; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_K_12_substr__MG1655_uid57779/genome/Escherichia_coli_K_12_substr__MG1655_uid57779_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_K_12_substr__MG1655_uid57779/genome/Escherichia_coli_K_12_substr__MG1655_uid57779_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_K_12_substr__MG1655_uid57779/genome/Escherichia_coli_K_12_substr__MG1655_uid57779_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_K_12_substr__MG1655_uid57779/genome/Escherichia_coli_K_12_substr__MG1655_uid57779_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	4319
; Sum of sequence lengths      	12957
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	4319
; total oligo occurrences      	4319
; 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	0.6367214633017	2750
tga	tga	0.2833989349386	1224
tag	tag	0.0689974531141	298
ggt	ggt	0.0006946052327	3
tat	tat	0.0006946052327	3
att	att	0.0004630701551	2
aag	aag	0.0004630701551	2
gct	gct	0.0004630701551	2
ccg	ccg	0.0004630701551	2
agg	agg	0.0004630701551	2
ggc	ggc	0.0004630701551	2
gta	gta	0.0004630701551	2
gtg	gtg	0.0004630701551	2
act	act	0.0004630701551	2
gcc	gcc	0.0004630701551	2
gaa	gaa	0.0004630701551	2
gca	gca	0.0004630701551	2
cag	cag	0.0004630701551	2
gtt	gtt	0.0002315350776	1
aat	aat	0.0002315350776	1
atg	atg	0.0002315350776	1
acg	acg	0.0002315350776	1
cgc	cgc	0.0002315350776	1
caa	caa	0.0002315350776	1
gcg	gcg	0.0002315350776	1
ctt	ctt	0.0002315350776	1
tac	tac	0.0002315350776	1
atc	atc	0.0002315350776	1
tcc	tcc	0.0002315350776	1
tgc	tgc	0.0002315350776	1
agc	agc	0.0002315350776	1
gat	gat	0.0002315350776	1
gac	gac	0.0002315350776	1
; Host name	rsat-tagc
; Job started	2014-06-19.082810
; Job done	2014-06-19.082810
; Seconds	0.32
;	user	0.32
;	system	0.01
;	cuser	0
;	csystem	0