; 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 7 -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_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_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              	7
; 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_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_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   	1.220703125e-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      	9765
; total overlapping occurrences	89
; total non overlapping occ    	9676
; alphabet size                	4
; nb possible oligomers        	8192
; oligomers tested for significance	5206
;
; 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
tgactaa	tgactaa|ttagtca	0.0001453173152	20	1.42	1.1e-16	6.0e-13	12.22	1	0	120
tgactca	tgactca|tgagtca	0.0001599636723	20	1.56	6.8e-16	3.6e-12	11.45	2	0	120
agtcagc	agtcagc|gctgact	0.0002377063923	22	2.32	1.1e-14	5.5e-11	10.26	3	0	132
agtcatc	agtcatc|gatgact	0.0001535140202	17	1.50	6.6e-13	3.4e-09	8.46	4	0	102
agtaagc	agtaagc|gcttact	0.0001955843672	18	1.91	2.9e-12	1.5e-08	7.82	5	0	108
actcagc	actcagc|gctgagt	0.0001888846412	16	1.84	1.5e-10	7.8e-07	6.11	6	0	96
cttagtc	cttagtc|gactaag	0.0001505158052	13	1.47	6.1e-09	3.2e-05	4.50	7	0	78
ctgactc	ctgactc|gagtcag	0.0001647400263	13	1.61	1.7e-08	9.1e-05	4.04	8	0	78
gtcagca	gtcagca|tgctgac	0.0002136799833	14	2.09	4.9e-08	2.5e-04	3.60	9	0	84
ttactaa	ttactaa|ttagtaa	0.0001212208143	11	1.18	5.4e-08	2.8e-04	3.55	10	0	66
ctgagtc	ctgagtc|gactcag	0.0001665965733	12	1.63	1.6e-07	8.3e-04	3.08	11	0	72
actaagc	actaagc|gcttagt	0.0001687098273	12	1.65	1.8e-07	9.5e-04	3.02	12	0	72
cttacta	cttacta|tagtaag	0.0001372883162	11	1.34	1.8e-07	9.6e-04	3.02	13	0	66
atgacta	atgacta|tagtcat	0.0001337033282	10	1.31	1.2e-06	6.3e-03	2.20	14	0	60
ctatcta	ctatcta|tagatag	0.0001383054422	10	1.35	1.6e-06	8.5e-03	2.07	15	0	60
gtaagca	gtaagca|tgcttac	0.0001734274743	11	1.69	1.8e-06	9.1e-03	2.04	16	0	66
attagta	attagta|tactaat	0.0001149149102	9	1.12	2.8e-06	1.5e-02	1.83	17	0	54
ctaaata	ctaaata|tatttag	0.0001532764202	9	1.50	2.7e-05	1.4e-01	0.85	18	0	54
ctcgtac	ctcgtac|gtacgag	0.0000608480402	6	0.59	3.7e-05	1.9e-01	0.72	19	0	36
atgactc	atgactc|gagtcat	0.0001336962993	8	1.31	6.6e-05	3.4e-01	0.46	20	0	48
cgtacga	cgtacga|tcgtacg	0.0000433686002	5	0.42	8e-05	4.2e-01	0.38	21	0	30
gcacaaa	gcacaaa|tttgtgc	0.0001069821392	7	1.04	0.00011	5.7e-01	0.25	22	0	42
agaagga	agaagga|tccttct	0.0001461298083	8	1.43	0.00012	6.3e-01	0.20	23	0	48
actaatc	actaatc|gattagt	0.0001120161903	7	1.09	0.00014	7.5e-01	0.13	24	0	42
ccgtacg	ccgtacg|cgtacgg	0.0000512282103	5	0.50	0.00017	9.0e-01	0.05	25	0	30
actaaat	actaaat|atttagt	0.0001157560143	7	1.13	0.00018	9.1e-01	0.04	26	0	42
gccgtac	gccgtac|gtacggc	0.0000823467813	6	0.80	0.00019	9.9e-01	0.01	27	0	36
; Host name	rsat
; Job started	2025-04-03.124459
; Job done	2025-04-03.124500
; Seconds	0.91
;	user	0.91
;	system	0.02
;	cuser	0.09
;	csystem	0.03
