; matrix-scan  -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/04/11/matrix-scan_2026-04-11.115129_FJd52T.matrix -pseudo 1 -decimals 1 -2str -origin end -bgfile $RSAT/public_html/data/genomes/Solanum_lycopersicum.SL5.0.SGN/oligo-frequencies/2nt_upstream-noorf_Solanum_lycopersicum.SL5.0.SGN-ovlp-1str.freq -bg_pseudo 0.01 -return limits -return sites -return pval -return rank -lth score 1 -lth pval 0 -uth pval 1e-4 -i $RSAT/public_html/tmp/www-data/2026/04/11/tmp_sequence_2026-04-11.115129_QfOqQ8.fasta -seq_format fasta -n score
; Slow counting mode            
; Input files
;	bg	$RSAT/public_html/data/genomes/Solanum_lycopersicum.SL5.0.SGN/oligo-frequencies/2nt_upstream-noorf_Solanum_lycopersicum.SL5.0.SGN-ovlp-1str.freq
;	input	$RSAT/public_html/tmp/www-data/2026/04/11/tmp_sequence_2026-04-11.115129_QfOqQ8.fasta
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/04/11/matrix-scan_2026-04-11.115129_FJd52T.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	file
;	Markov order  	1
;	Strand        	sensitive
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.35306
;		c	0.14789
;		g	0.14533
;		t	0.35371
; Thresholds	lower	upper
;	pval  	0    	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
SL2.50ch09:7426223..7427222	limit	START_END	D	-1000	-1	.	0	0	0	0
;
; Matrices
;	matrix	name                      	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	C2C2dof_tnt.Adof1_col_a_m1	21	4	1	-45.100	13.500	58.600	a:0.353 c:0.148 g:0.145 t:0.354 
;	2	HSF_tnt.HSF21_col_a_m1    	19	4	1	-45.900	19.400	65.300	a:0.353 c:0.148 g:0.145 t:0.354 
;	3	HSF_tnt.HSFA1E_col_a_m1   	13	4	1	-55.000	15.200	70.200	a:0.353 c:0.148 g:0.145 t:0.354 
; Number of sequences scanned	1
; Sum of sequence lengths	1000
; N residues           	0
; Matches per matrix
;	matrix	name                      	matches	scored
;	1	C2C2dof_tnt.Adof1_col_a_m1	0	1960
;	2	HSF_tnt.HSF21_col_a_m1	0	1964
;	3	HSF_tnt.HSFA1E_col_a_m1	0	1976
;		TOTAL          	0	5900
; Host name	rsat
; Job started	2026-04-11.115130
; Job done	2026-04-11.115133
; Seconds	3.35
;	user	3.35
;	system	0.02
;	cuser	0
;	csystem	0