; oligo-analysis  -v 1 -quick -i $RSAT/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/data/sequences/peak-motifs_test_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/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/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/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/data/sequences/peak-motifs_test_purged_ml40_mis3.fasta
; Input format                 	fasta
; Output file                  	$RSAT/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/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              	23
; Sum of sequence lengths      	10099
; 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      	6558
; total overlapping occurrences	87
; total non overlapping occ    	6471
; alphabet size                	4
; nb possible oligomers        	2080
; oligomers tested for significance	1850
; Sequences:
;	NZ_CP037899.1:7618-7818	200
;	NZ_CP037899.1:230205-230716	511
;	NZ_CP037899.1:644474-644930	456
;	NZ_CP037899.1:644474-644930	456
;	NZ_CP037899.1:645307-645628	321
;	NZ_CP037899.1:949092-950181	1089
;	NZ_CP037899.1:949092-950181	1089
;	NZ_CP037899.1:949092-950181	1089
;	NZ_CP037899.1:953361-953582	221
;	NZ_CP037899.1:1134619-1134882	263
;	NZ_CP037899.1:1164899-1165284	385
;	NZ_CP037899.1:1164899-1165284	385
;	NZ_CP037899.1:1277211-1277456	245
;	NZ_CP037899.1:1329900-1330336	436
;	NZ_CP037899.1:1329900-1330336	436
;	NZ_CP037899.1:1343835-1344167	332
;	NZ_CP037899.1:1508893-1509246	353
;	NZ_CP037899.1:1530412-1530753	341
;	NZ_CP037899.1:1640064-1640409	345
;	NZ_CP037899.1:1679730-1679930	200
;	NZ_CP037899.1:1681794-1682216	422
;	NZ_CP037899.1:2093304-2093628	324
;	NZ_CP037899.1:2135546-2135746	200
;
; 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
aaagaa	aaagaa|ttcttt	0.0019603747446	27	12.86	0.00038	7.0e-01	0.16	1	0	135
; Host name	rsat
; Job started	2025-03-02.091151
; Job done	2025-03-02.091151
; Seconds	0.29
;	user	0.29
;	system	0.03
;	cuser	0.08
;	csystem	0.01
