; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_96_0107_ensembl_72_GCA_000316765.1/genome/Escherichia_coli_96_0107_ensembl_72_GCA_000316765.1_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_96_0107_ensembl_72_GCA_000316765.1/genome/Escherichia_coli_96_0107_ensembl_72_GCA_000316765.1_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_96_0107_ensembl_72_GCA_000316765.1/genome/Escherichia_coli_96_0107_ensembl_72_GCA_000316765.1_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_96_0107_ensembl_72_GCA_000316765.1/genome/Escherichia_coli_96_0107_ensembl_72_GCA_000316765.1_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	2886
; Sum of sequence lengths      	8658
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	2886
; total oligo occurrences      	2886
; 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	0.5623700623701	1623
tga	tga	0.2983367983368	861
tag	tag	0.0755370755371	218
tgc	tgc	0.0034650034650	10
ggc	ggc	0.0034650034650	10
ggg	ggg	0.0024255024255	7
ccg	ccg	0.0024255024255	7
aaa	aaa	0.0024255024255	7
cac	cac	0.0024255024255	7
tgt	tgt	0.0017325017325	5
ctg	ctg	0.0017325017325	5
gca	gca	0.0017325017325	5
tcc	tcc	0.0017325017325	5
atc	atc	0.0017325017325	5
tat	tat	0.0017325017325	5
gat	gat	0.0013860013860	4
gcg	gcg	0.0013860013860	4
gct	gct	0.0013860013860	4
aat	aat	0.0013860013860	4
acg	acg	0.0013860013860	4
gac	gac	0.0013860013860	4
aca	aca	0.0013860013860	4
tgg	tgg	0.0013860013860	4
ggt	ggt	0.0013860013860	4
cgg	cgg	0.0013860013860	4
gaa	gaa	0.0010395010395	3
agg	agg	0.0010395010395	3
att	att	0.0010395010395	3
tta	tta	0.0010395010395	3
tct	tct	0.0010395010395	3
tcg	tcg	0.0010395010395	3
aag	aag	0.0010395010395	3
gtt	gtt	0.0010395010395	3
gga	gga	0.0010395010395	3
gcc	gcc	0.0010395010395	3
ttc	ttc	0.0006930006930	2
ttt	ttt	0.0006930006930	2
atg	atg	0.0006930006930	2
aac	aac	0.0006930006930	2
cga	cga	0.0006930006930	2
acc	acc	0.0006930006930	2
cat	cat	0.0006930006930	2
cct	cct	0.0006930006930	2
aga	aga	0.0006930006930	2
ata	ata	0.0006930006930	2
agc	agc	0.0006930006930	2
agt	agt	0.0006930006930	2
ctt	ctt	0.0003465003465	1
cca	cca	0.0003465003465	1
cgc	cgc	0.0003465003465	1
caa	caa	0.0003465003465	1
tac	tac	0.0003465003465	1
gta	gta	0.0003465003465	1
cag	cag	0.0003465003465	1
gag	gag	0.0003465003465	1
act	act	0.0003465003465	1
ctc	ctc	0.0003465003465	1
gtg	gtg	0.0003465003465	1
ttg	ttg	0.0003465003465	1
; Host name	jolitorax
; Job started	2013-09-30.070915
; Job done	2013-09-30.070916
; Seconds	1.47
;	user	1.47
;	system	0.07
;	cuser	0
;	csystem	0