; matrix-scan  -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/01/05/matrix-scan_2026-01-05.224600_oeaXwO.matrix -pseudo 1 -decimals 1 -2str -origin start -bginput -markov 1 -bg_pseudo 0.01 -return limits -return sites -return pval -return rank -lth score 1 -uth pval 1e-2 -i $RSAT/public_html/tmp/www-data/2026/01/05/tmp_sequence_2026-01-05.224600_etOxg6.fasta -seq_format fasta -n score
; Slow counting mode            
; Input files
;	input	$RSAT/public_html/tmp/www-data/2026/01/05/tmp_sequence_2026-01-05.224600_etOxg6.fasta
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/01/05/matrix-scan_2026-01-05.224600_oeaXwO.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
;	pval  	NA	0.01 
;	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
mir-71	limit	START_END	D	1	2551	.	0	0	0	0
mir-71	site	pha-4	R	1276	1285	CAGGCCAACA	5.7	1.4e-04	-8.882	3.858	1	1
mir-71	site	pha-4	R	1995	2004	CATACAAACA	5.7	1.4e-04	-8.882	3.858	2	2
mir-71	site	pha-4	R	2445	2454	AGAGCAGACA	2.3	3.5e-04	-7.957	3.456	3	3
mir-71	site	pha-4	R	581	590	AAAGTGAACA	2.1	4.1e-04	-7.804	3.389	4	4
mir-71	site	pha-4	D	1918	1927	TATCCAAACA	1.8	5.1e-04	-7.574	3.289	5	5
mir-71	site	pha-4	R	1254	1263	ACAGCCAACA	1.7	5.4e-04	-7.527	3.269	6	6
mir-71	site	pha-4	D	878	887	CATGTATACA	1.5	6.2e-04	-7.394	3.211	7	7
mir-71	site	pha-4	D	972	981	AAGGCATATA	1.3	6.9e-04	-7.282	3.162	8	8
;
; Matrices
;	matrix	name 	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	pha-4	10	4	1	-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	5084
;		TOTAL          	8	5084
; Host name	rsat
; Job started	2026-01-05.224601
; Job done	2026-01-05.224601
; Seconds	0.84
;	user	0.84
;	system	0.02
;	cuser	0.08
;	csystem	0.03