; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Rattus_norvegicus_Rnor_5.0/genome/Rattus_norvegicus_Rnor_5.0_stop_codons.wc -o $RSAT/public_html/data/genomes/Rattus_norvegicus_Rnor_5.0/genome/Rattus_norvegicus_Rnor_5.0_stop_codon_frequencies.tab
; 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/Rattus_norvegicus_Rnor_5.0/genome/Rattus_norvegicus_Rnor_5.0_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Rattus_norvegicus_Rnor_5.0/genome/Rattus_norvegicus_Rnor_5.0_stop_codon_frequencies.tab
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	26153
; Sum of sequence lengths      	78459
; discarded residues           	56	 (other letters than ACGT)
; discarded occurrences        	27	 (contain discarded residues)
; nb possible positions        	26126
; total oligo occurrences      	26126
; 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
tga	tga	0.2450432519329	6402
taa	taa	0.1482814054964	3874
tag	tag	0.1134502028630	2964
agg	agg	0.0794610732604	2076
aga	aga	0.0483809232183	1264
agc	agc	0.0277501339662	725
agt	agt	0.0221618311261	579
cag	cag	0.0107938452117	282
aag	aag	0.0102579805558	268
gag	gag	0.0100283242747	262
ctg	ctg	0.0094541835719	247
aaa	aaa	0.0092628033377	242
tgg	tgg	0.0084207303070	220
gaa	gaa	0.0083441782133	218
gga	gga	0.0082676261196	216
aca	aca	0.0078465896042	205
cct	cct	0.0076169333231	199
cca	cca	0.0075786572763	198
atg	atg	0.0072341728546	189
gcc	gcc	0.0068896884330	180
ctc	ctc	0.0068514123861	179
tgt	tgt	0.0066983081987	175
gtg	gtg	0.0066217561050	173
ggg	ggg	0.0064686519176	169
tgc	tgc	0.0062772716834	164
cac	cac	0.0062772716834	164
tcc	tcc	0.0062007195897	162
ccc	ccc	0.0060476154023	158
acc	acc	0.0058562351680	153
caa	caa	0.0058179591212	152
ggt	ggt	0.0057031309806	149
gca	gca	0.0056648549338	148
ggc	ggc	0.0056265788869	147
gat	gat	0.0056265788869	147
gac	gac	0.0055883028401	146
ttt	ttt	0.0055500267932	145
tca	tca	0.0055117507464	144
ctt	ctt	0.0053203705121	139
aac	aac	0.0052820944653	138
aat	aat	0.0052438184184	137
gct	gct	0.0052055423716	136
act	act	0.0051672663247	135
att	att	0.0050907142310	133
cat	cat	0.0049376100436	129
tct	tct	0.0048227819031	126
ttc	ttc	0.0047845058562	125
ttg	ttg	0.0044782974814	117
atc	atc	0.0042869172472	112
gtt	gtt	0.0041720891066	109
gta	gta	0.0041338130598	108
cta	cta	0.0040955370129	107
tat	tat	0.0039041567787	102
gtc	gtc	0.0038658807318	101
ata	ata	0.0030620837480	80
tta	tta	0.0029855316543	78
cgg	cgg	0.0029855316543	78
tac	tac	0.0029472556074	77
ccg	ccg	0.0027941514200	73
cgt	cgt	0.0024879430452	65
tcg	tcg	0.0019520783893	51
cgc	cgc	0.0019138023425	50
gcg	gcg	0.0017606981551	46
acg	acg	0.0017606981551	46
cga	cga	0.0016458700145	43
; Host name	n79
; Job started	2017-04-15.092543
; Job done	2017-04-15.092544
; Seconds	0.91
;	user	0.92
;	system	0.03
;	cuser	0
;	csystem	0