; matrix-scan  -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/07/27/matrix-scan_2026-07-27.113859_1ka1ZD.matrix -pseudo 1 -decimals 1 -2str -origin end -offset -200 -bginput -markov 1 -bg_pseudo 0.01 -return limits -return sites -return pval -return rank -lth score 1 -uth pval 1e-3 -i $RSAT/public_html/tmp/www-data/2026/07/27/tmp_sequence_2026-07-27.113859_5RoB0r.fasta -seq_format fasta -n score
; Slow counting mode            
; Input files
;	input	$RSAT/public_html/tmp/www-data/2026/07/27/tmp_sequence_2026-07-27.113859_5RoB0r.fasta
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/07/27/matrix-scan_2026-07-27.113859_1ka1ZD.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	input
;	Markov order  	1
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.33310
;		c	0.18237
;		g	0.16015
;		t	0.32438
; Thresholds	lower	upper
;	pval  	NA	0.001
;	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
F6'H1	limit	START_END	D	-1501	199	.	0	0	0	0
F6'H1	site	oligos_6-8nt_m2oligos_6-8nt_m2	D	-1485	-1474	AACCATGCCTAG	8.8	3.8e-05	-10.174	4.419	1	1
F6'H1	site	oligos_6-8nt_m2oligos_6-8nt_m2	D	-1456	-1445	AACCATGCCTAG	8.8	3.8e-05	-10.174	4.419	2	2
F6'H1	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	-507	-496	GTGCATGCAAGT	5.3	4.9e-04	-7.622	3.310	3	3
AT3G12900	limit	START_END	D	-1501	199	.	0	0	0	0
AT3G12900	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	169	180	TTTCACGCCGTT	8.6	4.9e-05	-9.926	4.311	1	1
AT3G12900	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	-682	-671	AGCCATGCCCCT	7.8	9.2e-05	-9.291	4.035	2	2
AT3G12900	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	-1347	-1336	TAACAAGCCTAA	5.7	3.5e-04	-7.961	3.457	3	3
AT3G12900	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	178	189	TATCATTCCTTT	5.4	4.5e-04	-7.712	3.349	4	4
AT3G12900	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	-1337	-1326	TTGCATGCAATA	5.1	5.8e-04	-7.454	3.237	5	5
AT3G12900	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	-414	-403	GTGCATGCGTCT	4.8	7.5e-04	-7.202	3.128	6	6
AT3G12900	site	oligos_6-8nt_m2oligos_6-8nt_m2	D	-1335	-1324	TTGCATGCAACT	4.5	9.4e-04	-6.973	3.028	7	7
CYP82C4	limit	START_END	D	-1069	199	.	0	0	0	0
CYP82C4	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	-719	-708	ATTCATGCGGTA	6.6	1.7e-04	-8.654	3.758	1	1
CYP82C4	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	-806	-795	ATGCATGNNNNN	5.6	3.8e-04	-7.881	3.423	2	2
CYP82C4	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	-580	-569	GGACCTGCCTTG	5.4	4.5e-04	-7.712	3.349	3	3
CYP82C4	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	-966	-955	ATTCATGCATGG	5.2	5.4e-04	-7.527	3.269	4	4
CYP82C4	site	oligos_6-8nt_m2oligos_6-8nt_m2	D	-635	-624	GTACATGCAAGT	5.1	5.8e-04	-7.454	3.237	5	5
CYP82C4	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	-146	-135	ATGCATGCACGA	4.6	8.6e-04	-7.058	3.065	6	6
CYP82C4	site	oligos_6-8nt_m2oligos_6-8nt_m2	D	-144	-133	GTGCATGCATTA	4.5	9.4e-04	-6.973	3.028	7	7
CYP82C4	site	oligos_6-8nt_m2oligos_6-8nt_m2	D	-697	-686	AAGCACGCAGGA	4.4	1.0e-03	-6.906	2.999	8	8
CYP82C4	site	oligos_6-8nt_m2oligos_6-8nt_m2	D	-78	-67	TCTCATGCGTTC	4.4	1.0e-03	-6.906	2.999	9	9
AT1G28680	limit	START_END	D	-1	199	.	0	0	0	0
AT1G28680	site	oligos_6-8nt_m2oligos_6-8nt_m2	D	6	17	ACCCATACCATT	5.1	5.8e-04	-7.454	3.237	1	1
ABCG37	limit	START_END	D	-1501	199	.	0	0	0	0
ABCG37	site	oligos_6-8nt_m2oligos_6-8nt_m2	D	89	100	AGCCAAGCCATG	6.6	1.7e-04	-8.654	3.758	1	1
ABCG37	site	oligos_6-8nt_m2oligos_6-8nt_m2	R	-667	-656	TCTCATACCAAT	5.3	4.9e-04	-7.622	3.310	2	2
COS1	limit	START_END	D	-51	199	.	0	0	0	0
RIBA1	limit	START_END	D	-1107	199	.	0	0	0	0
RIBC	limit	START_END	D	-78	199	.	0	0	0	0
;
; Matrices
;	matrix	name                          	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	oligos_6-8nt_m2oligos_6-8nt_m2	12	4	1	-26.400	10.600	37.000	a:0.333 c:0.182 g:0.160 t:0.324 
; Number of sequences scanned	8
; Sum of sequence lengths	8409
; N residues           	653
; Matches per matrix
;	matrix	name                          	matches	scored
;	1	oligos_6-8nt_m2oligos_6-8nt_m2	22	16642
;		TOTAL          	22	16642
; Host name	rsat
; Job started	2026-07-27.113900
; Job done	2026-07-27.113901
; Seconds	1.87
;	user	1.87
;	system	0.01
;	cuser	0.08
;	csystem	0.01