; matrix-scan  -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/07/27/matrix-scan_2026-07-27.113832_UFSSNo.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/2026/07/27/tmp_sequence_2026-07-27.113832_1qphsu.fasta -seq_format fasta -n score
; Slow counting mode            
; Input files
;	input	$RSAT/public_html/tmp/www-data/2026/07/27/tmp_sequence_2026-07-27.113832_1qphsu.fasta
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/07/27/matrix-scan_2026-07-27.113832_UFSSNo.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	input
;	Markov order  	1
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.33310
;		c	0.18237
;		g	0.16015
;		t	0.32438
; 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
F6'H1	limit	START_END	D	-1701	-1	.	0	0	0	0
F6'H1	site	oligos_6-8nt_m2oligos_6-8nt_m2	D	-1685	-1674	AACCATGCCTAG	8.8	3.8e-05	-10.174	4.419	1	1
F6'H1	site	oligos_6-8nt_m2oligos_6-8nt_m2	D	-1656	-1645	AACCATGCCTAG	8.8	3.8e-05	-10.174	4.419	2	2
AT3G12900	limit	START_END	D	-1701	-1	.	0	0	0	0
AT3G12900	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	-31	-20	TTTCACGCCGTT	8.6	4.9e-05	-9.926	4.311	1	1
AT3G12900	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	-882	-871	AGCCATGCCCCT	7.8	9.2e-05	-9.291	4.035	2	2
CYP82C4	limit	START_END	D	-1269	-1	.	0	0	0	0
AT1G28680	limit	START_END	D	-201	-1	.	0	0	0	0
ABCG37	limit	START_END	D	-1701	-1	.	0	0	0	0
COS1	limit	START_END	D	-251	-1	.	0	0	0	0
RIBA1	limit	START_END	D	-1307	-1	.	0	0	0	0
RIBC	limit	START_END	D	-278	-1	.	0	0	0	0
;
; Matrices
;	matrix	name                          	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	oligos_6-8nt_m2oligos_6-8nt_m2	12	4	1	-26.400	10.600	37.000	a:0.333 c:0.182 g:0.160 t:0.324 
; Number of sequences scanned	8
; Sum of sequence lengths	8409
; N residues           	653
; Matches per matrix
;	matrix	name                          	matches	scored
;	1	oligos_6-8nt_m2oligos_6-8nt_m2	4	16642
;		TOTAL          	4	16642
; Host name	rsat
; Job started	2026-07-27.113832
; Job done	2026-07-27.113834
; Seconds	1.76
;	user	1.76
;	system	0.04
;	cuser	0.12
;	csystem	0.01