| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnK-UUU-rps16 | LSC | 865 | 0.0371 | 0.99 | 76.1 | yes | View details |
| rps16-trnQ-UUG | LSC | 1654 | 0.0285 | 0.98 | 78.0 | yes | View details |
| trnT-UGU-trnL-UAA | LSC | 913 | 0.0450 | 0.92 | 77.5 | yes | View details |
| accD-psaI | LSC | 658 | 0.0390 | 0.98 | 77.0 | yes | View details |
| petA-psbJ | LSC | 988 | 0.0349 | 0.98 | 74.8 | yes | View details |
| ycf1 | IRb | 1074 | 0.0042 | 1.00 | 45.3 | no | View details |
| ndhF-rpl32 | SSC | 1143 | 0.0402 | 0.98 | 78.1 | yes | View details |
| ycf1 | SSC | 5703 | 0.0243 | 1.00 | 62.9 | yes | View details |
| atpH-atpI | LSC | 1134 | 0.0200 | 1.00 | 83.5 | yes | View details |
| trnH-GUG-psbA | LSC | 347 | 0.0462 | 0.98 | 81.6 | yes | View details |
| ndhC-trnV-UAC | LSC | 1156 | 0.0299 | 0.98 | 76.0 | yes | View details |
| trnS-GCU-trnG-UCC | LSC | 733 | 0.0282 | 0.99 | 75.3 | yes | View details |
| trnF-GAA-ndhJ | LSC | 684 | 0.0237 | 1.00 | 74.8 | yes | View details |
| trnT-GGU-psbD | LSC | 1407 | 0.0218 | 0.98 | 74.7 | yes | View details |
| trnG-GCC-trnM-CAU | LSC | 195 | 0.0400 | 0.97 | 74.6 | yes | View details |
| rpl32-trnL-UAG | SSC | 930 | 0.0317 | 1.00 | 73.7 | yes | View details |
| ycf4-cemA | LSC | 877 | 0.0211 | 1.00 | 71.4 | yes | View details |
| ccsA-ndhD | SSC | 281 | 0.0539 | 0.91 | 71.4 | 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
28
Genome length
157–158 kb
Candidate markers
271
Primer pairs
85
Genome-wide nucleotide diversity
Candidate markers
8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 271 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 |
|---|---|---|---|---|---|---|
| trnH-GUG-psbA_p1 | trnH-GUG-psbA | GATCCACTTGGCTACATCCG |
CCGTGCTAACCTTGGTATGG |
438–470 | 1.000 | 88.3 |
| trnH-GUG-psbA_p2 | trnH-GUG-psbA | CAATCCACTGCCTTGATCCA |
CCGTGCTAACCTTGGTATGG |
452–484 | 1.000 | 88.2 |
| trnH-GUG-psbA_p3 | trnH-GUG-psbA | AATCCACTGCCTTGATCCAC |
CCGTGCTAACCTTGGTATGG |
451–483 | 1.000 | 88.2 |
| trnH-GUG-psbA_p4 | trnH-GUG-psbA | ACAATCCACTGCCTTGATCC |
CCGTGCTAACCTTGGTATGG |
453–485 | 1.000 | 88.2 |
| trnH-GUG-psbA_p5 | trnH-GUG-psbA | GATCCACTTGGCTACATCCG |
ACCGTGCTAACCTTGGTATG |
439–471 | 1.000 | 87.8 |
| trnK-UUU-rps16_p1 | trnK-UUU-rps16 | CCTTTCAGGATCAGTCGTGG |
TCTATCCCAATGAGCCGTCT |
1186–1246 | 0.964 | 89.7 |
| trnK-UUU-rps16_p2 | trnK-UUU-rps16 | CCCTTTCAGGATCAGTCGTG |
TGTTGCTGCCGTTTTGAAAG |
1634–1693 | 0.964 | 89.3 |
| trnK-UUU-rps16_p3 | trnK-UUU-rps16 | CCTTTCAGGATCAGTCGTGG |
TGTTGCTGCCGTTTTGAAAG |
1633–1692 | 0.964 | 89.3 |
| trnK-UUU-rps16_p4 | trnK-UUU-rps16 | CCCTTTCAGGATCAGTCGTG |
GCCGTACGAGGAGAAAACTT |
1267–1305 | 0.929 | 87.7 |
| trnK-UUU-rps16_p5 | trnK-UUU-rps16 | CCTTTCAGGATCAGTCGTGG |
GCCGTACGAGGAGAAAACTT |
1266–1304 | 0.929 | 87.7 |
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | AACGGATCGTGTCCTTCAAG |
GAGGTTCGAATCCTTCCGTC |
1236–1753 | 1.000 | 90.7 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
GAGGTTCGAATCCTTCCGTC |
1219–1736 | 1.000 | 90.3 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | CAACGGATCGTGTCCTTCAA |
GAGGTTCGAATCCTTCCGTC |
1237–1754 | 1.000 | 89.7 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | CGGATCGTGTCCTTCAAGTC |
GAGGTTCGAATCCTTCCGTC |
1234–1751 | 1.000 | 88.4 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | GGATCGTGTCCTTCAAGTCG |
GAGGTTCGAATCCTTCCGTC |
1233–1750 | 1.000 | 88.4 |
| trnS-GCU-trnG-UCC_p1 | trnS-GCU-trnG-UCC | CAATCCGACGCTTTAGTCCA |
AGGGGGTTAATAGAACGAATCAC |
810–852 | 1.000 | 67.7 |
| trnS-GCU-trnG-UCC_p2 | trnS-GCU-trnG-UCC | AATCCGACGCTTTAGTCCAC |
AGGGGGTTAATAGAACGAATCAC |
809–851 | 1.000 | 67.7 |
| trnS-GCU-trnG-UCC_p3 | trnS-GCU-trnG-UCC | ACGGAAAGAGAGGGATTCGA |
AGGGGGTTAATAGAACGAATCAC |
864–906 | 1.000 | 66.5 |
| trnS-GCU-trnG-UCC_p4 | trnS-GCU-trnG-UCC | CAATCCGACGCTTTAGTCCA |
GGGGGTTAATAGAACGAATCACA |
809–851 | 1.000 | 66.1 |
| trnS-GCU-trnG-UCC_p5 | trnS-GCU-trnG-UCC | AATCCGACGCTTTAGTCCAC |
GGGGGTTAATAGAACGAATCACA |
808–850 | 1.000 | 66.1 |
| atpH-atpI_p1 | atpH-atpI | ATAACGGAAGCGGCAGAAAT |
CAAGCGGTATCCAAGCTCTT |
1011–1303 | 1.000 | 91.5 |
| atpH-atpI_p2 | atpH-atpI | TACCTTGACCAACTCCAGGT |
CAAGCGGTATCCAAGCTCTT |
1067–1359 | 1.000 | 90.9 |
| atpH-atpI_p3 | atpH-atpI | AATAACGGAAGCGGCAGAAA |
CAAGCGGTATCCAAGCTCTT |
1012–1304 | 1.000 | 90.3 |
| atpH-atpI_p4 | atpH-atpI | GCAGTACCTTGACCAACTCC |
CAAGCGGTATCCAAGCTCTT |
1071–1363 | 1.000 | 90.2 |
| atpH-atpI_p5 | atpH-atpI | TACCTTCTACAGCTTGGCCT |
CAAGCGGTATCCAAGCTCTT |
1094–1376 | 0.929 | 88.4 |
| trnT-GGU-psbD_p1 | trnT-GGU-psbD | GTGGTAGAGTAACGCCATGG |
ACAAAAACGAAACGGTCCCT |
1519–1573 | 1.000 | 89.4 |
| trnT-GGU-psbD_p2 | trnT-GGU-psbD | GTGGTAGAGTAACGCCATGG |
GACCGGACCAACCTACAAAA |
1533–1587 | 1.000 | 89.3 |
| trnT-GGU-psbD_p3 | trnT-GGU-psbD | TCAGTGGTAGAGTAACGCCA |
ACAAAAACGAAACGGTCCCT |
1522–1576 | 1.000 | 89.2 |
| trnT-GGU-psbD_p4 | trnT-GGU-psbD | TCAGTGGTAGAGTAACGCCA |
GACCGGACCAACCTACAAAA |
1536–1590 | 1.000 | 89.1 |
| trnT-GGU-psbD_p5 | trnT-GGU-psbD | GTGGTAGAGTAACGCCATGG |
TAGACCGGACCAACCTACAA |
1535–1589 | 1.000 | 88.9 |
Result downloads
Reference species (28)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Hydrangea alternifolia | NC_084217.1 | 157806 | View on NCBI ↗ |
| Hydrangea ampla | NC_044807.1 | 157294 | View on NCBI ↗ |
| Hydrangea arborescens | NC_084224.1 | 157898 | View on NCBI ↗ |
| Hydrangea aspera | MG524992.1 | 157637 | View on NCBI ↗ |
| Hydrangea barbara | NC_044832.1 | 157721 | View on NCBI ↗ |
| Hydrangea bifida | NC_084221.1 | 157826 | View on NCBI ↗ |
| Hydrangea caerulea | NC_044809.1 | 157765 | View on NCBI ↗ |
| Hydrangea chinensis | PQ593891.1 | 157706 | View on NCBI ↗ |
| Hydrangea daimingshanensis | NC_084220.1 | 157749 | View on NCBI ↗ |
| Hydrangea davidii | NC_050783.1 | 158054 | View on NCBI ↗ |
| Hydrangea febrifuga | NC_044841.1 | 157613 | View on NCBI ↗ |
| Hydrangea formosana | NC_084219.1 | 157335 | View on NCBI ↗ |
| Hydrangea heteromalla | NC_044842.1 | 157889 | View on NCBI ↗ |
| Hydrangea hirsuta | NC_084223.1 | 157652 | View on NCBI ↗ |
| Hydrangea hydrangeoides | NC_034935.1 | 157434 | View on NCBI ↗ |
| Hydrangea luteovenosa | NC_035662.1 | 157494 | View on NCBI ↗ |
| Hydrangea moellendorffii | NC_044805.1 | 157683 | View on NCBI ↗ |
| Hydrangea obtusifolia | NC_044833.1 | 157469 | View on NCBI ↗ |
| Hydrangea paniculata | NC_044829.1 | 157881 | View on NCBI ↗ |
| Hydrangea petiolaris | NC_034936.1 | 157692 | View on NCBI ↗ |
| Hydrangea platyarguta | NC_044806.1 | 157515 | View on NCBI ↗ |
| Hydrangea quercifolia | NC_084225.1 | 158163 | View on NCBI ↗ |
| Hydrangea scandens | NC_084226.1 | 157525 | View on NCBI ↗ |
| Hydrangea schizomollis | NC_084229.1 | 157630 | View on NCBI ↗ |
| Hydrangea serrata | NC_034934.1 | 157730 | View on NCBI ↗ |
| Hydrangea serrata f. fertilis | KU140669.1 | 157730 | View on NCBI ↗ |
| Hydrangea strigosa | NC_057991.1 | 157905 | View on NCBI ↗ |
| Hydrangea viburnoides | NC_084228.1 | 157974 | View on NCBI ↗ |