; matrix-scan  -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/07/02/matrix-scan_2026-07-02.183507_CYO2Cy.matrix -pseudo 1 -decimals 1 -2str -origin end -bginput -markov 1 -bg_pseudo 0.01 -return limits -return sites -return pval -return rank -lth score 1 -uth pval 1e-3 -i $RSAT/public_html/tmp/www-data/2026/07/02/tmp_sequence_2026-07-02.183507_rhyhEf.fasta -seq_format fasta -n score
; Slow counting mode            
; Input files
;	input	$RSAT/public_html/tmp/www-data/2026/07/02/tmp_sequence_2026-07-02.183507_rhyhEf.fasta
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/07/02/matrix-scan_2026-07-02.183507_CYO2Cy.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	input
;	Markov order  	1
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.33393
;		c	0.18328
;		g	0.16879
;		t	0.31399
; Thresholds	lower	upper
;	pval  	NA	0.001
;	score 	1    	NA
; Output columns
;	1	seq_id
;	2	ft_type
;	3	ft_name
;	4	strand
;	5	start
;	6	end
;	7	sequence
;	8	weight
#seq_id	ft_type	ft_name	strand	start	end	sequence	weight	Pval	ln_Pval	sig	rank	rank_pm
CYP2C8_promoter	limit	START_END	D	-2871	-1	.	0	0	0	0
CYP2C8_promoter	site	RXRA::VDR	R	-857	-843	TGGATAAAGGGTTCA	5.8	1.2e-04	-9.057	3.933	1	1
CYP2C8_promoter	site	RXRA::VDR	D	-232	-218	GGTTCATTAGTTACA	5.3	1.6e-04	-8.729	3.791	2	2
CYP2C8_promoter	site	RXRA::VDR	R	-292	-278	TGGTGAAGGGGTTTG	4.9	2.1e-04	-8.474	3.680	3	3
CYP2C8_promoter	site	RXRA::VDR	D	-1443	-1429	TGGTCATGAAGATCT	3.7	4.5e-04	-7.702	3.345	4	4
CYP2C8_promoter	site	RXRA::VDR	D	-1022	-1008	GGGCCACCAAGATTG	3.3	5.7e-04	-7.462	3.241	5	5
CYP2C8_promoter	site	RXRA::VDR	D	-880	-866	AGGTGAGTGAGTCCA	3.3	5.7e-04	-7.462	3.241	6	6
CYP2C8_promoter	site	RXRA::VDR	R	-2585	-2571	AGGTCATAAATTCCC	2.9	7.3e-04	-7.226	3.138	7	7
CYP2C8_promoter	site	RXRA::VDR	R	-1082	-1068	GGGTTATGGTTTCCA	2.5	9.2e-04	-6.994	3.037	8	8
CYP2C8_promoter	site	RXRA::VDR	R	-1028	-1014	TGGTGGCCCGGTTTA	2.3	1.0e-03	-6.884	2.990	9	9
;
; Matrices
;	matrix	name     	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	RXRA::VDR	15	4	1	-34.100	17.700	51.800	a:0.334 c:0.183 g:0.169 t:0.314 
; Number of sequences scanned	1
; Sum of sequence lengths	2871
; N residues           	0
; Matches per matrix
;	matrix	name     	matches	scored
;	1	RXRA::VDR      	9	5714
;		TOTAL          	9	5714
; Host name	rsat
; Job started	2026-07-02.183507
; Job done	2026-07-02.183509
; Seconds	1.29
;	user	1.29
;	system	0.02
;	cuser	0.08
;	csystem	0.01