Markers + reference

Schisandra

6 species · Schisandraceae · Austrobaileyales

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Species 6
Genome length 145–147 kb
Candidate markers 231
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 231 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
matK-rps16 LSC 1545 0.0198 1.00 54.7 yes View details
trnS-GCT-trnR-TCT LSC 1891 0.0265 0.98 73.7 yes View details
atpF-atpH LSC 502 0.0507 1.00 78.6 yes View details
atpH-atpI LSC 1117 0.0410 0.97 69.2 yes View details
psbM-trnD-GTC LSC 977 0.0229 0.98 67.0 yes View details
trnD-GTC-trnY-GTA LSC 412 0.0464 0.99 82.9 yes View details
ycf2 LSC 7032 0.0139 1.00 50.1 yes View details
ndhF-rpl32 SSC 1010 0.0419 0.99 79.0 yes View details
rps8-rpl14 LSC 172 0.0262 1.00 75.5 yes View details
psbI-trnS-GCT LSC 155 0.0773 0.99 71.4 yes View details
trnE-TTC-trnT-GGT LSC 370 0.0319 1.00 70.7 yes View details
trnT-TGT-trnF-GAA LSC 1519 0.0184 1.00 69.9 yes View details
trnL-TAG-ccsA SSC 103 0.0537 0.99 66.5 yes View details
psaA-ycf3 LSC 633 0.0184 1.00 65.3 yes View details
rps16-trnQ-TTG LSC 1786 0.0205 1.00 63.9 yes View details
rps15-ycf1 SSC 383 0.0264 0.96 63.5 yes View details
petB-petD LSC 853 0.0052 0.99 63.4 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
matK-rps16_p1 matK-rps16 AGGAAACGTTGTTGGCAAGA GGAACTTCGAGTTAATCAAACGA 1629–1661 1.000 50.9
matK-rps16_p2 matK-rps16 AGGAAACGTTGTTGGCAAGA AGGAACTTCGAGTTAATCAAACG 1630–1662 1.000 50.9
matK-rps16_p3 matK-rps16 AAGTGCGTAGATCGACTCCT GGAACTTCGAGTTAATCAAACGA 1666–1698 1.000 50.8
matK-rps16_p4 matK-rps16 TGCGTAGATCGACTCCTGAA GGAACTTCGAGTTAATCAAACGA 1663–1695 1.000 50.8
matK-rps16_p5 matK-rps16 AAGTGCGTAGATCGACTCCT AGGAACTTCGAGTTAATCAAACG 1667–1699 1.000 50.8
rps16-trnQ-TTG_p1 rps16-trnQ-TTG ATCATGTCGTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 1520–2037 1.000 86.1
rps16-trnQ-TTG_p2 rps16-trnQ-TTG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1508–2025 1.000 85.6
rps16-trnQ-TTG_p3 rps16-trnQ-TTG ATCATGTCGTTCAAGTCGCA CTCGGAGGTTCGAATCCTTC 1524–2041 1.000 85.0
rps16-trnQ-TTG_p4 rps16-trnQ-TTG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1512–2029 1.000 84.5
rps16-trnQ-TTG_p5 rps16-trnQ-TTG ATCATGTCGTTCAAGTCGCA TACTCGGAGGTTCGAATCCT 1526–2043 1.000 83.2
psbI-trnS-GCT_p1 psbI-trnS-GCT CTCCATCAAGCAAAGACGGT TGGACTAAAGCGTCGGATTG 549–567 1.000 87.6
psbI-trnS-GCT_p2 psbI-trnS-GCT CTCCATCAAGCAAAGACGGT GTGGACTAAAGCGTCGGATT 550–568 1.000 87.6
psbI-trnS-GCT_p3 psbI-trnS-GCT TATTCCGGTCCCCCACAATA TGGACTAAAGCGTCGGATTG 530–547 0.833 79.9
psbI-trnS-GCT_p4 psbI-trnS-GCT TTTTCTTCGCCAAATTGCCC TGGACTAAAGCGTCGGATTG 857–860 0.667 67.6
psbI-trnS-GCT_p5 psbI-trnS-GCT TTTTCTTCGCCAAATTGCCC GTGGACTAAAGCGTCGGATT 858–861 0.667 67.6
trnS-GCT-trnR-TCT_p1 trnS-GCT-trnR-TCT CAATCCGACGCTTTAGTCCA AGAAGACCTCTGTCCTATCCA 1417–1977 1.000 71.8
trnS-GCT-trnR-TCT_p2 trnS-GCT-trnR-TCT AATCCGACGCTTTAGTCCAC AGAAGACCTCTGTCCTATCCA 1416–1976 1.000 71.7
trnS-GCT-trnR-TCT_p3 trnS-GCT-trnR-TCT CAATCCGACGCTTTAGTCCA AGGTTTAGAAGACCTCTGTCCT 1423–1983 1.000 71.1
trnS-GCT-trnR-TCT_p4 trnS-GCT-trnR-TCT AATCCGACGCTTTAGTCCAC AGGTTTAGAAGACCTCTGTCCT 1422–1982 1.000 71.1
trnS-GCT-trnR-TCT_p5 trnS-GCT-trnR-TCT CGGAGAGAGAGGGATTCGAA AGAAGACCTCTGTCCTATCCA 1470–2030 1.000 69.1
atpF-atpH_p1 atpF-atpH GAAAGAATCGGTTACATTTTTCA GCTTTTATTTGCGAATCCTTTTGT 538–576 1.000 51.7
atpF-atpH_p2 atpF-atpH AAAGAATCGGTTACATTTTTCA GCTTTTATTTGCGAATCCTTTTGT 537–575 1.000 51.7
atpF-atpH_p3 atpF-atpH GAAAGAATCGGTTACATTTTTCAT GCTTTTATTTGCGAATCCTTTTGT 538–576 1.000 51.7
atpF-atpH_p4 atpF-atpH AAGAATCGGTTACATTTTTCAT GCTTTTATTTGCGAATCCTTTTGT 536–574 1.000 51.7
atpF-atpH_p5 atpF-atpH GAAAGAATCGGTTACATTTTTCA GCTTTTATTTGCGAATCCTTTTG 538–576 1.000 51.7
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT CAAACAATTCCAACCGACGG 1471–1728 1.000 88.2
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT TATGGTCCTTGGGTTCCCTT 1384–1641 1.000 88.1
atpH-atpI_p3 atpH-atpI AGCAAGGTCAAGGCAATCAA CAAACAATTCCAACCGACGG 1746–2004 1.000 88.0
atpH-atpI_p4 atpH-atpI AGCAAGGTCAAGGCAATCAA TATGGTCCTTGGGTTCCCTT 1659–1917 1.000 87.9
atpH-atpI_p5 atpH-atpI TAGGTCCCAGGTATCGTGTC CAAACAATTCCAACCGACGG 2157–2212 0.667 70.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Schisandra chinensis NC_034908.1 146859 View on NCBI ↗
Schisandra henryi PV747847.1 146882 View on NCBI ↗
Schisandra plena PQ282136.1 145490 View on NCBI ↗
Schisandra propinqua PQ037862.1 145302 View on NCBI ↗
Schisandra repanda NC_061938.1 146620 View on NCBI ↗
Schisandra sphenanthera NC_037145.1 146843 View on NCBI ↗