| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnS-GCU-trnC-GCA | LSC | 787 | 0.0031 | 1.00 | 55.0 | yes | View details |
| trnY-GUA-rpoB | LSC | 1223 | 0.0030 | 1.00 | 59.6 | yes | View details |
| trnT-UGU-trnL-UAA | LSC | 621 | 0.0042 | 1.00 | 61.4 | yes | View details |
| trnF-GAA-ndhJ | LSC | 657 | 0.0032 | 1.00 | 52.2 | yes | View details |
| ndhC-trnV-UAC | LSC | 714 | 0.0063 | 1.00 | 69.1 | yes | View details |
| accD-psaI | LSC | 889 | 0.0093 | 0.97 | 65.9 | yes | View details |
| ndhD | SSC | 1503 | 0.0013 | 1.00 | 35.7 | yes | View details |
| trnL-UAG-rpl32 | SSC | 825 | 0.0025 | 1.00 | 46.4 | yes | View details |
| rpl32-ndhF | SSC | 1044 | 0.0040 | 0.99 | 61.4 | yes | View details |
| ndhF | SSC | 2226 | 0.0012 | 1.00 | 35.1 | yes | View details |
| trnT-GGU-psbD | LSC | 1314 | 0.0016 | 1.00 | 64.8 | yes | View details |
| rpl22-rps19 | LSC | 80 | 0.0117 | 1.00 | 59.3 | yes | View details |
| ycf4-cemA | LSC | 906 | 0.0027 | 1.00 | 58.7 | yes | View details |
| rbcL-accD | LSC | 546 | 0.0035 | 1.00 | 58.6 | yes | View details |
| atpA-trnR-UCU | LSC | 135 | 0.0086 | 1.00 | 55.7 | yes | View details |
| psaC-ndhD | SSC | 111 | 0.0252 | 1.00 | 55.6 | yes | View details |
| rps16-trnQ-UUG | LSC | 973 | 0.0028 | 1.00 | 55.1 | yes | View details |
| ycf1 | SSC | 5064 | 0.0019 | 1.00 | 53.4 | yes | View details |
| clpP-psbB | LSC | 500 | 0.0026 | 1.00 | 53.0 | yes | View details |
| petD | LSC | 1210 | 0.0017 | 1.00 | 52.4 | yes | View details |
| ycf1 | IRa | 564 | 0.0002 | 1.00 | 26.0 | no | 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
36
Genome length
151–152 kb
Candidate markers
268
Primer pairs
100
Genome-wide nucleotide diversity
Candidate markers
10 hotspot labels from the diversity plot in genomic order, plus the top 11 remaining regions by MarkerSeek score (out of 268 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 |
|---|---|---|---|---|---|---|
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
GAGGTTCGAATCCTTCCGTC |
1040–1071 | 1.000 | 81.2 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | TGCTTTCTACCGCATCGTTT |
GAGGTTCGAATCCTTCCGTC |
1029–1060 | 1.000 | 80.8 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | TTGCTTTCTACCGCATCGTT |
GAGGTTCGAATCCTTCCGTC |
1030–1061 | 1.000 | 80.8 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | CGGATCGTGTCCTTCAAGTC |
GAGGTTCGAATCCTTCCGTC |
1055–1086 | 1.000 | 79.4 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | GGATCGTGTCCTTCAAGTCG |
GAGGTTCGAATCCTTCCGTC |
1054–1085 | 1.000 | 79.4 |
| trnS-GCU-trnC-GCA_p1 | trnS-GCU-trnC-GCA | ACGGAAAGAGAGGGATTCGA |
CCGGATTTGAACTGGGGAAA |
936–946 | 1.000 | 81.5 |
| trnS-GCU-trnC-GCA_p2 | trnS-GCU-trnC-GCA | ACGGAAAGAGAGGGATTCGA |
AAAAGGATTTGCAGTCCCCC |
918–928 | 1.000 | 79.4 |
| trnS-GCU-trnC-GCA_p3 | trnS-GCU-trnC-GCA | CTTTCGTCCACTCAGCCATC |
CCGGATTTGAACTGGGGAAA |
872–882 | 1.000 | 77.9 |
| trnS-GCU-trnC-GCA_p4 | trnS-GCU-trnC-GCA | AACGGAAAGAGAGGGATTCG |
CCGGATTTGAACTGGGGAAA |
937–947 | 1.000 | 77.3 |
| trnS-GCU-trnC-GCA_p5 | trnS-GCU-trnC-GCA | CTTTCGTCCACTCAGCCATC |
AAAAGGATTTGCAGTCCCCC |
854–864 | 1.000 | 75.8 |
| trnY-GUA-rpoB_p1 | trnY-GUA-rpoB | AGATTGGCAAATTGTTGGGC |
AGTTCTTCTGTCAAACCCTGA |
1376–1412 | 1.000 | 64.2 |
| trnY-GUA-rpoB_p2 | trnY-GUA-rpoB | CAACGAATTTACAGTCCGCC |
AGTTCTTCTGTCAAACCCTGA |
1323–1359 | 1.000 | 64.1 |
| trnY-GUA-rpoB_p3 | trnY-GUA-rpoB | AACGAATTTACAGTCCGCCC |
AGTTCTTCTGTCAAACCCTGA |
1322–1358 | 1.000 | 63.9 |
| trnY-GUA-rpoB_p4 | trnY-GUA-rpoB | GATTGGCAAATTGTTGGGCC |
AGTTCTTCTGTCAAACCCTGA |
1375–1411 | 1.000 | 63.7 |
| trnY-GUA-rpoB_p5 | trnY-GUA-rpoB | AGATTGGCAAATTGTTGGGC |
TCAAACCCTGATCAATGAACCT |
1366–1402 | 1.000 | 62.9 |
| atpA-trnR-UCU_p1 | atpA-trnR-UCU | TTTACCGAGGAAGCAGAAGC |
GCAATGAAAAGCGTCCATTGT |
280–306 | 1.000 | 75.0 |
| atpA-trnR-UCU_p2 | atpA-trnR-UCU | TACTTCAGGAACAAGCAGCC |
GCAATGAAAAGCGTCCATTGT |
219–245 | 1.000 | 74.9 |
| atpA-trnR-UCU_p3 | atpA-trnR-UCU | TTTACCGAGGAAGCAGAAGC |
GCAATGAAAAGCGTCCATTG |
280–306 | 1.000 | 74.2 |
| atpA-trnR-UCU_p4 | atpA-trnR-UCU | CAGGAACAGAGGGAACGTTT |
GCAATGAAAAGCGTCCATTGT |
241–267 | 1.000 | 74.1 |
| atpA-trnR-UCU_p5 | atpA-trnR-UCU | TACTTCAGGAACAAGCAGCC |
GCAATGAAAAGCGTCCATTG |
219–245 | 1.000 | 74.1 |
| trnT-GGU-psbD_p1 | trnT-GGU-psbD | GTAAGCCCTCGGTTCAGATC |
GAAACGGTCCCTACGTAACC |
1148–1463 | 0.806 | 75.7 |
| trnT-GGU-psbD_p2 | trnT-GGU-psbD | GTGACCCGTTCAGGAATTCA |
GAAACGGTCCCTACGTAACC |
1222–1537 | 0.778 | 74.9 |
| trnT-GGU-psbD_p3 | trnT-GGU-psbD | CAGTGACCCGTTCAGGAATT |
GAAACGGTCCCTACGTAACC |
1224–1539 | 0.778 | 74.8 |
| trnT-GGU-psbD_p4 | trnT-GGU-psbD | GTGACCCGTTCAGGAATTCA |
GGACCAGCCTACAAAAACGA |
1240–1555 | 0.778 | 74.0 |
| trnT-GGU-psbD_p5 | trnT-GGU-psbD | TACAGTGACCCGTTCAGGAA |
GAAACGGTCCCTACGTAACC |
1226–1541 | 0.778 | 74.0 |
| trnT-UGU-trnL-UAA_p1 | trnT-UGU-trnL-UAA | GCGATGCTCTAACCTCTGAG |
CCGTAGCGTCTACCGATTTC |
502–736 | 1.000 | 83.8 |
| trnT-UGU-trnL-UAA_p2 | trnT-UGU-trnL-UAA | GGAATCGAACCGATGACCAT |
CCGTAGCGTCTACCGATTTC |
534–768 | 1.000 | 82.8 |
| trnT-UGU-trnL-UAA_p3 | trnT-UGU-trnL-UAA | GCGATGCTCTAACCTCTGAG |
CGTCTACCGATTTCGCCATA |
496–730 | 1.000 | 82.5 |
| trnT-UGU-trnL-UAA_p4 | trnT-UGU-trnL-UAA | GGAATCGAACCGATGACCAT |
CGTCTACCGATTTCGCCATA |
528–762 | 1.000 | 81.5 |
| trnT-UGU-trnL-UAA_p5 | trnT-UGU-trnL-UAA | GCGATGCTCTAACCTCTGAG |
CGTAGCGTCTACCGATTTCG |
501–735 | 1.000 | 80.9 |
Result downloads
Reference species (36)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Linochilus alveolatus | NC_034847.1 | 152265 | View on NCBI ↗ |
| Linochilus antioquensis | NC_034876.1 | 152027 | View on NCBI ↗ |
| Linochilus apiculatus | NC_034902.1 | 152277 | View on NCBI ↗ |
| Linochilus camargoanus | NC_034897.1 | 152249 | View on NCBI ↗ |
| Linochilus cayambensis | NC_034886.1 | 151206 | View on NCBI ↗ |
| Linochilus cinerascens | NC_034850.1 | 152169 | View on NCBI ↗ |
| Linochilus colombianus | NC_034861.1 | 152314 | View on NCBI ↗ |
| Linochilus coriaceus | NC_034899.1 | 152290 | View on NCBI ↗ |
| Linochilus costaricensis | NC_034879.1 | 152048 | View on NCBI ↗ |
| Linochilus eriophorus | NC_034874.1 | 151802 | View on NCBI ↗ |
| Linochilus floribundus | NC_034857.1 | 151768 | View on NCBI ↗ |
| Linochilus frontinensis | NC_034893.1 | 152365 | View on NCBI ↗ |
| Linochilus glutinosus | NC_034875.1 | 152229 | View on NCBI ↗ |
| Linochilus heterophyllus | NC_034896.1 | 152223 | View on NCBI ↗ |
| Linochilus huertasii | NC_034812.1 | 151684 | View on NCBI ↗ |
| Linochilus inesianus | NC_034895.1 | 152328 | View on NCBI ↗ |
| Linochilus jaramilloi | NC_034894.1 | 151879 | View on NCBI ↗ |
| Linochilus jenesanus | NC_034829.1 | 150924 | View on NCBI ↗ |
| Linochilus juajibioyi | NC_034822.1 | 152282 | View on NCBI ↗ |
| Linochilus lacunosus | NC_034878.1 | 152247 | View on NCBI ↗ |
| Linochilus mutiscuanus | NC_034827.1 | 152282 | View on NCBI ↗ |
| Linochilus oblongifolius | NC_034818.1 | 152282 | View on NCBI ↗ |
| Linochilus obtusus | NC_034814.1 | 152179 | View on NCBI ↗ |
| Linochilus ochraceus | NC_034903.1 | 151555 | View on NCBI ↗ |
| Linochilus phylicoides | NC_034873.1 | 152172 | View on NCBI ↗ |
| Linochilus revolutus | NC_034863.1 | 151823 | View on NCBI ↗ |
| Linochilus rhododendroides | NC_034820.1 | 152289 | View on NCBI ↗ |
| Linochilus rhomboidalis | NC_034859.1 | 152186 | View on NCBI ↗ |
| Linochilus romeroi | NC_034885.1 | 152275 | View on NCBI ↗ |
| Linochilus rosmarinifolius | NC_034900.1 | 152216 | View on NCBI ↗ |
| Linochilus rupestris | NC_034865.1 | 152027 | View on NCBI ↗ |
| Linochilus schultzii | NC_034892.1 | 152252 | View on NCBI ↗ |
| Linochilus tachirensis | NC_034825.1 | 152197 | View on NCBI ↗ |
| Linochilus tenuifolius | NC_034860.1 | 151911 | View on NCBI ↗ |
| Linochilus venezuelensis | NC_034887.1 | 152173 | View on NCBI ↗ |
| Linochilus violaceus | NC_034817.1 | 151387 | View on NCBI ↗ |