Cluster set at subtree whose root is Cryptodira (rel. 194)

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Cluster IDParent clusterTaxIDsGIsGeneraLminLmaxMAD1Defline of longest sequenceTree2
0105896502559 0.981Gopherus agassizii voucher HBS109173 anonymous locus TB02 genomic sequence.
11069107521680 0.954Terrapene carolina voucher HBS27360 anonymous locus TB07 genomic sequence.
21079107393393 1.000Terrapene carolina voucher HBS27360 anonymous locus TB17 genomic sequence.
3356716034365587 0.919Emydoidea blandingii voucher HBS108703 anonymous nuclear locus TB29, genomic sequence.
4108675559643 0.977Chrysemys picta dorsalis voucher HBS27637 anonymous locus TB49 genomic sequence.
51099107534632 0.978Chrysemys picta bellii voucher HBS27688 anonymous locus TB53 genomic sequence.
6110896620693 0.972Chrysemys picta dorsalis voucher HBS27637 anonymous locus TB59 genomic sequence.
736886614690 0.968Graptemys geographica voucher HBS23396 anonymous locus TB81 genomic sequence.
81119107682689 0.996Cuora zhoui voucher HBS41855 anonymous locus TB82 genomic sequence.
9112674556586 0.983Pseudemys concinna floridana voucher HBS108683 anonymous locus TB86 genomic sequence.
10113785445586 0.941Gopherus agassizii voucher HBS109173 anonymous locus TB95 genomic sequence.
13116581443202621301 0.513Caretta caretta mitochondrial genes for tRNA-Thr, tRNA-Pro, D-loop, tRNA-Phe, partial and complete sequence.
1442181323513982325 0.378Malaclemys terrapin voucher MVZ 257697 tRNA-Gly gene, partial sequence; NADH dehydrogenase subunit 3 (ND3) gene, complete cds; tRNA-Arg gene, complete sequence; NADH dehydrogenase subunit 4L (ND4L) gene, complete cds; tRNA-His gene, complete sequence; NADH dehydrogenase subunit 4 (ND4) gene, complete cds; tRNA-Ser gene, complete sequence; and tRNA-Xle gene, partial sequence; mitochondrial.
15133362717752562118 0.404Pseudemys 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.
161176027429407967 0.735Cuora pani clone Cpa1_MVZ230512 hepatocyte nuclear factor 1-alpha (HNFAL) gene, intron 2.
1714170730532461151 0.808Cuora galbinifrons voucher FMNH 256544 RNA fingerprint protein 35 (R35) gene, intron 1.
181186121925402847 0.891Actinemys marmorata recombination activating gene 1 (RAG-1) gene, partial cds.
1911940237166941147 0.913Mauremys mutica clone Mm1_MVZ230476 reelin gene, exons 61, 62 and partial cds.
201204411619227679 0.886Indotestudo forstenii voucher HBS108633 anonymous locus TB73 genomic sequence.
2112136170173791047 0.655Terrapene carolina triunguis voucher HBS27365 transforming growth factor beta 2 gene, intron 5.
22122303010356746 0.964Pseudemys rubriventris voucher JJW 1056 ETS oncogene (ETS) gene, intron.
23123587131422734 0.846Heosemys spinosa voucher HBS109889 nerve growth factor beta polypeptide (NGF) gene, partial cds.
24124469220200516 0.828Platysternon megacephalum glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene, intron 11 and partial cds.
25125393914451693 0.924Cuora flavomarginata vimentin (Vim) gene, intron 4 and partial cds.
2612647220772105 0.996Graptemys pseudogeographica isolate pseB NADH dehydrogenase subunit 2 (ND2) gene, complete cds; tRNA-Trp, tRNA-Ala, tRNA-Asn, tRNA-Cys, and tRNA-Tyr genes, complete sequence; and cytochrome c oxidase subunit 1 (COX1) gene, partial cds; mitochondrial.
2712713142340344 0.997Graptemys versa DNA sequence.
28128131313188189 0.999Terrapene carolina NADH dehydrogenase subunit 3 (ND3) gene, partial cds; mitochondrial.
305165383662431266 0.559Pelodiscus parviformis isolate 001 cytochrome oxidase subunit I gene, partial cds; mitochondrial.
31130777491583 0.978Geochelone sulcata voucher MVZ238888 ATP-binding cassette sub-family E member 1 (ABCE1) mRNA, partial cds.
35134131312371394 0.996Malaclemys terrapin voucher MVZ257705 chromobox-like protein 3 (CBX3) mRNA, partial cds.
38137666276276 1.000Apalone ferox voucher MVZ241535 Down syndrome critical region 3 (DSCR3) mRNA, partial cds.
41140777300330 0.972Geoemyda spengleri voucher MVZ257081 eukaryotic translation initiation factor 3 subunit M (EIF3M) mRNA, partial cds.
46145998330413 0.974Sternotherus minor voucher MVZ241528 G1-S phase transition protein 1 (GSPT1) mRNA, partial cds.
49148666268273 0.996Hardella thurjii voucher MVZ248392 4-hydroxyphenylpyruvate dioxygenase (HPD) mRNA, partial cds.
53152776523563 0.984Apalone ferox voucher MVZ241535 nuclear factor I/A transcript variant 5 (NFIA005) mRNA, partial cds.
56155777386386 1.000Hardella thurjii voucher MVZ248392 nuclear transcription factor Y beta (NFYB) mRNA, partial cds.
59158998202380 0.912Hardella thurjii voucher MVZ248392 ornithine aminotransferase (OAT) mRNA, partial cds.
609111110259315 0.963Testudo graeca voucher MVZ234282 ornithine decarboxylase antizyme 1 (OAZ1) mRNA, partial cds.
61159444431431 1.000Eretmochelys imbricata voucher MVZ233242 Obg-like ATPase 1 (OLA1) mRNA, partial cds.
62160666321535 0.880Testudo hermanni voucher MVZ244866 polyA-binding protein cytoplasmic 1 (PABPC1) mRNA, partial cds.
64162131312288427 0.931Deirochelys reticularia voucher MVZ230923 programmed cell death 10 (PDCD10) mRNA, partial cds.
68166444604653 0.981Testudo hermanni voucher MVZ244866 proteasome 26S subunit ATPase 6 (PSMC6) mRNA, partial cds.
71169242420392407 0.999Pangshura smithii voucher MVZ248394 ribosomal protein L4 (RPL4) mRNA, partial cds.
7210171715459480 0.987Malayemys subtrijuga voucher MVZ230474 ribosomal protein L7a (RPL7A) mRNA, partial cds.
7639323230332339 0.998Mauremys mutica voucher MVZ230487 ribosomal protein S14 (RPS14) mRNA, partial cds.
77173131312386387 1.000Pseudemys concinna voucher MVZ241520 iron-sulfur succinate dehydrogenase complex subunit B (SDHB) mRNA, partial cds.
78174666504708 0.952Sternotherus minor voucher MVZ241528 SEC13-like protein (SEC13) mRNA, partial cds.
79175777324459 0.958Rhinoclemmys pulcherrima voucher MVZ230924 SEC62-like protein (SEC62) mRNA, partial cds.
80176111110489496 0.998Malaclemys terrapin voucher MVZ257705 serum/glucocorticoid regulated kinase 1 (SGK1) mRNA, partial cds.
81177131312436484 0.989Rhinoclemmys pulcherrima voucher MVZ230924 suppressor of mec-8 and unc-52-like protein (SMU1) mRNA, partial cds.
8217811119539606 0.986Malaclemys terrapin voucher MVZ257705 sorting nexin 6 (SNX6) mRNA, partial cds.
83179888395450 0.894Sternotherus minor voucher MVZ241528 mitochondrial superoxide dismutase 2 (SOD2) mRNA, partial cds; nuclear gene for mitochondrial product.
84180998200312 0.857Sternotherus carinatus voucher MVZ238123 signal recognition particle 54kDa (SRP54) mRNA, partial cds.
88184999279301 0.985Apalone ferox voucher MVZ241535 ubiquitin-conjugating enzyme E2K (UBE2K) mRNA, partial cds.
89185111110218280 0.960Sternotherus minor voucher MVZ241528 ubiquitin-conjugating enzyme E2N (UBE2N) mRNA, partial cds.
91187666280280 1.000Claudius angustatus voucher MVZ164771 ubiquitin-conjugating enzyme E2 variant 2 (UBE2V2) mRNA, partial cds.
92188131311562567 0.999Sternotherus carinatus voucher MVZ238123 voltage-dependent anion channel 1 (VDAC1) mRNA, partial cds.
93189555400451 0.962Geochelone sulcata voucher MVZ238888 vacuolar protein sorting 29-like protein (VPS29) mRNA, partial cds.
94190888522528 0.990Testudo hermanni voucher MVZ244866 Wilms tumor 1-associated protein (WTAP) mRNA, partial cds.
10512174605622821154 0.366Mauremys japonica voucher ANUM26080206 12S ribosomal RNA and tRNA-Val genes, complete sequence; and 16S ribosomal RNA gene, partial sequence; mitochondrial.
106114727754279602 0.947Dipsochelys arnoldi oocyte maturation factor Mos (Cmos) gene, partial cds.
1072015696172831020 0.574Nilssonia nigricans partial odc gene for ornithine decarboxylase, specimen voucher MTD:TD:3415, exons 6-7.
10883707729614704 0.898Staurotypus triporcatus recombination activating protein 1 (RAG1) gene, partial cds.
1090113200464411476 0.469Caretta caretta isolate CC_Atlantic recombination activating protein 2 (RAG-2) gene, partial cds.
1178338612710912869 0.926Caretta caretta isolate CC_Atlantic recombination activating protein 1 (RAG-1) gene, partial cds.
141252377922446660 0.958Heosemys spinosa voucher HBS117759 aryl hydrocarbon receptor 1 (AHR) gene, partial cds.
142864294295441011 0.641Lepidochelys olivacea isolate LO_Pacific brain-derived neurotrophic factor (BDNF) gene, partial cds.
143213378022554648 0.964Trionyx triunguis voucher TtSDZ bone morphogenetic protein 2 (BMP2) gene, partial cds.
144253327018389568 0.962Platysternon megacephalum high mobility group protein B2 (HMG-2) gene, intron and partial cds.
145254357321275699 0.947Cyclemys fusca voucher CAS 210070 KIAA0398 protein gene, partial cds; and intron.
146255285617349854 0.800Dermochelys coriacea proteasome (prosome, macropain) 26S subunit, ATPase, 1 (PSMC1) gene, intron and partial cds.
147256306317442907 0.781Heosemys depressa voucher HBS112432 paired box protein (PAX1P1) gene, intron.
148257367922514673 0.901Trionyx triunguis voucher TtSDZ anonymous locus TB01 genomic sequence.
149212285518601882 0.779Macrochelys temminckii zinc finger homeobox protein (ZEB2) gene, partial cds.
164313545253217700 0.766Kachuga tecta 16S ribosomal RNA gene, partial sequence; mitochondrial.
16537121512176220 0.944Kinosternon flavescens U17 snoRNA gene.
203445559991701 0.902Pelodiscus sinensis japonicus L-lactate dehydrogenase A (LDH-A) mRNA, complete cds.
2044355512001295 0.985Pelodiscus sinensis japonicus L-lactate dehydrogenase B (LDH-B) mRNA, complete cds.
230389666395600 0.866Testudo horsfieldii DNA, SINE franking sequence of BCr01 locus.
231390121210188194 0.978Siebenrockiella crassicollis DNA, BKs52 locus sequence.
232391888153193 0.935Cuora amboinensis DNA, SINE flanking sequence of BOr04 locus.
233392555214414 0.897Kachuga smithii DNA, BHa25 locus sequence containing a SINE unit.
239398555274439 0.703Testudo horsfieldii DNA, SINE and its flanking sequence of TKe17 locus.
241400444262437 0.723Testudo horsfieldii DNA, SINE and its flanking sequence of TKe83 locus.
24240110109219459 0.701Cuora amboinensis DNA, SINE and its flanking sequence of BHa65 locus.
243402101010242507 0.709Cuora mouhotii DNA, SINE and its flanking sequence of BHa74 locus.
244403666248449 0.631Kachuga smithii DNA, SINE and its flanking sequence of BKs29 locus.
245404131311191386 0.631Heosemys annandalii DNA, SINE and its flanking sequence of BHg36 locus.
246405777164175 0.985Geoemyda spengleri DNA, SINE flanking sequence of BMr20 locus.
247406202018135211 0.882Heosemys annandalii DNA, SINE flanking sequence of BMm74 locus.
248407887149169 0.965Emys orbicularis DNA, SINE flanking sequence of BHg10 locus.
249408111110192424 0.666Sacalia bealei DNA, SINE and its flanking sequence of BHa68 locus.
250409997281517 0.875Mauremys sinensis DNA, SINE and its flanking sequence of BOs57 locus.
251410161612142166 0.973Sacalia bealei DNA, SINE flanking sequence of BKs11 locus.
252411666242455 0.686Kachuga smithii DNA, SINE and its flanking sequence of TTh23 locus.
253412888145200 0.963Rhinoclemmys punctularia punctularia DNA, SINE flanking sequence of BMr15 locus.
2855187553336527 0.918Terrapene carolina triunguis haplotype 27 D-loop, partial sequence; mitochondrial.
2864857607524574 0.963Gopherus polyphemus isolate GPOR35 olfactory receptor 35 gene, partial cds.
298495595548564 0.984Gopherus polyphemus isolate GPOR37 olfactory receptor 37 pseudogene, partial sequence.
32143341727661273 0.863Gopherus berlanderi NADH dehydrogenase subunit 3 (ND3) gene, partial cds; tRNA-Arg gene, complete sequence; NADH dehydrogenase subunit 4L (ND4L) gene, complete cds; and NADH dehydrogenase subunit 4 (ND4) gene, partial cds; mitochondrial.
354466304122521706 0.908Rhinoclemmys diademata orphan G protein-coupled receptor R35 (R35) gene, intron 1.
35546713138396424 0.944Caretta caretta 12S ribosomal RNA gene, partial sequence; mitochondrial.
380493484534649 0.879Caretta caretta CCOR1 gene for olfactory receptor, partial cds.
38911776279377 0.941Leucocephalon yuwonoi voucher MVZ241499 ribosomal protein L11 (RPL11) mRNA, partial cds.
392517171717203295 0.959Malayemys subtrijuga voucher MVZ230474 proteasome subunit alpha type 6 (PSMA6) mRNA, partial cds.
469628775281472 0.738Mauremys japonica DNA, SINE and its flanking sequence of BOs55 locus.
470629665239425 0.709Mauremys mutica kami DNA, SINE and its flanking sequence of BOs74 locus.
471630888317563 0.703Mauremys japonica DNA, SINE and its flanking sequence of BCr61 locus.
472631666186228 0.965Testudo horsfieldii DNA, SINE flanking sequence of BMm105 locus.
473632444229231 0.995Mauremys japonica DNA, SINE flanking sequence of BPm30 locus.
474633777119128 0.973Rhinoclemmys punctularia punctularia DNA, SINE flanking sequence of BHg33 locus.
475634121212220420 0.609Melanochelys trijuga DNA, SINE and its flanking sequence of BHa59 locus.
47663510109258470 0.721Sacalia bealei DNA, SINE and its flanking sequence of BMr49 locus.
477636775153462 0.618Mauremys sinensis DNA, SINE and its flanking sequence of BOs68 locus.
478637444158173 0.977Heosemys annandalii DNA, SINE flanking sequence of BOs151 locus.
479638775235433 0.682Mauremys sinensis DNA, SINE and its flanking sequence of BOs94 locus.
481640775209496 0.686Mauremys mutica kami DNA, SINE and its flanking sequence of BMm103 locus.
48264111117222548 0.679Mauremys mutica kami DNA, CryIC SINE and its flanking sequence of BMm85 locus.
483642998184448 0.643Sacalia bealei DNA, SINE and its flanking sequence of BHg23 locus.
484643111110237461 0.611Heosemys grandis DNA, SINE and its flanking sequence of BHg12 locus.
485644888139140 0.996Cuora amboinensis DNA, SINE flanking sequence of BHg16 locus.
486645554234448 0.710Kachuga smithii DNA, SINE and its flanking sequence of BKs85 locus.
487646775265465 0.634Mauremys sinensis DNA, SINE and its flanking sequence of BOs33 locus.
488647665275469 0.661Mauremys sinensis DNA, SINE and its flanking sequence of BOs52 locus.
489648665214410 0.606Mauremys sinensis DNA, SINE and its flanking sequence of BOs80 locus.
494653997302499 0.665Kachuga smithii DNA, CryIC SINE and its flanking sequence of BKs31 locus.
508663216042387787 0.792Chelonoidis nigra isolate AGO6 D-loop, partial sequence; mitochondrial.
5096645262309380 0.970Geochelone carbonaria isolate red actin gene, partial intron sequence.
5106655402231330 0.945Geochelone pardalis isolate to aldolase 1 gene, intron and partial cds.
5126675262484585 0.980Geochelone nigra isolate P244 calmodulin gene, intron and partial cds.
5136685152293295 1.000Geochelone nigra isolate PB3 creatine kinase gene, intron 6 and partial cds.
514669530218052063 0.969Geochelone carbonaria isolate red 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, complete sequence; and 5.8S ribosomal RNA gene, partial sequence.
569734141422597972 0.771Mauremys leprosa voucher MNCN 23659 NADH dehydrogenase subunit 1 (ND1) gene, complete cds; mitochondrial.
57073513402635706 0.996Cuora trifasciata voucher KFBG 021325338 nerve growth factor beta polypeptide gene, partial cds.
573727664257456 0.712Mauremys japonica DNA, SINE and its flanking sequence of BOs60 locus.
574728664227432 0.611Cuora mouhotii DNA, SINE and its flanking sequence of BPm20 locus.
5757389156237390 0.840Heosemys annandalii DNA, SINE and its flanking sequence of BMr20 locus.
58072612128139158 0.937Geoclemys hamiltonii histone H4 gene, partial sequence.
5827309107188200 0.964Lissemys punctata punctata 12S ribosomal RNA gene, partial sequence; mitochondrial.
697876444940940 1.000Eretmochelys imbricata HoxD11 (HoxD11) gene, partial cds.
69887744412761276 1.000Eretmochelys imbricata HoxA13 (HoxA13) gene, partial cds.
699878494468468 1.000Lepidochelys olivacea haplotype 9 recombination activating protein 1 (Rag1) gene, partial cds.
7038825154371566 0.780Caretta caretta anonymous nuclear DNA from locus pdCM12 isolate CC98.
7048835214377591 0.777Caretta caretta anonymous nuclear DNA from locus pdCM14 isolate CC98.
726927444482615 0.846Apalone mutica doublesex and mab-3 related transcription factor 1 (Dmrt1) mRNA, partial cds.
728929444261296 0.921Apalone mutica nuclear receptor subfamily 0 group B member 1 mRNA, partial cds.
85110426252390403 0.984Nilssonia formosa partial odc gene intron, specimen voucher MTD:TD:5865.
852999512414312008 0.758Palea steindachneri 16S ribosomal RNA gene, complete sequence; mitochondrial.
8841034818210731145 0.950Sternotherus odoratus mitochondrial control region, complete sequence.
9182194447591176 0.911Carettochelys insculpta cullin-associated and neddylation-dissociated 1 gene, partial cds.

  1 Maximum Alignment Density
   2 Trees are unrooted RAxML trees based on Muscle alignments. Expect performance to deteriorate with low MAD 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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