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DNA Surveillance

Species identification with DNA
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Search Cluster (Simple) Cluster (Advanced) Maximum Likelihood Example Data

General details for dataset 'Rattus_DLoop_v3'

Loci: Control Region (v3)
Domain: Rattus
Alignment: 60 sequences, 538 sites
Alignment scoring
-ACGT
A1.0-1.0-1.0-1.0
C-1.01.0-1.0-1.0
G-1.0-1.01.0-1.0
T-1.0-1.0-1.01.0
Create/extend = -3.0/-1.0
Substitution model
-ACGT
A-1.04.01.0
C1.0-1.04.0
G4.01.0-1
T1.04.01-
(A,G,C,T) = (0.3286, 0.2219, 0.1132, 0.33630000000000004)

Sequence details

Main sequences
IDNameGroupSample OriginSample SourceMuseum AccessionGenBank Accession
DiMa080d rattus diardi (diardii clade)diardiiKuala Lumpur, MalaysiaSAMABTC64907 EF186294
DiMa126d rattus diardi (diardii clade)diardiiKuala Lumpur, MalaysiaSAMABTC64906 EF186298
ExCI031d exulans (exulans clade)exulansAitutaki, Cook IslandsE M-S- EF186299
ExCI032d exulans (exulans clade)exulansAitutaki, Cook IslandsE M-S- EF186300
ExIn023d exulans (exulans clade)exulansCibodas Forest, IndonesiaSAMABTC48011 EF186306
ExPN024d exulans (exulans clade)exulansYuro, Papua New GuineaSAMABTC43078 EF186312
ExSa029d exulans (exulans clade)exulansManua, SamoaE M-S- EF186315
ExSa030d exulans (exulans clade)exulansManua, SamoaE M-S- EF186316
ExTh026d exulans (exulans clade)exulansThailandSAMABTC 8553 EF186317
FlHk045d flavipectus (tanezumi clade)tanezumiHong Kong, ChinaSAMABTC 8489 EF186320
FuAu056d fuscipes assimilis (fuscipes clade)fuscipesLismore, AustraliaSAMABTC51715 EF186321
FuAu057d fuscipes coracius (fuscipes clade)fuscipesMt Windsor, Queensland, AustraliaSAMABTC51727 EF186322
FuAu059d fuscipes fuscipes (fuscipes clade)fuscipes26k W Manjimup, AustraliaSAMABTC 8615 EF186324
HoSu044d hoffmanni (hoffmanni clade)hoffmanniTangoa, Sulawesi, IndonesiaSAMABTC65754 EF186326
HoSu061d hoffmanni (hoffmanni clade)hoffmanniMt Nokilalaki, Sulawesi, IndonesiaSAMABTC65809 EF186327
KaSL063d kandianus (diardii clade)diardiiSri LankaSAMABTC 8529 EF186329
LeAu069d leucopus cooktownensis (leucopus clade)leucopusMt Simons, 19mls S Cooktown Queensland, AustraliaSAMABTC 8447 EF186333
LeAu071d leucopus leucopus (leucopus clade)leucopusRocky River Queensland, AustraliaSAMABTC 8493 EF186335
LePN066d leucopus (verecundus clade)verecundusHaia, Central Highland Province, Papua New GuineaSAMABTC42808 EF186336
LuAu126d lutreolus (lutreolus clade)lutreolusTasmaniaSAMABTC51762 GU570661
LuAu127d lutreolus (lutreolus clade)lutreolusMyall Lakes, New South WalesSAMABTC51720 GU570666
LuAu128d lutreolus (lutreolus clade)lutreolusJervois, South AustraliaSAMABTC27458 GU570667
MoPN046d mordax (PNG 1 clade)PNG 1Nokopo, Morobe Province, Papua New GuineaSAMABTC48962 EF186338
NiPN072d niobe (PNG 1 clade)PNG 1Bundi, Madang Province, Papua New GuineaSAMABTC49306 EF186341
NiPN073d niobe (PNG 2 clade)PNG 2Magidobo, Southern Highland Province, Papua New GuineaSAMABTC45409 EF186342
NiPN074d niobe (PNG 2 clade)PNG 2Mt Karimui, Central Highland Province, Papua New GuineaSAMABTC43906 EF186343
NiPN075d niobe (PNG 3 clade)PNG 3near Kosipe Mt Albert Edward Central Province, Papua New GuineaSAMABTC42503 EF186344
NiPN077d niobe (PNG 3 clade)PNG 3Sol River, West Sepik Province, Papua New GuineaSAMABTC47145 EF186345
Noxx001d norvegicus (norvegicus clade)norvegicuslaboratory strainGenBank- NC_001665
Noxx049d norvegicus (norvegicus clade)norvegicuslaboratory strainGenBank- AY172581
PrPN123d praetor (PNG 1 clade)PNG 1Munbil, West Sepik Province, Papua New GuineaSAMABTC47271 EF186351
PrPN124d praetor (PNG 1 clade)PNG 1Munbil, West Sepik Province, Papua New GuineaSAMABTC47273 EF186352
RaNZ004d rattus (rattus clade)rattusTitirangi, New ZealandE M-S- EF186355
RaPN009d rattus (villosissimus clade)villosissimusMoitaka, National Capital District, Papua New GuineaSAMABTC44857 EF186356
RaPN010d rattus (rattus clade)rattusSideia Is., Milne Bay Province, Papua New GuineaSAMABTC50177 EF186357
RaPN079d rattus (villosissimus clade)villosissimusMoitaka, National Capital District, Papua New GuineaSAMABTC44858 EF186358
RuPN055d ruber (PNG 1 clade)PNG 1Yuro, Central Highland Province, Papua New GuineaSAMABTC43216 EF186361
SoAu087d sordidus (sordidus clade)sordidusIngham, Queensland, AustraliaSAMABTC51664 EF186363
SoAu088d sordidus (sordidus clade)sordidusSir Edward Pellew Is. Northern Territory, AustraliaSAMABTC41164 EF186364
StIn090d steini (PNG 1 clade)PNG 1Bogor Botanic Gardens, Java, IndonesiaSAMABTC44036 EF186366
StPN047d steini (PNG 1 clade)PNG 1Nokopo, MP, Papua New GuineaSAMABTC49035 EF186368
TaIn018d tanezumi (tanezumi clade)tanezumiJakarta, Java, IndonesiaSAMABTC47993 EF186376
TaIn019d tanezumi (tiomanicus clade)tiomanicusJakarta, Java, IndonesiaSAMABTC47994 EF186377
TaIn022d tanezumi (tanezumi clade)tanezumiYogyakarta, Java, IndonesiaSAMABTC47983 EF186380
TaIn100d tanezumi (diardii clade)diardiiJakarta, Java, IndonesiaSAMABTC47997 EF186383
TaIn103d tanezumi (diardii clade)diardiiJakarta, Java, IndonesiaSAMABTC48000 EF186386
TaIn107d tanezumi (tanezumi clade)tanezumiYogyakarta, Java, IndonesiaSAMABTC47984 EF186387
TaJp014d tanezumi (tanezumi clade)tanezumiAnami Island, JapanSAMABTC 8487 EF186393
TaSu105d tanezumi (diardii clade)diardiinorthern Sulawesi, IndonesiaSAMABTC48005 EF186397
TiIn050d tiomanicus (tiomanicus clade)tiomanicusCibodas forest, Java, IndonesiaSAMABTC48026 EF186398
TuAu114d tunneyi (tunneyi clade)tunneyiLitchfield, NP, Northern Territory, AustraliaSAMABTC29636 EF186400
TuAu118d tunneyi (tunneyi clade)tunneyiYarraman, Queensland, AustraliaSAMABTC51688 EF186403
VePN053d verecundus (verecundus clade)verecundusBobole, Southern Highland Province, Papua New GuineaSAMABTC45161 EF186404
VePN119d verecundus (PNG 3 clade)PNG 3Bundi, Madang Province, Papua New GuineaSAMABTC49292 EF186405
VePN120d verecundus (verecundus clade)verecundusNoru, Central Highland Province, Papua New GuineaSAMABTC43510 EF186406
ViAu123d villosissimus (villosissumus clade)villosissimusPurni Bore, South AustraliaSAMABTC00548 GU570668
ViAu124d villosissimus (villosissumus clade)villosissimusPalparara, south west QueenslandSAMABTC23632 GU570669
ViAu125d villosissimus (villosissumus clade)villosissimusSir Edward Pellow Is., Northern TerritorySAMABTC41137 GU570670
ViAu129d villosissimus (villosissumus clade)villosissimusSouth AustraliaSAMABTC00549 GU570663
Outgroup sequences
IDNameGroup Sample OriginSample SourceMuseum AccessionGenBank Accession
MusR052d M. musculus domesticusUnspecifiedwestern EuropeGenBank- NC_006914