| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| rps4-psbM | Genome | 328 | 0.0139 | 0.99 | 47.8 | yes | View details |
| rps2 | Genome | 720 | 0.0036 | 1.00 | 33.0 | yes | View details |
| trnR-UCU-trnS-GCU | Genome | 765 | 0.0127 | 0.98 | 60.2 | yes | View details |
| trnF-GAA-trnfM-CAU | Genome | 352 | 0.0105 | 1.00 | 49.8 | yes | View details |
| rpl2 | Genome | 1276 | 0.0060 | 1.00 | 48.8 | yes | View details |
| rps15-psaC | Genome | 306 | 0.0257 | 1.00 | 68.5 | yes | View details |
| psaC | Genome | 246 | 0.0038 | 1.00 | 23.3 | yes | View details |
| trnL-AUG-ycf1 | Genome | 396 | 0.0192 | 0.99 | 52.9 | yes | View details |
| trnfM-CAU-atpE | Genome | 64 | 0.0569 | 0.95 | 73.8 | yes | View details |
| rpoC2-rps2 | Genome | 132 | 0.0458 | 0.88 | 73.2 | yes | View details |
| psaC-ccsA | Genome | 106 | 0.0412 | 1.00 | 66.1 | yes | View details |
| psaJ-rpl33 | Genome | 124 | 0.0247 | 0.93 | 65.7 | yes | View details |
| psbZ-trnG-UCC | Genome | 148 | 0.0121 | 1.00 | 59.7 | yes | View details |
| ycf3 | Genome | 1790 | 0.0054 | 1.00 | 59.7 | yes | View details |
| clpP-psbB | Genome | 1176 | 0.0074 | 0.99 | 59.0 | yes | View details |
| rps11-rpl36 | Genome | 83 | 0.0351 | 1.00 | 58.7 | yes | View details |
| psbJ-psbL | Genome | 125 | 0.0198 | 1.00 | 57.9 | 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. | |||||||
Species
35
Genome length
89–110 kb
Candidate markers
201
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 201 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 |
|---|---|---|---|---|---|---|
| psbZ-trnG-UCC_p1 | psbZ-trnG-UCC | CTTTCGCTTTCCCAGAAGGT |
CGTCTTCTCCTTGGCAAAGA |
288–372 | 1.000 | 85.2 |
| psbZ-trnG-UCC_p2 | psbZ-trnG-UCC | CTTTCGCTTTCCCAGAAGGT |
TGAGGTCACGGGTTCAAATC |
360–444 | 1.000 | 84.9 |
| psbZ-trnG-UCC_p3 | psbZ-trnG-UCC | CTTTCGCTTTCCCAGAAGGT |
ATGGTTATTTTGTGGGCGGA |
326–410 | 0.971 | 83.5 |
| psbZ-trnG-UCC_p4 | psbZ-trnG-UCC | CTTTCGCTTTCCCAGAAGGT |
TGGTTATTTTGTGGGCGGAT |
325–409 | 0.971 | 83.5 |
| psbZ-trnG-UCC_p5 | psbZ-trnG-UCC | ACCTATCGCTTTCGCTTTCC |
CGTCTTCTCCTTGGCAAAGA |
296–380 | 1.000 | 83.1 |
| ycf3_p1 | ycf3 | CCTGGGGTGGACATAATTGG |
CATTCCAAAAGGAACTGAAGCA |
1929–1964 | 1.000 | 64.6 |
| ycf3_p2 | ycf3 | CCTGGGGTGGACATAATTGG |
TCCAAAAGGAACTGAAGCAA |
1926–1961 | 1.000 | 64.4 |
| ycf3_p3 | ycf3 | CCTGGGGTGGACATAATTGG |
TTCCAAAAGGAACTGAAGCA |
1927–1962 | 1.000 | 64.3 |
| ycf3_p4 | ycf3 | CCTGGGGTGGACATAATTGG |
TCCAAAAGGAACTGAAGCAAA |
1926–1961 | 1.000 | 62.8 |
| ycf3_p5 | ycf3 | CCTGGGGTGGACATAATTGG |
TTCCAAAAGGAACTGAAGCAA |
1927–1962 | 1.000 | 62.8 |
| rps4-psbM_p1 | rps4-psbM | CTGTTGACCCCTGAGCATTT |
AAGTGGTAAGGCAGAGGACT |
1044–1075 | 1.000 | 86.1 |
| rps4-psbM_p2 | rps4-psbM | TGCCGTAATTGTCGTTCTGT |
AAGTGGTAAGGCAGAGGACT |
1006–1037 | 1.000 | 85.8 |
| rps4-psbM_p3 | rps4-psbM | CTGTTGACCCCTGAGCATTT |
CAAGTGGTAAGGCAGAGGAC |
1045–1076 | 1.000 | 85.5 |
| rps4-psbM_p4 | rps4-psbM | CAAATCCCTCTCTTTCCGCA |
AAGTGGTAAGGCAGAGGACT |
1492–1528 | 1.000 | 84.3 |
| rps4-psbM_p5 | rps4-psbM | CTGTTGACCCCTGAGCATTT |
CTGGGTGTCGCCTACTTTTT |
997–1028 | 0.971 | 83.9 |
| rpoC2-rps2_p1 | rpoC2-rps2 | GCCGGTACTGGAAAATGGAA |
TGATGTCCGAGATGAACTGC |
197–280 | 0.971 | 86.7 |
| rpoC2-rps2_p2 | rpoC2-rps2 | GCCGGTACTGGAAAATGGAA |
GATGTCCGAGATGAACTGCT |
196–279 | 0.971 | 84.4 |
| rpoC2-rps2_p3 | rpoC2-rps2 | AGTAGTAAAATACCCGCCGG |
TGATGTCCGAGATGAACTGC |
194–295 | 1.000 | 82.3 |
| rpoC2-rps2_p4 | rpoC2-rps2 | GCCGGTACTGGAAAATGGAA |
TGTCCGAGATGAACTGCTAC |
194–277 | 0.971 | 81.7 |
| rpoC2-rps2_p5 | rpoC2-rps2 | GCCGGTACTGGAAAATGGAA |
GTCCGAGATGAACTGCTACT |
193–276 | 0.971 | 79.3 |
| rps2_p1 | rps2 | AGAAAAGTCATAGATTCCGTAG |
GCTTTGCGCTTACTTCGAAA |
808 | 1.000 | 41.3 |
| rps2_p2 | rps2 | CGTAGGAATGGAAATTCTTTTAGAGA |
GCTTTGCGCTTACTTCGAAA |
791 | 1.000 | 41.2 |
| rps2_p3 | rps2 | CGTAGGAATGGAAATTCTTTT |
GCTTTGCGCTTACTTCGAAA |
791 | 1.000 | 41.2 |
| rps2_p4 | rps2 | TCTTTTAGAGAAGAGAAAAGCA |
GCTTTGCGCTTACTTCGAAA |
776 | 1.000 | 41.2 |
| rps2_p5 | rps2 | CGTAGGAATGGAAATTCTTTTAGAG |
GCTTTGCGCTTACTTCGAAA |
791 | 1.000 | 41.2 |
| trnR-UCU-trnS-GCU_p1 | trnR-UCU-trnS-GCU | AGAAGACCTCTGTCCTATCCA |
CTTTGGTCCTCTCAGCCATC |
793–856 | 1.000 | 71.2 |
| trnR-UCU-trnS-GCU_p2 | trnR-UCU-trnS-GCU | AGGTTTAGAAGACCTCTGTCCT |
CTTTGGTCCTCTCAGCCATC |
799–862 | 1.000 | 70.5 |
| trnR-UCU-trnS-GCU_p3 | trnR-UCU-trnS-GCU | AGAAGACCTCTGTCCTATCCA |
CGGAGAGAGAGGGATTCGAA |
857–920 | 1.000 | 68.8 |
| trnR-UCU-trnS-GCU_p4 | trnR-UCU-trnS-GCU | AGAAGACCTCTGTCCTATCCA |
GAACCCTCGATACGGGATTG |
840–903 | 0.943 | 67.7 |
| trnR-UCU-trnS-GCU_p5 | trnR-UCU-trnS-GCU | AGGTTTAGAAGACCTCTGTCCT |
GAACCCTCGATACGGGATTG |
846–909 | 0.943 | 67.0 |
Result downloads
Reference species (35)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Ephedra alata | MG594447.1 | 88898 | View on NCBI ↗ |
| Ephedra altissima | MG594448.1 | 89125 | View on NCBI ↗ |
| Ephedra americana | MG594450.1 | 89249 | View on NCBI ↗ |
| Ephedra andina | MG594451.1 | 89243 | View on NCBI ↗ |
| Ephedra antisyphilitica | MG594452.1 | 89158 | View on NCBI ↗ |
| Ephedra aphylla | MG594453.1 | 89066 | View on NCBI ↗ |
| Ephedra breana | MG594455.1 | 89275 | View on NCBI ↗ |
| Ephedra chilensis | MG594456.1 | 89243 | View on NCBI ↗ |
| Ephedra ciliata | MG594457.1 | 88907 | View on NCBI ↗ |
| Ephedra coryi | MG594458.1 | 89203 | View on NCBI ↗ |
| Ephedra distachya | MG594459.1 | 89103 | View on NCBI ↗ |
| Ephedra equisetina | NC_011954.1 | 109518 | View on NCBI ↗ |
| Ephedra fedtschenkoae | MG594462.1 | 89158 | View on NCBI ↗ |
| Ephedra foliata | MG594465.1 | 89039 | View on NCBI ↗ |
| Ephedra fragilis | MG594466.1 | 89094 | View on NCBI ↗ |
| Ephedra frustillata | MG594468.1 | 89255 | View on NCBI ↗ |
| Ephedra funerea | MG594469.1 | 89191 | View on NCBI ↗ |
| Ephedra gerardiana | MG594470.1 | 89184 | View on NCBI ↗ |
| Ephedra likiangensis | MG594472.1 | 89122 | View on NCBI ↗ |
| Ephedra lomatolepis | MG594473.1 | 89162 | View on NCBI ↗ |
| Ephedra major | MG594474.1 | 89324 | View on NCBI ↗ |
| Ephedra milleri | MG594475.1 | 89143 | View on NCBI ↗ |
| Ephedra minuta | MG594476.1 | 89374 | View on NCBI ↗ |
| Ephedra nevadensis | MG594478.1 | 89276 | View on NCBI ↗ |
| Ephedra pachyclada | MG594479.1 | 89107 | View on NCBI ↗ |
| Ephedra pedunculata | MG594480.1 | 89214 | View on NCBI ↗ |
| Ephedra przewalskii | NC_058775.1 | 109569 | View on NCBI ↗ |
| Ephedra rupestris | MG594483.1 | 89249 | View on NCBI ↗ |
| Ephedra somalensis | MG594485.1 | 89134 | View on NCBI ↗ |
| Ephedra strobilacea | MG594487.1 | 89166 | View on NCBI ↗ |
| Ephedra torreyana | MG594489.1 | 89299 | View on NCBI ↗ |
| Ephedra transitoria | MG594490.1 | 89216 | View on NCBI ↗ |
| Ephedra trifurca | MG594491.1 | 89367 | View on NCBI ↗ |
| Ephedra tweediana | MG594492.1 | 89310 | View on NCBI ↗ |
| Ephedra viridis | MG594493.1 | 89280 | View on NCBI ↗ |