; matrix-scan  -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/06/17/matrix-scan_2026-06-17.050225_NapA3Z.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_2026-06-17.050225_zvXRbV.fasta -seq_format fasta -n score
; Slow counting mode            
; Input files
;	input	$RSAT/public_html/tmp/www-data/2026/06/17/tmp_sequence_2026-06-17.050225_zvXRbV.fasta
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/06/17/matrix-scan_2026-06-17.050225_NapA3Z.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	input
;	Markov order  	1
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.34242
;		c	0.18661
;		g	0.15145
;		t	0.31953
; 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
BVRB_3g059400|Beta_vulgaris.RefBeet-1.2.2.60|BVRB_3g059400	limit	START_END	D	-255	199	.	0	0	0	0
BVRB_3g059400|Beta_vulgaris.RefBeet-1.2.2.60|BVRB_3g059400	site	oligos_6-8nt_m10oligos_6-8nt_m10	R	-136	-125	GAATCATGCCTT	7.5	7.8e-05	-9.464	4.110	1	1
BVRB_4g096340|Beta_vulgaris.RefBeet-1.2.2.60|BVRB_4g096340	limit	START_END	D	-1501	199	.	0	0	0	0
T459_03445|Capsicum_annuum.ASM51225v2.60|T459_03445	limit	START_END	D	-1501	199	.	0	0	0	0
T459_31204|Capsicum_annuum.ASM51225v2.60|T459_31204	limit	START_END	D	-1501	199	.	0	0	0	0
T459_31204|Capsicum_annuum.ASM51225v2.60|T459_31204	site	oligos_6-8nt_m10oligos_6-8nt_m10	D	-122	-111	GTTTCATGCCAC	7.5	7.8e-05	-9.464	4.110	1	1
AUR62023693.v1.0|Chenopodium_quinoa.PI614886.392.v1.JGI|AUR62023693.v1.0	limit	START_END	D	-1501	199	.	0	0	0	0
AUR62023693.v1.0|Chenopodium_quinoa.PI614886.392.v1.JGI|AUR62023693.v1.0	site	oligos_6-8nt_m10oligos_6-8nt_m10	D	-62	-51	GAAGCATGCCGC	8.8	2.2e-05	-10.735	4.662	1	1
AUR62023693.v1.0|Chenopodium_quinoa.PI614886.392.v1.JGI|AUR62023693.v1.0	site	oligos_6-8nt_m10oligos_6-8nt_m10	R	-105	-94	GATTCATGCCTT	7.7	6.3e-05	-9.670	4.200	2	2
Cla97C08G153070|Citrullus_lanatus.Cla97_v1.62|Cla97C08G153070	limit	START_END	D	-1501	199	.	0	0	0	0
MELO3C011439.2|Cucumis_melo.Melonv4.60|MELO3C011439.2	limit	START_END	D	-1501	199	.	0	0	0	0
Csa_6G366300|Cucumis_sativus.ASM407v2.60|Csa_6G366300	limit	START_END	D	-1501	199	.	0	0	0	0
HanXRQr2_Chr13g0574171|Helianthus_annuus.HanXRQr2.0-SUNRISE.60|HanXRQr2_Chr13g0574171	limit	START_END	D	-1501	199	.	0	0	0	0
HanXRQr2_Chr13g0574181|Helianthus_annuus.HanXRQr2.0-SUNRISE.60|HanXRQr2_Chr13g0574181	limit	START_END	D	-1501	199	.	0	0	0	0
gene-LSAT_8X33320|Lactuca_sativa.Lsat_Salinas_v7.60|gene-LSAT_8X33320	limit	START_END	D	-1501	199	.	0	0	0	0
gene-LSAT_8X33320|Lactuca_sativa.Lsat_Salinas_v7.60|gene-LSAT_8X33320	site	oligos_6-8nt_m10oligos_6-8nt_m10	D	-996	-985	ACGCCATGGCTA	7.7	6.3e-05	-9.670	4.200	1	1
gene25542|Medicago_truncatula.MtrunA17r50ANR.60|gene25542	limit	START_END	D	-1501	199	.	0	0	0	0
107761937|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107761937	limit	START_END	D	-1501	199	.	0	0	0	0
107793142|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107793142	limit	START_END	D	-1501	199	.	0	0	0	0
107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548	limit	START_END	D	-1501	199	.	0	0	0	0
107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548	site	oligos_6-8nt_m10oligos_6-8nt_m10	R	-77	-66	GTCCCATGCCGG	9.8	6.6e-06	-11.933	5.183	1	1
107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548	site	oligos_6-8nt_m10oligos_6-8nt_m10	R	-52	-41	GTCCCATGCCTT	9.5	1.0e-05	-11.515	5.001	2	2
107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548	site	oligos_6-8nt_m10oligos_6-8nt_m10	D	-45	-34	GGGACATGCCGA	7.9	5.1e-05	-9.878	4.290	3	3
107812499|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107812499	limit	START_END	D	-1501	199	.	0	0	0	0
107812499|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107812499	site	oligos_6-8nt_m10oligos_6-8nt_m10	R	-115	-104	GTCCCATGCCTT	9.5	1.0e-05	-11.515	5.001	1	1
gene-LOC110794951|Spinacia_oleracea.GCF020520425.1.RefSeq|gene-LOC110794951	limit	START_END	D	-1501	199	.	0	0	0	0
AT3G13610|Arabidopsis_thaliana.TAIR10.60|F6'H1	limit	START_END	D	-1501	199	.	0	0	0	0
AT3G13610|Arabidopsis_thaliana.TAIR10.60|F6'H1	site	oligos_6-8nt_m10oligos_6-8nt_m10	D	-1486	-1475	CAACCATGCCTA	9.3	1.2e-05	-11.292	4.904	1	1
AT3G13610|Arabidopsis_thaliana.TAIR10.60|F6'H1	site	oligos_6-8nt_m10oligos_6-8nt_m10	D	-1457	-1446	CAACCATGCCTA	9.3	1.2e-05	-11.292	4.904	2	2
GSBRNA2T00023848001|Brassica_napus.AST_PRJEB5043_v1.60|BnaC05g39690D	limit	START_END	D	-1448	199	.	0	0	0	0
GSBRNA2T00023848001|Brassica_napus.AST_PRJEB5043_v1.60|BnaC05g39690D	site	oligos_6-8nt_m10oligos_6-8nt_m10	D	-883	-872	AGTCCATGCCTC	9.8	6.6e-06	-11.933	5.183	1	1
GSBRNA2T00023848001|Brassica_napus.AST_PRJEB5043_v1.60|BnaC05g39690D	site	oligos_6-8nt_m10oligos_6-8nt_m10	D	-138	-127	GAAGCATGCCAT	8.0	4.7e-05	-9.965	4.328	2	2
GSBRNA2T00023848001|Brassica_napus.AST_PRJEB5043_v1.60|BnaC05g39690D	site	oligos_6-8nt_m10oligos_6-8nt_m10	D	-894	-883	GAACCATGCATA	7.7	6.3e-05	-9.670	4.200	3	3
GSBRNA2T00104708001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA05g25780D	limit	START_END	D	-1501	199	.	0	0	0	0
GSBRNA2T00104708001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA05g25780D	site	oligos_6-8nt_m10oligos_6-8nt_m10	D	-891	-880	AGTCCATGCCTC	9.8	6.6e-06	-11.933	5.183	1	1
GSBRNA2T00104708001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA05g25780D	site	oligos_6-8nt_m10oligos_6-8nt_m10	D	-138	-127	GAAGCATGCCAT	8.0	4.7e-05	-9.965	4.328	2	2
GSBRNA2T00104708001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA05g25780D	site	oligos_6-8nt_m10oligos_6-8nt_m10	D	-902	-891	GAACCATGCATA	7.7	6.3e-05	-9.670	4.200	3	3
GSBRNA2T00123637001|Brassica_napus.AST_PRJEB5043_v1.60|BnaC03g38030D	limit	START_END	D	-1501	199	.	0	0	0	0
GSBRNA2T00123637001|Brassica_napus.AST_PRJEB5043_v1.60|BnaC03g38030D	site	oligos_6-8nt_m10oligos_6-8nt_m10	D	-1248	-1237	GAACCATGCCCA	10.1	4.1e-06	-12.407	5.388	1	1
GSBRNA2T00123637001|Brassica_napus.AST_PRJEB5043_v1.60|BnaC03g38030D	site	oligos_6-8nt_m10oligos_6-8nt_m10	D	-1236	-1225	GTCCCATGCTTC	7.3	9.4e-05	-9.271	4.027	2	2
GSBRNA2T00137685001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA03g32900D	limit	START_END	D	-1459	199	.	0	0	0	0
GSBRNA2T00137685001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA03g32900D	site	oligos_6-8nt_m10oligos_6-8nt_m10	D	-992	-981	GAACCATGCCCA	10.1	4.1e-06	-12.407	5.388	1	1
GSBRNA2T00137685001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA03g32900D	site	oligos_6-8nt_m10oligos_6-8nt_m10	D	-980	-969	GTACCATGCTTC	7.7	6.3e-05	-9.670	4.200	2	2
A03p040480.1_BraROA|Brassica_rapa_ro18.SCU_BraROA_2.3.60|A03p040480.1_BraROA	limit	START_END	D	-1426	199	.	0	0	0	0
A03p040480.1_BraROA|Brassica_rapa_ro18.SCU_BraROA_2.3.60|A03p040480.1_BraROA	site	oligos_6-8nt_m10oligos_6-8nt_m10	D	-804	-793	GAGCCTTGCCTC	8.8	2.2e-05	-10.735	4.662	1	1
GLYMA_07G124400|Glycine_max.Glycine_max_v2.1.60|GLYMA_07G124400	limit	START_END	D	-1501	199	.	0	0	0	0
GLYMA_07G124400|Glycine_max.Glycine_max_v2.1.60|GLYMA_07G124400	site	oligos_6-8nt_m10oligos_6-8nt_m10	D	-263	-252	GTTGCATGCCCC	8.7	2.4e-05	-10.639	4.620	1	1
gene-Lalb_Chr13g0290931|Lupinus_albus.CNRS_Lalb_10.GCA_009771035.1.NCBI|gene-Lalb_Chr13g0290931	limit	START_END	D	-1501	199	.	0	0	0	0
gene-Lalb_Chr13g0290931|Lupinus_albus.CNRS_Lalb_10.GCA_009771035.1.NCBI|gene-Lalb_Chr13g0290931	site	oligos_6-8nt_m10oligos_6-8nt_m10	D	-431	-420	CGGACATGCCGG	8.3	3.4e-05	-10.277	4.463	1	1
107763182|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107763182	limit	START_END	D	-1501	199	.	0	0	0	0
107785648|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107785648	limit	START_END	D	-1501	199	.	0	0	0	0
107796566|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107796566	limit	START_END	D	-1501	199	.	0	0	0	0
107796566|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107796566	site	oligos_6-8nt_m10oligos_6-8nt_m10	R	140	151	ACTCCATGCCCT	9.3	1.2e-05	-11.292	4.904	1	1
107787976|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107787976	limit	START_END	D	-1501	199	.	0	0	0	0
107787976|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107787976	site	oligos_6-8nt_m10oligos_6-8nt_m10	D	-77	-66	GACCCATGCATA	7.7	6.3e-05	-9.670	4.200	1	1
Prudul26B000915|Prunus_dulcis.ALMONDv2.60|Prudul26B000915	limit	START_END	D	-773	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	-1501	199	.	0	0	0	0
;
; Matrices
;	matrix	name                            	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	oligos_6-8nt_m10oligos_6-8nt_m10	12	4	1	-21.300	12.500	33.800	a:0.342 c:0.187 g:0.151 t:0.320 
; Number of sequences scanned	32
; Sum of sequence lengths	51020
; N residues           	10767
; Matches per matrix
;	matrix	name                            	matches	scored
;	1	oligos_6-8nt_m10oligos_6-8nt_m10	26	101336
;		TOTAL          	26	101336
; Host name	rsat
; Job started	2026-06-17.050225
; Job done	2026-06-17.050233
; Seconds	7.97
;	user	7.98
;	system	0.02
;	cuser	0.11
;	csystem	0.02