| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnH-GUG-psbA | Genome | 397 | 0.0219 | 1.00 | 55.0 | yes | View details |
| petA-psbJ | Genome | 1160 | 0.0157 | 1.00 | 61.7 | yes | View details |
| ycf2 | Genome | 6972 | 0.0026 | 1.00 | 37.9 | yes | View details |
| rpl32-trnL-UAG | Genome | 1385 | 0.0086 | 1.00 | 60.2 | yes | View details |
| ycf1 | Genome | 5640 | 0.0061 | 1.00 | 45.1 | yes | View details |
| trnL-CAA-trnH-GUG | Genome | 3528 | 0.0033 | 1.00 | 49.3 | no | View details |
| rps19-rpl2 | Genome | 79 | 0.0224 | 1.00 | 67.2 | yes | View details |
| ndhF-rpl32 | Genome | 1122 | 0.0077 | 1.00 | 61.1 | yes | View details |
| trnS-GCU-trnG-UCC | Genome | 818 | 0.0035 | 1.00 | 53.1 | yes | View details |
| ycf4-cemA | Genome | 911 | 0.0025 | 1.00 | 52.4 | yes | View details |
| psaA-ycf3 | Genome | 639 | 0.0009 | 1.00 | 50.3 | yes | View details |
| trnK-UUU-rps16 | Genome | 825 | 0.0035 | 0.99 | 49.6 | yes | View details |
| ndhC-trnV-UAC | Genome | 1851 | 0.0019 | 1.00 | 48.8 | yes | View details |
| rpl2-trnI-CAU | Genome | 416 | 0.0101 | 0.98 | 48.2 | yes | View details |
| trnC-GCA-petN | Genome | 1056 | 0.0041 | 1.00 | 47.6 | yes | View details |
| psbC-trnS-UGA | Genome | 214 | 0.0218 | 1.00 | 47.4 | 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
153–159 kb
Candidate markers
256
Primer pairs
75
Genome-wide nucleotide diversity
Candidate markers
6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 256 candidates).
Primer pairs
Showing the top 30 of 75 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 |
TCAGTGCTATGCATGGTTCC |
844–852 | 1.000 | 83.2 |
| trnH-GUG-psbA_p2 | trnH-GUG-psbA | GATCCACTTGGCTACATCCG |
CAGTGCTATGCATGGTTCCT |
843–851 | 1.000 | 83.1 |
| trnH-GUG-psbA_p3 | trnH-GUG-psbA | CAATCCACTGCCTTGATCCA |
TCAGTGCTATGCATGGTTCC |
858–866 | 1.000 | 83.0 |
| trnH-GUG-psbA_p4 | trnH-GUG-psbA | AATCCACTGCCTTGATCCAC |
TCAGTGCTATGCATGGTTCC |
857–865 | 1.000 | 83.0 |
| trnH-GUG-psbA_p5 | trnH-GUG-psbA | ACAATCCACTGCCTTGATCC |
TCAGTGCTATGCATGGTTCC |
859–867 | 1.000 | 83.0 |
| trnK-UUU-rps16_p1 | trnK-UUU-rps16 | AAAGCCGAGTACTCTACCGT |
AAAAAGGCGCTCAACCTACA |
945–957 | 1.000 | 81.7 |
| trnK-UUU-rps16_p2 | trnK-UUU-rps16 | AAGCCGAGTACTCTACCGTT |
AAAAAGGCGCTCAACCTACA |
944–956 | 1.000 | 81.7 |
| trnK-UUU-rps16_p3 | trnK-UUU-rps16 | AAAAGACCATAGCCGCACTT |
AAAAAGGCGCTCAACCTACA |
966–978 | 1.000 | 81.4 |
| trnK-UUU-rps16_p4 | trnK-UUU-rps16 | CCGCACTTAAAAGCCGAGTA |
AAAAAGGCGCTCAACCTACA |
954–966 | 1.000 | 80.8 |
| trnK-UUU-rps16_p5 | trnK-UUU-rps16 | AAGCCGAGTACTCTACCGTT |
CTTGAAAAAGGCGCTCAACC |
948–960 | 1.000 | 80.1 |
| trnS-GCU-trnG-UCC_p1 | trnS-GCU-trnG-UCC | ATTAGCAATCCGCCGCTTTA |
AGGAATCAAACGAAAGATCCCT |
814–943 | 1.000 | 64.2 |
| trnS-GCU-trnG-UCC_p2 | trnS-GCU-trnG-UCC | GCTTTAGTCCACTCAGCCAT |
AGGAATCAAACGAAAGATCCCT |
800–929 | 1.000 | 61.2 |
| trnS-GCU-trnG-UCC_p3 | trnS-GCU-trnG-UCC | AGAAGAAACGGAGAGAGGGG |
AGGAATCAAACGAAAGATCCCT |
870–999 | 1.000 | 61.0 |
| trnS-GCU-trnG-UCC_p4 | trnS-GCU-trnG-UCC | AGTCCACTCAGCCATCTCTC |
AGGAATCAAACGAAAGATCCCT |
795–924 | 1.000 | 60.4 |
| trnS-GCU-trnG-UCC_p5 | trnS-GCU-trnG-UCC | ATTAGCAATCCGCCGCTTTA |
GGAATCAAACGAAAGATCCCT |
813–942 | 1.000 | 60.3 |
| trnC-GCA-petN_p1 | trnC-GCA-petN | TTTTGTATCGTTTTGGCGGC |
AGCCCAAGCGAGACTTACTA |
1134–1170 | 1.000 | 82.3 |
| trnC-GCA-petN_p2 | trnC-GCA-petN | CTGCAAATCCTTTCTCCCCA |
AGCCCAAGCGAGACTTACTA |
1090–1126 | 1.000 | 81.2 |
| trnC-GCA-petN_p3 | trnC-GCA-petN | TGCAAATCCTTTCTCCCCAG |
AGCCCAAGCGAGACTTACTA |
1089–1125 | 1.000 | 81.2 |
| trnC-GCA-petN_p4 | trnC-GCA-petN | GCAAATCCTTTCTCCCCAGT |
AGCCCAAGCGAGACTTACTA |
1088–1124 | 1.000 | 81.2 |
| trnC-GCA-petN_p5 | trnC-GCA-petN | ACTGCAAATCCTTTCTCCCC |
AGCCCAAGCGAGACTTACTA |
1091–1127 | 1.000 | 81.1 |
| psbC-trnS-UGA_p1 | psbC-trnS-UGA | CCTGTTCTTTCCATGACCCC |
GAGAGATGGCTGAGTGGTTG |
336–337 | 1.000 | 81.4 |
| psbC-trnS-UGA_p2 | psbC-trnS-UGA | CCTGTTCTTTCCATGACCCC |
GGCTGAGTGGTTGATAGCTC |
329–330 | 1.000 | 81.2 |
| psbC-trnS-UGA_p3 | psbC-trnS-UGA | CCTGTTCTTTCCATGACCCC |
AGCTCTGGTCTTGAAAACCG |
314–315 | 1.000 | 80.8 |
| psbC-trnS-UGA_p4 | psbC-trnS-UGA | CCTGTTCTTTCCATGACCCC |
GGGTTCGAATCCCTCTCTCT |
267–268 | 1.000 | 80.6 |
| psbC-trnS-UGA_p5 | psbC-trnS-UGA | AGCTGCAGCAGGATTTGAAA |
GAGAGATGGCTGAGTGGTTG |
379–380 | 1.000 | 79.4 |
| psaA-ycf3_p1 | psaA-ycf3 | GCCCATTCCTCGAAAGAAGT |
TGGTTGAAGATCGCAAGGAG |
663–751 | 1.000 | 82.7 |
| psaA-ycf3_p2 | psaA-ycf3 | GCCCATTCCTCGAAAGAAGT |
GTTGAAGATCGCAAGGAGGT |
661–749 | 1.000 | 82.7 |
| psaA-ycf3_p3 | psaA-ycf3 | GCCCATTCCTCGAAAGAAGT |
GTCCGATCAAGCTGCTGAAT |
736–824 | 1.000 | 80.8 |
| psaA-ycf3_p4 | psaA-ycf3 | TGTTCTTGAGAAATGGCCGG |
TGGTTGAAGATCGCAAGGAG |
688–776 | 1.000 | 79.9 |
| psaA-ycf3_p5 | psaA-ycf3 | TGTTCTTGAGAAATGGCCGG |
GTTGAAGATCGCAAGGAGGT |
686–774 | 1.000 | 79.9 |
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 |
|---|---|---|---|
| Cinnamomum appelianum | NC_065099.1 | 152748 | View on NCBI ↗ |
| Cinnamomum aromaticum | NC_046019.1 | 152763 | View on NCBI ↗ |
| Cinnamomum austrosinense | NC_065100.1 | 152847 | View on NCBI ↗ |
| Cinnamomum austroyunnanense | OR264215.1 | 153595 | View on NCBI ↗ |
| Cinnamomum balansae | PQ576718.1 | 152747 | View on NCBI ↗ |
| Cinnamomum bejolghota | OR264216.1 | 153937 | View on NCBI ↗ |
| Cinnamomum burmanni | NC_065101.1 | 152740 | View on NCBI ↗ |
| Cinnamomum caudiferum | MT621633.1 | 152719 | View on NCBI ↗ |
| Cinnamomum chartophyllum | NC_065102.1 | 158657 | View on NCBI ↗ |
| Cinnamomum daphnoides | NC_084288.1 | 152765 | View on NCBI ↗ |
| Cinnamomum guizhouense | NC_085205.1 | 152739 | View on NCBI ↗ |
| Cinnamomum iners | NC_065103.1 | 152741 | View on NCBI ↗ |
| Cinnamomum jensenianum | OR264227.1 | 154121 | View on NCBI ↗ |
| Cinnamomum kotoense | NC_050346.1 | 154010 | View on NCBI ↗ |
| Cinnamomum liangii | OR264229.1 | 154122 | View on NCBI ↗ |
| Cinnamomum longepaniculatum | NC_065104.1 | 152722 | View on NCBI ↗ |
| Cinnamomum migao | NC_058709.1 | 152711 | View on NCBI ↗ |
| Cinnamomum mollifolium | OR264234.1 | 154082 | View on NCBI ↗ |
| Cinnamomum osmophloeum | MT384386.1 | 152654 | View on NCBI ↗ |
| Cinnamomum parthenoxylon | OR264235.1 | 153999 | View on NCBI ↗ |
| Cinnamomum pauciflorum | NC_065105.1 | 152703 | View on NCBI ↗ |
| Cinnamomum pingbienense | NC_065106.1 | 152628 | View on NCBI ↗ |
| Cinnamomum pittosporoides | NC_048978.1 | 152730 | View on NCBI ↗ |
| Cinnamomum rigidissimum | OR264239.1 | 153377 | View on NCBI ↗ |
| Cinnamomum rufotomentosum | NC_065107.1 | 152727 | View on NCBI ↗ |
| Cinnamomum septentrionale | NC_065108.1 | 152726 | View on NCBI ↗ |
| Cinnamomum subavenium | OR264243.1 | 154087 | View on NCBI ↗ |
| Cinnamomum tamala | NC_065109.1 | 152790 | View on NCBI ↗ |
| Cinnamomum tonkinense | OR264246.1 | 153973 | View on NCBI ↗ |
| Cinnamomum verum | NC_035236.1 | 152766 | View on NCBI ↗ |
| Cinnamomum wilsonii | OR264247.1 | 154009 | View on NCBI ↗ |