; matrix-scan  -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/06/05/matrix-scan_2026-06-05.171059_TQ9uZN.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_2026-06-05.171059_F3hgWw.fasta -seq_format fasta -n score
; Slow counting mode            
; Input files
;	input	$RSAT/public_html/tmp/www-data/2026/06/05/tmp_sequence_2026-06-05.171059_F3hgWw.fasta
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/06/05/matrix-scan_2026-06-05.171059_TQ9uZN.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	input
;	Markov order  	1
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.31206
;		c	0.18282
;		g	0.14868
;		t	0.35644
; 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_9g215540|Beta_vulgaris.RefBeet-1.2.2.60|BVRB_9g215540	limit	START_END	D	-701	-1	.	0	0	0	0
BVRB_9g215540|Beta_vulgaris.RefBeet-1.2.2.60|BVRB_9g215540	site	oligos_6-8nt_m3oligos_6-8nt_m3	R	-274	-261	GAAAAGGCATGGGT	10.7	2.8e-06	-12.800	5.559	1	1
BVRB_9g215540|Beta_vulgaris.RefBeet-1.2.2.60|BVRB_9g215540	site	oligos_6-8nt_m3oligos_6-8nt_m3	R	-611	-598	ATGAAGGCATGTAA	10.1	5.7e-06	-12.072	5.243	2	2
BVRB_9g215540|Beta_vulgaris.RefBeet-1.2.2.60|BVRB_9g215540	site	oligos_6-8nt_m3oligos_6-8nt_m3	R	-65	-52	CAGAAGACATGATT	8.8	2.2e-05	-10.724	4.657	3	3
T459_35378|Capsicum_annuum.ASM51225v2.60|T459_35378	limit	START_END	D	-701	-1	.	0	0	0	0
T459_35378|Capsicum_annuum.ASM51225v2.60|T459_35378	site	oligos_6-8nt_m3oligos_6-8nt_m3	R	-205	-192	TGGAAGCCATGAAT	9.4	1.2e-05	-11.344	4.926	1	1
T459_32000|Capsicum_annuum.ASM51225v2.60|T459_32000	limit	START_END	D	-701	-1	.	0	0	0	0
AUR62013165.v1.0|Chenopodium_quinoa.PI614886.392.v1.JGI|AUR62013165.v1.0	limit	START_END	D	-701	-1	.	0	0	0	0
AUR62013165.v1.0|Chenopodium_quinoa.PI614886.392.v1.JGI|AUR62013165.v1.0	site	oligos_6-8nt_m3oligos_6-8nt_m3	R	-444	-431	AAAAAGGCATGGGT	10.3	4.5e-06	-12.316	5.349	1	1
AUR62013165.v1.0|Chenopodium_quinoa.PI614886.392.v1.JGI|AUR62013165.v1.0	site	oligos_6-8nt_m3oligos_6-8nt_m3	R	-205	-192	CAGAAGCCATGATT	10.1	5.7e-06	-12.072	5.243	2	2
Cla97C08G147910|Citrullus_lanatus.Cla97_v1.62|Cla97C08G147910	limit	START_END	D	-450	-1	.	0	0	0	0
Cla97C10G192540|Citrullus_lanatus.Cla97_v1.62|Cla97C10G192540	limit	START_END	D	-701	-1	.	0	0	0	0
MELO3C024826.2|Cucumis_melo.Melonv4.60|MELO3C024826.2	limit	START_END	D	-701	-1	.	0	0	0	0
MELO3C024827.2|Cucumis_melo.Melonv4.60|MELO3C024827.2	limit	START_END	D	-701	-1	.	0	0	0	0
Csa_4G111580|Cucumis_sativus.ASM407v2.60|Csa_4G111580	limit	START_END	D	-701	-1	.	0	0	0	0
Csa_4G111590|Cucumis_sativus.ASM407v2.60|Csa_4G111590	limit	START_END	D	-701	-1	.	0	0	0	0
Csa_4G111590|Cucumis_sativus.ASM407v2.60|Csa_4G111590	site	oligos_6-8nt_m3oligos_6-8nt_m3	R	-111	-98	GAAAAGGCATAATA	9.5	1.1e-05	-11.446	4.971	1	1
Csa_6G029440|Cucumis_sativus.ASM407v2.60|Csa_6G029440	limit	START_END	D	-701	-1	.	0	0	0	0
HanXRQr2_Chr10g0444301|Helianthus_annuus.HanXRQr2.0-SUNRISE.60|HanXRQr2_Chr10g0444301	limit	START_END	D	-701	-1	.	0	0	0	0
HanXRQr2_Chr10g0444301|Helianthus_annuus.HanXRQr2.0-SUNRISE.60|HanXRQr2_Chr10g0444301	site	oligos_6-8nt_m3oligos_6-8nt_m3	R	-84	-71	TGGAAGCCATGAAT	9.4	1.2e-05	-11.344	4.926	1	1
HanXRQr2_Chr10g0444301|Helianthus_annuus.HanXRQr2.0-SUNRISE.60|HanXRQr2_Chr10g0444301	site	oligos_6-8nt_m3oligos_6-8nt_m3	R	-69	-56	CAGAAGACATGTTA	7.1	1.0e-04	-9.185	3.989	2	2
HanXRQr2_Chr16g0751271|Helianthus_annuus.HanXRQr2.0-SUNRISE.60|HanXRQr2_Chr16g0751271	limit	START_END	D	-701	-1	.	0	0	0	0
gene-LSAT_5X108740|Lactuca_sativa.Lsat_Salinas_v7.60|gene-LSAT_5X108740	limit	START_END	D	-701	-1	.	0	0	0	0
gene-LSAT_5X108740|Lactuca_sativa.Lsat_Salinas_v7.60|gene-LSAT_5X108740	site	oligos_6-8nt_m3oligos_6-8nt_m3	R	-45	-32	CAGAAGACATGTTA	7.1	1.0e-04	-9.185	3.989	1	1
gene-LSAT_9X115140|Lactuca_sativa.Lsat_Salinas_v7.60|gene-LSAT_9X115140	limit	START_END	D	-701	-1	.	0	0	0	0
gene7299|Medicago_truncatula.MtrunA17r50ANR.60|gene7299	limit	START_END	D	-701	-1	.	0	0	0	0
107780053|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107780053	limit	START_END	D	-701	-1	.	0	0	0	0
107789601|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107789601	limit	START_END	D	-701	-1	.	0	0	0	0
107789601|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107789601	site	oligos_6-8nt_m3oligos_6-8nt_m3	R	-596	-583	GTATTGGCATGAAT	8.2	4.0e-05	-10.136	4.402	1	1
gene-LOC110802506|Spinacia_oleracea.GCF020520425.1.RefSeq|gene-LOC110802506	limit	START_END	D	-701	-1	.	0	0	0	0
gene-LOC110802506|Spinacia_oleracea.GCF020520425.1.RefSeq|gene-LOC110802506	site	oligos_6-8nt_m3oligos_6-8nt_m3	R	-200	-187	GAAAAGGCATGGGT	10.7	2.8e-06	-12.800	5.559	1	1
;
; Matrices
;	matrix	name                          	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	oligos_6-8nt_m3oligos_6-8nt_m3	14	4	1	-32.700	13.700	46.400	a:0.312 c:0.183 g:0.149 t:0.356 
; Number of sequences scanned	19
; Sum of sequence lengths	13068
; N residues           	2546
; Matches per matrix
;	matrix	name                          	matches	scored
;	1	oligos_6-8nt_m3oligos_6-8nt_m3	12	25642
;		TOTAL          	12	25642
; Host name	rsat
; Job started	2026-06-05.171059
; Job done	2026-06-05.171102
; Seconds	2.88
;	user	2.88
;	system	0.02
;	cuser	0.1
;	csystem	0.02