Markers + reference

Lespedeza

9 species · Fabaceae · Fabales

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Species 9
Genome length 149–149 kb
Candidate markers 264
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

14 hotspot labels from the diversity plot in genomic order, plus the top 7 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf3-psaA LSC 681 0.0082 0.99 54.9 yes View details
psbZ-trnS-UGA LSC 335 0.0081 1.00 42.8 yes View details
trnS-UGA-psbC LSC 227 0.0323 1.00 56.7 yes View details
psbD-trnT-GGU LSC 1372 0.0071 0.99 53.2 yes View details
trnC-GCA-rpoB LSC 1151 0.0074 1.00 51.0 yes View details
atpA-trnR-UCU LSC 335 0.0095 0.99 51.6 yes View details
psbI-psbK LSC 456 0.0107 1.00 41.6 yes View details
trnQ-UUG-rps16 LSC 418 0.0230 1.00 66.4 yes View details
accD-psaI LSC 354 0.0116 0.99 46.5 yes View details
ycf4-cemA LSC 437 0.0133 1.00 59.4 yes View details
petA-psbJ LSC 865 0.0117 1.00 55.5 yes View details
trnP-UGG-psaJ LSC 252 0.0176 1.00 51.5 yes View details
psaJ-rpl33 LSC 470 0.0097 1.00 51.6 yes View details
rpl32-trnL-UAG SSC 547 0.0090 1.00 51.8 yes View details
trnR-UCU-trnG-UCC LSC 109 0.0303 0.98 63.5 yes View details
trnE-UUC-psbM LSC 445 0.0074 0.99 57.0 yes View details
trnG-UCC-trnS-GCU LSC 425 0.0084 1.00 56.7 yes View details
atpH-atpF LSC 580 0.0040 0.99 55.8 yes View details
ndhF-rpl32 SSC 616 0.0069 0.96 52.6 yes View details
trnL-UAA-trnT-UGU LSC 891 0.0068 1.00 51.3 yes View details
rps3-rps19 LSC 475 0.0092 0.99 51.2 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnL-UAA-trnT-UGU_p1 trnL-UAA-trnT-UGU GCGTCTACCTATTTCGCCAT GCGATGCTCTAACCTCTGAG 947–992 1.000 80.6
trnL-UAA-trnT-UGU_p2 trnL-UAA-trnT-UGU CCCATTGTGAATTCCAGGGT GCGATGCTCTAACCTCTGAG 1034–1079 1.000 79.7
trnL-UAA-trnT-UGU_p3 trnL-UAA-trnT-UGU GCGTCTACCTATTTCGCCAT GGATTCGAACCGATGACCAT 979–1024 1.000 79.7
trnL-UAA-trnT-UGU_p4 trnL-UAA-trnT-UGU CCCATTGTGAATTCCAGGGT GGATTCGAACCGATGACCAT 1066–1111 1.000 78.8
trnL-UAA-trnT-UGU_p5 trnL-UAA-trnT-UGU TGCCCATTGTGAATTCCAGG GCGATGCTCTAACCTCTGAG 1036–1081 1.000 78.1
ycf3-psaA_p1 ycf3-psaA AAGTTGCGGAGTCTTGGTTT TTTCACTTCTGGTTCCGGTG 831–842 1.000 82.2
ycf3-psaA_p2 ycf3-psaA TTGGTTGAAGATCACTGGGC TTTCACTTCTGGTTCCGGTG 743–754 1.000 82.2
ycf3-psaA_p3 ycf3-psaA TGGTTTAATCAAGCCGCTGA TTTCACTTCTGGTTCCGGTG 817–828 1.000 81.1
ycf3-psaA_p4 ycf3-psaA AGATCACTGGGCGTTTTGAA TTTCACTTCTGGTTCCGGTG 735–746 1.000 80.8
ycf3-psaA_p5 ycf3-psaA AAGCTATAGCCCTTACCCCC TTTCACTTCTGGTTCCGGTG 786–797 1.000 80.7
psbZ-trnS-UGA_p1 psbZ-trnS-UGA ACTTGACCAACCTTCAGGAG CAACCACTCAGCCATCTCTC 457–462 1.000 74.7
psbZ-trnS-UGA_p2 psbZ-trnS-UGA ACTTGACCAACCTTCAGGAG TTCGCCGAGAAAAAGGAGAG 542–547 1.000 73.9
psbZ-trnS-UGA_p3 psbZ-trnS-UGA ACTTGACCAACCTTCAGGAG GTTTTCAAGACCGGGGCTAT 477–482 1.000 73.8
psbZ-trnS-UGA_p4 psbZ-trnS-UGA GGAGAAGCAAATACAACGGG CAACCACTCAGCCATCTCTC 441–446 1.000 72.7
psbZ-trnS-UGA_p5 psbZ-trnS-UGA CTTGACCAACCTTCAGGAGA CAACCACTCAGCCATCTCTC 456–461 1.000 72.4
trnS-UGA-psbC_p1 trnS-UGA-psbC GAGAGATGGCTGAGTGGTTG TGATCGAGATTTGGAACCTGT 365 1.000 68.6
trnS-UGA-psbC_p2 trnS-UGA-psbC GAGAGATGGCTGAGTGGTTG TCGAGATTTGGAACCTGTTCT 362 1.000 68.1
trnS-UGA-psbC_p3 trnS-UGA-psbC ATAGCCCCGGTCTTGAAAAC TGATCGAGATTTGGAACCTGT 345 1.000 68.0
trnS-UGA-psbC_p4 trnS-UGA-psbC GCTTTTGGAGAGATGGCTGA TGATCGAGATTTGGAACCTGT 372 1.000 67.7
trnS-UGA-psbC_p5 trnS-UGA-psbC AGCTTTTGGAGAGATGGCTG TGATCGAGATTTGGAACCTGT 373 1.000 67.6
psbD-trnT-GGU_p1 psbD-trnT-GGU CACAAAAACGAAACGGTCCC GTGGTAGAGTAACGCCATGG 1513–1548 1.000 81.1
psbD-trnT-GGU_p2 psbD-trnT-GGU CCACAAAAACGAAACGGTCC GTGGTAGAGTAACGCCATGG 1514–1549 1.000 81.1
psbD-trnT-GGU_p3 psbD-trnT-GGU CCCACAAAAACGAAACGGTC GTGGTAGAGTAACGCCATGG 1515–1550 1.000 81.1
psbD-trnT-GGU_p4 psbD-trnT-GGU CACAAAAACGAAACGGTCCC TCAGTGGTAGAGTAACGCCA 1516–1551 1.000 80.9
psbD-trnT-GGU_p5 psbD-trnT-GGU CCACAAAAACGAAACGGTCC TCAGTGGTAGAGTAACGCCA 1517–1552 1.000 80.9
trnE-UUC-psbM_p1 trnE-UUC-psbM TCAACTTCCGTTCGTAGCAC AGGAACTAGAATAAACAGTGCAGT 591–607 1.000 48.1
trnE-UUC-psbM_p2 trnE-UUC-psbM GCTGCCTCCTTGAAAGAGAG AGGAACTAGAATAAACAGTGCAGT 544–560 1.000 48.0
trnE-UUC-psbM_p3 trnE-UUC-psbM TGTCCTGAACCACTAGACGA AGGAACTAGAATAAACAGTGCAGT 523–539 1.000 48.0
trnE-UUC-psbM_p4 trnE-UUC-psbM CTGAACCACTAGACGATGGG AGGAACTAGAATAAACAGTGCAGT 519–535 1.000 45.6
trnE-UUC-psbM_p5 trnE-UUC-psbM TCAACTTCCGTTCGTAGCAC GGAACTAGAATAAACAGTGCAGT 590–606 1.000 45.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Lespedeza bicolor NC_046836.1 148930 View on NCBI ↗
Lespedeza buergeri NC_061375.1 149065 View on NCBI ↗
Lespedeza cuneata NC_057455.1 149029 View on NCBI ↗
Lespedeza davidii PV032006.1 149040 View on NCBI ↗
Lespedeza inschanica PQ652319.1 149015 View on NCBI ↗
Lespedeza juncea PQ652320.1 148975 View on NCBI ↗
Lespedeza maritima NC_044115.1 149022 View on NCBI ↗
Lespedeza tricolor NC_064210.1 149038 View on NCBI ↗
Lespedeza virginica NC_067538.1 149183 View on NCBI ↗