Markers + reference

Exbucklandia

3 species · Hamamelidaceae · Saxifragales

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Species 3
Genome length 161–161 kb
Candidate markers 272
Primer pairs 115

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps2 LSC 735 0.0027 1.00 33.2 yes View details
psbM-trnD-GUC LSC 1130 0.0035 1.00 56.4 yes View details
trnT-GGU-psbD LSC 1410 0.0043 1.00 61.5 yes View details
rps4-trnT-UGU LSC 357 0.0037 1.00 47.7 yes View details
trnT-UGU-trnL-UAA LSC 1150 0.0046 1.00 47.1 yes View details
ycf4 LSC 555 0.0036 1.00 40.3 yes View details
petA-psbJ LSC 1044 0.0038 1.00 48.7 yes View details
ycf15-trnL-CAA IRb 623 0.0053 1.00 62.2 yes View details
rpl32-trnL-UAG SSC 1239 0.0038 0.99 62.0 yes View details
psaC SSC 246 0.0027 1.00 31.2 yes View details
rps15-ycf1 SSC 375 0.0071 1.00 44.4 yes View details
ycf1 SSC 5580 0.0019 1.00 43.2 yes View details
trnL-CAA-ycf15 IRa 623 0.0053 1.00 62.2 yes View details
trnC-GCA-petN LSC 855 0.0031 1.00 61.2 yes View details
ndhF-rpl32 SSC 1152 0.0029 1.00 61.1 yes View details
rpl20-rps12 LSC 771 0.0035 1.00 61.0 yes View details
ndhC-trnV-UAC LSC 1141 0.0029 1.00 60.7 yes View details
matK-trnK-UUU LSC 704 0.0028 1.00 60.6 yes View details
accD-psaI LSC 688 0.0029 1.00 60.6 yes View details
psbE-petL LSC 1289 0.0026 1.00 60.4 yes View details
atpH-atpI LSC 1126 0.0018 1.00 60.2 yes View details
rpoA LSC 1014 0.0020 1.00 60.0 yes View details
rps16 LSC 1102 0.0018 1.00 59.9 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 115 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU CCATGATCATGAGCAAGTGC AACGGTAGAGTACTCGGCTT 835 1.000 72.7
matK-trnK-UUU_p2 matK-trnK-UUU CCATGATCATGAGCAAGTGC ACGGTAGAGTACTCGGCTTT 834 1.000 72.7
matK-trnK-UUU_p3 matK-trnK-UUU CCATGATCATGAGCAAGTGC GCGACTGTATCTACACACCC 891 1.000 72.4
matK-trnK-UUU_p4 matK-trnK-UUU CCATGATCATGAGCAAGTGC CGTCGTGCAATCCAATCTCT 926 1.000 71.2
matK-trnK-UUU_p5 matK-trnK-UUU CCATGATCATGAGCAAGTGC GGGTTGCTAACTCAACGGTA 848 1.000 70.4
rps16_p1 rps16 TATACGAGTCATCCCCACCC ACCGGTTCCAAACTAGAGGA 1167–1169 1.000 80.1
rps16_p2 rps16 AGTCATCCCCACCCTCTTTT ACCGGTTCCAAACTAGAGGA 1161–1163 1.000 78.3
rps16_p3 rps16 GTCATCCCCACCCTCTTTTT ACCGGTTCCAAACTAGAGGA 1160–1162 1.000 75.3
rps16_p4 rps16 GAGTCATCCCCACCCTCTTT ACCGGTTCCAAACTAGAGGA 1162–1164 1.000 74.5
rps16_p5 rps16 GAGTCATCCCCACCCTCTT ACCGGTTCCAAACTAGAGGA 1162–1164 1.000 72.1
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT CGAATCCATGGAGGGTCATC 1183 1.000 78.7
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT CGAATCCATGGAGGGTCATC 1239 1.000 78.1
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA CGAATCCATGGAGGGTCATC 1184 1.000 77.5
atpH-atpI_p4 atpH-atpI GCAGTACCTTGACCAACTCC CGAATCCATGGAGGGTCATC 1243 1.000 77.5
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC CGAATCCATGGAGGGTCATC 1198 1.000 77.3
rps2_p1 rps2 GGAACCCAAGGACCGTATTC TTGGATTGATGCGAGCAGAA 1843–1844 1.000 79.2
rps2_p2 rps2 GGAACCCAAGGACCGTATTC AGGCCTGAAAGAGAACGTTG 1659–1660 1.000 79.2
rps2_p3 rps2 GGAACCCAAGGACCGTATTC AAAGAGGAAGTGTGGGGAGA 1226 1.000 79.2
rps2_p4 rps2 GGAACCCAAGGACCGTATTC AAGAGGAAGTGTGGGGAGAA 1225 1.000 79.2
rps2_p5 rps2 GGAACCCAAGGACCGTATTC ACCGCTCGAGTTTTAGCAAA 1712–1713 1.000 79.1
trnC-GCA-petN_p1 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC AGTCCACCTCTTCCCCATAC 1032–1036 1.000 79.2
trnC-GCA-petN_p2 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC GTCCACCTCTTCCCCATACT 1031–1035 1.000 79.2
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGTCCACCTCTTCCCCATAC 976–980 1.000 79.0
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GTCCACCTCTTCCCCATACT 975–979 1.000 79.0
trnC-GCA-petN_p5 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC AGCCCAAGCGAGACTTACTA 973–977 1.000 79.0
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 1241–1242 1.000 58.7
psbM-trnD-GUC_p2 psbM-trnD-GUC AGGAACTAGAATGAACAGTGCA TTCAATTGGTCAGAGCACCG 1248–1249 1.000 55.6
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC GTTCAATTGGTCAGAGCACC 1242–1243 1.000 54.6
psbM-trnD-GUC_p4 psbM-trnD-GUC GGAACTAGAATGAACAGTGCAG TTCAATTGGTCAGAGCACCG 1247–1248 1.000 53.1
psbM-trnD-GUC_p5 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TCAATTGGTCAGAGCACCG 1240–1241 1.000 52.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Exbucklandia longipetala NC_086777.1 160723 View on NCBI ↗
Exbucklandia populnea NC_065400.1 160744 View on NCBI ↗
Exbucklandia tonkinensis NC_071203.1 160814 View on NCBI ↗