; matrix-scan  -v 1 -matrix_format tab -m $RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.195953_6ewexx.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_2026-04-30.193419_fEUhtg.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_2026-04-30.193419_fEUhtg.fasta.fasta.fasta
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.195953_6ewexx.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
borD	site	matrix-scan_2026-04-30	R	-52	-41	ATTTTTTTCATG	7.0	1.0e-04	-9.197	3.994	1	1
ompT	limit	START_END	D	-474	-1	.	0	0	0	0
ybeF	limit	START_END	D	-309	-1	.	0	0	0	0
ybeF	site	matrix-scan_2026-04-30	R	-75	-64	ATTTTATTCATG	7.5	3.1e-05	-10.368	4.503	1	1
ybjX	limit	START_END	D	-165	-1	.	0	0	0	0
ybjX	site	matrix-scan_2026-04-30	D	-163	-152	ATTTTCTGAATA	7.1	8.1e-05	-9.420	4.091	1	1
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	-194	-183	ATTTTTTCATTG	7.1	8.1e-05	-9.420	4.091	1	1
slyB	limit	START_END	D	-324	-1	.	0	0	0	0
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
yrbL	site	matrix-scan_2026-04-30	R	-221	-210	ATTTTCTTATTG	8.5	6.5e-07	-14.250	6.189	1	1
zntA	limit	START_END	D	-124	-1	.	0	0	0	0
hdeD	limit	START_END	D	-305	-1	.	0	0	0	0
hdeD	site	matrix-scan_2026-04-30	D	-81	-70	ATTTTCTTCTTA	7.1	8.1e-05	-9.420	4.091	1	1
gadE	limit	START_END	D	-362	-1	.	0	0	0	0
gadA	limit	START_END	D	-261	-1	.	0	0	0	0
gadA	site	matrix-scan_2026-04-30	D	-90	-79	ACTTTTTTATTG	7.1	8.1e-05	-9.420	4.091	1	1
yhjC	limit	START_END	D	-570	-1	.	0	0	0	0
yiaG	limit	START_END	D	-484	-1	.	0	0	0	0
yiaG	site	matrix-scan_2026-04-30	R	-367	-356	ATTTTCTCCATG	7.9	9.9e-06	-11.525	5.005	1	1
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	12	4	1	-35.100	9.000	44.100	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	8	12514
;		TOTAL          	8	12514
; Host name	rsat
; Job started	2026-04-30.195953
; Job done	2026-04-30.195955
; Seconds	1.34
;	user	1.34
;	system	0.02
;	cuser	0.1
;	csystem	0.02