAA 1 73 0 ATAACCTTTT 0.959767 -96 TTGGGTGTTGTAAACCTATATCTAATCTTT 1 108 1 TAAACCTATA 0.870343 -61 AAACCTATATCTAATCTTTAAAATAAATTA 1 119 1 CTAATCTTTA 0.851932 -50 AAAATAAATTAAAACATTTTTTTACTTTCG 1 138 1 AAAACATTTT 0.636 -31 GATTATATTAATATTTTTCTATTCGCA 2 8 1 TTAATATTTT 0.739337 -56 CTCTTTTTCATAAATCTTTTTTCTTTTTCA 3 24 1 TAAATCTTTT 0.805118 -35 TAAGTCTTTATATTAAAACT 5 13 0 TAAGTCTTTA 0.909859 -10 ********** Masking position 3 Map Score: 4.07725 Number of sites scoring better than the average of aligned sites = 1529 Number in coding regions = 1423 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 5 TCTAATCTTTAAAATAAATTAAAACATTTT 1 128 1 AAAATAAATT 0.947627 -41 CTCCGAAAGTAAAAAAATGTTTTAATTTAT 1 141 0 AAAAAAATGT 0.866279 -28 CGAATAGAAAAATATTAATATAATC 2 6 0 AATATTAATA 0.707558 -58 GTTTTTCATAAAAATAATGCGAATAGAAAA 2 25 0 AAAATAATGC 0.870422 -39 TTTGAAAAAGAAAAAAGATTTATGAAAAAG 3 26 0 AAAAAAGATT 0.788485 -33 AATATAAATTAAAAGCT 4 1 1 AATATAAATT 0.916407 -17 CAAGTTTTAATATAAAGACTTA 5 9 1 AATATAAAGA 0.933759 -14 ********** Masking position 4 Map Score: 2.40512 Number of sites scoring better than the average of aligned sites = 286 Number in coding regions = 218 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 6 ********** No masking Map Score: 7.69818e-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: 7.69818e-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: 7.69818e-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