| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnH-GUG-psbA | LSC | 373 | 0.0162 | 0.95 | 60.7 | yes | View details |
| trnK-UUU-rps16 | LSC | 1051 | 0.0137 | 0.99 | 69.4 | yes | View details |
| rps16-trnQ-UUG | LSC | 985 | 0.0134 | 0.97 | 74.0 | yes | View details |
| trnG-UCC-trnR-UCU | LSC | 285 | 0.0266 | 0.98 | 69.7 | yes | View details |
| rpoB-trnC-GCA | LSC | 1146 | 0.0118 | 0.99 | 62.5 | yes | View details |
| trnE-UUC-trnT-GGU | LSC | 667 | 0.0080 | 0.99 | 65.8 | yes | View details |
| trnT-GGU-psbD | LSC | 1261 | 0.0086 | 0.99 | 71.4 | yes | View details |
| psbZ-trnG-GCC | LSC | 673 | 0.0125 | 0.98 | 70.1 | yes | View details |
| ndhF-rpl32 | SSC | 1385 | 0.0170 | 0.99 | 81.8 | yes | View details |
| rpl32-trnL-UAG | SSC | 1504 | 0.0158 | 0.98 | 75.0 | yes | View details |
| psbK-psbI | LSC | 461 | 0.0128 | 1.00 | 73.4 | yes | View details |
| trnC-GCA-petN | LSC | 1028 | 0.0112 | 0.99 | 72.8 | yes | View details |
| trnT-UGU-trnL-UAA | LSC | 1211 | 0.0091 | 0.99 | 71.7 | yes | View details |
| atpH-atpI | LSC | 1266 | 0.0051 | 0.99 | 68.4 | yes | View details |
| petN-psbM | LSC | 1309 | 0.0086 | 0.99 | 65.1 | yes | View details |
| trnL-UAG-ccsA | SSC | 111 | 0.0362 | 1.00 | 64.8 | yes | View details |
| psbE-petL | LSC | 1253 | 0.0071 | 0.98 | 63.5 | 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
41
Genome length
159–163 kb
Candidate markers
265
Primer pairs
90
Genome-wide nucleotide diversity
Candidate markers
10 hotspot labels from the diversity plot in genomic order, plus the top 7 remaining regions by MarkerSeek score (out of 265 candidates).
Primer pairs
Showing the top 30 of 90 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 |
CCTAGCGGCTGTAGAAGTTC |
398–445 | 0.854 | 83.4 |
| trnH-GUG-psbA_p2 | trnH-GUG-psbA | GATCCACTTGGCTACATCCG |
CTAGCGGCTGTAGAAGTTCC |
397–444 | 0.854 | 83.4 |
| trnH-GUG-psbA_p3 | trnH-GUG-psbA | CAATCCACTGCCTTGATCCA |
CCTAGCGGCTGTAGAAGTTC |
412–459 | 0.854 | 83.4 |
| trnH-GUG-psbA_p4 | trnH-GUG-psbA | CAATCCACTGCCTTGATCCA |
CTAGCGGCTGTAGAAGTTCC |
411–458 | 0.854 | 83.4 |
| trnH-GUG-psbA_p5 | trnH-GUG-psbA | AATCCACTGCCTTGATCCAC |
CTAGCGGCTGTAGAAGTTCC |
410–457 | 0.854 | 83.4 |
| trnK-UUU-rps16_p1 | trnK-UUU-rps16 | AGTCGCGGTCTTACAAACTC |
GGAACTTCGCCTTAATCACCA |
1176–1219 | 0.951 | 78.4 |
| trnK-UUU-rps16_p2 | trnK-UUU-rps16 | AGTCGCGGTCTTACAAACTC |
TGGAACTTCGCCTTAATCACC |
1177–1220 | 0.951 | 78.4 |
| trnK-UUU-rps16_p3 | trnK-UUU-rps16 | GTCGCGGTCTTACAAACTCT |
GGAACTTCGCCTTAATCACCA |
1175–1218 | 0.951 | 78.4 |
| trnK-UUU-rps16_p4 | trnK-UUU-rps16 | GTCGCGGTCTTACAAACTCT |
TGGAACTTCGCCTTAATCACC |
1176–1219 | 0.951 | 78.4 |
| trnK-UUU-rps16_p5 | trnK-UUU-rps16 | AAGCCGAGTACTCTACCGTT |
GGAACTTCGCCTTAATCACCA |
1092–1135 | 0.951 | 77.9 |
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | GTATCCTTCAAGTCGCACGT |
GAGGTTCGAATCCTTCCGTC |
804–1073 | 1.000 | 91.3 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | ACGTTGCCTTCTACCACATC |
GAGGTTCGAATCCTTCCGTC |
788–1057 | 1.000 | 90.6 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | GTTGCCTTCTACCACATCGT |
GAGGTTCGAATCCTTCCGTC |
786–1055 | 1.000 | 90.6 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | CACGTTGCCTTCTACCACAT |
GAGGTTCGAATCCTTCCGTC |
789–1058 | 1.000 | 89.9 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | TCGTATCCTTCAAGTCGCAC |
GAGGTTCGAATCCTTCCGTC |
806–1075 | 1.000 | 89.2 |
| psbK-psbI_p1 | psbK-psbI | GTTTGGCAAGCTGCTGTAAG |
GGATTACGTCCCGGATCATT |
365–597 | 1.000 | 84.1 |
| psbK-psbI_p2 | psbK-psbI | CTTTTGTTTGGCAAGCTGCT |
GGATTACGTCCCGGATCATT |
370–602 | 1.000 | 84.0 |
| psbK-psbI_p3 | psbK-psbI | GTTTGGCAAGCTGCTGTAAG |
TCTTCACGTCCAGGATTACG |
377–609 | 1.000 | 83.3 |
| psbK-psbI_p4 | psbK-psbI | CTTTTGTTTGGCAAGCTGCT |
TCTTCACGTCCAGGATTACG |
382–614 | 1.000 | 83.2 |
| psbK-psbI_p5 | psbK-psbI | TGGCAAGCTGCTGTAAGTTT |
GGATTACGTCCCGGATCATT |
362–594 | 1.000 | 82.1 |
| trnG-UCC_p1 | trnG-UCC | TCCTCGGGTTAACGCTCTAA |
ACAGAGATAGAAAGATAAAGTAAGCA |
925–933 | 0.927 | 41.5 |
| trnG-UCC_p2 | trnG-UCC | TCCTCGGGTTAACGCTCTAA |
CAGAGATAGAAAGATAAAGTAAGCACA |
924–932 | 0.902 | 40.4 |
| trnG-UCC_p3 | trnG-UCC | TCCTCGGGTTAACGCTCTAA |
ACAGAGATAGAAAGATAAAGTAAGCAC |
925–933 | 0.902 | 40.4 |
| trnG-UCC_p4 | trnG-UCC | TCCTCGGGTTAACGCTCTAA |
AGAGATAGAAAGATAAAGTAAGCACA |
923–931 | 0.902 | 40.4 |
| trnG-UCC_p5 | trnG-UCC | TTAAGTCCTCGGGTTAACGC |
CAGAGATAGAAAGATAAAGTAAGCACA |
929–937 | 0.878 | 39.3 |
| trnG-UCC-trnR-UCU_p1 | trnG-UCC-trnR-UCU | AGCCTTCCAAGCTAACGATG |
AGAAGACCTCTGTCCTATCCA |
320–378 | 1.000 | 74.2 |
| trnG-UCC-trnR-UCU_p2 | trnG-UCC-trnR-UCU | CCTAGCCTTCCAAGCTAACG |
AGAAGACCTCTGTCCTATCCA |
323–381 | 1.000 | 73.9 |
| trnG-UCC-trnR-UCU_p3 | trnG-UCC-trnR-UCU | AGCCTTCCAAGCTAACGATG |
AGGTTTAGAAGACCTCTGTCCT |
326–384 | 1.000 | 73.4 |
| trnG-UCC-trnR-UCU_p4 | trnG-UCC-trnR-UCU | CCTAGCCTTCCAAGCTAACG |
AGGTTTAGAAGACCTCTGTCCT |
329–387 | 1.000 | 73.2 |
| trnG-UCC-trnR-UCU_p5 | trnG-UCC-trnR-UCU | ACCAAAGTTTCACGTTCGGT |
AGAAGACCTCTGTCCTATCCA |
390–448 | 1.000 | 71.7 |
Result downloads
Reference species (41)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Ficus adhatodifolia | PZ094988.1 | 160560 | View on NCBI ↗ |
| Ficus altissima | NC_053895.1 | 160251 | View on NCBI ↗ |
| Ficus anserina | NC_069046.1 | 160267 | View on NCBI ↗ |
| Ficus auriculata | NC_053837.1 | 162558 | View on NCBI ↗ |
| Ficus beipeiensis | NC_050048.1 | 160595 | View on NCBI ↗ |
| Ficus benjamina | NC_053836.1 | 160268 | View on NCBI ↗ |
| Ficus carica | NC_035237.1 | 160602 | View on NCBI ↗ |
| Ficus concinna | MZ128521.1 | 160331 | View on NCBI ↗ |
| Ficus curtipes | NC_053833.1 | 160772 | View on NCBI ↗ |
| Ficus dinganensis | OK375500.1 | 160018 | View on NCBI ↗ |
| Ficus erecta | PQ526733.1 | 160427 | View on NCBI ↗ |
| Ficus erecta var. sieboldii | PP291717.1 | 160604 | View on NCBI ↗ |
| Ficus eximia | PZ094984.1 | 160640 | View on NCBI ↗ |
| Ficus formosana | NC_059898.1 | 160606 | View on NCBI ↗ |
| Ficus guizhouensis | NC_069047.1 | 160209 | View on NCBI ↗ |
| Ficus heteromorpha | NC_053835.1 | 160333 | View on NCBI ↗ |
| Ficus hirta | NC_051532.1 | 160357 | View on NCBI ↗ |
| Ficus hispida | PQ037185.1 | 160341 | View on NCBI ↗ |
| Ficus howii | NC_069045.1 | 160169 | View on NCBI ↗ |
| Ficus lyrata | NC_053838.1 | 160369 | View on NCBI ↗ |
| Ficus microcarpa | NC_053834.1 | 160735 | View on NCBI ↗ |
| Ficus natalensis | NC_070396.1 | 160561 | View on NCBI ↗ |
| Ficus pandurata | PQ526731.1 | 160390 | View on NCBI ↗ |
| Ficus pandurata var. angustifolia | NC_063593.1 | 160526 | View on NCBI ↗ |
| Ficus periptera | PZ094992.1 | 160405 | View on NCBI ↗ |
| Ficus polynervis | NC_069048.1 | 160356 | View on NCBI ↗ |
| Ficus populifolia | NC_069638.1 | 160610 | View on NCBI ↗ |
| Ficus pubigera | NC_069049.1 | 160299 | View on NCBI ↗ |
| Ficus pumila | NC_058617.1 | 160248 | View on NCBI ↗ |
| Ficus racemosa | NC_028185.1 | 159473 | View on NCBI ↗ |
| Ficus sagittata | PZ094990.1 | 160309 | View on NCBI ↗ |
| Ficus sarmentosa | NC_061976.1 | 160183 | View on NCBI ↗ |
| Ficus sarmentosa var. impressa | ON257114.1 | 160293 | View on NCBI ↗ |
| Ficus sarmentosa var. lacrymans | ON257105.1 | 160385 | View on NCBI ↗ |
| Ficus sarmentosa var. nipponica | PP291719.1 | 160337 | View on NCBI ↗ |
| Ficus sarmentosa var. sarmentosa | ON257110.1 | 160355 | View on NCBI ↗ |
| Ficus sarmentosa var. thunbergii | PP291720.1 | 160276 | View on NCBI ↗ |
| Ficus stenophylla | PQ526736.1 | 160464 | View on NCBI ↗ |
| Ficus subpisocarpa | NC_073014.1 | 160708 | View on NCBI ↗ |
| Ficus tannoensis | PZ094989.1 | 160624 | View on NCBI ↗ |
| Ficus virens | NC_053832.1 | 162798 | View on NCBI ↗ |