| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| rps16-trnQ-UUG | LSC | 992 | 0.0071 | 0.96 | 59.9 | yes | View details |
| trnS-GCU-trnG-UCC | LSC | 1284 | 0.0075 | 1.00 | 57.2 | yes | View details |
| trnR-UCU-atpA | LSC | 446 | 0.0087 | 0.98 | 58.4 | yes | View details |
| ndhC-trnM-CAU | LSC | 1497 | 0.0070 | 1.00 | 67.9 | yes | View details |
| ycf1 | IRb | 1218 | 0.0011 | 1.00 | 31.5 | no | View details |
| ndhF | SSC | 2247 | 0.0024 | 1.00 | 39.6 | yes | View details |
| ndhF-rpl32 | SSC | 1145 | 0.0089 | 0.98 | 67.1 | yes | View details |
| rpl32-trnL-UAG | SSC | 1197 | 0.0089 | 0.99 | 68.5 | yes | View details |
| ccsA-ndhD | SSC | 269 | 0.0243 | 1.00 | 56.9 | yes | View details |
| ycf1 | SSC | 5709 | 0.0040 | 1.00 | 49.3 | yes | View details |
| psaA-ycf3 | LSC | 696 | 0.0056 | 1.00 | 68.2 | yes | View details |
| rps19 | LSC | 223 | 0.0185 | 1.00 | 65.1 | yes | View details |
| ycf1-ndhF | SSC | 66 | 0.0863 | 1.00 | 63.6 | yes | View details |
| atpH-atpI | LSC | 1241 | 0.0033 | 0.99 | 62.3 | yes | View details |
| rps2-rpoC2 | LSC | 229 | 0.0113 | 0.99 | 60.8 | yes | View details |
| ycf3 | LSC | 2079 | 0.0017 | 1.00 | 60.5 | yes | View details |
| trnT-GGU-psbD | LSC | 1372 | 0.0053 | 1.00 | 60.0 | yes | View details |
| rps4-trnT-UGU | LSC | 484 | 0.0065 | 1.00 | 59.2 | yes | View details |
| rps15-ycf1 | SSC | 375 | 0.0102 | 0.99 | 58.6 | yes | View details |
| rpoB-trnC-GCA | LSC | 1062 | 0.0044 | 1.00 | 58.5 | 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
44
Genome length
161–161 kb
Candidate markers
272
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 272 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 |
|---|---|---|---|---|---|---|
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | AACGGATCGTGTCCTTCAAG |
GTCGAATAGAAATGGGGCGT |
292–1143 | 1.000 | 87.0 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | AACGGATCGTGTCCTTCAAG |
GAGGTTCGAATCCTTCCGTC |
293–1083 | 1.000 | 87.0 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
GTCGAATAGAAATGGGGCGT |
275–1126 | 1.000 | 86.6 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
GAGGTTCGAATCCTTCCGTC |
276–1066 | 1.000 | 86.6 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | CAACGGATCGTGTCCTTCAA |
GTCGAATAGAAATGGGGCGT |
293–1144 | 1.000 | 86.0 |
| trnS-GCU-trnG-UCC_p1 | trnS-GCU-trnG-UCC | CAATCCGACGCTTTAGTCCA |
ACGAATCACACTTTTACCACT |
264–1413 | 1.000 | 59.9 |
| trnS-GCU-trnG-UCC_p2 | trnS-GCU-trnG-UCC | AATCCGACGCTTTAGTCCAC |
ACGAATCACACTTTTACCACT |
263–1412 | 1.000 | 59.9 |
| trnS-GCU-trnG-UCC_p3 | trnS-GCU-trnG-UCC | CAATCCGACGCTTTAGTCCA |
AGAACGAATCACACTTTTACCAC |
266–1416 | 1.000 | 58.7 |
| trnS-GCU-trnG-UCC_p4 | trnS-GCU-trnG-UCC | CAATCCGACGCTTTAGTCCA |
GAACGAATCACACTTTTACCACT |
266–1415 | 1.000 | 58.7 |
| trnS-GCU-trnG-UCC_p5 | trnS-GCU-trnG-UCC | AATCCGACGCTTTAGTCCAC |
GAACGAATCACACTTTTACCACT |
265–1414 | 1.000 | 58.7 |
| trnR-UCU-atpA_p1 | trnR-UCU-atpA | GGTTCAAATCCTATTGGACGC |
GAGGAAGCAGAAGCCCTTTT |
350–2704 | 1.000 | 72.8 |
| trnR-UCU-atpA_p2 | trnR-UCU-atpA | GGTTCAAATCCTATTGGACGC |
TTTACCGAGGAAGCAGAAGC |
356–2710 | 1.000 | 72.7 |
| trnR-UCU-atpA_p3 | trnR-UCU-atpA | GGTTCAAATCCTATTGGACGC |
AGGAAGCAGAAGCCCTTTTG |
349–2703 | 1.000 | 70.5 |
| trnR-UCU-atpA_p4 | trnR-UCU-atpA | GGTTCAAATCCTATTGGACGC |
GGAAGCAGAAGCCCTTTTGA |
348–2702 | 1.000 | 70.5 |
| trnR-UCU-atpA_p5 | trnR-UCU-atpA | TGGATAGGACAGAGGTCTTCT |
GAGGAAGCAGAAGCCCTTTT |
385–2704 | 1.000 | 69.8 |
| atpH-atpI_p1 | atpH-atpI | AATAGAAGCAAGCCCGACAG |
GCGAATCCATGGAAGGTCAT |
1246–1368 | 1.000 | 85.8 |
| atpH-atpI_p2 | atpH-atpI | ATAACGGAAGCGGCAGAAAT |
GCGAATCCATGGAAGGTCAT |
1212–1334 | 1.000 | 85.8 |
| atpH-atpI_p3 | atpH-atpI | AATAGAAGCAAGCCCGACAG |
TTTTTGCAACCTTAGCTGCG |
1276–1398 | 1.000 | 84.9 |
| atpH-atpI_p4 | atpH-atpI | ATAACGGAAGCGGCAGAAAT |
TTTTTGCAACCTTAGCTGCG |
1242–1364 | 1.000 | 84.9 |
| atpH-atpI_p5 | atpH-atpI | AGCCAATCCAGCAGCAATAA |
GCGAATCCATGGAAGGTCAT |
1228–1350 | 1.000 | 84.8 |
| rps2-rpoC2_p1 | rps2-rpoC2 | GTGCCATTCGAGGATTCCAT |
TCGAGTGGGAAATGAAAGACA |
437–451 | 1.000 | 71.9 |
| rps2-rpoC2_p2 | rps2-rpoC2 | AACTCCTGCTCCCATCATCT |
TCGAGTGGGAAATGAAAGACA |
394–408 | 1.000 | 71.9 |
| rps2-rpoC2_p3 | rps2-rpoC2 | TGCTCCCATCATCTCTTCCA |
TCGAGTGGGAAATGAAAGACA |
388–402 | 1.000 | 71.9 |
| rps2-rpoC2_p4 | rps2-rpoC2 | AAGGTGCCATTCGAGGATTC |
TCGAGTGGGAAATGAAAGACA |
440–454 | 1.000 | 71.7 |
| rps2-rpoC2_p5 | rps2-rpoC2 | TCCTGCTCCCATCATCTCTT |
TCGAGTGGGAAATGAAAGACA |
391–405 | 1.000 | 71.3 |
| rpoB-trnC-GCA_p1 | rpoB-trnC-GCA | TCCTCAGTTCTACCCCCAAG |
CCGGATTTGAACTGGGGAAA |
1144–1160 | 1.000 | 82.5 |
| rpoB-trnC-GCA_p2 | rpoB-trnC-GCA | TCCTCAGTTCTACCCCCAAG |
AAAAGGATTTGCAGTCCCCC |
1126–1142 | 1.000 | 80.4 |
| rpoB-trnC-GCA_p3 | rpoB-trnC-GCA | TCAGTTCTACCCCCAAGCAT |
CCGGATTTGAACTGGGGAAA |
1141–1157 | 1.000 | 80.3 |
| rpoB-trnC-GCA_p4 | rpoB-trnC-GCA | TTCCTCAGTTCTACCCCCAA |
CCGGATTTGAACTGGGGAAA |
1145–1161 | 1.000 | 79.5 |
| rpoB-trnC-GCA_p5 | rpoB-trnC-GCA | TTTCCTCAGTTCTACCCCCA |
CCGGATTTGAACTGGGGAAA |
1146–1162 | 1.000 | 79.5 |
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 |
|---|---|---|---|
| Spyridium bifidum subsp. wanillae | OK624205.1 | 161141 | View on NCBI ↗ |
| Spyridium burragorang | NC_064102.1 | 161057 | View on NCBI ↗ |
| Spyridium cinereum | NC_064074.1 | 161190 | View on NCBI ↗ |
| Spyridium coactilifolium | NC_064075.1 | 161048 | View on NCBI ↗ |
| Spyridium coalitum | NC_064076.1 | 161332 | View on NCBI ↗ |
| Spyridium cordatum | NC_064013.1 | 161321 | View on NCBI ↗ |
| Spyridium daltonii | NC_064077.1 | 161174 | View on NCBI ↗ |
| Spyridium daphnoides | NC_064078.1 | 160884 | View on NCBI ↗ |
| Spyridium eriocephalum var. eriocephalum | NC_064014.1 | 161219 | View on NCBI ↗ |
| Spyridium eriocephalum var. glabrisepalum | OK624227.1 | 161140 | View on NCBI ↗ |
| Spyridium fontis-woodii | NC_064079.1 | 161117 | View on NCBI ↗ |
| Spyridium furculentum | NC_064080.1 | 161167 | View on NCBI ↗ |
| Spyridium gunnii | NC_064081.1 | 161236 | View on NCBI ↗ |
| Spyridium halmaturinum | NC_064015.1 | 161175 | View on NCBI ↗ |
| Spyridium lawrencei | NC_064082.1 | 161329 | View on NCBI ↗ |
| Spyridium leucopogon | NC_064083.1 | 161118 | View on NCBI ↗ |
| Spyridium majoranifolium | NC_064084.1 | 161247 | View on NCBI ↗ |
| Spyridium microcephalum | NC_064085.1 | 161255 | View on NCBI ↗ |
| Spyridium minutum | NC_064086.1 | 161280 | View on NCBI ↗ |
| Spyridium montanum | NC_064087.1 | 161138 | View on NCBI ↗ |
| Spyridium mucronatum subsp. mucronatum | OK624256.1 | 161311 | View on NCBI ↗ |
| Spyridium mucronatum subsp. multiflorum | OK624258.1 | 161301 | View on NCBI ↗ |
| Spyridium mucronatum subsp. recurvum | OK624259.1 | 161241 | View on NCBI ↗ |
| Spyridium nitidum | NC_064088.1 | 160972 | View on NCBI ↗ |
| Spyridium obcordatum | NC_064089.1 | 161037 | View on NCBI ↗ |
| Spyridium obovatum var. velutinum | OK624270.1 | 161304 | View on NCBI ↗ |
| Spyridium oligocephalum | NC_064090.1 | 161326 | View on NCBI ↗ |
| Spyridium parvifolium | NC_064016.1 | 161202 | View on NCBI ↗ |
| Spyridium parvifolium var. parvifolium | MH234313.1 | 161012 | View on NCBI ↗ |
| Spyridium phylicoides | NC_064091.1 | 161210 | View on NCBI ↗ |
| Spyridium polycephalum | NC_064092.1 | 161411 | View on NCBI ↗ |
| Spyridium scabridum | NC_064093.1 | 161338 | View on NCBI ↗ |
| Spyridium scortechinii | NC_064094.1 | 160870 | View on NCBI ↗ |
| Spyridium spadiceum | NC_064095.1 | 160918 | View on NCBI ↗ |
| Spyridium stenophyllum subsp. renovatum | OK624312.1 | 161110 | View on NCBI ↗ |
| Spyridium stenophyllum subsp. stenophyllum | OK624319.1 | 161090 | View on NCBI ↗ |
| Spyridium subochreatum | NC_064096.1 | 161124 | View on NCBI ↗ |
| Spyridium thymifolium | NC_064097.1 | 161126 | View on NCBI ↗ |
| Spyridium tricolor | NC_064098.1 | 161181 | View on NCBI ↗ |
| Spyridium ulicinum | NC_064099.1 | 161292 | View on NCBI ↗ |
| Spyridium vexilliferum var. latifolium | OK624336.1 | 161164 | View on NCBI ↗ |
| Spyridium vexilliferum var. vexilliferum | OK624338.1 | 161017 | View on NCBI ↗ |
| Spyridium villosum | NC_064100.1 | 161217 | View on NCBI ↗ |
| Spyridium waterhousei | NC_064101.1 | 161360 | View on NCBI ↗ |