; oligo-analysis  -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/06/17/tmp_sequence_2026-06-17.142701_7fH52a.fasta.purged -format fasta -lth occ_sig 0 -uth rank 50 -return occ,proba,rank -2str -noov -quick_if_possible -seqtype dna -markov 2 -pseudo 0.01 -l 5 -o $RSAT/public_html/tmp/www-data/2026/06/17/oligo-analysis_2026-06-17.142701_4DoJCc_5nt.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              	5
; Input file                   	$RSAT/public_html/tmp/www-data/2026/06/17/tmp_sequence_2026-06-17.142701_7fH52a.fasta.purged
; Input format                 	fasta
; Output file                  	$RSAT/public_html/tmp/www-data/2026/06/17/oligo-analysis_2026-06-17.142701_4DoJCc_5nt.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   	1.953125e-05
; Sequence type                	DNA
; Nb of sequences              	1
; Sum of sequence lengths      	20509
; 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      	20505
; total overlapping occurrences	523
; total non overlapping occ    	19982
; alphabet size                	4
; nb possible oligomers        	512
; oligomers tested for significance	510
; Sequences:
;	3-UTseq836-UTL128-SPB	20509
;
; 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
agatg	agatg|catct	0.0023656644700	80	48.51	2.1e-05	1.1e-02	1.97	1	0	320
cttca	cttca|tgaag	0.0037644721000	114	77.19	5.1e-05	2.6e-02	1.58	2	0	456
ggaga	ggaga|tctcc	0.0014773909300	53	30.29	0.00012	5.9e-02	1.23	3	0	212
cttta	cttta|taaag	0.0043371475000	124	88.93	0.00025	1.3e-01	0.90	4	1	496
cgata	cgata|tatcg	0.0012630608800	44	25.90	0.00073	3.7e-01	0.43	5	0	176
gttga	gttga|tcaac	0.0025777690000	77	52.86	0.00106	5.4e-01	0.27	6	0	308
ctccc	ctccc|gggag	0.0009654272800	35	19.80	0.00125	6.4e-01	0.19	7	1	140
; Host name	rsat
; Job started	2026-06-17.142701
; Job done	2026-06-17.142701
; Seconds	0.21
;	user	0.21
;	system	0.01
;	cuser	0.1
;	csystem	0.01