; 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 6 -expfreq $RSAT/public_html/tmp/www-data/2025/09/18/peak-motifs.2025-09-18.095753_2025-09-18.095753_7F5dVY/results/oligos_6nt_test_vs_ctrl/peak-motifs_oligos_bg_from_ctrl_6nt-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_6nt_test_vs_ctrl/peak-motifs_oligos-2str-noov_6nt_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              	6
; 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_6nt_test_vs_ctrl/peak-motifs_oligos-2str-noov_6nt_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_6nt_test_vs_ctrl/peak-motifs_oligos_bg_from_ctrl_6nt-2str-noov.tab
; Pseudo-frequency             	0.01
; Pseudo-frequency per oligo   	4.80769230769231e-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      	454865
; total overlapping occurrences	4845
; total non overlapping occ    	450020
; alphabet size                	4
; nb possible oligomers        	2080
; oligomers tested for significance	2080
;
; 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
atggag	atggag|ctccat	0.0007922194229	428	360.35	0.00029	5.9e-01	0.23	1	0	2140
; Host name	rsat
; Job started	2025-09-18.095824
; Job done	2025-09-18.095824
; Seconds	0.41
;	user	0.41
;	system	0.01
;	cuser	0.17
;	csystem	0.03
