; matrix-scan  -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/05/29/matrix-scan_2026-05-29.151518_1A13s9.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/2026/05/29/tmp_sequence_2026-05-29.151518_NS5bVn.fasta -seq_format fasta -n score
; Slow counting mode            
; Input files
;	input	$RSAT/public_html/tmp/www-data/2026/05/29/tmp_sequence_2026-05-29.151518_NS5bVn.fasta
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/05/29/matrix-scan_2026-05-29.151518_1A13s9.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	input
;	Markov order  	1
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.35281
;		c	0.19966
;		g	0.14836
;		t	0.29917
; 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
AT3G13610|Arabidopsis_thaliana.TAIR10.60|F6'H1	site	dyads_test_vs_ctrl_m1	D	23	41	TAAGCATGGTGAGAGCCAT	8.9	1.4e-05	-11.147	4.841	1	1
GSBRNA2T00023848001|Brassica_napus.AST_PRJEB5043_v1.60|BnaC05g39690D	limit	START_END	D	-501	199	.	0	0	0	0
GSBRNA2T00104708001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA05g25780D	limit	START_END	D	-501	199	.	0	0	0	0
GSBRNA2T00123637001|Brassica_napus.AST_PRJEB5043_v1.60|BnaC03g38030D	limit	START_END	D	-501	199	.	0	0	0	0
GSBRNA2T00123637001|Brassica_napus.AST_PRJEB5043_v1.60|BnaC03g38030D	site	dyads_test_vs_ctrl_m1	D	-135	-117	CAAGCATGGTGAGAGCCAT	8.5	2.0e-05	-10.815	4.697	1	1
GSBRNA2T00137685001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA03g32900D	limit	START_END	D	-501	199	.	0	0	0	0
GSBRNA2T00137685001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA03g32900D	site	dyads_test_vs_ctrl_m1	D	-145	-127	CAAGCATGGTGAGAGCCAT	8.5	2.0e-05	-10.815	4.697	1	1
A03p040480.1_BraROA|Brassica_rapa_ro18.SCU_BraROA_2.3.60|A03p040480.1_BraROA	limit	START_END	D	-501	199	.	0	0	0	0
A03p040480.1_BraROA|Brassica_rapa_ro18.SCU_BraROA_2.3.60|A03p040480.1_BraROA	site	dyads_test_vs_ctrl_m1	D	-145	-127	CAAGCATGGTGAGAGCCAT	8.5	2.0e-05	-10.815	4.697	1	1
GLYMA_07G124400|Glycine_max.Glycine_max_v2.1.60|GLYMA_07G124400	limit	START_END	D	-501	199	.	0	0	0	0
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
107763182|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107763182	limit	START_END	D	-501	199	.	0	0	0	0
107785648|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107785648	limit	START_END	D	-501	199	.	0	0	0	0
107796566|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107796566	limit	START_END	D	-501	199	.	0	0	0	0
107796566|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107796566	site	dyads_test_vs_ctrl_m1	D	-43	-25	ATGGCATGCCAATTGCCTA	9.7	7.3e-06	-11.832	5.139	1	1
107796566|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107796566	site	dyads_test_vs_ctrl_m1	R	-43	-25	TAGGCAATTGGCATGCCAT	8.8	1.6e-05	-11.055	4.801	2	2
107787976|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107787976	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	dyads_test_vs_ctrl_m1	19	4	1	-33.900	19.400	53.300	a:0.353 c:0.200 g:0.148 t:0.299 
; Number of sequences scanned	15
; Sum of sequence lengths	10247
; N residues           	1059
; Matches per matrix
;	matrix	name                 	matches	scored
;	1	dyads_test_vs_ctrl_m1	6	19954
;		TOTAL          	6	19954
; Host name	rsat
; Job started	2026-05-29.151518
; Job done	2026-05-29.151521
; Seconds	3
;	user	3
;	system	0.01
;	cuser	0.1
;	csystem	0.02