; oligo-analysis -v 1 -quick -i $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/data/sequences/peak-motifs_test_maxlen1000_purged_ml30_mis0.fasta -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 100 -return occ,proba,rank -2str -noov -seqtype dna -l 6 -markov 3 -pseudo 0.01 -o $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3.tab ; Citation: van Helden et al. (1998). J Mol Biol 281(5), 827-42. ; Program version 1.169 ; Quick counting mode ; Detection of over-represented words (right-tail test) ; Oligomer length 6 ; Input file $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/data/sequences/peak-motifs_test_maxlen1000_purged_ml30_mis0.fasta ; Input format fasta ; Output file $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/oligos_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3.tab ; Discard overlapping matches ; Counted on both strands ; grouped by pairs of reverse complements ; Background model Markov ; Background estimation method Markov model estimated from input sequences ; Markov chain order 3 ; Pseudo-frequency 0.01 ; Pseudo-frequency per oligo 4.80769230769231e-06 ; Sequence type DNA ; Nb of sequences 109 ; Sum of sequence lengths 108923 ; discarded residues NA (quick mode) (other letters than ACGT) ; discarded occurrences NA (quick mode) (contain discarded residues) ; nb possible positions NA (quick mode) ; total oligo occurrences 107326 ; total overlapping occurrences 721 ; total non overlapping occ 106605 ; alphabet size 4 ; nb possible oligomers 2080 ; oligomers tested for significance 2077 ; ; column headers ; 1 seq oligomer sequence ; 2 identifier oligomer identifier ; 3 exp_freq expected relative frequency ; 4 occ observed occurrences ; 5 exp_occ expected occurrences ; 6 occ_P occurrence probability (binomial) ; 7 occ_E E-value for occurrences (binomial) ; 8 occ_sig occurrence significance (binomial) ; 9 rank rank ; 10 ovl_occ number of overlapping occurrences (discarded from the count) ; 11 forbocc forbidden positions (to avoid self-overlap) #seq identifier exp_freq occ exp_occ occ_P occ_E occ_sig rank ovl_occ forbocc aagaga aagaga|tctctt 0.0004779345800 82 51.29 4.7e-05 9.9e-02 1.01 1 0 410 ctcttc ctcttc|gaagag 0.0004776162891 81 51.26 7.6e-05 1.6e-01 0.80 2 0 405 atcgac atcgac|gtcgat 0.0004342487485 75 46.61 7.9e-05 1.6e-01 0.79 3 0 375 acaaaa acaaaa|ttttgt 0.0011063622948 162 118.74 9.4e-05 2.0e-01 0.71 4 0 810 gctaaa gctaaa|tttagc 0.0005965451160 96 64.02 0.00011 2.4e-01 0.62 5 0 480 ggtaga ggtaga|tctacc 0.0003281869297 59 35.22 0.00016 3.2e-01 0.49 6 0 295 ggcaaa ggcaaa|tttgcc 0.0010448238142 152 112.14 0.00020 4.1e-01 0.39 7 0 760 agagat agagat|atctct 0.0004166579051 70 44.72 0.00028 5.9e-01 0.23 8 2 350 tcggca tcggca|tgccga 0.0005637646404 89 60.51 0.00036 7.4e-01 0.13 9 0 445 ; Host name biow ; Job started 2014-09-05.202713 ; Job done 2014-09-05.202714 ; Seconds 0.8 ; user 0.8 ; system 0.02 ; cuser 0.25 ; csystem 0.02