; matrix-scan  -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/06/17/matrix-scan_2026-06-17.053330_3kEBCx.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_2026-06-17.053330_RiqLoT.fasta -seq_format fasta -n score
; Slow counting mode            
; Input files
;	input	$RSAT/public_html/tmp/www-data/2026/06/17/tmp_sequence_2026-06-17.053330_RiqLoT.fasta
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/06/17/matrix-scan_2026-06-17.053330_3kEBCx.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	input
;	Markov order  	1
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.33425
;		c	0.18710
;		g	0.15730
;		t	0.32135
; 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
AT2G44050|Arabidopsis_thaliana.TAIR10.60|COS1	limit	START_END	D	-51	199	.	0	0	0	0
GSBRNA2T00101444001|Brassica_napus.AST_PRJEB5043_v1.60|BnaC03g24640D	limit	START_END	D	-136	199	.	0	0	0	0
GSBRNA2T00139024001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA03g20600D	limit	START_END	D	-184	199	.	0	0	0	0
GLYMA_08G087500|Glycine_max.Glycine_max_v2.1.60|GLYMA_08G087500	limit	START_END	D	-1501	199	.	0	0	0	0
gene-Lalb_Chr13g0292401|Lupinus_albus.CNRS_Lalb_10.GCA_009771035.1.NCBI|gene-Lalb_Chr13g0292401	limit	START_END	D	-1501	199	.	0	0	0	0
Prudul26B014047|Prunus_dulcis.ALMONDv2.60|Prudul26B014047	limit	START_END	D	-143	199	.	0	0	0	0
Prudul26B014047|Prunus_dulcis.ALMONDv2.60|Prudul26B014047	site	dyads_test_vs_ctrl_m1dyads_test_vs_ctrl_m1	D	-17	2	TAGGCAAGCGGCAAGCCTAT	10.0	5.2e-06	-12.157	5.280	1	1
Prudul26B014047|Prunus_dulcis.ALMONDv2.60|Prudul26B014047	site	dyads_test_vs_ctrl_m1dyads_test_vs_ctrl_m1	R	-18	1	TAGGCTTGCCGCTTGCCTAA	7.8	4.5e-05	-10.004	4.345	2	2
PRUPE_7G270800|Prunus_persica.Prunus_persica_NCBIv2.60|PRUPE_7G270800	limit	START_END	D	-1	199	.	0	0	0	0
Solyc08g015660.ITAG4.0|Solanum_lycopersicum.ITAG4.0.JGI|Solyc08g015660.ITAG4.0	limit	START_END	D	-1501	199	.	0	0	0	0
BVRB_4g071180|Beta_vulgaris.RefBeet-1.2.2.60|BVRB_4g071180	limit	START_END	D	-1415	199	.	0	0	0	0
T459_28413|Capsicum_annuum.ASM51225v2.60|T459_28413	limit	START_END	D	-1501	199	.	0	0	0	0
AUR62039389.v1.0|Chenopodium_quinoa.PI614886.392.v1.JGI|AUR62039389.v1.0	limit	START_END	D	-1501	199	.	0	0	0	0
Cla97C05G087480|Citrullus_lanatus.Cla97_v1.62|Cla97C05G087480	limit	START_END	D	-1501	199	.	0	0	0	0
MELO3C006644.2|Cucumis_melo.Melonv4.60|MELO3C006644.2	limit	START_END	D	-1501	199	.	0	0	0	0
Csa_3G821020|Cucumis_sativus.ASM407v2.60|Csa_3G821020	limit	START_END	D	-1501	199	.	0	0	0	0
HanXRQr2_Chr13g0590341|Helianthus_annuus.HanXRQr2.0-SUNRISE.60|HanXRQr2_Chr13g0590341	limit	START_END	D	-1501	199	.	0	0	0	0
gene-LSAT_6X52001|Lactuca_sativa.Lsat_Salinas_v7.60|gene-LSAT_6X52001	limit	START_END	D	-1501	199	.	0	0	0	0
gene-LSAT_6X52001|Lactuca_sativa.Lsat_Salinas_v7.60|gene-LSAT_6X52001	site	dyads_test_vs_ctrl_m1dyads_test_vs_ctrl_m1	R	-135	-116	GTTGCATTGTTCATGCTTTA	10.3	3.8e-06	-12.480	5.420	1	1
gene-LSAT_6X52001|Lactuca_sativa.Lsat_Salinas_v7.60|gene-LSAT_6X52001	site	dyads_test_vs_ctrl_m1dyads_test_vs_ctrl_m1	D	-134	-115	AAAGCATGAACAATGCAACT	10.1	4.8e-06	-12.253	5.321	2	2
gene14703|Medicago_truncatula.MtrunA17r50ANR.60|gene14703	limit	START_END	D	-1501	199	.	0	0	0	0
;
; Matrices
;	matrix	name                                      	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	dyads_test_vs_ctrl_m1dyads_test_vs_ctrl_m1	20	4	1	-33.100	17.000	50.100	a:0.334 c:0.187 g:0.157 t:0.321 
; Number of sequences scanned	17
; Sum of sequence lengths	21841
; N residues           	5555
; Matches per matrix
;	matrix	name                                      	matches	scored
;	1	dyads_test_vs_ctrl_m1dyads_test_vs_ctrl_m1	4	43036
;		TOTAL          	4	43036
; Host name	rsat
; Job started	2026-06-17.053330
; Job done	2026-06-17.053336
; Seconds	5.88
;	user	5.88
;	system	0.03
;	cuser	0.12
;	csystem	0