; matrix-scan  -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.111703_JrUZaG.matrix -pseudo 1 -decimals 1 -2str -origin end -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/2026/04/30/tmp_sequence_2026-04-30.111533_YCQqp0.fasta.fasta -seq_format fasta -n score
; Slow counting mode            
; Input files
;	input	$RSAT/public_html/tmp/www-data/2026/04/30/tmp_sequence_2026-04-30.111533_YCQqp0.fasta.fasta
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.111703_JrUZaG.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	input
;	Markov order  	1
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.43547
;		c	0.10591
;		g	0.13268
;		t	0.32595
; 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
gp11_Padj	limit	START_END	D	-80	-1	.	0	0	0	0
gp11_Padj	site	assembly_8	R	-45	-34	GATATTTAAATT	8.6	2.0e-05	-10.831	4.704	1	1
gp12	limit	START_END	D	-85	-1	.	0	0	0	0
gp12	site	assembly_8	R	-46	-35	GATATTTAAAGC	9.5	2.1e-07	-15.356	6.669	1	1
gp12	site	assembly_1	D	-73	-62	TTTCTTCTAAAC	9.3	6.2e-06	-11.989	5.207	2	1
gp12	site	assembly_9	R	-85	-74	GATGGAAAGAGA	7.7	5.2e-05	-9.871	4.287	3	1
gp13	limit	START_END	D	-85	-1	.	0	0	0	0
gp13	site	assembly_2	D	-65	-53	TTTTTATCGAAAA	9.7	5.2e-06	-12.168	5.285	1	1
gp13	site	assembly_2	D	-39	-27	AGTTTATCGAAAA	9.7	5.2e-06	-12.168	5.285	2	2
gp13	site	assembly_8	R	-27	-16	GGTATTTAAATT	8.6	2.0e-05	-10.831	4.704	3	1
gp13	site	assembly_1	R	-54	-43	ACTCTTCTATTT	8.1	4.4e-05	-10.032	4.357	4	1
gp14	limit	START_END	D	-85	-1	.	0	0	0	0
gp14	site	assembly_2	D	-54	-42	GATTTGTCGAAAA	9.4	7.1e-06	-11.850	5.146	1	1
gp14	site	assembly_8	R	-42	-31	AATATTTAAATT	7.9	5.2e-05	-9.868	4.286	2	1
gp14	site	assembly_1	D	-85	-74	ATTCTTCTTAAT	8.0	5.3e-05	-9.846	4.276	3	1
gp15	limit	START_END	D	-85	-1	.	0	0	0	0
gp15	site	assembly_9	D	-61	-50	AGAAGAAAGACA	8.2	1.2e-05	-11.311	4.912	1	1
gp15	site	assembly_1	R	-78	-67	TTTTTTCTAACT	8.7	1.3e-05	-11.277	4.897	2	1
gp15	site	assembly_8	R	-43	-32	GATATTTAAATT	8.6	2.0e-05	-10.831	4.704	3	1
gp16	limit	START_END	D	-85	-1	.	0	0	0	0
gp16	site	assembly_8	R	-47	-36	GATATTTAAAGA	8.1	3.9e-05	-10.144	4.405	1	1
gp16	site	assembly_1	D	-34	-23	ATTTTTCTAATG	8.1	4.4e-05	-10.032	4.357	2	1
gp17	limit	START_END	D	-85	-1	.	0	0	0	0
gp17	site	assembly_2	R	-70	-58	TTTTTATCGAATT	8.4	2.6e-05	-10.569	4.590	1	1
gp17	site	assembly_9	D	-61	-50	AAAAGAAAGATA	7.6	6.5e-05	-9.641	4.187	2	1
gp17	site	assembly_9	D	-57	-46	GAAAGATAGAGA	7.5	8.7e-05	-9.352	4.061	3	2
;
; Matrices
;	matrix	name      	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	assembly_1	12	4	1	-23.800	10.600	34.400	a:0.435 c:0.106 g:0.133 t:0.326 
;	2	assembly_2	13	4	1	-21.000	11.800	32.800	a:0.435 c:0.106 g:0.133 t:0.326 
;	3	assembly_8	12	4	1	-30.700	9.300	40.000	a:0.435 c:0.106 g:0.133 t:0.326 
;	4	assembly_9	12	4	1	-22.200	10.700	32.900	a:0.435 c:0.106 g:0.133 t:0.326 
; Number of sequences scanned	7
; Sum of sequence lengths	590
; N residues           	0
; Matches per matrix
;	matrix	name      	matches	scored
;	1	assembly_1     	5	1026
;	2	assembly_2     	4	1012
;	3	assembly_8     	6	1026
;	4	assembly_9     	4	1026
;		TOTAL          	19	4090
; Host name	rsat
; Job started	2026-04-30.111703
; Job done	2026-04-30.111705
; Seconds	1.63
;	user	1.63
;	system	0.03
;	cuser	0.11
;	csystem	0.02