; matrix-scan  -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/03/29/matrix-scan_2026-03-29.162011_HYdv3a.matrix -pseudo 1 -decimals 1 -2str -origin end -bginput -markov 1 -bg_pseudo 0.01 -return limits -return pval -uth pval 0.0001 -i $RSAT/public_html/tmp/www-data/2026/03/29/tmp_sequence_2026-03-29.162011_H8IXsK.fasta -seq_format fasta -n score
; Quick counting mode           
; Input files
;	input	$RSAT/public_html/tmp/www-data/2026/03/29/tmp_sequence_2026-03-29.162011_H8IXsK.fasta
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/03/29/matrix-scan_2026-03-29.162011_HYdv3a.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	input
;	Markov order  	1
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.30182
;		c	0.20504
;		g	0.20354
;		t	0.28959
; Thresholds	lower	upper
;	pval  	NA	0.0001
; 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
chromosome_GRCh38_10_1_133797422_1:88066000-88068000()_enhA1	limit	START_END	D	-2000	-1	.	0	0	0	0
chromosome_GRCh38_10_1_133797422_1:88092000-88094000()_enhA2	limit	START_END	D	-2000	-1	.	0	0	0	0
chromosome_GRCh38_10_1_133797422_1:88112000-88114000()_enhA3	limit	START_END	D	-2000	-1	.	0	0	0	0
chromosome_GRCh38_10_1_133797422_1:88272000-88274000()_enhB1	limit	START_END	D	-2000	-1	.	0	0	0	0
chromosome_GRCh38_10_1_133797422_1:88322000-88324000()_enhB2	limit	START_END	D	-2000	-1	.	0	0	0	0
chromosome_GRCh38_10_1_133797422_1:88388000-88390000()_enhG	limit	START_END	D	-2000	-1	.	0	0	0	0
chromosome_GRCh38_10_1_133797422_1:88066000-88068000()_enhA1	site	rwAATTAAAcyy	D	-1599	-1588	GCAATTAAACTG	9.4	1.1e-05	-11.418	4.959
chromosome_GRCh38_10_1_133797422_1:88066000-88068000()_enhA1	site	rwAATTAAAcyy	R	-1100	-1089	AAAATTAAATTT	7.8	7.5e-05	-9.498	4.125
chromosome_GRCh38_10_1_133797422_1:88066000-88068000()_enhA1	site	rwAATTAAAcyy	R	-935	-924	AGAATTAAACCC	9.1	1.5e-05	-11.107	4.824
chromosome_GRCh38_10_1_133797422_1:88066000-88068000()_enhA1	site	rwAATTAAAcyy	D	-376	-365	GAAATTAAAGTG	7.9	5.7e-05	-9.772	4.244
chromosome_GRCh38_10_1_133797422_1:88092000-88094000()_enhA2	site	rwAATTAAAcyy	D	-211	-200	GAAATTAAATAG	8.0	5.1e-05	-9.884	4.292
chromosome_GRCh38_10_1_133797422_1:88112000-88114000()_enhA3	site	rwAATTAAAcyy	D	-968	-957	AGAATTAAATCC	7.5	9.3e-05	-9.283	4.032
chromosome_GRCh38_10_1_133797422_1:88272000-88274000()_enhB1	site	rwAATTAAAcyy	R	-1666	-1655	AAAATTAAAATA	7.7	7.5e-05	-9.498	4.125
chromosome_GRCh38_10_1_133797422_1:88272000-88274000()_enhB1	site	rwAATTAAAcyy	R	-137	-126	ATAATGAAACGT	8.2	4.1e-05	-10.102	4.387
chromosome_GRCh38_10_1_133797422_1:88322000-88324000()_enhB2	site	rwAATTAAAcyy	D	-1367	-1356	TCAATTAAACTT	8.6	2.8e-05	-10.483	4.553
chromosome_GRCh38_10_1_133797422_1:88322000-88324000()_enhB2	site	rwAATTAAAcyy	R	-246	-235	TTAATTAAATCC	7.7	7.5e-05	-9.498	4.125
chromosome_GRCh38_10_1_133797422_1:88322000-88324000()_enhB2	site	rwAATTAAAcyy	D	-242	-231	TTAATTAAACTA	9.0	1.7e-05	-10.982	4.770
chromosome_GRCh38_10_1_133797422_1:88388000-88390000()_enhG	site	rwAATTAAAcyy	R	-1804	-1793	TAAATTAAACAT	8.9	2.0e-05	-10.820	4.699
chromosome_GRCh38_10_1_133797422_1:88388000-88390000()_enhG	site	rwAATTAAAcyy	R	-1546	-1535	CAAATTAAACTG	8.8	2.5e-05	-10.597	4.602
chromosome_GRCh38_10_1_133797422_1:88388000-88390000()_enhG	site	rwAATTAAAcyy	D	-1220	-1209	GTAATCAAACTC	8.3	3.7e-05	-10.205	4.432
chromosome_GRCh38_10_1_133797422_1:88388000-88390000()_enhG	site	rwAATTAAAcyy	D	-845	-834	ACAATTAAAATC	7.9	5.7e-05	-9.772	4.244
chromosome_GRCh38_10_1_133797422_1:88388000-88390000()_enhG	site	rwAATTAAAcyy	R	-490	-479	GTAATTAAAGCA	7.5	9.3e-05	-9.283	4.032
;
; Matrices
;	matrix	name        	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	rwAATTAAAcyy	12	4	0	-22.800	10.500	33.300	a:0.302 c:0.205 g:0.204 t:0.290 
; Number of sequences scanned	6
; Sum of sequence lengths	12000
; N residues           	0
; Matches per matrix
;	matrix	name        	matches	scored
;	1	rwAATTAAAcyy   	16	0
;		TOTAL          	16	0
; Host name	rsat
; Job started	2026-03-29.162011
; Job done	2026-03-29.162012
; Seconds	0.57
;	user	0.57
;	system	0.02
;	cuser	0.5
;	csystem	0.04