; oligo-analysis  -quick -v 1 -2str -i $RSAT/public_html/data/genomes/Spinacia_oleracea.GCF020520425.1.RefSeq/genome/Spinacia_oleracea.GCF020520425.1.RefSeq_upstream.fasta.gz -format fasta -seqtype dna -noov -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-noov-2str.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-noov-2str.freq
; Discard overlapping matches
; Counted on both strands
; 	grouped by pairs of reverse complements
; 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
; total overlapping occurrences	9152248
; total non overlapping occ    	105706244
; alphabet size                	4
; nb possible oligomers        	10
; 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
;	5	ovl_occ        	number of overlapping occurrences (discarded from the count)
;	6	forbocc        	forbidden positions (to avoid self-overlap)
#seq	id	obs_freq	occ	ovl_occ	forbocc
aa	aa|tt	0.1718586467251	19739425	7383677	19739425
ac	ac|gt	0.1044504484701	11997021	0	11997021
ag	ag|ct	0.1066612993665	12250956	0	12250956
at	at|at	0.0962674575250	11057135	0	11057135
ca	ca|tg	0.1215395375381	13959848	0	13959848
cc	cc|gg	0.0649584533985	7461030	1768571	7461030
cg	cg|cg	0.0258141818543	2964978	0	2964978
ga	ga|tc	0.1128315353470	12959660	0	12959660
gc	gc|gc	0.0312887792398	3593782	0	3593782
ta	ta|ta	0.0846468452677	9722409	0	9722409
; Host name	baobab
; Job started	2026-04-10.210219
; Job done	2026-04-10.210232
; Seconds	0.48
;	user	0.48
;	system	0.08
;	cuser	23.28
;	csystem	1.11
