Markers + reference

Leplaea

3 species · Meliaceae · Sapindales

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Species 3
Genome length 160–161 kb
Candidate markers 260
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 260 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-psbA LSC 371 0.0147 0.98 57.8 yes View details
rps16-trnQ LSC 1411 0.0029 0.99 52.7 yes View details
rpoB-trnC LSC 1231 0.0016 0.99 41.2 yes View details
psaA-ycf3 LSC 664 0.0060 1.00 50.2 yes View details
trnT-trnL LSC 975 0.0060 0.80 49.4 yes View details
psbB LSC 1527 0.0000 1.00 29.7 yes View details
rpl16 LSC 1450 0.0042 0.99 50.2 yes View details
ndhF SSC 2235 0.0042 1.00 44.3 yes View details
ndhF-rpl32 SSC 983 0.0089 0.99 46.7 yes View details
ccsA-ndhD SSC 321 0.0232 0.98 50.6 yes View details
ndhA SSC 2217 0.0039 1.00 59.8 yes View details
rbcL LSC 1437 0.0023 1.00 60.2 yes View details
psbH-petB LSC 113 0.0118 1.00 60.0 yes View details
clpP1 LSC 2078 0.0029 1.00 59.9 yes View details
petN-psbM LSC 1254 0.0027 1.00 59.6 yes View details
psbE-petL LSC 1439 0.0009 1.00 59.3 yes View details
psbK-psbI LSC 389 0.0018 0.95 59.1 yes View details
trnQ-psbK LSC 354 0.0075 1.00 58.4 yes View details
trnS-trnG LSC 793 0.0034 0.99 58.4 yes View details
trnM-rps14 LSC 162 0.0082 1.00 52.9 yes View details
psbT-psbN LSC 65 0.0205 1.00 51.9 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-psbA_p1 trnH-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 441–483 1.000 81.1
trnH-psbA_p2 trnH-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 455–497 1.000 81.0
trnH-psbA_p3 trnH-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 454–496 1.000 81.0
trnH-psbA_p4 trnH-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 456–498 1.000 81.0
trnH-psbA_p5 trnH-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 490–532 1.000 78.7
rps16-trnQ_p1 rps16-trnQ AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1468–1484 1.000 79.5
rps16-trnQ_p2 rps16-trnQ CATAGCGGATCATGGCCTTC GAGGTTCGAATCCTTCCGTC 1488–1504 1.000 76.1
rps16-trnQ_p3 rps16-trnQ AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGGTATTC 1489–1505 1.000 75.8
rps16-trnQ_p4 rps16-trnQ CGGATCATGGCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1483–1499 1.000 75.0
rps16-trnQ_p5 rps16-trnQ GGATCATGGCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1482–1498 1.000 75.0
trnQ-psbK_p1 trnQ-psbK GAATACCGGGACCAAAACCC CGGGCAATTTGGCGAATAAA 483 1.000 74.1
trnQ-psbK_p2 trnQ-psbK GACCAAAACCCGTTGCCTTA CGGGCAATTTGGCGAATAAA 474 1.000 73.0
trnQ-psbK_p3 trnQ-psbK GAATACCGGGACCAAAACCC TCGGGCAATTTGGCGAATAA 484 1.000 72.1
trnQ-psbK_p4 trnQ-psbK ACTCTGGGACGGAAGGATTC CGGGCAATTTGGCGAATAAA 511 1.000 71.9
trnQ-psbK_p5 trnQ-psbK CGAATACCGGGACCAAAACC CGGGCAATTTGGCGAATAAA 484 1.000 71.1
psbK-psbI_p1 psbK-psbI TGGCAAGCTGCTGTAAGTTT GGGATTACGTCCTGGATCAT 493–512 1.000 68.5
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT TTTTTATTCTTCGCGCCCGG 511–530 1.000 68.2
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT GGGATTACGTCCTGGATCATT 493–512 1.000 66.6
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT TTTTATTCTTCGCGCCCGG 510–529 1.000 65.4
psbK-psbI_p5 psbK-psbI TGGCAAGCTGCTGTAAGTTT TTTTTATTCTTCGCGCCCG 511–530 1.000 64.8
trnS-trnG_p1 trnS-trnG CCGACGCTTTAATCCACTCA AGGGGATTAATCGAACGAATCA 872 1.000 59.3
trnS-trnG_p2 trnS-trnG CCGACGCTTTAATCCACTCA CGAACGAATCACACTTTTACCA 861 1.000 59.0
trnS-trnG_p3 trnS-trnG CCGACGCTTTAATCCACTCA GGGGATTAATCGAACGAATCAC 871 1.000 59.0
trnS-trnG_p4 trnS-trnG ACGGAAAGAGAGGGATTCGA AGGGGATTAATCGAACGAATCA 930 1.000 58.1
trnS-trnG_p5 trnS-trnG ACGGAAAGAGAGGGATTCGA CGAACGAATCACACTTTTACCA 919 1.000 57.8
rpoB-trnC_p1 rpoB-trnC ATTCCCGCATTTCCATCTCC AAAAGGATTTGCAGTCCCCC 1301–1311 1.000 78.0
rpoB-trnC_p2 rpoB-trnC ATTCCCGCATTTCCATCTCC GCGACACCCAGATTTGAACT 1326–1336 1.000 77.0
rpoB-trnC_p3 rpoB-trnC GCATTTCCATCTCCGAGCAT AAAAGGATTTGCAGTCCCCC 1295–1305 1.000 74.9
rpoB-trnC_p4 rpoB-trnC ATTCCCGCATTTCCATCTCC TTTGTTGATCAGGCGACACC 1338–1348 1.000 74.7
rpoB-trnC_p5 rpoB-trnC ACATTCCCGCATTTCCATCT AAAAGGATTTGCAGTCCCCC 1303–1313 1.000 74.5

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
Leplaea cedrata MZ274126.1 160609 View on NCBI ↗
Leplaea laurentii MZ274127.1 160470 View on NCBI ↗
Leplaea thompsonii MZ274128.1 160499 View on NCBI ↗