| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnH-GUG-psbA | LSC | 527 | 0.0375 | 0.98 | 73.5 | yes | View details |
| trnK-UUU-rps16 | LSC | 1039 | 0.0366 | 1.00 | 82.8 | yes | View details |
| psbK-psbI | LSC | 420 | 0.0327 | 1.00 | 79.1 | yes | View details |
| trnS-GCU-trnG-UCC | LSC | 1147 | 0.0289 | 1.00 | 69.9 | yes | View details |
| trnD-GUC-trnY-GUA | LSC | 535 | 0.0789 | 1.00 | 80.3 | yes | View details |
| trnP-UGG-psaJ | LSC | 716 | 0.0358 | 1.00 | 80.4 | yes | View details |
| ndhF | SSC | 2226 | 0.0187 | 1.00 | 56.3 | yes | View details |
| ndhF-rpl32 | SSC | 1318 | 0.0373 | 0.98 | 75.0 | yes | View details |
| ndhG-ndhI | SSC | 567 | 0.0338 | 0.95 | 70.3 | yes | View details |
| ycf1 | SSC | 5589 | 0.0224 | 1.00 | 57.0 | yes | View details |
| trnE-UUC-trnT-GGU | LSC | 837 | 0.0275 | 1.00 | 77.0 | yes | View details |
| ccsA-ndhD | SSC | 298 | 0.0459 | 0.99 | 74.4 | yes | View details |
| psbI-trnS-GCU | LSC | 142 | 0.0753 | 1.00 | 72.5 | yes | View details |
| accD-psaI | LSC | 725 | 0.0264 | 0.99 | 71.6 | yes | View details |
| psaC-ndhE | SSC | 290 | 0.0320 | 0.99 | 70.1 | yes | View details |
| trnT-GGU-psbD | LSC | 1527 | 0.0204 | 1.00 | 69.5 | yes | View details |
| trnW-CCA-trnP-UGG | LSC | 185 | 0.0314 | 1.00 | 69.4 | yes | View details |
| psbZ-trnG-GCC | LSC | 607 | 0.0278 | 0.97 | 69.1 | yes | View details |
| psbA-trnK-UUU | LSC | 379 | 0.0298 | 0.98 | 68.8 | 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
21
Genome length
157–158 kb
Candidate markers
264
Primer pairs
95
Genome-wide nucleotide diversity
Candidate markers
10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 264 candidates).
Primer pairs
Showing the top 30 of 95 primer pairs (ranked by primer score).
| Primer ID | Label | Forward | Reverse | Amplicon (bp) | Cross-species rate | Score |
|---|---|---|---|---|---|---|
| trnH-GUG-psbA_p1 | trnH-GUG-psbA | AATCCACTTGGCTACATCCG |
TGCTCACAACTTCCCTCTAGA |
598–674 | 1.000 | 80.5 |
| trnH-GUG-psbA_p2 | trnH-GUG-psbA | AATCCACTTGGCTACATCCG |
CCCTCTAGATCTAGCTGCTGT |
586–662 | 1.000 | 80.3 |
| trnH-GUG-psbA_p3 | trnH-GUG-psbA | AATCCACTTGGCTACATCCG |
TCCCTCTAGATCTAGCTGCTG |
587–663 | 1.000 | 80.1 |
| trnH-GUG-psbA_p4 | trnH-GUG-psbA | AATCCACTTGGCTACATCCG |
GCATGAACGTAATGCTCACA |
610–686 | 1.000 | 79.9 |
| trnH-GUG-psbA_p5 | trnH-GUG-psbA | AATCCACTTGGCTACATCCG |
CGTAATGCTCACAACTTCCC |
603–679 | 1.000 | 79.9 |
| psbA-trnK-UUU_p1 | psbA-trnK-UUU | TACAGAAGCGACCCCATAGG |
CTAGTTCCGGGTTCGAATCC |
461–508 | 1.000 | 84.5 |
| psbA-trnK-UUU_p2 | psbA-trnK-UUU | TTTTCGGTGCTGGTTATCCA |
CTAGTTCCGGGTTCGAATCC |
483–530 | 1.000 | 84.4 |
| psbA-trnK-UUU_p3 | psbA-trnK-UUU | ATCCAGTTACAGAAGCGACC |
CTAGTTCCGGGTTCGAATCC |
468–515 | 1.000 | 83.7 |
| psbA-trnK-UUU_p4 | psbA-trnK-UUU | AGTTACAGAAGCGACCCCAT |
CTAGTTCCGGGTTCGAATCC |
464–511 | 1.000 | 83.4 |
| psbA-trnK-UUU_p5 | psbA-trnK-UUU | CGGTTTTCGGTGCTGGTTAT |
CTAGTTCCGGGTTCGAATCC |
486–533 | 1.000 | 82.2 |
| trnK-UUU-rps16_p1 | trnK-UUU-rps16 | AGTACGGACGAATCCATTGC |
CCATCTACCGAATCGTTGCA |
1078–1233 | 1.000 | 91.0 |
| trnK-UUU-rps16_p2 | trnK-UUU-rps16 | GTACGGACGAATCCATTGCT |
CCATCTACCGAATCGTTGCA |
1077–1232 | 1.000 | 91.0 |
| trnK-UUU-rps16_p3 | trnK-UUU-rps16 | AGTACGGACGAATCCATTGC |
TCGATCCCGAAGAGAAGGAA |
1050–1205 | 1.000 | 90.4 |
| trnK-UUU-rps16_p4 | trnK-UUU-rps16 | GTACGGACGAATCCATTGCT |
TCGATCCCGAAGAGAAGGAA |
1049–1204 | 1.000 | 90.4 |
| trnK-UUU-rps16_p5 | trnK-UUU-rps16 | AAGCCGAGTACTCTACCGTT |
CCATCTACCGAATCGTTGCA |
1021–1176 | 1.000 | 90.1 |
| psbK-psbI_p1 | psbK-psbI | GTTTGGCAAGCTGCTGTAAG |
TTTTATTCCTCACGCCCAGG |
450–602 | 1.000 | 89.2 |
| psbK-psbI_p2 | psbK-psbI | TGGCAAGCTGCTGTAAGTTT |
TTTTATTCCTCACGCCCAGG |
447–599 | 1.000 | 87.2 |
| psbK-psbI_p3 | psbK-psbI | TTGGCAAGCTGCTGTAAGTT |
TTTTATTCCTCACGCCCAGG |
448–600 | 1.000 | 87.2 |
| psbK-psbI_p4 | psbK-psbI | TTTGGCAAGCTGCTGTAAGT |
TTTTATTCCTCACGCCCAGG |
449–601 | 1.000 | 87.2 |
| psbK-psbI_p5 | psbK-psbI | GTTTGGCAAGCTGCTGTAAG |
ATTCCTCACGCCCAGGATTA |
446–598 | 1.000 | 86.3 |
| psbI-trnS-GCU_p1 | psbI-trnS-GCU | AATCCTGGGCGTGAGGAATA |
TAAAGCGGCGGATTGCTAAT |
231–238 | 1.000 | 87.8 |
| psbI-trnS-GCU_p2 | psbI-trnS-GCU | ATCCTGGGCGTGAGGAATAA |
TAAAGCGGCGGATTGCTAAT |
230–237 | 1.000 | 87.8 |
| psbI-trnS-GCU_p3 | psbI-trnS-GCU | TAATCCTGGGCGTGAGGAAT |
TAAAGCGGCGGATTGCTAAT |
232–239 | 1.000 | 87.8 |
| psbI-trnS-GCU_p4 | psbI-trnS-GCU | AATCCTGGGCGTGAGGAATA |
ATTGGGAGAGATGGCTGAGT |
255–262 | 1.000 | 86.9 |
| psbI-trnS-GCU_p5 | psbI-trnS-GCU | ATCCTGGGCGTGAGGAATAA |
ATTGGGAGAGATGGCTGAGT |
254–261 | 1.000 | 86.9 |
| trnS-GCU-trnG-UCC_p1 | trnS-GCU-trnG-UCC | ACGGAAAGAGAGGGATTCGA |
TACCACTAAACTATACCCGC |
1256–1342 | 1.000 | 57.5 |
| trnS-GCU-trnG-UCC_p2 | trnS-GCU-trnG-UCC | ACGGAAAGAGAGGGATTCGA |
TTACCACTAAACTATACCCGC |
1257–1343 | 1.000 | 56.4 |
| trnS-GCU-trnG-UCC_p3 | trnS-GCU-trnG-UCC | ATTAGCAATCCGCCGCTTTA |
TACCACTAAACTATACCCGC |
1207–1293 | 0.905 | 54.4 |
| trnS-GCU-trnG-UCC_p4 | trnS-GCU-trnG-UCC | ATTAGCAATCCGCCGCTTTA |
TTACCACTAAACTATACCCGC |
1208–1294 | 0.905 | 53.3 |
| trnS-GCU-trnG-UCC_p5 | trnS-GCU-trnG-UCC | ATTAGCAATCCGCCGCTTTA |
TTTACCACTAAACTATACCCGC |
1209–1295 | 0.905 | 51.6 |
Result downloads
Reference species (21)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Stephania brachyandra | PZ122807.1 | 157702 | View on NCBI ↗ |
| Stephania cephalantha | NC_067079.1 | 158052 | View on NCBI ↗ |
| Stephania chingtungensis | OR166989.1 | 157747 | View on NCBI ↗ |
| Stephania dicentrinifera | OR166986.1 | 157594 | View on NCBI ↗ |
| Stephania dielsiana | NC_054337.1 | 156843 | View on NCBI ↗ |
| Stephania dolichopoda | PZ122811.1 | 157716 | View on NCBI ↗ |
| Stephania epigaea | NC_058988.1 | 157738 | View on NCBI ↗ |
| Stephania excentrica | OR166995.1 | 156997 | View on NCBI ↗ |
| Stephania hainanensis | PX092667.1 | 156701 | View on NCBI ↗ |
| Stephania herbacea | PV975265.1 | 157727 | View on NCBI ↗ |
| Stephania hernandiifolia | PP175339.1 | 157748 | View on NCBI ↗ |
| Stephania japonica | NC_029432.1 | 157719 | View on NCBI ↗ |
| Stephania japonica var. discolor | OR166987.1 | 157748 | View on NCBI ↗ |
| Stephania kuinanensis | OR166996.1 | 157517 | View on NCBI ↗ |
| Stephania kwangsiensis | NC_048524.1 | 156624 | View on NCBI ↗ |
| Stephania lincangensis | PZ122815.1 | 158235 | View on NCBI ↗ |
| Stephania longa | PV975267.1 | 157758 | View on NCBI ↗ |
| Stephania longipes | PV975268.1 | 158129 | View on NCBI ↗ |
| Stephania macrantha | PZ122808.1 | 158079 | View on NCBI ↗ |
| Stephania viridiflavens | PZ122814.1 | 158039 | View on NCBI ↗ |
| Stephania yunnanensis | NC_087726.1 | 158146 | View on NCBI ↗ |