; 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 7 -markov 4 -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_7nt_mkv4/peak-motifs_oligos-2str-noov_7nt_mkv4.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/2025/05/26/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_7nt_mkv4/peak-motifs_oligos-2str-noov_7nt_mkv4.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           	4
; Pseudo-frequency             	0.01
; Pseudo-frequency per oligo   	1.220703125e-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      	38002
; total overlapping occurrences	458
; total non overlapping occ    	37544
; alphabet size                	4
; nb possible oligomers        	8192
; oligomers tested for significance	6772
;
; 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
aaaaagg	aaaaagg|ccttttt	0.0016109676663	114	61.22	1.1e-09	7.1e-06	5.15	1	0	684
aaaggca	aaaggca|tgccttt	0.0007020328263	58	26.68	1e-07	6.9e-04	3.16	2	0	348
aaaaggc	aaaaggc|gcctttt	0.0008766510062	67	33.31	1.8e-07	1.3e-03	2.90	3	0	402
caacaaa	caacaaa|tttgttg	0.0007293281162	58	27.72	3.4e-07	2.3e-03	2.63	4	0	348
aacaaaa	aacaaaa|ttttgtt	0.0012296572863	84	46.73	5.8e-07	3.9e-03	2.41	5	3	504
actaaaa	actaaaa|ttttagt	0.0004321370463	40	16.42	6.1e-07	4.2e-03	2.38	6	0	240
gcaacaa	gcaacaa|ttgttgc	0.0004863969662	42	18.48	1.8e-06	1.2e-02	1.90	7	0	252
agcaaca	agcaaca|tgttgct	0.0005397252962	41	20.51	4.4e-05	3.0e-01	0.53	8	0	246
tagataa	tagataa|ttatcta	0.0001549553612	17	5.89	0.00014	9.5e-01	0.02	9	0	102
; Host name	rsat
; Job started	2025-05-26.211242
; Job done	2025-05-26.211243
; Seconds	0.89
;	user	0.89
;	system	0.04
;	cuser	0.12
;	csystem	0.01
