; oligo-analysis  -v 1 -quick -i $RSAT/public_html/tmp/www-data/2025/04/03/peak-motifs.2025-04-03.124448_2025-04-03.124448_OhsrJC/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 2 -pseudo 0.01 -o $RSAT/public_html/tmp/www-data/2025/04/03/peak-motifs.2025-04-03.124448_2025-04-03.124448_OhsrJC/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2.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/2025/04/03/peak-motifs.2025-04-03.124448_2025-04-03.124448_OhsrJC/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta
; Input format                 	fasta
; Output file                  	$RSAT/public_html/tmp/www-data/2025/04/03/peak-motifs.2025-04-03.124448_2025-04-03.124448_OhsrJC/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2.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   	4.80769230769231e-06
; Sequence type                	DNA
; Nb of sequences              	150
; Sum of sequence lengths      	15000
; 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      	9898
; total overlapping occurrences	106
; total non overlapping occ    	9792
; alphabet size                	4
; nb possible oligomers        	2080
; oligomers tested for significance	2013
;
; 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
agtcag	agtcag|ctgact	0.0007622559546	30	7.54	5.5e-10	1.1e-06	5.96	1	0	150
gagtca	gagtca|tgactc	0.0005399316546	25	5.34	6e-10	1.2e-06	5.92	2	0	125
gactaa	gactaa|ttagtc	0.0004931353446	22	4.88	1.2e-08	2.4e-05	4.62	3	0	110
tagtca	tagtca|tgacta	0.0005396287146	23	5.34	1.3e-08	2.6e-05	4.59	4	0	115
gctgac	gctgac|gtcagc	0.0008274375546	29	8.19	1.3e-08	2.6e-05	4.59	5	0	145
gcttac	gcttac|gtaagc	0.0006782009946	25	6.71	4.9e-08	9.8e-05	4.01	6	1	125
gactca	gactca|tgagtc	0.0005435629746	21	5.38	2.6e-07	5.3e-04	3.28	7	0	105
tactaa	tactaa|ttagta	0.0004537184946	19	4.49	2.9e-07	5.8e-04	3.23	8	0	95
agtaag	agtaag|cttact	0.0006305701146	22	6.24	7.3e-07	1.5e-03	2.83	9	0	110
tcagca	tcagca|tgctga	0.0008988452646	27	8.90	7.7e-07	1.5e-03	2.81	10	0	135
gatgac	gatgac|gtcatc	0.0005341916346	20	5.29	8e-07	1.6e-03	2.79	11	0	100
tagtaa	tagtaa|ttacta	0.0004485368346	18	4.44	1.1e-06	2.1e-03	2.67	12	0	90
taagca	taagca|tgctta	0.0008610262746	25	8.52	3.4e-06	6.9e-03	2.16	13	0	125
actaat	actaat|attagt	0.0004499901546	17	4.45	4.6e-06	9.2e-03	2.03	14	0	85
actaag	actaag|cttagt	0.0005412394446	18	5.36	1.3e-05	2.7e-02	1.57	15	0	90
agtcat	agtcat|atgact	0.0006171665046	19	6.11	2.2e-05	4.5e-02	1.35	16	0	95
cgtacg	cgtacg|cgtacg	0.0000879701673	7	0.87	3.5e-05	7.1e-02	1.15	17	0	35
ccgtac	ccgtac|gtacgg	0.0002825276946	12	2.80	3.7e-05	7.4e-02	1.13	18	0	60
atttag	atttag|ctaaat	0.0005523620946	17	5.47	5.9e-05	1.2e-01	0.93	19	0	85
cggcca	cggcca|tggccg	0.0005622017046	17	5.56	7.2e-05	1.5e-01	0.84	20	0	85
cacgtg	cacgtg|cacgtg	0.0001098358023	7	1.09	0.00014	2.8e-01	0.56	21	0	35
actcag	actcag|ctgagt	0.0006035797446	17	5.97	0.00017	3.3e-01	0.48	22	0	85
ctaagc	ctaagc|gcttag	0.0008033013546	20	7.95	0.00023	4.7e-01	0.33	23	0	100
aggcgg	aggcgg|ccgcct	0.0004558212546	14	4.51	0.00026	5.2e-01	0.29	24	0	70
tagata	tagata|tatcta	0.0005804048346	16	5.74	0.00032	6.4e-01	0.19	25	0	80
; Host name	rsat
; Job started	2025-04-03.124455
; Job done	2025-04-03.124455
; Seconds	0.33
;	user	0.33
;	system	0.02
;	cuser	0.09
;	csystem	0.01
