; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_96_0109_ensembl_72_GCA_000318425.1/genome/Escherichia_coli_96_0109_ensembl_72_GCA_000318425.1_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_96_0109_ensembl_72_GCA_000318425.1/genome/Escherichia_coli_96_0109_ensembl_72_GCA_000318425.1_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_0109_ensembl_72_GCA_000318425.1/genome/Escherichia_coli_96_0109_ensembl_72_GCA_000318425.1_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_96_0109_ensembl_72_GCA_000318425.1/genome/Escherichia_coli_96_0109_ensembl_72_GCA_000318425.1_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	4211
; Sum of sequence lengths      	12633
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	4211
; total oligo occurrences      	4211
; 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	0.5326525765851	2243
tga	tga	0.3044407504156	1282
tag	tag	0.0786036570886	331
tgg	tgg	0.0033246259796	14
gtg	gtg	0.0028496794111	12
atg	atg	0.0026122061268	11
cga	cga	0.0026122061268	11
gac	gac	0.0026122061268	11
ggc	ggc	0.0026122061268	11
gat	gat	0.0023747328426	10
ttt	ttt	0.0023747328426	10
agg	agg	0.0021372595583	9
ctg	ctg	0.0021372595583	9
cgc	cgc	0.0021372595583	9
aat	aat	0.0021372595583	9
acc	acc	0.0021372595583	9
aaa	aaa	0.0021372595583	9
tgt	tgt	0.0018997862740	8
gct	gct	0.0018997862740	8
tgc	tgc	0.0018997862740	8
ggg	ggg	0.0018997862740	8
ccg	ccg	0.0018997862740	8
cgg	cgg	0.0018997862740	8
gcc	gcc	0.0018997862740	8
tat	tat	0.0018997862740	8
aac	aac	0.0016623129898	7
acg	acg	0.0016623129898	7
cag	cag	0.0016623129898	7
gag	gag	0.0016623129898	7
ctc	ctc	0.0016623129898	7
ata	ata	0.0016623129898	7
gca	gca	0.0014248397055	6
tcg	tcg	0.0014248397055	6
gtc	gtc	0.0014248397055	6
gga	gga	0.0014248397055	6
ttc	ttc	0.0011873664213	5
gaa	gaa	0.0011873664213	5
cgt	cgt	0.0011873664213	5
ggt	ggt	0.0011873664213	5
aag	aag	0.0011873664213	5
tca	tca	0.0011873664213	5
agc	agc	0.0011873664213	5
agt	agt	0.0011873664213	5
att	att	0.0009498931370	4
gta	gta	0.0009498931370	4
atc	atc	0.0009498931370	4
cca	cca	0.0007124198528	3
gcg	gcg	0.0007124198528	3
ccc	ccc	0.0007124198528	3
aca	aca	0.0007124198528	3
cat	cat	0.0007124198528	3
act	act	0.0007124198528	3
aga	aga	0.0007124198528	3
tac	tac	0.0004749465685	2
gtt	gtt	0.0004749465685	2
cac	cac	0.0004749465685	2
tct	tct	0.0002374732843	1
tcc	tcc	0.0002374732843	1
; Host name	jolitorax
; Job started	2013-09-30.071535
; Job done	2013-09-30.071536
; Seconds	1.65
;	user	1.65
;	system	0.07
;	cuser	0
;	csystem	0