; dna-pattern  -v 1 -pl $RSAT/public_html/tmp/www-data/2026/04/21/dna-pattern_2026-04-21.101312_jNTU83.pat -i $RSAT/public_html/tmp/www-data/2026/04/21/tmp_sequence_2026-04-21.101312_BoiO4g.fasta -format fasta -return sites -origin -0 -N 4 -noov -2str -subst 1
; Citation: van Helden et al. (2000). Yeast 16(2), 177-187.
; Input file           	$RSAT/public_html/tmp/www-data/2026/04/21/tmp_sequence_2026-04-21.101312_BoiO4g.fasta
; Input format         	fasta
; Pattern file         	$RSAT/public_html/tmp/www-data/2026/04/21/dna-pattern_2026-04-21.101312_jNTU83.pat
; Search method        	IUPAC
; Threshold            	0
; Allowed substitutions	1
; Return fields
;                     	sites
; Patterns
; 	seq	id	score
; 	GCCGCC	GCC-box	1
; 	TAAGAGCCGCC	GCC-box	1
; 	GCCGCC	DRE	1
; 	GCCGAC	CRT	1
; 	ACCGAC	CRT	1
; 	GAAATTTC	VWRE	1
; 	CACCG	CEI	1
; 
; Matching positions
; PatID	Strand	Pattern	SeqID	Start	End	matching_seq	Score
GCC-box	D	GCCGCC	pro-9590	-270	-265	GCAGCC	0.83
DRE	D	GCCGCC	pro-9590	-270	-265	GCAGCC	0.83
CRT	R	GCCGAC	pro-9590	-1802	-1797	GCCCAC	0.83
CRT	D	ACCGAC	pro-9590	-1204	-1199	ACCTAC	0.83
CRT	D	ACCGAC	pro-9590	-679	-674	ACCGAT	0.83
CRT	D	ACCGAC	pro-9590	-452	-447	ACCCAC	0.83
CRT	D	ACCGAC	pro-9590	-174	-169	ACCTAC	0.83
CRT	R	ACCGAC	pro-9590	-1710	-1705	ACCGAA	0.83
CRT	R	ACCGAC	pro-9590	-1210	-1205	ACCGAT	0.83
CRT	R	ACCGAC	pro-9590	-786	-781	ACCTAC	0.83
CRT	R	ACCGAC	pro-9590	-372	-367	ACTGAC	0.83
VWRE	DR	GAAATTTC	pro-9590	-1777	-1770	AAAATTTC	0.88
VWRE	DR	GAAATTTC	pro-9590	-1510	-1503	GCAATTTC	0.88
VWRE	DR	GAAATTTC	pro-9590	-1447	-1440	AAAATTTC	0.88
VWRE	DR	GAAATTTC	pro-9590	-475	-468	GAAATTTA	0.88
CEI	D	CACCG	pro-9590	-1201	-1197	TACCG	0.80
CEI	D	CACCG	pro-9590	-680	-676	GACCG	0.80
CEI	D	CACCG	pro-9590	-453	-449	CACCC	0.80
CEI	D	CACCG	pro-9590	-202	-198	CAACG	0.80
CEI	R	CACCG	pro-9590	-1804	-1800	CACCC	0.80
CEI	R	CACCG	pro-9590	-1708	-1704	TACCG	0.80
CEI	R	CACCG	pro-9590	-1208	-1204	TACCG	0.80
CEI	R	CACCG	pro-9590	-527	-523	CATCG	0.80
CEI	R	CACCG	pro-9590	-221	-217	TACCG	0.80
; Host name	rsat
; Job started	2026-04-21.101312
; Job done	2026-04-21.101312
; Seconds	0.13
;	user	0.13
;	system	0.01
;	cuser	0
;	csystem	0