; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_dec7d_ensembl_72_GCA_000249755.2/genome/Escherichia_coli_dec7d_ensembl_72_GCA_000249755.2_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_dec7d_ensembl_72_GCA_000249755.2/genome/Escherichia_coli_dec7d_ensembl_72_GCA_000249755.2_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_dec7d_ensembl_72_GCA_000249755.2/genome/Escherichia_coli_dec7d_ensembl_72_GCA_000249755.2_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_dec7d_ensembl_72_GCA_000249755.2/genome/Escherichia_coli_dec7d_ensembl_72_GCA_000249755.2_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	5397
; Sum of sequence lengths      	16191
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	5397
; total oligo occurrences      	5397
; 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	0.5888456549935	3178
tga	tga	0.3266629609042	1763
tag	tag	0.0811561978877	438
atg	atg	0.0005558643691	3
tcg	tcg	0.0003705762461	2
gac	gac	0.0003705762461	2
agc	agc	0.0003705762461	2
ccc	ccc	0.0003705762461	2
ttt	ttt	0.0001852881230	1
gat	gat	0.0001852881230	1
acc	acc	0.0001852881230	1
ata	ata	0.0001852881230	1
gtt	gtt	0.0001852881230	1
gcc	gcc	0.0001852881230	1
ctc	ctc	0.0001852881230	1
; Host name	jolitorax
; Job started	2013-09-30.191217
; Job done	2013-09-30.191218
; Seconds	1.84
;	user	1.84
;	system	0.1
;	cuser	0
;	csystem	0.01