; oligo-analysis  -v 1 -quick -i $RSAT/public_html/tmp/www-data/2025/09/18/peak-motifs.2025-09-18.095753_2025-09-18.095753_7F5dVY/data/sequences/peak-motifs_test_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 -expfreq $RSAT/public_html/tmp/www-data/2025/09/18/peak-motifs.2025-09-18.095753_2025-09-18.095753_7F5dVY/results/oligos_7nt_test_vs_ctrl/peak-motifs_oligos_bg_from_ctrl_7nt-2str-noov.tab -pseudo 0.01 -o $RSAT/public_html/tmp/www-data/2025/09/18/peak-motifs.2025-09-18.095753_2025-09-18.095753_7F5dVY/results/oligos_7nt_test_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_test_vs_ctrl.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/2025/09/18/peak-motifs.2025-09-18.095753_2025-09-18.095753_7F5dVY/data/sequences/peak-motifs_test_purged_ml40_mis3.fasta
; Input format                 	fasta
; Output file                  	$RSAT/public_html/tmp/www-data/2025/09/18/peak-motifs.2025-09-18.095753_2025-09-18.095753_7F5dVY/results/oligos_7nt_test_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_test_vs_ctrl.tab
; Discard overlapping matches
; Counted on both strands
; 	grouped by pairs of reverse complements
; Background model             	exp_file
; Background estimation method 	Frequency file
; Expected frequency file      	$RSAT/public_html/tmp/www-data/2025/09/18/peak-motifs.2025-09-18.095753_2025-09-18.095753_7F5dVY/results/oligos_7nt_test_vs_ctrl/peak-motifs_oligos_bg_from_ctrl_7nt-2str-noov.tab
; Pseudo-frequency             	0.01
; Pseudo-frequency per oligo   	1.220703125e-06
; Sequence type                	DNA
; Nb of sequences              	2996
; Sum of sequence lengths      	602196
; 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      	451923
; total overlapping occurrences	4253
; total non overlapping occ    	447670
; alphabet size                	4
; nb possible oligomers        	8192
; oligomers tested for significance	8191
;
; 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
gaaacta	gaaacta|tagtttc	0.0000740568780	59	33.47	4.2e-05	3.4e-01	0.47	1	0	354
gactctc	gactctc|gagagtc	0.0000676301567	54	30.56	8e-05	6.6e-01	0.18	2	0	324
ctcacaa	ctcacaa|ttgtgag	0.0000997637633	73	45.09	8.1e-05	6.6e-01	0.18	3	0	438
attcatg	attcatg|catgaat	0.0001297551294	90	58.64	8.6e-05	7.0e-01	0.15	4	1	540
; Host name	rsat
; Job started	2025-09-18.095826
; Job done	2025-09-18.095827
; Seconds	0.91
;	user	0.91
;	system	0.02
;	cuser	0.18
;	csystem	0.03
