| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnH-GUG-psbA | LSC | 307 | 0.0492 | 0.87 | 77.3 | yes | View details |
| rps16-trnQ-UUG | LSC | 1307 | 0.0199 | 0.99 | 71.7 | yes | View details |
| trnS-GCU-trnG-UCC | LSC | 582 | 0.0277 | 0.98 | 74.3 | yes | View details |
| rps2-rpoC2 | LSC | 4894 | 0.0129 | 0.99 | 59.6 | yes | View details |
| trnE-UUC-trnT-GGU | LSC | 1023 | 0.0262 | 0.98 | 83.0 | yes | View details |
| ndhC-trnV-UAC | LSC | 1499 | 0.0258 | 0.99 | 86.3 | yes | View details |
| atpB-rbcL | LSC | 763 | 0.0196 | 0.96 | 70.2 | yes | View details |
| accD | LSC | 1788 | 0.0164 | 0.99 | 65.8 | yes | View details |
| clpP | LSC | 2260 | 0.0149 | 0.99 | 65.6 | yes | View details |
| ycf1 | IRb | 6030 | 0.0083 | 0.98 | 54.7 | no | View details |
| ndhF | SSC | 2241 | 0.0213 | 1.00 | 66.0 | yes | View details |
| ycf1 | IRa | 6030 | 0.0088 | 0.98 | 55.0 | yes | View details |
| trnT-UGU-trnL-UAA | LSC | 817 | 0.0117 | 1.00 | 79.2 | yes | View details |
| atpH-atpI | LSC | 1118 | 0.0102 | 1.00 | 73.6 | yes | View details |
| trnC-GCA-petN | LSC | 907 | 0.0106 | 0.99 | 73.5 | yes | View details |
| psaA-ycf3 | LSC | 788 | 0.0146 | 1.00 | 72.2 | yes | View details |
| rpl16 | LSC | 1569 | 0.0137 | 1.00 | 70.8 | yes | View details |
| trnQ-UUG-psbK | LSC | 487 | 0.0187 | 0.97 | 70.7 | yes | View details |
| rpl20-rps12 | LSC | 890 | 0.0173 | 0.99 | 70.6 | yes | View details |
| rbcL-accD | LSC | 824 | 0.0208 | 1.00 | 70.2 | yes | View details |
| trnK-UUU-rps16 | LSC | 799 | 0.0195 | 0.97 | 69.9 | yes | View details |
| petN-psbM | LSC | 806 | 0.0119 | 0.97 | 69.9 | 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
27
Genome length
175–179 kb
Candidate markers
291
Primer pairs
105
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 291 candidates).
Primer pairs
Showing the top 30 of 105 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 |
TTCCCTCTAGACCTAGCTGC |
343–396 | 1.000 | 90.4 |
| trnH-GUG-psbA_p2 | trnH-GUG-psbA | CAATCCACTGCCTTGATCCA |
TTCCCTCTAGACCTAGCTGC |
357–410 | 1.000 | 90.3 |
| trnH-GUG-psbA_p3 | trnH-GUG-psbA | AATCCACTGCCTTGATCCAC |
TTCCCTCTAGACCTAGCTGC |
356–409 | 1.000 | 90.3 |
| trnH-GUG-psbA_p4 | trnH-GUG-psbA | ACAATCCACTGCCTTGATCC |
TTCCCTCTAGACCTAGCTGC |
358–411 | 1.000 | 90.3 |
| trnH-GUG-psbA_p5 | trnH-GUG-psbA | CGCATGGTGGATTCACAATC |
TTCCCTCTAGACCTAGCTGC |
372–425 | 1.000 | 87.6 |
| trnK-UUU-rps16_p1 | trnK-UUU-rps16 | GCTCGTTGCTTTGTCTTTCC |
GCCGTACGAGGAGAAAACTT |
1335–1508 | 1.000 | 90.9 |
| trnK-UUU-rps16_p2 | trnK-UUU-rps16 | TCAGGATCAGTCGTGGTCTT |
GCCGTACGAGGAGAAAACTT |
1144–1315 | 1.000 | 90.8 |
| trnK-UUU-rps16_p3 | trnK-UUU-rps16 | CCCTTTCAGGATCAGTCGTG |
GCCGTACGAGGAGAAAACTT |
1149–1269 | 0.963 | 89.2 |
| trnK-UUU-rps16_p4 | trnK-UUU-rps16 | CCTTTCAGGATCAGTCGTGG |
GCCGTACGAGGAGAAAACTT |
1148–1268 | 0.963 | 89.2 |
| trnK-UUU-rps16_p5 | trnK-UUU-rps16 | TCCCTTTCAGGATCAGTCGT |
GCCGTACGAGGAGAAAACTT |
1150–1270 | 0.963 | 88.8 |
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | TTCTACTCGAGCTCCATCGT |
AGCAGCTTGCCAAACAAAAG |
1735–2341 | 1.000 | 91.2 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | TTCTACTCGAGCTCCATCGT |
CTTACAGCAGCTTGCCAAAC |
1740–2346 | 1.000 | 91.2 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | AACTTGCTCGAATGGGATCC |
AGCAGCTTGCCAAACAAAAG |
1851–2457 | 0.963 | 89.7 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | AACTTGCTCGAATGGGATCC |
CTTACAGCAGCTTGCCAAAC |
1856–2462 | 0.963 | 89.7 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | GATTCCCGCGTGATACACTT |
AGCAGCTTGCCAAACAAAAG |
1921–2527 | 0.963 | 89.6 |
| trnQ-UUG-psbK_p1 | trnQ-UUG-psbK | GACCAAAACCCGTTGCCTTA |
AAAAAGCGTAGGCCTCGG |
621–695 | 1.000 | 68.2 |
| trnQ-UUG-psbK_p2 | trnQ-UUG-psbK | AAAACCCGTTGCCTTACCAC |
AAAAAGCGTAGGCCTCGG |
617–691 | 1.000 | 65.9 |
| trnQ-UUG-psbK_p3 | trnQ-UUG-psbK | ACCAAAACCCGTTGCCTTAC |
AAAAAGCGTAGGCCTCGG |
620–694 | 1.000 | 65.9 |
| trnQ-UUG-psbK_p4 | trnQ-UUG-psbK | CAAAACCCGTTGCCTTACCA |
AAAAAGCGTAGGCCTCGG |
618–692 | 1.000 | 65.9 |
| trnQ-UUG-psbK_p5 | trnQ-UUG-psbK | AAACCCGTTGCCTTACCAC |
AAAAAGCGTAGGCCTCGG |
616–690 | 1.000 | 63.4 |
| trnS-GCU-trnG-UCC_p1 | trnS-GCU-trnG-UCC | ATTAGCAATCCGCCGCTTTA |
ACGAATCACACTTTTACCACT |
623–1159 | 1.000 | 63.4 |
| trnS-GCU-trnG-UCC_p2 | trnS-GCU-trnG-UCC | ATTAGCAATCCGCCGCTTTA |
AACGAATCACACTTTTACCACT |
624–1160 | 1.000 | 61.5 |
| trnS-GCU-trnG-UCC_p3 | trnS-GCU-trnG-UCC | GCTTTAGTCCACTCAGCCAT |
ACGAATCACACTTTTACCACT |
609–1145 | 1.000 | 60.4 |
| trnS-GCU-trnG-UCC_p4 | trnS-GCU-trnG-UCC | ATTAGCAATCCGCCGCTTTA |
TACCACTAAACTATACCCGC |
609–1145 | 1.000 | 59.6 |
| trnS-GCU-trnG-UCC_p5 | trnS-GCU-trnG-UCC | AGTCCACTCAGCCATCTCTC |
ACGAATCACACTTTTACCACT |
604–1140 | 1.000 | 59.6 |
| atpH-atpI_p1 | atpH-atpI | ATAACGGAAGCGGCAGAAAT |
CGCGGCTTATATCGGTGAAT |
1095–1264 | 1.000 | 87.0 |
| atpH-atpI_p2 | atpH-atpI | GCGATACCCTCTACAGCTTG |
CGCGGCTTATATCGGTGAAT |
1182–1351 | 1.000 | 85.9 |
| atpH-atpI_p3 | atpH-atpI | AATAACGGAAGCGGCAGAAA |
CGCGGCTTATATCGGTGAAT |
1096–1265 | 1.000 | 85.8 |
| atpH-atpI_p4 | atpH-atpI | ATAACGGAAGCGGCAGAAAT |
TTTTTGCAACTTTAGCCGCG |
1111–1280 | 1.000 | 85.1 |
| atpH-atpI_p5 | atpH-atpI | TACCCTCTACAGCTTGACCC |
CGCGGCTTATATCGGTGAAT |
1178–1347 | 0.963 | 84.3 |
Result downloads
Reference species (27)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Hoya angustifolia | NC_069566.1 | 176018 | View on NCBI ↗ |
| Hoya ariadna | NC_069568.1 | 179069 | View on NCBI ↗ |
| Hoya caudata | NC_069569.1 | 176907 | View on NCBI ↗ |
| Hoya commutata | NC_067958.1 | 176458 | View on NCBI ↗ |
| Hoya dimorpha | NC_067959.1 | 177711 | View on NCBI ↗ |
| Hoya exilis | MW719054.1 | 178616 | View on NCBI ↗ |
| Hoya griffithii | NC_069565.1 | 176996 | View on NCBI ↗ |
| Hoya ignorata | MW719061.1 | 175892 | View on NCBI ↗ |
| Hoya kerrii | NC_069570.1 | 176967 | View on NCBI ↗ |
| Hoya lacunosa | NC_069564.1 | 175404 | View on NCBI ↗ |
| Hoya lanceolata | NC_067960.1 | 176739 | View on NCBI ↗ |
| Hoya lithophytica | MW719058.1 | 176580 | View on NCBI ↗ |
| Hoya lockii | NC_085235.1 | 177063 | View on NCBI ↗ |
| Hoya longifolia | NC_069560.1 | 177058 | View on NCBI ↗ |
| Hoya lyi | MW719055.1 | 176567 | View on NCBI ↗ |
| Hoya megalaster | MW719063.1 | 178169 | View on NCBI ↗ |
| Hoya meliflua | NC_069571.1 | 177130 | View on NCBI ↗ |
| Hoya monetteae | MW719053.1 | 176921 | View on NCBI ↗ |
| Hoya omlorii | MW719060.1 | 178525 | View on NCBI ↗ |
| Hoya ovalifolia | NC_069563.1 | 176748 | View on NCBI ↗ |
| Hoya pandurata | NC_069562.1 | 176320 | View on NCBI ↗ |
| Hoya pubicalyx | NC_069561.1 | 176709 | View on NCBI ↗ |
| Hoya radicalis | NC_067961.1 | 177347 | View on NCBI ↗ |
| Hoya rigida | NC_067962.1 | 176474 | View on NCBI ↗ |
| Hoya silvatica | NC_067963.1 | 175950 | View on NCBI ↗ |
| Hoya thomsonii | NC_067612.1 | 176631 | View on NCBI ↗ |
| Hoya verticillata | NC_085236.1 | 176429 | View on NCBI ↗ |