id	sid	tid	token	lemma	pos
2n49t150833	1	1	the	the	DET
2n49t150833	1	2	genetic	genetic	ADJ
2n49t150833	1	3	code	code	NOUN
2n49t150833	1	4	is	be	AUX
2n49t150833	1	5	degenerate	degenerate	ADJ
2n49t150833	1	6	,	,	PUNCT
2n49t150833	1	7	and	and	CCONJ
2n49t150833	1	8	synonymous	synonymous	ADJ
2n49t150833	1	9	codons	codon	NOUN
2n49t150833	1	10	are	be	AUX
2n49t150833	1	11	not	not	PART
2n49t150833	1	12	used	use	VERB
2n49t150833	1	13	with	with	ADP
2n49t150833	1	14	equal	equal	ADJ
2n49t150833	1	15	frequency	frequency	NOUN
2n49t150833	1	16	.	.	PUNCT
2n49t150833	2	1	rare	rare	ADJ
2n49t150833	2	2	codons	codon	NOUN
2n49t150833	2	3	are	be	AUX
2n49t150833	2	4	hypothesized	hypothesize	VERB
2n49t150833	2	5	to	to	PART
2n49t150833	2	6	be	be	AUX
2n49t150833	2	7	associated	associate	VERB
2n49t150833	2	8	with	with	ADP
2n49t150833	2	9	generally	generally	ADV
2n49t150833	2	10	slower	slow	ADJ
2n49t150833	2	11	translation	translation	NOUN
2n49t150833	2	12	and	and	CCONJ
2n49t150833	2	13	lower	low	ADJ
2n49t150833	2	14	translational	translational	ADJ
2n49t150833	2	15	accuracy	accuracy	NOUN
2n49t150833	2	16	.	.	PUNCT
2n49t150833	3	1	historically	historically	ADV
2n49t150833	3	2	,	,	PUNCT
2n49t150833	3	3	rare	rare	ADJ
2n49t150833	3	4	codons	codon	NOUN
2n49t150833	3	5	were	be	AUX
2n49t150833	3	6	believed	believe	VERB
2n49t150833	3	7	to	to	PART
2n49t150833	3	8	be	be	AUX
2n49t150833	3	9	deleterious	deleterious	ADJ
2n49t150833	3	10	,	,	PUNCT
2n49t150833	3	11	and	and	CCONJ
2n49t150833	3	12	were	be	AUX
2n49t150833	3	13	thought	think	VERB
2n49t150833	3	14	to	to	PART
2n49t150833	3	15	persist	persist	VERB
2n49t150833	3	16	in	in	ADP
2n49t150833	3	17	coding	code	VERB
2n49t150833	3	18	sequences	sequence	NOUN
2n49t150833	3	19	mostly	mostly	ADV
2n49t150833	3	20	as	as	ADP
2n49t150833	3	21	the	the	DET
2n49t150833	3	22	result	result	NOUN
2n49t150833	3	23	of	of	ADP
2n49t150833	3	24	random	random	ADJ
2n49t150833	3	25	genetic	genetic	ADJ
2n49t150833	3	26	drift	drift	NOUN
2n49t150833	3	27	.	.	PUNCT
2n49t150833	4	1	however	however	ADV
2n49t150833	4	2	,	,	PUNCT
2n49t150833	4	3	rare	rare	ADJ
2n49t150833	4	4	codons	codon	NOUN
2n49t150833	4	5	have	have	AUX
2n49t150833	4	6	also	also	ADV
2n49t150833	4	7	been	be	AUX
2n49t150833	4	8	hypothesized	hypothesize	VERB
2n49t150833	4	9	to	to	ADP
2n49t150833	4	10	encode	encode	ADJ
2n49t150833	4	11	translation	translation	NOUN
2n49t150833	4	12	rate	rate	NOUN
2n49t150833	4	13	,	,	PUNCT
2n49t150833	4	14	thus	thus	ADV
2n49t150833	4	15	promoting	promote	VERB
2n49t150833	4	16	proper	proper	ADJ
2n49t150833	4	17	co	co	NOUN
2n49t150833	4	18	-	-	NOUN
2n49t150833	4	19	translation	translation	NOUN
2n49t150833	4	20	folding	folding	NOUN
2n49t150833	4	21	of	of	ADP
2n49t150833	4	22	the	the	DET
2n49t150833	4	23	nascent	nascent	ADJ
2n49t150833	4	24	chain	chain	NOUN
2n49t150833	4	25	and	and	CCONJ
2n49t150833	4	26	allowing	allow	VERB
2n49t150833	4	27	time	time	NOUN
2n49t150833	4	28	for	for	ADP
2n49t150833	4	29	co	co	ADJ
2n49t150833	4	30	-	-	ADJ
2n49t150833	4	31	translational	translational	ADJ
2n49t150833	4	32	interactions	interaction	NOUN
2n49t150833	4	33	.	.	PUNCT
2n49t150833	5	1	prior	prior	ADJ
2n49t150833	5	2	work	work	NOUN
2n49t150833	5	3	by	by	ADP
2n49t150833	5	4	the	the	DET
2n49t150833	5	5	clark	clark	PROPN
2n49t150833	5	6	lab	lab	NOUN
2n49t150833	5	7	established	establish	VERB
2n49t150833	5	8	that	that	SCONJ
2n49t150833	5	9	rare	rare	ADJ
2n49t150833	5	10	codons	codon	NOUN
2n49t150833	5	11	form	form	NOUN
2n49t150833	5	12	clusters	cluster	NOUN
2n49t150833	5	13	within	within	ADP
2n49t150833	5	14	the	the	DET
2n49t150833	5	15	coding	code	VERB
2n49t150833	5	16	sequences	sequence	NOUN
2n49t150833	5	17	of	of	ADP
2n49t150833	5	18	most	most	ADJ
2n49t150833	5	19	species	specie	NOUN
2n49t150833	5	20	,	,	PUNCT
2n49t150833	5	21	raising	raise	VERB
2n49t150833	5	22	the	the	DET
2n49t150833	5	23	possibility	possibility	NOUN
2n49t150833	5	24	that	that	SCONJ
2n49t150833	5	25	these	these	DET
2n49t150833	5	26	clusters	cluster	NOUN
2n49t150833	5	27	resulted	result	VERB
2n49t150833	5	28	from	from	ADP
2n49t150833	5	29	positive	positive	ADJ
2n49t150833	5	30	selection	selection	NOUN
2n49t150833	5	31	.	.	PUNCT
2n49t150833	6	1	rare	rare	ADJ
2n49t150833	6	2	codons	codon	NOUN
2n49t150833	6	3	have	have	AUX
2n49t150833	6	4	been	be	AUX
2n49t150833	6	5	shown	show	VERB
2n49t150833	6	6	to	to	PART
2n49t150833	6	7	have	have	VERB
2n49t150833	6	8	functional	functional	ADJ
2n49t150833	6	9	significance	significance	NOUN
2n49t150833	6	10	in	in	ADP
2n49t150833	6	11	specific	specific	ADJ
2n49t150833	6	12	protein	protein	NOUN
2n49t150833	6	13	coding	code	VERB
2n49t150833	6	14	sequences	sequence	NOUN
2n49t150833	6	15	,	,	PUNCT
2n49t150833	6	16	but	but	CCONJ
2n49t150833	6	17	there	there	PRON
2n49t150833	6	18	is	be	VERB
2n49t150833	6	19	still	still	ADV
2n49t150833	6	20	no	no	DET
2n49t150833	6	21	consensus	consensus	NOUN
2n49t150833	6	22	on	on	ADP
2n49t150833	6	23	how	how	SCONJ
2n49t150833	6	24	widespread	widespread	ADJ
2n49t150833	6	25	such	such	ADJ
2n49t150833	6	26	mechanisms	mechanism	NOUN
2n49t150833	6	27	are	be	AUX
2n49t150833	6	28	or	or	CCONJ
2n49t150833	6	29	how	how	SCONJ
2n49t150833	6	30	to	to	PART
2n49t150833	6	31	identify	identify	VERB
2n49t150833	6	32	functional	functional	ADJ
2n49t150833	6	33	rare	rare	ADJ
2n49t150833	6	34	codon	codon	PROPN
2n49t150833	6	35	clusters	cluster	NOUN
2n49t150833	6	36	.	.	PUNCT
2n49t150833	7	1	the	the	DET
2n49t150833	7	2	studies	study	NOUN
2n49t150833	7	3	described	describe	VERB
2n49t150833	7	4	here	here	ADV
2n49t150833	7	5	seek	seek	VERB
2n49t150833	7	6	to	to	PART
2n49t150833	7	7	identify	identify	VERB
2n49t150833	7	8	genome	genome	NOUN
2n49t150833	7	9	-	-	PUNCT
2n49t150833	7	10	wide	wide	ADJ
2n49t150833	7	11	trends	trend	NOUN
2n49t150833	7	12	in	in	ADP
2n49t150833	7	13	codon	codon	ADJ
2n49t150833	7	14	usage	usage	NOUN
2n49t150833	7	15	to	to	PART
2n49t150833	7	16	aid	aid	VERB
2n49t150833	7	17	in	in	ADP
2n49t150833	7	18	building	building	NOUN
2n49t150833	7	19	hypotheses	hypothesis	NOUN
2n49t150833	7	20	about	about	ADP
2n49t150833	7	21	the	the	DET
2n49t150833	7	22	function	function	NOUN
2n49t150833	7	23	of	of	ADP
2n49t150833	7	24	rare	rare	ADJ
2n49t150833	7	25	codons	codon	NOUN
2n49t150833	7	26	and	and	CCONJ
2n49t150833	7	27	identifying	identify	VERB
2n49t150833	7	28	functionally	functionally	ADV
2n49t150833	7	29	significant	significant	ADJ
2n49t150833	7	30	codon	codon	NOUN
2n49t150833	7	31	usage	usage	NOUN
2n49t150833	7	32	.	.	PUNCT
2n49t150833	8	1	if	if	SCONJ
2n49t150833	8	2	rare	rare	ADJ
2n49t150833	8	3	codons	codon	NOUN
2n49t150833	8	4	modulate	modulate	VERB
2n49t150833	8	5	co	co	ADJ
2n49t150833	8	6	-	-	ADJ
2n49t150833	8	7	translational	translational	ADJ
2n49t150833	8	8	protein	protein	NOUN
2n49t150833	8	9	folding	folding	NOUN
2n49t150833	8	10	,	,	PUNCT
2n49t150833	8	11	their	their	PRON
2n49t150833	8	12	positions	position	NOUN
2n49t150833	8	13	are	be	AUX
2n49t150833	8	14	expected	expect	VERB
2n49t150833	8	15	to	to	PART
2n49t150833	8	16	be	be	AUX
2n49t150833	8	17	correlated	correlate	VERB
2n49t150833	8	18	with	with	ADP
2n49t150833	8	19	the	the	DET
2n49t150833	8	20	locations	location	NOUN
2n49t150833	8	21	of	of	ADP
2n49t150833	8	22	protein	protein	NOUN
2n49t150833	8	23	structural	structural	ADJ
2n49t150833	8	24	features	feature	NOUN
2n49t150833	8	25	.	.	PUNCT
2n49t150833	9	1	here	here	ADV
2n49t150833	9	2	we	we	PRON
2n49t150833	9	3	report	report	VERB
2n49t150833	9	4	that	that	SCONJ
2n49t150833	9	5	rare	rare	ADJ
2n49t150833	9	6	codon	codon	NOUN
2n49t150833	9	7	clusters	cluster	NOUN
2n49t150833	9	8	are	be	AUX
2n49t150833	9	9	enriched	enrich	VERB
2n49t150833	9	10	at	at	ADP
2n49t150833	9	11	predicted	predict	VERB
2n49t150833	9	12	domain	domain	NOUN
2n49t150833	9	13	boundaries	boundary	NOUN
2n49t150833	9	14	,	,	PUNCT
2n49t150833	9	15	at	at	ADP
2n49t150833	9	16	a	a	DET
2n49t150833	9	17	genome	genome	NOUN
2n49t150833	9	18	-	-	PUNCT
2n49t150833	9	19	wide	wide	ADJ
2n49t150833	9	20	level	level	NOUN
2n49t150833	9	21	,	,	PUNCT
2n49t150833	9	22	in	in	ADP
2n49t150833	9	23	both	both	PRON
2n49t150833	9	24	human	human	ADJ
2n49t150833	9	25	and	and	CCONJ
2n49t150833	9	26	e.	e.	PROPN
2n49t150833	9	27	coli	coli	PROPN
2n49t150833	9	28	.	.	PUNCT
2n49t150833	10	1	transmembrane	transmembrane	ADJ
2n49t150833	10	2	helices	helix	NOUN
2n49t150833	10	3	were	be	AUX
2n49t150833	10	4	also	also	ADV
2n49t150833	10	5	shown	show	VERB
2n49t150833	10	6	to	to	PART
2n49t150833	10	7	have	have	VERB
2n49t150833	10	8	biased	bias	VERB
2n49t150833	10	9	codon	codon	NOUN
2n49t150833	10	10	usage	usage	NOUN
2n49t150833	10	11	,	,	PUNCT
2n49t150833	10	12	but	but	CCONJ
2n49t150833	10	13	in	in	ADP
2n49t150833	10	14	this	this	DET
2n49t150833	10	15	case	case	NOUN
2n49t150833	10	16	codon	codon	NOUN
2n49t150833	10	17	usage	usage	NOUN
2n49t150833	10	18	preferences	preference	NOUN
2n49t150833	10	19	were	be	AUX
2n49t150833	10	20	associated	associate	VERB
2n49t150833	10	21	with	with	ADP
2n49t150833	10	22	codon	codon	PROPN
2n49t150833	10	23	gc	gc	PROPN
2n49t150833	10	24	content	content	NOUN
2n49t150833	10	25	rather	rather	ADV
2n49t150833	10	26	than	than	ADP
2n49t150833	10	27	commonness	commonness	ADJ
2n49t150833	10	28	or	or	CCONJ
2n49t150833	10	29	rareness	rareness	NOUN
2n49t150833	10	30	.	.	PUNCT
2n49t150833	11	1	functional	functional	ADJ
2n49t150833	11	2	sequence	sequence	NOUN
2n49t150833	11	3	features	feature	NOUN
2n49t150833	11	4	are	be	AUX
2n49t150833	11	5	often	often	ADV
2n49t150833	11	6	conserved	conserve	VERB
2n49t150833	11	7	in	in	ADP
2n49t150833	11	8	evolution	evolution	NOUN
2n49t150833	11	9	,	,	PUNCT
2n49t150833	11	10	so	so	ADV
2n49t150833	11	11	homologous	homologous	ADJ
2n49t150833	11	12	coding	code	VERB
2n49t150833	11	13	sequences	sequence	NOUN
2n49t150833	11	14	from	from	ADP
2n49t150833	11	15	multiple	multiple	ADJ
2n49t150833	11	16	eukaryotes	eukaryote	NOUN
2n49t150833	11	17	,	,	PUNCT
2n49t150833	11	18	archaea	archaea	ADJ
2n49t150833	11	19	,	,	PUNCT
2n49t150833	11	20	and	and	CCONJ
2n49t150833	11	21	bacteria	bacteria	NOUN
2n49t150833	11	22	were	be	AUX
2n49t150833	11	23	analyzed	analyze	VERB
2n49t150833	11	24	to	to	PART
2n49t150833	11	25	determine	determine	VERB
2n49t150833	11	26	if	if	SCONJ
2n49t150833	11	27	rare	rare	ADJ
2n49t150833	11	28	codon	codon	NOUN
2n49t150833	11	29	clusters	cluster	NOUN
2n49t150833	11	30	are	be	AUX
2n49t150833	11	31	conserved	conserve	VERB
2n49t150833	11	32	.	.	PUNCT
2n49t150833	12	1	this	this	DET
2n49t150833	12	2	study	study	NOUN
2n49t150833	12	3	revealed	reveal	VERB
2n49t150833	12	4	that	that	SCONJ
2n49t150833	12	5	such	such	ADJ
2n49t150833	12	6	conservation	conservation	NOUN
2n49t150833	12	7	is	be	AUX
2n49t150833	12	8	widespread	widespread	ADJ
2n49t150833	12	9	across	across	ADP
2n49t150833	12	10	the	the	DET
2n49t150833	12	11	tree	tree	NOUN
2n49t150833	12	12	of	of	ADP
2n49t150833	12	13	life	life	NOUN
2n49t150833	12	14	,	,	PUNCT
2n49t150833	12	15	and	and	CCONJ
2n49t150833	12	16	homolog	homolog	NOUN
2n49t150833	12	17	families	family	NOUN
2n49t150833	12	18	with	with	ADP
2n49t150833	12	19	conserved	conserved	ADJ
2n49t150833	12	20	rare	rare	ADJ
2n49t150833	12	21	codon	codon	NOUN
2n49t150833	12	22	clusters	cluster	NOUN
2n49t150833	12	23	are	be	AUX
2n49t150833	12	24	enriched	enrich	VERB
2n49t150833	12	25	in	in	ADP
2n49t150833	12	26	functions	function	NOUN
2n49t150833	12	27	associated	associate	VERB
2n49t150833	12	28	with	with	ADP
2n49t150833	12	29	growth	growth	NOUN
2n49t150833	12	30	and	and	CCONJ
2n49t150833	12	31	development	development	NOUN
2n49t150833	12	32	.	.	PUNCT
2n49t150833	13	1	finally	finally	ADV
2n49t150833	13	2	,	,	PUNCT
2n49t150833	13	3	the	the	DET
2n49t150833	13	4	functional	functional	ADJ
2n49t150833	13	5	significance	significance	NOUN
2n49t150833	13	6	of	of	ADP
2n49t150833	13	7	rare	rare	ADJ
2n49t150833	13	8	codons	codon	NOUN
2n49t150833	13	9	will	will	AUX
2n49t150833	13	10	have	have	VERB
2n49t150833	13	11	to	to	PART
2n49t150833	13	12	be	be	AUX
2n49t150833	13	13	verified	verify	VERB
2n49t150833	13	14	experimentally	experimentally	ADV
2n49t150833	13	15	.	.	PUNCT
2n49t150833	14	1	here	here	ADV
2n49t150833	14	2	we	we	PRON
2n49t150833	14	3	describe	describe	VERB
2n49t150833	14	4	the	the	DET
2n49t150833	14	5	design	design	NOUN
2n49t150833	14	6	of	of	ADP
2n49t150833	14	7	an	an	DET
2n49t150833	14	8	experimental	experimental	ADJ
2n49t150833	14	9	system	system	NOUN
2n49t150833	14	10	to	to	PART
2n49t150833	14	11	identify	identify	VERB
2n49t150833	14	12	the	the	DET
2n49t150833	14	13	effects	effect	NOUN
2n49t150833	14	14	of	of	ADP
2n49t150833	14	15	synonymous	synonymous	ADJ
2n49t150833	14	16	codon	codon	NOUN
2n49t150833	14	17	usage	usage	NOUN
2n49t150833	14	18	on	on	ADP
2n49t150833	14	19	the	the	DET
2n49t150833	14	20	fitness	fitness	NOUN
2n49t150833	14	21	of	of	ADP
2n49t150833	14	22	bacteria	bacteria	NOUN
2n49t150833	14	23	.	.	PUNCT