; matrix-scan  -v 1 -matrix_format tab -m $RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.194011_2N1Sdc.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_2026-04-30.193611_V56puB.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_2026-04-30.193611_V56puB.fasta.fasta.fasta
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.194011_2N1Sdc.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	input
;	Markov order  	1
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.25409
;		c	0.20989
;		g	0.19582
;		t	0.34021
; 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_2026-04-30.5	R	-155	-139	GACGTTAAAACGTCACG	15.8	3.0e-10	-21.911	9.516	1	1
mgtA	site	matrix-scan_2026-04-30.4	D	-167	-151	GATGCGTAAGGCCGTGA	14.6	4.4e-09	-19.235	8.354	2	1
mgtA	site	matrix-scan_2026-04-30.6	R	-72	-56	AGTCCCTCCGCACTGTC	14.4	1.7e-08	-17.868	7.760	3	1
mgtA	site	matrix-scan_2026-04-30.2	R	-74	-58	TCCCTCCGCACTGTCTG	13.8	3.8e-08	-17.076	7.416	4	1
mgtA	site	matrix-scan_2026-04-30.5	D	-152	-136	GACGTTTTAACGTCCCT	12.6	2.1e-07	-15.394	6.686	5	2
rstA	limit	START_END	D	-179	-1	.	0	0	0	0
rstA	site	matrix-scan_2026-04-30.4	D	-24	-8	GATGCGGAAGTCGGTTC	14.3	8.0e-09	-18.643	8.097	1	1
rstA	site	matrix-scan_2026-04-30.2	D	-97	-81	AAACAGCGCGGTGTATT	14.4	1.5e-08	-18.020	7.826	2	1
rstA	site	matrix-scan_2026-04-30.2	R	-98	-82	ATACACCGCGCTGTTTT	14.0	2.8e-08	-17.377	7.547	3	2
rstA	site	matrix-scan_2026-04-30.3	D	-157	-141	AACAAGTCATCAGTAGA	10.9	1.7e-06	-13.298	5.775	4	1
rstA	site	matrix-scan_2026-04-30.5	R	-81	-65	GATATAAAAACGTCACA	7.3	7.5e-05	-9.504	4.128	5	1
slyB	limit	START_END	D	-324	-1	.	0	0	0	0
slyB	site	matrix-scan_2026-04-30.3	R	-44	-28	AACAACCAATACGCGTT	14.7	1.7e-09	-20.180	8.764	1	1
slyB	site	matrix-scan_2026-04-30.6	R	-102	-86	AAGCATCCCTCATGGTC	14.8	8.7e-09	-18.559	8.060	2	1
slyB	site	matrix-scan_2026-04-30.6	R	-266	-250	GGTCATTCCGCATGGTA	14.4	1.7e-08	-17.868	7.760	3	2
slyB	site	matrix-scan_2026-04-30.5	R	-84	-68	CACCATGAAACGCCACG	12.7	1.8e-07	-15.540	6.749	4	1
slyB	site	matrix-scan_2026-04-30.2	R	-268	-252	TCATTCCGCATGGTATT	7.1	8.4e-05	-9.389	4.077	5	1
phoP	limit	START_END	D	-219	-1	.	0	0	0	0
phoP	site	matrix-scan_2026-04-30.3	R	-50	-34	AACAACCAGTACGCGCA	14.7	1.7e-09	-20.180	8.764	1	1
phoP	site	matrix-scan_2026-04-30.2	R	-32	-16	TAACAACGCATTGTCTT	14.0	2.8e-08	-17.377	7.547	2	1
phoP	site	matrix-scan_2026-04-30.6	R	-194	-178	AAGCAGGCCGGACAGCA	13.8	4.3e-08	-16.963	7.367	3	1
phoP	site	matrix-scan_2026-04-30.4	D	-208	-192	GTGCCGGATGGCGATGC	12.7	1.3e-07	-15.837	6.878	4	1
phoP	site	matrix-scan_2026-04-30.5	R	-28	-12	GACGTAACAACGCATTG	11.8	6.3e-07	-14.285	6.204	5	1
phoP	site	matrix-scan_2026-04-30.3	D	-104	-88	AACCACATAATCGCGTT	11.4	8.7e-07	-13.956	6.061	6	2
phoP	site	matrix-scan_2026-04-30.4	R	-26	-10	GTGACGTAACAACGCAT	8.8	1.8e-05	-10.926	4.745	7	2
phoP	site	matrix-scan_2026-04-30.3	R	-167	-151	AAAAAATAAAAAGCGGA	7.1	9.5e-05	-9.264	4.023	8	3
;
; Matrices
;	matrix	name                    	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	matrix-scan_2026-04-30.2	17	4	1	-27.400	16.700	44.100	a:0.254 c:0.210 g:0.196 t:0.340 
;	2	matrix-scan_2026-04-30.3	17	4	1	-27.400	16.400	43.800	a:0.254 c:0.210 g:0.196 t:0.340 
;	3	matrix-scan_2026-04-30.4	17	4	1	-27.400	16.800	44.200	a:0.254 c:0.210 g:0.196 t:0.340 
;	4	matrix-scan_2026-04-30.5	17	4	1	-27.400	17.500	44.900	a:0.254 c:0.210 g:0.196 t:0.340 
;	5	matrix-scan_2026-04-30.6	17	4	1	-27.400	16.300	43.700	a:0.254 c:0.210 g:0.196 t:0.340 
; Number of sequences scanned	4
; Sum of sequence lengths	913
; N residues           	0
; Matches per matrix
;	matrix	name                    	matches	scored
;	1	matrix-scan_2026-04-30.2	5	1698
;	2	matrix-scan_2026-04-30.3	5	1698
;	3	matrix-scan_2026-04-30.4	4	1698
;	4	matrix-scan_2026-04-30.5	5	1698
;	5	matrix-scan_2026-04-30.6	4	1698
;		TOTAL          	23	8490
; Host name	rsat
; Job started	2026-04-30.194011
; Job done	2026-04-30.194016
; Seconds	4.28
;	user	4.28
;	system	0.04
;	cuser	0.08
;	csystem	0.01