Markers + reference

Leucaena

2 species · Fabaceae · Fabales

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Species 2
Genome length 165–167 kb
Candidate markers 274
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 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 939 0.0426 0.85 72.2 yes View details
trnQ-UUG-psbK LSC 835 0.0414 0.78 68.9 yes View details
trnS-GCU-trnG-UCC LSC 1588 0.0273 0.72 61.3 yes View details
trnG-UCC-trnR-UCU LSC 499 0.0777 0.77 80.2 yes View details
trnC-GCA-petN LSC 1470 0.0251 0.92 71.1 yes View details
psbZ-trnG-GCC LSC 747 0.0490 0.93 85.5 yes View details
trnT-UGU-trnL-UAA LSC 1894 0.0438 0.82 76.5 yes View details
rbcL-accD LSC 1091 0.0294 0.97 64.0 yes View details
accD-psaI LSC 782 0.0488 0.86 88.4 yes View details
rps8-rpl14 LSC 702 0.0780 0.82 81.1 yes View details
rpl22-rps19 LSC 748 0.2271 0.86 96.1 yes View details
rpl33-rps18 LSC 533 0.0549 0.75 84.3 yes View details
atpF-atpH LSC 751 0.0328 0.93 81.7 yes View details
rps2-rpoC2 LSC 233 0.0472 1.00 79.6 yes View details
trnR-UCU-atpA LSC 505 0.0487 0.90 75.0 yes View details
trnL-UAA-trnF-GAA LSC 434 0.0315 0.95 74.3 yes View details
trnT-GGU-psbD LSC 1577 0.0228 0.97 74.2 yes View details
ycf1-ndhF SSC 74 0.1081 1.00 72.7 yes View details
petA-psbJ LSC 1334 0.0156 0.96 71.2 yes View details
trnK-UUU-rps16 LSC 1382 0.0244 0.95 68.4 yes View details
ndhF-rpl32 SSC 992 0.0282 0.93 68.0 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG AAAAAGGCGCTCAACCTACA 1540–1634 1.000 80.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 GAGTCGCACTTAAAAGCCGA AAAAAGGCGCTCAACCTACA 1541–1635 1.000 80.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA AAAAAGGCGCTCAACCTACA 1538–1632 1.000 79.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG CCTTGAAAAAGGCGCTCAAC 1545–1639 1.000 78.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG CTTGAAAAAGGCGCTCAACC 1544–1638 1.000 78.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 889–1019 1.000 86.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT GAGGTTCGAATCCTTCCGTC 891–1021 1.000 85.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA GAGGTTCGAATCCTTCCGTC 877–1007 1.000 84.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CATGTCTTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 892–1022 1.000 84.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TGTCTTTCAAGTCGCACGTT GAGGTTCGAATCCTTCCGTC 890–1020 1.000 83.4
trnQ-UUG-psbK_p1 trnQ-UUG-psbK AAAACCCGTTGCCTTACCG ACAGACCAAACTAAAGATATTAAGCA 755–896 1.000 46.6
trnQ-UUG-psbK_p2 trnQ-UUG-psbK CAAAACCCGTTGCCTTACC ACAGACCAAACTAAAGATATTAAGCA 756–897 1.000 46.6
trnQ-UUG-psbK_p3 trnQ-UUG-psbK CAAAACCCGTTGCCTTACCG ACAGACCAAACTAAAGATATTAAGCA 756–897 1.000 46.6
trnQ-UUG-psbK_p4 trnQ-UUG-psbK AAACCCGTTGCCTTACCG ACAGACCAAACTAAAGATATTAAGCA 754–895 1.000 46.6
trnQ-UUG-psbK_p5 trnQ-UUG-psbK AAAACCCGTTGCCTTACCG CAGACCAAACTAAAGATATTAAGCA 754–895 1.000 46.6
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGATCCATAGAACGAATCGCA 1238–1668 1.000 77.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GGATCCATAGAACGAATCGCA 1237–1667 1.000 77.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA GGATCCATAGAACGAATCGCA 1292–1722 1.000 76.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCACT 1227–1657 1.000 75.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCACT 1226–1656 1.000 75.8
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 489–579 1.000 71.8
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 492–582 1.000 71.6
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 495–585 1.000 71.1
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 498–588 1.000 70.9
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU ACCAAAGTTTCACGTTCGGT AGAAGACCTCTGTCCTATCCA 559–648 1.000 69.5
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ACTTCAGGAACAAGTAGAAAA 555–565 1.000 47.1
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ACTTCAGGAACAAGTAGAAAAA 555–565 1.000 47.1
trnR-UCU-atpA_p3 trnR-UCU-atpA GTTCAAATCCTATTGGACGCA ACTTCAGGAACAAGTAGAAAA 554–564 1.000 47.1
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT ACTTCAGGAACAAGTAGAAAA 590–600 1.000 47.0
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT ACTTCAGGAACAAGTAGAAAAA 590–600 1.000 47.0

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
Leucaena leucocephala PQ181007.1 167423 View on NCBI ↗
Leucaena trichandra NC_028733.1 164692 View on NCBI ↗