; dyad-analysis  -quick -v 1 -i $RSAT/public_html/data/genomes/Spinacia_oleracea.GCF020520425.1.RefSeq/genome/Spinacia_oleracea.GCF020520425.1.RefSeq_upstream-noorf.fasta.gz -format fasta -timeout 240000 -type any -seqtype dna -2str -ovlp -sp 0-20 -l 1 -return freq,occ -o $RSAT/public_html/data/genomes/Spinacia_oleracea.GCF020520425.1.RefSeq/oligo-frequencies/dyads_1nt_sp0-20_upstream-noorf_Spinacia_oleracea.GCF020520425.1.RefSeq-ovlp-2str.freq
; Citation: van Helden et al. (2000). Nucleic Acids Res. 28(8):1808-18.
; Program version              	1.78
; Input file                   	$RSAT/public_html/data/genomes/Spinacia_oleracea.GCF020520425.1.RefSeq/genome/Spinacia_oleracea.GCF020520425.1.RefSeq_upstream-noorf.fasta.gz
; Sequence type                	DNA
; Nb of sequences              	38318
; Sum of sequence lengths      	92348965
; Output file                  	$RSAT/public_html/data/genomes/Spinacia_oleracea.GCF020520425.1.RefSeq/oligo-frequencies/dyads_1nt_sp0-20_upstream-noorf_Spinacia_oleracea.GCF020520425.1.RefSeq-ovlp-2str.freq
; default return values        	occ,freq
; return values                	freq,occ
; Count overlapping matches
; Counted on both strands
; 	grouped by pairs of reverse complements
; Monad parameters             
; 	monad size                  	1
; 	monad positions              92348265
; 	    valid                    	92348265
; 	    discarded                	0 (contain other letters than ACGT)
; 	distinct monads              4
; Dyad parameters              
; 	dyad type                    any dyad
; 	minimal spacing              0
; 	maximal spacing              20
; 	distinct dyads               	210
; 	dyads tested for significance	0
;	Dyad counts per spacing
;		spacing	max_pos	occ	ACGT	nonACGT
;		sp 0		92310546	92310546	NA
;		sp 1				
;		sp 2				
;		sp 3				
;		sp 4				
;		sp 5				
;		sp 6				
;		sp 7				
;		sp 8				
;		sp 9				
;		sp 10				
;		sp 11				
;		sp 12				
;		sp 13				
;		sp 14				
;		sp 15				
;		sp 16				
;		sp 17				
;		sp 18				
;		sp 19				
;		sp 20				
; Estimation of expected dyad frequencies
;	Background model	monads
;	Monad calibration from input sequences
; column headers
;	1	seq            	
;	2	identifier     	
;	3	observed_freq  	observed frequency
;	4	occ            	observed occurrences
#seq   	identifier     	observed_freq	occ
an{0}a	an{0}a|tn{0}t	0.2400098142633	22155437
an{0}c	an{0}c|gn{0}t	0.1039052677686	9591552
an{0}g	an{0}g|cn{0}t	0.1048728495225	9680870
an{0}t	an{0}t|an{0}t	0.0984825395790	9090977
cn{0}a	cn{0}a|tn{0}g	0.1197054343065	11050074
cn{0}c	cn{0}c|gn{0}g	0.0785832964307	7254067
cn{0}g	cn{0}g|cn{0}g	0.0255195327303	2355722
gn{0}a	gn{0}a|tn{0}c	0.1112426201011	10268867
gn{0}c	gn{0}c|gn{0}c	0.0302519064290	2792570
tn{0}a	tn{0}a|tn{0}a	0.0874267388690	8070410
; Host name	baobab
; Job started	2026-04-10.205927
; Job done	2026-04-10.205944
; Seconds	0.5
;	user	0.5
;	system	0.06
;	cuser	32.38
;	csystem	1.76
