; matrix-scan  -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/06/05/matrix-scan_2026-06-05.172024_KVN9lY.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/2026/06/05/tmp_sequence_2026-06-05.172024_wMn9ed.fasta -seq_format fasta -n score
; Slow counting mode            
; Input files
;	input	$RSAT/public_html/tmp/www-data/2026/06/05/tmp_sequence_2026-06-05.172024_wMn9ed.fasta
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/06/05/matrix-scan_2026-06-05.172024_KVN9lY.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	input
;	Markov order  	1
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.35349
;		c	0.20221
;		g	0.14949
;		t	0.29482
; 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
AT3G13610|Arabidopsis_thaliana.TAIR10.60	limit	START_END	D	-701	-1	.	0	0	0	0
GSBRNA2T00023848001|	limit	START_END	D	-701	-1	.	0	0	0	0
GSBRNA2T00104708001|	limit	START_END	D	-701	-1	.	0	0	0	0
GSBRNA2T00104708001|	site	oligos_6-8nt_m3oligos_6-8nt_m3	R	-337	-324	TAGATGGCATGCTT	7.6	7.0e-05	-9.574	4.158	1	1
GSBRNA2T00123637001	limit	START_END	D	-701	-1	.	0	0	0	0
GSBRNA2T00123637001	site	oligos_6-8nt_m3oligos_6-8nt_m3	R	-495	-482	AAAAAGACATGTTT	7.4	8.3e-05	-9.397	4.081	1	1
GSBRNA2T00137685001	limit	START_END	D	-701	-1	.	0	0	0	0
GSBRNA2T00137685001	site	oligos_6-8nt_m3oligos_6-8nt_m3	R	-505	-492	AAAAAGACATGTTT	7.4	8.3e-05	-9.397	4.081	1	1
A03p040480.1_BraROA	limit	START_END	D	-701	-1	.	0	0	0	0
A03p040480.1_BraROA	site	oligos_6-8nt_m3oligos_6-8nt_m3	R	-505	-492	AAAAAGACATGTTT	7.4	8.3e-05	-9.397	4.081	1	1
GLYMA_07G124400|Glycine_max.Glycine_max_v2.1.60	limit	START_END	D	-701	-1	.	0	0	0	0
gene-Lalb_Chr13g0290931	limit	START_END	D	-701	-1	.	0	0	0	0
LOC107763182|	limit	START_END	D	-701	-1	.	0	0	0	0
LOC107763182|	site	oligos_6-8nt_m3oligos_6-8nt_m3	D	-371	-358	AGGAAAGCATGAGA	7.7	6.4e-05	-9.657	4.194	1	1
LOC107785648	limit	START_END	D	-701	-1	.	0	0	0	0
LOC107785648	site	oligos_6-8nt_m3oligos_6-8nt_m3	D	-276	-263	ATAAATGCATGTAA	7.2	9.9e-05	-9.215	4.002	1	1
LOC107796566	limit	START_END	D	-701	-1	.	0	0	0	0
LOC107787976	limit	START_END	D	-701	-1	.	0	0	0	0
Prudul26B000915	limit	START_END	D	-701	-1	.	0	0	0	0
PRUPE_6G006000	limit	START_END	D	-433	-1	.	0	0	0	0
Solyc11g072100.ITAG4.0	limit	START_END	D	-701	-1	.	0	0	0	0
;
; Matrices
;	matrix	name                          	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	oligos_6-8nt_m3oligos_6-8nt_m3	14	4	1	-32.700	13.500	46.200	a:0.353 c:0.202 g:0.149 t:0.295 
; Number of sequences scanned	15
; Sum of sequence lengths	10247
; N residues           	1298
; Matches per matrix
;	matrix	name                          	matches	scored
;	1	oligos_6-8nt_m3oligos_6-8nt_m3	6	20104
;		TOTAL          	6	20104
; Host name	rsat
; Job started	2026-06-05.172024
; Job done	2026-06-05.172026
; Seconds	2.22
;	user	2.22
;	system	0.02
;	cuser	0.08
;	csystem	0.01