| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnH-GUG-psbA | LSC | 400 | 0.0353 | 0.97 | 86.1 | yes | View details |
| psbM-trnD-GUC | LSC | 974 | 0.0117 | 1.00 | 68.2 | yes | View details |
| petA-psbJ | LSC | 1132 | 0.0189 | 1.00 | 70.4 | yes | View details |
| ycf1 | IRb | 1381 | 0.0017 | 1.00 | 35.9 | no | View details |
| ndhF-rpl32 | SSC | 1218 | 0.0152 | 0.93 | 75.3 | yes | View details |
| rpl32-trnL-UAG | SSC | 1392 | 0.0167 | 0.99 | 69.5 | yes | View details |
| ycf1 | SSC | 5568 | 0.0075 | 1.00 | 51.0 | yes | View details |
| psbE-petL | LSC | 1275 | 0.0089 | 1.00 | 72.1 | yes | View details |
| trnK-UUU-rps16 | LSC | 821 | 0.0058 | 1.00 | 64.8 | yes | View details |
| trnE-UUC-trnT-GGU | LSC | 720 | 0.0084 | 1.00 | 63.9 | yes | View details |
| petN-psbM | LSC | 1061 | 0.0062 | 1.00 | 63.5 | yes | View details |
| trnS-GGA-rps4 | LSC | 279 | 0.0159 | 1.00 | 63.3 | yes | View details |
| trnC-GCA-petN | LSC | 1065 | 0.0076 | 0.99 | 61.2 | yes | View details |
| rps16-trnQ-UUG | LSC | 1875 | 0.0087 | 1.00 | 60.9 | yes | View details |
| lhbA-trnG-GCC | LSC | 275 | 0.0116 | 1.00 | 59.8 | yes | View details |
| ycf4-cemA | LSC | 914 | 0.0085 | 1.00 | 59.0 | yes | View details |
| trnT-GGU-psbD | LSC | 1442 | 0.0056 | 1.00 | 58.4 | 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
27
Genome length
152–153 kb
Candidate markers
261
Primer pairs
80
Genome-wide nucleotide diversity
Candidate markers
7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 261 candidates).
Primer pairs
Showing the top 30 of 80 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 |
TTCCCTCTAGACCTAGCTGC |
410–478 | 1.000 | 90.4 |
| trnH-GUG-psbA_p2 | trnH-GUG-psbA | GATCCACTTGGCTACATCCG |
CCTCTAGACCTAGCTGCTGT |
407–475 | 0.963 | 89.0 |
| trnH-GUG-psbA_p3 | trnH-GUG-psbA | CAATCCACTGCCTTGATCCA |
CCTCTAGACCTAGCTGCTGT |
421–489 | 0.963 | 88.9 |
| trnH-GUG-psbA_p4 | trnH-GUG-psbA | AATCCACTGCCTTGATCCAC |
CCTCTAGACCTAGCTGCTGT |
420–488 | 0.963 | 88.9 |
| trnH-GUG-psbA_p5 | trnH-GUG-psbA | ACAATCCACTGCCTTGATCC |
CCTCTAGACCTAGCTGCTGT |
422–490 | 0.963 | 88.9 |
| trnK-UUU-rps16_p1 | trnK-UUU-rps16 | AAAGCCGAGTACTCTACCGT |
AAAAAGGCGCTCAACCTACA |
830–974 | 1.000 | 86.3 |
| trnK-UUU-rps16_p2 | trnK-UUU-rps16 | AAGCCGAGTACTCTACCGTT |
AAAAAGGCGCTCAACCTACA |
829–973 | 1.000 | 86.3 |
| trnK-UUU-rps16_p3 | trnK-UUU-rps16 | AAAAGACCATAGCCGCACTT |
AAAAAGGCGCTCAACCTACA |
851–995 | 1.000 | 86.0 |
| trnK-UUU-rps16_p4 | trnK-UUU-rps16 | CCGCACTTAAAAGCCGAGTA |
AAAAAGGCGCTCAACCTACA |
839–983 | 1.000 | 85.4 |
| trnK-UUU-rps16_p5 | trnK-UUU-rps16 | AAGCCGAGTACTCTACCGTT |
CTTGAAAAAGGCGCTCAACC |
833–977 | 1.000 | 84.7 |
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
GAGGTTCGAATCCTTCCGTC |
1760–2014 | 1.000 | 86.7 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | GGGTACAAGAATCCACAGCC |
GAGGTTCGAATCCTTCCGTC |
1793–2047 | 1.000 | 85.8 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
CTCGGAGGTTCGAATCCTTC |
1764–2018 | 1.000 | 85.6 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | GGGTACAAGAATCCACAGCC |
CTCGGAGGTTCGAATCCTTC |
1797–2051 | 1.000 | 84.7 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | GGTACAAGAATCCACAGCCA |
GAGGTTCGAATCCTTCCGTC |
1792–2046 | 0.963 | 81.9 |
| trnC-GCA-petN_p1 | trnC-GCA-petN | TTTTGTATCGTTTTGGCGGC |
AGCCCAAGCGAGACTTACTA |
1158–1187 | 1.000 | 84.2 |
| trnC-GCA-petN_p2 | trnC-GCA-petN | CTGCAAATCCTTTCTCCCCA |
AGCCCAAGCGAGACTTACTA |
1114–1143 | 1.000 | 83.1 |
| trnC-GCA-petN_p3 | trnC-GCA-petN | TGCAAATCCTTTCTCCCCAG |
AGCCCAAGCGAGACTTACTA |
1113–1142 | 1.000 | 83.1 |
| trnC-GCA-petN_p4 | trnC-GCA-petN | ACTGCAAATCCTTTCTCCCC |
AGCCCAAGCGAGACTTACTA |
1115–1144 | 1.000 | 83.1 |
| trnC-GCA-petN_p5 | trnC-GCA-petN | GCAAATCCTTTCTCCCCAGT |
AGCCCAAGCGAGACTTACTA |
1112–1141 | 1.000 | 83.1 |
| petN-psbM_p1 | petN-psbM | TAGTAAGTCTCGCTTGGGCT |
TGCTACTGCGTTGTTCATTCT |
1222–1235 | 1.000 | 72.3 |
| petN-psbM_p2 | petN-psbM | TAGTAAGTCTCGCTTGGGCT |
TGCTACTGCGTTGTTCATTC |
1222–1235 | 1.000 | 72.2 |
| petN-psbM_p3 | petN-psbM | GGGACACGATTCACATGGAT |
TGCTACTGCGTTGTTCATTCT |
1243–1256 | 1.000 | 70.9 |
| petN-psbM_p4 | petN-psbM | ATGGGGAAGAAGTGGACTCT |
TGCTACTGCGTTGTTCATTCT |
1161–1174 | 1.000 | 70.9 |
| petN-psbM_p5 | petN-psbM | GGGACACGATTCACATGGAT |
TGCTACTGCGTTGTTCATTC |
1243–1256 | 1.000 | 70.7 |
| psbM-trnD-GUC_p1 | psbM-trnD-GUC | AGAATGAACAACGCAGTAGCA |
AGTTCAATCGGTCAGAGCAC |
1059–1128 | 1.000 | 77.9 |
| psbM-trnD-GUC_p2 | psbM-trnD-GUC | GAATGAACAACGCAGTAGCA |
AGTTCAATCGGTCAGAGCAC |
1058–1127 | 1.000 | 77.8 |
| psbM-trnD-GUC_p3 | psbM-trnD-GUC | AGAATGAACAACGCAGTAGCA |
ATGCTGTACACCCCATTTCC |
1088–1157 | 1.000 | 77.3 |
| psbM-trnD-GUC_p4 | psbM-trnD-GUC | GAATGAACAACGCAGTAGCA |
ATGCTGTACACCCCATTTCC |
1087–1156 | 1.000 | 77.2 |
| psbM-trnD-GUC_p5 | psbM-trnD-GUC | GAATGAACAACGCAGTAGCAA |
AGTTCAATCGGTCAGAGCAC |
1058–1127 | 1.000 | 75.5 |
Result downloads
Reference species (27)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Litsea acutivena | NC_050362.1 | 152718 | View on NCBI ↗ |
| Litsea auriculata | NC_056809.1 | 152377 | View on NCBI ↗ |
| Litsea chunii | NC_056810.1 | 152081 | View on NCBI ↗ |
| Litsea coreana var. sinensis | MK674781.1 | 152834 | View on NCBI ↗ |
| Litsea cubeba | NC_048954.1 | 152725 | View on NCBI ↗ |
| Litsea cubeba var. formosana | OK054368.1 | 152739 | View on NCBI ↗ |
| Litsea dilleniifolia | NC_050363.1 | 152298 | View on NCBI ↗ |
| Litsea elongata | NC_050364.1 | 152793 | View on NCBI ↗ |
| Litsea garciae | PQ275788.1 | 152774 | View on NCBI ↗ |
| Litsea glutinosa | NC_050365.1 | 152748 | View on NCBI ↗ |
| Litsea honghoensis | NC_063701.1 | 152605 | View on NCBI ↗ |
| Litsea ichangensis | NC_056811.1 | 152747 | View on NCBI ↗ |
| Litsea japonica | NC_045267.1 | 152718 | View on NCBI ↗ |
| Litsea liyuyingi | NC_085194.1 | 152823 | View on NCBI ↗ |
| Litsea martabanica | NC_085191.1 | 152628 | View on NCBI ↗ |
| Litsea mollis | NC_050366.1 | 152736 | View on NCBI ↗ |
| Litsea monopetala | NC_050367.1 | 152705 | View on NCBI ↗ |
| Litsea moupinensis | NC_056812.1 | 152588 | View on NCBI ↗ |
| Litsea populifolia | NC_056813.1 | 152619 | View on NCBI ↗ |
| Litsea pungens | NC_050368.1 | 152655 | View on NCBI ↗ |
| Litsea rotundifolia var. oblongifolia | NC_085189.1 | 152796 | View on NCBI ↗ |
| Litsea rubescens | NC_056814.1 | 152581 | View on NCBI ↗ |
| Litsea sericea | NC_056815.1 | 152717 | View on NCBI ↗ |
| Litsea szemaois | NC_050369.1 | 152132 | View on NCBI ↗ |
| Litsea tibetana | MT621574.1 | 152594 | View on NCBI ↗ |
| Litsea tsinlingensis | NC_056816.1 | 152051 | View on NCBI ↗ |
| Litsea veitchiana | NC_056817.1 | 152578 | View on NCBI ↗ |