; 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