; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_dec2e_ensembl_72_GCA_000249235.2/genome/Escherichia_coli_dec2e_ensembl_72_GCA_000249235.2_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_dec2e_ensembl_72_GCA_000249235.2/genome/Escherichia_coli_dec2e_ensembl_72_GCA_000249235.2_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_dec2e_ensembl_72_GCA_000249235.2/genome/Escherichia_coli_dec2e_ensembl_72_GCA_000249235.2_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_dec2e_ensembl_72_GCA_000249235.2/genome/Escherichia_coli_dec2e_ensembl_72_GCA_000249235.2_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	5288
; Sum of sequence lengths      	15864
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	5288
; total oligo occurrences      	5288
; 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	0.5873676248109	3106
tga	tga	0.3203479576399	1694
tag	tag	0.0858547655068	454
gag	gag	0.0003782148260	2
act	act	0.0003782148260	2
aat	aat	0.0003782148260	2
aga	aga	0.0003782148260	2
cac	cac	0.0003782148260	2
tat	tat	0.0003782148260	2
ggg	ggg	0.0001891074130	1
ctt	ctt	0.0001891074130	1
tgg	tgg	0.0001891074130	1
ttt	ttt	0.0001891074130	1
gat	gat	0.0001891074130	1
cag	cag	0.0001891074130	1
tcg	tcg	0.0001891074130	1
acc	acc	0.0001891074130	1
atg	atg	0.0001891074130	1
cat	cat	0.0001891074130	1
gcg	gcg	0.0001891074130	1
gtc	gtc	0.0001891074130	1
aag	aag	0.0001891074130	1
ctc	ctc	0.0001891074130	1
cct	cct	0.0001891074130	1
tac	tac	0.0001891074130	1
cgg	cgg	0.0001891074130	1
tgc	tgc	0.0001891074130	1
gga	gga	0.0001891074130	1
atc	atc	0.0001891074130	1
ccc	ccc	0.0001891074130	1
aca	aca	0.0001891074130	1
; Host name	jolitorax
; Job started	2013-09-30.161801
; Job done	2013-09-30.161802
; Seconds	2.05
;	user	2.05
;	system	0.09
;	cuser	0
;	csystem	0