; dna-pattern  -v 1 -pl $RSAT/public_html/tmp/www-data/2026/04/21/dna-pattern_2026-04-21.092338_ruIdrV.pat -i $RSAT/public_html/tmp/www-data/2026/04/21/tmp_sequence_2026-04-21.092338_L7TYia.fasta -format fasta -return sites -origin -0 -N 4 -return limits -return scores -return rank -return table -return total -noov -2str -subst 0
; Citation: van Helden et al. (2000). Yeast 16(2), 177-187.
; Input file           	$RSAT/public_html/tmp/www-data/2026/04/21/tmp_sequence_2026-04-21.092338_L7TYia.fasta
; Input format         	fasta
; Pattern file         	$RSAT/public_html/tmp/www-data/2026/04/21/dna-pattern_2026-04-21.092338_ruIdrV.pat
; Search method        	regexp
; Threshold            	0
; Allowed substitutions	0
; Return fields
;                     	total
;                     	colsum
;                     	sites
;                     	limits
;                     	rank
;                     	scores
;                     	table
;                     	rowsum
; Patterns
; 	seq	id	score
; 	TTGNCN	TTGNCN	1
; 	NGNYANNMT	NGNYANNMT	1
; 
; Matching positions
; PatID	Strand	Pattern	SeqID	Start	End	matching_seq	Score
START_END	DR	-	KingstonB	-501	-1	-	0.00
TTGNCN	R	TTGNCN	KingstonB	-303	-298	ctgcTTGGCGtgcg	1.00
TTGNCN	R	TTGNCN	KingstonB	-34	-29	cgccTTGGCCtggg	1.00
NGNYANNMT	R	NGNYANNMT	KingstonB	-163	-155	gtggGGTCATTCTgtgc	1.00
#seq	rank	score	total	TTGNCN	NGNYANNMT
KingstonB	1	3	3	2	1
total	1	3	3	2	1
; Host name	rsat
; Job started	2026-04-21.092339
; Job done	2026-04-21.092339
; Seconds	0.1
;	user	0.1
;	system	0
;	cuser	0
;	csystem	0