Table S1. List of Gag Sequences

Taxon Accession number Seq Length
1 E.01_AE.CF.90.90CF11697_AF197340 AF197340 498
2 E.01_AE.CF.90.90CF402_U51188 U51188 498
3 E.01_AE.CF.90.90CF4071_AF197341 AF197341 498
4 E.01_AE.CN.97.97CNGX2F_AY008714 AY008714 498
5 E.01_AE.JP.93.93JP_NH1_AB052995 AB052995 495
6 E.01_AE.JP.93.NH25_AB070352 AB070352 498
7 E.01_AE.TH.90.CM235_AF259954 AF259954 498
8 E.01_AE.TH.90.CM240_U54771 U54771 503
9 E.01_AE.TH.93.93TH057_AF197338 AF197338 498
10 E.01_AE.TH.93.93TH065_AF197339 AF197339 496
11 E.01_AE.TH.93.93TH253_U51189 U51189 490
12 E.01_AE.TH.93.93TH902_AF170549 AF170549 498
13 E.01_AE.TH.95.95TNIH022_AB032740 AB032740 498
14 E.01_AE.TH.95.95TNIH047_AB032741 AB032741 498
15 E.01_AE.TH.97.97TH6_107_AY125894 AY125894 497
16 B.01B.CN.01.DH006_AB078706 AB078706 506
17 B.01B.MM.99.mCSW104_AB097867 AB097867 499
18 B.01B.TH.x.1269_AF490973 AF490973 501
19 B.01B.TH.x.CM237_AY167123 AY167123 500
20 B.01B.TH.x.NP1623_AF362994 AF362994 500
21 B.01B.TH.x.TH1326_AY082968 AY082968 500
22 B.01B.TH.x.TH283_AF468970 AF468970 500
23 B.01B.TH.x.TH9_95_AF490974 AF490974 502
24 C.01BC.MM.00.mCSW503_AB097866 AB097866 495
25 C.01BC.MM.99.mIDU107_AB097868 AB097868 491
26 G.01GHJKU.CD.97.97CDKTB49_AJ404325 AJ404325 499
27 02_AG.CM.99.pBD6_15_AY271690 AY271690 498
28 02_AG.FR.91.DJ263_AF063223 AF063223 492
29 02_AG.FR.91.DJ264_AF063224 AF063224 492
30 02_AG.GH.97.97GHAG1_AB049811 AB049811 492
31 02_AG.NG.x.IBNG_L39106 L39106 492
32 02_AG.SE.94.SE7812_AF107770 AF107770 492
33 02_AG.SN.98.MP1211_AJ251056 AJ251056 495
34 02_AG_0206.NE.00.NE36_AJ508597 AJ508597 491
35 02_AG_0206.NE.00.NE95_AJ508596 AJ508596 496
36 02_AG_0206.NE.97.NE03_AJ508595 AJ508595 492
37 02_AG_02A.GH.97.G829_AF184155 AF184155 491
38 02_AG_02A1.GH.97.AG2_AB052867 AB052867 503
39 02C.BE.93.VI1035_AJ276595 AJ276595 500
40 02O.CM.97.97CA_MP645M_O_AJ239083 AJ239083 495
41 03_AB.BY.00.98BY10443_AF414006 AF414006 498
42 03_AB.RU.97.KAL153_2_AF193276 AF193276 498
43 03_AB.RU.98.RU98001_AF193277 AF193277 498
44 04_cpx.CY.94.CY032_AF049337 AF049337 500
45 04_cpx.GR.91.97PVCH_AF119820 AF119820 500
46 04_cpx.GR.97.97PVMY_AF119819 AF119819 498
47 05_DF.BE.93.VI961_AF076998 AF076998 501
48 05_DF.BE.x.VI1310_AF193253 AF193253 502
49 05_DF.ES.99.X492_AY227107 AY227107 501
50 06_cpx.AU.96.BFP90_AF064699 AF064699 497
51 06_cpx.EE.01.EE0359_AY535659 AY535659 498
52 06_cpx.ML.95.95ML127_AJ288982 AJ288982 497
53 06_cpx.ML.95.95ML84_AJ245481 AJ245481 499
54 06_cpx.SN.97.97SE1078_AJ288981 AJ288981 502
55 06A1.BJ.x.B76_AJ293865 AJ293865 492
56 06A1.EE.01.EE0369_AY535660 AY535660 492
57 07_BC.CN.00.HH043_AB078681 AB078681 496
58 07_BC.CN.00.WS001_AB078694 AB078694 495
59 07_BC.CN.98.98CN009_AF286230 AF286230 495
60 08_BC.CN.00.HH025_AB078678 AB078678 491
61 08_BC.CN.00.HH033_AB078679 AB078679 491
62 08_BC.CN.00.HH040_AB078680 AB078680 491
63 08_BC.CN.00.HH049_AB078683 AB078683 491
64 08_BC.CN.00.HH057_AB078684 AB078684 492
65 08_BC.CN.00.HH063_AB078685 AB078685 485
66 08_BC.CN.00.HH068_AB078687 AB078687 491
67 08_BC.CN.00.HH072_AB078689 AB078689 491
68 08_BC.CN.00.HH083_AB078690 AB078690 490
69 08_BC.CN.00.HH090_AB078692 AB078692 491
70 08_BC.CN.00.HH093_AB078693 AB078693 492
71 08_BC.CN.00.WS002_AB078695 AB078695 491
72 08_BC.CN.00.WS009_AB078696 AB078696 491
73 08_BC.CN.00.WS030_AB078697 AB078697 491
74 08_BC.CN.00.WS031_AB078698 AB078698 491
75 08_BC.CN.00.WS035_AB078700 AB078700 491
76 08_BC.CN.00.WS039_AB078701 AB078701 491
77 08_BC.CN.00.WS041_AB078702 AB078702 491
78 08_BC.CN.01.DH003_AB078705 AB078705 489
79 08_BC.CN.01.DH015_AB078712 AB078712 491
80 08_BC.CN.01.DH020_AB078716 AB078716 492
81 08_BC.CN.97.97CNGX_7F_AY008716 AY008716 491
82 08_BC.CN.98.98CN006_AF286229 AF286229 495
83 09_cpx.SN.95.95SN1795_AY093603 AY093603 497
84 09_cpx.SN.95.95SN7808_AY093604 AY093604 493
85 10_CD.TZ.96.96TZ_BF061_AF289548 AF289548 500
86 10_CD.TZ.96.96TZ_BF071_AF289549 AF289549 500
87 10_CD.TZ.96.96TZ_BF110_AF289550 AF289550 497
88 11_cpx.CM.95.1816_AF492624 AF492624 496
89 11_cpx.CM.96.4496_AF492623 AF492623 497
90 11_cpx.CM.97.MP818_AJ291718 AJ291718 496
91 11_cpx.CM.99.99CMLB40_AF355337 AF355337 494
92 11_cpx.FR.99.MP1298_AJ291719 AJ291719 497
93 11_cpx.FR.99.MP1307_AJ291720 AJ291720 513
94 11_cpx.GR.x.GR17_AF179368 AF179368 409
95 12_BF.AR.97.A32879_AF408629 AF408629 496
96 12_BF.AR.97.A32989_AF408630 AF408630 492
97 12_BF.AR.99.ARMA159_AF385936 AF385936 492
98 12_BF.BR.99.BREPM107_AY771588 AY771588 495
99 12_BF.BR.99.BREPM108_AY771589 AY771589 497
100 12_BF.ES.02.X1241_AY536238 AY536238 498
101 12_BF.UY.99.URTR23_AF385934 AF385934 492
102 12_BF.UY.99.URTR35_AF385935 AF385935 498
103 13_cpx.CM.96.1849_AF460972 AF460972 506
104 13_cpx.CM.96.4164_AF460974 AF460974 505
105 14_BG.ES.00.X475_AF423758 AF423758 494
106 14_BG.ES.00.X623_AF450097 AF450097 494
107 14_BG.ES.99.X397_AF423756 AF423756 494
108 15_01B.TH.02.02TH_OUR1331_AF529572 AF529572 502
109 15_01B.TH.02.02TH_OUR1332_AF529573 AF529573 496
110 15_01B.TH.99.99TH_MU2079_AF516184 AF516184 497
111 15_01B.TH.99.99TH_R2399_AF530576 AF530576 496
112 16_A2D.KR.97.97KR004_AF286239 AF286239 499
113 A.KE.96.M133gag_AY772954 AY772954 499
114 A.KE.97.M104gag_AY772953 AY772953 501
115 A.KE.97.M141gag_AY772955 AY772955 512
116 A.KE.97.M21_ps1_AY772968 AY772968 493
117 A.KE.98.M178gag_AY772958 AY772958 498
118 A.KE.98.M264_gag_AY772970 AY772970 493
119 A.KE.98.M369gag_AY772971 AY772971 498
120 A.KE.98.M428gag_AY772986 AY772986 498
121 A.KE.99.M439gag_AY772985 AY772985 499
122 A1.KE.00.CQ891776_CQ891776 CQ891776 498
123 A1.KE.86.ML013_10_AY322184 AY322184 498
124 A1.KE.86.ML170_1986_AF539405 AF539405 498
125 A1.KE.94.Q23_17_AF004885 AF004885 498
126 A1.KE.97.ML605_3_AY322190 AY322190 496
127 A1.KE.97.ML752_AY322193 AY322193 499
128 A1.RU.03.03RU20_06_13_AY500393 AY500393 498
129 A1.SE.94.SE7253_AF069670 AF069670 497
130 A1.SE.94.SE7535_AF069671 AF069671 495
131 A1.SE.95.SE8538_AF069669 AF069669 496
132 A1.SE.95.SE8891_AF069673 AF069673 497
133 A1.SE.95.UGSE8131_AF107771 AF107771 492
134 A1.TZ.97.97TZ03_AF361873 AF361873 499
135 A1.UA.00.98UA0116_AF413987 AF413987 497
136 A1.UG.85.U455_M62320 M62320 493
137 A1.UG.92.92UG037_U51190 U51190 499
138 A1.UG.92.UG029_AB098332 AB098332 498
139 A1.UG.x.UG031_AB098330 AB098330 498
140 A1C.ET.91.E3099G_U92049 U92049 495
141 A1C.IN.95.95IN21301_AF067156 AF067156 491
142 A1C.KE.95.ML170_1995_AF539406 AF539406 498
143 A1C.RW.92.92RW009_06_U88823 U88823 494
144 A1C.SE.96.SE9488_AF071474 AF071474 495
145 A1C.TZ.97.97TZ09_AF361879 AF361879 493
146 A1CD.SE.95.SE8603_AF075702 AF075702 496
147 A1CDGKU.ZA.99.CM4_AF411964 AF411964 501
148 A1D.SE.93.SE6954_AF075701 AF075701 498
149 A1D.SE.94.SE7108_AF071473 AF071473 496
150 A1D.TZ.96.TZBFL0011_AF442569 AF442569 500
151 A1D.TZ.96.TZBFL0088_AF442570 AF442570 499
152 A1D.TZ.97.TZBFL0086_AF442566 AF442566 499
153 A1D.UG.90.UG266_AY352657 AY352657 497
154 A1D.UG.92.UG035_AY352656 AY352656 498
155 A1DHK.NO.97.97NOGIL3_AJ237565 AJ237565 498
156 A1DK.CD.85.MAL_X04415 X04415 505
157 A1G.BE.94.VI1197_AJ276596 AJ276596 493
158 A1G.NG.92.92NG003_U88825 U88825 497
159 A1GHU.GA.x.VI354_AF076474 AF076474 494
160 A1GJ.BW.98.BW2117_AF192135 AF192135 494
161 A1GU.CD.76.Z321_U76035 U76035 498
162 A1U.SE.93.SE6594_AF069672 AF069672 491
163 A2.CD.97.97CDKTB48_AF286238 AF286238 497
164 A2.CY.94.94CY017_41_AF286237 AF286237 496
165 A2.CY.94.CY034G_AF286247 AF286247 504
166 A2.CY.94.CY042GAG_AF286250 AF286250 382
167 A2.CY.94.CY049GAG_AF286253 AF286253 491
168 A2.KE.98.M389_clone17_AY772973 AY772973 495
169 A2C.ZA.98.DU178_AF411965 AF411965 495
170 A2C.ZM.89.ZAM174_21_U86771 U86771 490
171 A2C.ZM.90.ZAM184_U86780 U86780 494
172 A2C.ZM.x.ZAM716_17_U86779 U86779 490
173 A2D.KE.98.M389_clone10_AY772979 AY772979 497
174 A2D.KE.98.M389_clone11_AY772984 AY772984 378
175 A2G.CD.97.97CDKP58_AF316544 AF316544 503
176 AC.KE.97.ML672_AY322191 AY322191 491
177 AD.KE.97.M18gag_AY772959 AY772959 501
178 AD.KE.97.M21_clone8_AY772967 AY772967 506
179 AD.KE.98.M381gag_AY772972 AY772972 498
180 B.98PI1365px10 n/a 498
181 B.AR.00.ARMS008 AY037269 498
182 B.AR.02.02AR114146.DQ383746 DQ383746 492
183 B.AR.03.03AR137681.DQ383748 DQ383748 492
184 B.AR.04.04AR151516.DQ383752 DQ383752 497
185 B.AR.05.05AR163052.DQ383755 DQ383755 500
186 B.AR.98.ARCH054 AY037268 498
187 B.AR.99.ARMA132 AY037282 498
188 B.AU.04.Phcsffull04 AY818644 502
189 B.AU.86.MBC200_AF042100 AF042100 500
190 B.AU.87.MBC925_AF042101 AF042101 501
191 B.AU.93.MBC18_AF042102 AF042102 517
192 B.AU.95.MBCC54_AF042103 AF042103 500
193 B.AU.96.MBCC98_AF042104 AF042104 500
194 B.AU.96.MBCD36_AF042105 AF042105 500
195 B.AU.98.SC49_AF128998 AF128998 508
196 B.AU.x.1181_AF538302 AF538302 502
197 B.AU.x.1182_AF538303 AF538303 500
198 B.AU.x.2870718 AY857022 500
199 B.AU.x.3350218 AY857029 501
200 B.AU.x.3480277 AY857031 502
201 B.AU.x.4756961 AY857053 201
202 B.AU.x.9125091 AY857165 501
203 B.AU.x.C24_AF538304 AF538304 505
204 B.AU.x.C42_AF538305 AF538305 500
205 B.AU.x.C76_AF538306 AF538306 502
206 B.AU.x.C92_AF538307 AF538307 500
207 B.AU.x.VH_AF146728 AF146728 506
208 B.BO.99.BOL0122 AY037270 499
209 B.BR.89.BZ167_AY173956 AY173956 502
210 B.BR.99.BREPM11931.DQ085869 DQ085869 493
211 B.CA.92.CANC2FULL_AY779559 AY779559 500
212 B.CA.96.CANA1FULL_AY779564 AY779564 500
213 B.CA.96.WC10C_10_AY314061 AY314061 504
214 B.CA.97.CANB3FULL_AY779553 AY779553 503
215 B.CN.01.DH001_AB078703 AB078703 501
216 B.CN.01.DH002_AB078704 AB078704 500
217 B.CN.01.DH011_AB078709 AB078709 501
218 B.CN.01.DH013_AB078711 AB078711 501
219 B.CN.02.02HNsc11.DQ007903 DQ007903 493
220 B.CN.02.02HNsmx2_AY275557 AY275557 500
221 B.CN.02.02HNsq4_AY275555 AY275555 500
222 B.CN.x.CNHN24_AY180905 AY180905 500
223 B.CN.x.RL42_U71182 U71182 505
224 B.CO.01.PCM001 AY561236 497
225 B.CO.01.PCM013 AY561237 501
226 B.CO.01.PCM034 AY561238 498
227 B.CO.01.PCM074 AY561240 501
228 B.DE.86.D31_U43096 U43096 500
229 B.DE.86.HAN_U43141 U43141 499
230 B.DE.x.20_AJ437030 AJ437030 501
231 B.DE.x.21_AJ437035 AJ437035 501
232 B.DE.x.22_AJ437036 AJ437036 500
233 B.DE.x.23_AJ437041 AJ437041 499
234 B.DE.x.24_AJ437042 AJ437042 417
235 B.DE.x.26_AJ437047 AJ437047 500
236 B.DE.x.27_AJ437048 AJ437048 503
237 B.DE.x.28_AJ437053 AJ437053 509
238 B.DE.x.30_AJ437056 AJ437056 515
239 B.ES.89.89SP061.AJ006287 AJ006287 496
240 B.FR.83.HXB2_LAI_IIIB_BRU_K03455 K03455 500
241 B.FR.85.LW123.U12055 U12055 493
242 B.FR.92.92FR AY713411 493
243 B.GA.88.OYI_M26727 M26727 499
244 B.GB.83.CAM1_D10112 D10112 500
245 B.GB.86.GB8_AJ271445 AJ271445 507
246 B.GB.x.MANC_U23487 U23487 500
247 B.GE.03.03GEMZ004.DQ207940 DQ207940 488
248 B.JP.04.04JPDR6075B.AB221126 AB221126 493
249 B.JP.86.JH31_M21137 M21137 500
250 B.JP.x.0_5_AB083565 AB083565 505
251 B.JP.x.PATIENT_IMS1_AB074049 AB074049 503
252 B.JP.x.PATIENT_IMS2_AB074053 AB074053 499
253 B.JP.x.PATIENT_IMS3_AB074054 AB074054 500
254 B.JP.x.PATIENT_IMS4_AB074058 AB074058 497
255 B.JP.x.PATIENT_IMS5_AB074059 AB074059 210
256 B.JP.x.PATIENT_IMS7_AB074064 AB074064 500
257 B.JP.x.PATIENT_IMS8_AB074069 AB074069 499
258 B.KR.04.04KJin8 DQ295195 493
259 B.KR.04.04KMH5.DQ295193 DQ295193 493
260 B.KR.04.04LHS6 AY839827 498
261 B.KR.04.04LSK7.DQ295192 DQ295192 496
262 B.KR.97.WK_AF224507 AF224507 500
263 B.MM.99.mSTD101_AB097870 AB097870 503
264 B.NL.00.671_00T103_AY423386 AY423386 510
265 B.NL.86.3202A21_U34604 U34604 500
266 'B.NL.86.H434-8-A3.AY970946' AY970946 493
267 B.RU.04.04RU128005_AY682547 AY682547 500
268 B.RU.04.04RU129005_AY751406 AY751406 506
269 B.RU.04.04RU139089_AY751407 AY751407 501
270 B.RU.04.04RU139095_AY819715 AY819715 499
271 B.TH.90.BK132_AY173951 AY173951 500
272 B.TH.96.96TH AY713408 491
273 B.TW.94.TWCYS_AF086817 AF086817 500
274 B.US.01.Ac_06_AY268493 AY268493 500
275 B.US.82.5048 AY835759 493
276 B.US.83.5018 AY835777 493
277 B.US.83.5082 AY835770 493
278 B.US.83.5084 AY835754 493
279 B.US.83.5096 AY835748 493
280 B.US.83.RF_M17451 M17451 501
281 B.US.83.SF2_K02007 K02007 502
282 B.US.84.5019 AY835779 493
283 B.US.84.5160 AY835762 495
284 B.US.84.MNCG_M17449 M17449 506
285 B.US.84.NY5CG_M38431 M38431 500
286 B.US.84.SF33_AY352275 AY352275 503
287 B.US.85.5077 AY835769 493
288 B.US.85.5157 AY835755 493
289 'B.US.85.Ba-L.AB221005' AB221005 496
290 B.US.85.WCIPR_U69584 U69584 500
291 B.US.86.5113 AY835757 493
292 B.US.86.5127 AY835774 493
293 B.US.86.AD87_AF004394 AF004394 500
294 B.US.86.JRCSF M38429 503
295 B.US.86.JRFL_U63632 U63632 498
296 B.US.86.YU_2_M93258 M93258 500
297 B.US.87.BC_L02317 L02317 500
298 B.US.88.WR27_AF286365 AF286365 500
299 B.US.89.5073 AY835766 493
300 B.US.89.P896_U39362 U39362 500
301 B.US.90.90US AY713412 491
302 B.US.90.US1_AY173952 AY173952 499
303 B.US.90.US2_AY173953 AY173953 500
304 B.US.90.US3_AY173954 AY173954 500
305 B.US.90.US4_AY173955 AY173955 499
306 B.US.90.WEAU160_U21135 U21135 500
307 B.US.91.DH12_3_AF069140 AF069140 495
308 B.US.93.WCD32P0793.DQ487188 DQ487188 498
309 B.US.94.94US AY713410 491
310 B.US.96.1027_03 AY331291 497
311 B.US.96.1057_01_AY331292 AY331292 505
312 B.US.96.1299_d22_AY308761 AY308761 500
313 B.US.96.5155 AY835753 498
314 B.US.97.1001_07_AY331282 AY331282 501
315 B.US.97.1006_08_AY331284 AY331284 498
316 B.US.97.1012_08_AY331285 AY331285 494
317 B.US.97.1013_03_AY331287 AY331287 500
318 B.US.97.1018_06_AY331289 AY331289 500
319 B.US.97.Ac_06_AY247251 AY247251 501
320 B.US.97.ARES2_AB078005 AB078005 499
321 B.US.98.1058_08 AY331294 494
322 B.US.98.98USHVTN1925c1_AY560107 AY560107 502
323 B.US.98.98USHVTN3605c9_AY560108 AY560108 499
324 B.US.98.98USHVTN8229c6_AY560109 AY560109 501
325 B.US.98.98USHVTN941c1_AY560110 AY560110 504
326 B.US.PIC1660r030512 n/a 506
327 B.US.PIC1663r030619 n/a 497
328 B.US.PIC1667r030827 n/a 501
329 B.US.PIC1671r031103 n/a 497
330 B.US.PIC1676r031229 n/a 500
331 B.US.PIC1683r040302 n/a 497
332 B.US.PIC1689c040413 n/a 499
333 B.US.PIC1690c040428 n/a 500
334 B.US.PIC1691c040520 n/a 504
335 B.US.PIC1693c040526 n/a 499
336 B.US.PIC1695r040607 n/a 504
337 B.US.PIC1696r040607 n/a 496
338 B.US.PIC1698c040609 n/a 496
339 B.US.PIC1701r040707 n/a 497
340 B.US.PIC1706c040913 n/a 497
341 B.US.PIC1707r041102 n/a 500
342 B.US.x.11BP_1031_AY786858 AY786858 500
343 B.US.x.13BP_1115_AY786939 AY786939 499
344 B.US.x.1BP_1024_AY786817 AY786817 500
345 B.US.x.MDR1_AY206647 AY206647 499
346 B.US.x.MDR2_AY206648 AY206648 520
347 B.US.x.MDR3_AY206649 AY206649 505
348 B.US.x.NC7_AF049495 AF049495 502
349 B.US.x.NL43E9_AF070521 AF070521 500
350 B.US.x.P2_AY206654 AY206654 500
351 B.US.x.R1_AY206650 AY206650 502
352 B.US.x.R3_PDC1_AY206652 AY206652 495
353 B.US.x.UCD_1_AY679786 AY679786 499
354 B.US.x.WT1_PDC1_AY206656 AY206656 495
355 B.US.x.WT2_AY206657 AY206657 501
356 B.US.x.WT3_PDC1_AY206658 AY206658 502
357 B.US.x.WT4_AY206659 AY206659 508
358 B.US.x.WT5_AY206660 AY206660 503
359 B.US.x.WT6_PDC1_AY206661 AY206661 505
360 B.US.x.WT7_PDC1_AY206662 AY206662 500
361 B.US.x.WT8_AY206663 AY206663 500
362 B.US.x.WT9_AY206664 AY206664 500
363 B.US00PIC1362 n/a 504
364 B.US00PIC1484 n/a 497
365 B.US03PIC1647 n/a 503
366 B.US03PIC1664 n/a 497
367 B.US93PIC1034 n/a 501
368 B.US94PIC1060 n/a 504
369 B.US97PIC1212 n/a 502
370 B.US97PIC1238 n/a 498
371 B.US98PIC1294 n/a 502
372 B.US98PIC131119.3 n/a 505
373 B.US99PIC1433 n/a 498
374 B.US99PIC1444 n/a 501
375 B.UY.01.01UYTRA1092 AY781126 498
376 B.YE.x.02YE519 AY795908 502
377 B.ZA.03.03ZAPS045MB2.DQ396398 DQ396398 493
378 BC.CN.00.HH069_AB078688 AB078688 491
379 BC.CN.00.HH069_AP005206 AP005206 491
380 BC.CN.00.HH086_AB078691 AB078691 491
381 BC.CN.01.DH008_AB078707 AB078707 497
382 BC.CN.01.DH009_AB078708 AB078708 500
383 BC.CN.01.DH012_AB078710 AB078710 495
384 BC.CN.01.DH016_AB078713 AB078713 499
385 BC.CN.01.DH017_AB078714 AB078714 492
386 BC.CN.01.DH019_AB078715 AB078715 504
387 BC.CN.x.HH003_AB090997 AB090997 491
388 BC.CN.x.HH004_AB090998 AB090998 491
389 BC.CN.x.HH029_AB090999 AB090999 491
390 BC.MM.99.mIDU103_AB097873 AB097873 503
391 BC.MM.99.mIDU106_AB097869 AB097869 499
392 BF.AR.97.A050_AF408631 AF408631 492
393 BF.AR.97.A32878_AF408632 AF408632 498
394 BF.AR.99.A025_AF408626 AF408626 499
395 BF.AR.99.A027_AF332867 AF332867 492
396 BF.AR.99.A047_AF408627 AF408627 492
397 BF.AR.99.A063_AF408628 AF408628 492
398 BF.BR.94.94BR_RJ_41_AY455781 AY455781 491
399 BF.BR.99.99UFRJ_9_AY455783 AY455783 264
400 BF.BR.99.BREPM269_AY771591 AY771591 500
401 BF.CL.01.CH3_AY536233 AY536233 500
402 BF.CL.01.CH6_AY536234 AY536234 496
403 BF.ES.02.R140_AY536237 AY536237 496
404 BF.VE.99.V62_AY536236 AY536236 498
405 BF1.BR.93.93BR029_4_AF005495 AF005495 500
406 BG.ES.99.X254_AF423755 AF423755 496
407 C.BR.04.04BR013_AY727522 AY727522 501
408 C.BR.04.04BR021_AY727523 AY727523 493
409 C.BR.04.04BR038_AY727524 AY727524 500
410 C.BR.04.04BR073_AY727525 AY727525 492
411 C.BR.04.04BR137_AY727526 AY727526 504
412 C.BR.04.04BR142_AY727527 AY727527 505
413 C.BR.92.BR025_d_U52953 U52953 496
414 C.BR.98.98BR004_AF286228 AF286228 493
415 C.BW.00.00BW07621_AF443088 AF443088 492
416 C.BW.00.00BW076820_AF443089 AF443089 492
417 C.BW.00.00BW087421_AF443090 AF443090 502
418 C.BW.00.00BW147127_AF443091 AF443091 489
419 C.BW.00.00BW16162_AF443092 AF443092 501
420 C.BW.00.00BW1686_AF443093 AF443093 491
421 C.BW.00.00BW17593_AF443094 AF443094 492
422 C.BW.00.00BW17732_AF443095 AF443095 492
423 C.BW.00.00BW17835_AF443096 AF443096 504
424 C.BW.00.00BW17956_AF443097 AF443097 492
425 C.BW.00.00BW18113_AF443098 AF443098 500
426 C.BW.00.00BW18595_AF443099 AF443099 492
427 C.BW.00.00BW18802_AF443100 AF443100 492
428 C.BW.00.00BW192113_AF443101 AF443101 492
429 C.BW.00.00BW20361_AF443102 AF443102 496
430 C.BW.00.00BW20636_AF443103 AF443103 490
431 C.BW.00.00BW20872_AF443104 AF443104 501
432 C.BW.00.00BW2127214_AF443105 AF443105 499
433 C.BW.00.00BW21283_AF443106 AF443106 503
434 C.BW.00.00BW22767_AF443107 AF443107 502
435 C.BW.00.00BW38193_AF443108 AF443108 495
436 C.BW.00.00BW38428_AF443109 AF443109 508
437 C.BW.00.00BW38713_AF443110 AF443110 493
438 C.BW.00.00BW3876_9_AF443111 AF443111 492
439 C.BW.00.00BW3886_8_AF443112 AF443112 499
440 C.BW.00.00BW3891_6_AF443113 AF443113 496
441 C.BW.00.00BW3970_2_AF443114 AF443114 491
442 C.BW.00.00BW5031_1_AF443115 AF443115 498
443 C.BW.96.96BW01B22_AF110961 AF110961 492
444 C.BW.96.96BW0402_AF110962 AF110962 492
445 C.BW.96.96BW0502_AF110967 AF110967 502
446 C.BW.96.96BW06K18_AF290030 AF290030 493
447 C.BW.96.96BW1104_AF110969 AF110969 490
448 C.BW.96.96BW1210_AF110972 AF110972 494
449 C.BW.96.96BW15B03_AF110973 AF110973 492
450 C.BW.96.96BW1626_AF110978 AF110978 492
451 C.BW.96.96BW17_AF110979 AF110979 490
452 C.BW.96.96BWM032_AF443075 AF443075 493
453 C.BW.96.96BWMO1_5_AF443074 AF443074 500
454 C.BW.98.98BWMC122_AF443076 AF443076 490
455 C.BW.98.98BWMC134_AF443077 AF443077 490
456 C.BW.98.98BWMC14A3_AF443078 AF443078 491
457 C.BW.98.98BWMO1410_AF443079 AF443079 501
458 C.BW.98.98BWMO18D5_AF443080 AF443080 501
459 C.BW.98.98BWMO36A5_AF443081 AF443081 500
460 C.BW.98.98BWMO37D5_AF443082 AF443082 488
461 C.BW.99.99BW393212_AF443083 AF443083 504
462 C.BW.99.99BW46424_AF443084 AF443084 492
463 C.BW.99.99BW4745_AF443085 AF443085 497
464 C.BW.99.99BW47547_AF443086 AF443086 492
465 C.BW.99.99BWMC168_AF443087 AF443087 499
466 C.ET.86.ETH2220_U46016 U46016 504
467 C.IL.98.98IS002_AF286233 AF286233 496
468 C.IN.00.NARI_GAG_1_AY484419 AY484419 486
469 C.IN.00.NARI_GAG_2_AY484420 AY484420 492
470 C.IN.00.NARI_GAG_3_AY484421 AY484421 491
471 C.IN.00.NARI_GAG_6_AY484424 AY484424 492
472 C.IN.01.NARI_GAG_4_AY484422 AY484422 491
473 C.IN.01.NARI_GAG_5_AY484423 AY484423 487
474 C.IN.93.93IN101_AB023804 AB023804 491
475 C.IN.93.93IN904_AF067157 AF067157 491
476 C.IN.93.93IN905_AF067158 AF067158 491
477 C.IN.93.93IN9999_AF067154 AF067154 500
478 C.IN.94.94IN11246_AF067159 AF067159 488
479 C.IN.94.94IN476_AF286223 AF286223 491
480 C.IN.95.95IN21068_AF067155 AF067155 491
481 C.IN.98.98IN012_AF286231 AF286231 492
482 C.IN.98.98IN022_AF286232 AF286232 494
483 C.IN.99.01IN565_14_AY049711 AY049711 500
484 C.IN.99.49587_AF533140 AF533140 491
485 C.IN.x.33840_AF533123 AF533123 491
486 C.IN.x.50322_AF533128 AF533128 491
487 C.IN.x.50437_AF533129 AF533129 491
488 C.IN.x.50542_AF533133 AF533133 496
489 C.IN.x.50561_AF533132 AF533132 491
490 C.IN.x.50581_AF533125 AF533125 491
491 C.IN.x.50813_AF533126 AF533126 488
492 C.IN.x.50823_AF533135 AF533135 492
493 C.IN.x.50950_AF533130 AF533130 491
494 C.IN.x.60080_AF533118 AF533118 491
495 C.IN.x.60133_AF533119 AF533119 491
496 C.IN.x.60161_AF533120 AF533120 491
497 C.IN.x.60615_AF533127 AF533127 491
498 C.IN.x.70177_AF533131 AF533131 491
499 C.IN.x.80496_AF533134 AF533134 491
500 C.IN.x.C_GAG_221_AF209990 AF209990 491
501 C.IN.x.IMP1_AF533137 AF533137 491
502 C.IN.x.IMP6_AF533141 AF533141 491
503 C.IN.x.MYA1_AF533139 AF533139 491
504 C.MM.99.mIDU101_3_AB097871 AB097871 491
505 C.TZ.01.A246_CQ891779 CQ891779 501
506 C.TZ.98.98TZ013_AF286234 AF286234 499
507 C.TZ.98.98TZ017_AF286235 AF286235 502
508 C.ZA.00.1119MB_AY463229 AY463229 491
509 C.ZA.00.1134MB_AY463217 AY463217 493
510 C.ZA.00.1157M3M_AY585266 AY585266 492
511 C.ZA.00.1165MB_AY463230 AY463230 495
512 C.ZA.00.1168MB_AY463231 AY463231 497
513 C.ZA.00.1170MB_AY463225 AY463225 491
514 C.ZA.00.1171MB_AY463232 AY463232 492
515 C.ZA.00.1176MB_AY463218 AY463218 492
516 C.ZA.00.1178MB_AY463233 AY463233 491
517 C.ZA.00.1192M3M_AY463219 AY463219 491
518 C.ZA.00.1195MB_AY463220 AY463220 494
519 C.ZA.00.1197MB_AY463234 AY463234 491
520 C.ZA.00.1210MB_AY463221 AY463221 492
521 C.ZA.00.1214MB_AY463236 AY463236 493
522 C.ZA.00.1217MB_AY463226 AY463226 491
523 C.ZA.00.1225MB_AY463227 AY463227 492
524 C.ZA.00.1228MB_AY463222 AY463222 483
525 C.ZA.00.J38MA_AY463228 AY463228 506
526 C.ZA.01.01ZATM45_AY228557 AY228557 503
527 C.ZA.01.J54Ma_AY463223 AY463223 492
528 C.ZA.03.SK023B2_AY772690 AY772690 492
529 C.ZA.03.SK029B2_AY772691 AY772691 490
530 C.ZA.03.SK033B2_AY772692 AY772692 492
531 C.ZA.03.SK040B1_AY703908 AY703908 494
532 C.ZA.03.SK041B1_AY772693 AY772693 497
533 C.ZA.03.SK043B1_AY772700 AY772700 505
534 C.ZA.03.SK065B1_AY772694 AY772694 503
535 C.ZA.03.SK112B1_AY772695 AY772695 498
536 C.ZA.03.SK116B1_AY772696 AY772696 492
537 C.ZA.04.SK133B1_AY772698 AY772698 493
538 C.ZA.04.SK134B1_AY703909 AY703909 498
539 C.ZA.04.SK143B1_AY703910 AY703910 493
540 C.ZA.04.SK144B1_AY703911 AY703911 492
541 C.ZA.04.SK164B1_AY772699 AY772699 492
542 C.ZA.97.97ZA003_AY118165 AY118165 489
543 C.ZA.97.97ZA009_AY118166 AY118166 503
544 C.ZA.97.97ZA012_AF286227 AF286227 495
545 C.ZA.98.98ZA445_AY158533 AY158533 493
546 C.ZA.98.98ZA502_AY158534 AY158534 491
547 C.ZA.98.98ZA528_AY158535 AY158535 498
548 C.ZA.98.CTSC2_AY043176 AY043176 492
549 C.ZA.98.TV001_AY162223 AY162223 497
550 C.ZA.98.TV002_AY162224 AY162224 496
551 C.ZA.98.TV003_AF391254 AF391254 491
552 C.ZA.98.TV004A_AF391255 AF391255 492
553 C.ZA.98.TV006B_AF391258 AF391258 409
554 C.ZA.98.TV007_AF391259 AF391259 499
555 C.ZA.98.TV008A_AF391260 AF391260 491
556 C.ZA.98.TV010_AF391262 AF391262 493
557 C.ZA.98.TV012_AY162225 AY162225 487
558 C.ZA.98.TV013B_AF391266 AF391266 508
559 C.ZA.98.TV014_AF391267 AF391267 491
560 C.ZA.98.TV018_AF391268 AF391268 492
561 C.ZA.98.TV019A_AF391269 AF391269 492
562 C.ZA.99.99ZACM9_AF411967 AF411967 495
563 C.ZA.99.99ZATM10_AY228556 AY228556 495
564 C.ZA.99.DU151_AY043173 AY043173 492
565 C.ZA.99.DU179_AY043174 AY043174 491
566 C.ZA.99.DU422_g2_AF544010 AF544010 492
567 C.ZA.99.ZASW7_AF411966 AF411966 499
568 C.ZM.96.96ZM651_AF286224 AF286224 494
569 C.ZM.96.96ZM751_AF286225 AF286225 498
570 C.ZM.x.HIV1084i_AY805330 AY805330 493
571 CD.BW.00.00BWMO351_AY074891 AY074891 491
572 CD.KE.97.ML249_AY322187 AY322187 500
573 CD.KE.97.pWCML249_AY445524 AY445524 500
574 D.CD.83.ELI_K03454 K03454 500
575 D.CD.83.NDK_M27323 M27323 497
576 D.CD.84.84ZR085_U88822 U88822 502
577 D.CD.85.Z2Z6_M22639 M22639 501
578 D.KE.97.M115gag_AY772952 AY772952 497
579 D.KE.97.M150gag_AY772956 AY772956 500
580 D.KE.97.M160gag_AY772957 AY772957 500
581 D.KE.97.ML415_2_AY322189 AY322189 500
582 D.KE.98.M389_16_AY772980 AY772980 500
583 D.TD.99.MN011_AJ519488 AJ519488 502
584 D.TD.99.MN012_AJ519489 AJ519489 502
585 D.UG.92.92UG001_AJ320484 AJ320484 500
586 D.UG.94.94UG114_U88824 U88824 502
587 D.UG.99.CQ891769_CQ891769 CQ891769 492
588 D.UG.99.CQ891770_CQ891770 CQ891770 499
589 D.ZA.84.R2_AY773338 AY773338 501
590 D.ZA.85.R214_AY773339 AY773339 500
591 D.ZA.85.R286_AY773340 AY773340 502
592 D.ZA.86.R482_AY773341 AY773341 501
593 F1.BE.93.VI850_AF077336 AF077336 491
594 F1.BR.89.BZ126_AY173957 AY173957 492
595 F1.BR.93.93BR020_1_AF005494 AF005494 492
596 F1.CD.x.VI174_L11782 L11782 488
597 F1.FI.93.FIN9363_AF075703 AF075703 493
598 F1.FR.96.MP411_AJ249238 AJ249238 494
599 F1.RW.x.VI69_L11796 L11796 487
600 F2.CM.95.MP255_AJ249236 AJ249236 492
601 F2.CM.95.MP257_AJ249237 AJ249237 496
602 F2KU.BE.94.VI1126_AF076475 AF076475 496
603 G.BE.96.DRCBL_AF084936 AF084936 490
604 G.ES.00.X558_AF423760 AF423760 493
605 G.ES.99.X138_AF450098 AF450098 494
606 G.KE.93.HH8793_1_1_AF061640 AF061640 497
607 G.SE.93.SE6165_AF061642 AF061642 495
608 GKU.SE.95.SE8646_AY352654 AY352654 506
609 GKU.SE.95.SE9010_AY352655 AY352655 499
610 H.BE.93.VI991_AF190127 AF190127 498
611 H.BE.93.VI997_AF190128 AF190128 499
612 H.CF.90.056_AF005496 AF005496 500
613 J.SE.93.SE7887_AF082394 AF082394 497
614 K.BE.x.VI325_L11789 L11789 487
615 K.CD.97.EQTB11C_AJ249235 AJ249235 495
616 K.CM.96.MP535_AJ249239 AJ249239 495
617 U.CD.83.83CD003_AF286236 AF286236 499
618 U.CD.90.90CD121E12_AF457101 AF457101 496
619 U.GR.99.GR303_AY046058 AY046058 492