Markers + reference

Chesneya

2 species · Fabaceae · Fabales

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Species 2
Genome length 127–129 kb
Candidate markers 223
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 223 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
accD Genome 1800 0.2613 0.79 78.6 yes View details
petA-psbJ Genome 1161 0.2328 0.83 88.6 yes View details
rps12-psbB Genome 1283 0.2115 0.98 82.1 yes View details
rpl23-ycf2 Genome 1079 0.1346 0.70 76.2 yes View details
ndhB-ycf1 Genome 748 0.1294 0.57 70.8 yes View details
trnL-UAA-trnN-GUU Genome 680 0.0675 0.96 85.2 yes View details
atpH-atpF Genome 602 0.1014 0.95 85.1 yes View details
rps8-rpl14 Genome 782 0.1200 0.83 84.0 yes View details
psbK-trnQ-UUG Genome 614 0.1097 0.92 83.9 yes View details
trnN-GUU-trnR-ACG Genome 610 0.0612 0.96 82.7 yes View details
trnG-GCC-psbZ Genome 683 0.0872 0.89 81.5 yes View details
trnV-UAC-ndhC Genome 435 0.0962 0.96 81.1 yes View details
trnS-UGA-psbC Genome 209 0.0813 1.00 80.2 yes View details
trnL-CAA-trnT-UGU Genome 1641 0.0851 0.75 80.0 yes View details
trnfM-CAU-trnG-GCC Genome 150 0.0902 0.89 80.0 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
trnV-UAC-ndhC_p1 trnV-UAC-ndhC ATCAGAGCACAGGGAGTCAT GCCTAGGACTAGATCGTGGT 1253–1255 1.000 83.4
trnV-UAC-ndhC_p2 trnV-UAC-ndhC ATCAGAGCACAGGGAGTCAT TGCCTAGGACTAGATCGTGG 1254–1256 1.000 83.3
trnV-UAC-ndhC_p3 trnV-UAC-ndhC ATCAGAGCACAGGGAGTCAT TTTCATAGTTACCGTGCCCG 1294–1296 1.000 83.2
trnV-UAC-ndhC_p4 trnV-UAC-ndhC GCACAAGGGCTATAGCTCAG TTTCATAGTTACCGTGCCCG 1745–1761 1.000 83.1
trnV-UAC-ndhC_p5 trnV-UAC-ndhC GCACAAGGGCTATAGCTCAG GCCTAGGACTAGATCGTGGT 1704–1720 1.000 83.1
trnL-CAA-trnT-UGU_p1 trnL-CAA-trnT-UGU TAGCGTCTACCAATTTCGCC GCGATGCTCTAACCTCTGAG 1575–1700 1.000 87.5
trnL-CAA-trnT-UGU_p2 trnL-CAA-trnT-UGU TAGCGTCTACCAATTTCGCC GGAATCGAACCGATGACCAT 1607–1732 1.000 86.6
trnL-CAA-trnT-UGU_p3 trnL-CAA-trnT-UGU AGTCCGTAGCGTCTACCAAT GCGATGCTCTAACCTCTGAG 1581–1706 1.000 86.1
trnL-CAA-trnT-UGU_p4 trnL-CAA-trnT-UGU CCCATTGTGAATTCCAGGGT GCGATGCTCTAACCTCTGAG 1660–1785 1.000 85.9
trnL-CAA-trnT-UGU_p5 trnL-CAA-trnT-UGU CCCATTGTGAATTCCAGGGT GGAATCGAACCGATGACCAT 1692–1817 1.000 85.0
trnfM-CAU-trnG-GCC_p1 trnfM-CAU-trnG-GCC GTAGCTCGCAAGGCTCATAA TCTTTGCCAAGGAGAAGACG 237–257 1.000 84.7
trnfM-CAU-trnG-GCC_p2 trnfM-CAU-trnG-GCC TAGCTCGCAAGGCTCATAAC TCTTTGCCAAGGAGAAGACG 236–256 1.000 84.7
trnfM-CAU-trnG-GCC_p3 trnfM-CAU-trnG-GCC TCTTCCGGAGTAGAGCAACT TCTTTGCCAAGGAGAAGACG 279 0.500 56.9
trnfM-CAU-trnG-GCC_p4 trnfM-CAU-trnG-GCC TCTTCCGGAGTAGAGCAACT GCGGATGCGGATATAGTTGA 312 0.500 55.3
trnfM-CAU-trnG-GCC_p5 trnfM-CAU-trnG-GCC TAGCTCGCAAGGCTCATAAC GCGGATGCGGATATAGTTGA 289 0.500 55.3
trnG-GCC-psbZ_p1 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA AGTGGGTATTCTTAATTCTCTCA 761–896 1.000 49.1
trnG-GCC-psbZ_p2 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA AGTGGGTATTCTTAATTCTCTCATCT 761–896 1.000 49.1
trnG-GCC-psbZ_p3 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA TGGGTATTCTTAATTCTCTCATCTCT 759–894 1.000 49.1
trnG-GCC-psbZ_p4 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA AGTGGGTATTCTTAATTCTCTCATC 761–896 1.000 49.1
trnG-GCC-psbZ_p5 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA GTGGGTATTCTTAATTCTCTCATCT 760–895 1.000 49.1
trnS-UGA-psbC_p1 trnS-UGA-psbC GAGAGATGGCTGAGTGGTTG TAGGTCATTTATGGCACGCG 408–411 1.000 79.8
trnS-UGA-psbC_p2 trnS-UGA-psbC GCTGAGTGGTTGATAGCTCC TAGGTCATTTATGGCACGCG 400–403 1.000 79.6
trnS-UGA-psbC_p3 trnS-UGA-psbC GGCTGAGTGGTTGATAGCTC TAGGTCATTTATGGCACGCG 401–404 1.000 79.6
trnS-UGA-psbC_p4 trnS-UGA-psbC GGTTGATAGCTCCGGTCTTG TAGGTCATTTATGGCACGCG 393–396 1.000 79.6
trnS-UGA-psbC_p5 trnS-UGA-psbC GCTTTTGGAGAGATGGCTGA TAGGTCATTTATGGCACGCG 415–418 1.000 78.9
atpH-atpF_p1 atpH-atpF ATTTGCGAATCCTTTTGTTT GATGGCCAGTAACTCAAGCA 671–741 1.000 50.0
atpH-atpF_p2 atpH-atpF ATTTGCGAATCCTTTTGTTT TGGCCAGTAACTCAAGCAAA 669–739 1.000 50.0
atpH-atpF_p3 atpH-atpF ATTTGCGAATCCTTTTGTTT ATGGCCAGTAACTCAAGCAA 670–740 1.000 50.0
atpH-atpF_p4 atpH-atpF ATTTGCGAATCCTTTTGTTT CGGATGGCCAGTAACTCAAG 673–743 1.000 49.9
atpH-atpF_p5 atpH-atpF ATTTGCGAATCCTTTTGTTT ATCAAACCCGAAACTTCCGG 693–763 1.000 49.7

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
Chesneya acaulis NC_063688.1 128629 View on NCBI ↗
Chesneya polystichoides PV870846.1 127217 View on NCBI ↗