The defective MuERV sequences have numerous in-frame terminators and frameshifts. In some places, the alignment can not be objectively defended and reasonable alternative alignments would trade frameshfits for in-frame terminators. Regions of poor alignment among MuERV sequences correspond to regions of poor conservation among active retroviruses. Regions of relatively secure alignment used for phylogenetic reconstructions are indicated.
Numbers refer to base under final digit and match numbering system in the GenBank files defined in overview. For the numbering of MuERVC, see MuERVC-C105 sequence It is AF049340 with the 718 bp L1C105 insert removed starting at coordinate 180. First letters of gag-pol codons have been capitalized. All 3 letters of in-frame terminators have been capitalized.
SCH 6/3/98
630 640 650 660 670 680
MoMLV AtgGgcCagActGttAccActCccTtaAgtTtgAccTtaGgtCacTggAaaGatGtcGag
||||| || | | | || || | | || || |||||||| ||||||
GALV AtgGgaCaaGatAatTctAccCctAtcTccCtcActCtaAatCacTggAgaGatGtgAga
640 650 660 670 680 690
|||||| | | | ||||| | | || |||| || || || | ||| || |
MuRVY AtgGgaAagActGtgAcgAccCcaCtaAcaCttActCagAacCatTGAAcaGacGttAtg
1080 1090 1100 1110 1120 1130
| ||| |||||| |||||||| |||| | ||| |||| || || || ||||
MuRRS ActGgaCggActGtaAcgAccCccCtaAgtTtgActTtaGacCacTggActGaaGttAga
1250 1260 1270 1280 1290 1300
MuERVC >>>>>>>>>>>>>>>>>>>>>>>>>>>>> This portion not cloned >>>>>>
Met --> start of gag MA domain
690 700 710 720 730
MoMLV CggAtc...GctCacAacCagTcgGtaGatGtcAagAagAgaCgtTggGttAccTtcTgc
| |||||||| | || || || |||| ||| || ||| || |||||
GALV AcaAgg...GctCacAatCtaTccGtgGaaAtcAaaAagGgaAaaTggCagActTtcTgt
700 710 720 730 740
|| ||| || ||||||| | | | || |||| |||||| ||||| ||||| ||
MuRVY ActAgg..gGccAacAatCttTtcTttGatGtcAagAagGgaCctTggCaaActTttTgc
1140 1150 1160 1170 1180 1190
| ||| ||| | || |||| | || | |||||||| |||||||| ||||| |||
MuRRS TcaAgg...GccCatAacCttTcaGtaGaaAttAagAagGggCctTggCagActTtcTgc
1310 1320 1330 1340 1350 1360
MuERVC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
740 750 760 770 780 790
MoMLV TctGcaGaaTggCcaAccTttAacGtcGgaTggCcgCgaGacGgcAccTttAacCgaGac
|| | || ||||| || || ||| || ||||| | || || || ||||| |
GALV TccTccGagTggCccAcaTtcGgcGtgGggTggCcaCcgGagGgaActTttAatCtcTct
750 760 770 780 790 800
||||| | ||||| | || || ||||| ||||| || |||||| ||||| || ||
MuRVY TccTctAaaTggCcaGctTttGgtGtgGgcTggCctTcgCagGgaAatTttAgcCtgCct
1200 1210 1220 1230 1240 1250
|||| | | ||| ||||| ||| ||| | | | || | |||| | | ||
MuRRS GccTccGagTAGCcgActTttAatGtaAaaTggTcaCtgGaaGggActTtt.ggTttAct
1370 1380 1390 1400 1410 1420
MuERVC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
800 810 820 830 840 850
MoMLV CtcAtcAccCagGttAagAtcAagGtcTttTcaCctGgcCcgCatGgaCacCcaGacCag
|||| ||||| | | |||||| | ||||| || |||||
GALV GtcAttTttGcaGttAaaAagAttGtcTttCagGagAac...GggGgaCatCcgGacCaa
810 820 830 840 850 860
|| ||| | | || || || | |||||| || || ||||| || |
MuRVY GttAttCtaGgtGtcAa....GttAttTttCagActGca...GgaGggCatCctGatCcg
1260 1270 1280 1290 1300
|||| | | || || || ||||||||| || | || || | ||||
MuRRS CttAtcTttGaaGttAaaGccAttGttTttCagAgtGgaCctGggTccCacCtgGatCaa
1430 1440 1450 1460 1470 1480
MuERVC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
860 870 880 890 900 910
MoMLV GtcCccTacAtcGtgAccTggGaaGccTtgGctTttGacCccCctCccTggGtcAagCcc
|| || || |||||| ||| | | | | || | ||||| || ||||| ||
GALV GttCcaTatAtcGtgGtaTggCagGacCtcGccCagAatCccCcaCcaTggGtgCcaGcc
870 880 890 900 910 920
|| || ||||| | || |||||||| || | || |||| ||||| || || ||
MuRVY GtaCctTatAtaAttGtgTggCagGatCtgGtaCaaAatCtgCcaCccTGACtgGgtTcc
1310 1320 1330 1340 1350 1360
||||| || | || ||| || || | | | |
MuRRS CagCctTac..................CtcAttCagAatTcaCcgCcaTAAAtcAaaCca
1490 1500 1510 1520
MuERVC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
End of portion used as MA-><----------
920 930 940 950 960
MoMLV TttGtaCacCctAagCctCcg............CctCctCttCctCcaTccGccCcgTct
| | | | |
GALV Tcc..................GccAagGtcGctGttGtcTctGatAccCga.........
930 940 950
| || | ||| || || | | || ||| |
MuRVY TggActTccGgaGctGagGcaGcgAtgGtgGcaGtaGcaT..GaaAccGaaAatGat...
1370 1380 1390 1400 1410 1420
||| |
MuRRS TggGtt......................................................
1530
MuERVC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
--- alignment considered unreliable in this region
970 980 990 1000 1010
MoMLV CtcCccCttGaaCctCctCgtTcgAccCcgCctCgaTccTcc......CttTatCcaGcc
|| ||| | || | || || ||| || || | || || ||
GALV AgaCcaGttGcgGggAggCcaTcaGctCctCccCgaCccCcc......AtcTacCcgGca
960 970 980 990 1000 1010
|||||| | | | | | || ||||| ||||| || | |
MuRVY AgaCcaTgcGggTcaGccCagAgcAcgTtcCatCggCccCctGagG..AtcTatCctGaa
1430 1440 1450 1460 1470 1480
|||||| |||| | | | | |
MuRRS CccCcaTgcCtcTcaGagCccTccCccGgaTgcTccCatGca..................
1540 1550 1560 1570
MuERVC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>GAtcTatCcaGag
1 10
1020 1030 1040 1050
MoMLV ...........................CtcActCctTctCtaGgcGccAaaCctAaaCct
GALV AcaGacGacTta................................................
1020
| || ||
MuRVY AttGatGatGcc................................................
1490
MuRRS ............CtcGagTggGtcAgcAcaGtgAccTcgCttTctGcc...CtaAaa.ag
1580 1590 1600 1610
| || ||| |||
MuERVC AtaGaaGaaCctCcaGaaTggTgtTacAcc..............................
20 30 40
1060 1070 1080 1090 1100 1110
MoMLV CaaGttCttTctGacAgtGggGggCcgCtcAtcGacCtaCttAcaGaaGacCccCcgCct
||| || | | ||||||||
GALV ...........................CtcCtcCtcTctGaaCccAcg...CccCcgCcc
1030 1040 1050
|| | ||| || || ||
MuRVY ........................TttTtcAttGacTccTtc.........CcaCccCct
1500 1510 1520
| | ||
MuRRS CagTccCtg...............CacCtgGctCtgAgaTtgCta...............
1620 1630 1640
MuERVC ...................................................CcaCccCaa
50
1120 1130 1140 1150 1160 1170
MoMLV TatAggGacCcaAgaCcaCccCctTccGacAggGacGgaAatGgtGgaGaaGcgAccCct
||| || || ||||||||| | | | | | || | ||
GALV TatCcgGcgGcaCtgCcaCccCctCtgGccCctCagGcgAtcGgaCcgCcgTcaGgcCag
1060 1070 1080 1090 1100 1110
|| || | | ||| || | ||| | | || | | |
MuRVY TacCccCaaAgaActTctAatCctGatCccTcaCagCtgCccAccCcaGcaGacCccAgg
1530 1540 1550 1560 1570 1580
MuRRS ............................................................
MuERVC TatCccCaaCtgAtcCccTccCagAtcTctCaaCagGgtGctGctGgtGatGcgGaa...
60 70 80 90 100
1180 1190 1200 1210 1220
MoMLV GcgGgaGagGcaCcgGacCccTccCcaAtgGcaTctCgcCtaCgtGggAgaCgg...Gag
| || || || || || | | | | ||
GALV AtgCccGatAgtAgcGatCctGagGggCcaGccGctGggAccAggAgtCgcCgtGccCgc
1120 1130 1140 1150 1160 1170
|| || | || || | ||||| || || | ||
MuRVY GtgGccTctGtg.........AcaGgaCcgTtgGgaGggActCctAgcTgcGaaGtcCat
1590 1600 1610 1620 1630
| | |||||| | ||||| | ||| | ||| |||
MuRRS ...AagGcaCagTctGagGacCgaGgaCctAcaGctGggAccCggAgcCgaCaaGccCag
1650 1660 1670 1680 1690 1700
||||| | ||||| | || ||| | ||| |||
MuERVC .....................GagGgaCcaGctGctGgaAacCaaAgcTggAgaGctCag
110 120 130 140
1230 1240 1250 1260 1270
MoMLV CccCctGtgGcc..................GacTccActAccTcgCagGcaTtcCccCtc
|| | | | ||||||||| | || ||||||
GALV AgtCcaGcaGac......AacTcgGgtCctGacTccAct......GtgAttTtgCccCtc
1180 1190 1200 1210 1220
||| ||| || || || || |||||| || |||||| |
MuRVY AgtTcaGagAggGaaGtgAa.TctAaaCcaGatTccAct......GttGctTtgCctTta
1640 1650 1660 1670 1680
||| | | | || || | ||| |||||
MuRRS AgtCccCcaGca......GatGaaGctCttGac...AccActTctGcc..tTttCctTtg
1710 1720 1730 1740 1750
|| || | | ||| ||| || | |||||
MuERVC AgcCcaGag...............GgaCcaGacTcaAcc......AccGagCtaCctTta
150 160 170 180
1280 1290 1300
MoMLV CgcGcaGga......GgaAac...............GgaCagCtt.........CaaTac
|| || | ||| | || |||||
GALV CgaGccAta......GgaCcc...CcgGccGagCccAatGgcCtgGtcCctCtaCaaTat
1230 1240 1250 1260 1270
|||| ||||| || | | |||| | || ||
MuRVY AgaGctTatGtaGgaGgaCc..tgCccAtgCccCggGg.CagTtaAtcCcaTtgCagTac
1690 1700 1710 1720 1730 1740
||||| || || ||| | || | | | | ||
MuRRS TGAGctGtg......GgcAacCtgTccAcaGacAggCagTctCtgCagAccCtcTAATat
1760 1770 1780 1790 1800
|| ||| | | ||||| | ||||| |||| ||||
MuERVC CatActTat......GgcCctCctCcaGcaGacCccGggCaaTtgCagCccCttCaaTac
190 200 210 220 230 240
alignment considered unreliable -------------><--
1310 1320 1330 1340
MoMLV TggCcgTtcTccTct............TctGacCttTacAacTggAaaAatAatAacCct
||||| || ||||| | || ||||| || |||||| |||| | ||
GALV TggCctTttTccTca............GcaGatCttTatAatTggAaaTctAatCatCcc
1280 1290 1300 1310 1320
||||| ||||| | |||||| | ||||| |||| ||
MuRVY TggCcaTttTcaTtgAtaGatAtgTtgGcaGatAtgTatAac........aTatCacTcc
1750 1760 1770 1780 1790
||||| ||||||| || ||| |||| ||
MuRRS TggCctTttTcaTca............GctGatCtgTacAatTAG...............
1810 1820 1830 1840
|| |||||||| ||| ||||||| || ||||||
MuERVC TgtCctTttTccTca............TctGatCtcTatAatTAGAagAcaAatCatGcc
250 260 270 280
--- Region used as CA domain
1350 1360 1370 1380 1390 1400
MoMLV TctTttTctGaaGatCcaGgtAaaCtgAcaGctCtgAtcGagTctGttCtcAtcAccCat
|||||||||||| | |||| || || | || | |||||| || | || |||||
GALV TctTttTctGaaAacCcaGcaGgtCtcAcgGggCtcCttGagTctCttAtgTtcTccCat
1330 1340 1350 1360 1370 1380
||||| || | || || |||| | || || |||||||||| || ||||||||| |
MuRVY TctTtcTcaTAGAatCccTcaGgcTtaAcaGgaCtcCttGagTtcCtaAtgTtcTccTac
1800 1810 1820 1830 1840 1850
MuRRS ............................................................
MuERVC GccTtcTct.....cTccTcaAgcCttActAatCtaAtaGaaTctCtcAtgTtcTctCat
290 300 310 320 330 340
1410 1420 1430 1440 1450 1460
MoMLV CagCccAccTggGacGacTgtCagCagCtgTtgGggActCtgCtgAccGgaGaaGaaAaa
|||||||| |||||||| || || ||||| | || ||| | ||| || |||
GALV CagCccActTggGacGatTgcCaaCagCtcCtaCagAttCttTtcAccActGagGaaCgg
1390 1400 1410 1420 1430 1440
|||||||||||||| || ||||| || || | ||| | | || | ||||| || |
MuRVY CagCccActTggGatGacTgcCagCaaCttTtgCagGtcCccTttAgaActGaaGagAga
1860 1870 1880 1890 1900 1910
MuRRS ............................................................
MuERVC CaaCctActTggGatGacTgtCagCagCttTtaCagGttCttTtcAccAcaGggGagAag
350 360 370 380 390 400
1470 1480 1490 1500 1510 1520
MoMLV CaaCggGtgCtcTtaGagGctAga...AagGcgGtgCggGgcGatGatGggCgcCccAct
|| | | ||| | ||||| | || || | || || ||||| ||| ||
GALV GaaAgaAttCtcCtgGagGccCgc...AaaAatGtcCttGggGacAatGggGccCctAca
1450 1460 1470 1480 1490
|| || || || || || ||| | ||||| |||| || ||||| |||| ||
MuRVY GagAggAtcCtgCtaGaaGccAgaA..AaaAacGtcCcaGgaCcaGatGggAccCccAct
1920 1930 1940 1950 1960 1970
MuRRS ............................................................
MuERVC GaaAagAttTggCtgGagGcaAga...AaaAatGtgCtaGggGctAatAgaCtaCtgAca
410 420 430 440 450 460
1530 1540 1550 1560 1570 1580
MoMLV CaaCtgCccAatGaaGtcGatGccGctTttCccCtcGagCgcCcaGacTggGatTacAcc
|| || || | ||| || || |||||| | || || |||||||||||| |
GALV CagCtcGagAacCtcAttAatGagGccTtcCccCtcAatCgaCctCacTggGatTacAac
1500 1510 1520 1530 1540 1550
| ||| ||||| || |||| || |||||| | || || || || | |||
MuRVY AatCtcCccAacCttAtaAatGcaGctTtcCccTtgGccCgtTctGccTtaGagTtcAat
1980 1990 2000 2010 2020 2030
|| || | ||||| ||| ||| | | | | | |||
MuRRS ..................AacGctGggTtcCctCtgGacCggCcaGatTAGAacTacAac
1850 1860 1870 1880
| || || ||||||||| | || || ||| || |||
MuERVC CaaGttCtgAatGaaAtaGatGcaGgaTtcCctCtgAcaTgtCctGacTAGGacCctAac
470 480 490 500 510 520
1590 1600 1610 1620 1630 1640
MoMLV AccCagGcaGgtAggAacCacCtaGtcCacTatCgc...CagTtgCtcCtaGcgGgtCtc
|| ||||||||| | | || | ||| ||| | | || | || ||||||
GALV AcaGccGcaGgtAggGagCgtCttCtgGtcTacCgc...CggActCtaGtgGcaGgtCtc
1560 1570 1580 1590 1600 1610
|| | || |||||||||||| |||||| | |||||||||||||||| |
MuRVY ActGtgAaaGatAggGagCgtCtcAcaGtcTacTGA...TggActCtaGtgGcaGggAta
2040 2050 2060 2070 2080
|| | ||| || |||| | | ||||| ||||| || ||||||| ||
MuRRS AcaGcaCaaGgtAagGagAggTtgAcaGttTacTgg..cCggGctCtaGt.......Cta
1890 1900 1910 1920 1930
| | |||||| |||| ||||||| ||| | | |||||||| || ||
MuERVC AggCctGaaGgtAggGagCagTtgAcaAttTtcCgc...CggGctCtgGtaGcaGgaCtg
530 540 550 560 570
1650 1660 1670 1680 1690 1700
MoMLV CaaAacGcgGgcAgaAgcCccAccAatTtgGccAagGtaAaaGgaAtaAcaCaaGggCcc
|| || | | | || ||||||||||| ||||||| || | || || ||
GALV AaaGggGcaGctCggCgtCctAccAatTtgGctAagGtaAgaGagGtcTtgCagGgaCcg
1620 1630 1640 1650 1660 1670
| |||| || || | || ||||||||||| |||||||||| ||| | ||||| |
MuRVY GagCggGctGcaTggTGACccAccAatTtgGccTAGGtaAgaGaaGtcCttCagGgtTca
2090 2100 2110 2120 2130 2140
|| | || | | |||||||||||||| ||||||||||||| | |||||
MuRRS AagGgaGcgAtgAgaCgcCccAccAatTtgGctAagGtaAgaGaaGtgAtgCagGgcCtt
1940 1950 1960 1970 1980 1990
| ||||| || ||||||||| |||||| ||||||||||| | | || || |
MuERVC AgaGgaGctGgcAggTgcCccAccAgtTtgGccAagGtaAgaGagAtcCtaCaaGggTta
580 590 600 610 620 630
1710 1720 1730 1740 1750 1760
MoMLV AatGagTctCccTcgGccTtcCtaGagAgaCttAagGaaGccTatCgcAggTacActCct
|| | || |||| ||| |||| | || | ||| |||||| | || ||||||||
GALV GcaGaaCccCctTcgGttTtcTtaGaaCgcCtgAtgGagGccTatAggAgaTacActCcg
1680 1690 1700 1710 1720 1730
|| | || || ||||||||| ||| || |||||| | ||||||||||| ||
MuRVY AtgGagCtgCccTccAttTtcTtaGcaCgaCtaAtgGagTctTatAggAgaTa..gcCca
2150 2160 2170 2180 2190 2200
| |||| || || |||| |||| | || | || || ||||||| || |
MuRRS AcaGagCccCcaTctGttTttTtaGaaAgaTtgAtaGaaGctTatAgaTacTatActTct
2000 2010 2020 2030 2040 2050
| || |||| | | || | |||||| |||| || || || | || ||| |
MuERVC AagGaaCccCtaAcaGtgTgtTtaGagCacCccTtaGagGcaTacAggCatTacActCcc
640 650 660 670 680 690
1770 1780 1790 1800 1810 1820
MoMLV TatGacCctGagGacCcaGggCaaGaaActAatGtgTctAtgTctTtc...AttTggCag
| ||| || || ||| | || || | ||| | || || | |||
GALV TttGatCccTctTctGagGgaCaaCagGctGcgGtcGccAtgGccTtt...AtcGgaCag
1740 1750 1760 1770 1780 1790
|||||||| |||| ||||| ||| || ||||| | || || || |||
MuRVY TttGatCc.TctT....aGgaCagCagC....tGtaGccAtaGatTta..cAttGgtCag
2210 2220 2230 2240 2250
||| | || | | || | || || || || | |||
MuRRS TttAacCcgAccTctGagGgtTAACaaGccGcgGttGctAtgGctTtt............
2060 2070 2080 2090 2100
||| |||| | || ||| | |||| | | || || |
MuERVC TttGacCctAtaTcaGagAgcCaaCagGtgAcaGtaGccA..............TggCag
700 710 720 730 740
1830 1840 1850 1860 1870
MoMLV TctGccCca......GacAttGggAgaAagTtaGagAggTtaGaaGatTtaAaaAacAag
|| |||||| || || || ||||||| ||||| |||| | | | || |
GALV TcaGccCca......GatAtcAagAaaAagTtaCagAggCtaGagGggCtcCagGacTat
1800 1810 1820 1830 1840
|| | | | ||||| | || ||||||||||||| ||||||| ||||| || |||
MuRVY TctGacTct......GatAttAtgAgaAagTtaCagAggTtaGagGgtCtcCaaGatTat
2260 2270 2280 2290 2300
| | | || |
MuRRS ...........................................aaAgaTtaCatGccAtg
2110
| | | || | |
MuERVC TctGctTctGacAt.GacAtcAggAgaAggTtaCatTgtCtaGagGgtCtgCaaCcaTta
750 760 770 780 790 800
1880 1890 1900 1910 1920
MoMLV AcgCttGgaGatTtgGttAgaGag...GcaGaaAagAtcTttAatAaaCgaGaa...Acc
| | |||||| || | |||| ||||||||| | | |||| |||| ||
GALV TccTtaCaaGatTtaGtaAaaGag...GcaGaaAagGtgTacCatAagAgaGag...Aca
1850 1860 1870 1880 1890
| | ||| ||||||||||||| || || || |||||||| ||||||||| ||
MuRVY ActCtgCaaCatTtaGtaAaaGaaA..GctGagAaaGtgTacCacAagAgaGag...Act
2310 2320 2330 2340 2350 2360
|| | ||| ||||||| || || || |||| ||||| | |||| |||| |
MuRRS GctTtaCaaGatTtaGttAagGag...GcaCagAagGtgTatCccAagGgaGaaT..Aag
2120 2130 2140 2150 2160 2170
|||| |||||| | ||||||||| ||| |||| ||||| | ||| |||| |
MuERVC TctTtgCaaGatCtgGttAagGag...GcaGagAaaGtgTacCatAagAgaGag...Act
810 820 830 840 850
End region used as CA ------------
1930 1940 1950 1960 1970 1980
MoMLV CcgGaaGaaAga......GagGaaCgtAtcAggAgaGaaAcaGagGaaAaaGaaGaaCgc
||||||||| | ||| | | | || |||| ||||| || ||
GALV GaaGaaGaaAga......CaaGaaAgaGaaAaaAagGagGcaGaaGaaAagGagAggCgg
1900 1910 1920 1930 1940 1950
|| ||||||| ||||| |||||| | || |||| ||| |||| || | |||
MuRVY GagGaaGaaAag......CaaGagAgaGaaGagAaaGagGtaGagGaaAgaGaaAacCgg
2370 2380 2390 2400 2410
|||| ||
MuRRS AggGaaAgaAga................................................
2180
|| | |
MuERVC GaaAaaTAAGaaAaaA..CgaGaaAgaGaaAagAgaGagGctGagGcaAgaGaaAgcAga
860 870 880 890 900 910
-----------><--- Alignment not used through to pol domain
although pro region has some usable segments.
1990 2000 2010 2020 2030 2040
MoMLV CgtAggAcaGagGatGagCagAaaGagAaaGaaAgaGatCgtAggAgaCatAgaGagAtg
| ||| | || | | | | ||
GALV .................................CgcGatAggCcgAagAaaAaaAacTtg
1960 1970 1980
| || | | | || | | ||||||
MuRVY .................................CatGaaCgcCagGagGatAggAacTtg
2420 2430 2440
|||| ||||| ||
MuRRS .............................................CagGagAggAatTta
2190 2200
|| || || ||||||
MuERVC .................................TGAGatAgaAggCaaGaaAgaAatTta
920 930 940
2050 2060 2070 2080
MoMLV AgcAagCtaTtgGccActGtcGttAgt..................GgaCagAaaCag...
| || | ||||| | || || ||| || |
GALV ActAaaAttCtgGccGcaGtaGtaAgt..................AgaGaaGggTccAca
1990 2000 2010 2020
||||| ||| |||| ||||| ||| || ||||| | ||
MuRVY ActAagAttTtgGcgGcaGtgGtaGgt..................GgaGaaAgtTcaGag
2450 2460 2470 2480
| | ||||||||| |||| ||||| | | | |||||
MuRRS AgcAggAttTtgGccTcaGtaGtaGggGaaTgtAaaGaa......AggAacGggCcaGag
2210 2220 2230 2240 2250
| | |||||| | || | ||| || || ||| || || || ||
MuERVC ActAagAttTtaGatAcaTtcAcaGgtGat...AagGaaGttTatAgaAaaGgtAgaGga
950 960 970 980 990
2090 2100
MoMLV GatAgaCagGgaGga..............................GaaCgaAggAgg...
| ||| ||| ||| | ||
GALV GgtAggCagAcaGggAacCtgAgcAacCagGcaAagAagAcaCctAggGatGgaAga...
2030 2040 2050 2060 2070
| ||| ||||| ||||| ||||| ||||| | | || | || |||
MuRVY AagGgtCagTcaGggTacCtgCgcAacAggGcaAgaAgaCccCcaGgaGaaCagAga...
2490 2500 2510 2520 2530 2540
|| | || ||||||||||| |||||| || | ||| || | | |||
MuRRS AatAgaTAGAcaGggTacCtgGgcAacAagGaaCccAga...CctAaaAgaAgaAgaTct
2260 2270 2280 2290 2300 2310
| ||| ||||||||||||||||||||| | || ||| ||| | | |||
MuERVC AgtAggCagAcaGggTacCtgGgcAacAcaGgaCtgAgaAgaCctCagAacTccAgaGaa
1000 1010 1020 1030 1040 1050
2110 2120 2130 2140 2150
MoMLV .........TccCaaCtcGatCgcGacCagTgtGccTacTgcAaaGaaAagGggCacTgg
| | ||| || |||||||| || ||||| ||||| ||||| || |||
GALV .........CctCcaCtaGacAaaGacCagTgcGcaTacTgtAaaGagAagGgcCatTgg
2080 2090 2100 2110 2120 2130
|||||||| || |||||||| ||| ||||||| || | || | |||||
MuRVY .........CctCcaCttGagAaaGacCacTgcAcaTacTgcAagAaaAaaGaaTatTgg
2550 2560 2570 2580 2590
| ||||| ||||| || | || |||||| |||||| | || ||
MuRRS ...GtcCagAagAttTtaGagAagGacCaaTgtGccTatTgcAagGaaAaaGgaCatAgg
2320 2330 2340 2350 2360
|| | | || |||||||||||||| | | ||| ||||| ||||| ||
MuERVC CctTcaCaaCcaCctCtgGatAagGacCaaTgtGcaTgcTacAaaGaaAagGgaCacTgg
1060 1070 1080 1090 1100 1110
2160 2170 2180 2190 2200 2210
MoMLV GctAaaGatTgtCccAagAaaCcaCgaGgaCctCggGgaCcaAgaCccCagAccTccCtc
|| | ||| |||||| ||| | | | | | || || |
GALV GcaAgaGaaTgtCccCgaAaaAaa.........CacGtcAgaGaaGccAagGttCtaGcc
2140 2150 2160 2170 2180
|| ||||| || || ||| | || | | ||| ||| ||
MuRVY GccAgaGacTgcCcaAaaAag............AagCagAggGgcCcaAagTatCtgCcc
2600 2610 2620 2630 2640
|| |||| |||||||| || ||| |||| ||| ||| ||| |
MuRRS GcaCgaGaaTgcCcaAagAaaA...........AagGgaAggGccCctAagGtcCtgAct
2370 2380 2390 2400 2410
||| |||| ||||| | ||| | || | || |||||||| ||
MuERVC GcaAgaGacTgcCccAgaAaaGagAca......GatAccAgaCcaCccAagGtcCttAcc
1120 1130 1140 1150 1160 1170
2220 2230 2240 2250 2260 2270
MoMLV CtgAccCtaGatGacTAG...GgaGgtCagGgtCagGagCccCccCctGaaCccAggAta
|||||| ||||| || |||||||| ||| |||| ||| ||||| ||| ||
GALV ......CtaGatAacTAG...GggAgtCagGgtTcgGacCccCtcCccGaaCctAggGta
2190 2200 2210 2220 2230
||| || || || |||| ||| |||| |||||||||| | |||||||||
MuRVY Tt....GaaGaaGacAag...GgaAgtCggGgcTcgGtcCccCtcCccAagCctAggGta
2650 2660 2670 2680 2690
| |||| || || | || |||||||| | ||||||||| |||||||||||
MuRRS Ctg...AaaGatGatAaa...TggAgaCggGgcTcaGggCccCtcCccGagCctAggGta
2420 2430 2440 2450 2460 2470
|| | ||| | | ||||| ||||||||| ||||||||| || ||||||||
MuERVC CtaGaaGatGatAacTAG...GggAgaTggGgcTcaGacCccCtcCccAagTctAggGta
1180 1190 1200 1210 1220 1230
Gag Ter
2280 2290 2300 2310 2320 2330
MoMLV AccCtcAaaGtcGggGggCaaCcc...GtcAccTtcCtgGtaGatActGggGccCaaCac
|| || | || | |||| ||| | |||||||| || || || || ||||
GALV AcaCtgActGtgGagGggAccCcc...AttGagTtcCtgGtcGacAccGgaGctGaaCat
2240 2250 2260 2270 2280
|| | ||||||||||| ||| || | || || | ||||| ||||||||| ||
MuRVY ActCacTctGtgGagGggTtaCccCc.GttAatTttCtaAtaGacAcaGgaGctGaaTat
2700 2710 2720 2730 2740 2750
|| | ||| | | | || | ||||| |||| |||||||| || ||| ||
MuRRS AccCtgAtgGtgAaaGagActCca...AtgGatTttTtaAttGacAcaGggGcaGaaCat
2480 2490 2500 2510 2520
||||| | ||| | | ||| || | |||||| | |||| || || ||||| |
MuERVC AccCtaActGtgGagGggAccCcc...AcgGatTtcCttGttGatAccGgaGcaGagTtt
1240 1250 1260 1270 1280
2340 2350 2360 2370 2380 2390
MoMLV TccGtgCtgAccCaaAatCctGgaCccCtaAgtGatAagTctGccTggGtcCaaGggGct
|| || |||||||| ||| || | | | || |||| ||
GALV TcaGtaTtgAccCaaCccAtgGgaAaaGtaGggTccAgaCggAcgGtcGtgGaaGgaGcg
2290 2300 2310 2320 2330 2340
||||| ||||| |||| | ||| || |||| || | || | || |||
MuRVY TcaGtcTtgActGaaCctTtaGgaCaaTtaGgaTcaAagAagAttTtaGttAtcCcaGcc
2760 2770 2780 2790 2800 2810
|| || |||| | || | || ||||| | || | | |||| || ||||
MuRRS TctGtgTtgAaaCatCcaCtgAgaAaaTtaAaaAatAaaAgaAccAtaGtgAttGgaGcc
2530 2540 2550 2560 2570 2580
|| || ||||| | |||||| | ||||| | || || | ||| |||| || || ||
MuERVC TcaGtcCtgAaaGagCcaCtgGggAaaTtgAggAacAagAaaActGtaGtaAtcGgcGct
1290 1300 1310 1320 1330 1340
2400 2410 2420 2430 2440 2450
MoMLV ActGgaGgaAagCggTatCgcTggAccAcgGatCgcAaaGtaCatCtaGctAccGgtAag
|| || | ||| || | ||||||||| | | || | | | |
GALV AcaGgcAgcAagGtcTacCccTggAccAcaAaaAgaCttTtaAaaAttGgaCatAaaCaa
2350 2360 2370 2380 2390 2400
|| || |||||| | || |||||||| || ||||| ||||| | || ||| | || ||
MuRVY ActGgtAgcAagCttTatCccTggAcaAccAaaAggAttTtaGacAtaGgaAaaAatAaa
2820 2830 2840 2850 2860 2870
|||||| || | || |||||||| || | | | | |||| | || ||| ||
MuRRS ActGgtCagAaaCaaTacCccTggAccActGcaTgcActGtaGatCtgGggAaaGgcCaa
2590 2600 2610 2620 2630 2640
||||||||||||||||| | |||||||||| | | | ||| |||| | | |||||
MuERVC ActGgtCagAaaCaaTatTctTggAccActGatAggAaaCttGatTtgGgaAgaAgcCaa
1350 1360 1370 1380 1390 1400
2460 2470 2480 2490 2500 2510
MoMLV GtcAccCacTctTtcCtcCatGtaCcaGacTgtCccTatCctCtgTtaGgaAgaGatTtg
|| |||||||| ||||| |||| || || || ||||||||| || || || |
GALV GtgAccCacTccTtcCtgGtcAtaCccGagTgcCctGctCctCtgTtgGgcAggGacCtc
2410 2420 2430 2440 2450 2460
||||| || || || || || ||||| |||||||| || || ||| | ||| |||||||
MuRVY GtgAcgCatTctTttCttGtgAtaCctGagTgcCcaGcaCccCtgCtaGgcTggGacCtt
2880 2890 2900 2910 2920 2930
|||| ||||| || | || || |||||||| || |||| || ||||| | || ||
MuRRS GtgAgtCatTccTtcTtgGtcAttCctGagTgtCccAcaCcgCttCtaGgaAgaGatCtg
2650 2660 2670 2680 2690 2700
|| ||||| |||| | ||||||||||| |||||||| || | |||| ||||| |
MuERVC GtaGctCatTacTtcCtcGtcAttCctGaaTgtCccAccCcaTtgTtaGggAgaGacTta
1410 1420 1430 1440 1450 1460
2520 2530 2540 2550 2560 2570
MoMLV CtgActAaaCtaAaaGccCaaAtcCacTttGagGgaTcaGgaGctCagGttAtgGgaCca
|| || |||||||| ||||| ||||| ||| | || | ||||| | | |
GALV CtaAccAaaCtaAagGccCagAtcCagTttTccGctGagGgcCcaCagGtaAcaTggGga
2470 2480 2490 2500 2510 2520
| ||| | || || || |||||||| | |||| || || ||||| |||||
MuRVY TgtAaaAaaTtgAaaGcaCaaGtcCagTttActTctGatGgaCctGagGtaTcaTggAag
2940 2950 2960 2970 2980 2990
| ||||| || || || || ||||| | || || || ||| | ||| |
MuRRS ...ActAaaTtaAagGccCagAtcGgaTttAccTAAGaaGggCcgAgaGtaActTggGaa
2710 2720 2730 2740 2750 2760
| |||||||| ||||| || || | | ||||| | ||| |||| ||
MuERVC CtaTcaAaaTtaAaaGccCaaAtaAacTtcTctTtgGaaGgaActTcaGtcTctTGACaa
1470 1480 1490 1500 1510 1520
2580 2590 2600 2610 2620 2630
MoMLV AtgGggCagCccCtgCaaGtgTtgAccCtaAatAtaGaaGatGagCatCggCtaCatGag
| || || |||||| | ||||| || | || ||||||||
GALV Gaa...CgcCctActAtgTgcCtgGtcCtaAacCtgGaaGaaGaaTacCgaCtaCatGaa
2530 2540 2550 2560 2570 2580
| | ||| | || |||| | ||||||||||| | || || |||
MuRVY AagAatCca...GtgGcaTgcTtaGttTtaAatTtaGaaGaaGaaTatCacCtcCacGaa
3000 3010 3020 3030 3040 3050
|| | | ||||| | | | || |||||||| | | || |||
MuRRS Tct...CccAccTccGtaGtcTtaGccCtgCagCttGagGaaGaaTacCgaTtgCatGaa
2770 2780 2790 2800 2810 2820
|| | ||| || | ||||| | | | || |||||||| |||| |||||
MuERVC Gtc...CctAtcTctAtaAttTtaGctTtaAacTtaGaaGaaGaaTatAgaTtaCatGag
1530 1540 1550 1560 1570 1580
2640 2650 2660 2670 2680 2690
MoMLV AccTcaAaaGagCcaGatGttTctCtaGggTccAcaTggCtgTctGatTttCctCagGcc
| || | ||| | | | | ||||| ||| || |
GALV AagCcaGtaCcc......TccTctAtcGacCcaTccTggCtcCagCttTtcCccActGta
2590 2600 2610 2620 2630 2640
|| | | | | | ||| || ||
MuRVY CagAagTctGagAct......TtaCccTttAaaGaaCgaTtgAcaGgtTttCcaGagGtt
3060 3070 3080 3090 3100
| | || | | | ||||| | ||||| | ||| || |
MuRRS GgcAtaAagCaaAcaGagGtgCcaGacCtaAaaGacTggTtgActGctTtcCctAgaGca
2830 2840 2850 2860 2870 2880
| | | || | | |||||| | ||| |||
MuERVC CctCaaGccCcaTcaAgaAaaGtaCtaGaaGggAccTggTtaGagAgaTatCctCaaGct
1590 1600 1610 1620 1630 1640
2700 2710 2720 2730 2740 2750
MoMLV TggGcgGaaAccGggGgcAtgGgaCtgGcaGttCgcCaaGctCctCtgAtcAtaCctCtg
||||| |||| | ||||||||||| || || | || || | || ||
GALV TggGcaGaaAgaGccGgcAtgGgaCtaGccAatCaaGtcCcaCcaGtgGtaGtaGagCta
2650 2660 2670 2680 2690 2700
|||||||| || || |||| | |||| | ||||| ||||| |||| ||||||
MuRVY TggGcaGagCagGctGggAtgGaaTtaGctAggCaaGtgCcaCccAacAtaGtcGagCta
3110 3120 3130 3140 3150 3160
||||||||| || || |||||| | ||| ||| || || | || | ||
MuRRS TggGcaGagActGcaGgcAtgGaaAtgGctGtcAgaGttCccCctGtgGttGtgGgaCtg
2890 2900 2910 2920 2930 2940
||||||||||||| ||| ||| | ||| || || ||| | | ||||| |||
MuERVC TggGcaGagActGgaGgtAtgAgaGagGcaAagAggGtgCccTccAtcAttGtgAtgCtg
1650 1660 1670 1680 1690 1700
<- Begin pol domain
2760 2770 2780 2790 2800 2810
MoMLV AaaGcaAccTctAccCccGtgTccAtaAaaCaaTacCccAtgTcaCaaGaaGccAgaCtg
| | || | | || ||| | | |||||| || ||| ||||||| |
GALV AgaTcaGgtGccTcaCcaGtgGctGttCgaCaaTatCcaAtgAgcAaaGaaGctCggGaa
2710 2720 2730 2740 2750 2760
| | | |||| ||| | | || | ||||| || ||||| ||| ||| |
MuRVY AaaAtgGctGccAaaCccAttTcaGtcAggCaaTacCccAtgAgtCaaGggGctAaaAac
3170 3180 3190 3200 3210 3220
|| | || ||| | || || ||| ||||| || ||||| | || | | |
MuRRS AagAcgGatGcaAccCctAtaGgaGtgCaaCaaTatCcaAtgAgcCgtAaaGcaAgaGat
2950 2960 2970 2980 2990 3000
|| || | || || ||||| | | |||||| || |||| | | || |||
MuERVC AaaActGgtGtgActCctAtcTgg.taTGACaaTacCccAtgAacAaaGagGccCaaGag
1710 1720 1730 1740 1750 1760
2820 2830 2840 2850 2860 2870
MoMLV GggAtcAagCccCacAtaCagAgaCtgTtgGacCagGgaAtaCtgGtaCccTgcCagTcc
|| |||| |||||||| |||| | | |||| || | |||| ||||| | |||
GALV GgtAtcAgaCccCacAtcCagAagTtcCtaGacCtaGggGtcTtgGtgCccTgtCggTcg
2770 2780 2790 2800 2810 2820
| || |||| || ||||||| | ||| | | || | ||||| || || | |||
MuRVY AgcAttCgaCcaCatAtcCagAgaCtgCtaTAACagGgtAtaTtgGtcCcgTGACagTcc
3230 3240 3250 3260 3270 3280
| || | |||||||| |||||||| || || ||||| ||||| || || |||||
MuRRS GgaAtcAggCcaCatAttCagAgaCtaTtaCaaTtaGgtAttTtgGtaCctTgcCagTca
3010 3020 3030 3040 3050 3060
|| ||||| || || ||||| || | | | | ||||||| | |||||
MuERVC GgcAtcAgaCctCacAttCaaAg....GtgAggTctGatGttTtgGtcAt.TatCagTct
1770 1780 1790 1800 1810
2880 2890 2900 2910 2920 2930
MoMLV CccTggAacAcgCccCtgCtaCccGttAagAaaCcaGggActAatGatTatAggCctGtc
|||||||| || || |||||||| || || || |||||||| ||||| ||| |||| ||
GALV CccTggAatAccCctCtgCtaCctGtaAaaAagCcaGggAccAatGacTatCggCcaGtt
2830 2840 2850 2860 2870 2880
| ||||||||||| | || || || || || ||||| ||||||||| ||| ||
MuRVY CatTggAatAccCccTtcCtgCcaGtgTgtAaaCctGggAcaAatGacTatGtgCctGtc
3290 3300 3310 3320 3330 3340
| |||||||| || || ||| | || |||||||| || | |||||| || |||
MuRRS CccTggAatActCctTtaCtgTcgGtaAagAaaCctGgcAcgAgtGacTacTGACcaGtc
3070 3080 3090 3100 3110 3120
|||||||||||||| || || | || || || || ||||| | ||| || | |||||
MuERVC CccTggAatActCcaTtgCtaCcaGttAaaAagCcaGgcActAatGatTatCggCcaGta
1820 1830 1840 1850 1860 1870
2940 2950 2960 2970 2980 2990
MoMLV CagGatCtgAgaGaaGtc...AacAagCggGtgGaaGacAtcCacCccAccGtgCccAac
|| || ||||||||| | || || |||| | || || || ||||| || || |||
GALV CaaGacCtgAgaGaaAtt...AatAaaAggGtaCagGatAttCatCccAcaGtcCcaAac
2890 2900 2910 2920 2930
|| ||| | ||| || | ||||| |||||||||| ||||| | || || || |||
MuRVY CagGacTtaAgaAaaGtcC..AatAagCggGtaCagGacAttCaaTcaActGtgCccAac
3350 3360 3370 3380 3390 3400
|| ||| | ||| | ||| |||||| |||| || || ||||| ||||||| || ||
MuRRS CaaGacCtgAgaGagGtc...AatAagAggGtcCaaGatAttCacCcaActGttCctAat
3130 3140 3150 3160 3170 3180
|||||| | ||||| || || || || || ||||||||||| || ||||| |||||
MuERVC CaaGacTtaAgaGaaGta...AacAaaAgaGtaCaaGatAttCatCctActGtcCctAac
1880 1890 1900 1910 1920 1930
3000 3010 3020 3030 3040 3050
MoMLV CctTacAacCtcTtgAgcGggCtcCcaCcgTccCacCagTggTacActGtgCttGatTta
|||||||| || |||| || || || | | |||||| | || | ||| |
GALV CctTacAatCttCtgAgtTccCttCcgCctAgcTatActTggTacTcaGtcTtaGatCtc
2940 2950 2960 2970 2980 2990
||| |||| | ||||||||| | || ||| | |||||| | ||| | ||| |
MuRVY CctCacAacTtgCtgAgtTccTtaCcaCctGaaCggTccTggTacActGtcCtgGatTtg
3410 3420 3430 3440 3450 3460
|| | ||| | || || || | || || || | ||||| || || || |||||
MuRRS CccTatAacCtcCtcAgcTcaCtcCctCcgGagCaaAaaTggTatAcaGtaCttGatTta
3190 3200 3210 3220 3230 3240
||||| | || ||||| || ||||| || || | ||||||||| ||||| || |
MuERVC CccTacA.tCtaCtcAgtTctCtcCccCctGacAgaCaaTggTatAtgGtaCtgGacCtg
1940 1950 1960 1970 1980 1990
3060 3070 3080 3090 3100 3110
MoMLV AagGatGccTttTtcTgcCtgAgaCtcCacCccAccAgtCagCctCtcTtcGccTttGag
|||||||||||||||||||| || || || |||| ||| ||||| || ||||| || |||
GALV AagGatGccTttTtcTgcCtcAggCtaCatCccAacAgcCagCcgCtgTtcGcgTtcGag
3000 3010 3020 3030 3040 3050
|| |||||||||||||| ||||| |||| | ||||| || | |||| || || |||
MuRVY AaaGatGccTttTtcTgtCtcAgaTtaCacCtgAacAgtCaaCttCtgTgtGctTttGag
3470 3480 3490 3500 3510 3520
|||||||| || || || || | ||||| | ||| || | | | || ||||||
MuRRS AaaGatGctTtcTttTgcCtgAagTtaCatCccTccAgcCagCccAtaTtcGccTttGag
3250 3260 3270 3280 3290 3300
|| || | |||| ||||| || |||||||| || | || || || ||||||
MuERVC AagGacAc..tcTtcTgcCtaAaaCtaCatCccAtgAgtTggGtaAtcTttGctTttGag
2000 2010 2020 2030 2040 2050
3120 3130 3140 3150 3160
MoMLV TggAgaGatCcaGagAtgGgaAtcTcaGgaCaaTtgAccTggAccAgaCtcCcaCag...
|||| ||| ||||| | || | | |||| || |||||||||| | || |||||
GALV TggAaaGacCcaGaaAaaGgtAacAcaGgtCagCtgAccTggAcgCggCtaCcaCaa...
3060 3070 3080 3090 3100 3110
||| |||| ||| ||| | || |||||||| | | ||| |||| | |||
MuRVY TggGggTacCctGaaGgaGgaTatAcgGgtCagCtaAttTtgActAggCtgCgaCagA..
3530 3540 3550 3560 3570 3580
||| | | ||||| ||| | ||||| || | | | || || | |||
MuRRS TggAgaGatCctGacActGgaCaaAcgGgaCaaTtgAccTggAtgTggTAACccCag...
3310 3320 3330 3340 3350
|||||||| || || | ||||| | |||||| | || |||| | || ||
MuERVC TggAgaGacCcaGatTcgGgaCagGctGgaCaaCtaActTggAcaCatTtgCctCaa...
2060 2070 2080 2090 2100
3170 3180 3190 3200 3210 3220
MoMLV GgtTtcAaaAacAgtCccAccCtgTttGatGagGcaCtgCacAgaGacCtaGcaGacTtc
|| ||||| ||| |||||| || || || ||||| || ||| |||| | || |||
GALV GggTtcAagAacTctCccActCtcTtcGacGagGccCtcCacCgaGatTtgGctCccTtt
3120 3130 3140 3150 3160 3170
|| ||||| || || |||||| | || || || | |||||| | | |||||
MuRVY GgaTtcAaaAatTcaCccActTttTttGatGaaGtgGtcCacCacAacCttAtgTccTtt
3590 3600 3610 3620 3630 3640
| |||||||| || ||||| |||||||||| | | || | | | |||||
MuRRS GagTtcAaaAacTccCccAccCttTttGatGagGctCtaCatCgaGatTtaGccTccTtc
3360 3370 3380 3390 3400 3410
| ||||| ||||| || || || ||||||||||| || || | || || || |||
MuERVC GgaTtcAagAacTctCctActCtcTttGatGagGccCtcCacTggGacTtgGcaCagTtc
2110 2120 2130 2140 2150 2160
3230 3240 3250 3260 3270 3280
MoMLV CggAtcCagCacCcaGacTtgAtcCtgCtaCagTacGtgGatGacTtaCtgCtgGccGcc
|| || |||| | || | | || || || ||||| ||| | || ||||||||
GALV AggGccCtcAacCccCagGtgGtgTtaCtcCaaTatGtgGacGacCtcTtgGtgGccGcc
3180 3190 3200 3210 3220 3230
|||| | |||| ||| | | || | |||| || || | | | || ||
MuRVY AggGaaCagAacCtcCaaAttTctCtcCtgGagTatGgaGatGatTtaAtcCttGcaGct
3650 3660 3670 3680 3690 3700
| | | ||| ||| | |||| || | |||| ||||| || ||||||| ||
MuRRS CgaGctGaaAacTccCagGtaActCtgCttCaaTatGttGatGacTtgCtcCttGctGca
3420 3430 3440 3450 3460 3470
| | |||||| |||| | |||| ||||| |||||||||||| ||| ||||||||
MuERVC AgtTcaGaaAacCccCaaAttTctCtcCttCagTatGttGatGacCggCttCttGctGcc
2170 2180 2190 2200 2210 2220
3290 3300 3310 3320 3330 3340
MoMLV ActTctGagCtaGacTgcCaaCaaGgtActCggGccCtgTtaCaaAccCtaGggAacCtc
| | | ||||||| || |||| || | | || ||||| || | || |
GALV CccAcaTatGaaGacTgcAaaAaaGgaAcaCagAagCtcTtaCagGagTtaAgtAagTtg
3240 3250 3260 3270 3280 3290
| || | ||| ||| | | | ||||||| || | || |||| | |||
MuRVY TcaAccCagGaaCtgTgcCttGacAggAtcAagAagCttCtaAatGaaAaaAgtGaaTtg
3710 3720 3730 3740 3750 3760
| || | | ||| | | | ||||| | ||| ||| |||| |||
MuRRS AccAcgGa.AgaGaaTgcTggCagGgaAccAagAgaTtgCtaGcaGaaCtgGgtGagTtg
3480 3490 3500 3510 3520 3530
||||| | ||| ||| | | ||| | ||| ||| || |||||| || | || |||
MuERVC AccAccAagCaaGagTgcAgaCtaGgaCctGagAaaTtaCtgGcaGaaTtgAgcGaaTtg
2230 2240 2250 2260 2270 2280
3350 3360 3370 3380 3390 3400
MoMLV GggTatCggGccTcgGccAagAaaGccCaaAttTgcCagAaaCagGtcAagTatCtgGgg
||||| |||| ||||| ||||| ||||| | ||||||| | | |||| |||||||||
GALV GggTacCggGtaTcgGctAagAagGccCagCtcTgcCagAgaGaaGtcAccTatCtgGgg
3300 3310 3320 3330 3340 3350
| |||| ||||||| || ||||| ||||| | || | ||||| || ||
MuRVY GtgTac........tCctAagAaaGctCagCtaTgcCatAtgGacTtgAccTacCtaGga
3770 3780 3790 3800 3810
| ||| | |||| ||||| |||||||| || ||||| || |||||| ||
MuRRS GgtTacCggGccTctGctAaaAaaGccCagCtaTgtCagAtgGaaGtgGtcTacCtgAga
3540 3550 3560 3570 3580 3590
| ||| ||| | |||| |||| |||| | || |||| ||||| |||| || |
MuERVC AgaTacAagGcaCccActAatAaaGtcCagAttTgcCagAcaGaaGtaAccTacTtgGgt
2290 2300 2310 2320 2330 2340
3410 3420 3430 3440 3450 3460
MoMLV TatCttCtaAaaGagGgtCagAgaTggCtgActGagGccAgaAaaGagActGtgAtgGgg
|| || || || || || | |||||||| || ||| |||| | ||||| |||
GALV TacCtaCtcAagGaaGgaAaaAgaTggCtaAccCcaGccCgaAagGctActGttAtgAaa
3360 3370 3380 3390 3400 3410
||| ||| |||||||| ||| | || ||| ||||| ||||| ||| |
MuRVY TacTccCtcCgaGaaGgaAagCagTggTtcTccGaaGctGgaAagAagActGtgAtgCag
3820 3830 3840 3850 3860 3870
|| | | || || | ||| | |||| | | || ||| |||| | |||||||| ||
MuRRS TatActC..CggGatGaaAaaCggTggCtgAcaGagGctAgaAaaAggActGtgActCaa
3600 3610 3620 3630 3640 3650
||||||| ||| | |||| |||||||||||| ||| |||| |||||||||||||
MuERVC TatActCtcAggGgaGggAaaCagTggCtgAcaGaaGctCagAaaAagActGtgActCaa
2350 2360 2370 2380 2390 2400
3470 3480 3490 3500 3510 3520
MoMLV CagCctActCcgAagAccCctCgaCaaCtaAggGagTtcCtaGggAcgGcaGgcTtcTgt
||| ||| | |||||| |||| | | || || ||||| || || || |||||
GALV AtcCctGttCctAcgAccCccAgaCagGtcCgtGaaTttCtaGgcActGccGgaTtcTgc
3420 3430 3440 3450 3460 3470
||||| || || || | |||| || ||||| ||||| || | || || || ||
MuRVY AtcCcaAccCccAccActCtgTGACaaGtaCgtGagTttCtgGgaAagGcaGgcTttTgt
3880 3890 3900 3910 3920 3930
|| ||||| || | |||| |||| || | || || |||| | || || || ||
MuRRS AtaCcaActCcgGctActCcaAgaCagGtgAgaGaaTtcTtgGgcActGctGggTtcTgc
3660 3670 3680 3690 3700 3710
|| || | || | || | | |||||||| ||||| |||||| |||||||| ||
MuERVC AtcCccAtcCcaAcaAccTcgAagCagGtgAggGaaTttCtgGgcAtgGctGggTttTgt
2410 2420 2430 2440 2450 2460
3530 3540 3550 3560 3570 3580
MoMLV CgcCtcTggAtcCctGggTttGcaGaaAtgGcaGccCccTtgTacCctCtcAccAaaAcg
| |||||||||||||||||||| |||| || ||||||||||| || || ||| |
GALV AggCtcTggAtcCctGggTttGctTccCtgGctGcaCccTtgTacCccCtaAcaAaaGag
3480 3490 3500 3510 3520 3530
|| ||||| || || | || | |||| ||||| ||||||| || || |||||
MuRVY AgaCtcTGAAtaCcaGagTccAcaAtgTtgGcgGcaCctCtgTacCcaCtcActAaaGaa
3940 3950 3960 3970 3980 3990
||||| || ||||| | || |||| |||| || || | ||| || || |||
MuRRS AgaCttTggAtaCctGggTttAcaAcaCtgGctGccCcc...CatGtaCtgAccAagGaa
3720 3730 3740 3750 3760 3770
|| || ||||| || | ||| | || ||||| ||||| | || || || ||
MuERVC AggCtcTggAtcCcaAgcTttGccActCtgGcaGccCcaCtcTacCccCttActAaaGag
2470 2480 2490 2500 2510 2520
3590 3600 3610 3620 3630 3640
MoMLV GggActCtgTttAatTggGgcCcaGacCaaCaaAagGccTatCaaGaaAtcAagCaaGct
| | | |||| |||| || || || |||| | | | | || || ||||
GALV AgcAtcCctTttAttTggActGagGaaCatCagCagGctTttGacCacAtaAaaAaaGcc
3540 3550 3560 3570 3580 3590
| |||| || | ||||| |||||||| || | || ||| || || ||| ||
MuRVY AaaGtcCcgTtcAccTggAcaGagGaaCacCaaAaaGccTttAacAgcAcaAagGctGct
4000 4010 4020 4030 4040 4050
| | || | ||| ||
MuRRS AgtGgaGaaTttAga.....................................agGagGcc
3780 3790
| || || | | |||||
MuERVC ActGcgActTtcTcaTggAccCccAtaCacCaaGagGccTttAaaGagAttAaaAagGcc
2530 2540 2550 2560 2570 2580
3650 3660 3670 3680 3690 3700
MoMLV CttCtaActGccCcaGccCtgGggTtgCcaGatTtgActAagCccTttGaaCtcTttGtc
| || | ||||| || ||| | ||||| | || ||||| || || | | |
GALV TtgCtgTcaGccCctGcaTtgGccCtcCcaGacCtcAccAagCcaTtcActCtaTatAta
3600 3610 3620 3630 3640 3650
|||| || ||| || |||||||| ||||| | || ||||| ||||| |||| |
MuRVY CtgCttGcaAccCagGctTtgGccCtgCcaGatTtgActAagCctTtcAccAtaTacGtt
4060 4070 4080 4090 4100 4110
||||| | | | || ||||| ||||||||| | || ||||| |||| | | || |||
MuRRS CtgCtgActGcgCcaGc.TtgGcaCtgCcaGatCtaAccAagCccTtcAtcCtcTatGtt
3800 3810 3820 3830 3840 3850
|||| | ||| ||||| | || || | || || || ||||| |||| || |||||
MuERVC TtgCttAgtGcaCcaGcaCtaGccCttCtgGacCtgActAagCctTtcActCtaTatGta
2590 2600 2610 2620 2630 2640
End pol----><---Begin RNAse domain
3710 3720 3730 3740 3750 3760
MoMLV GacGagAagCagGgcTacGccAaaGgtGtcCtaAcgCaaAaaCtgGgaCctTggCgtCgg
|| |||| ||| ||| || || || || || | | ||||| ||||| |||
GALV GatGagAgaGccGgcGtgGccCggGgaGtgCtcActCagActTtaGgaCccTggCggCgg
3660 3670 3680 3690 3700 3710
|||||| ||| || || ||||| |||| || ||||||||| | || |||||| | |
MuRVY GatGagCcaGctGgaGtaGccCgcAgaGtcCtgActCagActCtgGggCccTggAagAg.
4120 4130 4140 4150 4160 4170
|||||| || || || ||| | ||||| || ||||| |||| ||||| ||| ||||
MuRRS GatGagAggGcgGggGtgGccAgaAgaGttCttTctCagGctCtaGggCcgTggGagAgg
3860 3870 3880 3890 3900 3910
|| | || || || | || ||| | | || | || ||||| ||||| | | | |
MuERVC GacAaaAgtGcaGgaAtaGcgAgaGggTtcCtgAccCaaGctCtgGggCcaTAGAaaCga
2650 2660 2670 2680 2690 2700
3770 3780 3790 3800 3810 3820
MoMLV CcgGtgGccTacCtgTccAaaAagCtaGacCcaGtaGcaGctGggTggCccCctTgcCta
|| || || || || || ||||| || || || || || |||||||| | |||||
GALV CcaGtaGcaTatCtaTcaAaaAaaCtgGatCcgGtgGccAgcGggTggCcaAccTgcCtg
3720 3730 3740 3750 3760 3770
||||| || || || || |||||| |||| || || ||||| | ||||| |||||||
MuRVY CcaGtgGccTacCtgTctAaaAaaTtgGacCcaGttGccAgtGaaTggCccTccTgcCta
4180 4190 4200 4210 4220 4230
| ||||| || ||||||| || |||||||||| ||||||| ||||||| | | ||
MuRRS CtgGtgGcaTatTtgTctAagAagCtgGacCcaGtgGccAgtGgaTggCccAcaCgtTta
3920 3930 3940 3950 3960 3970
| ||||| || ||||| | || | ||||||||||||||||| ||||| | | |||
MuERVC CctGtgGccTacTtgTc.AtaAaaTtaGacCcaGtgGccAgtGggTggCcaTctTgcTta
2710 2720 2730 2740 2750 2760
3830 3840 3850 3860 3870 3880
MoMLV CggAtgGtaGcaGccAttGccGtaCtgAcaAagGatGcaGgcAagCtaAccAtgGgaCag
||| ||||| | || | || || || || | ||| ||||| |||||||
GALV AaaGcgGttGcaGcaGtaGcaCtcCttCtcAaaGacGctGatAagTtaAccTtgGgaCaa
3780 3790 3800 3810 3820 3830
||||| | | |||||||| || ||| | ||||| ||| ||| | || | || ||
MuRVY AaaGccAtcActGcaGtaGccCtaCttGttAaaGatActGgcAagCttActCtaGgtCag
4240 4250 4260 4270 4280 4290
|| ||| | || ||||||||||||| ||||| ||| ||| ||| | ||||| || |||
MuRRS AagGccGttGctAcaGtaGccCtaCtcGttAagGatGctGacAaaTtaActCtgGgaCag
3980 3990 4000 4010 4020 4030
|| || | || | || || ||||| | || |||||||||||| | ||||| || ||
MuERVC AaaGctAtcActGctGtgGcaCtaCttCtcAaaGatGctGacAaaCtgActCtaGgtCaa
2770 2780 2790 2800 2810 2820
3890 3900 3910 3920 3930 3940
MoMLV CcaCtaGtcAttCtgGccCccCatGcaGtaGagGcaCtaGtcAaaCaaCccCccGacCgc
| | | || ||||| | || | || ||||||||||||||
GALV AatGtgActGtgAttGctTccCatAgcCtcGaaAgcAtcGtgCggCaaCccCccGacCgg
3840 3850 3860 3870 3880 3890
|||||| || || || ||||| | | || || || | || ||||| ||||
MuRVY CatGtgAgtG.aAtcActCccCatGcgTtaAagAgtAttGtaTGACagCccCctGacCat
4300 4310 4320 4330 4340 4350
|| | | || | | | ||||| | | | || ||| | | |||||| | ||||
MuRRS CaaAtaActGtaGtaGccCccCacTctCttGaaAgcAttAtcCgtCagCccTcaGacCga
4040 4050 4060 4070 4080 4090
| || | ||||||| |||| | | | ||||||||| | | || || | || |
MuERVC CgaActAtaGtaGtaGacCcc.atGccAtaGaaAgcAttGttAgaCaaCcaCctGatCac
2830 2840 2850 2860 2870 2880
3950 3960 3970 3980 3990 4000
MoMLV TggCttTccAacGccCggAtgActCacTatCagGccTtgCttTtgGacAcgGacCggGtc
||| | |||| ||| | |||||||| || ||| | |||| || | || ||||
GALV TggAtgAccAatGccAgaAtgActCatTacCagAgcCtgCtgTta...AatGaaAggGta
3900 3910 3920 3930 3940 3950
|||||||| |||||| | ||||| || |||||||||||| || || ||||| | ||
MuRVY TggAtgAcaAatGccCggAtgAccCacTacCagAgcCtgTtgCta...AatGacCgaGtg
4360 4370 4380 4390 4400
||||||||||||||| |||||| ||||||||||| |||||||| | ||| | ||
MuRRS TggAtgAcaAatGccTAGAtgActCacTacCagAgtCtgTtgCtg...ActGaaTggGtc
4100 4110 4120 4130 4140 4150
|||||||| ||||| |||| || || ||||| || || ||| ||||| | ||
MuERVC TggAtgActAatGctCgcAtgAtcCatTatCagAgcCtcTttCtg...ActGagAgaGtg
2890 2900 2910 2920 2930 2940
4010 4020 4030 4040 4050 4060
MoMLV CagTtcGgaCcgGtgGtaGccCtgAacCcgGctAcgCtgCtcCcaCtgCctGagGaa...
||| | || | | ||| ||||| ||||| || || ||| | ||||
GALV TcgTttGcgCccCctGctGtcCtaAacCcaGctAccCtaCttCcaGtcGagTcgGaaGcc
3960 3970 3980 3990 4000 4010
| ||||| | ||||| ||| || || | ||||| || || | | |
MuRVY ActTttGccCtaCctGccAtcCacAatCctAccAccCtcCtcCccAagAcgGatGccTct
4410 4420 4430 4440 4450 4460
|||| | ||||| || | ||| ||| ||
MuRRS GtgTttGttCctCctGctAttCtcAacCctGcc...........................
4160 4170 4180
|||| || |||||| | || || |||||
MuERVC CagTttAcaCccCctGctGtcCtaAatCctGctAccTtgCtgCcaTAAGtcTacGacTcc
2950 2960 2970 2980 2990 3000
4070 4080 4090 4100 4110 4120
MoMLV GggCtgCaaCacAacTgcCttGatAtcCtgGccGaaGccCacGgaAccCgaCccGacCta
| |||| ||| || ||||| ||||||| ||||| |||| ||||||
GALV AccCcaGtgCacAggTgcTcaGaaAtcCtcGccGaaGaaActGgaActCgaCgaGacCta
4020 4030 4040 4050 4060 4070
||| || ||| || | | | ||| || |||||||||||| | || || ||
MuRVY AccTggGtaCacCaaTgtGctGtaTacCtgGctGaaGaaActGgaTcgAgaAagGatCtg
4470 4480 4490 4500 4510 4520
|| || |||||
MuRRS ..............................................cgCaaAgtGatCta
4190
| | || ||
MuERVC CtaCcaGtaCacCagTgtAtgGacAtcCtgGctGaaGaaAccAgaActAggAaaGacCtc
3010 3020 3030 3040 3050 3060
4130 4140 4150 4160 4170 4180
MoMLV AcgGacCagCcgCtcCcaGacGccGacCacAccTggTacAcgGatGgaAgcAgtCtcTta
||||| || | || | | | |||||||| || || || |||||| || |
GALV GaaGacCaaCcaTtgCccGgg...GtgCcaAccTggTatAcaGacGgtAgcAgtTtcAtc
4080 4090 4100 4110 4120
|||| | | | ||| || ||||| |||||| ||||| ||||| || || |
MuRVY ActGacCgaActTggCcaGgt...GtgCctGacTggTacAcaGatGgtAgaAgcTttGtg
4530 4540 4550 4560 4570 4580
||||| | ||||||||| || || ||||||||||||| || || || || |
MuRRS CgtGacCagCcgTggCcaGgt...GttCcaAacTggTacAcaGacGgaAgcAgtTtcCta
4200 4210 4220 4230 4240 4250
| |||||| |||||||| || |||||||||||||| | ||||| || |
MuERVC AcaGgcCagCcaTggCcaGgc...TgcCccAacTggTacAcaGatAgtAgcAgcTttTtg
3070 3080 3090 3100 3110 3120
4190 4200 4210 4220 4230 4240
MoMLV CaaGagGgaCagCgtAagGcgGgaGctGcgGtgAccAccGagAccGagGtaAtcTggGct
|| || | || | || || || || | | | | | ||||||
GALV AcgGaaGgtAaaCggAgaGcaGggGccCcgAtcGtaGatGgcAagCggAcgGtaTggGct
4130 4140 4150 4160 4170 4180
||| || ||| |||||||| | | | || || | || | | |||||
MuRVY GtgGagGgaAaaTAAAgaGcaGgaGagGcaGtgGttGacAgaAaaCatGtaAttTggGca
4590 4600 4610 4620 4630 4640
|||
MuRRS GtgA........................................................
||
MuERVC GttGaaAgaAagTGAAaaGcaGggGcaGcaGtgGtcAacGgaAaaCaaActAtcTggGcc
3130 3140 3150 3160 3170 3180
4250 4260 4270 4280 4290 4300
MoMLV AaaGccCtgCcaGccGggAcaTccGctCagCggGctGaaCtgAtaGcaCtcAccCagGcc
| |||||||| || || || || ||| ||||||||| |||| | || |||||
GALV AgcAgcCtgCcaGaaGgtAcgTcaGccCagAagGctGaaCtaGtaGccTtgAcgCagGca
4190 4200 4210 4220 4230 4240
|| || |||||||| || || || ||||||||||| || | | | || | ||
MuRVY AgtTAACttCcaGaaGgaActTcgGctCagAagGctGagCtcCtgAcgCtaActAaaGct
4650 4660 4670 4680 4690 4700
MuRRS ............................................................
MuERVC AgcAgcTtgCctGaaGggAcgAcaGccCagAgaGcaGagCtaAtcAcaCtcAccCaaGcc
3190 3200 3210 3220 3230 3240
4310 4320 4330 4340 4350 4360
MoMLV CtaAagAtgGca...GaaGgtAagAagCtaAatGttTatActGatAgcCgtTatGctTtt
|| |||| ||||| || || | || | || || || ||| | |||||||||
GALV TtaCgcCtgGcc...GaaGgaAaaAacAtcAacAtcTacAcgGacAgcAggTatGctTtt
4250 4260 4270 4280 4290 4300
| | |||||| ||||| || ||||| || ||||| |||||| |||||||||
MuRVY CtgCagCtgGccA..GaaGgtAagGcaAtcAatAttTacActGacAgcCacTatGctTtt
4710 4720 4730 4740 4750 4760
MuRRS ............................................................
MuERVC TtgCggCtgGca...Gaa...GagAacAttAatAtcTacAcaGacAgcAggCatGctTtc
3250 3260 3270 3280 3290
4370 4380 4390 4400 4410 4420
MoMLV GctActGccCatAtcCatGgaGaaAtaTacAgaAggCgtGggTtgCtcAcaTcaGaaGgc
|| ||||| ||||| ||||| | |||||| | | | ||| ||||||| || | ||
GALV GccActGctCatAttCatGggGcaAtaTatAagCagAggGggCtgCtcActTctGctGga
4310 4320 4330 4340 4350 4360
||||| || || ||||||| ||| || |||| || |||||||| || ||||| || ||
MuRVY GccAcaGccCacAttCatGagGccAtcTatAgaCaaAggGggCtaCttActTcgGcaGgc
4770 4780 4790 4800 4810 4820
MuRRS ............................................................
MuERVC GccAccGctCatAtaCatGggGcaA...........AggGggTtaTtcAcaTctGctGgg
3300 3310 3320 3330 3340
4430 4440 4450 4460 4470 4480
MoMLV AaaGagAtcAaaAatAaaGacGagAtcTtgGccCtaCtaAaaGccCtcTttCtgCccAaa
||||| |||||||| ||||| || || |||||||| ||| | ||| || ||| || |
GALV AaaGatAtcAaaAacAaaGagGaaAttTtgGccCtgCtaGagGccAtcCatCtcCctAgg
4370 4380 4390 4400 4410 4420
|| || || ||||| ||||| ||||| |||||||| |||||||| || || | || | |
MuRVY AagGaaAttAaaAatAaaGaaGaaAtcTtgGccCtcCtaGagGctAtaCacAtgCccAag
4830 4840 4850 4860 4870 4880
MuRRS ............................................................
MuERVC AaaGatAttAaaAgtAaaGaaGaaAtcTtgAgcCtaTtaGaaGtcAtaCacTtgAc.Aaa
3350 3360 3370 3380 3390 3400
4490 4500 4510 4520 4530 4540
MoMLV AgaCttAgcAtaAtcCatTgtCcaGgaCatCaaAagGgaCacAgcGccGagGctAgaGgc
| | ||| ||||| ||||| || || || | |||| | | | | ||| | ||
GALV CggGtcGccAttAtcCacTgtCctGgcCacCagAggGgaAgtAacCctGtgGccActGgg
4430 4440 4450 4460 4470 4480
|| ||||| |||| ||| | |||||| || | ||| |||| ||| ||
MuRVY AaaGtgGccAtcAtcCtcTgcCttGgcCatCaaAagGggCaaGgtGctGtaGccCagGga
4890 4900 4910 4920 4930 4940
MuRRS ............................................................
MuERVC AacCtgGccAtcAtaCatTgcCctGgtCacCagAaaGgcCatGgtGccAtaGcaAagGga
3410 3420 3430 3440 3450 3460
4550 4560 4570 4580 4590 4600
MoMLV AacCggAtgGctGacCaaGcgGccCgaAagGcaGccAtcAcaGagActCcaGacAccTct
||||||| ||| ||| | || || | || ||| | ||
GALV AacCggAggGccGacGagGctGcaAagCaaGccGccCtg..................Tcg
4490 4500 4510 4520
|| | || ||| | || || || || | | | |
MuRVY AatCagAtgGcaGgtTggGtgGccAaaCagGtgGtaCaaGgcAtcCctGcgCtg.ccTgt
4950 4960 4970 4980 4990 5000
MuRRS ............................................................
MuERVC AatCagGtgGctGacCtgGctGccAcaCagGcaGccCaaGgaGctAtgAtcCtcAtaGct
3470 3480 3490 3500 3510 3520
End region used for RNAse-----><-Align unreliable--...
4610 4620 4630 4640 4650
MoMLV AccCtcCtcAtaGaaAatTcaTcaCccTac.........AccTcaGaaCatTttCatTac
||| | | | | | ||
GALV AccAgaGtgCtgGcaGgaActAca....................................
4530 4540 4550
| | | || | | | |
MuRVY AgaGag...AtaGaaGaaCcaAaaGagAcc.........CcaGagAtcAgtTttGa.Tac
5010 5020 5030 5040 5050
MuRRS ............................................................
MuERVC AgaGagAaaAatAaaGaaCttAagGatCatTatGaaCtcAaaGccAcaGgcTttGacTac
3530 3540 3550 3560 3570 3580
4660 4670 4680 4690
MoMLV AcaGtgActGatAtaAagGac.........CtaAccAagTtgGggGccAtt......Tat
|| | | | | | || | |
GALV ...............AaaCct.........CaaGagCcaAtcGagCccGct......Caa
4560 4570 4580
| | || | | | |
MuRVY AccTccAaaGatTatGagAtgAatGaaGaaCttGaaGaaCaaGggAagTccAaaGgaTtt
5060 5070 5080 5090 5100 5110
MuRRS ............................................................
MuERVC ActCcaGaaGatCagGaaCtaAcaGgcAaaAtaCctGagAtaTgt...Agg......Tat
3590 3600 3610 3620 3630
4700 4710 4720 4730 4740 4750
MoMLV GatAaaAcaAagAagTatTggGtcTacCaaGgaAaaCctGtgAtgCctGacCagTttAct
|| || || | | | | | | ||||||| |
GALV GaaAagAccAggCcg..................AggGagCtcAccCctGacCgg...Gga
4590 4600 4610 4620
| || | | || | | |||
MuRVY AgcTacCatGggAtaGcaAgaAcaAaaGaaGg.AaaAttAttTtgCccTatAgaGaaGga
5120 5130 5140 5150 5160
MuRRS ............................................................
MuERVC ActCccCagGaaGtgGctAagAccCaaGatGgtTgcTtgGtcCtgCccAccAaaGaaGga
3640 3650 3660 3670 3680 3690
4760 4770 4780 4790 4800 4810
MoMLV TttGaaTtaTtaGacTttCttCatCagCtgActCacCtcAgcTtcTcaAaaAtgAagGct
||||| | | | |||||| | |||||| | | ||| |
GALV AaaGaaTtcAttAagCggTtaCatCagTtaActCacTtaGgaCcaGaaAagCttCtcCaa
4630 4640 4650 4660 4670 4680
|| | || | || || | |||| | || || | ||| || | || | |
MuRVY AagGcaTatGtaAaaCgcAtcCatCccCtgAcaCatCtgGgaGcaAagAaaTtgTgtGat
5170 5180 5190 5200 5210 5220
MuRRS ............................................................
MuERVC CaaCaaTatGtaGccAatGtaCacCagCtcAtgCacTtaGaaActAagAatCtcAaaGaa
3700 3710 3720 3730 3740 3750
4820 4830 4840 4850 4860 4870
MoMLV CtcCtaGagAgaAgcCacAgtCccTacTacAtgCtgAacCggGatCgaAcaCtcAaaAat
|| | | | | | | ||| | ||||| | || | |
GALV CtaGtgAacCgt......AccAgcCtcCtcAtcCcgAacCtcCaaTctGcaGttCgcGaa
4690 4700 4710 4720 4730
| | | | | | | | | || | | ||
MuRVY TAAAtcCagTcc......TcaAacTatTatGtgCtcAggCtaCtaGac......GaaCaa
5230 5240 5250 5260 5270
MuRRS ............................................................
MuERVC AttGttAagAac......TcaAacTacTatGttAtaAaaCtgTtcAacGttGccCagGag
3760 3770 3780 3790 3800
4880 4890 4900 4910 4920 4930
MoMLV AtcActGagAccTgcAaaGctTgtGcaCaaGtcAacGccAgcAagTctGccGttAaaCag
|||| || | |||||||| || || || | | |
GALV GtcAccAgtCagTgtCagGctTgtGccAtgActAatGcgGtcAccAccTacAgaGagAcc
4740 4750 4760 4770 4780 4790
|| || | || | | ||| || | | |||||| | | ||| | ||
MuRVY GtaActAaaTccTgc.aaGtgTgtTccCtaAttAatGctGcaCgcCccTttAatGaaCaa
5280 5290 5300 5310 5320 5330
MuRRS ............................................................
MuERVC AttGttAatAaaTgcCaaGccTgtGccCtcAccAatGccAggCacCacAagAacGtcCcc
3810 3820 3830 3840 3850 3860
4940 4950 4960 4970 4980 4990
MoMLV GgaActAggGtcCgcGggCatCggCccGgcActCatTggGagAtcGatTtcAccGagAta
|||| ||| || || |||| |||||| | |||||| | || ||||| || |||
GALV GgaAaaAggCaaCgaGgaGatCgaCccGgcGtgTacTggGagGtaGacTtcAcaGaaAta
4800 4810 4820 4830 4840 4850
|||||| | |||| || ||| |||| || || |||||||| ||||||||||| || ||
MuRVY GgaAaaCgaCaaCtgGggGatAgaCctGgaGttTacTggGaaGtaGacTtcActGagAtc
5340 5350 5360 5370 5380 5390
MuRRS ............................................................
MuERVC GgaAggTggCtaAgaGgtGacCggCcaGggGcaTacTGAAaaGtaAatTttActGaaGtt
3870 3880 3890 3900 3910 3920
<-- begin region used as Int domain
5000 5010 5020 5030 5040 5050
MoMLV AagCccGgaTtgTatGgcTatAaaTatCttCtaGttTttAtaGatAccTttTctGgcTgg
||||| || |||||| | || ||||| |||| || |||||||| || || || |||
GALV AagCctGgtCggTatGgaAacAagTatCtgTtaGtaTtcAtaGatActTtcTccGgaTgg
4860 4870 4880 4890 4900 4910
|| || || ||||| || || || | |||| |||||||| |||||||| ||||||
MuRVY AaaCcaGgaAaaTatGgtAatAaaTAGTtaCtaGttTtcAtaGacActTtcTcaGgaTgg
5400 5410 5420 5430 5440 5450
|||||| |||| || || |||||||||
MuRRS ...............................aaGttTttGtaGatAccTttTcaGgaTgg
4260 4270 4280
||||||| |||| || |||| ||| |||
MuERVC AaaCcaGccAagTacGgtAatAaaTatCtaTtaGttTttAtaGacActTttTGAGggTgg
3930 3940 3950 3960 3970 3980
5060 5070 5080 5090 5100 5110
MoMLV AtaGaaGccTtcCcaAccAagAaaGaaAccGccAagGtcGtaAccAagAagCtaCtaGag
||||||| || || ||||| | ||||| ||| |||| || || || ||||
GALV GtaGaaGctTttCctAccAaaActGaaAcgGccCtaAtcGtcTgtAaaAaaAtaTtaGaa
4920 4930 4940 4950 4960 4970
|||||||| || || ||||| ||||||| || | | || || || || | |||
MuRVY GtaGaaGccTtcCccAccAagTctGaaActGctCagGtgGtgAccAagAagAtcGttGaa
5460 5470 5480 5490 5500 5510
|| || |||| | | || || |||||||| | || ||| || || ||| | ||
MuRRS GtgGagGccTacAcaAcaAa.AaaGaaActGccAatGttGtgTttAaaAaaAtcCtaAaa
4290 4300 4310 4320 4330 4340
|| || |||||||||||| || || || |
MuERVC ........................GagAccGccAatGttGtgAc...gAagAtaTtaGag
3990 4000 4010 4020
5120 5130 5140 5150 5160 5170
MoMLV GagAtcTtcCccAggTtcGgcAtgCctCagGtaTtgGgaActGacAatGggCctGccTtc
|| || | ||| | ||||| || ||| ||||| | || | |||||||| || |||||
GALV GaaAttCtaCccCgcTtcGggAtcCctAagGtaCtcGggTcaGacAatGgcCcgGccTtt
4980 4990 5000 5010 5020 5030
|| || ||||||| || |||||||| | ||| | | | || ||||| || || |||
MuRVY GagAtcCtaCccCagTttGggAtcCccAgtGtaAtaTgcTtgGaaAatGggCctGcaTtt
5520 5530 5540 5550 5560 5570
| || | || | |||| | || || | |||||| | | || |||| || | | |
MuRRS AaaAttTttCctCggTttAgaAtaCctAagGtaAtaGggTctGacAatGaaCccAccTct
4350 4360 4370 4380 4390 4400
||||||| || | ||| | | ||||||||| | || ||||||| ||| ||
MuERVC GaaAttTtcCcaAgaTttGgcA.cCctAagGtaCttTcaTcaGacAatGgcCcc.tcTtc
4030 4040 4050 4060 4070
5180 5190 5200 5210 5220 5230
MoMLV GtcTccAagGtgAgtCagAcaGtgGccGatCtgTtgGggAttGatTggAaaTtaCatTgt
|| | |||| |||||| | ||||| || ||||||| ||||||| |||||||||
GALV GttGctCagGtaAgtCagGgaCtgGccActCaaCtgGggAtaAatTggAagTtaCatTgt
5040 5050 5060 5070 5080 5090
||||| ||||||||||||| | | ||||| || |||||| |||||||||||| |||||
MuRVY GttGccCagGtaAgtCagGaaTtaGccAcaCatTtgGggAacAatTggAagTtaTatTgt
5580 5590 5600 5610 5620 5630
||||||||||||||||||| | | |||| || ||||||| ||| ||| ||| |||||
MuRRS GttGccCagGtaAgtCagGgaCtgGccAtcCaaTtgGggAttGatTAGAaaTtaCatTgt
4410 4420 4430 4440 4450 4460
||||||||||||||||| | | |||| |||||||||||||||| ||| |||||||||
MuERVC GttGccCagGtaAgtCaaGcgTtaGccAgaCaaTtgGggAttGatTggAagTtaCatTgt
4080 4090 4100 4110 4120 4130
5240 5250 5260 5270 5280 5290
MoMLV GcaTacAgaCccCaaAgcTcaGgcCagGtaGaaAgaAtgAatAgaAccAtcAagGagAct
|| || |||||||| |||||||| ||||||||||||||||| ||||| || || |||||
GALV GcgTatAgaCccCagAgcTcaGgtCagGtaGaaAgaAtgAacAgaAcaAttAaaGagAcc
5100 5110 5120 5130 5140 5150
|| |||| ||||||||| |||| |||||||| |||||||||| || | ||||| |||
MuRVY GctTatAaaCccCagAgaTcaGtaGagGtaGaaGgaAtgAacAggActCtaAaaGaaAcc
5640 5650 5660 5670 5680 5690
| ||||| ||||||||| |||| |||||||| | | | |||| ||| |
MuRRS GttTatAgaCccCagAgtTcaGgcTAGGtaGaaAg........gaAaaAaaAaaAaaAac
4470 4480 4490 4500 4510
||||||||| ||||||||||| | || |||| | ||| | |||| |||
MuERVC GttTatAgaAccCagAgtTcaAgaCagTtaGagCggAtaAatAgaAcaTtaAaaGaaAca
4140 4150 4160 4170 4180 4190
5300 5310 5320 5330 5340 5350
MoMLV TtaActAaaTtaAcgCttGcaActGgcTctAgaGacTggGtgCtcCtaCtcCccTtaGcc
|| || |||||| | | | || || | |||||||||| ||| || ||||||||
GALV TtgAccAaaTtaGccTtaGagAccGgtGgaAaaGacTggGtgAccCtcCttCccTtaGcg
5160 5170 5180 5190 5200 5210
| || |||||||| || |||||| |||| |||||||||||||||||||||||||| | |
MuRVY CtaActAaaTtaGctTttGagAccAgtGgtAaaGacTggGtgAccCtcCttCccTttGtg
5700 5710 5720 5730 5740 5750
| ||||||||| || |||||| | | | ||||| |||||||||||||||
MuRRS TtgActAaaTtaAtcTtaGagAccGgcAgaAgtTacTggAcaGccCtcCttCccTttGct
4520 4530 4540 4550 4560 4570
|| |||||||| |||||||| ||| ||| | ||| |||| |||||| |||| |
MuERVC TtaActAaaTtgGctTtaGagActGgcTGAAaaGatTggGcaGctCtcCttTccTtcCcc
4200 4210 4220 4230 4240 4250
5360 5370 5380 5390 5400 5410
MoMLV CtgTacCgaGccCgcAacAcgCcgGgcCccCatGgcCtcAccCcaTatGagAtcTtaTat
||| | ||| | || || || |||| ||| | || || ||||| || | |||
GALV CtgCttAggGccAggAatAccCctGgcCggTttGgtTtaActCctTatGaaAttCtcTat
5220 5230 5240 5250 5260 5270
|| ||||||||| | || || ||||| | || || | ||||||||||||||||| ||
MuRVY CtcCttAggGccCgaAacAcaCctGggTgtTtcGgcAttActCctTatGaaAttCtaCat
5760 5770 5780 5790 5800 5810
| | | | | |||||||| || || ||||||| ||| |||| || ||
MuRRS TtgTtcCgtGttAggAacAcaCcaGgaAaaTttAagCttActCcaTatAaaAtcCtgTat
4580 4590 4600 4610 4620 4630
|||||| | || |||||| ||||| |||||||| |||| || | | || |||| ||
MuERVC TtgTtcTGAGtaCagAacAccCcaGggAaaTttAaaCttAaaCccTttGaaCtcCtcCat
4260 4270 4280 4290 4300 4310
5420 5430 5440 5450 5460 5470
MoMLV GggGcaCccCcgCccCttGtaAacTtcCctGacCctGacAtgAcaAga......GttAct
|| | ||| || ||| | | | | || || | | ||
GALV GgaGgaCcaCccCccAtaCttGagTctGgaGaaActTtgGgtCccGat......GatAga
5280 5290 5300 5310 5320
|| |||||||||||| | ||||||| || | ||| | || | |
MuRVY GggGgaCcaCccCccTtgAccGagTctGatGagAtaTtgTatTccAgtGctGacTctTcc
5820 5830 5840 5850 5860 5870
||||| | ||| | | | ||| | ||| | | | | |
MuRRS GggGggGggGctCccCcgCtcActAaaGtaAagAgaGtgTtaGatCctTtaAaaTttAac
4640 4650 4660 4670 4680 4690
||||| | ||| || | | | | ||
MuERVC GggGgaCccCccCccTtaAcaGaaGcaGggGgaAtgTttGacCctGat......GttCct
4320 4330 4340 4350 4360 4370
5480 5490 5500 5510 5520 5530
MoMLV AacAgcCccTctCtcCaaGctCacTtaCagGctCtcTacTtaGtcCagCacGaaGtcTgg
||| | |||||||| ||||| | | | || | | || |||||
GALV TttCtcCctGtcTtaTttActCacTtaAagGctTtaGaaAttGtaAggAccCaaAtcTgg
5330 5340 5350 5360 5370 5380
| | | || | ||||| || |||||||| |||||| |||| || || || ||||||
MuRVY TcaCccTctTctCtgTttAccCatTtaAagGccTtaGaaGttGtcAgaAcaCagAtcTgg
5880 5890 5900 5910 5920 5930
| |||| ||||||| |||| ||| ||||||| ||||||| |||
MuRRS CctGgtCctTcaTtgTttAcaTgcAtaAaaGccCtaGaaGtgGtcAgaAacAccGccTGA
4700 4710 4720 4730 4740 4750
|| | | || | | || | || ||||||||| |||||| ||| ||||||
MuERVC TctTccCaaCccCtgCtaGctCgcTtgAagGccCtaGaaCtgGtcAaaAaaGatGccTGA
4380 4390 4400 4410 4420 4430
5540 5550 5560 5570 5580 5590
MoMLV AgaCctCtgGcgGcaGccTacCaaGaaCaaCtgGacCgaCcgGtgGtaCctCacCctTac
| | | | || | | | |||||||| | |
GALV GacCagAtcAaaGagGtgTatAagCct......GgtAccGtaAcaAtcCctCacCcgTtc
5390 5400 5410 5420 5430 5440
|||||||| ||||| | || | || || | | || | || ||| ||||
MuRVY GacCagAttAaaGaaGcaTacAcaCca......GggAgcAgtGcaGtgCccCacAggTtc
5940 5950 5960 5970 5980 5990
|| ||| | ||||| || ||| |||| || | | || ||| ||||
MuRRS GagCagCtcAaaGagGccTacGaaCca......GgaGacTtgAtgAtaCcaCacCagTtc
4760 4770 4780 4790 4800 4810
|| ||| ||| | || |||||| || | | ||| | ||
MuERVC GaaTtgCtgAaa.aaAagTatGaaCca......AgaAccAccGcaGtgTcaCgtAaaTtt
4440 4450 4460 4470 4480
5600 5610 5620 5630 5640 5650
MoMLV CgaGtcGgcGacAcaGtgTggGtcCgcCgaCacCagActAagAacCtaGaaCctCgcTgg
| ||||| || |||| ||| | || || | | | | ||| || ||||| |||
GALV CagGtcGggGatCaaGtgCttGtcAgaCgcCatCgaCccAgcAgcCttGagCctCggTgg
5450 5460 5470 5480 5490 5500
|||||||| || ||| || ||| ||| |||||| | ||| | |||||| ||||||
MuRVY CagGtcGg.GacTcaGttCtgGtcTGACaaCatCgaGctGgcAtgCatGagCcaCggTgg
6000 6010 6020 6030 6040
||||| || || ||||||| ||||||| ||||||||||| | | | || | |
MuRRS CagGtgGgaGatGcaGttCtcGtcTGACgaCatCgaGctGagAatCtgAaaCctTgtTAA
4820 4830 4840 4850 4860 4870
|| | | ||| | || || |||| || || | | || || |||| |
MuERVC CaaAtaAggGatCctGtcCtgGtcTAGCgcCacTgtTccAgcAacCttGaaCccAaaTgg
4490 4500 4510 4520 4530 4540
5660 5670 5680 5690 5700 5710
MoMLV AaaGgaCctTacAcaGtcCtgCtgAccAccCccAccGccCtcAaaGtaGacGgcAtcGca
||||| || ||| || ||||||| ||||| ||||| | ||||| || || || ||
GALV AaaGgcCcaTacCtgGtgTtgCtgActAccCcgAccGcgGtaAaaGtcGatGgtAttGct
Met for env
5510 5520 5530 5540 5550 5560
|| || || || || ||| ||||||| | | | | | ||| || || | || |||
MuRVY AagGgaCctTatCtaGtgCtgCtgAccAgcGccGagGtcGcaAagGtaGacAggAtcGct
6050 6060 6070 6080 6090 6100
|| || ||| | ||||| ||||||| | || | | || | ||| | |||
MuRRS AaaGgcTctTgcAtcGtgCtaCtgAccAccCccActGctGtcAaaGaaGaaGgcAtcTac
4880 4890 4900 4910 4920 4930
||||| | | | | ||||| |||||
MuERVC AaaGgaCccTacCtgGtgCttCtgAc.....remainder MuERVC pol deleted
4550 4560 4570
Used as Int ---------><-- alignment unreliable--...
Trying to align the end of pol
or the beginning of env which
overlaps in a different frame
tends to produce conflicting
alignments, neither of which
is convincing.
5720 5730 5740 5750 5760
MoMLV GctTggAta...CacGccGccCacGtgAagGc...tGccGacCccGggGgtGgaCcaTcc
|| ||| | || || | ||| | || | ||| || || |
GALV GccTggGtc...CatGctTctCacCtcAaaCc...tGcaCcaCctTcgGcaCcaGatGag
Met (internal): better candidate for
homologue to initiator ATGs of env of
other viruses.
5570 5580 5590 5600 5610
|||||| || || || || ||| | ||| |||||| | || ||| ||
MuRVY GccTggAtc...CacGcaTccCacAtaAaaAa.AagGcaCcaAccA.gGatGaaGacGac
Met for env
possible pol ter
6110 6120 6130 6140 6150 6160
|| || | |||| | |
MuRRS GcaTgcCttT..CacGtaAagC remainder MuRRS pol deleted
4940 4950
5770 5780 5790 5800 5810 5820
MoMLV TctAgaCtgAcaTggCgcGttCaaCgcTctCaaAacCccTtaAaaAtaAggTtaAccCgc
Met for env
|| ||| | ||
GALV Tcc.........TggGagCtgGaaAagA................................
5620 5630
| ||| ||| |
MuRVY CtcAgaGaaAatTggAcaGtgGccGctA................................
6170 6180 6190
5830 5840 5850 5860 5870 5880
MoMLV GagGccCccTAAtccccttaattcttctgatgctcagaggggtcagtactgcttcgcccg
|| | | | | || | || | | | || | || ||
GALV ........ctGatCatCctCttAagCtgCgtAttCggCggCggCggGacGagTctGcaAa
5640 5650 5660 5670 5680
||||| || ||| | ||| | || | ||
MuRVY ........ctGatAatTctCaaActGtgCctT.........cgCtgTacAccAacCttGg
6200 6210 6220 6230
<-- Begin Env conserved seq. in overlapping frame.
GALV and MoMLV frameshift relative to one another
in C terminal of pol and finish at different
stop codons.
5890
MoMLV gctcc
GALV aTAA
5690
|||
MuRVY gTAA
6240