| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnK-TTT-rps16 | LSC | 806 | 0.0084 | 0.99 | 65.2 | yes | View details |
| trnS-GCT-trnG-GCC | LSC | 856 | 0.0070 | 1.00 | 45.7 | yes | View details |
| psbZ-trnG-GCC | LSC | 751 | 0.0117 | 0.98 | 63.2 | yes | View details |
| trnP-TGG-psaJ | LSC | 368 | 0.0072 | 1.00 | 52.8 | yes | View details |
| clpP | LSC | 2129 | 0.0061 | 1.00 | 48.0 | yes | View details |
| ndhF-rpl32 | SSC | 1078 | 0.0183 | 0.98 | 63.0 | yes | View details |
| rpl32-trnL-TAG | SSC | 1158 | 0.0092 | 1.00 | 50.3 | yes | View details |
| ccsA-ndhD | SSC | 319 | 0.0063 | 1.00 | 36.2 | yes | View details |
| ycf1 | SSC | 5664 | 0.0047 | 1.00 | 47.6 | yes | View details |
| rps19-rpl2 | IRb | 84 | 0.0238 | 1.00 | 67.7 | yes | View details |
| ndhC-trnV-UAC | LSC | 1223 | 0.0072 | 0.98 | 65.7 | yes | View details |
| atpF-atpH | LSC | 608 | 0.0057 | 0.97 | 65.2 | yes | View details |
| rbcL-accD | LSC | 721 | 0.0046 | 1.00 | 61.9 | yes | View details |
| ndhD | SSC | 1152 | 0.0046 | 1.00 | 61.7 | yes | View details |
| trnR-TCT-atpA | LSC | 124 | 0.0376 | 1.00 | 61.4 | yes | View details |
| trnA-TGC-rrn23S | IRb | 172 | 0.0039 | 1.00 | 60.6 | yes | View details |
| rrn23S-trnA-TGC | IRa | 172 | 0.0039 | 1.00 | 60.6 | yes | View details |
| rpl2-trnH-GTG | IRa | 92 | 0.0217 | 1.00 | 60.6 | no | View details |
| trnR-ACG-trnN-GTT | IRb | 597 | 0.0022 | 1.00 | 60.1 | 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
3
Genome length
160–161 kb
Candidate markers
267
Primer pairs
90
Genome-wide nucleotide diversity
Candidate markers
9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 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-TTT-rps16_p1 | trnK-TTT-rps16 | AAGCCGAGTACTCTACCGTT |
AAAAGGAGCTCAACCCACAG |
933–943 | 1.000 | 80.3 |
| trnK-TTT-rps16_p2 | trnK-TTT-rps16 | AAAGCCGAGTACTCTACCGT |
AAAAGGAGCTCAACCCACAG |
934–944 | 1.000 | 80.2 |
| trnK-TTT-rps16_p3 | trnK-TTT-rps16 | CCGCACTTAAAAGCCGAGTA |
AAAAGGAGCTCAACCCACAG |
943–953 | 1.000 | 79.3 |
| trnK-TTT-rps16_p4 | trnK-TTT-rps16 | TACCGTTGAGTTAGCAACCC |
AAAAGGAGCTCAACCCACAG |
920–930 | 1.000 | 77.9 |
| trnK-TTT-rps16_p5 | trnK-TTT-rps16 | AAGCCGAGTACTCTACCGTT |
AAGAAGGCGGGGGTTTTTAC |
893–903 | 1.000 | 77.4 |
| trnS-GCT-trnG-GCC_p1 | trnS-GCT-trnG-GCC | CAATCCGACGCTTTAGTCCA |
TGTTCGGAATATGAATCAAACCG |
980–988 | 1.000 | 53.0 |
| trnS-GCT-trnG-GCC_p2 | trnS-GCT-trnG-GCC | AATCCGACGCTTTAGTCCAC |
TGTTCGGAATATGAATCAAACCG |
979–987 | 1.000 | 52.9 |
| trnS-GCT-trnG-GCC_p3 | trnS-GCT-trnG-GCC | CAATCCGACGCTTTAGTCCA |
ACGAATCACACTTTTACCACT |
924–932 | 1.000 | 52.5 |
| trnS-GCT-trnG-GCC_p4 | trnS-GCT-trnG-GCC | AATCCGACGCTTTAGTCCAC |
ACGAATCACACTTTTACCACT |
923–931 | 1.000 | 52.5 |
| trnS-GCT-trnG-GCC_p5 | trnS-GCT-trnG-GCC | CGCACAACGGATTAGCAATC |
TGTTCGGAATATGAATCAAACCG |
995–1003 | 1.000 | 52.2 |
| trnR-TCT-atpA_p1 | trnR-TCT-atpA | GGTTCAAATCCTATTGGACGC |
CATTCACTGAGGAAGCGGAA |
226–248 | 1.000 | 68.0 |
| trnR-TCT-atpA_p2 | trnR-TCT-atpA | GGTTCAAATCCTATTGGACGC |
CTGAGGAAGCGGAAACACTT |
220–242 | 1.000 | 67.9 |
| trnR-TCT-atpA_p3 | trnR-TCT-atpA | GGTTCAAATCCTATTGGACGC |
TTCACTGAGGAAGCGGAAAC |
224–246 | 1.000 | 67.8 |
| trnR-TCT-atpA_p4 | trnR-TCT-atpA | GGTTCAAATCCTATTGGACGC |
TGAGGAAGCGGAAACACTTT |
219–241 | 1.000 | 66.1 |
| trnR-TCT-atpA_p5 | trnR-TCT-atpA | GGTTCAAATCCTATTGGACGC |
AGACATTCACTGAGGAAGCG |
229–251 | 1.000 | 65.7 |
| atpF-atpH_p1 | atpF-atpH | CAGTGACCCAAGGAAACGAA |
TGGGTTGGTTGTAGCATTGG |
686–698 | 1.000 | 79.5 |
| atpF-atpH_p2 | atpF-atpH | CAGTGACCCAAGGAAACGAA |
GCATTGGCGCTTTTATTTGC |
673–685 | 1.000 | 79.0 |
| atpF-atpH_p3 | atpF-atpH | ATTAAACCCGAAACTCCCGG |
TGGGTTGGTTGTAGCATTGG |
714–726 | 1.000 | 78.7 |
| atpF-atpH_p4 | atpF-atpH | ATTAAACCCGAAACTCCCGG |
GCATTGGCGCTTTTATTTGC |
701–713 | 1.000 | 78.2 |
| atpF-atpH_p5 | atpF-atpH | CAGTGACCCAAGGAAACGAA |
CCGAGGCAGAGGGAAAAATA |
756–768 | 1.000 | 76.5 |
| psbZ-trnG-GCC_p1 | psbZ-trnG-GCC | TTGCTTCTCCTGATGGTTGG |
CGTCTTCTCCTTGGCAAAGA |
895–908 | 1.000 | 80.0 |
| psbZ-trnG-GCC_p2 | psbZ-trnG-GCC | GCTTCTCCTGATGGTTGGTT |
CGTCTTCTCCTTGGCAAAGA |
893–906 | 1.000 | 80.0 |
| psbZ-trnG-GCC_p3 | psbZ-trnG-GCC | CTCCTGATGGTTGGTTGAGT |
CGTCTTCTCCTTGGCAAAGA |
889–902 | 1.000 | 74.7 |
| psbZ-trnG-GCC_p4 | psbZ-trnG-GCC | TGCTTCTCCTGATGGTTGGT |
CGTCTTCTCCTTGGCAAAGA |
894–907 | 1.000 | 74.2 |
| psbZ-trnG-GCC_p5 | psbZ-trnG-GCC | TCTCCTGATGGTTGGTTGAG |
CGTCTTCTCCTTGGCAAAGA |
890–903 | 1.000 | 72.4 |
| ndhC-trnV-UAC_p1 | ndhC-trnV-UAC | ACCCTTTCTAATCGGGGCTA |
CGGTTCAAGTCCGTATAGCC |
1357–1373 | 1.000 | 79.8 |
| ndhC-trnV-UAC_p2 | ndhC-trnV-UAC | CGGGGCTAAAACTCCAGAAA |
CGGTTCAAGTCCGTATAGCC |
1345–1361 | 1.000 | 79.7 |
| ndhC-trnV-UAC_p3 | ndhC-trnV-UAC | ACCCTTTCTAATCGGGGCTA |
GGTTCAAGTCCGTATAGCCC |
1356–1372 | 1.000 | 79.1 |
| ndhC-trnV-UAC_p4 | ndhC-trnV-UAC | CGGGGCTAAAACTCCAGAAA |
GGTTCAAGTCCGTATAGCCC |
1344–1360 | 1.000 | 79.0 |
| ndhC-trnV-UAC_p5 | ndhC-trnV-UAC | ATCGGGGCTAAAACTCCAGA |
CGGTTCAAGTCCGTATAGCC |
1347–1363 | 1.000 | 77.9 |
Result downloads
Reference species (3)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Theobroma bicolor | NC_073584.1 | 160317 | View on NCBI ↗ |
| Theobroma cacao | NC_014676.2 | 160619 | View on NCBI ↗ |
| Theobroma grandiflorum | NC_054233.1 | 160606 | View on NCBI ↗ |