; matrix-scan  -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/07/27/matrix-scan_2026-07-27.154705_9Bk7TV.matrix -pseudo 1 -decimals 1 -2str -origin end -offset -200 -bgfile $RSAT/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.60/oligo-frequencies/3nt_upstream-noorf_Arabidopsis_thaliana.TAIR10.60-ovlp-1str.freq -bg_pseudo 0.01 -return limits -return sites -return pval -return rank -return normw -lth score 1 -uth pval 1e-3 -lth normw 0.8 -i $RSAT/public_html/tmp/www-data/2026/07/27/tmp_sequence_2026-07-27.154705_zW3a1Z.fasta -seq_format fasta -n score
; Slow counting mode            
; Input files
;	input	$RSAT/public_html/tmp/www-data/2026/07/27/tmp_sequence_2026-07-27.154705_zW3a1Z.fasta
;	bg	$RSAT/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.60/oligo-frequencies/3nt_upstream-noorf_Arabidopsis_thaliana.TAIR10.60-ovlp-1str.freq
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/07/27/matrix-scan_2026-07-27.154705_9Bk7TV.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	file
;	Markov order  	2
;	Strand        	sensitive
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.34590
;		c	0.15669
;		g	0.15366
;		t	0.34374
; Thresholds	lower	upper
;	normw 	0.8  	NA
;	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	normw	rank	rank_pm
ON_F6'H1	limit	START_END	D	-1501	199	.	0	0	0	0
ON_F6'H1	site	oligos_6-8nt_m4oligos_6-8nt_m4	D	-1475	-1462	AGTCTCACGCTTCT	6.3	1.8e-04	-8.615	3.741	0.8367	1	1
ON_F6'H1	site	oligos_6-8nt_m4oligos_6-8nt_m4	R	-986	-973	TGGTTCATGTCTAA	5.2	4.0e-04	-7.837	3.403	0.8118	2	2
ON_S8H	limit	START_END	D	-1501	199	.	0	0	0	0
ON_S8H	site	oligos_6-8nt_m4oligos_6-8nt_m4	R	-682	-669	TGAGCCATGCCCCT	8.0	5.1e-05	-9.879	4.290	0.8753	1	1
ON_S8H	site	oligos_6-8nt_m4oligos_6-8nt_m4	R	-414	-401	TGGTGCATGCGTCT	7.6	6.9e-05	-9.580	4.161	0.8662	2	2
ON_S8H	site	oligos_6-8nt_m4oligos_6-8nt_m4	D	-1337	-1324	TATTGCATGCAACT	6.8	1.3e-04	-8.975	3.898	0.8481	3	3
ON_S8H	site	oligos_6-8nt_m4oligos_6-8nt_m4	R	-1337	-1324	AGTTGCATGCAATA	6.6	1.5e-04	-8.835	3.837	0.8435	4	4
ON_S8H	site	oligos_6-8nt_m4oligos_6-8nt_m4	D	-414	-401	AGACGCATGCACCA	5.4	3.4e-04	-7.978	3.465	0.8163	5	5
ON_S8H	site	oligos_6-8nt_m4oligos_6-8nt_m4	R	-117	-104	TGCATAATGCCAAG	4.7	5.5e-04	-7.510	3.262	0.8005	6	6
ON_CYP82C4	limit	START_END	D	-1069	199	.	0	0	0	0
ON_CYP82C4	site	oligos_6-8nt_m4oligos_6-8nt_m4	D	-80	-67	TGTCTCATGCGTTC	10.1	6.7e-06	-11.917	5.176	0.9229	1	1
ON_CYP82C4	site	oligos_6-8nt_m4oligos_6-8nt_m4	D	-806	-793	NNNNNCATGCATAC	6.1	2.1e-04	-8.471	3.679	0.8322	2	2
ON_CYP82C4	site	oligos_6-8nt_m4oligos_6-8nt_m4	R	-359	-346	AGATCCATGCATAA	5.9	2.4e-04	-8.327	3.616	0.8277	3	3
ON_CYP82C4	site	oligos_6-8nt_m4oligos_6-8nt_m4	R	-966	-953	TGATTCATGCATGG	5.8	2.6e-04	-8.250	3.583	0.8254	4	4
ON_CYP82C4	site	oligos_6-8nt_m4oligos_6-8nt_m4	D	-637	-624	TAGTACATGCAAGT	5.2	4.0e-04	-7.837	3.403	0.8118	5	5
ON_COSY	limit	START_END	D	-1	199	.	0	0	0	0
ON_COSY	site	oligos_6-8nt_m4oligos_6-8nt_m4	D	4	17	AGACCCATACCATT	5.9	2.4e-04	-8.327	3.616	0.8277	1	1
ON_ABCG37	limit	START_END	D	-1501	199	.	0	0	0	0
ON_ABCG37	site	oligos_6-8nt_m4oligos_6-8nt_m4	R	-858	-845	TGACACAGGCCTCC	9.2	1.8e-05	-10.934	4.748	0.9025	1	1
ON_ABCG37	site	oligos_6-8nt_m4oligos_6-8nt_m4	R	-126	-113	TAACACATGCTATC	6.7	1.4e-04	-8.901	3.866	0.8458	2	2
ON_ABCG37	site	oligos_6-8nt_m4oligos_6-8nt_m4	D	-851	-838	TGTGTCATGCTGAT	5.9	2.4e-04	-8.327	3.616	0.8277	3	3
ON_ABCG37	site	oligos_6-8nt_m4oligos_6-8nt_m4	D	-425	-412	GGTTTCATGCTGCG	5.8	2.6e-04	-8.250	3.583	0.8254	4	4
ON_ABCG37	site	oligos_6-8nt_m4oligos_6-8nt_m4	D	-1289	-1276	TATCACATGCATGA	5.4	3.4e-04	-7.978	3.465	0.8163	5	5
ON_ABCG37	site	oligos_6-8nt_m4oligos_6-8nt_m4	R	-1285	-1272	AACTTCATGCATGT	4.9	4.8e-04	-7.645	3.320	0.8050	6	6
OFF_DMRL	limit	START_END	D	-51	199	.	0	0	0	0
OFF_RIBA1	limit	START_END	D	-1107	199	.	0	0	0	0
OFF_RIBA1	site	oligos_6-8nt_m4oligos_6-8nt_m4	R	-577	-564	TGACCCATGCAACA	8.6	3.1e-05	-10.379	4.507	0.8889	1	1
OFF_RIBA1	site	oligos_6-8nt_m4oligos_6-8nt_m4	D	-909	-896	AGATTCATGTCATG	5.5	3.2e-04	-8.040	3.492	0.8186	2	2
OFF_RIBA1	site	oligos_6-8nt_m4oligos_6-8nt_m4	R	-314	-301	GATCTCATGACTAT	5.3	3.7e-04	-7.912	3.436	0.8141	3	3
OFF_RIBC	limit	START_END	D	-78	199	.	0	0	0	0
;
; Matrices
;	matrix	name                          	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	oligos_6-8nt_m4oligos_6-8nt_m4	14	4	1	-30.600	13.500	44.100	a:0.346 c:0.157 g:0.154 t:0.344 
; Number of sequences scanned	8
; Sum of sequence lengths	8409
; N residues           	653
; Matches per matrix
;	matrix	name                          	matches	scored
;	1	oligos_6-8nt_m4oligos_6-8nt_m4	23	16610
;		TOTAL          	23	16610
; Host name	rsat
; Job started	2026-07-27.154705
; Job done	2026-07-27.154708
; Seconds	3.13
;	user	3.13
;	system	0.03
;	cuser	0
;	csystem	0