pima.sh alignment of gag sequences displayed with print-pima.sh.
Page 1.1
1 15 16 30 31 45 46 60 61 75 76 90
1 clus1-ML --------------- --------------- ------AhrrfXRFh aXXXLLksXEGCXra fXXLXXXXXTGikXL rhLdNXffXadfaHX 54
2 clus1-ML.7 --hXsSfLsXnsfDs fEqaRLRPXGKKKYX aKHaaWAhrrfkRFG LXEsLLEsrEGCrKI asVLXPfXPTGSEjL KhLdNXfCVadCaHX 88
3 clus1-ML.2.7 --ARsSVLsGKKADE LEnaRLRPGGKKKYX LKHaVWAANrLDRFG LAESLLEsKEGCQKI aiVLXPfVPTGSENL KSLdNTVCVIWCIHA 88
4 clus1-ML.1.2.7 --ARsSVLSGKKADE LEKaRLRPGGKKKYM LKHVVWAANELDRFG LAESLLEsKEGCQKI aiVLXPLVPTGSENL KSLdNTVCVIWCIHA 88
5 sivmm251r.1.2.7 MGARNSVLSGKKADE LEKIRLRPGGKKKYM LKHVVWAANELDRFG LAESLLENKEGCQKI LSVLAPLVPTGSENL KSLYNTVCVIWCIHA 90
6 sivstm.1.2.7 MGARSSVLSGKKADE LEKVRLRPGGKKKYM LKHVVWAANELDRFG LAESLLESKEGCQKI ITVLEPLVPTGSENL KSLFNTVCVIWCIHA 90
7 hiv2rod.2.7 MGARNSVLRGKKADE LERIRLRPGGKKKYR LKHIVWAANKLDRFG LAESLLESKEGCQKI LTVLDPMVPTGSENL KSLFNTVCVIWCIHA 90
8 clus1-ML.5.7 --hhsSALsXRsLDs FEqIRLRPsGKKKYQ IKHLIWAGKEMERFG LHEnLLEirEGCrKI IEVLXPLEPTGSEGL KhLFNLfCVadCaHX 88
9 sivagm3.5.7 MGAATSALNRRQLDK FEHIRLRPTGKKKYQ IKHLIWAGKEMERFG LHERLLESEEGCKKI IEVLYPLEPTGSEGL KSLFNLVCVLFCVHK 90
10 sivagm677.5.7 MGGGHSALSGRSLDT FEKIRLRPNGKKKYQ IKHLIWAGKEMERFG LHEKLLETKEGCQKI IEVLTPLEPTGSEGL KALFNLCCVIWCIHA 90
11 clus1-ML.6 --ARASVLsGGKLDX WEKInLRPGGKKXYX fKHLVWASRELXRFA aNXXLLkTXEGCXra fXQLQXhLrTGikEL rSLdNXaAXLdfaHr 88
12 clus1-ML.4.6 --ARASVLsGGKLDX WEKInLRPGGKKXYX fKHLVWASRELXRFA LNXXLLkTXEGCXQa frQLQPhLrTGTkEL rSLdNXaAXLdCaHr 88
13 clus1-ML.3.4.6 --ARASVLSGGKLDX WEKIRLRPGGKKKYR fKHLVWASRELERFA LNPXLLkTXEGCXQa aoQLQPhLrTGTEEL rSLFNfaAXLdCaHQ 88
14 hivlbv217.3.4.6 MGARASVLSGGKLDE WEKIRLRPGGKKKYR MKHLVWASRELERFA LNPGLLETTEGCQQI LQQLQPSLQTGTEEL KSLFNAVAVLWCIHQ 90
15 hivvi557.3.4.6 MGARASVLSGGKLDA WEKIRLRPGGKKKYR LKHLVWASRELERFA LNPDLLDTAEGCLQL IEQLQPALKTGTEEL QSLFNLLATLYCVHQ 90
16 hivug268.4.6 MGARASVLRGGKLDT WEKIKLRPGGKKCYM MKHLVWASRELGRFA LNSGLLETSEGCKQI MKQLQPALQTGTDEL RSLYNTVATLYCVHK 90
17 hiv1bz163b.6 MGARASVLSGGKLDA WEKIRLRPGGKKKYS LKHLVWASRELERFA INPGLLETSEGCQKI IGQLQSSLQTGSEEL RSLYNTVAVLYFVHQ 90
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91 105 106 120 121 135 136 150 151 165 166 180
1 clus1-ML XXXVnrTrXAXXXar rXXXXXsXsXrXXgg gggXXXXXXXrXXXf ggggggggggggXrX XjXXXHXXaSPRTLN AWVKfaEEKXdhXEa 144
2 clus1-ML.7 krrVKrTEXAXXXVr rXfXfXsXsXrXXXX ssrXihjXXXrXXjf XVggggggggggXrX jjXdXHXPLSPRTLN AWVKfaEEKndGAEa 178
3 clus1-ML.2.7 EEKVKrTEXAKQaVr RHLVfETGTApsMPX TSRPTAPXSXnGGNY PV----------Qra GGNYXHaPLSPRTLN AWVKLaEEKKFGAEV 168
4 clus1-ML.1.2.7 EEKVKHTEEAKQaVr RHLVVETGTApsMPX TSRPTAPXSGRGGNY PV----------QQa GGNYVHLPLSPRTLN AWVKLaEEKKFGAEV 168
5 sivmm251r.1.2.7 EEKVKHTEEAKQIVQ RHLVVETGTAETMPK TSRPTAPSSGRGGNY PV----------QQI GGNYVHLPLSPRTLN AWVKLIEEKKFGAEV 170
6 sivstm.1.2.7 EEKVKHTEEAKQVVK RHLVVETGTANKMPA TSRPTAPPSGRGGNY PV----------QQV GGNYVHLPLSPRTLN AWVKLVEEKKFGAEV 170
7 hiv2rod.2.7 EEKVKDTEGAKQIVR RHLVAETGTAEKMPS TSRPTAPSSEKGGNY PV----------QHV GGNYTHIPLSPRTLN AWVKLVEEKKFGAEV 170
8 clus1-ML.5.7 krrVKDTEEAVfXVn QXfHLVkKprrAXnr ssETihjXXXpsnjf XVggggggggggXpQ jNAWaHXPLSPRTLN AWVKfVEEKndGAEa 178
9 sivagm3.5.7 DKEVKDTEEAVAIVR QCCHLVEKERNAERN TTETSSGQKKNDKGV TVPPGGSQNFPAQQQ GNAWIHVPLSPRTLN AWVKAVEEKKFGAEI 180
10 sivagm677.5.7 EQKVKDTEEAVVTVK QHYHLVDKNEKAAKK KNETTAPPGGESRNY PV----------VNQ NNAWVHQPLSPRTLN AWVKCVEEKRWGAEV 170
11 clus1-ML.6 XaXVnDTKEALkrar rXQrrXQpnXrsAgg gggXXXXaSQNYPIV ------------QNf QGQXVHQXaSPRTLN AWVKVaEEKAFSPEV 166
12 clus1-ML.4.6 XIXVnDTKEALkrar rXQrrXQpnXosAgg ggglXXraSQNYPIV ------------QNf QGQXVHQXaSPRTLN AWVKVaEEKAFSPEV 166
13 clus1-ML.3.4.6 RIXVKDTKEALErar rXQrrSQpnXQQAgg DKGljsraSQNYPIV ------------QNA QGQXVHQXISPRTLN AWVKVVEEKAFSPEV 166
14 hivlbv217.3.4.6 RIGVKDTKEALEEVE KRQKNSQQKIQQA-- DKGDNSQVSQNYPIV ------------QNA QGQMVHQPISPRTLN AWVKVVEEKAFSPEV 166
15 hivvi557.3.4.6 RIDVKDTKEALEKLK EAQNKSQNRTQQATG DKGNGNKISQNYPIV ------------QNA QGQPVHQAISPRTLN AWVKVVEEKAFSPEV 168
16 hivug268.4.6 GIEVRDTKEALDKIE EEQNKIQQKTETA-- ---DKGKVSQNYPIV ------------QNL QGQMVHQALSPRTLN AWVKVIEEKAFSPEV 163
17 hiv1bz163b.6 RVEVKDTKEALDKLE EEQNKSQQKTKQA-- --AADKGVSQNYPIV ------------QNL QGQMVHQSISPRTLN AWVKVIEEKAFSPEV 164
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181 195 196 210 211 225 226 240 241 255 256 270
1 clus1-ML aPXFsALSEGfXXXD aNXfLNXaGXHQhAf QfankXINEEAAggX XXXXXXXXXXXXjXX XrXXXhsXfhXTiiX XooXXXXfsXpjXaX 234
2 clus1-ML.7 VPXFQALSEGCXXYD aNQfLNfaGkHQhAf QIankaINEEAAggX XXXXXXXjXXXXGQL RkPsGSDIAGTTSiX pEQaoWXdsXpjXaX 268
3 clus1-ML.2.7 VPGFQALSEGCTPYD INQfLNCVGkHQAAM QIInkIINEEAAggX XXXXXXXjXXXXGQL REPsGSDIAGTTSiX kEQIQWMdRXQNPaP 258
4 clus1-ML.1.2.7 VPGFQALSEGCTPYD INQfLNCVGkHQAAM QIInkIINEEAAggD fpXXrPXjXXXXGQL REPSGSDIAGTTSSX kEQIQWMYRQQNPIP 258
5 sivmm251r.1.2.7 VPGFQALSEGCTPYD INQMLNCVGDHQAAM QIIRDIINEEAA--D WDLQHPQPAPQQGQL REPSGSDIAGTTSSV DEQIQWMYRQQNPIP 258
6 sivstm.1.2.7 VPGFQALSEGCTPYD INQLLNCVGEHQAAM QIIKEIINEEAADWD MQHPQPPGPLPAGQL REPSGSDIAGTTSSP EEQIQWMYRQQNPIP 260
7 hiv2rod.2.7 VPGFQALSEGCTPYD INQMLNCVGDHQAAM QIIREIINEEAA-EW DVQHPIPGPLPAGQL REPRGSDIAGTTSTV EEQIQWMFRPQNPVP 259
8 clus1-ML.5.7 VPMFQALSEGCXXYD aNQMLNVaGDHQGAL QIaKEaINEEAAoWD XXHXPPAGPLPAGQL RDPsGSDIAGTTSia QEQaEWXdsANPRaD 268
9 sivagm3.5.7 VPMFQALSEGCTPYD INQMLNVLGDHQGAL QIVKEIINEEAAQWD IAHPPPAGPLPAGQL RDPRGSDIAGTTSTV QEQLEWIYTANPRVD 270
10 sivagm677.5.7 VPMFQALSEGCLSYD VNQMLNVIGDHQGAL QILKEVINEEAAEWD RTHRPPAGPLPAGQL RDPTGSDIAGTTSSI QEQIEWTFNANPRID 260
11 clus1-ML.6 IPMFiALSEGATPQD LNXMLNXVGGHQAAM QMLKDTINEEAA-EW DRaHPXrAGPaXPGQ fRkPRGSDIAGTTST LQEQIXWMTSNPPaP 255
12 clus1-ML.4.6 IPMFiALSEGATPQD LNXMLNXVGGHQAAM QMLKDTINEEAA-EW DRaHPXrAGPaXPGQ fRkPRGSDIAGTTST LQEQIXWMTSNPPIP 255
13 clus1-ML.3.4.6 IPMFSALSEGATPQD LNXMLNXVGGHQAAM QMLKDTINEEAA-EW DRaHPXrAGPIPPGQ fRkPRGSDIAGTTST LQEQIXWMTSNPPIP 255
14 hivlbv217.3.4.6 IPMFSALSEGATPQD LNTMLNTVGGHQAAM QMLKDTINEEAA-EW DRIHPQQAGPIPPGQ IRDPRGSDIAGTTST LQEQIRWMTSNPPIP 255
15 hivvi557.3.4.6 IPMFSALSEGATPQD LNAMLNIVGGHQAAM QMLKDTINEEAA-EW DRVHPVHAGPIPPGQ MREPRGSDIAGTTST LQEQIAWMTSNPPIP 257
16 hivug268.4.6 IPMFTALSEGATPQD LNTMLNTVGGHQAAM QMLKDTINEEAA-EW DRLHPVHAGPVAPGQ MREPRGSDIAGTTST LQEQINWMTSNPPIP 252
17 hiv1bz163b.6 IPMFSALSEGATPQD LNTMLNTVGGHQAAM QMLKDTINEEAA-EW DRLHPVQAGPIPPGQ IREPRGSDIAGTTST LQEQIQWMTSNPPVP 253
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271 285 286 300 301 315 316 330 331 345 346 360
1 clus1-ML VGXXYnnWaXaGLpK fVrMYsPXsaLDanQ GPKEXFrsYVDRFdK XaRAEQXXXXVKXWM TriLLaQNANPDC-- --------------- 307
2 clus1-ML.7 VGXXYRnWaXaGLQK fVrMYNPXsaLDanQ GPKEXFrsYVDRFYK haRAEQXXXXVKpWM TriLLaQNANPDCKa aLKGLGfrPTLEEML 358
3 clus1-ML.2.7 VGNIYRRWIQaGLQK CVRMYNPXNILDaKQ GPKEXFQSYVDRFYK SLRAEQXDXhVKNWM TrTLLaQNANPDCKL VLKGLGfNPTLEEML 348
4 clus1-ML.1.2.7 VGNIYRRWIQLGLQK CVRMYNPXNILDVKQ GPKEXFQSYVDRFYK SLRAEQXDXhVKNWM TrTLLIQNANPDCKL VLKGLGfNPTLEEML 348
5 sivmm251r.1.2.7 VGNIYRRWIQLGLQK CVRMYNPTNILDVKQ GPKEPFQSYVDRFYK SLRAEQTDAAVKNWM TQTLLIQNANPDCKL VLKGLGVNPTLEEML 348
6 sivstm.1.2.7 VGNIYRRWIQLGLQK CVRMYNPVNILDVKQ GPKETFQSYVDRFYK SLRAEQADPSVKNWM TRTLLIQNANPDCKL VLKGLGMNPTLEEML 350
7 hiv2rod.2.7 VGNIYRRWIQIGLQK CVRMYNPTNILDIKQ GPKEPFQSYVDRFYK SLRAEQTDPAVKNWM TQTLLVQNANPDCKL VLKGLGMNPTLEEML 349
8 clus1-ML.5.7 VGAXYRnWaILGLQK fVrMYNPXsVLDIRQ GPKEXFrDYVDRFYK AaRAEQAXXkVKpWM ToiLLIQNANPDCKa ILKGLGMrPTLEEML 358
9 sivagm3.5.7 VGAIYRRWIILGLQK CVKMYNPVSVLDIRQ GPKEAFKDYVDRFYK AIRAEQASGEVKQWM TESLLIQNANPDCKV ILKGLGMHPTLEEML 360
10 sivagm677.5.7 VGAQYRKWVILGLQK VVQMYNPQKVLDIRQ GPKEPFQDYVDRFYK ALRAEQAPQDVKNWM TQTLLIQNANPDCKL ILKGLGMNPTLEEML 350
11 clus1-ML.6 VGkIYKRWIILGLNK IVRMYSPVSILDInQ GPKEPFRDYVDRFFK XLRAEQATQkVKjWM TDTLLVQNANPDCrT ILnALGXGA------ 339
12 clus1-ML.4.6 VGkIYKRWIILGLNK IVRMYSPVSILDInQ GPKEPFRDYVDRFFK XLRAEQATQkVKjWM TDTLLVQNANPDCKT ILnALGXGAiaEEMM 345
13 clus1-ML.3.4.6 VGkIYKRWIILGLNK IVRMYSPVSILDIRQ GPKEPFRDYVDRFFK XLRAEQATQkVKjWM TDTLLVQNANPDCKT ILnALGXGAiaEEMM 345
14 hivlbv217.3.4.6 VGEIYKRWIILGLNK IVRMYSPVSILDIRQ GPKEPFRDYVDRFFK TLRAEQATQDVKNWM TDTLLVQNANPDCKT ILKALGPGATLEEMM 345
15 hivvi557.3.4.6 VGDIYKRWIILGLNK IVRMYSPVSILDIRQ GPKEPFRDYVDRFFK ALRAEQATQEVKGWM TDTLLVQNANPDCKT ILRALGQGASIEEMM 347
16 hivug268.4.6 VGEIYKRWIILGLNK IVRMYSPVSILDIKQ GPKEPFRDYVDRFFK TLRAEQATQDVKNWM TDTLLVQNANPDCKT ILRALGPGASLEEMM 342
17 hiv1bz163b.6 VGEIYKRWIILGLNK IVRMYSPVSILDIRQ GPKEPFRDYVDRFFK TLRAEQATQEVKGWM TDTLLVQNANPDCQT ILKALGPGAT----- 338
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361 375 376 390 391 405 406 420 421 435 436 450
1 clus1-ML --------------- --------------- --------------- --------------- --------------- --------------- 307
2 clus1-ML.7 XACQGVGGPXXKAna gggXfXXXXXXXjfX XXhXgggXXRXXfKC dNCGKXGHXXnoCXX PRrXXCfKCGrXXHX fXrCXXXXXXfXXXX 448
3 clus1-ML.2.7 TACQGVGGPGQKARL MAEALKEffXPXPaP FAAAgggXXRnXfKC WNCGKXGHiAnQCnh PRRQGCWKCGrXXHX MXrCPkRQfGFLGfG 438
4 clus1-ML.1.2.7 TACQGVGGPGQKARL MAEALKEffXPXPaP FAAAgrrXjRnXaKC WNCGKXGHiAnQCnh PRRQGCWKCGrXXHX MAKCPkRQfGFLGfG 438
5 sivmm251r.1.2.7 TACQGVGGPGQKARL MAEALKEALAPVPIP FAAAQKRGPRKPIKC WNCGKEGHSARQCRA PRRQGCWKCGKMDHV MAKCPDRQAGFLGLG 438
6 sivstm.1.2.7 TACQGVGGPGQKARL MAEALKEVFQPDPLP FAAA-QQQGRRTVKC WNCGKAGHTAKQCKG PRRQGCWKCGQQGHQ MAKCPERQVGFLGFG 439
7 hiv2rod.2.7 TACQGVGGPGQKARL MAEALKEVIGPAPIP FAAA---QQRKAFKC WNCGKEGHSARQCRA PRRQGCWKCGKPGHI MTNCPDRQAGFLGLG 436
8 clus1-ML.5.7 XACQGVGGPseKAKa g-gXfXXXXphQNMf QXGjQnXXPRjPaKC dNCGKFGHMQRoCXX PRrfnCfKCGKXGHf AKDCnjXXXXfXXXX 447
9 sivagm3.5.7 TACQGVGGPSYKAKV M-AEMMQNMQSQNMM QQGGQRGRPRPPVKC YNCGKFGHMQRQCPE PRKMRCLKCGKPGHL AKDCRGQVNFLGYGR 449
10 sivagm677.5.7 IACQGVGGPQHKAKL ---MVEMMSNGQNMV QVGPQKKGPRGPLKC FNCGKFGHMQRECKA PRQIKCFKCGKIGHM AKDCKNGQANFLGYG 437
11 clus1-ML.6 --------------- --------------- --------------- --------------- --------------- --------------- 339
12 clus1-ML.4.6 TACQGVGGPhHKAnV LAEAMSQfsXXXggf MMQnhNFKGXnnXIK CFlCGKEGHLARNCR APRKnGCWKCGnEGH QfKDCTERQANFLGK 435
13 clus1-ML.3.4.6 TACQGVGGPhHKAnV LAEAMSQfsXsAXgf MMQKGNFKGXRnXIK CFlCGKEGHLARNCR APRKnGCWKCGKEGH QfKDCTERQANFLGK 435
14 hivlbv217.3.4.6 TACQGVGGPSHKARV LAEAMSQASGTATAI MMQKGNFKGPRKNIK CFDCGKEGHLARNCR APRKRGCWKCGKEGH QMKDCTERQANFLGK 435
15 hivvi557.3.4.6 TACQGVGGPGHKAKV LAEAMSQVNTNAV-M MMQKGNFKGQRRIIK CFNCGKEGHLARNCR APRKKGCWKCGKEGH QLKDCTERQANFLGK 436
16 hivug268.4.6 TACQGVGGPGHKARV LAEAMSQANNIN--I MMQRSNFKGPKRIIK CFNCGKEGHLARNCR APRKKGCWKCGREGH QMKDCTERQANFLGK 430
17 hiv1bz163b.6 --------------- --------------- --------------- --------------- --------------- --------------- 338
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451 465 466 480 481 495 496 510 511 525 526 540
1 clus1-ML --------------- --------------- --------------- --------------- --------------- -------------1 307
2 clus1-ML.7 XfGXggggrXXXfXX XXXGasPTA------ --------------- --------------- --------------- -------------1 472
3 clus1-ML.2.7 PWGK--KPqNFPfAQ aXQGLTPTAPPXDPA --------------- --------------- --------------- -------------1 466
4 clus1-ML.1.2.7 PWGK--KPqNFPMAQ aXQGLTPTAPPEDPA --------------- --------------- --------------- -------------1 466
5 sivmm251r.1.2.7 PWGK--KPRNFPMAQ VHQGLTPTAPPEDPA VDLLKNYMQLGKQQR ESREKPYKEVTEDLL HLNSLFGGDQ----- -------------1 506
6 sivstm.1.2.7 PWGK--KPHNFPMAQ IPQGLTPTAPPEDPA ADLLRSYMQLGKKQR ESRKTPYKEVTEDLL HLNSLFGEDQ----- -------------1 507
7 hiv2rod.2.7 PWGK--KPRNFPVAQ VPQGLTPTAPPVDPA VDLLEKYMQQGKRQR EQRERPYKEVTEDLL HLEQGETPYREPPTE DLLHLNSLFGKDQ1 522
8 clus1-ML.5.7 efGhggggrXXpdXh XTaGaEPTAPPXXiX YDPAKKLLQQYA--- --------------- --------------- -------------1 489
9 sivagm3.5.7 WMGA----KPRNFPA ATLGVEPTAPPPPSP YDPAKKLLQQYADKG KQLREQRKKPPAVNP DWTEGYSLNSLFGED Q------------1 521
10 sivagm677.5.7 HWGGAKPRNFVQYRG DTVGLEPTAPPMETA YDPAKKLLQQYAEKG QRLREEREQTRKQKE KEVEDVSLSSLFGGD Q------------1 513
11 clus1-ML.6 --------------- --------------- --------------- --------------- --------------- -------------1 339
12 clus1-ML.4.6 IWXXrKGRPGNFLQs RPEPiAPPA------ --------------- --------------- --------------- -------------1 459
13 clus1-ML.3.4.6 IWXXrKGRPGNFLQs RPEPiAPPA------ --------------- --------------- --------------- -------------1 459
14 hivlbv217.3.4.6 IWPSHKGRPGNFLQN RPEPSAPPAESLGFG EEIAPSPKQEPKELY PLTSLKS-------- --------------- -------------1 487
15 hivvi557.3.4.6 IWSPNKGRPGNFLQS RPEPTAPPAESFGFG EEMTPPPKQERKDAE SPLTSLKS------- --------------- -------------1 489
16 hivug268.4.6 IWPPNKGRPGNFLQS RPEPTAPPAEPTAPP AESFRFEGTTPPPKQ EPKDREPLISLKS-- --------------- -------------1 488
17 hiv1bz163b.6 --------------- --------------- --------------- --------------- --------------- -------------1 338