; 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 7 -markov 4 -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_7nt_mkv4/peak-motifs_oligos-2str-noov_7nt_mkv4.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/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_7nt_mkv4/peak-motifs_oligos-2str-noov_7nt_mkv4.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           	4
; Pseudo-frequency             	0.01
; Pseudo-frequency per oligo   	1.220703125e-06
; 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      	194324
; total overlapping occurrences	1912
; total non overlapping occ    	192412
; alphabet size                	4
; nb possible oligomers        	8192
; oligomers tested for significance	7937
;
; 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
ccactgc	ccactgc|gcagtgg	0.0001670465283	61	32.46	5.1e-06	4.0e-02	1.40	1	0	366
aatgtat	aatgtat|atacatt	0.0002843924163	86	55.26	7.7e-05	6.1e-01	0.21	2	0	516
cactgca	cactgca|tgcagtg	0.0001960893662	64	38.10	8e-05	6.3e-01	0.20	3	0	384
gagtgca	gagtgca|tgcactc	0.0001069733282	40	20.79	0.00012	9.3e-01	0.03	4	0	240
; Host name	rsat
; Job started	2026-02-26.200644
; Job done	2026-02-26.200645
; Seconds	1.08
;	user	1.08
;	system	0.04
;	cuser	0.15
;	csystem	0.01
