; matrix-scan  -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/07/22/matrix-scan_2026-07-22.181541_eZ1FSW.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-4 -i $RSAT/public_html/tmp/www-data/2026/07/22/tmp_sequence_2026-07-22.181541_nCTfbS.fasta -seq_format fasta -n score
; Slow counting mode            
; Input files
;	input	$RSAT/public_html/tmp/www-data/2026/07/22/tmp_sequence_2026-07-22.181541_nCTfbS.fasta
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/07/22/matrix-scan_2026-07-22.181541_eZ1FSW.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	input
;	Markov order  	1
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.28219
;		c	0.23008
;		g	0.23106
;		t	0.25667
; Thresholds	lower	upper
;	pval  	NA	0.0001
;	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
Spic	limit	START_END	D	-2200	-1	.	0	0	0	0
Nfe2l2	limit	START_END	D	-2200	-1	.	0	0	0	0
Nfe2l2	site	Spic	D	-2144	-2131	ACAAGGAGGAAGTA	10.0	5.3e-06	-12.154	5.278	1	1
Nfe2l2	site	Spic	D	-1041	-1028	AAATAGAGTAAGTA	6.7	4.8e-05	-9.949	4.321	2	2
Brf2	limit	START_END	D	-2200	-1	.	0	0	0	0
Brf2	site	Spic	D	-2097	-2084	AAAAAGGGGGAGTG	7.3	3.3e-05	-10.331	4.487	1	1
Brf2	site	Nfe2l2	R	-666	-653	GTGAGAGAGCAGTA	7.8	5.4e-05	-9.829	4.269	2	1
Brf2	site	Spic	R	-951	-938	TCAAAGAGGATGTA	5.5	9.6e-05	-9.253	4.018	3	2
;
; Matrices
;	matrix	name  	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	Spic  	14	4	1	-53.600	16.000	69.600	a:0.282 c:0.230 g:0.231 t:0.257 
;	2	Nfe2l2	15	4	1	-37.300	15.700	53.000	a:0.282 c:0.230 g:0.231 t:0.257 
;	3	Nfe2l2	14	4	1	-22.700	13.100	35.800	a:0.282 c:0.230 g:0.231 t:0.257 
; Number of sequences scanned	3
; Sum of sequence lengths	6600
; N residues           	0
; Matches per matrix
;	matrix	name  	matches	scored
;	1	Spic           	4	13122
;	2	Nfe2l2         	0	13116
;	3	Nfe2l2         	1	13122
;		TOTAL          	5	39360
; Host name	rsat
; Job started	2026-07-22.181541
; Job done	2026-07-22.181546
; Seconds	4.97
;	user	4.97
;	system	0.02
;	cuser	0.12
;	csystem	0