TABLE 3.

Sequence ambiguities in TAN2 and TAN3 population sequences

Virus	Amplicona	Sequence ambiguityb	Position in genome	Protein	Codon	Encoded amino acidc
SIVcpzTAN2	B-C	C-T	1068	p24 Gag	239	P
	E-F	T-C	2969	RT	257	I
	E-F	A-C	3017	RT	273	G
	E-F	C-T	3047	RT	283	I
	*F	G/Ad	3057	RT	287	E/K
	F-G	G-A	3869	RT	557	R
	G-H	A-G	4397	IN	173	R
	G-H	A-G	4407	IN	177	I-A
	G-H	T-C	4408	IN	177	I-A
	H-I	A-G	5149	Vif	154	I-V
	H-I	T-C	5154	Vif	155	V
	J-K	T-C	6104	Env	74	P
	J-K	G-C	6123	Env	81	D/A-H
	*J-K	A/C-A	6124	Env	81	D/A-H
	J-K	T-C	6125	Env	81	D/A-H
	J-K	G-A	6153	Env	91	E-K
	*K	G/T	6417	Env	179	V-F
	K-L	A-G	7165	Env	428	K-R
	L-M	G-A	7625	Env	581	K
SIVcpzTAN3	*B	G/A	894	p24 Gag	27	V
	*B	C/T	909	p24 Gag	32	F
	E-F	G-T	3137	RT	313	E-D
	*F	A/T	3221	RT	341	I
	*F	G/A	3658	RT	487	R/K
	G-H	T-C	4241	IN	121	F
	G-H	G-A	4277	IN	133	A
	G-H	A-G	4280	IN	134	Q
	G-H	G-A	4292	IN	138	E
	G-H	A-G	4334	IN	152	E
	G-*H	T-C/T	4350	IN	158	L
	G-H	A-C	4406	IN	176	V
	H-I	A-G	5147	Vif	153	K-R
	J-K	C-T	6584	Env	236	Y
	J-K	A-C	6652	Env	259	Y-S
	J-K	G-C	6668	Env	264	V
	J-K	C-G	6728	Env	284	L
	J-K	A-C	6736	Env	287	K-T
	J-K	G-A	6737	Env	287	K-T
	J-K	A-G	6800	Env	308	E
	J-K	A-G	6831	Env	319	N-D
	J-K	G-A	6841	Env	322	R-K
	J-K	T-C	6872	Env	332	T
	J-K	C-T	6883	Env	336	T-I
	J-K	T-A	6890	Env	338	N-K
	J-K	T-G	6894	Env	340	F-V
	J-K	A-C	6957	Env	361	N-H
	J-K	G-T	6989	Env	371	K-N
	J-K	A-G	7002	Env	376	N-D
	J-K	A-G	7011	Env	379	R-E
	J-K	G-A	7012	Env	379	R-E
	J-K	G-A	7015	Env	380	R-K
	J-K	C-A	7022	Env	382	D-E

^aThe locations of TAN2 and TAN3 amplicons are shown in Fig. 3.

^bHyphens indicate nucleotide differences between adjoining fragments in regions of sequence overlap; slashes indicate positions of base mixtures; the latter are also highlighted by asterisks on the corresponding amplicons.

^cAmino acids encoded by the TAN2.69 and TAN3.1 infectious molecular clones are boldfaced.

^dInitially unrecognized double peak in TAN2.1 sequence chromatogram.