; oligo-analysis  -quick -v 1 -1str -i $RSAT/public_html/data/genomes/Spinacia_oleracea.GCF020520425.1.RefSeq/genome/Spinacia_oleracea.GCF020520425.1.RefSeq_upstream.fasta.gz -format fasta -seqtype dna -ovlp -l 2 -type dna -return freq,occ -o $RSAT/public_html/data/genomes/Spinacia_oleracea.GCF020520425.1.RefSeq/oligo-frequencies/2nt_upstream_Spinacia_oleracea.GCF020520425.1.RefSeq-ovlp-1str.freq
; Citation: van Helden et al. (1998). J Mol Biol 281(5), 827-42. 
; Program version              	1.169
; Quick counting mode          
; Oligomer length              	2
; Input file                   	$RSAT/public_html/data/genomes/Spinacia_oleracea.GCF020520425.1.RefSeq/genome/Spinacia_oleracea.GCF020520425.1.RefSeq_upstream.fasta.gz
; Input format                 	fasta
; Output file                  	$RSAT/public_html/data/genomes/Spinacia_oleracea.GCF020520425.1.RefSeq/oligo-frequencies/2nt_upstream_Spinacia_oleracea.GCF020520425.1.RefSeq-ovlp-1str.freq
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	38318
; Sum of sequence lengths      	114897616
; discarded residues           	NA (quick mode)	 (other letters than ACGT)
; discarded occurrences        	NA (quick mode)	 (contain discarded residues)
; nb possible positions        	NA (quick mode)
; total oligo occurrences      	114858492
; alphabet size                	4
; nb possible oligomers        	16
; oligomers tested for significance	0
;
; column headers
;	1	seq            	oligomer sequence
;	2	id             	oligomer identifier
;	3	obs_freq       	observed relative frequency
;	4	occ            	observed occurrences
#seq	id	obs_freq	occ
aa	aa	0.1175206705657	13498247
ac	ac	0.0515977869534	5926444
ag	ag	0.0538966069657	6190483
at	at	0.0962674575250	11057135
ca	ca	0.0599708465613	6888161
cc	cc	0.0392576806598	4509078
cg	cg	0.0258141818543	2964978
ct	ct	0.0527646924008	6060473
ga	ga	0.0571539281571	6564614
gc	gc	0.0312887792398	3593782
gg	gg	0.0410985980906	4720523
gt	gt	0.0528526615167	6070577
ta	ta	0.0846468452677	9722409
tc	tc	0.0556776071899	6395046
tg	tg	0.0615686909767	7071687
tt	tt	0.1186229660755	13624855
; Host name	baobab
; Job started	2026-04-10.210449
; Job done	2026-04-10.210502
; Seconds	0.49
;	user	0.5
;	system	0.05
;	cuser	21.2
;	csystem	1
