| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| psbA-trnK-UUU | LSC | 493 | 0.0490 | 0.98 | 78.6 | yes | View details |
| trnL-UAA-trnT-UGU | LSC | 1198 | 0.0329 | 1.00 | 82.1 | yes | View details |
| trnR-UCU-trnG-UCC | LSC | 441 | 0.0495 | 0.97 | 79.0 | yes | View details |
| trnP-UGG-psaJ | LSC | 723 | 0.0409 | 0.98 | 75.1 | yes | View details |
| ndhF-rpl32 | SSC | 741 | 0.0459 | 0.97 | 80.9 | yes | View details |
| rpl32-trnL-UAG | SSC | 1056 | 0.0695 | 0.89 | 73.2 | yes | View details |
| ndhG-ndhI | SSC | 754 | 0.0724 | 0.91 | 75.3 | yes | View details |
| ycf1 | SSC | 5307 | 0.0283 | 0.99 | 62.0 | yes | View details |
| rps8-rpl14 | LSC | 344 | 0.0404 | 0.99 | 76.9 | yes | View details |
| trnQ-UUG-rps16 | LSC | 431 | 0.0335 | 0.98 | 74.2 | yes | View details |
| trnS-UGA-psbC | LSC | 240 | 0.0405 | 0.97 | 73.9 | yes | View details |
| petN-trnC-GCA | LSC | 993 | 0.0250 | 0.98 | 73.9 | yes | View details |
| trnC-GCA-rpoB | LSC | 884 | 0.0259 | 1.00 | 73.8 | yes | View details |
| rps16 | LSC | 1169 | 0.0211 | 0.99 | 73.4 | yes | View details |
| rps16-accD | LSC | 707 | 0.0345 | 0.98 | 73.2 | yes | View details |
| psbD-trnT-GGU | LSC | 1273 | 0.0251 | 0.99 | 73.1 | yes | View details |
| accD-psaI | LSC | 487 | 0.0428 | 0.97 | 73.1 | 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. | |||||||
Species
40
Genome length
156–157 kb
Candidate markers
266
Primer pairs
85
Genome-wide nucleotide diversity
Candidate markers
8 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 266 candidates).
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 |
|---|---|---|---|---|---|---|
| psbA-trnK-UUU_p1 | psbA-trnK-UUU | ACGGTTTTCAGTGCTGGTTA |
ACTCCATCCGACTAGTTCCG |
547–661 | 1.000 | 84.4 |
| psbA-trnK-UUU_p2 | psbA-trnK-UUU | GCTCTCGCGTCTCTCTAAAA |
ACTCCATCCGACTAGTTCCG |
496–610 | 1.000 | 82.8 |
| psbA-trnK-UUU_p3 | psbA-trnK-UUU | ACGGTTTTCAGTGCTGGTTA |
ACTAGTTCCGGGTTCGAGTC |
537–651 | 1.000 | 82.7 |
| psbA-trnK-UUU_p4 | psbA-trnK-UUU | ACGGTTTTCAGTGCTGGTTA |
GACTAGTTCCGGGTTCGAGT |
538–652 | 1.000 | 82.7 |
| psbA-trnK-UUU_p5 | psbA-trnK-UUU | TACAGAAGCGACCCCATAGG |
ACTCCATCCGACTAGTTCCG |
521–635 | 1.000 | 82.4 |
| trnL-UAA-trnT-UGU_p1 | trnL-UAA-trnT-UGU | TAGCGTCTACCAATTTCGCC |
GCGATGCTCTAACCTCTGAG |
784–1370 | 1.000 | 90.4 |
| trnL-UAA-trnT-UGU_p2 | trnL-UAA-trnT-UGU | CGTTTCCATACCAAGGCTCA |
GCGATGCTCTAACCTCTGAG |
819–1405 | 1.000 | 90.1 |
| trnL-UAA-trnT-UGU_p3 | trnL-UAA-trnT-UGU | ACGTTTCCATACCAAGGCTC |
GCGATGCTCTAACCTCTGAG |
820–1406 | 1.000 | 90.1 |
| trnL-UAA-trnT-UGU_p4 | trnL-UAA-trnT-UGU | TAGCGTCTACCAATTTCGCC |
GGAATCGAACCGATGACCAT |
816–1402 | 1.000 | 89.5 |
| trnL-UAA-trnT-UGU_p5 | trnL-UAA-trnT-UGU | CCCATTGTTAATTCCGGGGT |
GCGATGCTCTAACCTCTGAG |
1318–1405 | 0.925 | 86.7 |
| trnS-UGA-psbC_p1 | trnS-UGA-psbC | CCGGTATAGTTCGCACCAAA |
CCGGTTCTTTCCATGACTCC |
313–329 | 1.000 | 89.8 |
| trnS-UGA-psbC_p2 | trnS-UGA-psbC | AAACCGGTATAGTTCGCACC |
CCGGTTCTTTCCATGACTCC |
316–332 | 1.000 | 89.8 |
| trnS-UGA-psbC_p3 | trnS-UGA-psbC | GAGAGATGGCTGAGTGGTTG |
CCGGTTCTTTCCATGACTCC |
352–368 | 1.000 | 89.7 |
| trnS-UGA-psbC_p4 | trnS-UGA-psbC | GCTGAGTGGTTGATAGCTCC |
CCGGTTCTTTCCATGACTCC |
344–360 | 1.000 | 89.5 |
| trnS-UGA-psbC_p5 | trnS-UGA-psbC | GGCTGAGTGGTTGATAGCTC |
CCGGTTCTTTCCATGACTCC |
345–361 | 1.000 | 89.5 |
| psbD-trnT-GGU_p1 | psbD-trnT-GGU | CCCACAAAAACGAAACGGTC |
GTGGTAGAGTAACGCCATGG |
1221–1461 | 1.000 | 90.1 |
| psbD-trnT-GGU_p2 | psbD-trnT-GGU | CACAAAAACGAAACGGTCCC |
GTGGTAGAGTAACGCCATGG |
1219–1459 | 0.950 | 88.1 |
| psbD-trnT-GGU_p3 | psbD-trnT-GGU | CCACAAAAACGAAACGGTCC |
GTGGTAGAGTAACGCCATGG |
1220–1460 | 0.950 | 88.1 |
| psbD-trnT-GGU_p4 | psbD-trnT-GGU | CACAAAAACGAAACGGTCCC |
TCAGTGGTAGAGTAACGCCA |
1222–1462 | 0.950 | 88.0 |
| psbD-trnT-GGU_p5 | psbD-trnT-GGU | CCACAAAAACGAAACGGTCC |
TCAGTGGTAGAGTAACGCCA |
1223–1463 | 0.950 | 88.0 |
| petN-trnC-GCA_p1 | petN-trnC-GCA | TTAAAGCAGCCCAAGCAAGA |
TTTCCCCAGTTCAAATCCGG |
1010–1093 | 1.000 | 91.3 |
| petN-trnC-GCA_p2 | petN-trnC-GCA | TTAAAGCAGCCCAAGCAAGA |
GGGGGACTGCAAATCCTTTT |
1028–1111 | 1.000 | 89.1 |
| petN-trnC-GCA_p3 | petN-trnC-GCA | GCCCAAGCAAGACTCACTAT |
TTTCCCCAGTTCAAATCCGG |
1002–1085 | 1.000 | 88.1 |
| petN-trnC-GCA_p4 | petN-trnC-GCA | AGCCCAAGCAAGACTCACTA |
TTTCCCCAGTTCAAATCCGG |
1003–1086 | 1.000 | 86.2 |
| petN-trnC-GCA_p5 | petN-trnC-GCA | GCCCAAGCAAGACTCACTAT |
GGGGGACTGCAAATCCTTTT |
1020–1103 | 1.000 | 85.9 |
| trnC-GCA-rpoB_p1 | trnC-GCA-rpoB | CCGGATTTGAACTGGGGAAA |
GACATTCCCGCATTTTCACC |
900–1029 | 1.000 | 89.1 |
| trnC-GCA-rpoB_p2 | trnC-GCA-rpoB | CCGGATTTGAACTGGGGAAA |
GCCCCGATCAATGAACCTAC |
961–1090 | 0.975 | 87.1 |
| trnC-GCA-rpoB_p3 | trnC-GCA-rpoB | AAAAGGATTTGCAGTCCCCC |
GACATTCCCGCATTTTCACC |
882–1011 | 1.000 | 86.9 |
| trnC-GCA-rpoB_p4 | trnC-GCA-rpoB | CCGGATTTGAACTGGGGAAA |
TAAGCCCCGATCAATGAACC |
964–1093 | 0.950 | 86.6 |
| trnC-GCA-rpoB_p5 | trnC-GCA-rpoB | CCGGATTTGAACTGGGGAAA |
AGCCCCGATCAATGAACCTA |
962–1091 | 0.975 | 86.4 |
Result downloads
Reference species (40)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Dalbergia armata | NC_049048.1 | 156246 | View on NCBI ↗ |
| Dalbergia assamica | NC_062094.1 | 155835 | View on NCBI ↗ |
| Dalbergia bariensis | NC_058538.1 | 156544 | View on NCBI ↗ |
| Dalbergia benthamii | NC_062096.1 | 156638 | View on NCBI ↗ |
| Dalbergia burmanica | PQ144600.1 | 155833 | View on NCBI ↗ |
| Dalbergia candenatensis | NC_062098.1 | 155947 | View on NCBI ↗ |
| Dalbergia cearensis | NC_049046.1 | 156314 | View on NCBI ↗ |
| Dalbergia chlorocarpa | NC_049047.1 | 155745 | View on NCBI ↗ |
| Dalbergia clarkei | PQ144626.1 | 156314 | View on NCBI ↗ |
| Dalbergia cochinchinensis | NC_058539.1 | 156576 | View on NCBI ↗ |
| Dalbergia cultrata | NC_044117.1 | 156385 | View on NCBI ↗ |
| Dalbergia dyeriana | PQ144613.1 | 155951 | View on NCBI ↗ |
| Dalbergia frutescens | NC_049044.1 | 156105 | View on NCBI ↗ |
| Dalbergia gardneriana | OR159810.1 | 156284 | View on NCBI ↗ |
| Dalbergia hainanensis | NC_036961.1 | 156073 | View on NCBI ↗ |
| Dalbergia hancei | NC_062095.1 | 155859 | View on NCBI ↗ |
| Dalbergia horrida | PQ144621.1 | 156172 | View on NCBI ↗ |
| Dalbergia hupeana | NC_058536.1 | 155829 | View on NCBI ↗ |
| Dalbergia lakhonensis | PQ144630.1 | 156354 | View on NCBI ↗ |
| Dalbergia lanceolaria | PQ144617.1 | 156492 | View on NCBI ↗ |
| Dalbergia latifolia | PQ144619.1 | 156154 | View on NCBI ↗ |
| Dalbergia matthewii | PQ144623.1 | 155891 | View on NCBI ↗ |
| Dalbergia melanoxylon | PQ144625.1 | 156415 | View on NCBI ↗ |
| Dalbergia millettii | NC_062097.1 | 155907 | View on NCBI ↗ |
| Dalbergia millettii var. mimosoides | NC_063304.1 | 155773 | View on NCBI ↗ |
| Dalbergia obovata | NC_049045.1 | 156012 | View on NCBI ↗ |
| Dalbergia obtusifolia | NC_063303.1 | 156419 | View on NCBI ↗ |
| Dalbergia odorifera | NC_049008.1 | 156049 | View on NCBI ↗ |
| Dalbergia pinnata | PQ144639.1 | 156603 | View on NCBI ↗ |
| Dalbergia polyadelpha | PQ144637.1 | 156861 | View on NCBI ↗ |
| Dalbergia rimosa | PQ144604.1 | 155936 | View on NCBI ↗ |
| Dalbergia rostrata | OR159816.1 | 156133 | View on NCBI ↗ |
| Dalbergia sericea | PQ144627.1 | 156314 | View on NCBI ↗ |
| Dalbergia sissoo | NC_049043.1 | 155863 | View on NCBI ↗ |
| Dalbergia stipulacea | PQ144611.1 | 156604 | View on NCBI ↗ |
| Dalbergia tonkinensis | NC_049007.1 | 156090 | View on NCBI ↗ |
| Dalbergia travancorica | PQ144624.1 | 155891 | View on NCBI ↗ |
| Dalbergia vietnamensis | NC_049050.1 | 156088 | View on NCBI ↗ |
| Dalbergia volubilis | PQ144620.1 | 156354 | View on NCBI ↗ |
| Dalbergia yunnanensis | NC_049009.1 | 155823 | View on NCBI ↗ |