; 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_m2/peak-motifs_dyads_m2.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_m2/peak-motifs_dyads_m2_sites.tab
; Quick counting mode           
; Input files
;	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
;	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
; 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_m2/peak-motifs_dyads_m2.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_m2/peak-motifs_dyads_m2_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_m2	R	-541	-522	CAGGAGTTTACAACCCGAAG	11.6
NZ_CP037899.1:949092-950181	site	dyads_m2	D	-247	-228	GAGGAACACCGGTGGCGAAG	9.0
NZ_CP037899.1:949092-950181	site	dyads_m2	D	-209	-190	CCTGACTCTGATACACGAAA	8.7
NZ_CP037899.1:949092-950181	site	dyads_m2	R	103	122	CACGACACGAGCTGACGACA	12.7
NZ_CP037899.1:949092-950181	site	dyads_m2	D	286	305	AGGGAAGCAAGACCGCGAGG	10.9
NZ_CP037899.1:949092-950181	site	dyads_m2	R	352	371	CCGGCTTCACGAAGGCGAGT	8.0
NZ_CP037899.1:949092-950181	site	dyads_m2	R	513	532	ACGGCTACCTTGTTACGACT	9.8
NZ_CP037899.1:949092-950181	site	dyads_m2	R	-541	-522	CAGGAGTTTACAACCCGAAG	11.6
NZ_CP037899.1:949092-950181	site	dyads_m2	D	-247	-228	GAGGAACACCGGTGGCGAAG	9.0
NZ_CP037899.1:949092-950181	site	dyads_m2	D	-209	-190	CCTGACTCTGATACACGAAA	8.7
NZ_CP037899.1:949092-950181	site	dyads_m2	R	103	122	CACGACACGAGCTGACGACA	12.7
NZ_CP037899.1:949092-950181	site	dyads_m2	D	286	305	AGGGAAGCAAGACCGCGAGG	10.9
NZ_CP037899.1:949092-950181	site	dyads_m2	R	352	371	CCGGCTTCACGAAGGCGAGT	8.0
NZ_CP037899.1:949092-950181	site	dyads_m2	R	513	532	ACGGCTACCTTGTTACGACT	9.8
NZ_CP037899.1:949092-950181	site	dyads_m2	R	-541	-522	CAGGAGTTTACAACCCGAAG	11.6
NZ_CP037899.1:949092-950181	site	dyads_m2	D	-247	-228	GAGGAACACCGGTGGCGAAG	9.0
NZ_CP037899.1:949092-950181	site	dyads_m2	D	-209	-190	CCTGACTCTGATACACGAAA	8.7
NZ_CP037899.1:949092-950181	site	dyads_m2	R	103	122	CACGACACGAGCTGACGACA	12.7
NZ_CP037899.1:949092-950181	site	dyads_m2	D	286	305	AGGGAAGCAAGACCGCGAGG	10.9
NZ_CP037899.1:949092-950181	site	dyads_m2	R	352	371	CCGGCTTCACGAAGGCGAGT	8.0
NZ_CP037899.1:949092-950181	site	dyads_m2	R	513	532	ACGGCTACCTTGTTACGACT	9.8
NZ_CP037899.1:953361-953582	site	dyads_m2	R	-36	-17	CAGGATGCGATGAGCCGACA	11.8
NZ_CP037899.1:1164899-1165284	site	dyads_m2	D	142	161	AAGGCCGCAACACACCGATG	11.1
NZ_CP037899.1:1164899-1165284	site	dyads_m2	D	142	161	AAGGCCGCAACACACCGATG	11.1
NZ_CP037899.1:1508893-1509246	site	dyads_m2	R	-84	-65	TCGGACATAGCGATACGAAC	9.5
NZ_CP037899.1:2135546-2135746	site	dyads_m2	D	51	70	AAGGATTTTCCAATCCGATC	7.6
;
; Matrices
;	matrix	name    	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	dyads_m2	20	4	0	-31.600	14.100	45.700	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_m2       	26	0
;		TOTAL          	26	0
; Host name	rsat
; Job started	2025-03-02.091349
; Job done	2025-03-02.091349
; Seconds	0.12
;	user	0.12
;	system	0.02
;	cuser	0.1
;	csystem	0.01
