; matrix-scan  -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/06/17/matrix-scan_2026-06-17.025816_Aflznt.matrix -pseudo 1 -decimals 1 -2str -origin end -offset -200 -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/2026/06/17/tmp_sequence_2026-06-17.025816_925GNQ.fasta -seq_format fasta -n score
; Slow counting mode            
; Input files
;	input	$RSAT/public_html/tmp/www-data/2026/06/17/tmp_sequence_2026-06-17.025816_925GNQ.fasta
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/06/17/matrix-scan_2026-06-17.025816_Aflznt.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	input
;	Markov order  	1
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.35356
;		c	0.20630
;		g	0.15199
;		t	0.28815
; 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|F6'H1	limit	START_END	D	-501	199	.	0	0	0	0
GSBRNA2T00023848001|Brassica_napus.AST_PRJEB5043_v1.60|BnaC05g39690D	limit	START_END	D	-501	199	.	0	0	0	0
GSBRNA2T00023848001|Brassica_napus.AST_PRJEB5043_v1.60|BnaC05g39690D	site	oligos_6-8nt_m2oligos_6-8nt_m2	D	-300	-289	AAACATGCCAGT	9.0	2.1e-05	-10.773	4.679	1	1
GSBRNA2T00023848001|Brassica_napus.AST_PRJEB5043_v1.60|BnaC05g39690D	site	oligos_6-8nt_m2oligos_6-8nt_m2	D	-137	-126	AAGCATGCCATA	8.9	2.6e-05	-10.548	4.581	2	2
GSBRNA2T00104708001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA05g25780D	limit	START_END	D	-501	199	.	0	0	0	0
GSBRNA2T00104708001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA05g25780D	site	oligos_6-8nt_m2oligos_6-8nt_m2	D	-295	-284	AAACATGCCAGT	9.0	2.1e-05	-10.773	4.679	1	1
GSBRNA2T00104708001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA05g25780D	site	oligos_6-8nt_m2oligos_6-8nt_m2	D	-137	-126	AAGCATGCCATC	8.1	7.4e-05	-9.506	4.128	2	2
GSBRNA2T00123637001|Brassica_napus.AST_PRJEB5043_v1.60|BnaC03g38030D	limit	START_END	D	-501	199	.	0	0	0	0
GSBRNA2T00137685001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA03g32900D	limit	START_END	D	-501	199	.	0	0	0	0
A03p040480.1_BraROA|Brassica_rapa_ro18.SCU_BraROA_2.3.60|A03p040480.1_BraROA	limit	START_END	D	-501	199	.	0	0	0	0
GLYMA_07G124400|Glycine_max.Glycine_max_v2.1.60|GLYMA_07G124400	limit	START_END	D	-501	199	.	0	0	0	0
GLYMA_07G124400|Glycine_max.Glycine_max_v2.1.60|GLYMA_07G124400	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	-18	-7	ATTCATGCCGGG	8.9	2.6e-05	-10.548	4.581	1	1
gene-Lalb_Chr13g0290931|Lupinus_albus.CNRS_Lalb_10.GCA_009771035.1.NCBI|gene-Lalb_Chr13g0290931	limit	START_END	D	-501	199	.	0	0	0	0
Prudul26B000915|Prunus_dulcis.ALMONDv2.60|Prudul26B000915	limit	START_END	D	-501	199	.	0	0	0	0
PRUPE_6G006000|Prunus_persica.Prunus_persica_NCBIv2.60|PRUPE_6G006000	limit	START_END	D	-233	199	.	0	0	0	0
Solyc11g072100.ITAG4.0|Solanum_lycopersicum.ITAG4.0.JGI|Solyc11g072100.ITAG4.0	limit	START_END	D	-501	199	.	0	0	0	0
;
; Matrices
;	matrix	name                          	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	oligos_6-8nt_m2oligos_6-8nt_m2	12	4	1	-23.100	11.000	34.100	a:0.354 c:0.206 g:0.152 t:0.288 
; Number of sequences scanned	11
; Sum of sequence lengths	7443
; N residues           	1059
; Matches per matrix
;	matrix	name                          	matches	scored
;	1	oligos_6-8nt_m2oligos_6-8nt_m2	5	14644
;		TOTAL          	5	14644
; Host name	rsat
; Job started	2026-06-17.025816
; Job done	2026-06-17.025818
; Seconds	1.53
;	user	1.53
;	system	0.02
;	cuser	0.11
;	csystem	0.02