; matrix-scan  -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/06/02/matrix-scan_2026-06-02.102816_c2WoGT.matrix -pseudo 1 -decimals 1 -2str -origin end -bginput -markov 1 -bg_pseudo 0.01 -return limits -return pval -uth pval 0.0002 -i $RSAT/public_html/tmp/www-data/2026/06/02/tmp_sequence_2026-06-02.102816_YkgQ3U.fasta -seq_format fasta -n score
; Quick counting mode           
; Input files
;	input	$RSAT/public_html/tmp/www-data/2026/06/02/tmp_sequence_2026-06-02.102816_YkgQ3U.fasta
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/06/02/matrix-scan_2026-06-02.102816_c2WoGT.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	input
;	Markov order  	1
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.28891
;		c	0.21973
;		g	0.20122
;		t	0.29014
; Thresholds	lower	upper
;	pval  	NA	0.0002
; 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
PAS_chr1-1_0097	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr1-1_0118	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr1-1_0226	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr1-3_0119	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr1-3_0312	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr1-4_0327	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr1-4_0329	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr1-4_0338	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr1-4_0392	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr1-4_0393	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr1-4_0431	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr1-4_0668	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr2-1_0037	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr2-1_0189	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr2-1_0242	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr2-1_0313	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr2-1_0472	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr2-1_0640	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr2-1_0767	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr2-1_0853	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr2-2_0022	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr2-2_0127	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr2-2_0131	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr2-2_0208	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr2-2_0236	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr2-2_0288	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr3_0078	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr3_0095	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr3_0188	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr3_0349	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr3_0445	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr3_0648	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr3_0744	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr3_0841	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr3_0932	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr3_0987	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr3_1068	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr3_1214	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr3_1230	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr4_0042	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr4_0146	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr4_0147	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr4_0151	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr4_0191	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr4_0248	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr4_0314	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr4_0336	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr4_0407	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr4_0470	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr4_0488	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr4_0593	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr4_0627	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr4_0704	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr4_0762	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr4_0809	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_FragB_0015	limit	START_END	D	-800	-1	.	0	0	0	0
;
; Matrices
;	matrix	name	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	CRZ1	6	4	0	-19.400	7.000	26.400	a:0.289 c:0.220 g:0.201 t:0.290 
; Number of sequences scanned	56
; Sum of sequence lengths	44800
; N residues           	0
; Matches per matrix
;	matrix	name	matches	scored
;	1	CRZ1           	0	0
;		TOTAL          	0	0
; Host name	rsat
; Job started	2026-06-02.102816
; Job done	2026-06-02.102817
; Seconds	0.23
;	user	0.23
;	system	0.01
;	cuser	0.24
;	csystem	0.03