; matrix-scan  -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/06/17/matrix-scan_2026-06-17.054834_jDc3jj.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_2026-06-17.054834_SnfRin.fasta -seq_format fasta -n score
; Slow counting mode            
; Input files
;	input	$RSAT/public_html/tmp/www-data/2026/06/17/tmp_sequence_2026-06-17.054834_SnfRin.fasta
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/06/17/matrix-scan_2026-06-17.054834_jDc3jj.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_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_m9oligos_6-8nt_m9	R	-891	-879	ACAAGCATGAGAA	9.6	9.7e-06	-11.541	5.012	1	1
T459_31204|Capsicum_annuum.ASM51225v2.60|T459_31204	site	oligos_6-8nt_m9oligos_6-8nt_m9	R	-122	-110	AGTGGCATGAAAC	8.0	6.2e-05	-9.682	4.205	2	2
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_m9oligos_6-8nt_m9	D	-63	-51	CGAAGCATGCCGC	9.7	8.4e-06	-11.688	5.076	1	1
AUR62023693.v1.0|Chenopodium_quinoa.PI614886.392.v1.JGI|AUR62023693.v1.0	site	oligos_6-8nt_m9oligos_6-8nt_m9	D	-106	-94	AAAGGCATGAATC	8.2	5.1e-05	-9.880	4.291	2	2
AUR62023693.v1.0|Chenopodium_quinoa.PI614886.392.v1.JGI|AUR62023693.v1.0	site	oligos_6-8nt_m9oligos_6-8nt_m9	R	-653	-641	AAGAGCATGACAT	8.1	5.6e-05	-9.782	4.248	3	3
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_Chr13g0574171|Helianthus_annuus.HanXRQr2.0-SUNRISE.60|HanXRQr2_Chr13g0574171	site	oligos_6-8nt_m9oligos_6-8nt_m9	R	-167	-155	GGATGCATGAGAA	8.2	5.1e-05	-9.880	4.291	1	1
HanXRQr2_Chr13g0574171|Helianthus_annuus.HanXRQr2.0-SUNRISE.60|HanXRQr2_Chr13g0574171	site	oligos_6-8nt_m9oligos_6-8nt_m9	R	-66	-54	GGATGCATGAGAA	8.2	5.1e-05	-9.880	4.291	2	2
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_m9oligos_6-8nt_m9	D	-927	-915	AGAAGCAGGAAGT	8.1	5.6e-05	-9.782	4.248	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
107761937|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107761937	site	oligos_6-8nt_m9oligos_6-8nt_m9	D	-132	-120	AAAGGCATGAGAC	7.8	7.5e-05	-9.491	4.122	1	1
107793142|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107793142	limit	START_END	D	-1501	199	.	0	0	0	0
107793142|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107793142	site	oligos_6-8nt_m9oligos_6-8nt_m9	R	-381	-369	CAAAGCATGACTC	8.9	2.5e-05	-10.603	4.605	1	1
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_m9oligos_6-8nt_m9	R	-693	-681	CAAAGCATGACTC	8.9	2.5e-05	-10.603	4.605	1	1
107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548	site	oligos_6-8nt_m9oligos_6-8nt_m9	R	-925	-913	ATAAGCATGCATC	8.1	5.6e-05	-9.782	4.248	2	2
107812499|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107812499	limit	START_END	D	-1501	199	.	0	0	0	0
gene-LOC110794951|Spinacia_oleracea.GCF020520425.1.RefSeq|gene-LOC110794951	limit	START_END	D	-1501	199	.	0	0	0	0
gene-LOC110794951|Spinacia_oleracea.GCF020520425.1.RefSeq|gene-LOC110794951	site	oligos_6-8nt_m9oligos_6-8nt_m9	D	1	13	AAAGGCATGAAAC	8.2	5.1e-05	-9.880	4.291	1	1
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_m9oligos_6-8nt_m9	R	-1474	-1462	AGAAGCGTGAGAC	7.7	8.2e-05	-9.407	4.085	1	1
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_m9oligos_6-8nt_m9	D	-139	-127	CGAAGCATGCCAT	8.7	3.1e-05	-10.381	4.509	1	1
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_m9oligos_6-8nt_m9	D	-139	-127	CGAAGCATGCCAT	8.7	3.1e-05	-10.381	4.509	1	1
GSBRNA2T00123637001|Brassica_napus.AST_PRJEB5043_v1.60|BnaC03g38030D	limit	START_END	D	-1501	199	.	0	0	0	0
GSBRNA2T00137685001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA03g32900D	limit	START_END	D	-1459	199	.	0	0	0	0
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_m9oligos_6-8nt_m9	D	-865	-853	GGATGCATGACCT	7.8	7.5e-05	-9.491	4.122	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_m9oligos_6-8nt_m9	D	-18	-6	CCCGGCATGAATT	7.7	8.2e-05	-9.407	4.085	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
107763182|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107763182	limit	START_END	D	-1501	199	.	0	0	0	0
107763182|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107763182	site	oligos_6-8nt_m9oligos_6-8nt_m9	D	-91	-79	GAAAGCATGAGAA	8.9	2.5e-05	-10.603	4.605	1	1
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
107787976|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107787976	limit	START_END	D	-1501	199	.	0	0	0	0
Prudul26B000915|Prunus_dulcis.ALMONDv2.60|Prudul26B000915	limit	START_END	D	-773	199	.	0	0	0	0
Prudul26B000915|Prunus_dulcis.ALMONDv2.60|Prudul26B000915	site	oligos_6-8nt_m9oligos_6-8nt_m9	R	-218	-206	ACATGCATGCATT	7.9	6.8e-05	-9.598	4.168	1	1
PRUPE_6G006000|Prunus_persica.Prunus_persica_NCBIv2.60|PRUPE_6G006000	limit	START_END	D	-233	199	.	0	0	0	0
PRUPE_6G006000|Prunus_persica.Prunus_persica_NCBIv2.60|PRUPE_6G006000	site	oligos_6-8nt_m9oligos_6-8nt_m9	R	38	50	ACATGCATGCATT	7.9	6.8e-05	-9.598	4.168	1	1
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_m9oligos_6-8nt_m9	13	4	1	-27.900	11.400	39.300	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_m9oligos_6-8nt_m9	21	101272
;		TOTAL          	21	101272
; Host name	rsat
; Job started	2026-06-17.054835
; Job done	2026-06-17.054843
; Seconds	8.63
;	user	8.63
;	system	0.03
;	cuser	0.08
;	csystem	0.02