; oligo-analysis  -v 1 -quick -i $RSAT/public_html/tmp/www-data/2025/05/26/peak-motifs.2025-05-26.211230_2025-05-26.211230_ZHQlvw/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/2025/05/26/peak-motifs.2025-05-26.211230_2025-05-26.211230_ZHQlvw/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/2025/05/26/peak-motifs.2025-05-26.211230_2025-05-26.211230_ZHQlvw/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta
; Input format                 	fasta
; Output file                  	$RSAT/public_html/tmp/www-data/2025/05/26/peak-motifs.2025-05-26.211230_2025-05-26.211230_ZHQlvw/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              	705
; Sum of sequence lengths      	157204
; 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      	38184
; total overlapping occurrences	570
; total non overlapping occ    	37614
; alphabet size                	4
; nb possible oligomers        	2080
; oligomers tested for significance	2032
;
; 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
aaaagg	aaaagg|cctttt	0.0026372238846	177	100.70	3.8e-12	7.8e-09	8.11	1	0	885
aaaggc	aaaggc|gccttt	0.0013982963046	94	53.39	3.2e-07	6.4e-04	3.19	2	0	470
aacaaa	aacaaa|tttgtt	0.0019810360446	123	75.64	3.5e-07	7.1e-04	3.15	3	7	615
gcaaca	gcaaca|tgttgc	0.0007742111946	58	29.56	2.4e-06	4.9e-03	2.31	4	0	290
caacaa	caacaa|ttgttg	0.0011102439246	74	42.39	6.9e-06	1.4e-02	1.86	5	1	370
aagcaa	aagcaa|ttgctt	0.0010183521246	67	38.88	2.6e-05	5.3e-02	1.27	6	0	335
aagaaa	aagaaa|tttctt	0.0023557767846	131	89.95	2.9e-05	5.8e-02	1.24	7	5	655
agcaac	agcaac|gttgct	0.0006440261946	47	24.59	3.8e-05	7.6e-02	1.12	8	0	235
gagcaa	gagcaa|ttgctc	0.0009558059046	62	36.50	7.5e-05	1.5e-01	0.82	9	0	310
acaaaa	acaaaa|ttttgt	0.0024602910846	133	93.94	8.3e-05	1.7e-01	0.77	10	3	665
ctcagc	ctcagc|gctgag	0.0006135183546	43	23.43	0.00018	3.7e-01	0.43	11	0	215
aaggca	aaggca|tgcctt	0.0012006220146	72	45.84	0.00021	4.3e-01	0.37	12	0	360
ataaat	ataaat|atttat	0.0009354406146	59	35.72	0.00022	4.5e-01	0.35	13	2	295
agagca	agagca|tgctct	0.0011016517146	67	42.07	0.00024	4.8e-01	0.32	14	0	335
ctaccc	ctaccc|gggtag	0.0003139245546	26	11.99	0.00030	6.1e-01	0.21	15	0	130
ggctga	ggctga|tcagcc	0.0005598554046	39	21.38	0.00039	8.0e-01	0.10	16	0	195
caagaa	caagaa|ttcttg	0.0011257097046	67	42.98	0.00041	8.4e-01	0.07	17	0	335
; Host name	rsat
; Job started	2025-05-26.211238
; Job done	2025-05-26.211238
; Seconds	0.38
;	user	0.38
;	system	0.04
;	cuser	0.12
;	csystem	0.01
