; 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/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_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/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_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/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_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/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_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_CP037899.1:7618-7818	site	oligos_6nt_mkv2_m1	D	-3	6	TCAAAGAAGT	7.5
;
; Matrices
;	matrix	name              	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	oligos_6nt_mkv2_m1	10	4	0	-23.400	8.600	32.000	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	oligos_6nt_mkv2_m1	1	0
;		TOTAL          	1	0
; Host name	rsat
; Job started	2025-03-02.091346
; Job done	2025-03-02.091346
; Seconds	0.14
;	user	0.14
;	system	0.01
;	cuser	0.1
;	csystem	0.02
; 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/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_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/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_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/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_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/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_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_CP037899.1:230205-230716	site	oligos_7nt_mkv2_m1	R	62	72	GGCCGCAACTT	8.1
NZ_CP037899.1:644474-644930	site	oligos_7nt_mkv2_m1	R	-173	-163	TTCGGCAACAT	9.6
NZ_CP037899.1:644474-644930	site	oligos_7nt_mkv2_m1	R	-173	-163	TTCGGCAACAT	9.6
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	-128	-118	TCCGCCAACGC	8.1
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	49	59	TTCAGCAACTG	8.3
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	D	138	148	TCCCGCAACGA	8.7
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	165	175	TTCGGCAACTG	10.4
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	479	489	TTCGACAACCT	8.4
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	523	533	TACGGCTACCT	8.3
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	-128	-118	TCCGCCAACGC	8.1
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	49	59	TTCAGCAACTG	8.3
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	D	138	148	TCCCGCAACGA	8.7
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	165	175	TTCGGCAACTG	10.4
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	479	489	TTCGACAACCT	8.4
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	523	533	TACGGCTACCT	8.3
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	-128	-118	TCCGCCAACGC	8.1
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	49	59	TTCAGCAACTG	8.3
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	D	138	148	TCCCGCAACGA	8.7
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	165	175	TTCGGCAACTG	10.4
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	479	489	TTCGACAACCT	8.4
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	523	533	TACGGCTACCT	8.3
NZ_CP037899.1:1164899-1165284	site	oligos_7nt_mkv2_m1	R	-104	-94	ATCGGCAACTG	8.4
NZ_CP037899.1:1164899-1165284	site	oligos_7nt_mkv2_m1	R	46	56	TCCGGCAACTA	10.0
NZ_CP037899.1:1164899-1165284	site	oligos_7nt_mkv2_m1	D	144	154	GGCCGCAACAC	7.5
NZ_CP037899.1:1164899-1165284	site	oligos_7nt_mkv2_m1	R	-104	-94	ATCGGCAACTG	8.4
NZ_CP037899.1:1164899-1165284	site	oligos_7nt_mkv2_m1	R	46	56	TCCGGCAACTA	10.0
NZ_CP037899.1:1164899-1165284	site	oligos_7nt_mkv2_m1	D	144	154	GGCCGCAACAC	7.5
NZ_CP037899.1:2093304-2093628	site	oligos_7nt_mkv2_m1	R	-76	-66	AGCGGCAACGC	8.3
;
; Matrices
;	matrix	name              	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	oligos_7nt_mkv2_m1	11	4	0	-27.200	11.100	38.300	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	oligos_7nt_mkv2_m1	28	0
;		TOTAL          	28	0
; Host name	rsat
; Job started	2025-03-02.091347
; Job done	2025-03-02.091347
; Seconds	0.12
;	user	0.12
;	system	0.03
;	cuser	0.09
;	csystem	0.02
; 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
; 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
; 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_m3/peak-motifs_dyads_m3.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_m3/peak-motifs_dyads_m3_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_m3/peak-motifs_dyads_m3.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_m3/peak-motifs_dyads_m3_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_CP037899.1:230205-230716	site	dyads_m3	R	-169	-140	CCACCGAGCGCTCCCAGGTGGAGTCCAGCA	10.5
NZ_CP037899.1:949092-950181	site	dyads_m3	R	-396	-367	TAACCTCCTACACACCCTTTACGCCCAGTA	12.9
NZ_CP037899.1:949092-950181	site	dyads_m3	D	-212	-183	GTACCTGACTCTGATACACGAAAGCTAGGG	13.2
NZ_CP037899.1:949092-950181	site	dyads_m3	R	-210	-181	TCCCCTAGCTTTCGTGTATCAGAGTCAGGT	14.1
NZ_CP037899.1:949092-950181	site	dyads_m3	D	-166	-137	ATACCCCGGTAGTCCTAGCCGTAAACGGTG	9.1
NZ_CP037899.1:949092-950181	site	dyads_m3	D	24	53	TTACCAGGCCTTGACATGCCGTGTTCAGTT	15.1
NZ_CP037899.1:949092-950181	site	dyads_m3	R	181	210	TCCCCGTTATACGAGGCAGTCTGTTCAGAG	10.9
NZ_CP037899.1:949092-950181	site	dyads_m3	R	190	219	CCACCTTCCTCCCCGTTATACGAGGCAGTC	14.2
NZ_CP037899.1:949092-950181	site	dyads_m3	R	431	460	CAACCAGCTTTCAGGATGTGACGGGCGGTG	12.6
NZ_CP037899.1:949092-950181	site	dyads_m3	R	-396	-367	TAACCTCCTACACACCCTTTACGCCCAGTA	12.9
NZ_CP037899.1:949092-950181	site	dyads_m3	D	-212	-183	GTACCTGACTCTGATACACGAAAGCTAGGG	13.2
NZ_CP037899.1:949092-950181	site	dyads_m3	R	-210	-181	TCCCCTAGCTTTCGTGTATCAGAGTCAGGT	14.1
NZ_CP037899.1:949092-950181	site	dyads_m3	D	-166	-137	ATACCCCGGTAGTCCTAGCCGTAAACGGTG	9.1
NZ_CP037899.1:949092-950181	site	dyads_m3	D	24	53	TTACCAGGCCTTGACATGCCGTGTTCAGTT	15.1
NZ_CP037899.1:949092-950181	site	dyads_m3	R	181	210	TCCCCGTTATACGAGGCAGTCTGTTCAGAG	10.9
NZ_CP037899.1:949092-950181	site	dyads_m3	R	190	219	CCACCTTCCTCCCCGTTATACGAGGCAGTC	14.2
NZ_CP037899.1:949092-950181	site	dyads_m3	R	431	460	CAACCAGCTTTCAGGATGTGACGGGCGGTG	12.6
NZ_CP037899.1:949092-950181	site	dyads_m3	R	-396	-367	TAACCTCCTACACACCCTTTACGCCCAGTA	12.9
NZ_CP037899.1:949092-950181	site	dyads_m3	D	-212	-183	GTACCTGACTCTGATACACGAAAGCTAGGG	13.2
NZ_CP037899.1:949092-950181	site	dyads_m3	R	-210	-181	TCCCCTAGCTTTCGTGTATCAGAGTCAGGT	14.1
NZ_CP037899.1:949092-950181	site	dyads_m3	D	-166	-137	ATACCCCGGTAGTCCTAGCCGTAAACGGTG	9.1
NZ_CP037899.1:949092-950181	site	dyads_m3	D	24	53	TTACCAGGCCTTGACATGCCGTGTTCAGTT	15.1
NZ_CP037899.1:949092-950181	site	dyads_m3	R	181	210	TCCCCGTTATACGAGGCAGTCTGTTCAGAG	10.9
NZ_CP037899.1:949092-950181	site	dyads_m3	R	190	219	CCACCTTCCTCCCCGTTATACGAGGCAGTC	14.2
NZ_CP037899.1:949092-950181	site	dyads_m3	R	431	460	CAACCAGCTTTCAGGATGTGACGGGCGGTG	12.6
NZ_CP037899.1:953361-953582	site	dyads_m3	R	37	66	GAACTGTCTCACGACGTTCTGAACCCAGCT	7.8
NZ_CP037899.1:953361-953582	site	dyads_m3	R	77	106	GAACCCCTCAGATCTCCAGCGCCCACAGTG	9.1
NZ_CP037899.1:1508893-1509246	site	dyads_m3	D	119	148	TAACCTAATATAAATTAGGCAGATCCAGTA	9.0
NZ_CP037899.1:1530412-1530753	site	dyads_m3	R	127	156	TAACCAATACCTTTGTTACGATGCGCAGAA	9.6
;
; Matrices
;	matrix	name    	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	dyads_m3	30	4	0	-43.600	19.900	63.500	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_m3       	29	0
;		TOTAL          	29	0
; Host name	rsat
; Job started	2025-03-02.091349
; Job done	2025-03-02.091350
; Seconds	0.17
;	user	0.17
;	system	0.02
;	cuser	0.09
;	csystem	0.01
; 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/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_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/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_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/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_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/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_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_CP037899.1:7618-7818	site	oligos_6nt_mkv2_m1	D	-3	6	TCAAAGAAGT	7.5
;
; Matrices
;	matrix	name              	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	oligos_6nt_mkv2_m1	10	4	0	-23.400	8.600	32.000	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	oligos_6nt_mkv2_m1	1	0
;		TOTAL          	1	0
; Host name	rsat
; Job started	2025-03-02.091346
; Job done	2025-03-02.091346
; Seconds	0.14
;	user	0.14
;	system	0.01
;	cuser	0.1
;	csystem	0.02
; 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/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_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/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_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/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_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/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_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_CP037899.1:230205-230716	site	oligos_7nt_mkv2_m1	R	62	72	GGCCGCAACTT	8.1
NZ_CP037899.1:644474-644930	site	oligos_7nt_mkv2_m1	R	-173	-163	TTCGGCAACAT	9.6
NZ_CP037899.1:644474-644930	site	oligos_7nt_mkv2_m1	R	-173	-163	TTCGGCAACAT	9.6
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	-128	-118	TCCGCCAACGC	8.1
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	49	59	TTCAGCAACTG	8.3
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	D	138	148	TCCCGCAACGA	8.7
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	165	175	TTCGGCAACTG	10.4
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	479	489	TTCGACAACCT	8.4
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	523	533	TACGGCTACCT	8.3
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	-128	-118	TCCGCCAACGC	8.1
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	49	59	TTCAGCAACTG	8.3
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	D	138	148	TCCCGCAACGA	8.7
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	165	175	TTCGGCAACTG	10.4
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	479	489	TTCGACAACCT	8.4
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	523	533	TACGGCTACCT	8.3
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	-128	-118	TCCGCCAACGC	8.1
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	49	59	TTCAGCAACTG	8.3
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	D	138	148	TCCCGCAACGA	8.7
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	165	175	TTCGGCAACTG	10.4
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	479	489	TTCGACAACCT	8.4
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	523	533	TACGGCTACCT	8.3
NZ_CP037899.1:1164899-1165284	site	oligos_7nt_mkv2_m1	R	-104	-94	ATCGGCAACTG	8.4
NZ_CP037899.1:1164899-1165284	site	oligos_7nt_mkv2_m1	R	46	56	TCCGGCAACTA	10.0
NZ_CP037899.1:1164899-1165284	site	oligos_7nt_mkv2_m1	D	144	154	GGCCGCAACAC	7.5
NZ_CP037899.1:1164899-1165284	site	oligos_7nt_mkv2_m1	R	-104	-94	ATCGGCAACTG	8.4
NZ_CP037899.1:1164899-1165284	site	oligos_7nt_mkv2_m1	R	46	56	TCCGGCAACTA	10.0
NZ_CP037899.1:1164899-1165284	site	oligos_7nt_mkv2_m1	D	144	154	GGCCGCAACAC	7.5
NZ_CP037899.1:2093304-2093628	site	oligos_7nt_mkv2_m1	R	-76	-66	AGCGGCAACGC	8.3
;
; Matrices
;	matrix	name              	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	oligos_7nt_mkv2_m1	11	4	0	-27.200	11.100	38.300	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	oligos_7nt_mkv2_m1	28	0
;		TOTAL          	28	0
; Host name	rsat
; Job started	2025-03-02.091347
; Job done	2025-03-02.091347
; Seconds	0.12
;	user	0.12
;	system	0.03
;	cuser	0.09
;	csystem	0.02
; 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
; 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
; 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_m3/peak-motifs_dyads_m3.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_m3/peak-motifs_dyads_m3_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_m3/peak-motifs_dyads_m3.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_m3/peak-motifs_dyads_m3_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_CP037899.1:230205-230716	site	dyads_m3	R	-169	-140	CCACCGAGCGCTCCCAGGTGGAGTCCAGCA	10.5
NZ_CP037899.1:949092-950181	site	dyads_m3	R	-396	-367	TAACCTCCTACACACCCTTTACGCCCAGTA	12.9
NZ_CP037899.1:949092-950181	site	dyads_m3	D	-212	-183	GTACCTGACTCTGATACACGAAAGCTAGGG	13.2
NZ_CP037899.1:949092-950181	site	dyads_m3	R	-210	-181	TCCCCTAGCTTTCGTGTATCAGAGTCAGGT	14.1
NZ_CP037899.1:949092-950181	site	dyads_m3	D	-166	-137	ATACCCCGGTAGTCCTAGCCGTAAACGGTG	9.1
NZ_CP037899.1:949092-950181	site	dyads_m3	D	24	53	TTACCAGGCCTTGACATGCCGTGTTCAGTT	15.1
NZ_CP037899.1:949092-950181	site	dyads_m3	R	181	210	TCCCCGTTATACGAGGCAGTCTGTTCAGAG	10.9
NZ_CP037899.1:949092-950181	site	dyads_m3	R	190	219	CCACCTTCCTCCCCGTTATACGAGGCAGTC	14.2
NZ_CP037899.1:949092-950181	site	dyads_m3	R	431	460	CAACCAGCTTTCAGGATGTGACGGGCGGTG	12.6
NZ_CP037899.1:949092-950181	site	dyads_m3	R	-396	-367	TAACCTCCTACACACCCTTTACGCCCAGTA	12.9
NZ_CP037899.1:949092-950181	site	dyads_m3	D	-212	-183	GTACCTGACTCTGATACACGAAAGCTAGGG	13.2
NZ_CP037899.1:949092-950181	site	dyads_m3	R	-210	-181	TCCCCTAGCTTTCGTGTATCAGAGTCAGGT	14.1
NZ_CP037899.1:949092-950181	site	dyads_m3	D	-166	-137	ATACCCCGGTAGTCCTAGCCGTAAACGGTG	9.1
NZ_CP037899.1:949092-950181	site	dyads_m3	D	24	53	TTACCAGGCCTTGACATGCCGTGTTCAGTT	15.1
NZ_CP037899.1:949092-950181	site	dyads_m3	R	181	210	TCCCCGTTATACGAGGCAGTCTGTTCAGAG	10.9
NZ_CP037899.1:949092-950181	site	dyads_m3	R	190	219	CCACCTTCCTCCCCGTTATACGAGGCAGTC	14.2
NZ_CP037899.1:949092-950181	site	dyads_m3	R	431	460	CAACCAGCTTTCAGGATGTGACGGGCGGTG	12.6
NZ_CP037899.1:949092-950181	site	dyads_m3	R	-396	-367	TAACCTCCTACACACCCTTTACGCCCAGTA	12.9
NZ_CP037899.1:949092-950181	site	dyads_m3	D	-212	-183	GTACCTGACTCTGATACACGAAAGCTAGGG	13.2
NZ_CP037899.1:949092-950181	site	dyads_m3	R	-210	-181	TCCCCTAGCTTTCGTGTATCAGAGTCAGGT	14.1
NZ_CP037899.1:949092-950181	site	dyads_m3	D	-166	-137	ATACCCCGGTAGTCCTAGCCGTAAACGGTG	9.1
NZ_CP037899.1:949092-950181	site	dyads_m3	D	24	53	TTACCAGGCCTTGACATGCCGTGTTCAGTT	15.1
NZ_CP037899.1:949092-950181	site	dyads_m3	R	181	210	TCCCCGTTATACGAGGCAGTCTGTTCAGAG	10.9
NZ_CP037899.1:949092-950181	site	dyads_m3	R	190	219	CCACCTTCCTCCCCGTTATACGAGGCAGTC	14.2
NZ_CP037899.1:949092-950181	site	dyads_m3	R	431	460	CAACCAGCTTTCAGGATGTGACGGGCGGTG	12.6
NZ_CP037899.1:953361-953582	site	dyads_m3	R	37	66	GAACTGTCTCACGACGTTCTGAACCCAGCT	7.8
NZ_CP037899.1:953361-953582	site	dyads_m3	R	77	106	GAACCCCTCAGATCTCCAGCGCCCACAGTG	9.1
NZ_CP037899.1:1508893-1509246	site	dyads_m3	D	119	148	TAACCTAATATAAATTAGGCAGATCCAGTA	9.0
NZ_CP037899.1:1530412-1530753	site	dyads_m3	R	127	156	TAACCAATACCTTTGTTACGATGCGCAGAA	9.6
;
; Matrices
;	matrix	name    	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	dyads_m3	30	4	0	-43.600	19.900	63.500	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_m3       	29	0
;		TOTAL          	29	0
; Host name	rsat
; Job started	2025-03-02.091349
; Job done	2025-03-02.091350
; Seconds	0.17
;	user	0.17
;	system	0.02
;	cuser	0.09
;	csystem	0.01
; 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/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_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/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_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/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_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/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_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_CP037899.1:7618-7818	site	oligos_6nt_mkv2_m1	D	-3	6	TCAAAGAAGT	7.5
;
; Matrices
;	matrix	name              	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	oligos_6nt_mkv2_m1	10	4	0	-23.400	8.600	32.000	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	oligos_6nt_mkv2_m1	1	0
;		TOTAL          	1	0
; Host name	rsat
; Job started	2025-03-02.091346
; Job done	2025-03-02.091346
; Seconds	0.14
;	user	0.14
;	system	0.01
;	cuser	0.1
;	csystem	0.02
; 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/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_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/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_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/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_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/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_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_CP037899.1:230205-230716	site	oligos_7nt_mkv2_m1	R	62	72	GGCCGCAACTT	8.1
NZ_CP037899.1:644474-644930	site	oligos_7nt_mkv2_m1	R	-173	-163	TTCGGCAACAT	9.6
NZ_CP037899.1:644474-644930	site	oligos_7nt_mkv2_m1	R	-173	-163	TTCGGCAACAT	9.6
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	-128	-118	TCCGCCAACGC	8.1
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	49	59	TTCAGCAACTG	8.3
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	D	138	148	TCCCGCAACGA	8.7
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	165	175	TTCGGCAACTG	10.4
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	479	489	TTCGACAACCT	8.4
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	523	533	TACGGCTACCT	8.3
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	-128	-118	TCCGCCAACGC	8.1
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	49	59	TTCAGCAACTG	8.3
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	D	138	148	TCCCGCAACGA	8.7
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	165	175	TTCGGCAACTG	10.4
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	479	489	TTCGACAACCT	8.4
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	523	533	TACGGCTACCT	8.3
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	-128	-118	TCCGCCAACGC	8.1
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	49	59	TTCAGCAACTG	8.3
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	D	138	148	TCCCGCAACGA	8.7
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	165	175	TTCGGCAACTG	10.4
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	479	489	TTCGACAACCT	8.4
NZ_CP037899.1:949092-950181	site	oligos_7nt_mkv2_m1	R	523	533	TACGGCTACCT	8.3
NZ_CP037899.1:1164899-1165284	site	oligos_7nt_mkv2_m1	R	-104	-94	ATCGGCAACTG	8.4
NZ_CP037899.1:1164899-1165284	site	oligos_7nt_mkv2_m1	R	46	56	TCCGGCAACTA	10.0
NZ_CP037899.1:1164899-1165284	site	oligos_7nt_mkv2_m1	D	144	154	GGCCGCAACAC	7.5
NZ_CP037899.1:1164899-1165284	site	oligos_7nt_mkv2_m1	R	-104	-94	ATCGGCAACTG	8.4
NZ_CP037899.1:1164899-1165284	site	oligos_7nt_mkv2_m1	R	46	56	TCCGGCAACTA	10.0
NZ_CP037899.1:1164899-1165284	site	oligos_7nt_mkv2_m1	D	144	154	GGCCGCAACAC	7.5
NZ_CP037899.1:2093304-2093628	site	oligos_7nt_mkv2_m1	R	-76	-66	AGCGGCAACGC	8.3
;
; Matrices
;	matrix	name              	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	oligos_7nt_mkv2_m1	11	4	0	-27.200	11.100	38.300	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	oligos_7nt_mkv2_m1	28	0
;		TOTAL          	28	0
; Host name	rsat
; Job started	2025-03-02.091347
; Job done	2025-03-02.091347
; Seconds	0.12
;	user	0.12
;	system	0.03
;	cuser	0.09
;	csystem	0.02
; 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
; 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
; 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_m3/peak-motifs_dyads_m3.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_m3/peak-motifs_dyads_m3_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_m3/peak-motifs_dyads_m3.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_m3/peak-motifs_dyads_m3_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_CP037899.1:230205-230716	site	dyads_m3	R	-169	-140	CCACCGAGCGCTCCCAGGTGGAGTCCAGCA	10.5
NZ_CP037899.1:949092-950181	site	dyads_m3	R	-396	-367	TAACCTCCTACACACCCTTTACGCCCAGTA	12.9
NZ_CP037899.1:949092-950181	site	dyads_m3	D	-212	-183	GTACCTGACTCTGATACACGAAAGCTAGGG	13.2
NZ_CP037899.1:949092-950181	site	dyads_m3	R	-210	-181	TCCCCTAGCTTTCGTGTATCAGAGTCAGGT	14.1
NZ_CP037899.1:949092-950181	site	dyads_m3	D	-166	-137	ATACCCCGGTAGTCCTAGCCGTAAACGGTG	9.1
NZ_CP037899.1:949092-950181	site	dyads_m3	D	24	53	TTACCAGGCCTTGACATGCCGTGTTCAGTT	15.1
NZ_CP037899.1:949092-950181	site	dyads_m3	R	181	210	TCCCCGTTATACGAGGCAGTCTGTTCAGAG	10.9
NZ_CP037899.1:949092-950181	site	dyads_m3	R	190	219	CCACCTTCCTCCCCGTTATACGAGGCAGTC	14.2
NZ_CP037899.1:949092-950181	site	dyads_m3	R	431	460	CAACCAGCTTTCAGGATGTGACGGGCGGTG	12.6
NZ_CP037899.1:949092-950181	site	dyads_m3	R	-396	-367	TAACCTCCTACACACCCTTTACGCCCAGTA	12.9
NZ_CP037899.1:949092-950181	site	dyads_m3	D	-212	-183	GTACCTGACTCTGATACACGAAAGCTAGGG	13.2
NZ_CP037899.1:949092-950181	site	dyads_m3	R	-210	-181	TCCCCTAGCTTTCGTGTATCAGAGTCAGGT	14.1
NZ_CP037899.1:949092-950181	site	dyads_m3	D	-166	-137	ATACCCCGGTAGTCCTAGCCGTAAACGGTG	9.1
NZ_CP037899.1:949092-950181	site	dyads_m3	D	24	53	TTACCAGGCCTTGACATGCCGTGTTCAGTT	15.1
NZ_CP037899.1:949092-950181	site	dyads_m3	R	181	210	TCCCCGTTATACGAGGCAGTCTGTTCAGAG	10.9
NZ_CP037899.1:949092-950181	site	dyads_m3	R	190	219	CCACCTTCCTCCCCGTTATACGAGGCAGTC	14.2
NZ_CP037899.1:949092-950181	site	dyads_m3	R	431	460	CAACCAGCTTTCAGGATGTGACGGGCGGTG	12.6
NZ_CP037899.1:949092-950181	site	dyads_m3	R	-396	-367	TAACCTCCTACACACCCTTTACGCCCAGTA	12.9
NZ_CP037899.1:949092-950181	site	dyads_m3	D	-212	-183	GTACCTGACTCTGATACACGAAAGCTAGGG	13.2
NZ_CP037899.1:949092-950181	site	dyads_m3	R	-210	-181	TCCCCTAGCTTTCGTGTATCAGAGTCAGGT	14.1
NZ_CP037899.1:949092-950181	site	dyads_m3	D	-166	-137	ATACCCCGGTAGTCCTAGCCGTAAACGGTG	9.1
NZ_CP037899.1:949092-950181	site	dyads_m3	D	24	53	TTACCAGGCCTTGACATGCCGTGTTCAGTT	15.1
NZ_CP037899.1:949092-950181	site	dyads_m3	R	181	210	TCCCCGTTATACGAGGCAGTCTGTTCAGAG	10.9
NZ_CP037899.1:949092-950181	site	dyads_m3	R	190	219	CCACCTTCCTCCCCGTTATACGAGGCAGTC	14.2
NZ_CP037899.1:949092-950181	site	dyads_m3	R	431	460	CAACCAGCTTTCAGGATGTGACGGGCGGTG	12.6
NZ_CP037899.1:953361-953582	site	dyads_m3	R	37	66	GAACTGTCTCACGACGTTCTGAACCCAGCT	7.8
NZ_CP037899.1:953361-953582	site	dyads_m3	R	77	106	GAACCCCTCAGATCTCCAGCGCCCACAGTG	9.1
NZ_CP037899.1:1508893-1509246	site	dyads_m3	D	119	148	TAACCTAATATAAATTAGGCAGATCCAGTA	9.0
NZ_CP037899.1:1530412-1530753	site	dyads_m3	R	127	156	TAACCAATACCTTTGTTACGATGCGCAGAA	9.6
;
; Matrices
;	matrix	name    	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	dyads_m3	30	4	0	-43.600	19.900	63.500	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_m3       	29	0
;		TOTAL          	29	0
; Host name	rsat
; Job started	2025-03-02.091349
; Job done	2025-03-02.091350
; Seconds	0.17
;	user	0.17
;	system	0.02
;	cuser	0.09
;	csystem	0.01
