; matrix-scan  -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/07/27/matrix-scan_2026-07-27.105918_fhZfeZ.matrix -pseudo 1 -decimals 1 -2str -origin end -bginput -markov 1 -bg_pseudo 0.01 -return limits -return sites -lth score 4 -i $RSAT/public_html/tmp/www-data/2026/07/27/tmp_sequence_2026-07-27.105918_LNaSzX.fasta -seq_format fasta -n score
; Quick counting mode           
; Input files
;	input	$RSAT/public_html/tmp/www-data/2026/07/27/tmp_sequence_2026-07-27.105918_LNaSzX.fasta
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/07/27/matrix-scan_2026-07-27.105918_fhZfeZ.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	input
;	Markov order  	1
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.33100
;		c	0.19057
;		g	0.17166
;		t	0.30677
; Thresholds	lower	upper
;	score 	4    	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
COS1	limit	START_END	D	-251	-1	.	0
RIBA1	limit	START_END	D	-1307	-1	.	0
AT2G20690	limit	START_END	D	-278	-1	.	0
RIBA1	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	-721	-710	TGACATACCAAC	4.1
RIBA1	site	oligos_6-8nt_m2oligos_6-8nt_m2	D	-603	-592	CTTCATACCATA	4.2
;
; Matrices
;	matrix	name                          	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	oligos_6-8nt_m2oligos_6-8nt_m2	12	4	0	-26.600	10.500	37.100	a:0.331 c:0.191 g:0.172 t:0.307 
; Number of sequences scanned	3
; Sum of sequence lengths	1836
; N residues           	122
; Matches per matrix
;	matrix	name                          	matches	scored
;	1	oligos_6-8nt_m2oligos_6-8nt_m2	2	0
;		TOTAL          	2	0
; Host name	rsat
; Job started	2026-07-27.105918
; Job done	2026-07-27.105918
; Seconds	0.16
;	user	0.16
;	system	0.02
;	cuser	0.12
;	csystem	0.02