; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_ec1869_ensembl_72_GCA_000303335.1/genome/Escherichia_coli_ec1869_ensembl_72_GCA_000303335.1_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_ec1869_ensembl_72_GCA_000303335.1/genome/Escherichia_coli_ec1869_ensembl_72_GCA_000303335.1_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_ec1869_ensembl_72_GCA_000303335.1/genome/Escherichia_coli_ec1869_ensembl_72_GCA_000303335.1_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_ec1869_ensembl_72_GCA_000303335.1/genome/Escherichia_coli_ec1869_ensembl_72_GCA_000303335.1_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	2830
; Sum of sequence lengths      	8490
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	2830
; total oligo occurrences      	2830
; 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	0.5318021201413	1505
tga	tga	0.3141342756184	889
tag	tag	0.0710247349823	201
gga	gga	0.0053003533569	15
gaa	gaa	0.0049469964664	14
cgg	cgg	0.0045936395760	13
ggg	ggg	0.0042402826855	12
cac	cac	0.0031802120141	9
tgt	tgt	0.0028268551237	8
tgc	tgc	0.0028268551237	8
cag	cag	0.0028268551237	8
tat	tat	0.0028268551237	8
atg	atg	0.0024734982332	7
gcg	gcg	0.0024734982332	7
ccg	ccg	0.0024734982332	7
ggc	ggc	0.0021201413428	6
aga	aga	0.0021201413428	6
agc	agc	0.0021201413428	6
cca	cca	0.0017667844523	5
acg	acg	0.0017667844523	5
ggt	ggt	0.0017667844523	5
cgc	cgc	0.0014134275618	4
tgg	tgg	0.0014134275618	4
aaa	aaa	0.0014134275618	4
aag	aag	0.0014134275618	4
cct	cct	0.0014134275618	4
gtg	gtg	0.0014134275618	4
atc	atc	0.0014134275618	4
ctt	ctt	0.0010600706714	3
ctg	ctg	0.0010600706714	3
ttt	ttt	0.0010600706714	3
gct	gct	0.0010600706714	3
tac	tac	0.0010600706714	3
aca	aca	0.0010600706714	3
gca	gca	0.0010600706714	3
act	act	0.0010600706714	3
ttc	ttc	0.0007067137809	2
aac	aac	0.0007067137809	2
tta	tta	0.0007067137809	2
cgt	cgt	0.0007067137809	2
cta	cta	0.0007067137809	2
cga	cga	0.0007067137809	2
tcg	tcg	0.0007067137809	2
acc	acc	0.0007067137809	2
gtc	gtc	0.0007067137809	2
tca	tca	0.0007067137809	2
gtt	gtt	0.0007067137809	2
agt	agt	0.0007067137809	2
agg	agg	0.0003533568905	1
gat	gat	0.0003533568905	1
tct	tct	0.0003533568905	1
aat	aat	0.0003533568905	1
caa	caa	0.0003533568905	1
gac	gac	0.0003533568905	1
ccc	ccc	0.0003533568905	1
ctc	ctc	0.0003533568905	1
tcc	tcc	0.0003533568905	1
ttg	ttg	0.0003533568905	1
; Host name	jolitorax
; Job started	2013-09-30.234646
; Job done	2013-09-30.234646
; Seconds	1.5
;	user	1.5
;	system	0.07
;	cuser	0
;	csystem	0