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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_COI_100'

Loci: Cytochrome Oxidase I (v3)
Domain: Pos 101-300
Alignment: 84 sequences, 200 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-1.07.01.0
C1.0-1.07.0
G7.01.0-1
T1.07.01-
(A,G,C,T) = (0.3403, 0.2617, 0.1256, 0.2724)

Sequence details

Main sequences
IDNameGroupSample OriginSample SourceMuseum AccessionGenBank Accession
DiMa080c rattus diardi (diardii clade)diardiiKuala Lumpur, MalaysiaSAMABTC64907 EF186528
DiMa126c rattus diardi (diardii clade)diardiiKuala Lumpur, MalaysiaSAMABTC64906 EF186524
ExCI031c exulans (exulans clade)exulansAitutaki, Cook IslandsE M-S- EF186529
ExCI032c exulans (exulans clade)exulansAitutaki, Cook IslandsE M-S- EF186530
ExIn023c exulans (exulans clade)exulansCibodas Forest, IndonesiaSAMABTC48011 EF186536
ExPN024c exulans (exulans clade)exulansYuro, Papua New GuineaSAMABTC43078 EF186542
ExSa029c exulans (exulans clade)exulansManua, Samoa E M-S- EF186545
ExSa030c exulans (exulans clade)exulansManua, SamoaE M-S- EF186545
ExTh026c exulans (exulans clade)exulansThailandSAMABTC 8553 EF186547
FlHk045c flavipectus (tanezumi clade)tanezumiHong Kong, ChinaSAMABTC 8489 EF186555
FuAu056c fuscipes assimilis (fuscipes clade)fuscipesLismore, AustraliaSAMABTC51715 EF186550
FuAu057c fuscipes coracius (fuscipes clade)fuscipesMt Windsor, Queensland, AustraliaSAMABTC51727 EF186551
FuAu059c fuscipes fuscipes (fuscipes clade)fuscipes26k W Manjimup, AustraliaSAMABTC 8615 EF186553
HoSu044c hoffmanni (hoffmanni clade)hoffmanniTangoa, Sulawesi, IndonesiaSAMABTC65754 EF186556
HoSu061c hoffmanni (hoffmanni clade)hoffmanniMt Nokilalaki, Sulawesi, IndonesiaSAMABTC65809 EF186557
KaSL063c kandianus (diardii clade)diardiiSri LankaSAMABTC 8529 EF186559
LeAu069c leucopus cooktownensis (leucopus clade)leucopusMt Simons, 19mls S Cooktown Queensland, AustraliaSAMABTC 8447 EF186562
LeAu071c leucopus leucopus (leucopus clade)leucopusRocky River Queensland, AustraliaSAMABTC 8493 EF186567
LePN066c leucopus (verecundus clade)verecundusHaia, Central Highland Province, Papua New GuineaSAMABTC42808 EF186564
MoPN046c mordax (PNG 1 clade)PNG 1Nokopo, Morobe Province, Papua New GuineaSAMABTC48962 EF186568
NiPN072c niobe (PNG 1 clade)PNG 1Bundi, Madang Province, Papua New GuineaSAMABTC49306 EF186571
NiPN073c niobe (PNG 2 clade)PNG 2Magidobo, Southern Highland Province, Papua New GuineaSAMABTC45409 EF186572
NiPN074c niobe (PNG 2 clade)PNG 2Mt Karimui, Central Highland Province, Papua New GuineaSAMABTC43906 EF186573
NiPN075c niobe (PNG 3 clade)PNG 3near Kosipe Mt Albert Edward Central Province, Papua New GuineaSAMABTC42503 EF186574
NiPN077c niobe (PNG 3 clade)PNG 3Sol River, West Sepik Province, Papua New GuineaSAMABTC47145 EF186575
NoDe048c norvegicus (norvegicus clade)norvegicusCopenhagen, DenmarkGenBank- AJ428514
Noxx001c norvegicus (norvegicus clade)norvegicuslaboratory strainGenBank- NC_001665
PrPN123c praetor (PNG 1 clade)PNG 1Munbil, West Sepik Province, Papua New GuineaSAMABTC47271 EF186581
PrPN124c praetor (PNG 1 clade)PNG 1Munbil, West Sepik Province, Papua New GuineaSAMABTC47273 EF186582
RaNZ004c rattus (rattus clade)rattusTitirangi, New Zealandtrapped- EF186585
RaPN009c rattus (villosissimus clade)villosissimusMoitaka, National Capital District, Papua New GuineaSAMABTC44857 EF186586
RaPN010c rattus (rattus clade)rattusSideia Is., Milne Bay Province, Papua New GuineaSAMABTC50177 EF186587
RaPN079c rattus (villosissimus clade)villosissimusMoitaka, National Capital District, Papua New GuineaSAMABTC44858 EF186588
RuPN055c ruber (PNG 1 clade)PNG 1Yuro, Central Highland Province, Papua New GuineaSAMABTC43216 EF186591
SoAu087c sordidus (sordidus clade)sordidusIngham, Queensland, AustraliaSAMABTC51664 EF186593
SoAu088c sordidus (sordidus clade)sordidusSir Edward Pellew Is. Northern Territory, AustraliaSAMABTC41164 EF186594
StIn090c steini (PNG 1 clade)PNG 1Bogor Botanic Gardens, Java, IndonesiaSAMABTC44036 EF186596
StPN047c steini (PNG 1 clade)PNG 1Nokopo, MP, Papua New GuineaSAMABTC49035 EF186598
TaIn018c tanezumi (tanezumi clade)tanezumiJakarta, Java, IndonesiaSAMABTC47993 EF186606
TaIn019c tanezumi (tiomanicus clade)tiomanicusJakarta, Java, IndonesiaSAMABTC47994 EF186607
TaIn022c tanezumi (tanezumi clade)tanezumiYogyakarta, Java, IndonesiaSAMABTC47983 EF186610
TaIn100c tanezumi (diardii clade)diardiiJakarta, Java, IndonesiaSAMABTC47997 EF186613
TaIn103c tanezumi (diardii clade)diardiiJakarta, Java, IndonesiaSAMABTC48000 EF186616
TaIn107c tanezumi (tanezumi clade)tanezumiYogyakarta, Java, IndonesiaSAMABTC47984 EF186617
TaJp014c tanezumi (tanezumi clade)tanezumiAnami Island, JapanSAMABTC 8487 EF186623
TaSu105c tanezumi (diardii clade)diardiinorthern Sulawesi, IndonesiaSAMABTC48005 EF186627
TiIn050c tiomanicus (tiomanicus clade)tiomanicusCibodas forest, Java, IndonesiaSAMABTC48026 EF186628
TuAu114c tunneyi (tunneyi clade)tunneyiLitchfield NP, Northern Territory, AustraliaSAMABTC29636 EF186630
TuAu118c tunneyi (tunneyi clade)tunneyiYarraman, Queensland, AustraliaSAMABTC51688 EF186633
VePN053c verecundus (verecundus clade)verecundusBobole, Southern Highland Province, Papua New GuineaSAMABTC45161 EF186634
VePN119c verecundus (PNG 3 clade)PNG 3Bundi, Madang Province, Papua New GuineaSAMABTC49292 EF186635
VePN120c verecundus (verecundus clade)verecundusNoru, Central Highland Province, Papua New GuineaSAMABTC43510 EF186636
GU570676 lutreolus (lutreolus clade)lutreolusMyall Lakes, New South WalesSAMABTC51720 GU570676
GU570677 lutreolus (lutreolus clade)lutreolusJervois, South AustraliaSAMABTC27458 GU570677
GU570661 lutreolus (lutreolus clade)lutreolusTasmaniaSAMABTC51762 GU570661
GU570678 villosissimus (villosissumus clade)villosissimusPurni Bore, South AustraliaSAMABTC00548 GU570678
GU570679 villosissimus (villosissumus clade)villosissimusPalparara, south west QueenslandSAMABTC23632 GU570679
GU570680 villosissimus (villosissumus clade)villosissimusSir Edward Pellow Is., Northern TerritorySAMABTC41137 GU570680
GU570663 villosissimus (villosissumus clade)villosissimusSouth AustraliaSAMABTC00549 GU570663
HM217495 rattus (rattus clade)rattusMadagascarPages et al. 2010 BMC EvolBio 10:184.MDZ10Mada HM217495
HM217498 rattus (rattus clade)rattusIndiaPages et al. 2010 BMC EvolBio 10:184.ratcosT820 HM217498
HM217496 rattus (rattus clade)rattusOmanPages et al. 2010 BMC EvolBio 10:184.ratcosR12 HM217496
HM217497 rattus (rattus clade)rattusTanzaniaPages et al. 2010 BMC EvolBio 10:184.ratcosTE4262 HM217497
HM217522 tiomanicus (tiomanicus clade)tiomanicusNakhon Sri Thammarat, ThailandPages et al. 2010 BMC EvolBio 10:184.R1833 HM217522
HM217525 andamanensis (andamanensis clade)andamanensisKanchanaburi, ThailandPages et al. 2010 BMC EvolBio 10:184.R2953 HM217525
HM217533 andamanensis (andamanensis clade)andamanensisKanchanaburi, ThailandPages et al. 2010 BMC EvolBio 10:184.R3087 HM217533
HM217540 tanezumi (tanezumi clade)tanezumiKanchanaburi, ThailandPages et al. 2010 BMC EvolBio 10:184.R3214 HM217540
HM217582 tanezumi (tanezumi clade)tanezumiPhrae, ThailandPages et al. 2010 BMC EvolBio 10:184.R4424 HM217582
HM217494 tanezumi (tanezumi clade)tanezumiLuang Prabang, Lao PDRPages et al. 2010 BMC EvolBio 10:184.L0194 HM217494
HM217581 losea (losea clade)loseaLoei, ThailandPages et al. 2010 BMC EvolBio 10:184.R4402 HM217581
HM217512 losea (losea clade)loseaNakhon Ratchasima, Thailand Pages et al. 2010 BMC EvolBio 10:184.R1015 HM217512
HM217570 losea (losea clade)loseaPhrae, ThailandPages et al. 2010 BMC EvolBio 10:184.R4203 HM217570
HM217505 losea (losea clade)loseaRatchaburi, ThailandPages et al. 2010 BMC EvolBio 10:184.R0237 HM217505
HM217508 exulans (exulans clade)exulansRatchaburi, ThailandPages et al. 2010 BMC EvolBio 10:184.R0284 HM217508
HM217557 exulans (exulans clade)exulansSurat Thani, ThailandPages et al. 2010 BMC EvolBio 10:184.R3563 HM217557
HM217595 exulans (exulans clade)exulansNan, ThailandPages et al. 2010 BMC EvolBio 10:184.R5349 HM217595
HM217484 argentiventer (argentiventer clade)argentiventerVeal Renh, CambodiaPages et al. 2010 BMC EvolBio 10:184.CB0001 HM217484
HM217486 argentiventer (argentiventer clade)argentiventerVeal Renh, CambodiaPages et al. 2010 BMC EvolBio 10:184.CB0104 HM217486
HM217504 norvegicus (norvegicus clade)norvegicusRatchaburi, ThailandPages et al. 2010 BMC EvolBio 10:184.R0223 HM217504
HM217499 norvegicus (norvegicus clade)norvegicusCambodiaPages et al. 2010 BMC EvolBio 10:184.RNO 032 HM217499
HM217492 nitidus (nitidus clade)nitidusLuang Prabang, Lao PDRPages et al. 2010 BMC EvolBio 10:184.L0180 HM217492
HM217493 nitidus (nitidus clade)nitidusLuang Prabang, Lao PDRPages et al. 2010 BMC EvolBio 10:184.L0192 HM217493
HM217488 nitidus (nitidus clade)nitidusLuang Prabang, Lao PDRPages et al. 2010 BMC EvolBio 10:184.L0010 HM217488
Outgroup sequences
IDNameGroup Sample OriginSample SourceMuseum AccessionGenBank Accession
MusR052c M. musculus domesticusUnspecifiedwestern EuropeGenBank- NC_006914