AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i193_dna_polymerase_aquae_reg_300.orf -o193_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 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 0.975618 -159 TAAAAAAATGTTTTAATTTATTTTAAAGAT 1 132 0 TTTTAATTTA 0.974188 -37 TAAAACATTTTTTTACTTTCGGAGGTGGAT 1 147 1 TTTTACTTTC 0.959187 -22 AATAGAAAAATATTAATATAATC 2 4 0 TATTAATATA 0.705261 -60 TATATTAATATTTTTCTATTCGCATTATTT 2 14 1 TTTTTCTATT 0.896341 -50 TCCTTTAGGGTTTTTCATAAAAATAATGCG 2 34 0 TTTTTCATAA 0.881031 -30 CCTTCCCCTCTTTTTCATAAATCTTTTTTC 3 17 1 TTTTTCATAA 0.881031 -42 TCATAAATCTTTTTTCTTTTTCAAAGGAGG 3 31 1 TTTTTCTTTT 0.950246 -28 AGCTTTTAATTTATATT 4 5 0 TTTTAATTTA 0.974188 -13 CAAGTTTTAATATAAAGACTTA 5 5 1 TTTTAATATA 0.944325 -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 0.994028 -149 TTCCAAACTTCTTCCTTTGGGTGTTGTAAA 1 92 1 CTTCCTTTGG 0.989306 -77 ACATCCACCTCCGAAAGTAAAAAA 1 155 0 CCACCTCCGA 0.952065 -14 AGCACTTACCTCCTTTAGGGTTTTTCAT 2 46 0 CCTCCTTTAG 0.991349 -18 TTTTCCTTCCCCTCTTTTTCATAAATCTTT 3 13 1 CCTCTTTTTC 0.935298 -46 GGCTCAGACCTCCTTTGAAAAAGAAAAA 3 41 0 CCTCCTTTGA 0.996248 -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 CTGGTTTTACATTACTGAGAATT 1 4 0 ATTACTGAGA 0.984354 -165 TTATTCTTCTAATACTGGGAGCTATCGGAC 1 43 1 AATACTGGGA 0.993956 -126 TTTTCATAAAAATAATGCGAATAGAAAAAT 2 23 0 AATAATGCGA 0.983683 -41 ********** Masking position 4 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 AAAATGTTTTAATTTATTTTAAAGATTAGA 1 128 0 AATTTATTTT 0.948286 -41 ATAAATTAAAACATTTTTTTACTTTCGGAG 1 141 1 ACATTTTTTT 0.871852 -28 GATTATATTAATATTTTTCTATTCG 2 6 1 TATTAATATT 0.717572 -58 TTTTCTATTCGCATTATTTTTATGAAAAAC 2 25 1 GCATTATTTT 0.875862 -39 CTTTTTCATAAATCTTTTTTCTTTTTCAAA 3 26 1 AATCTTTTTT 0.796279 -33 AGCTTTTAATTTATATT 4 1 0 AATTTATATT 0.916506 -17 TAAGTCTTTATATTAAAACTTG 5 9 0 TCTTTATATT 0.936728 -14 ********** Masking position 7 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