; matrix-scan  -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/07/23/matrix-scan_2026-07-23.092211_6yxeBs.matrix -pseudo 1 -decimals 1 -2str -origin end -bginput -markov 1 -bg_pseudo 0.01 -return limits -return sites -lth score 1 -i $RSAT/public_html/tmp/www-data/2026/07/23/retrieve-seq_2026-07-23.091839_qH7BlP.fasta.fasta -seq_format fasta -n score
; Quick 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_2026-07-23.092211_6yxeBs.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
;	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
gene25542	limit	START_END	D	-1701	-1	.	0
gene7299	limit	START_END	D	-1701	-1	.	0
gene22259	limit	START_END	D	-201	-1	.	0
gene3683	limit	START_END	D	-1701	-1	.	0
gene14703	limit	START_END	D	-1701	-1	.	0
gene14702	limit	START_END	D	-1701	-1	.	0
gene25542	site	oligos_6-8nt_m7oligos_6-8nt_m7	R	-1519	-1505	TGGTAGATCAATGTT	3.1
gene25542	site	oligos_6-8nt_m7oligos_6-8nt_m7	D	-1514	-1500	TGATCTACCACATAC	2.5
gene25542	site	oligos_6-8nt_m7oligos_6-8nt_m7	D	-911	-897	TTATCGTATAACGTA	3.4
gene25542	site	oligos_6-8nt_m7oligos_6-8nt_m7	D	-879	-865	TGAGCGACAAAAATT	5.2
gene25542	site	oligos_6-8nt_m7oligos_6-8nt_m7	R	-749	-735	CGGTACACCAACCCT	5.4
gene25542	site	oligos_6-8nt_m7oligos_6-8nt_m7	R	-244	-230	GTGGGCAACAACTTA	2.3
gene25542	site	oligos_6-8nt_m7oligos_6-8nt_m7	R	-189	-175	TGAGCGATCAAGCCT	9.3
gene25542	site	oligos_6-8nt_m7oligos_6-8nt_m7	D	-184	-170	TGATCGCTCAAACAT	2.0
gene7299	site	oligos_6-8nt_m7oligos_6-8nt_m7	D	-1152	-1138	TTCGAAAACAACTTA	2.3
gene22259	site	oligos_6-8nt_m7oligos_6-8nt_m7	R	-19	-5	CAGGCGACCCCGGGC	1.2
gene3683	site	oligos_6-8nt_m7oligos_6-8nt_m7	D	-1681	-1667	AAAGAGAATAAACCA	1.0
gene3683	site	oligos_6-8nt_m7oligos_6-8nt_m7	D	-1259	-1245	ATAGCCACCACCATA	6.5
gene3683	site	oligos_6-8nt_m7oligos_6-8nt_m7	R	-957	-943	ATGGGAATCAAGGTT	1.3
gene3683	site	oligos_6-8nt_m7oligos_6-8nt_m7	D	-819	-805	CAGGCCATGAACTCC	2.2
gene3683	site	oligos_6-8nt_m7oligos_6-8nt_m7	D	-803	-789	TGGGCCACCACCAGC	2.3
gene3683	site	oligos_6-8nt_m7oligos_6-8nt_m7	R	-580	-566	TGGTCGTTCAGATTC	1.0
gene3683	site	oligos_6-8nt_m7oligos_6-8nt_m7	D	-575	-561	TGAACGACCATCATA	2.7
gene14703	site	oligos_6-8nt_m7oligos_6-8nt_m7	D	-1658	-1644	AAGGATAACAGCTCT	3.1
gene14703	site	oligos_6-8nt_m7oligos_6-8nt_m7	D	-1591	-1577	GAGGACATCAACCAT	4.6
gene14703	site	oligos_6-8nt_m7oligos_6-8nt_m7	D	-1556	-1542	TGATTGATCAAAGCT	1.1
gene14703	site	oligos_6-8nt_m7oligos_6-8nt_m7	D	-1434	-1420	AAAGCGCCTAAACTC	3.8
gene14703	site	oligos_6-8nt_m7oligos_6-8nt_m7	R	-1374	-1360	TAAGATATGAACTTT	2.1
gene14703	site	oligos_6-8nt_m7oligos_6-8nt_m7	D	-911	-897	AAAGCTAACACAATT	2.2
gene14703	site	oligos_6-8nt_m7oligos_6-8nt_m7	R	-793	-779	CTAGAGATCAAGTTT	7.0
gene14703	site	oligos_6-8nt_m7oligos_6-8nt_m7	R	-607	-593	AAGGAGAAAAAAGTT	2.2
gene14703	site	oligos_6-8nt_m7oligos_6-8nt_m7	D	-452	-438	CCGCCGACCAAGTTG	4.4
gene14703	site	oligos_6-8nt_m7oligos_6-8nt_m7	D	-383	-369	TCGGCGATATACCTA	3.8
gene14703	site	oligos_6-8nt_m7oligos_6-8nt_m7	D	-162	-148	CGCTCCAACACCGCC	1.1
gene14702	site	oligos_6-8nt_m7oligos_6-8nt_m7	R	-1001	-987	CCAGATACTAAAGTT	1.6
gene14702	site	oligos_6-8nt_m7oligos_6-8nt_m7	D	-509	-495	AAAGAAACCAAGTTT	3.7
gene14702	site	oligos_6-8nt_m7oligos_6-8nt_m7	R	-394	-380	TGCGACCCCAACATT	1.3
gene14702	site	oligos_6-8nt_m7oligos_6-8nt_m7	R	-356	-342	TTGGCCTCTAGCGCT	1.7
gene14702	site	oligos_6-8nt_m7oligos_6-8nt_m7	D	-63	-49	TGAGATATCAAGTCT	3.6
;
; Matrices
;	matrix	name                          	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	oligos_6-8nt_m7oligos_6-8nt_m7	15	4	0	-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	33	0
;		TOTAL          	33	0
; Host name	rsat
; Job started	2026-07-23.092212
; Job done	2026-07-23.092212
; Seconds	0.17
;	user	0.17
;	system	0.01
;	cuser	0.11
;	csystem	0.02