Cluster set at subtree whose root is 'Testudines'

Click here to see taxon by cluster Data Availability Matrix
Cluster IDParent clusterTaxIDsGIsLminLmaxMAD1Q2Tcfi3Defline of longest sequenceTree4
0-838390755 0.797- 0.000Phrynops williamsi mitochondrial cytochrome c oxidase subunit I-like (COI) gene, partial sequence.
1-149343349700 0.768- 0.000Kachuga tecta 16S ribosomal RNA gene, partial sequence; mitochondrial.
2-1899323981597 0.502- 0.000Mauremys mutica NADH dehydrogenase subunit 4 gene, complete cds; and tRNA-His, tRNA-Ser, and tRNA-Leu genes, complete sequence; mitochondrial.
3-114185357602 0.938- 0.000Geochelone denticulata oocyte maturation factor Mos (Cmos) gene, partial cds.
4-2525252414 0.931- 0.000Pelusios sinnuatus cytochrome c oxidase subunit 1 (COI) gene, partial cds; mitochondrial.
7-150415298440 0.914- 0.000Chelonia mydas 12S ribosomal RNA gene, partial sequence; mitochondrial.
8-30718242561264 0.624- 0.000Chelonia mydas voucher CHE-GT1 cytochrome b (cytb) gene, complete cds; mitochondrial.-
9-1385534691151 0.822- 0.000Cuora bourreti voucher FMNH 261578 RNA fingerprint protein 35 (R35) gene, intron 1.
11-314516382869 0.954- 0.000Caretta caretta isolate CC_Atlantic recombination activating protein 1 (RAG-1) gene, partial cds.
29-1316176220 0.948- 0.000Kinosternon flavescens U17 snoRNA gene.
30-55119365587 0.956- 0.000Terrapene carolina voucher HBS27240 anonymous nuclear locus TB29, genomic sequence.
31-1111614700 0.961- 0.000Emydura macquarii voucher HBS100714 anonymous locus TB81 genomic sequence.
32-819355466 0.855- 0.000Elseya sp. albagula haplotype ESP11 control region, partial sequence; mitochondrial.
36-5512001295 0.972- 0.000Pelodiscus sinensis japonicus L-lactate dehydrogenase B (LDH-B) mRNA, complete cds.
37-559991701 0.827- 0.000Trachemys scripta L-lactate dehydrogenase A (LDH-A) mRNA, complete cds.
38-29351412719438 0.877- 0.000Testudo marginata voucher MVZ 247484 mitochondrion, complete genome.
40-5516002684 0.708- 0.000Trachemys scripta 12S ribosomal RNA gene, complete sequence; tRNA-Val gene, complete sequence; 16S ribosomal RNA gene, complete sequence; and tRNA-Leu gene, partial sequence; mitochondrial genes for mitochondrial products.
41-44675694 0.992- 0.000Chelydra serpentina voucher AMCC 101071 28S ribosomal RNA gene, partial sequence.
55-910521680 0.954- 0.000Chrysemys picta dorsalis voucher HBS27637 anonymous locus TB07 genomic sequence.
56-1011393393 1.000- 0.000Graptemys geographica voucher HBS23396 anonymous locus TB17 genomic sequence.
57-910682689 0.996- 0.000Chrysemys picta bellii voucher MVZ238119 anonymous locus TB82 genomic sequence.
58-3146550718 0.953- 0.000Caretta caretta isolate CC_Pacific brain-derived neurotrophic factor (BDNF) gene, partial cds.
59-851184411476 0.492- 0.000Caretta caretta isolate CC_Atlantic recombination activating protein 2 (RAG-2) gene, partial cds.
60-953340516 0.873- 0.000Trachemys scripta glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene, intron 11 and partial cds.
61-1313188189 0.999- 0.000Apalone ferox NADH dehydrogenase subunit 3 (ND3) gene, partial cds; mitochondrial.
63-1919446649 0.974- 0.000Pelomedusa subrufa aryl hydrocarbon receptor 1 (AHR) gene, partial cds.
64-1919676722 0.992- 0.000Pelomedusa subrufa nerve growth factor beta polypeptide (NGF) gene, partial cds.
65-1919554626 0.984- 0.000Carettochelys insculpta bone morphogenetic protein 2 (BMP2) gene, partial cds.
66-1616389568 0.941- 0.000Platysternon megacephalum high mobility group protein B2 (HMG-2) gene, intron and partial cds.
67-55249407856 0.827- 0.000Cuora pani clone Cpa2MVZ230513 hepatocyte nuclear factor 1-alpha (HNFAL) gene, intron 2.
68-1717654699 0.975- 0.000Kinosternon flavescens KIAA0398 protein gene, partial cds; and intron.
69-1717349854 0.770- 0.000Dermochelys coriacea proteasome (prosome, macropain) 26S subunit, ATPase, 1 (PSMC1) gene, intron and partial cds.
70-1515630884 0.853- 0.000Testudo graeca paired box protein (PAX1P1) gene, intron.
71-1818629668 0.991- 0.000Carettochelys insculpta anonymous locus TB01 genomic sequence.
72-1717601881 0.938- 0.000Psammobates pardalis zinc finger homeobox protein (ZEB2) gene, partial cds.
73-89502559 0.981- 0.000Cuora zhoui voucher HBS41855 anonymous locus TB02 genomic sequence.
74-67559643 0.977- 0.000Chrysemys picta dorsalis voucher HBS27637 anonymous locus TB49 genomic sequence.
75-910534632 0.978- 0.000Terrapene carolina voucher HBS27360 anonymous locus TB53 genomic sequence.
76-89620693 0.972- 0.000Chrysemys picta dorsalis voucher HBS27637 anonymous locus TB59 genomic sequence.
77-67556586 0.983- 0.000Pseudemys concinna floridana voucher HBS108683 anonymous locus TB86 genomic sequence.
78-78445586 0.941- 0.000Gopherus agassizii voucher HBS109173 anonymous locus TB95 genomic sequence.
88-7104519649 0.852- 0.000Caretta caretta CCOR1 gene for olfactory receptor, partial cds.
96-411525649 0.859- 0.000Caretta caretta CCOR3 gene for olfactory receptor, partial cds.
102-44261296 0.921- 0.000Trachemys scripta Dax1 (Dax1) mRNA, partial cds.
103-49123577847 0.884- 0.000Macrochelys temminckii recombination activating gene 1 (RAG-1) gene, partial cds.
104-412316941147 0.915- 0.000Mauremys mutica clone Mm1_MVZ230476 reelin gene, exons 61, 62 and partial cds.
105-3378227679 0.895- 0.000Indotestudo forstenii voucher HBS108633 anonymous locus TB73 genomic sequence.
106-311553791047 0.657- 0.000Chrysemys picta voucher HBS26210 transforming growth factor beta 2 gene, intron 5.
110-418542622118 0.282- 0.000Pseudemys concinna haplotype 65 cytochrome b-like (cytb) gene, partial sequence; tRNA-Thr and tRNA-Pro genes, control region, and tRNA-Phe gene, complete sequence; and 12S ribosomal RNA gene, partial sequence; mitochondrial.
111-1314340344 0.997- 0.000Graptemys flavimaculata DNA sequence.
116-1313576623 0.935- 0.000Chinemys reevesi neurotrophin-3 (nt-3) gene, partial cds.
117-88339440 0.949- 0.000Pelomedusa subrufa proopiomelanocortin (POMC) mRNA, partial sequence.
118-5153642862 0.768- 0.000Erymnochelys madagascariensis recombination activating protein 1 (RAG1) gene, partial cds.
178-417324520 0.913- 0.000Podocnemis unifilis isolate PounB4 mitochondrial control region, partial sequence.
203-1616142166 0.973- 0.000Melanochelys trijuga DNA, SINE flanking sequence of BKs11 locus.
204-88317563 0.703- 0.000Mauremys japonica DNA, SINE and its flanking sequence of BCr61 locus.
207-66186228 0.965- 0.000Testudo horsfieldii DNA, SINE flanking sequence of BMm105 locus.
208-44229231 0.995- 0.000Mauremys japonica DNA, SINE flanking sequence of BPm30 locus.
209-1010258470 0.721- 0.000Sacalia bealei DNA, SINE and its flanking sequence of BMr49 locus.
210-2020135211 0.882- 0.000Heosemys annandalii DNA, SINE flanking sequence of BMm74 locus.
211-1111222548 0.679- 0.000Mauremys mutica kami DNA, CryIC SINE and its flanking sequence of BMm85 locus.
212-88153193 0.935- 0.000Cuora amboinensis DNA, SINE flanking sequence of BOr04 locus.
293-361484071597 0.495- 0.000Trachemys scripta cytochrome C oxidase subunit 1 (cox1) mRNA, mitochondrial gene encoding mitochondrial protein, partial cds.
341-66395600 0.866- 0.000Testudo horsfieldii DNA, SINE franking sequence of BCr01 locus.
342-1212188194 0.978- 0.000Siebenrockiella crassicollis DNA, BKs52 locus sequence.
343-55214414 0.897- 0.000Heosemys grandis DNA, BHa25 locus sequence containing a SINE unit.
347-55274439 0.703- 0.000Testudo horsfieldii DNA, SINE and its flanking sequence of TKe17 locus.
349-44262437 0.723- 0.000Testudo horsfieldii DNA, SINE and its flanking sequence of TKe83 locus.
350-1010219459 0.701- 0.000Cuora amboinensis DNA, SINE and its flanking sequence of BHa65 locus.
351-1010242507 0.709- 0.000Cuora mouhotii DNA, SINE and its flanking sequence of BHa74 locus.
352-66248449 0.631- 0.000Kachuga smithii DNA, SINE and its flanking sequence of BKs29 locus.
353-1313191386 0.631- 0.000Heosemys annandalii DNA, SINE and its flanking sequence of BHg36 locus.
354-77164175 0.984- 0.000Geoemyda spengleri DNA, SINE flanking sequence of BMr20 locus.
355-88149169 0.964- 0.000Emys orbicularis DNA, SINE flanking sequence of BHg10 locus.
356-1111192424 0.666- 0.000Sacalia bealei DNA, SINE and its flanking sequence of BHa68 locus.
357-99281517 0.875- 0.000Mauremys sinensis DNA, SINE and its flanking sequence of BOs57 locus.
358-66242455 0.686- 0.000Kachuga smithii DNA, SINE and its flanking sequence of TTh23 locus.
359-88145200 0.963- 0.000Heosemys annandalii DNA, SINE flanking sequence of BMr15 locus.
400-3080521706 0.822- 0.000Rhinoclemmys diademata orphan G protein-coupled receptor R35 (R35) gene, intron 1.
402-1111396424 0.945- 0.000Caretta caretta 12S ribosomal RNA gene, partial sequence; mitochondrial.
434-17589387787 0.791- 0.000Chelonoidis nigra isolate PBL29 D-loop, partial sequence; mitochondrial.
435-425309380 0.969- 0.000Geochelone carbonaria isolate red actin gene, partial intron sequence.
436-439231325 0.958- 0.000Geochelone nigra isolate ESP4 aldolase 1 gene, intron and partial cds.
438-425484585 0.979- 0.000Geochelone nigra isolate ME4 calmodulin gene, intron and partial cds.
439-414293295 1.000- 0.000Geochelone chilensis isolate 8136 creatine kinase gene, intron 6 and partial cds.
440-42918052063 0.968- 0.000Geochelone carbonaria isolate red 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, complete sequence; and 5.8S ribosomal RNA gene, partial sequence.
555-77281472 0.738- 0.000Mauremys japonica DNA, SINE and its flanking sequence of BOs55 locus.
556-66239425 0.709- 0.000Mauremys mutica kami DNA, SINE and its flanking sequence of BOs74 locus.
557-77119128 0.973- 0.000Rhinoclemmys punctularia punctularia DNA, SINE flanking sequence of BHg33 locus.
558-1212220420 0.609- 0.000Melanochelys trijuga DNA, SINE and its flanking sequence of BHa59 locus.
559-77153462 0.618- 0.000Mauremys reevesii DNA, SINE and its flanking sequence of BOs68 locus.
560-44158173 0.977- 0.000Heosemys annandalii DNA, SINE flanking sequence of BOs151 locus.
561-77235433 0.682- 0.000Mauremys japonica DNA, SINE and its flanking sequence of BOs94 locus.
563-77209496 0.686- 0.000Mauremys mutica kami DNA, SINE and its flanking sequence of BMm103 locus.
564-1010184448 0.629- 0.000Sacalia bealei DNA, SINE and its flanking sequence of BHg23 locus.
565-1111237461 0.611- 0.000Heosemys annandalii DNA, SINE and its flanking sequence of BHg12 locus.
566-88139140 0.996- 0.000Mauremys reevesii DNA, SINE flanking sequence of BHg16 locus.
567-55234448 0.710- 0.000Kachuga smithii DNA, SINE and its flanking sequence of BKs85 locus.
568-77265465 0.634- 0.000Mauremys sinensis DNA, SINE and its flanking sequence of BOs33 locus.
569-66275469 0.661- 0.000Mauremys sinensis DNA, SINE and its flanking sequence of BOs52 locus.
570-66214410 0.606- 0.000Mauremys sinensis DNA, SINE and its flanking sequence of BOs80 locus.
586-99302499 0.665- 0.000Kachuga smithii DNA, CryIC SINE and its flanking sequence of BKs31 locus.
607-1019237390 0.826- 0.000Heosemys annandalii DNA, SINE and its flanking sequence of BMr20 locus.
609-66227432 0.611- 0.000Cuora mouhotii DNA, SINE and its flanking sequence of BPm20 locus.
613-1010139158 0.933- 0.000Geoclemys hamiltonii histone H4 gene, partial sequence.
614-66257456 0.712- 0.000Mauremys japonica DNA, SINE and its flanking sequence of BOs60 locus.
616-1343597972 0.833- 0.000Mauremys leprosa voucher MNCN 23659 NADH dehydrogenase subunit 1 (ND1) gene, complete cds; mitochondrial.
619-1016296376 0.935- 0.000Cyclemys oldhamii voucher BMNH 1947.3.5.63 cytochrome b (cytb) gene, partial cds; mitochondrial.
673-515371566 0.780- 0.000Chelonia mydas anonymous nuclear DNA clone CM12.
674-521377591 0.777- 0.000Chelonia mydas anonymous nuclear DNA clone CM14.
682-44940940 1.000- 0.000Eretmochelys imbricata HoxD11 (HoxD11) gene, partial cds.
683-4412761276 1.000- 0.000Eretmochelys imbricata HoxA13 (HoxA13) gene, partial cds.
927-81810731145 0.950- 0.000Sternotherus odoratus mitochondrial control region, complete sequence.

  1 Maximum Alignment Density
  2 "Q" alignment comparison score between default Clustal W and Muscle alignments
  3 Level of resolution (consensus fork index) of the strict consensus tree built from the two bootstrap trees from Clustal W and Muscle alignments.
  4 Trees are unrooted majority rule consensus trees from 'fast bootstrap parsimony' algorithm in PAUP* 4.0 using default ClustalW alignments. Expect performance to deteriorate with low MAD or Q scores, large number of taxa, and high sequence divergence (largely owing to alignment problems). Only trees for (taxon) phylogenetically informative clusters with fewer than 1000 sequences are generated.


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