; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_chi7122_ensembl_72_GCA_000307205.1/genome/Escherichia_coli_chi7122_ensembl_72_GCA_000307205.1_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_chi7122_ensembl_72_GCA_000307205.1/genome/Escherichia_coli_chi7122_ensembl_72_GCA_000307205.1_stop_codon_frequencies
; Citation: van Helden et al. (1998). J Mol Biol 281(5), 827-42. 
; Program version              	1.169
; Slow counting mode           
; Oligomer length              	3
; Input file                   	$RSAT/public_html/data/genomes/Escherichia_coli_chi7122_ensembl_72_GCA_000307205.1/genome/Escherichia_coli_chi7122_ensembl_72_GCA_000307205.1_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_chi7122_ensembl_72_GCA_000307205.1/genome/Escherichia_coli_chi7122_ensembl_72_GCA_000307205.1_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	4598
; Sum of sequence lengths      	13794
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	4598
; total oligo occurrences      	4598
; alphabet size                	4
; nb possible oligomers        	64
; 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
taa	taa	0.6076555023923	2794
tga	tga	0.2951283166594	1357
tag	tag	0.0767725097869	353
ttg	ttg	0.0013049151805	6
gat	gat	0.0008699434537	4
gcg	gcg	0.0008699434537	4
cag	cag	0.0008699434537	4
act	act	0.0008699434537	4
agg	agg	0.0006524575903	3
ttt	ttt	0.0006524575903	3
cgc	cgc	0.0006524575903	3
atg	atg	0.0006524575903	3
tta	tta	0.0006524575903	3
tgg	tgg	0.0006524575903	3
ccg	ccg	0.0006524575903	3
tcg	tcg	0.0006524575903	3
ttc	ttc	0.0004349717268	2
tgt	tgt	0.0004349717268	2
ctt	ctt	0.0004349717268	2
att	att	0.0004349717268	2
tct	tct	0.0004349717268	2
acg	acg	0.0004349717268	2
cgt	cgt	0.0004349717268	2
tac	tac	0.0004349717268	2
ggc	ggc	0.0004349717268	2
ctc	ctc	0.0004349717268	2
cct	cct	0.0004349717268	2
cgg	cgg	0.0004349717268	2
ata	ata	0.0004349717268	2
gga	gga	0.0004349717268	2
atc	atc	0.0004349717268	2
tat	tat	0.0004349717268	2
aac	aac	0.0002174858634	1
caa	caa	0.0002174858634	1
gta	gta	0.0002174858634	1
tgc	tgc	0.0002174858634	1
cga	cga	0.0002174858634	1
aca	aca	0.0002174858634	1
ggg	ggg	0.0002174858634	1
gca	gca	0.0002174858634	1
cat	cat	0.0002174858634	1
aaa	aaa	0.0002174858634	1
aag	aag	0.0002174858634	1
aga	aga	0.0002174858634	1
agc	agc	0.0002174858634	1
gcc	gcc	0.0002174858634	1
cac	cac	0.0002174858634	1
agt	agt	0.0002174858634	1
; Host name	jolitorax
; Job started	2013-09-30.111925
; Job done	2013-09-30.111926
; Seconds	1.78
;	user	1.78
;	system	0.07
;	cuser	0
;	csystem	0