Markers + reference

Helwingia

3 species · Helwingiaceae · Aquifoliales

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Species 3
Genome length 158–159 kb
Candidate markers 263
Primer pairs 85

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 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 323 0.0144 1.00 52.9 yes View details
rps2 LSC 711 0.0000 1.00 26.7 yes View details
rpoC2 LSC 4152 0.0010 1.00 46.9 yes View details
trnE-UUC-trnT-GGU LSC 978 0.0041 1.00 63.0 yes View details
psbE LSC 252 0.0000 1.00 23.8 yes View details
psbE-petL LSC 1285 0.0036 1.00 49.9 yes View details
petL-petG LSC 174 0.0460 1.00 54.4 yes View details
ycf1 IRb 1101 0.0000 1.00 46.4 no View details
ndhE SSC 306 0.0000 1.00 19.8 yes View details
ycf1 SSC 5538 0.0008 1.00 53.0 yes View details
trnF-GAA-ndhJ LSC 674 0.0020 1.00 60.0 yes View details
trnS-GCU-trnT-CGU LSC 730 0.0009 1.00 59.5 yes View details
ycf3-trnS-GGA LSC 881 0.0008 1.00 59.5 yes View details
ndhD SSC 1503 0.0009 1.00 59.3 yes View details
rps16-trnQ-UUG LSC 2232 0.0006 1.00 57.7 yes View details
trnG-GCC-trnM-CAU LSC 182 0.0000 0.99 53.6 yes View details
rpl23-trnH-GUG IRa 1640 0.0012 1.00 52.3 no View details
trnD-GUC LSC 74 0.0180 1.00 51.5 yes View details
psbK-psbI LSC 395 0.0034 1.00 48.8 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 441–447 1.000 77.5
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 455–461 1.000 77.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 454–460 1.000 77.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 456–462 1.000 77.4
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 442–448 1.000 77.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TTCCTTCTCTTCGGGATCGA GAGGTTCGAATCCTTCCGTC 2307–2308 1.000 78.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCAACGATTTGATAGACGGC GAGGTTCGAATCCTTCCGTC 2278–2279 1.000 76.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGGGATCGAACATCAATTGC GAGGTTCGAATCCTTCCGTC 2296–2297 1.000 76.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CTTCCTTCTCTTCGGGATCG GAGGTTCGAATCCTTCCGTC 2308–2309 1.000 75.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TTCCTTCTCTTCGGGATCGA TTCGGAGGTTCGAATCCTTC 2311–2312 1.000 73.7
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG CGTCCTGGATCATTAGAGAGG 514–516 1.000 64.4
psbK-psbI_p2 psbK-psbI CGTCGATGTTATGCCAGTCA CGTCCTGGATCATTAGAGAGG 563–565 1.000 64.2
psbK-psbI_p3 psbK-psbI TCGTCGATGTTATGCCAGTC CGTCCTGGATCATTAGAGAGG 564–566 1.000 63.2
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT CGTCCTGGATCATTAGAGAGG 511–513 1.000 62.4
psbK-psbI_p5 psbK-psbI TTGGCAAGCTGCTGTAAGTT CGTCCTGGATCATTAGAGAGG 512–514 1.000 62.4
trnS-GCU-trnT-CGU_p1 trnS-GCU-trnT-CGU ATTAGCAATCCGCCGCTTTA GCAAACCGAAAGACCCCTTA 845–846 1.000 79.1
trnS-GCU-trnT-CGU_p2 trnS-GCU-trnT-CGU ACGGAAAGAGAGGGATTCGA GCAAACCGAAAGACCCCTTA 894–895 1.000 78.2
trnS-GCU-trnT-CGU_p3 trnS-GCU-trnT-CGU CGAAAACCTCGTACAACGGA GCAAACCGAAAGACCCCTTA 864–865 1.000 77.5
trnS-GCU-trnT-CGU_p4 trnS-GCU-trnT-CGU GCTTTAGTCCACTCAGCCAT GCAAACCGAAAGACCCCTTA 831–832 1.000 76.1
trnS-GCU-trnT-CGU_p5 trnS-GCU-trnT-CGU AGTCCACTCAGCCATCTCTC GCAAACCGAAAGACCCCTTA 826–827 1.000 75.3
rps2_p1 rps2 AAGCCAAAGCAACAGTCGTA TTACCCGGCGAACTAATTGG 1990–1991 1.000 79.6
rps2_p2 rps2 ATGGACTTGGAAACCCCCTA TTACCCGGCGAACTAATTGG 1674–1675 1.000 79.4
rps2_p3 rps2 AAGCCAAAGCAACAGTCGTA AATGTCTACGGCCAATCGAC 1455 1.000 79.3
rps2_p4 rps2 ATGGACTTGGAAACCCCCTA AATGTCTACGGCCAATCGAC 1139 1.000 79.1
rps2_p5 rps2 AAGCCAAAGCAACAGTCGTA AGGCCTGAAAGAGAACGTTG 1790–1791 1.000 78.9
rpoC2_p1 rpoC2 GCGAAGGGGAAACTAGACTG AGTGATTGCTGAGATTCGCG 218 1.000 74.9
rpoC2_p2 rpoC2 AGCGAAGGGGAAACTAGACT AGTGATTGCTGAGATTCGCG 219 1.000 74.5
rpoC2_p3 rpoC2 CTAGACTGGATCTGCATGGC AGTGATTGCTGAGATTCGCG 206 1.000 73.7
rpoC2_p4 rpoC2 TAGACTGGATCTGCATGGCT AGTGATTGCTGAGATTCGCG 205 1.000 73.4
rpoC2_p5 rpoC2 GAGCGAAGGGGAAACTAGAC AGTGATTGCTGAGATTCGCG 220 1.000 72.6

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
Helwingia chinensis NC_058619.1 158483 View on NCBI ↗
Helwingia himalaica NC_031370.1 158362 View on NCBI ↗
Helwingia japonica PP056233.1 158525 View on NCBI ↗