; oligo-analysis  -v 1 -quick -i $RSAT/public_html/tmp/www-data/2026/02/26/peak-motifs.2026-02-26.200629_2026-02-26.200629_uoww0v/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 100 -return occ,proba,rank -2str -noov -seqtype dna -l 8 -markov 5 -pseudo 0.01 -o $RSAT/public_html/tmp/www-data/2026/02/26/peak-motifs.2026-02-26.200629_2026-02-26.200629_uoww0v/results/oligos_8nt_mkv5/peak-motifs_oligos-2str-noov_8nt_mkv5.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              	8
; Input file                   	$RSAT/public_html/tmp/www-data/2026/02/26/peak-motifs.2026-02-26.200629_2026-02-26.200629_uoww0v/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta
; Input format                 	fasta
; Output file                  	$RSAT/public_html/tmp/www-data/2026/02/26/peak-motifs.2026-02-26.200629_2026-02-26.200629_uoww0v/results/oligos_8nt_mkv5/peak-motifs_oligos-2str-noov_8nt_mkv5.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           	5
; Pseudo-frequency             	0.01
; Pseudo-frequency per oligo   	3.03988326848249e-07
; Sequence type                	DNA
; Nb of sequences              	226
; Sum of sequence lengths      	226000
; 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      	193970
; total overlapping occurrences	910
; total non overlapping occ    	193060
; alphabet size                	4
; nb possible oligomers        	32896
; oligomers tested for significance	26923
;
; column headers
;	1	seq            	oligomer sequence
;	2	id             	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	id	exp_freq	occ	exp_occ	occ_P	occ_E	occ_sig	rank	ovl_occ	forbocc
cattttac	cattttac|gtaaaatg	0.0000645284157	30	12.52	1.9e-05	5.2e-01	0.29	1	0	210
ggagtgca	ggagtgca|tgcactcc	0.0000369887937	21	7.17	2.1e-05	5.6e-01	0.26	2	0	147
cactccag	cactccag|ctggagtg	0.0000629201607	29	12.20	3e-05	8.2e-01	0.09	3	0	203
; Host name	rsat
; Job started	2026-02-26.200648
; Job done	2026-02-26.200652
; Seconds	3.96
;	user	3.96
;	system	0.12
;	cuser	0.24
;	csystem	0.04
