; matrix-scan  -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/07/17/matrix-scan_2026-07-17.091622_jhu4Ih.matrix -pseudo 1 -decimals 1 -2str -origin end -bginput -markov 1 -bg_pseudo 0.01 -return limits -return sites -return pval -return normw -lth score 1 -uth pval 1e-4 -i $RSAT/public_html/tmp/www-data/2026/07/17/tmp_sequence_2026-07-17.091622_HFJkst.fasta -seq_format fasta -n score
; Slow counting mode            
; Input files
;	input	$RSAT/public_html/tmp/www-data/2026/07/17/tmp_sequence_2026-07-17.091622_HFJkst.fasta
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/07/17/matrix-scan_2026-07-17.091622_jhu4Ih.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	input
;	Markov order  	1
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.20136
;		c	0.20128
;		g	0.59177
;		t	0.00559
; 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	normw
sequence_1	limit	START_END	D	-11	-1	.	0	0	0	0
;
; Matrices
;	matrix	name   	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	Kr     	8	4	1	-23.700	28.400	52.100	a:0.201 c:0.201 g:0.592 t:0.006 
;	2	Med    	6	4	1	-14.400	19.800	34.200	a:0.201 c:0.201 g:0.592 t:0.006 
;	3	Stat92E	9	4	1	-12.500	16.200	28.700	a:0.201 c:0.201 g:0.592 t:0.006 
;	4	bcd    	6	4	1	-19.600	18.800	38.400	a:0.201 c:0.201 g:0.592 t:0.006 
;	5	eve    	15	4	1	-32.800	33.400	66.200	a:0.201 c:0.201 g:0.592 t:0.006 
;	6	gt     	10	4	1	-22.000	39.000	61.000	a:0.201 c:0.201 g:0.592 t:0.006 
;	7	hb     	8	4	1	-26.800	37.800	64.600	a:0.201 c:0.201 g:0.592 t:0.006 
;	8	kni    	8	4	1	-15.900	28.900	44.800	a:0.201 c:0.201 g:0.592 t:0.006 
;	9	pan    	8	4	1	-18.200	24.700	42.900	a:0.201 c:0.201 g:0.592 t:0.006 
;	10	prd    	8	4	1	-18.500	11.900	30.400	a:0.201 c:0.201 g:0.592 t:0.006 
;	11	tin    	6	4	1	-15.000	14.900	29.900	a:0.201 c:0.201 g:0.592 t:0.006 
;	12	ttk    	7	4	1	-15.400	10.100	25.500	a:0.201 c:0.201 g:0.592 t:0.006 
; Number of sequences scanned	1
; Sum of sequence lengths	11
; N residues           	0
; Matches per matrix
;	matrix	name   	matches	scored
;	1	Kr             	0	8
;	2	Med            	0	12
;	3	Stat92E        	0	6
;	4	bcd            	0	12
;	5	eve            	0	0
;	6	gt             	0	4
;	7	hb             	0	8
;	8	kni            	0	8
;	9	pan            	0	8
;	10	prd            	0	8
;	11	tin            	0	12
;	12	ttk            	0	10
;		TOTAL          	0	96
; Host name	rsat
; Job started	2026-07-17.091622
; Job done	2026-07-17.091625
; Seconds	2.21
;	user	2.21
;	system	0.02
;	cuser	0.11
;	csystem	0.02