; matrix-scan  -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/07/27/matrix-scan_2026-07-27.133622_Ilm2rh.matrix -pseudo 1 -decimals 1 -2str -origin end -offset -200 -bgfile $RSAT/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.60/oligo-frequencies/2nt_upstream-noorf_Arabidopsis_thaliana.TAIR10.60-ovlp-1str.freq -bg_pseudo 0.01 -return limits -return sites -return pval -return rank -return normw -lth score 1 -uth pval 1e-3 -i $RSAT/public_html/tmp/www-data/2026/07/27/tmp_sequence_2026-07-27.133622_txPplH.fasta -seq_format fasta -n score
; Slow counting mode            
; Input files
;	input	$RSAT/public_html/tmp/www-data/2026/07/27/tmp_sequence_2026-07-27.133622_txPplH.fasta
;	bg	$RSAT/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.60/oligo-frequencies/2nt_upstream-noorf_Arabidopsis_thaliana.TAIR10.60-ovlp-1str.freq
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/07/27/matrix-scan_2026-07-27.133622_Ilm2rh.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	file
;	Markov order  	1
;	Strand        	sensitive
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.34589
;		c	0.15671
;		g	0.15366
;		t	0.34374
; Thresholds	lower	upper
;	pval  	NA	0.001
;	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	normw	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
GSBRNA2T00101444001|Brassica_napus.AST_PRJEB5043_v1.60|BnaC03g24640D	site	oligos_6-8nt_m2oligos_6-8nt_m2	D	79	90	CAACACGCCGTC	5.8	2.9e-04	-8.154	3.541	0.8607	1	1
GSBRNA2T00139024001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA03g20600D	limit	START_END	D	-184	199	.	0	0	0	0
GSBRNA2T00139024001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA03g20600D	site	oligos_6-8nt_m2oligos_6-8nt_m2	D	42	53	CAACACGCCGTC	5.8	2.9e-04	-8.154	3.541	0.8607	1	1
GLYMA_08G087500|Glycine_max.Glycine_max_v2.1.60|GLYMA_08G087500	limit	START_END	D	-1501	199	.	0	0	0	0
GLYMA_08G087500|Glycine_max.Glycine_max_v2.1.60|GLYMA_08G087500	site	oligos_6-8nt_m2oligos_6-8nt_m2	D	-1084	-1073	TCTCATGNNNNN	5.5	3.8e-04	-7.874	3.420	0.8525	1	1
GLYMA_08G087500|Glycine_max.Glycine_max_v2.1.60|GLYMA_08G087500	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	-969	-958	TACCATGNNNNN	5.3	4.5e-04	-7.697	3.343	0.8470	2	2
GLYMA_08G087500|Glycine_max.Glycine_max_v2.1.60|GLYMA_08G087500	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	-1317	-1306	TGACATGCACGG	4.6	8.1e-04	-7.117	3.091	0.8279	3	3
GLYMA_08G087500|Glycine_max.Glycine_max_v2.1.60|GLYMA_08G087500	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	140	151	GGTCATGCACAA	4.6	8.1e-04	-7.117	3.091	0.8279	4	4
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
gene-Lalb_Chr13g0292401|Lupinus_albus.CNRS_Lalb_10.GCA_009771035.1.NCBI|gene-Lalb_Chr13g0292401	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	-2	9	TTGCAAGCCACT	6.3	1.8e-04	-8.607	3.738	0.8743	1	1
Prudul26B014047|Prunus_dulcis.ALMONDv2.60|Prudul26B014047	limit	START_END	D	-143	199	.	0	0	0	0
Prudul26B014047|Prunus_dulcis.ALMONDv2.60|Prudul26B014047	site	oligos_6-8nt_m2oligos_6-8nt_m2	D	162	173	ACTCATGCCTCC	7.9	7.5e-05	-9.498	4.125	0.9180	1	1
Prudul26B014047|Prunus_dulcis.ALMONDv2.60|Prudul26B014047	site	oligos_6-8nt_m2oligos_6-8nt_m2	D	-9	2	CGGCAAGCCTAT	5.7	3.2e-04	-8.061	3.501	0.8579	2	2
Prudul26B014047|Prunus_dulcis.ALMONDv2.60|Prudul26B014047	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	-11	0	AGGCTTGCCGCT	5.3	4.5e-04	-7.697	3.343	0.8470	3	3
PRUPE_7G270800|Prunus_persica.Prunus_persica_NCBIv2.60|PRUPE_7G270800	limit	START_END	D	-1	199	.	0	0	0	0
PRUPE_7G270800|Prunus_persica.Prunus_persica_NCBIv2.60|PRUPE_7G270800	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	2	13	TGACATTCCTAT	4.8	7.0e-04	-7.269	3.157	0.8333	1	1
PRUPE_7G270800|Prunus_persica.Prunus_persica_NCBIv2.60|PRUPE_7G270800	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	50	61	AGCCATTCCTAA	4.8	7.0e-04	-7.269	3.157	0.8333	2	2
Solyc08g015660.ITAG4.0|Solanum_lycopersicum.ITAG4.0.JGI|Solyc08g015660.ITAG4.0	limit	START_END	D	-1501	199	.	0	0	0	0
Solyc08g015660.ITAG4.0|Solanum_lycopersicum.ITAG4.0.JGI|Solyc08g015660.ITAG4.0	site	oligos_6-8nt_m2oligos_6-8nt_m2	D	-492	-481	CTGCATGCCATC	7.2	1.0e-04	-9.169	3.982	0.8989	1	1
Solyc08g015660.ITAG4.0|Solanum_lycopersicum.ITAG4.0.JGI|Solyc08g015660.ITAG4.0	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	-680	-669	TAGCATGCGCAT	6.2	2.0e-04	-8.507	3.694	0.8716	2	2
Solyc08g015660.ITAG4.0|Solanum_lycopersicum.ITAG4.0.JGI|Solyc08g015660.ITAG4.0	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	-1390	-1379	AGTCATACCAAA	6.0	2.4e-04	-8.329	3.617	0.8661	3	3
Solyc08g015660.ITAG4.0|Solanum_lycopersicum.ITAG4.0.JGI|Solyc08g015660.ITAG4.0	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	-1491	-1480	AAGTATGCCTAA	5.4	4.1e-04	-7.793	3.384	0.8497	4	4
Solyc08g015660.ITAG4.0|Solanum_lycopersicum.ITAG4.0.JGI|Solyc08g015660.ITAG4.0	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	-494	-483	TGGCATGCAGTC	5.1	5.4e-04	-7.523	3.267	0.8415	5	5
;
; Matrices
;	matrix	name                          	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	oligos_6-8nt_m2oligos_6-8nt_m2	12	4	1	-25.700	10.900	36.600	a:0.346 c:0.157 g:0.154 t:0.344 
; Number of sequences scanned	8
; Sum of sequence lengths	6618
; N residues           	1277
; Matches per matrix
;	matrix	name                          	matches	scored
;	1	oligos_6-8nt_m2oligos_6-8nt_m2	17	13060
;		TOTAL          	17	13060
; Host name	rsat
; Job started	2026-07-27.133623
; Job done	2026-07-27.133624
; Seconds	1.46
;	user	1.46
;	system	0.02
;	cuser	0
;	csystem	0