; matrix-scan  -v 1 -matrix_format tab -m $RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.194012_wmkHmU.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/retrieve-seq_2026-04-30.193449_sojowF.fasta.fasta.fasta -seq_format fasta -n score
; Slow counting mode            
; Input files
;	input	$RSAT/public_html/tmp/www-data/2026/04/30/retrieve-seq_2026-04-30.193449_sojowF.fasta.fasta.fasta
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.194012_wmkHmU.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	input
;	Markov order  	1
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.26937
;		c	0.22894
;		g	0.18969
;		t	0.31199
; 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
mgtA	limit	START_END	D	-191	-1	.	0	0	0	0
mgtA	site	matrix-scan_2026-04-30.4	R	-101	-85	GAAATGTCTTCAGGCGT	15.6	2.2e-10	-22.225	9.652	1	1
mgtA	site	matrix-scan_2026-04-30.2	D	-157	-141	GCCGTGACGTTTTAACG	15.2	1.9e-09	-20.075	8.718	2	1
mgtA	site	matrix-scan_2026-04-30.2	R	-150	-134	GCAGGGACGTTAAAACG	14.8	5.7e-09	-18.978	8.242	3	2
mgtA	site	matrix-scan_2026-04-30.6	D	-80	-64	CTGTTTCAGACAGTGCG	14.4	1.6e-08	-17.970	7.804	4	1
mgtA	site	matrix-scan_2026-04-30.5	D	-79	-63	TGTTTCAGACAGTGCGG	14.2	2.2e-08	-17.644	7.663	5	1
mgtA	site	matrix-scan_2026-04-30.5	R	-138	-122	TAATAAAGCTGAGCAGG	11.2	1.4e-06	-13.509	5.867	6	2
rstA	limit	START_END	D	-179	-1	.	0	0	0	0
rstA	site	matrix-scan_2026-04-30.5	D	-34	-18	TGTGGAAGATGATGCGG	16.3	2.3e-10	-22.198	9.641	1	1
rstA	site	matrix-scan_2026-04-30.6	D	-35	-19	TTGTGGAAGATGATGCG	14.8	9.0e-09	-18.523	8.045	2	1
rstA	site	matrix-scan_2026-04-30.4	D	-90	-74	GCGGTGTATTGTGACGT	11.7	7.0e-07	-14.173	6.155	3	1
rstA	site	matrix-scan_2026-04-30.2	R	-102	-86	ACCGCGCTGTTTTTACT	10.0	5.2e-06	-12.163	5.282	4	1
phoP	limit	START_END	D	-219	-1	.	0	0	0	0
phoP	site	matrix-scan_2026-04-30.6	D	-38	-22	TTGTTGAAGACAATGCG	15.4	2.4e-09	-19.858	8.624	1	1
phoP	site	matrix-scan_2026-04-30.5	D	-37	-21	TGTTGAAGACAATGCGT	14.9	6.5e-09	-18.847	8.185	2	1
phoP	site	matrix-scan_2026-04-30.2	R	-23	-7	GTGGTGACGTAACAACG	13.4	6.7e-08	-16.514	7.172	3	1
phoP	site	matrix-scan_2026-04-30.5	D	-75	-59	TAATTAAGACAGGGAGA	8.6	2.2e-05	-10.744	4.666	4	2
phoP	site	matrix-scan_2026-04-30.6	D	-76	-60	ATAATTAAGACAGGGAG	7.6	5.4e-05	-9.828	4.268	5	2
yrbL	limit	START_END	D	-264	-1	.	0	0	0	0
yrbL	site	matrix-scan_2026-04-30.3	R	-144	-128	AAGGTTTTCTTAAGGTT	14.6	5.3e-09	-19.055	8.275	1	1
yrbL	site	matrix-scan_2026-04-30.3	D	-125	-109	GAGGCATTGTTTAGGTT	14.5	7.0e-09	-18.772	8.153	2	2
yrbL	site	matrix-scan_2026-04-30.4	R	-79	-63	GAAATATTTTCTGACGA	14.3	1.4e-08	-18.054	7.841	3	1
yrbL	site	matrix-scan_2026-04-30.3	D	-114	-98	TAGGTTTTGTTTAAGTT	13.3	6.7e-08	-16.519	7.174	4	3
yrbL	site	matrix-scan_2026-04-30.4	D	-72	-56	AAAATATTTCCAGGAGA	12.1	4.0e-07	-14.727	6.396	5	2
yrbL	site	matrix-scan_2026-04-30.6	D	-89	-73	ATACTGGAGATCGTCAG	11.7	7.6e-07	-14.087	6.118	6	1
yrbL	site	matrix-scan_2026-04-30.3	R	-223	-207	GTGATTTTCTTATTGTC	10.9	1.8e-06	-13.204	5.735	7	4
;
; Matrices
;	matrix	name                    	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	matrix-scan_2026-04-30.2	17	4	1	-27.400	17.000	44.400	a:0.269 c:0.229 g:0.190 t:0.312 
;	2	matrix-scan_2026-04-30.3	17	4	1	-27.400	16.400	43.800	a:0.269 c:0.229 g:0.190 t:0.312 
;	3	matrix-scan_2026-04-30.4	17	4	1	-27.400	15.900	43.300	a:0.269 c:0.229 g:0.190 t:0.312 
;	4	matrix-scan_2026-04-30.5	17	4	1	-27.400	17.100	44.500	a:0.269 c:0.229 g:0.190 t:0.312 
;	5	matrix-scan_2026-04-30.6	17	4	1	-27.400	16.500	43.900	a:0.269 c:0.229 g:0.190 t:0.312 
; Number of sequences scanned	4
; Sum of sequence lengths	853
; N residues           	0
; Matches per matrix
;	matrix	name                    	matches	scored
;	1	matrix-scan_2026-04-30.2	4	1578
;	2	matrix-scan_2026-04-30.3	4	1578
;	3	matrix-scan_2026-04-30.4	4	1578
;	4	matrix-scan_2026-04-30.5	5	1578
;	5	matrix-scan_2026-04-30.6	5	1578
;		TOTAL          	22	7890
; Host name	rsat
; Job started	2026-04-30.194012
; Job done	2026-04-30.194017
; Seconds	4.57
;	user	4.57
;	system	0.03
;	cuser	0.1
;	csystem	0.01