; matrix-scan  -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/06/18/matrix-scan_2026-06-18.094009_ETLMrs.matrix -pseudo 1 -decimals 1 -2str -origin end -bgfile $RSAT/public_html/data/genomes/Homo_sapiens_GRCh38/oligo-frequencies/2nt_upstream-noorf_Homo_sapiens_GRCh38-ovlp-1str.freq -bg_pseudo 0.01 -return limits -return sites -return pval -return rank -lth score 1 -uth pval 5e-3 -i $RSAT/public_html/tmp/www-data/2026/06/18/tmp_sequence_2026-06-18.094009_gJMTGU.fasta -seq_format fasta -n score
; Slow counting mode            
; Input files
;	input	$RSAT/public_html/tmp/www-data/2026/06/18/tmp_sequence_2026-06-18.094009_gJMTGU.fasta
;	bg	$RSAT/public_html/data/genomes/Homo_sapiens_GRCh38/oligo-frequencies/2nt_upstream-noorf_Homo_sapiens_GRCh38-ovlp-1str.freq
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/06/18/matrix-scan_2026-06-18.094009_ETLMrs.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	file
;	Markov order  	1
;	Strand        	sensitive
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.28149
;		c	0.21988
;		g	0.22090
;		t	0.27773
; Thresholds	lower	upper
;	pval  	NA	0.005
;	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
hg38_dna	limit	START_END	D	-1601	-1	.	0	0	0	0
hg38_dna	limit	START_END	D	-1601	-1	.	0	0	0	0
hg38_dna	limit	START_END	D	-1601	-1	.	0	0	0	0
;
; Matrices
;	matrix	name  	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	TOPORS	17	4	1	-78.500	23.200	101.700	a:0.281 c:0.220 g:0.221 t:0.278 
; Number of sequences scanned	3
; Sum of sequence lengths	4803
; N residues           	0
; Matches per matrix
;	matrix	name  	matches	scored
;	1	TOPORS         	0	9510
;		TOTAL          	0	9510
; Host name	rsat
; Job started	2026-06-18.094009
; Job done	2026-06-18.094011
; Seconds	2.47
;	user	2.47
;	system	0.02
;	cuser	0
;	csystem	0