| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| petN-psbM | LSC | 518 | 0.0043 | 1.00 | 48.1 | yes | View details |
| psbC-trnS-UGA | LSC | 248 | 0.0087 | 0.95 | 49.7 | yes | View details |
| ndhC-trnV-UAC | LSC | 938 | 0.0037 | 0.99 | 63.5 | yes | View details |
| ycf4-cemA | LSC | 838 | 0.0036 | 1.00 | 56.7 | yes | View details |
| petA-psbJ | LSC | 821 | 0.0065 | 1.00 | 58.4 | yes | View details |
| clpP | LSC | 1982 | 0.0021 | 0.99 | 47.2 | yes | View details |
| ndhI-ndhG | SSC | 386 | 0.0103 | 0.98 | 56.8 | yes | View details |
| psaC | SSC | 246 | 0.0000 | 1.00 | 20.9 | yes | View details |
| ndhD-ccsA | SSC | 268 | 0.0113 | 1.00 | 64.9 | yes | View details |
| ccsA | SSC | 969 | 0.0009 | 1.00 | 42.8 | yes | View details |
| rpl32-ndhF | SSC | 882 | 0.0015 | 0.99 | 63.7 | yes | View details |
| trnK-UUU-rps16 | LSC | 850 | 0.0017 | 1.00 | 61.1 | yes | View details |
| atpI-atpH | LSC | 1157 | 0.0014 | 1.00 | 57.8 | yes | View details |
| trnT-GGU-psbD | LSC | 1188 | 0.0015 | 0.99 | 57.7 | yes | View details |
| rps16-trnQ-UUG | LSC | 978 | 0.0029 | 0.98 | 56.8 | yes | View details |
| trnL-UAG-rpl32 | SSC | 786 | 0.0026 | 0.99 | 56.4 | yes | View details |
| rsp19-trnH-GUG | IRa | 2 | 0.0000 | 1.00 | 56.2 | no | View details |
| psaA-ycf3 | LSC | 742 | 0.0030 | 0.99 | 56.1 | yes | View details |
| rpl16-rps3 | LSC | 1193 | 0.0018 | 1.00 | 55.5 | 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
31
Genome length
151–151 kb
Candidate markers
272
Primer pairs
90
Genome-wide nucleotide diversity
Candidate markers
10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 272 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 |
|---|---|---|---|---|---|---|
| trnK-UUU-rps16_p1 | trnK-UUU-rps16 | AAAGCCGAGTACTCTACCGT |
TTCCTTGAAAAAGGCGCTCA |
982–992 | 1.000 | 79.1 |
| trnK-UUU-rps16_p2 | trnK-UUU-rps16 | AAGCCGAGTACTCTACCGTT |
TTCCTTGAAAAAGGCGCTCA |
981–991 | 1.000 | 79.1 |
| trnK-UUU-rps16_p3 | trnK-UUU-rps16 | TCAGTCGTGGTCTTCCAAAC |
TTCCTTGAAAAAGGCGCTCA |
1067–1077 | 1.000 | 78.4 |
| trnK-UUU-rps16_p4 | trnK-UUU-rps16 | CCGATGGTATGGACGAATCC |
TTCCTTGAAAAAGGCGCTCA |
1044–1053 | 0.968 | 78.2 |
| trnK-UUU-rps16_p5 | trnK-UUU-rps16 | CGATGGTATGGACGAATCCC |
TTCCTTGAAAAAGGCGCTCA |
1043–1052 | 0.968 | 78.2 |
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
GAGGTTCGAATCCTTCCGTC |
1046–1070 | 1.000 | 81.5 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | CGGATCGTGTCCTTCAAGTC |
GAGGTTCGAATCCTTCCGTC |
1061–1085 | 1.000 | 79.7 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | GGATCGTGTCCTTCAAGTCG |
GAGGTTCGAATCCTTCCGTC |
1060–1084 | 1.000 | 79.7 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | CCAAGAGCACCTTCATTCCT |
GAGGTTCGAATCCTTCCGTC |
1117–1141 | 1.000 | 78.5 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
TTCGGAGGTTCGAATCCTTC |
1050–1074 | 1.000 | 76.8 |
| petN-psbM_p1 | petN-psbM | TAGTAAGTCTCGCTTGGGCT |
TGCTACTGCACTGTTCATTT |
680–701 | 1.000 | 60.6 |
| petN-psbM_p2 | petN-psbM | TAGTAAGTCTCGCTTGGGCT |
TGCTACTGCACTGTTCATTTT |
680–701 | 1.000 | 58.9 |
| petN-psbM_p3 | petN-psbM | ATAGTAAGTCTCGCTTGGGC |
TGCTACTGCACTGTTCATTT |
681–702 | 1.000 | 54.7 |
| petN-psbM_p4 | petN-psbM | CTCGCTTGGGCTGCTTTAAT |
TGCTACTGCACTGTTCATTT |
672–693 | 1.000 | 54.6 |
| petN-psbM_p5 | petN-psbM | TGGGCTGCTTTAATGGTAGTC |
TGCTACTGCACTGTTCATTT |
666–687 | 1.000 | 53.8 |
| atpI-atpH_p1 | atpI-atpH | CCCGTCATGTTCCTTGGATT |
ATAACGGAAGCGGCAGAAAT |
1285–1297 | 1.000 | 81.6 |
| atpI-atpH_p2 | atpI-atpH | CCCGTCATGTTCCTTGGATT |
TACCTTGACCAACTCCAGGT |
1341–1353 | 1.000 | 80.9 |
| atpI-atpH_p3 | atpI-atpH | CCCGTCATGTTCCTTGGATT |
AGCCAATCCAGCAGCAATAA |
1301–1313 | 1.000 | 80.7 |
| atpI-atpH_p4 | atpI-atpH | CCCGTCATGTTCCTTGGATT |
AATAACGGAAGCGGCAGAAA |
1286–1298 | 1.000 | 80.5 |
| atpI-atpH_p5 | atpI-atpH | CCCGTCATGTTCCTTGGATT |
GCAGTACCTTGACCAACTCC |
1345–1357 | 1.000 | 80.3 |
| trnT-GGU-psbD_p1 | trnT-GGU-psbD | ATGGTAACGCGTAAACCCTC |
GAAACGGTCCCTACGTAACC |
1305–1319 | 1.000 | 82.8 |
| trnT-GGU-psbD_p2 | trnT-GGU-psbD | GTAATCCCATGGTAACGCGT |
GAAACGGTCCCTACGTAACC |
1313–1327 | 1.000 | 82.5 |
| trnT-GGU-psbD_p3 | trnT-GGU-psbD | ATGGTAACGCGTAAACCCTC |
GGACCAGCCTACAAAAACGA |
1323–1337 | 1.000 | 82.0 |
| trnT-GGU-psbD_p4 | trnT-GGU-psbD | GTAATCCCATGGTAACGCGT |
GGACCAGCCTACAAAAACGA |
1331–1345 | 1.000 | 81.6 |
| trnT-GGU-psbD_p5 | trnT-GGU-psbD | CGACCCGTTCAGGAATTCAA |
GAAACGGTCCCTACGTAACC |
1366–1380 | 1.000 | 81.2 |
| psbC-trnS-UGA_p1 | psbC-trnS-UGA | CCTGTTCTTTCCATGACCCC |
GAGAGATGGCTGAGTGGTTG |
358–366 | 1.000 | 81.9 |
| psbC-trnS-UGA_p2 | psbC-trnS-UGA | TCTTCGTAGGGCATTTGTGG |
GAGAGATGGCTGAGTGGTTG |
441–449 | 1.000 | 81.7 |
| psbC-trnS-UGA_p3 | psbC-trnS-UGA | CCTGTTCTTTCCATGACCCC |
GTCTTTCGGAGAGATGGCTG |
366–374 | 1.000 | 81.4 |
| psbC-trnS-UGA_p4 | psbC-trnS-UGA | TCTTCGTAGGGCATTTGTGG |
GTCTTTCGGAGAGATGGCTG |
449–457 | 1.000 | 81.3 |
| psbC-trnS-UGA_p5 | psbC-trnS-UGA | TCTTCGTAGGGCATTTGTGG |
TCTTTCGGAGAGATGGCTGA |
448–456 | 1.000 | 80.6 |
Result downloads
Reference species (31)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Aldama anchusifolia | NC_053291.1 | 151330 | View on NCBI ↗ |
| Aldama arenaria | NC_053292.1 | 151345 | View on NCBI ↗ |
| Aldama bakeriana | NC_053294.1 | 151376 | View on NCBI ↗ |
| Aldama bracteata | NC_053295.1 | 151339 | View on NCBI ↗ |
| Aldama canescens | NC_053296.1 | 151386 | View on NCBI ↗ |
| Aldama corumbensis | NC_053297.1 | 151327 | View on NCBI ↗ |
| Aldama discolor | NC_057171.1 | 151360 | View on NCBI ↗ |
| Aldama excelsa | NC_057172.1 | 151312 | View on NCBI ↗ |
| Aldama filifolia | NC_053279.1 | 151333 | View on NCBI ↗ |
| Aldama fusiformis | NC_053280.1 | 151314 | View on NCBI ↗ |
| Aldama gardneri | NC_053281.1 | 151312 | View on NCBI ↗ |
| Aldama goyazii | NC_053282.1 | 151279 | View on NCBI ↗ |
| Aldama grandiflora | NC_053283.1 | 151353 | View on NCBI ↗ |
| Aldama kunthiana | NC_053284.1 | 151327 | View on NCBI ↗ |
| Aldama linearis | NC_053285.1 | 151314 | View on NCBI ↗ |
| Aldama macrorhiza | NC_053286.1 | 151314 | View on NCBI ↗ |
| Aldama megapotamica | NC_053287.1 | 151363 | View on NCBI ↗ |
| Aldama nudibasilaris | NC_053288.1 | 151316 | View on NCBI ↗ |
| Aldama nudicaulis | NC_053289.1 | 151333 | View on NCBI ↗ |
| Aldama pilosa | NC_053290.1 | 151354 | View on NCBI ↗ |
| Aldama revoluta | NC_057173.1 | 151376 | View on NCBI ↗ |
| Aldama robusta | NC_057174.1 | 151343 | View on NCBI ↗ |
| Aldama rubra | NC_057175.1 | 151322 | View on NCBI ↗ |
| Aldama santacatarinensis | NC_057176.1 | 151362 | View on NCBI ↗ |
| Aldama squalida | NC_057177.1 | 151399 | View on NCBI ↗ |
| Aldama tenuifolia | NC_057178.1 | 151372 | View on NCBI ↗ |
| Aldama trichophylla | NC_053298.1 | 151353 | View on NCBI ↗ |
| Aldama tuberosa | NC_057179.1 | 151323 | View on NCBI ↗ |
| Aldama tukumanensis | NC_057180.1 | 151336 | View on NCBI ↗ |
| Aldama veredensis | NC_057181.1 | 151331 | View on NCBI ↗ |
| Aldama vernonioides | NC_057182.1 | 151221 | View on NCBI ↗ |