Cluster set at subtree whose root is 'Pleurodira'

Click here to see taxon by cluster Data Availability Matrix
Cluster IDParent clusterTaxIDsGIsLminLmaxMAD1Q2Tcfi3Defline of longest sequenceTree4
0077390755 0.883- 0.000Phrynops williamsi mitochondrial cytochrome c oxidase subunit I-like (COI) gene, partial sequence.
113134349677 0.713- 0.000Phrynops hogei 16S ribosomal RNA gene, partial sequence; mitochondrial gene for mitochondrial product.
28712417417 1.000- 0.000Platemys platycephala isolate AK10229 cytochrome b (cytb) gene, partial cds; mitochondrial.
32814732737 0.997- 0.000Pelomedusa subrufa NADH dehydrogenase subunit 4 (ND4) gene, partial cds; mitochondrial.
542525252414 0.931- 0.000Pelusios sinnuatus cytochrome c oxidase subunit 1 (COI) gene, partial cds; mitochondrial.
6511876876 1.000- 0.000Chelodina longicollis atrial natriuretic peptide (ANP) mRNA, complete cds.-
7611249249 1.000- 0.000Chelodina longicollis glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA, partial cds.-
872838298398 0.948- 0.000Erymnochelys madagascariensis mitochondrial partial 12S rRNA gene, isolate ErymadaI.
98141244881044 0.524- 0.000Peltocephalus dumeriliana mitochondrial partial cytb gene for cytochrome b.
1091720925977 0.969- 0.000Phrynops gibbus RNA fingerprint fragment 35 (R35) gene, intron 1.
111011773773 1.000- 0.000Chelodina longicollis B-type natriuretic peptide (BNP) mRNA, complete cds.-
12117827902793 0.999- 0.000Podocnemis expansa recombination activating gene 1 (RAG-1) gene, partial cds.
131211162162 1.000- 0.000Chelodina rugosa microsatellite T12 sequence.-
141311124124 1.000- 0.000Chelodina rugosa microsatellite T14 sequence.-
151411125125 1.000- 0.000Chelodina rugosa microsatellite T17 sequence.-
161511164164 1.000- 0.000Chelodina rugosa microsatellite T26 sequence.-
171611162162 1.000- 0.000Chelodina rugosa microsatellite T42 sequence.-
181711141141 1.000- 0.000Chelodina rugosa microsatellite T44 sequence.-
191811148148 1.000- 0.000Chelodina rugosa microsatellite T80 sequence.-
201911146146 1.000- 0.000Chelodina rugosa microsatellite T87 sequence.-
212011165165 1.000- 0.000Chelodina rugosa microsatellite T58 sequence.-
222111240240 1.000- 0.000Chelodina rugosa microsatellite T11 sequence.-
232211369369 1.000- 0.000Chelodina rugosa microsatellite T15 sequence.-
242311345345 1.000- 0.000Chelodina rugosa microsatellite T31 sequence.-
252411262262 1.000- 0.000Chelodina rugosa microsatellite T39 sequence.-
262511223223 1.000- 0.000Chelodina rugosa microsatellite T41 sequence.-
272611242242 1.000- 0.000Chelodina rugosa microsatellite T47 sequence.-
282711450450 1.000- 0.000Chelodina rugosa microsatellite T67 sequence.-
292811138138 1.000- 0.000Chelodina rugosa microsatellite T27 sequence.-
302933215215 1.000- 0.000Chelodina novaeguineae u17 snoRNA gene.-
313033577582 0.996- 0.000Podocnemis expansa voucher HBS109191 anonymous locus TB29 genomic sequence.-
323133678700 0.979- 0.000Emydura macquarii voucher HBS100714 anonymous locus TB81 genomic sequence.-
3332819355466 0.855- 0.000Elseya sp. albagula haplotype ESP11 control region, partial sequence; mitochondrial.
343311389389 1.000- 0.000Platemys platycephala 12S mitochondrial rRNA, mitochondrial gene, partial sequence.-
35341144804480 1.000- 0.000Acanthochelys spixii retrotransposon CR1-like LINE, copmlete sequence.-
363513290388 0.907- 0.000Acanthochelys spixii CR1-like LINE DNA, partial sequence.-
37361112121212 1.000- 0.000Chelodina siebenrocki L-lactate dehydrogenase B (LDH-B) mRNA, complete cds.-
383711999999 1.000- 0.000Chelodina siebenrocki L-lactate dehydrogenase A (LDH-A) mRNA, complete cds.-
39112129310421329 0.890- 0.000Podocnemis expansa isolate G6 D-loop, partial sequence; mitochondrial.-
4011311168168 1.000- 0.000Podocnemis expansa microsatellite PE344 sequence.-
4111411317317 1.000- 0.000Podocnemis expansa microsatellite PE519 sequence.-
4211511252252 1.000- 0.000Podocnemis expansa microsatellite PE1075 sequence.-
435868610718 0.979- 0.000Pelomedusa subrufa brain-derived neurotrophic factor (BDNF) gene, partial cds.
441161111576580 0.999- 0.000Pelomedusa subrufa neurotrophin-3 (NT-3) gene, partial cds.
4511766373440 0.970- 0.000Pelomedusa subrufa proopiomelanocortin (POMC) mRNA, partial sequence.
4611866728862 0.937- 0.000Erymnochelys madagascariensis recombination activating protein 1 (RAG1) gene, partial cds.
475611393393 1.000- 0.000Podocnemis expansa voucher HBS109191 anonymous locus TB17 genomic sequence.-
4811911330330 1.000- 0.000Podocnemis expansa mitochondrial partial D-loop, isolate PEXP1.-
49277783805 0.978- 0.000Podocnemis sextuberculata mitochondrial nd4 gene (partial), tRNA-His gene and tRNA-Ser gene (partial).
50599106361193 0.580- 0.000Pelomedusa subrufa recombination activating protein 2 (RAG-2) gene, partial cds.
5112011165165 1.000- 0.000Erymnochelys madagascariensis clone 59HDZ188 microsatellite sequence.-
5212112212226 0.969- 0.000Erymnochelys madagascariensis clone 59HDZ397 microsatellite sequence.-
5312211220220 1.000- 0.000Erymnochelys madagascariensis clone 59HDZ196 microsatellite sequence.-
5412311237237 1.000- 0.000Erymnochelys madagascariensis clone 59HDZ234 microsatellite sequence.-
5512411106106 1.000- 0.000Erymnochelys madagascariensis clone 59HDZ242 microsatellite sequence.-
5612511311311 1.000- 0.000Erymnochelys madagascariensis clone 59HDZ327 microsatellite sequence.-
5712611201201 1.000- 0.000Erymnochelys madagascariensis clone 59HDZ499 microsatellite sequence.-
5812711229229 1.000- 0.000Erymnochelys madagascariensis clone 59HDZ669 microsatellite sequence.-
5912811154154 1.000- 0.000Erymnochelys madagascariensis clone 59HDZ777 microsatellite sequence.-
6012911152152 1.000- 0.000Erymnochelys madagascariensis clone 59HDZ897 microsatellite sequence.-
613911397397 1.000- 0.000Pelomedusa subrufa voucher RAX 2055 (at KU) seventh in absentia gene, partial cds.-
621301124542454 1.000- 0.000Pelomedusa subrufa voucher RAX 2055 (at KU) 12S ribosomal RNA gene, partial sequence; tRNA-Val gene, complete sequence; and 16S ribosomal RNA gene, partial sequence; mitochondrial.-
634111694694 1.000- 0.000Pelomedusa subrufa voucher RAX 2055 (at KU) 28S ribosomal RNA gene, partial sequence.-
64131111678716787 1.000- 0.000Pelomedusa subrufa, complete mitochondrial genome.-
6513211782782 1.000- 0.000Pelomedusa subrufa mitochondrial nd4 gene (partial), tRNA-His gene and tRNA-Ser gene (partial).-
666311649649 1.000- 0.000Pelomedusa subrufa aryl hydrocarbon receptor 1 (AHR) gene, partial cds.-
676411722722 1.000- 0.000Pelomedusa subrufa nerve growth factor beta polypeptide (NGF) gene, partial cds.-
686511560560 1.000- 0.000Pelomedusa subrufa bone morphogenetic protein 2 (BMP2) gene, partial cds.-
696611548548 1.000- 0.000Pelomedusa subrufa high mobility group protein B2 (HMG-2) gene, intron and partial cds.-
706711627627 1.000- 0.000Pelomedusa subrufa hepatocyte nuclear factor 1-alpha (HNFAL) gene, intron 2.-
716911667667 1.000- 0.000Pelomedusa subrufa proteasome (prosome, macropain) 26S subunit, ATPase, 1 (PSMC1) gene, intron and partial cds.-
727011716716 1.000- 0.000Pelomedusa subrufa paired box protein (PAX1P1) gene, intron.-
737211743743 1.000- 0.000Pelomedusa subrufa zinc finger homeobox protein (ZEB2) gene, partial cds.-
7413411528528 1.000- 0.000Hydromedusa tectifera mitochondrial control region, partial sequence.-
751351111201120 1.000- 0.000Pelusios subniger alpha enolase mRNA, partial cds.-
7613611519519 1.000- 0.000Pelusios subniger recombination-activating gene 1 (RAG1) gene, partial cds.-
776211909909 1.000- 0.000Pelusios subniger dopamine receptor type 1b (dbdr) gene, partial cds.-
785111507507 1.000- 0.000Pelusios subniger acetylcholinergic receptor M4 (acm4) gene, partial cds.-
795211751751 1.000- 0.000Pelusios subniger dopamine receptor type 1a (dadr) gene, partial cds.-
805311523523 1.000- 0.000Pelusios subniger transcription factor sox-9 (sox9) gene, partial cds.-
8115714491541 0.950- 0.000Hydromedusa maximiliani mitochondrial control region, partial sequence.-
8215813374391 0.979- 0.000Hydromedusa maximiliani clone Hmaxmb1b cytochrome b-like gene, partial sequence; mitochondrial gene for mitochondrial product.-
8315911164164 1.000- 0.000Podocnemis unifilis clone Puni_1A5 microsatellite sequence.-
8416011348348 1.000- 0.000Podocnemis unifilis clone Puni_1B2 microsatellite sequence.-
8516111260260 1.000- 0.000Podocnemis unifilis clone Puni_1B11 microsatellite sequence.-
8616211165165 1.000- 0.000Podocnemis unifilis clone Puni_1C3 microsatellite sequence.-
8716311136136 1.000- 0.000Podocnemis unifilis clone Puni_1C9 microsatellite sequence.-
8816411218218 1.000- 0.000Podocnemis unifilis clone Puni_1B10 microsatellite sequence.-
8916511129129 1.000- 0.000Podocnemis unifilis clone Puni_1D9 microsatellite sequence.-
9016611163163 1.000- 0.000Podocnemis unifilis clone Puni_1D11 microsatellite sequence.-
9116711166166 1.000- 0.000Podocnemis unifilis clone Puni_1D12 microsatellite sequence.-
9216811203203 1.000- 0.000Podocnemis unifilis clone Puni_1E1 microsatellite sequence.-
9316911189189 1.000- 0.000Podocnemis unifilis clone Puni_1F10 microsatellite sequence.-
9417011381381 1.000- 0.000Podocnemis unifilis clone Puni_1H8 microsatellite sequence.-
9517111171171 1.000- 0.000Podocnemis unifilis clone Puni_1H9 microsatellite sequence.-
9617211151151 1.000- 0.000Podocnemis unifilis clone Puni_2A9 microsatellite sequence.-
9717311250250 1.000- 0.000Podocnemis unifilis clone Puni_2C11 microsatellite sequence.-
9817411219219 1.000- 0.000Podocnemis unifilis clone Puni_2D9 microsatellite sequence.-
9917511157157 1.000- 0.000Podocnemis unifilis clone Puni_2D10 microsatellite sequence.-
10017611240240 1.000- 0.000Podocnemis unifilis clone Puni_2E7 microsatellite sequence.-
10117711283283 1.000- 0.000Podocnemis unifilis clone Puni_2F6 microsatellite sequence.-
102178417324520 0.913- 0.000Podocnemis unifilis isolate PounB4 mitochondrial control region, partial sequence.
10318211784784 1.000- 0.000Peltocephalus dumeriliana mitochondrial nd4 gene (partial), tRNA-His gene and tRNA-Ser gene (partial).-
1041831111491149 1.000- 0.000Pelusios castaneus myf-5 gene for myogenic factor 5, partial cds.-
10518511323323 1.000- 0.000Podocnemis vogli mitochondrial partial D-loop.-
10618611188188 1.000- 0.000Mesoclemmys nasutus NADH dehydrogenase subunit 3 (ND3) gene, partial cds; mitochondrial.-
10718711189189 1.000- 0.000Macrochelodina parkeri NADH dehydrogenase subunit 3 (ND3) gene, partial cds; mitochondrial.-

  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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