; matrix-scan  -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/07/23/matrix-scan_2026-07-23.092403_yDnYNa.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-4 -i $RSAT/public_html/tmp/www-data/2026/07/23/retrieve-seq_2026-07-23.091839_qH7BlP.fasta.fasta -seq_format fasta -n score
; Slow 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_2026-07-23.092403_yDnYNa.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
;	pval  	NA	0.0001
;	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
gene25542	limit	START_END	D	-1501	199	.	0	0	0	0
gene7299	limit	START_END	D	-1501	199	.	0	0	0	0
gene22259	limit	START_END	D	-1	199	.	0	0	0	0
gene3683	limit	START_END	D	-1501	199	.	0	0	0	0
gene3683	site	oligos_6-8nt_m1	D	-523	-511	CGGCACCACCATA	12.6	8.7e-08	-16.256	7.060	1	1
gene3683	site	oligos_6-8nt_m1	D	-310	-298	CGCCACTACCACC	12.0	3.0e-07	-15.036	6.530	2	2
gene3683	site	oligos_6-8nt_m1	D	-298	-286	CTCCAGCACCACC	11.7	4.8e-07	-14.545	6.317	3	3
gene3683	site	oligos_6-8nt_m1	D	-601	-589	GGCCACCACCAGC	11.3	9.2e-07	-13.899	6.036	4	4
gene3683	site	oligos_6-8nt_m1	D	-1057	-1045	AGCCACCACCATA	11.0	1.5e-06	-13.424	5.830	5	5
gene3683	site	oligos_6-8nt_m1	D	-694	-682	CAGCACCACCACT	10.9	1.6e-06	-13.316	5.783	6	6
gene3683	site	oligos_6-8nt_m1	D	-697	-685	ATCCAGCACCACC	10.4	3.4e-06	-12.605	5.474	7	7
gene3683	site	oligos_6-8nt_m1	D	-1069	-1057	GGGCAGCACCATA	9.5	9.7e-06	-11.544	5.013	8	8
gene3683	site	oligos_6-8nt_m1	D	-526	-514	CAGCGGCACCACC	9.2	1.4e-05	-11.199	4.863	9	9
gene3683	site	oligos_6-8nt_m1	D	-892	-880	GTTCACTACCACC	9.1	1.5e-05	-11.091	4.817	10	10
gene3683	site	oligos_6-8nt_m1	D	-598	-586	CACCACCAGCATA	9.1	1.5e-05	-11.091	4.817	11	11
gene3683	site	oligos_6-8nt_m1	D	-835	-823	CAACAGCACCATA	9.0	1.7e-05	-11.002	4.778	12	12
gene3683	site	oligos_6-8nt_m1	D	-910	-898	TGCCACCACTACC	8.9	1.9e-05	-10.893	4.731	13	13
gene3683	site	oligos_6-8nt_m1	D	-784	-772	ACCCGCCACCATA	8.4	3.1e-05	-10.375	4.506	14	14
gene3683	site	oligos_6-8nt_m1	D	-304	-292	TACCACCTCCAGC	8.1	4.2e-05	-10.076	4.376	15	15
gene3683	site	oligos_6-8nt_m1	D	-775	-763	CATAACCACCATA	7.9	5.1e-05	-9.888	4.295	16	16
gene3683	site	oligos_6-8nt_m1	R	-143	-131	CTGGACGACCACG	7.7	6.2e-05	-9.694	4.210	17	17
gene3683	site	oligos_6-8nt_m1	D	-841	-829	GCCCACCAACAGC	7.2	9.8e-05	-9.234	4.010	18	18
gene3683	site	oligos_6-8nt_m1	D	-376	-364	CTGAACGACCATC	7.2	9.8e-05	-9.234	4.010	19	19
gene14703	limit	START_END	D	-1501	199	.	0	0	0	0
gene14703	site	oligos_6-8nt_m1	D	-670	-658	CTTCACCACCAAC	10.4	3.4e-06	-12.605	5.474	1	1
gene14703	site	oligos_6-8nt_m1	D	43	55	CAACACCGCCACC	10.0	5.5e-06	-12.112	5.260	2	2
gene14703	site	oligos_6-8nt_m1	D	46	58	CACCGCCACCCGC	8.4	3.1e-05	-10.375	4.506	3	3
gene14702	limit	START_END	D	-1501	199	.	0	0	0	0
;
; Matrices
;	matrix	name           	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	oligos_6-8nt_m1	13	4	1	-28.000	14.300	42.300	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_m1	22	17268
;		TOTAL          	22	17268
; Host name	rsat
; Job started	2026-07-23.092403
; Job done	2026-07-23.092405
; Seconds	1.81
;	user	1.81
;	system	0.02
;	cuser	0.11
;	csystem	0.01