| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| psbA | LSC | 1062 | 0.0075 | 1.00 | 58.0 | yes | View details |
| trnS-GCU-trnR-UCU | LSC | 1808 | 0.0237 | 0.99 | 80.5 | yes | View details |
| trnR-UCU-atpA | LSC | 309 | 0.0482 | 0.98 | 85.5 | yes | View details |
| rpoB-trnC-GCA | LSC | 1419 | 0.0196 | 1.00 | 78.4 | yes | View details |
| trnD-GUC-trnY-GUA | LSC | 491 | 0.0270 | 0.93 | 72.9 | yes | View details |
| ndhC-trnV-UAC | LSC | 665 | 0.0244 | 0.97 | 72.3 | yes | View details |
| petA-psbJ | LSC | 905 | 0.0216 | 1.00 | 86.2 | yes | View details |
| ycf1 | SSC | 1899 | 0.0044 | 1.00 | 59.4 | no | View details |
| ndhF-rpl32 | SSC | 1014 | 0.0451 | 0.89 | 85.9 | yes | View details |
| ccsA-ndhD | SSC | 319 | 0.0360 | 1.00 | 78.0 | yes | View details |
| ycf1 | SSC | 5508 | 0.0143 | 1.00 | 72.0 | yes | View details |
| trnH-GUG-psbA | LSC | 236 | 0.0637 | 0.94 | 90.2 | yes | View details |
| trnT-UGU-trnL-UAA | LSC | 825 | 0.0197 | 0.98 | 85.2 | yes | View details |
| accD-psaI | LSC | 847 | 0.0194 | 1.00 | 84.5 | yes | View details |
| atpH-atpI | LSC | 951 | 0.0158 | 0.98 | 82.4 | yes | View details |
| atpF-atpH | LSC | 511 | 0.0180 | 1.00 | 82.1 | yes | View details |
| atpB-rbcL | LSC | 822 | 0.0099 | 1.00 | 81.7 | yes | View details |
| ndhE-ndhG | SSC | 222 | 0.0282 | 1.00 | 79.8 | yes | View details |
| rps16-trnQ-UUG | LSC | 1010 | 0.0225 | 0.97 | 78.8 | yes | View details |
| rps8-rpl14 | LSC | 308 | 0.0305 | 0.99 | 78.6 | yes | View details |
| rpl14-rps3 | LSC | 1696 | 0.0125 | 1.00 | 78.4 | 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
44
Genome length
153–159 kb
Candidate markers
263
Primer pairs
100
Genome-wide nucleotide diversity
Candidate markers
11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 263 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 | GATCCACTTGGCTACATCCG |
GCGCTAACCTTGGTATGGAA |
268–366 | 0.932 | 88.0 |
| trnH-GUG-psbA_p2 | trnH-GUG-psbA | CAATCCACTGCCTTGATCCA |
GCGCTAACCTTGGTATGGAA |
282–380 | 0.932 | 87.9 |
| trnH-GUG-psbA_p3 | trnH-GUG-psbA | AATCCACTGCCTTGATCCAC |
GCGCTAACCTTGGTATGGAA |
281–379 | 0.932 | 87.9 |
| trnH-GUG-psbA_p4 | trnH-GUG-psbA | ACAATCCACTGCCTTGATCC |
GCGCTAACCTTGGTATGGAA |
283–381 | 0.932 | 87.9 |
| trnH-GUG-psbA_p5 | trnH-GUG-psbA | GATCCACTTGGCTACATCCG |
CCTCTAGACCTAGCTGCTGT |
218–316 | 0.886 | 85.9 |
| psbA_p1 | psbA | TCAAAAACTCGTCTAAATTCAGACT |
AGAATTCGTGTGCTTGGGAG |
1151–1159 | 0.886 | 42.5 |
| psbA_p2 | psbA | TCAAAAACTCGTCTAAATTCAGACT |
AGAGAATTCGTGTGCTTGGG |
1153–1161 | 0.886 | 42.5 |
| psbA_p3 | psbA | TCAAAAACTCGTCTAAATTCAGACT |
GAGAATTCGTGTGCTTGGGA |
1152–1160 | 0.886 | 42.5 |
| psbA_p4 | psbA | TCAAAAACTCGTCTAAATTCAGACT |
TGGGAGTCCCTGATGATGAA |
1137–1145 | 0.886 | 42.4 |
| psbA_p5 | psbA | TCAAAAACTCGTCTAAATTCAGACT |
TTGGGAGTCCCTGATGATGA |
1138–1146 | 0.886 | 42.4 |
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | CGTTGCTTTCTACCACATCG |
GAGGTTCGAATCCTTCCGTC |
828–1093 | 1.000 | 85.1 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | GCACGTTGCTTTCTACCACA |
GAGGTTCGAATCCTTCCGTC |
831–1096 | 1.000 | 82.9 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | TAAGAATCCACGGACGATCC |
GAGGTTCGAATCCTTCCGTC |
864–1129 | 1.000 | 82.0 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | CGTTGCTTTCTACCACATCG |
TTCGGAGGTTCGAATCCTTC |
832–1097 | 1.000 | 80.4 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | CGTTGCTTTCTACCACATCG |
TAAGGCAACGGGTTTTGGTC |
858–1123 | 0.977 | 79.4 |
| trnS-GCU-trnR-UCU_p1 | trnS-GCU-trnR-UCU | CAATCCGACGCTTTAGTCCA |
AGAACTTGCGTCCAATAGGA |
1882–1986 | 1.000 | 80.4 |
| trnS-GCU-trnR-UCU_p2 | trnS-GCU-trnR-UCU | AATCCGACGCTTTAGTCCAC |
AGAACTTGCGTCCAATAGGA |
1881–1985 | 1.000 | 80.4 |
| trnS-GCU-trnR-UCU_p3 | trnS-GCU-trnR-UCU | CAATCCGACGCTTTAGTCCA |
ACATAGAAGAACTTGCGTCCA |
1889–1993 | 1.000 | 78.5 |
| trnS-GCU-trnR-UCU_p4 | trnS-GCU-trnR-UCU | AATCCGACGCTTTAGTCCAC |
ACATAGAAGAACTTGCGTCCA |
1888–1992 | 1.000 | 78.5 |
| trnS-GCU-trnR-UCU_p5 | trnS-GCU-trnR-UCU | CAATCCGACGCTTTAGTCCA |
AAGAACTTGCGTCCAATAGGA |
1883–1987 | 1.000 | 78.4 |
| trnR-UCU-atpA_p1 | trnR-UCU-atpA | CCAAACCCGAAGCCAAAAAG |
CATTCACCGAGGAAGCAGAA |
450–522 | 0.841 | 83.8 |
| trnR-UCU-atpA_p2 | trnR-UCU-atpA | CCAAACCCGAAGCCAAAAAG |
AAGACATTCACCGAGGAAGC |
454–526 | 0.818 | 82.8 |
| trnR-UCU-atpA_p3 | trnR-UCU-atpA | CCAAACCCGAAGCCAAAAAG |
TTCACCGAGGAAGCAGAATC |
448–520 | 0.841 | 81.5 |
| trnR-UCU-atpA_p4 | trnR-UCU-atpA | CCGAAGCCAAAAAGCAAGAA |
CATTCACCGAGGAAGCAGAA |
444–516 | 0.841 | 80.8 |
| trnR-UCU-atpA_p5 | trnR-UCU-atpA | CCAAACCCGAAGCCAAAAAG |
CCGAGGAAGCAGAATCCATT |
444–516 | 0.795 | 80.0 |
| atpF-atpH_p1 | atpF-atpH | ATTAAACCCGAAACTCCCGG |
GGATTGGTTGTCGCTTTAGC |
617–655 | 1.000 | 86.7 |
| atpF-atpH_p2 | atpF-atpH | GGCCCAAGGAAAGGAAAGAA |
GGATTGGTTGTCGCTTTAGC |
585–623 | 0.932 | 84.8 |
| atpF-atpH_p3 | atpF-atpH | GGCCCAAGGAAAGGAAAGAA |
CGGAGGGAAAAATACGAGGT |
650–688 | 0.932 | 83.7 |
| atpF-atpH_p4 | atpF-atpH | GGCCCAAGGAAAGGAAAGAA |
GCGGAGGGAAAAATACGAGG |
651–689 | 0.909 | 82.7 |
| atpF-atpH_p5 | atpF-atpH | GGCCCAAGGAAAGGAAAGAA |
GGCGGAGGGAAAAATACGAG |
652–690 | 0.909 | 82.7 |
Result downloads
Reference species (44)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Phyllagathis calisaurea | MK994865.1 | 155458 | View on NCBI ↗ |
| Phyllagathis cavaleriei | MK994795.1 | 156406 | View on NCBI ↗ |
| Phyllagathis cavaleriei var. wilsoniana | MK994854.1 | 155868 | View on NCBI ↗ |
| Phyllagathis chongzuoensis | NC_069574.1 | 155850 | View on NCBI ↗ |
| Phyllagathis cymigera | MK994864.1 | 156317 | View on NCBI ↗ |
| Phyllagathis dispar | MK994910.1 | 155978 | View on NCBI ↗ |
| Phyllagathis elattandra | MK994830.1 | 155370 | View on NCBI ↗ |
| Phyllagathis elliptica | NC_068148.1 | 156017 | View on NCBI ↗ |
| Phyllagathis erecta | MK994811.1 | 156360 | View on NCBI ↗ |
| Phyllagathis fengii | MK994818.1 | 156336 | View on NCBI ↗ |
| Phyllagathis gigantifolia | MK994779.1 | 156350 | View on NCBI ↗ |
| Phyllagathis griffithii | NC_068190.1 | 156135 | View on NCBI ↗ |
| Phyllagathis gymnantha | MK994918.1 | 156607 | View on NCBI ↗ |
| Phyllagathis hainanensis | NC_058699.1 | 156123 | View on NCBI ↗ |
| Phyllagathis hispida | MK994783.1 | 156365 | View on NCBI ↗ |
| Phyllagathis hispidissima | MK994857.1 | 156166 | View on NCBI ↗ |
| Phyllagathis lii | MK994924.1 | 156958 | View on NCBI ↗ |
| Phyllagathis longifolia | NC_068150.1 | 155784 | View on NCBI ↗ |
| Phyllagathis longiradiosa | MK994807.1 | 155849 | View on NCBI ↗ |
| Phyllagathis melastomatoides | MK994914.1 | 155822 | View on NCBI ↗ |
| Phyllagathis millelunata | MK994916.1 | 157069 | View on NCBI ↗ |
| Phyllagathis nudipes | MK994787.1 | 156251 | View on NCBI ↗ |
| Phyllagathis oligotricha | MK994799.1 | 156278 | View on NCBI ↗ |
| Phyllagathis osmantha | MK994915.1 | 156987 | View on NCBI ↗ |
| Phyllagathis ovalifolia | MK994814.1 | 155632 | View on NCBI ↗ |
| Phyllagathis phyllioides | NC_068181.1 | 156682 | View on NCBI ↗ |
| Phyllagathis prostrata | MK994919.1 | 155851 | View on NCBI ↗ |
| Phyllagathis rajah | MK994921.1 | 156105 | View on NCBI ↗ |
| Phyllagathis rotundifolia | MK994912.1 | 156274 | View on NCBI ↗ |
| Phyllagathis rufa | MK994890.1 | 157556 | View on NCBI ↗ |
| Phyllagathis scortechinii | MK994911.1 | 156108 | View on NCBI ↗ |
| Phyllagathis sessilifolia | MK994926.1 | 156038 | View on NCBI ↗ |
| Phyllagathis setotheca var. setotuba | MK994840.1 | 156158 | View on NCBI ↗ |
| Phyllagathis stellata | MK994920.1 | 158960 | View on NCBI ↗ |
| Phyllagathis stenophylla | MK994793.1 | 155832 | View on NCBI ↗ |
| Phyllagathis suberalata | MK994927.1 | 156068 | View on NCBI ↗ |
| Phyllagathis subrotunda | NC_068186.1 | 155394 | View on NCBI ↗ |
| Phyllagathis tentaculifera | MK994782.1 | 156440 | View on NCBI ↗ |
| Phyllagathis tetrandra | MK994817.1 | 154818 | View on NCBI ↗ |
| Phyllagathis tuberculata | NC_068188.1 | 156140 | View on NCBI ↗ |
| Phyllagathis velutina | MK994812.1 | 156001 | View on NCBI ↗ |
| Phyllagathis wallacei | MK994781.1 | 156719 | View on NCBI ↗ |
| Phyllagathis wenshanensis | NC_068168.1 | 153453 | View on NCBI ↗ |
| Phyllagathis xinyiensis | MK994844.1 | 155462 | View on NCBI ↗ |