; dna-pattern  -v 1 -pl $RSAT/public_html/tmp/www-data/2026/05/18/dna-pattern_2026-05-18.082357_b24kZG.pat -i $RSAT/public_html/tmp/www-data/2026/05/18/tmp_sequence_2026-05-18.082357_UwH74y.fasta -format fasta -return sites -origin -0 -N 4 -return limits -noov -2str -subst 0
; Citation: van Helden et al. (2000). Yeast 16(2), 177-187.
; Input file           	$RSAT/public_html/tmp/www-data/2026/05/18/tmp_sequence_2026-05-18.082357_UwH74y.fasta
; Input format         	fasta
; Pattern file         	$RSAT/public_html/tmp/www-data/2026/05/18/dna-pattern_2026-05-18.082357_b24kZG.pat
; Search method        	regexp
; Threshold            	0
; Allowed substitutions	0
; Return fields
;                     	sites
;                     	limits
; Patterns
; 	seq	id	score
; 	GAGTHCA	GAGTHCA	1
; 	AAWTTCRG	AAWTTCRG	1
; 	TYCTATATGGACTCT	TYCTATATGGACTCT	1
; 	TAATCTCGTATTGGG	TAATCTCGTATTGGG	1
; 	CTTYYAATATTCCTT	CTTYYAATATTCCTT	1
; 	TAWTTYYRAATTKT	TAWTTYYRAATTKT	1
; 	AATATTCCTTATTTT	AATATTCCTTATTTT	1
; 	GCGSGGGS	GCGSGGGS	1
; 	AAAARAARAG	AAAARAARAG	1
; 	TTCCTACTTG	TTCCTACTTG	1
; 	RAATAAAAATAAAA	RAATAAAAATAAAA	1
; 	WAGAGTAT	WAGAGTAT	1
; 
; Matching positions
; PatID	Strand	Pattern	SeqID	Start	End	matching_seq	Score
START_END	DR	-	AAP1	-2356	-1	-	0.00
AAWTTCRG	D	AAWTTCRG	AAP1	-2091	-2084	cacaAATTTCAGtcac	1.00
AAWTTCRG	R	AAWTTCRG	AAP1	-1851	-1844	aaggAATTTCGGtcac	1.00
AAAARAARAG	D	AAAARAARAG	AAP1	-1645	-1636	caacAAAAGAAGAGgagg	1.00
AAAARAARAG	D	AAAARAARAG	AAP1	-261	-252	gaagAAAAAAAAAGaagc	1.00
WAGAGTAT	D	WAGAGTAT	AAP1	-1116	-1109	aaggTAGAGTATcaca	1.00
; Host name	rsat
; Job started	2026-05-18.082357
; Job done	2026-05-18.082357
; Seconds	0.11
;	user	0.11
;	system	0
;	cuser	0
;	csystem	0