; matrix-scan  -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/01/05/matrix-scan_2026-01-05.212041_nA43g7.matrix -pseudo 1 -decimals 1 -2str -origin end -bginput -markov 1 -bg_pseudo 0.01 -return limits -return sites -lth score 1 -i $RSAT/public_html/tmp/www-data/2026/01/05/tmp_sequence_2026-01-05.212041_XWEK9A.fasta -seq_format fasta -n score
; Quick counting mode           
; Input files
;	input	$RSAT/public_html/tmp/www-data/2026/01/05/tmp_sequence_2026-01-05.212041_XWEK9A.fasta
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/01/05/matrix-scan_2026-01-05.212041_nA43g7.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	input
;	Markov order  	1
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.23603
;		c	0.23327
;		g	0.22786
;		t	0.30283
; Thresholds	lower	upper
;	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
mir-71	limit	START_END	D	-2551	-1	.	0
mir-71	site	pha-4	R	-1971	-1962	AAAGTGAACA	2.1
mir-71	site	pha-4	D	-1674	-1665	CATGTATACA	1.5
mir-71	site	pha-4	D	-1580	-1571	AAGGCATATA	1.3
mir-71	site	pha-4	R	-1298	-1289	ACAGCCAACA	1.7
mir-71	site	pha-4	R	-1276	-1267	CAGGCCAACA	5.7
mir-71	site	pha-4	D	-634	-625	TATCCAAACA	1.8
mir-71	site	pha-4	R	-557	-548	CATACAAACA	5.7
mir-71	site	pha-4	R	-107	-98	AGAGCAGACA	2.3
;
; Matrices
;	matrix	name 	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	pha-4	10	4	0	-69.200	11.300	80.500	a:0.236 c:0.233 g:0.228 t:0.303 
; Number of sequences scanned	1
; Sum of sequence lengths	2551
; N residues           	0
; Matches per matrix
;	matrix	name 	matches	scored
;	1	pha-4          	8	0
;		TOTAL          	8	0
; Host name	rsat
; Job started	2026-01-05.212041
; Job done	2026-01-05.212041
; Seconds	0.15
;	user	0.15
;	system	0.02
;	cuser	0.11
;	csystem	0.02