; matrix-scan  -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/07/23/matrix-scan_2026-07-23.092250_zqfA2D.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/2026/07/23/retrieve-seq_2026-07-23.091839_qH7BlP.fasta.fasta -seq_format fasta -n score
; Slow counting mode            
; Input files
;	input	$RSAT/public_html/tmp/www-data/2026/07/23/retrieve-seq_2026-07-23.091839_qH7BlP.fasta.fasta
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/07/23/matrix-scan_2026-07-23.092250_zqfA2D.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	input
;	Markov order  	1
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.34027
;		c	0.18532
;		g	0.16609
;		t	0.30832
; 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
gene25542	limit	START_END	D	-1501	199	.	0	0	0	0
gene25542	site	oligos_6-8nt_m7oligos_6-8nt_m7	R	11	25	TGAGCGATCAAGCCT	9.2	1.1e-05	-11.396	4.949	1	1
gene7299	limit	START_END	D	-1501	199	.	0	0	0	0
gene22259	limit	START_END	D	-1	199	.	0	0	0	0
gene3683	limit	START_END	D	-1501	199	.	0	0	0	0
gene3683	site	oligos_6-8nt_m7oligos_6-8nt_m7	D	-1059	-1045	ATAGCCACCACCATA	6.4	9.7e-05	-9.243	4.014	1	1
gene14703	limit	START_END	D	-1501	199	.	0	0	0	0
gene14703	site	oligos_6-8nt_m7oligos_6-8nt_m7	R	-593	-579	CTAGAGATCAAGTTT	7.0	6.3e-05	-9.677	4.203	1	1
gene14702	limit	START_END	D	-1501	199	.	0	0	0	0
;
; Matrices
;	matrix	name                          	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	oligos_6-8nt_m7oligos_6-8nt_m7	15	4	1	-41.400	15.900	57.300	a:0.340 c:0.185 g:0.166 t:0.308 
; Number of sequences scanned	6
; Sum of sequence lengths	8706
; N residues           	0
; Matches per matrix
;	matrix	name                          	matches	scored
;	1	oligos_6-8nt_m7oligos_6-8nt_m7	3	17244
;		TOTAL          	3	17244
; Host name	rsat
; Job started	2026-07-23.092251
; Job done	2026-07-23.092253
; Seconds	2.21
;	user	2.21
;	system	0.04
;	cuser	0.11
;	csystem	0.02