Markers + reference

Eurya

5 species · Pentaphylacaceae · Ericales

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Species 5
Genome length 157–157 kb
Candidate markers 262
Primer pairs 95

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1700 0.0015 1.00 52.1 yes View details
atpH-atpI LSC 1112 0.0013 1.00 44.7 yes View details
petN-psbM LSC 1137 0.0028 1.00 49.9 yes View details
ycf3-trnS-GGA LSC 821 0.0017 1.00 49.3 yes View details
ndhC-trnV-UAC LSC 1175 0.0020 1.00 52.3 yes View details
ycf2-trnL-CAA IRb 709 0.0023 1.00 45.5 yes View details
ycf1 SSC 5628 0.0004 1.00 45.3 yes View details
ndhB-trnL-CAA IRa 554 0.0000 1.00 34.7 yes View details
trnL-CAA-ycf2 IRa 709 0.0023 1.00 45.5 yes View details
rpl23-trnH-GUG IRa 1598 0.0031 0.99 51.1 no View details
trnT-GGU-psbD LSC 1099 0.0004 0.95 56.0 yes View details
ycf4-cemA LSC 902 0.0007 1.00 52.5 yes View details
petA-psbJ LSC 995 0.0012 1.00 50.8 yes View details
rbcL-accD LSC 592 0.0014 1.00 48.4 yes View details
ndhF-rpl32 SSC 914 0.0004 1.00 48.0 yes View details
rpoC2 LSC 4173 0.0004 1.00 46.6 yes View details
atpI-rps2 LSC 208 0.0058 1.00 45.6 yes View details
rpoC1 LSC 2813 0.0004 1.00 45.0 yes View details
rbcL LSC 1428 0.0011 1.00 45.0 yes View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAAATTGAAATGGGGCGTGG 1846–1871 1.000 79.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 1829–1854 1.000 79.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1788–1813 1.000 79.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GTCGAGTCAAGAGCACCTTT GAAATTGAAATGGGGCGTGG 1900–1925 1.000 79.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1771–1796 1.000 78.7
trnG-UCC_p1 trnG-UCC CCAATTCCCCTGTTCGACAA AGAGGGTATATAAGAGAGGATC 825 1.000 40.1
trnG-UCC_p2 trnG-UCC TTGATTACGCCCAATTCCCC AGAGGGTATATAAGAGAGGATC 835 1.000 40.1
trnG-UCC_p3 trnG-UCC GATTACGCCCAATTCCCCTG AGAGGGTATATAAGAGAGGATC 833 1.000 40.1
trnG-UCC_p4 trnG-UCC TTCCCCTGTTCGACAAAAGA AGAGGGTATATAAGAGAGGATC 821 1.000 40.1
trnG-UCC_p5 trnG-UCC CCAATTCCCCTGTTCGACAA TAGAGGGTATATAAGAGAGGATC 826 1.000 40.1
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1200 1.000 75.8
atpH-atpI_p2 atpH-atpI TACCTTCTACAGCTTGGCCT TTTTTGCAACTTTAGCCGCG 1283 1.000 75.7
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT TTTTTGCAACTTTAGCCGCG 1256 1.000 75.2
atpH-atpI_p4 atpH-atpI AGCCAATCCAGCAGCAATAA TTTTTGCAACTTTAGCCGCG 1216 1.000 74.9
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTTGCAACTTTAGCCGCG 1201 1.000 74.6
atpI-rps2_p1 atpI-rps2 ATGTTGGCCTACTTCCACAC ATTTCGATTCCAGCGAACGA 391 1.000 79.0
atpI-rps2_p2 atpI-rps2 ATGTTGGCCTACTTCCACAC TTTCGATTCCAGCGAACGAT 390 1.000 79.0
atpI-rps2_p3 atpI-rps2 GGCCATGGACTTGGAAACTT ATTTCGATTCCAGCGAACGA 428 1.000 77.6
atpI-rps2_p4 atpI-rps2 GGCCATGGACTTGGAAACTT TTTCGATTCCAGCGAACGAT 427 1.000 77.6
atpI-rps2_p5 atpI-rps2 CTTGGCCATGGACTTGGAAA TTTCGATTCCAGCGAACGAT 430 1.000 77.6
rpoC2_p1 rpoC2 ATGTTACTGCATGGATCGGG ATTAGGAATTCGTTGGGCCC 200 1.000 78.2
rpoC2_p2 rpoC2 ATGTTACTGCATGGATCGGG GGCCCTTTAGGAACAGCTTT 185 1.000 78.2
rpoC2_p3 rpoC2 ATGTTACTGCATGGATCGGG AATTCGTTGGGCCCTTTAGG 194 1.000 77.5
rpoC2_p4 rpoC2 ATGTTACTGCATGGATCGGG GGAATTCGTTGGGCCCTTTA 196 1.000 77.5
rpoC2_p5 rpoC2 GTTACTGCATGGATCGGGAT ATTAGGAATTCGTTGGGCCC 198 1.000 75.9
rpoC1_p1 rpoC1 TTCCCACGGGTCTCATAGAA TTGCTCGTTCGAGAACTACG 2955 1.000 77.8
rpoC1_p2 rpoC1 TAGTTGAACCGGAGAGACCC TTGCTCGTTCGAGAACTACG 2978 1.000 76.2
rpoC1_p3 rpoC1 ATTCCCACGGGTCTCATAGA TTGCTCGTTCGAGAACTACG 2956 1.000 76.0
rpoC1_p4 rpoC1 TCCCACGGGTCTCATAGAAT TTGCTCGTTCGAGAACTACG 2954 1.000 76.0
rpoC1_p5 rpoC1 TTCCCACGGGTCTCATAGAA TTCGATTGCTCGTTCGAGAA 2960 1.000 75.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Eurya kueichowensis PP999694.1 157228 View on NCBI ↗
Eurya loquaiana NC_050937.1 157218 View on NCBI ↗
Eurya muricata PP078679.1 157188 View on NCBI ↗
Eurya nitida PQ834811.1 157191 View on NCBI ↗
Eurya rubiginosa var. attenuata ON729444.1 157215 View on NCBI ↗