; oligo-analysis -v 1 -quick -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/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 7 -markov 2 -pseudo 0.01 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2.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 7 ; Input file $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000_purged_ml30_mis0.fasta ; Input format fasta ; Output file $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2.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 2 ; Pseudo-frequency 0.01 ; Pseudo-frequency per oligo 1.220703125e-06 ; Sequence type DNA ; Nb of sequences 109 ; Sum of sequence lengths 11009 ; 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 10355 ; total overlapping occurrences 78 ; total non overlapping occ 10277 ; alphabet size 4 ; nb possible oligomers 8192 ; oligomers tested for significance 5144 ; ; 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 aggagta aggagta|tactcct 0.0000710612225 7 0.74 1.2e-05 6.3e-02 1.20 1 0 42 attgatc attgatc|gatcaat 0.0003624499597 14 3.75 3.9e-05 2.0e-01 0.70 2 0 84 attcacc attcacc|ggtgaat 0.0001828809779 9 1.89 0.00016 8.2e-01 0.09 3 0 54 agatcaa agatcaa|ttgatct 0.0003214555587 12 3.33 0.00018 9.5e-01 0.02 4 0 72 ; Host name biow ; Job started 2014-09-06.011306 ; Job done 2014-09-06.011307 ; Seconds 1.46 ; user 1.46 ; system 0.03 ; cuser 0.24 ; csystem 0.02