; 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 6 -markov 3 -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_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3.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/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_6nt_mkv3/peak-motifs_oligos-2str-noov_6nt_mkv3.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           	3
; Pseudo-frequency             	0.01
; Pseudo-frequency per oligo   	4.80769230769231e-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      	194731
; total overlapping occurrences	2254
; total non overlapping occ    	192477
; alphabet size                	4
; nb possible oligomers        	2080
; oligomers tested for significance	2077
;
; 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
aaataa	aaataa|ttattt	0.0020023071846	509	389.91	4.5e-09	9.3e-06	5.03	1	21	2545
aagcaa	aagcaa|ttgctt	0.0007870109046	221	153.26	1.6e-07	3.4e-04	3.47	2	2	1105
aacaaa	aacaaa|tttgtt	0.0013651233846	353	265.83	2e-07	4.1e-04	3.39	3	15	1765
ccaggc	ccaggc|gcctgg	0.0006011453346	171	117.06	1.8e-06	3.7e-03	2.43	4	3	855
aataaa	aataaa|tttatt	0.0019591857546	473	381.51	3.4e-06	7.0e-03	2.16	5	21	2365
aatgta	aatgta|tacatt	0.0008000214846	214	155.79	5.7e-06	1.2e-02	1.93	6	2	1070
cctccc	cctccc|gggagg	0.0006744013746	184	131.33	8.2e-06	1.7e-02	1.77	7	7	920
cactgc	cactgc|gcagtg	0.0005710077546	158	111.19	1.7e-05	3.5e-02	1.45	8	0	790
attcaa	attcaa|ttgaat	0.0008378434446	218	163.15	2.4e-05	5.1e-02	1.29	9	1	1090
tacata	tacata|tatgta	0.0005304365646	145	103.29	6.2e-05	1.3e-01	0.89	10	5	725
atacat	atacat|atgtat	0.0006941528646	181	135.17	9.9e-05	2.1e-01	0.69	11	5	905
acccag	acccag|ctgggt	0.0005930867346	158	115.49	0.00010	2.1e-01	0.68	12	0	790
gaaata	gaaata|tatttc	0.0012017238846	293	234.01	0.00011	2.3e-01	0.64	13	0	1465
aaagaa	aaagaa|ttcttt	0.0018324548646	427	356.84	0.00017	3.5e-01	0.46	14	10	2135
atttta	atttta|taaaat	0.0017182712346	402	334.60	0.00019	3.9e-01	0.41	15	12	2010
aaaata	aaaata|tatttt	0.0022013862846	502	428.68	0.00030	6.1e-01	0.21	16	9	2510
aaacaa	aaacaa|ttgttt	0.0013468133346	319	262.27	0.00038	7.8e-01	0.11	17	22	1595
aattac	aattac|gtaatt	0.0006472981446	166	126.05	0.00038	7.9e-01	0.10	18	4	830
cccagg	cccagg|cctggg	0.0007119788046	180	138.64	0.00043	8.9e-01	0.05	19	0	900
; Host name	rsat
; Job started	2026-02-26.200637
; Job done	2026-02-26.200638
; Seconds	0.37
;	user	0.37
;	system	0.02
;	cuser	0.11
;	csystem	0.02
