; matrix-scan  -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab
; Quick counting mode           
; Input files
;	bg	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt
;	input	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/data/sequences/peak-motifs_test.fasta
; Matrix files
;	matrix 1	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tf
; Sequence format      	fasta
; Output files
;	output	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab
; Pseudo counts        	1
; Background model
;	Method        	file
;	Markov order  	1
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.30609
;		c	0.19676
;		g	0.20512
;		t	0.29203
; Thresholds	lower	upper
;	score 	7.5  	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
NZ_CP037899.1:949092-950181	site	dyads_m1	R	-350	-338	AAGCAAAGGGATT	7.9
NZ_CP037899.1:949092-950181	site	dyads_m1	D	-310	-298	TAGCTAGAGGACC	8.6
NZ_CP037899.1:949092-950181	site	dyads_m1	R	45	57	CAGCAACTGAACA	10.3
NZ_CP037899.1:949092-950181	site	dyads_m1	R	161	173	CGGCAACTGGACA	12.0
NZ_CP037899.1:949092-950181	site	dyads_m1	R	-350	-338	AAGCAAAGGGATT	7.9
NZ_CP037899.1:949092-950181	site	dyads_m1	D	-310	-298	TAGCTAGAGGACC	8.6
NZ_CP037899.1:949092-950181	site	dyads_m1	R	45	57	CAGCAACTGAACA	10.3
NZ_CP037899.1:949092-950181	site	dyads_m1	R	161	173	CGGCAACTGGACA	12.0
NZ_CP037899.1:949092-950181	site	dyads_m1	R	-350	-338	AAGCAAAGGGATT	7.9
NZ_CP037899.1:949092-950181	site	dyads_m1	D	-310	-298	TAGCTAGAGGACC	8.6
NZ_CP037899.1:949092-950181	site	dyads_m1	R	45	57	CAGCAACTGAACA	10.3
NZ_CP037899.1:949092-950181	site	dyads_m1	R	161	173	CGGCAACTGGACA	12.0
NZ_CP037899.1:1134619-1134882	site	dyads_m1	D	67	79	AAGCAAGAGGAAA	8.7
NZ_CP037899.1:1164899-1165284	site	dyads_m1	D	-32	-20	CTGCAAATGGAGA	8.4
NZ_CP037899.1:1164899-1165284	site	dyads_m1	D	-32	-20	CTGCAAATGGAGA	8.4
NZ_CP037899.1:1640064-1640409	site	dyads_m1	R	58	70	GAGCAGATGGATT	8.7
NZ_CP037899.1:2093304-2093628	site	dyads_m1	R	-49	-37	AGGCAGCTGGACT	10.1
NZ_CP037899.1:2135546-2135746	site	dyads_m1	D	-71	-59	CAGCAATAGGAAC	8.7
NZ_CP037899.1:2135546-2135746	site	dyads_m1	D	-30	-18	CAGCAGATGGAAT	9.7
NZ_CP037899.1:2135546-2135746	site	dyads_m1	D	45	57	AGGCAAAAGGATT	8.0
;
; Matrices
;	matrix	name    	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	dyads_m1	13	4	0	-27.200	12.100	39.300	a:0.306 c:0.197 g:0.205 t:0.292 
; Number of sequences scanned	23
; Sum of sequence lengths	10099
; N residues           	0
; Matches per matrix
;	matrix	name    	matches	scored
;	1	dyads_m1       	20	0
;		TOTAL          	20	0
; Host name	rsat
; Job started	2025-03-02.091348
; Job done	2025-03-02.091348
; Seconds	0.17
;	user	0.17
;	system	0.01
;	cuser	0.08
;	csystem	0.02
