| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnH-GUG-psbA | LSC | 328 | 0.0771 | 0.97 | 73.4 | yes | View details |
| rps16-trnQ-UUG | LSC | 816 | 0.0501 | 0.98 | 84.3 | yes | View details |
| trnS-GCU-trnG-UCC | LSC | 671 | 0.0536 | 0.95 | 80.4 | yes | View details |
| ycf1 | IRb | 1131 | 0.0124 | 1.00 | 50.1 | no | View details |
| ndhF-rpl32 | SSC | 401 | 0.0494 | 1.00 | 77.3 | yes | View details |
| rpl32-trnL-UAG | SSC | 690 | 0.0514 | 1.00 | 80.3 | yes | View details |
| ycf1 | SSC | 5493 | 0.0425 | 1.00 | 75.8 | yes | View details |
| ndhC-trnV-UAC | LSC | 935 | 0.0403 | 1.00 | 79.3 | yes | View details |
| trnT-UGU-trnL-UAA | LSC | 672 | 0.0383 | 0.99 | 78.8 | yes | View details |
| trnT-GGU-psbD | LSC | 1117 | 0.0328 | 1.00 | 78.4 | yes | View details |
| ycf4-cemA | LSC | 683 | 0.0376 | 0.98 | 77.7 | yes | View details |
| petN-psbM | LSC | 1000 | 0.0398 | 0.99 | 77.0 | yes | View details |
| trnK-UUU-rps16 | LSC | 515 | 0.0464 | 1.00 | 75.2 | yes | View details |
| rpoB-trnC-GCA | LSC | 1144 | 0.0333 | 1.00 | 74.7 | yes | View details |
| trnW-CCA-trnP-UGG | LSC | 163 | 0.0631 | 0.99 | 73.7 | yes | View details |
| ndhG-ndhI | SSC | 352 | 0.0592 | 0.98 | 72.0 | 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. | |||||||
Species
32
Genome length
149–152 kb
Candidate markers
272
Primer pairs
75
Genome-wide nucleotide diversity
Candidate markers
7 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 272 candidates).
Primer pairs
Showing the top 30 of 75 primer pairs (ranked by primer score).
| Primer ID | Label | Forward | Reverse | Amplicon (bp) | Cross-species rate | Score |
|---|---|---|---|---|---|---|
| trnH-GUG-psbA_p1 | trnH-GUG-psbA | GATCCACTTGGCTACATCCG |
GAGTGGGAGCTTAGTTTCCG |
880–1029 | 0.969 | 89.6 |
| trnH-GUG-psbA_p2 | trnH-GUG-psbA | CAATCCACTGCCTTGATCCA |
GAGTGGGAGCTTAGTTTCCG |
894–1043 | 0.969 | 89.6 |
| trnH-GUG-psbA_p3 | trnH-GUG-psbA | AATCCACTGCCTTGATCCAC |
GAGTGGGAGCTTAGTTTCCG |
893–1042 | 0.969 | 89.6 |
| trnH-GUG-psbA_p4 | trnH-GUG-psbA | ACAATCCACTGCCTTGATCC |
GAGTGGGAGCTTAGTTTCCG |
895–1044 | 0.969 | 89.6 |
| trnH-GUG-psbA_p5 | trnH-GUG-psbA | GATCCACTTGGCTACATCCG |
AAGCTCCAACAAACGGCTAA |
228–377 | 0.750 | 80.8 |
| trnK-UUU-rps16_p1 | trnK-UUU-rps16 | AAGGTAGAAGATTCGGGGGT |
GCCGTACGAGGAGAAAACTT |
1506–1549 | 0.969 | 87.8 |
| trnK-UUU-rps16_p2 | trnK-UUU-rps16 | AGGTAGAAGATTCGGGGGTT |
GCCGTACGAGGAGAAAACTT |
1505–1548 | 0.969 | 87.8 |
| trnK-UUU-rps16_p3 | trnK-UUU-rps16 | TCTAGCCGCACTTAAAAGCC |
GCCGTACGAGGAGAAAACTT |
854–875 | 0.969 | 86.4 |
| trnK-UUU-rps16_p4 | trnK-UUU-rps16 | AAGGTAGAAGATTCGGGGGT |
TCTATCCCAATGAGCCGTCT |
1450–1493 | 0.781 | 79.6 |
| trnK-UUU-rps16_p5 | trnK-UUU-rps16 | AGGTAGAAGATTCGGGGGTT |
TCTATCCCAATGAGCCGTCT |
1449–1492 | 0.781 | 79.6 |
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
GAGGTTCGAATCCTTCCGTC |
769–1075 | 1.000 | 90.3 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
GTCTCGCTATTCGGAGGTTC |
782–1088 | 1.000 | 89.9 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
CGGGTTTTGGTCTCGCTATT |
791–1004 | 0.906 | 85.0 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | AAAAATCCACAACGGGTCGT |
GAGGTTCGAATCCTTCCGTC |
796–1009 | 0.875 | 83.9 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | AAAAATCCACAACGGGTCGT |
GTCTCGCTATTCGGAGGTTC |
809–1022 | 0.875 | 83.5 |
| trnS-GCU-trnG-UCC_p1 | trnS-GCU-trnG-UCC | CAATCCGACGCTTTAGTCCA |
CATCGTTAGCTTGGAAGGCT |
1298–1482 | 1.000 | 91.7 |
| trnS-GCU-trnG-UCC_p2 | trnS-GCU-trnG-UCC | AATCCGACGCTTTAGTCCAC |
CATCGTTAGCTTGGAAGGCT |
1297–1481 | 1.000 | 91.7 |
| trnS-GCU-trnG-UCC_p3 | trnS-GCU-trnG-UCC | CAATCCGACGCTTTAGTCCA |
TAGTCGACGCCAATTCAGTG |
1270–1430 | 0.688 | 79.4 |
| trnS-GCU-trnG-UCC_p4 | trnS-GCU-trnG-UCC | AATCCGACGCTTTAGTCCAC |
TAGTCGACGCCAATTCAGTG |
1269–1429 | 0.688 | 79.4 |
| trnS-GCU-trnG-UCC_p5 | trnS-GCU-trnG-UCC | CCTCGCCTTTGAGCCTTTAT |
TAGTCGACGCCAATTCAGTG |
1812–1972 | 0.688 | 78.3 |
| rpoB-trnC-GCA_p1 | rpoB-trnC-GCA | CGAGCCCATATCCTTGCTTT |
ACTTCTTCCCCACACTACGA |
1833–2010 | 0.750 | 81.4 |
| rpoB-trnC-GCA_p2 | rpoB-trnC-GCA | CGAGCCCATATCCTTGCTTT |
TTCTTCCCCACACTACGAGT |
1831–2008 | 0.750 | 81.4 |
| rpoB-trnC-GCA_p3 | rpoB-trnC-GCA | TTGTTTCCTACTCACGCGAG |
TTCTTCCCCACACTACGAGT |
1847–2024 | 0.750 | 81.1 |
| rpoB-trnC-GCA_p4 | rpoB-trnC-GCA | CCGCCTACACAAGCAAATTG |
ACTTCTTCCCCACACTACGA |
2025–2202 | 0.750 | 80.9 |
| rpoB-trnC-GCA_p5 | rpoB-trnC-GCA | CCGCCTACACAAGCAAATTG |
TTCTTCCCCACACTACGAGT |
2023–2200 | 0.750 | 80.9 |
| petN-psbM_p1 | petN-psbM | ACTCGTAGTGTGGGGAAGAA |
CCCTTATTTCCCCGGGATTG |
1250–1806 | 1.000 | 91.9 |
| petN-psbM_p2 | petN-psbM | TCGTAGTGTGGGGAAGAAGT |
CCCTTATTTCCCCGGGATTG |
1248–1804 | 1.000 | 91.9 |
| petN-psbM_p3 | petN-psbM | ACTCGTAGTGTGGGGAAGAA |
TCATTCTAGTACCGACCGCT |
593–1154 | 1.000 | 91.6 |
| petN-psbM_p4 | petN-psbM | TCGTAGTGTGGGGAAGAAGT |
TCATTCTAGTACCGACCGCT |
591–1152 | 1.000 | 91.6 |
| petN-psbM_p5 | petN-psbM | TCCGGGAAAAATTGCATCCA |
CCCTTATTTCCCCGGGATTG |
1576–2132 | 0.906 | 87.7 |
Result downloads
Reference species (32)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Elsholtzia angustifolia | NC_067948.1 | 151337 | View on NCBI ↗ |
| Elsholtzia argyi | PP357185.1 | 151272 | View on NCBI ↗ |
| Elsholtzia blanda | OR701859.1 | 151970 | View on NCBI ↗ |
| Elsholtzia bodinieri | PP357159.1 | 151517 | View on NCBI ↗ |
| Elsholtzia byeonsanensis | NC_064501.1 | 150628 | View on NCBI ↗ |
| Elsholtzia capituligera | PP357162.1 | 151943 | View on NCBI ↗ |
| Elsholtzia cephalantha | PP357230.1 | 149375 | View on NCBI ↗ |
| Elsholtzia ciliata | NC_067947.1 | 151148 | View on NCBI ↗ |
| Elsholtzia cyprianii | PP357156.1 | 151978 | View on NCBI ↗ |
| Elsholtzia densa | NC_056994.1 | 149095 | View on NCBI ↗ |
| Elsholtzia densa var. ianthina | MT083931.1 | 149118 | View on NCBI ↗ |
| Elsholtzia feddei | PP357223.1 | 151075 | View on NCBI ↗ |
| Elsholtzia fruticosa | NC_063697.1 | 151550 | View on NCBI ↗ |
| Elsholtzia glabra | PP357161.1 | 151524 | View on NCBI ↗ |
| Elsholtzia heterophylla | PP357160.1 | 151510 | View on NCBI ↗ |
| Elsholtzia kachinensis | PP357165.1 | 151166 | View on NCBI ↗ |
| Elsholtzia lamprophylla | PP357234.1 | 151520 | View on NCBI ↗ |
| Elsholtzia litangensis | PP357202.1 | 151520 | View on NCBI ↗ |
| Elsholtzia luteola | PP357199.1 | 151016 | View on NCBI ↗ |
| Elsholtzia minima | NC_068005.1 | 151199 | View on NCBI ↗ |
| Elsholtzia myosurus | PP357155.1 | 151531 | View on NCBI ↗ |
| Elsholtzia ochroleuca | PP357187.1 | 151525 | View on NCBI ↗ |
| Elsholtzia pilosa | PP357163.1 | 151928 | View on NCBI ↗ |
| Elsholtzia pygmaea | PP357243.1 | 151119 | View on NCBI ↗ |
| Elsholtzia rugulosa | NC_050945.1 | 151952 | View on NCBI ↗ |
| Elsholtzia saxatilis | PP357166.1 | 150791 | View on NCBI ↗ |
| Elsholtzia souliei | PP357167.1 | 150850 | View on NCBI ↗ |
| Elsholtzia splendens | NC_063558.1 | 151224 | View on NCBI ↗ |
| Elsholtzia stachyodes | PP357157.1 | 151980 | View on NCBI ↗ |
| Elsholtzia stauntonii | PP357164.1 | 151579 | View on NCBI ↗ |
| Elsholtzia strobilifera | PP357224.1 | 150956 | View on NCBI ↗ |
| Elsholtzia winitiana | PP357194.1 | 151958 | View on NCBI ↗ |