Markers + reference

Cunninghamia

2 species · Cupressaceae · Cupressales

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Species 2
Genome length 135–135 kb
Candidate markers 232
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 232 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA Genome 1062 0.0000 1.00 40.0 yes View details
rps2 Genome 696 0.0000 1.00 27.3 yes View details
trnI-trnV Genome 2958 0.0007 1.00 56.3 yes View details
rpl16 Genome 1323 0.0008 1.00 59.2 yes View details
rps12-ycf1 Genome 1760 0.0006 0.89 61.8 yes View details
trnF-accD Genome 1751 0.0006 1.00 58.6 yes View details
trnI-psbA Genome 134 NA 1.00 64.2 no View details
psbD-trnT Genome 1398 0.0000 0.99 59.3 yes View details
ycf3-psaA Genome 609 0.0000 1.00 58.9 yes View details
trnI-ycf2 Genome 644 0.0000 1.00 58.9 yes View details
psaI-ycf4 Genome 601 0.0000 1.00 58.9 yes View details
ycf2 Genome 7035 0.0000 0.97 55.2 yes View details
rps2-atpI Genome 246 0.0041 1.00 54.8 yes View details
matK-trnK Genome 697 0.0000 1.00 40.0 yes View details
trnK-rps16 Genome 715 0.0000 1.00 40.0 yes View details
rps16 Genome 1061 0.0000 1.00 40.0 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA TGGCCAAGCAGCTAAAAAGA TGCGATTGGATCACTAGCAC 786 1.000 79.5
psbA_p2 psbA CTACTGGCCAAGCAGCTAAA TGCGATTGGATCACTAGCAC 790 1.000 78.6
psbA_p3 psbA CATAGTGCTGATGCCCAGAG TGCGATTGGATCACTAGCAC 828 1.000 78.6
psbA_p4 psbA TACTACTGGCCAAGCAGCTA TGCGATTGGATCACTAGCAC 792 1.000 78.4
psbA_p5 psbA TGGCCAAGCAGCTAAAAAGA GCGATTGGATCACTAGCACT 785 1.000 78.1
matK-trnK_p1 matK-trnK TGCGTAAAGATCTTCCCGAA ACTGCGTATTCCACTTCGAC 861 1.000 71.6
matK-trnK_p2 matK-trnK TGCGTAAAGATCTTCCCGAA GCGTATTCCACTTCGACTGT 858 1.000 71.6
matK-trnK_p3 matK-trnK TTGCGTAAAGATCTTCCCGA ACTGCGTATTCCACTTCGAC 862 1.000 71.6
matK-trnK_p4 matK-trnK TTGCGTAAAGATCTTCCCGA GCGTATTCCACTTCGACTGT 859 1.000 71.6
matK-trnK_p5 matK-trnK TGCGTAAAGATCTTCCCGAA TGCGTATTCCACTTCGACTG 859 1.000 71.6
trnK-rps16_p1 trnK-rps16 AGTACTTCATCCGAACGTGC TTAGGAGCTCAACCTACGGG 892–893 1.000 75.8
trnK-rps16_p2 trnK-rps16 CATCCGAACGTGCAAAAGAC TTAGGAGCTCAACCTACGGG 885–886 1.000 75.5
trnK-rps16_p3 trnK-rps16 TCATCCGAACGTGCAAAAGA TTAGGAGCTCAACCTACGGG 886–887 1.000 74.8
trnK-rps16_p4 trnK-rps16 GTACTTCATCCGAACGTGCA TTAGGAGCTCAACCTACGGG 891–892 1.000 73.5
trnK-rps16_p5 trnK-rps16 ACTTCATCCGAACGTGCAAA TTAGGAGCTCAACCTACGGG 889–890 1.000 72.6
rps16_p1 rps16 GGACCTAGACGTAGACGCAT TCCATTTTGTATCAGATCAAAGA 1115 1.000 40.0
rps16_p2 rps16 GGACCTAGACGTAGACGCAT TCCATTTTGTATCAGATCAAAGATCT 1115 1.000 40.0
rps16_p3 rps16 TTGGACCTAGACGTAGACGC TCCATTTTGTATCAGATCAAAGA 1117 1.000 40.0
rps16_p4 rps16 TTGGACCTAGACGTAGACGC TCCATTTTGTATCAGATCAAAGATCT 1117 1.000 40.0
rps16_p5 rps16 GGACCTAGACGTAGACGCAT TCCATTTTGTATCAGATCAAAGATC 1115 1.000 40.0
ycf3-psaA_p1 ycf3-psaA TGGTTTGATCAAGCTGCTGA AGAAATGACCGGGTTTAGCC 813–814 1.000 76.9
ycf3-psaA_p2 ycf3-psaA TGGTTTGATCAAGCTGCTGA GGATCCCTCTCCACTACGAT 769–770 1.000 75.5
ycf3-psaA_p3 ycf3-psaA TGGAAACAAGCTATAGCGCT AGAAATGACCGGGTTTAGCC 789–790 1.000 73.6
ycf3-psaA_p4 ycf3-psaA TGGAAACAAGCTATAGCGCT GGATCCCTCTCCACTACGAT 745–746 1.000 72.2
ycf3-psaA_p5 ycf3-psaA GGTTTGATCAAGCTGCTGAG AGAAATGACCGGGTTTAGCC 812–813 1.000 71.8
psbD-trnT_p1 psbD-trnT AAGCAATAGACCGGACCAAC GCCCTTTTAACTCAGCGGTA 1576–1584 1.000 78.7
psbD-trnT_p2 psbD-trnT ACAAAACGGTCTCTGCGTAG GCCCTTTTAACTCAGCGGTA 1548–1556 1.000 77.8
psbD-trnT_p3 psbD-trnT AACAAAACGGTCTCTGCGTA GCCCTTTTAACTCAGCGGTA 1549–1557 1.000 77.8
psbD-trnT_p4 psbD-trnT AAGCAATAGACCGGACCAAC GGCGTAAGTCATCGGTTCAA 1539–1547 1.000 77.3
psbD-trnT_p5 psbD-trnT ACAAAACGGTCTCTGCGTAG GGCGTAAGTCATCGGTTCAA 1511–1519 1.000 76.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Cunninghamia lanceolata NC_021437.1 135334 View on NCBI ↗
Cunninghamia lanceolata var. konishii LC571741.1 135188 View on NCBI ↗