; matrix-scan  -v 1 -matrix_format tab -m $RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.195805_zheNGr.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/2026/04/30/retrieve-seq_2026-04-30.195733_BWJu75.fasta.fasta.fasta -seq_format fasta -n score
; Slow counting mode            
; Input files
;	input	$RSAT/public_html/tmp/www-data/2026/04/30/retrieve-seq_2026-04-30.195733_BWJu75.fasta.fasta.fasta
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.195805_zheNGr.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	input
;	Markov order  	1
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.30335
;		c	0.19690
;		g	0.19856
;		t	0.30118
; 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
insA	limit	START_END	D	-106	-1	.	0	0	0	0
borD	limit	START_END	D	-341	-1	.	0	0	0	0
ompT	limit	START_END	D	-474	-1	.	0	0	0	0
ybeF	limit	START_END	D	-309	-1	.	0	0	0	0
ybjX	limit	START_END	D	-165	-1	.	0	0	0	0
nudJ	limit	START_END	D	-60	-1	.	0	0	0	0
yncH	limit	START_END	D	-126	-1	.	0	0	0	0
gadC	limit	START_END	D	-206	-1	.	0	0	0	0
gadB	limit	START_END	D	-412	-1	.	0	0	0	0
gadB	site	matrix-scan_2026-04-30	R	-249	-233	GTGTTTTATGCTGTTAT	6.4	6.0e-05	-9.729	4.225	1	1
slyB	limit	START_END	D	-324	-1	.	0	0	0	0
slyB	site	matrix-scan_2026-04-30	D	-199	-183	GAATGTTTTGTTTATAA	6.5	4.8e-05	-9.951	4.322	1	1
mgrB	limit	START_END	D	-209	-1	.	0	0	0	0
ygdR	limit	START_END	D	-188	-1	.	0	0	0	0
ygeN	limit	START_END	D	-51	-1	.	0	0	0	0
higB	limit	START_END	D	-334	-1	.	0	0	0	0
yrbL	limit	START_END	D	-264	-1	.	0	0	0	0
zntA	limit	START_END	D	-124	-1	.	0	0	0	0
hdeD	limit	START_END	D	-305	-1	.	0	0	0	0
gadE	limit	START_END	D	-362	-1	.	0	0	0	0
gadA	limit	START_END	D	-261	-1	.	0	0	0	0
yhjC	limit	START_END	D	-570	-1	.	0	0	0	0
yiaG	limit	START_END	D	-484	-1	.	0	0	0	0
yidX	limit	START_END	D	-328	-1	.	0	0	0	0
yjbJ	limit	START_END	D	-166	-1	.	0	0	0	0
yjeT	limit	START_END	D	-132	-1	.	0	0	0	0
mgtA	limit	START_END	D	-191	-1	.	0	0	0	0
fecC	limit	START_END	D	-51	-1	.	0	0	0	0
;
; Matrices
;	matrix	name                  	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	matrix-scan_2026-04-30	17	4	1	-24.400	10.100	34.500	a:0.303 c:0.197 g:0.199 t:0.301 
; Number of sequences scanned	26
; Sum of sequence lengths	6543
; N residues           	0
; Matches per matrix
;	matrix	name                  	matches	scored
;	1	matrix-scan_2026-04-30	2	12254
;		TOTAL          	2	12254
; Host name	rsat
; Job started	2026-04-30.195805
; Job done	2026-04-30.195807
; Seconds	1.68
;	user	1.68
;	system	0.04
;	cuser	0.1
;	csystem	0.03