| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnH-GUG-psbA | LSC | 455 | 0.0348 | 0.91 | 69.1 | yes | View details |
| rps16-trnQ-UUG | LSC | 1738 | 0.0204 | 0.99 | 70.8 | yes | View details |
| psbZ-trnG-GCC | LSC | 273 | 0.0127 | 1.00 | 55.7 | yes | View details |
| trnT-UGU-trnL-UAA | LSC | 1122 | 0.0264 | 0.93 | 80.8 | yes | View details |
| accD-psaI | LSC | 813 | 0.0224 | 0.95 | 65.8 | yes | View details |
| petA-psbJ | LSC | 749 | 0.0242 | 1.00 | 72.5 | yes | View details |
| ycf1 | IRb | 1177 | 0.0024 | 1.00 | 40.0 | no | View details |
| ndhF | SSC | 2256 | 0.0104 | 1.00 | 49.4 | yes | View details |
| ndhF-rpl32 | SSC | 954 | 0.0205 | 0.99 | 73.8 | yes | View details |
| rpl32-trnL-UAG | SSC | 848 | 0.0280 | 0.98 | 75.3 | yes | View details |
| ndhD | SSC | 1503 | 0.0066 | 1.00 | 48.7 | yes | View details |
| ycf1 | SSC | 5613 | 0.0145 | 1.00 | 52.2 | yes | View details |
| trnG-GCC-trnfM-CAU | LSC | 141 | 0.0764 | 0.99 | 80.8 | yes | View details |
| rps19-rpl2 | IRb | 62 | 0.0601 | 0.95 | 76.9 | yes | View details |
| rpl2-trnH-GUG | IRa | 87 | 0.0458 | 0.98 | 74.8 | no | View details |
| ccsA-ndhD | SSC | 238 | 0.0539 | 1.00 | 73.0 | yes | View details |
| ndhC-trnV-UAC | LSC | 1065 | 0.0164 | 0.99 | 72.2 | yes | View details |
| rps15-ycf1 | SSC | 361 | 0.0241 | 1.00 | 68.9 | yes | View details |
| trnS-GCU-trnG-UCC | LSC | 649 | 0.0152 | 1.00 | 68.7 | yes | View details |
| psbI-trnS-GCU | LSC | 152 | 0.0215 | 0.99 | 67.8 | yes | View details |
| trnC-GCA-petN | LSC | 757 | 0.0129 | 1.00 | 66.6 | yes | View details |
| trnT-GGU-psbD | LSC | 1523 | 0.0143 | 0.98 | 65.9 | 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
17
Genome length
157–158 kb
Candidate markers
269
Primer pairs
100
Genome-wide nucleotide diversity
Candidate markers
12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 269 candidates).
Primer pairs
Showing the top 30 of 100 primer pairs (ranked by primer score).
| Primer ID | Label | Forward | Reverse | Amplicon (bp) | Cross-species rate | Score |
|---|---|---|---|---|---|---|
| trnH-GUG-psbA_p1 | trnH-GUG-psbA | CTGCCTTAATCCACTTGGCT |
TCAGTGCTATGCATGGTTCC |
710–1077 | 1.000 | 89.5 |
| trnH-GUG-psbA_p2 | trnH-GUG-psbA | CTGCCTTAATCCACTTGGCT |
CAGTGCTATGCATGGTTCCT |
709–1076 | 1.000 | 89.5 |
| trnH-GUG-psbA_p3 | trnH-GUG-psbA | ACTGCCTTAATCCACTTGGC |
TCAGTGCTATGCATGGTTCC |
711–1078 | 1.000 | 89.3 |
| trnH-GUG-psbA_p4 | trnH-GUG-psbA | CTGCCTTAATCCACTTGGCT |
GGTGTAGCTGGTGTATTCGG |
741–1108 | 1.000 | 89.1 |
| trnH-GUG-psbA_p5 | trnH-GUG-psbA | CTGCCTTAATCCACTTGGCT |
ATGCACCCATTCCACATGTT |
762–1129 | 1.000 | 89.0 |
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | AACGGATCGTGTCCTTCAAG |
GAGGTTCGAATCCTTCCGTC |
1820–1877 | 1.000 | 89.3 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
GAGGTTCGAATCCTTCCGTC |
1803–1860 | 1.000 | 89.0 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | CAACGGATCGTGTCCTTCAA |
GAGGTTCGAATCCTTCCGTC |
1821–1878 | 1.000 | 88.3 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | CGGATCGTGTCCTTCAAGTC |
GAGGTTCGAATCCTTCCGTC |
1818–1875 | 1.000 | 87.0 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | GGATCGTGTCCTTCAAGTCG |
GAGGTTCGAATCCTTCCGTC |
1817–1874 | 1.000 | 87.0 |
| psbI-trnS-GCU_p1 | psbI-trnS-GCU | CGTAATCCTGGACGTGAAGA |
TAAAGCGGCGGATTGCTAAT |
236–244 | 1.000 | 82.5 |
| psbI-trnS-GCU_p2 | psbI-trnS-GCU | CGTAATCCTGGACGTGAAGA |
ATTGGGAGAGATGGCTGAGT |
260–268 | 1.000 | 81.4 |
| psbI-trnS-GCU_p3 | psbI-trnS-GCU | CGTAATCCTGGACGTGAAGAA |
TAAAGCGGCGGATTGCTAAT |
236–244 | 1.000 | 80.2 |
| psbI-trnS-GCU_p4 | psbI-trnS-GCU | CTCTCTTCATCTTCGGGTTCC |
TAAAGCGGCGGATTGCTAAT |
274–282 | 1.000 | 80.0 |
| psbI-trnS-GCU_p5 | psbI-trnS-GCU | TCTCTTCATCTTCGGGTTCCT |
TAAAGCGGCGGATTGCTAAT |
273–281 | 1.000 | 80.0 |
| trnS-GCU-trnG-UCC_p1 | trnS-GCU-trnG-UCC | ATTAGCAATCCGCCGCTTTA |
AACCGAAAGACCCCTTAACT |
749–777 | 1.000 | 74.2 |
| trnS-GCU-trnG-UCC_p2 | trnS-GCU-trnG-UCC | ACGGAAAGAGAGGGATTCGA |
AACCGAAAGACCCCTTAACT |
798–826 | 1.000 | 72.9 |
| trnS-GCU-trnG-UCC_p3 | trnS-GCU-trnG-UCC | ATTAGCAATCCGCCGCTTTA |
AAACCGAAAGACCCCTTAACT |
750–778 | 1.000 | 72.3 |
| trnS-GCU-trnG-UCC_p4 | trnS-GCU-trnG-UCC | GCTTTAGTCCACTCAGCCAT |
AACCGAAAGACCCCTTAACT |
735–763 | 1.000 | 71.3 |
| trnS-GCU-trnG-UCC_p5 | trnS-GCU-trnG-UCC | ACGGAAAGAGAGGGATTCGA |
AAACCGAAAGACCCCTTAACT |
799–827 | 1.000 | 71.0 |
| trnC-GCA-petN_p1 | trnC-GCA-petN | TTTGGATCCTTTTGGCGACA |
AGCCCAAGCGAGACTTACTA |
866–905 | 1.000 | 87.2 |
| trnC-GCA-petN_p2 | trnC-GCA-petN | TTGGATCCTTTTGGCGACAT |
AGCCCAAGCGAGACTTACTA |
865–904 | 1.000 | 85.6 |
| trnC-GCA-petN_p3 | trnC-GCA-petN | TTTGGATCCTTTTGGCGACA |
AGAGTCCACTTCTTCCCCAT |
927–966 | 1.000 | 85.4 |
| trnC-GCA-petN_p4 | trnC-GCA-petN | GGGGGACTGCAAATCCTTTT |
AGCCCAAGCGAGACTTACTA |
829–868 | 1.000 | 84.6 |
| trnC-GCA-petN_p5 | trnC-GCA-petN | TTGGATCCTTTTGGCGACAT |
AGAGTCCACTTCTTCCCCAT |
926–965 | 1.000 | 83.8 |
| trnT-GGU-psbD_p1 | trnT-GGU-psbD | GGCGTAAGTCATCGGTTCAA |
GGACCAGCCTACAAAAACGA |
1610–1663 | 1.000 | 85.9 |
| trnT-GGU-psbD_p2 | trnT-GGU-psbD | GGCGTAAGTCATCGGTTCAA |
ACAAAAACGAAACGGTCCCT |
1600–1653 | 1.000 | 84.9 |
| trnT-GGU-psbD_p3 | trnT-GGU-psbD | GGCGTAAGTCATCGGTTCAA |
CAAAAACGAAACGGTCCCTC |
1599–1652 | 1.000 | 83.7 |
| trnT-GGU-psbD_p4 | trnT-GGU-psbD | GGCGTAAGTCATCGGTTCAA |
AGAGCAATAAACCGGACCAG |
1623–1676 | 1.000 | 83.6 |
| trnT-GGU-psbD_p5 | trnT-GGU-psbD | GGCGTAAGTCATCGGTTCAA |
ATAAACCGGACCAGCCTACA |
1617–1670 | 1.000 | 83.4 |
Result downloads
Reference species (17)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Diospyros blancoi | NC_033502.1 | 157745 | View on NCBI ↗ |
| Diospyros cathayensis | NC_039554.1 | 157689 | View on NCBI ↗ |
| Diospyros celebica | NC_046040.1 | 157643 | View on NCBI ↗ |
| Diospyros crassiflora | MZ274087.1 | 157874 | View on NCBI ↗ |
| Diospyros eriantha | NC_081462.1 | 157432 | View on NCBI ↗ |
| Diospyros glaucifolia | NC_030784.1 | 157593 | View on NCBI ↗ |
| Diospyros hainanensis | NC_042160.1 | 157999 | View on NCBI ↗ |
| Diospyros kaki | NC_030789.1 | 157784 | View on NCBI ↗ |
| Diospyros lotus | NC_030786.1 | 157590 | View on NCBI ↗ |
| Diospyros mespiliformis | MZ274088.1 | 157246 | View on NCBI ↗ |
| Diospyros morrisiana | NC_081461.1 | 157737 | View on NCBI ↗ |
| Diospyros nigra | NC_059001.1 | 157186 | View on NCBI ↗ |
| Diospyros oleifera | NC_030787.1 | 157724 | View on NCBI ↗ |
| Diospyros rhombifolia | NC_039556.1 | 157368 | View on NCBI ↗ |
| Diospyros sutchuensis | NC_067511.1 | 157917 | View on NCBI ↗ |
| Diospyros vaccinioides | NC_060861.1 | 157778 | View on NCBI ↗ |
| Diospyros virginiana | NC_039555.1 | 157761 | View on NCBI ↗ |