| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| rps16-trnQ-UUG | LSC | 1653 | 0.0531 | 0.98 | 80.9 | yes | View details |
| petN-psbM | LSC | 1091 | 0.0483 | 0.98 | 76.4 | yes | View details |
| ndhC-trnV-UAC | LSC | 1138 | 0.0513 | 0.99 | 82.5 | yes | View details |
| petA-psbJ | LSC | 989 | 0.0571 | 0.99 | 78.9 | yes | View details |
| ycf1 | IRb | 975 | 0.0174 | 1.00 | 50.4 | no | View details |
| ndhF | SSC | 2235 | 0.0292 | 1.00 | 63.4 | yes | View details |
| ndhF-rpl32 | SSC | 1162 | 0.0608 | 0.94 | 77.5 | yes | View details |
| rpl32-trnL-UAG | SSC | 847 | 0.0582 | 0.97 | 77.3 | yes | View details |
| rps15-ycf1 | SSC | 393 | 0.0609 | 0.97 | 71.7 | yes | View details |
| ycf1 | SSC | 5469 | 0.0417 | 1.00 | 72.4 | yes | View details |
| trnK-UUU-rps16 | LSC | 773 | 0.0504 | 0.96 | 80.1 | yes | View details |
| rpoB-trnC-GCA | LSC | 1184 | 0.0382 | 1.00 | 79.4 | yes | View details |
| trnT-GGU-psbD | LSC | 1383 | 0.0397 | 0.98 | 78.2 | yes | View details |
| trnT-UGU-trnL-UAA | LSC | 920 | 0.0432 | 0.94 | 78.2 | yes | View details |
| trnS-GCU-trnR-UCU | LSC | 1667 | 0.0356 | 0.93 | 78.1 | yes | View details |
| atpH-atpI | LSC | 969 | 0.0400 | 0.98 | 76.5 | yes | View details |
| ycf3-trnS-GGA | LSC | 784 | 0.0413 | 0.98 | 75.8 | yes | View details |
| trnL-UAA-trnF-GAA | LSC | 343 | 0.0452 | 1.00 | 74.6 | yes | View details |
| trnF-GAA-ndhJ | LSC | 690 | 0.0426 | 0.99 | 74.5 | yes | View details |
| trnE-UUC-trnT-GGU | LSC | 819 | 0.0499 | 0.97 | 74.1 | 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
35
Genome length
157–159 kb
Candidate markers
268
Primer pairs
95
Genome-wide nucleotide diversity
Candidate markers
10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 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 |
|---|---|---|---|---|---|---|
| trnK-UUU-rps16_p1 | trnK-UUU-rps16 | TCCCTCGCTTCATCCAAATG |
TGTTGCTGCCGTTTTGAAAG |
1507–1559 | 1.000 | 91.0 |
| trnK-UUU-rps16_p2 | trnK-UUU-rps16 | CTCATGGGAGAAGCCTTTCC |
TGTTGCTGCCGTTTTGAAAG |
1846–1902 | 1.000 | 91.0 |
| trnK-UUU-rps16_p3 | trnK-UUU-rps16 | TCCCTCGCTTCATCCAAATG |
TCTATCCCAATGAGCCGTCT |
1039–1089 | 0.971 | 89.8 |
| trnK-UUU-rps16_p4 | trnK-UUU-rps16 | TCCCTCGCTTCATCCAAATG |
AAAAAGGCGCTCAACCTACA |
896–946 | 0.914 | 88.0 |
| trnK-UUU-rps16_p5 | trnK-UUU-rps16 | CTCATGGGAGAAGCCTTTCC |
AAAAAGGCGCTCAACCTACA |
1233–1289 | 0.914 | 88.0 |
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
GAGGTTCGAATCCTTCCGTC |
1318–1835 | 1.000 | 90.3 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
TTCGGAGGTTCGAATCCTTC |
1322–1839 | 1.000 | 85.5 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | CGTTGCTTTCTACCACATCG |
GAGGTTCGAATCCTTCCGTC |
1310–1827 | 1.000 | 85.1 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | AGTCGCACGTTGCTTTCTAC |
GAGGTTCGAATCCTTCCGTC |
1317–1834 | 1.000 | 84.5 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
TAAGGCAACGGGTTTTGGTC |
1571–1865 | 0.914 | 82.0 |
| trnS-GCU-trnR-UCU_p1 | trnS-GCU-trnR-UCU | CAATCCGACGCTTTAGTCCA |
AGAAGACCTCTGTCCTATCCA |
1417–1750 | 1.000 | 75.6 |
| trnS-GCU-trnR-UCU_p2 | trnS-GCU-trnR-UCU | AATCCGACGCTTTAGTCCAC |
AGAAGACCTCTGTCCTATCCA |
1416–1749 | 1.000 | 75.5 |
| trnS-GCU-trnR-UCU_p3 | trnS-GCU-trnR-UCU | CAATCCGACGCTTTAGTCCA |
AGGTTTAGAAGACCTCTGTCCT |
1423–1756 | 1.000 | 74.9 |
| trnS-GCU-trnR-UCU_p4 | trnS-GCU-trnR-UCU | AATCCGACGCTTTAGTCCAC |
AGGTTTAGAAGACCTCTGTCCT |
1422–1755 | 1.000 | 74.9 |
| trnS-GCU-trnR-UCU_p5 | trnS-GCU-trnR-UCU | ACGGAAAGAGAGGGATTCGA |
AGAAGACCTCTGTCCTATCCA |
1471–1804 | 1.000 | 74.4 |
| atpH-atpI_p1 | atpH-atpI | TACCTTGACCAACTCCAGGT |
TTTTTGCAACTTTAGCCGCG |
1069–1313 | 0.943 | 84.7 |
| atpH-atpI_p2 | atpH-atpI | ATAACGGAAGCGGCAGAAAT |
TTTTTGCAACTTTAGCCGCG |
1013–1257 | 0.914 | 84.1 |
| atpH-atpI_p3 | atpH-atpI | ATAACGGAAGCGGCAGAAAT |
TAGGTGAATCCATGGAGGGT |
986–1230 | 0.914 | 83.6 |
| atpH-atpI_p4 | atpH-atpI | TACCTTGACCAACTCCAGGT |
TAGGTGAATCCATGGAGGGT |
1042–1286 | 0.914 | 83.0 |
| atpH-atpI_p5 | atpH-atpI | AATAACGGAAGCGGCAGAAA |
TTTTTGCAACTTTAGCCGCG |
1014–1258 | 0.914 | 83.0 |
| rpoB-trnC-GCA_p1 | rpoB-trnC-GCA | CCCTCATTTCCATCCCGAAG |
CCGGATTTGAACTGGGGAAA |
1120–1300 | 1.000 | 91.1 |
| rpoB-trnC-GCA_p2 | rpoB-trnC-GCA | CTCATTTCCATCCCGAAGCA |
CCGGATTTGAACTGGGGAAA |
1118–1298 | 1.000 | 91.0 |
| rpoB-trnC-GCA_p3 | rpoB-trnC-GCA | CCCTCATTTCCATCCCGAAG |
AAAAGGATTTGCAGTCCCCC |
1102–1282 | 1.000 | 88.9 |
| rpoB-trnC-GCA_p4 | rpoB-trnC-GCA | CTCATTTCCATCCCGAAGCA |
AAAAGGATTTGCAGTCCCCC |
1100–1280 | 1.000 | 88.8 |
| rpoB-trnC-GCA_p5 | rpoB-trnC-GCA | TCCCTCATTTCCATCCCGAA |
CCGGATTTGAACTGGGGAAA |
1121–1301 | 1.000 | 88.1 |
| petN-psbM_p1 | petN-psbM | TTTCACAGAGACAATGGGGC |
AGATCAAACAAGGATCCCGC |
1947–2297 | 0.457 | 67.3 |
| petN-psbM_p2 | petN-psbM | TTTCACAGAGACAATGGGGC |
TGGGAAGGTGGTCAGATGAT |
1670–2017 | 0.429 | 65.9 |
| petN-psbM_p3 | petN-psbM | GGGCCAGAATCCCTTTTTGA |
AGATCAAACAAGGATCCCGC |
1670–2017 | 0.400 | 63.5 |
| petN-psbM_p4 | petN-psbM | GGGCCAGAATCCCTTTTTGA |
TGGGAAGGTGGTCAGATGAT |
1393–1736 | 0.371 | 62.0 |
| petN-psbM_p5 | petN-psbM | TCCCTTTTTGACTCTTCGCC |
TGGGAAGGTGGTCAGATGAT |
1384–1727 | 0.286 | 57.1 |
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 |
|---|---|---|---|
| Cornus alba | NC_059720.1 | 158451 | View on NCBI ↗ |
| Cornus alternifolia | NC_044812.1 | 158716 | View on NCBI ↗ |
| Cornus bretschneideri | NC_060800.1 | 158270 | View on NCBI ↗ |
| Cornus canadensis | NC_044822.1 | 157153 | View on NCBI ↗ |
| Cornus capitata | NC_084212.1 | 157199 | View on NCBI ↗ |
| Cornus chinensis | NC_044815.1 | 158166 | View on NCBI ↗ |
| Cornus controversa | NC_030260.1 | 158674 | View on NCBI ↗ |
| Cornus disciflora | NC_044819.1 | 157331 | View on NCBI ↗ |
| Cornus elliptica | NC_056267.1 | 157400 | View on NCBI ↗ |
| Cornus eydeana | NC_044816.1 | 158345 | View on NCBI ↗ |
| Cornus florida | NC_044820.1 | 157538 | View on NCBI ↗ |
| Cornus florida var. urbiniana | MN380671.1 | 157584 | View on NCBI ↗ |
| Cornus hongkongensis | NC_084123.1 | 156954 | View on NCBI ↗ |
| Cornus hongkongensis subsp. elegans | OR597582.1 | 157197 | View on NCBI ↗ |
| Cornus hongkongensis subsp. ferruginea | OR597579.1 | 157291 | View on NCBI ↗ |
| Cornus hongkongensis subsp. gigantea | OR597583.1 | 156980 | View on NCBI ↗ |
| Cornus hongkongensis subsp. melanotricha | OR597580.1 | 157288 | View on NCBI ↗ |
| Cornus hongkongensis subsp. tonkinensis | OR597581.1 | 156965 | View on NCBI ↗ |
| Cornus kousa | NC_044818.1 | 157154 | View on NCBI ↗ |
| Cornus kousa subsp. chinensis | PV164577.1 | 157283 | View on NCBI ↗ |
| Cornus macrophylla | NC_044810.1 | 158482 | View on NCBI ↗ |
| Cornus multinervosa | NC_084211.1 | 157365 | View on NCBI ↗ |
| Cornus nuttallii | NC_044821.1 | 156671 | View on NCBI ↗ |
| Cornus oblonga | NC_044811.1 | 157731 | View on NCBI ↗ |
| Cornus officinalis | NC_042746.1 | 158257 | View on NCBI ↗ |
| Cornus peruviana | NC_044825.1 | 158830 | View on NCBI ↗ |
| Cornus sanguinea | NC_044817.1 | 158510 | View on NCBI ↗ |
| Cornus sericea | PP811661.1 | 158244 | View on NCBI ↗ |
| Cornus sessilis | NC_044814.1 | 158445 | View on NCBI ↗ |
| Cornus suecica | NC_044823.1 | 157114 | View on NCBI ↗ |
| Cornus sunhangii | NC_060994.1 | 157446 | View on NCBI ↗ |
| Cornus unalaschkensis | NC_044824.1 | 157182 | View on NCBI ↗ |
| Cornus volkensii | NC_044813.1 | 158227 | View on NCBI ↗ |
| Cornus walteri | NC_058318.1 | 158198 | View on NCBI ↗ |
| Cornus wilsoniana | NC_063837.1 | 158158 | View on NCBI ↗ |