| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnG-UCC-trnT-GGU | LSC | 1961 | 0.0076 | 1.00 | 56.6 | yes | View details |
| trnD-GUC-psbM | LSC | 1056 | 0.0036 | 1.00 | 44.6 | yes | View details |
| rpoC2 | LSC | 4521 | 0.0010 | 1.00 | 37.2 | yes | View details |
| rbcL-psaI | LSC | 1245 | 0.0032 | 1.00 | 48.6 | yes | View details |
| trnP-UGG-psaJ | LSC | 388 | 0.0014 | 1.00 | 31.9 | yes | View details |
| rpl16 | LSC | 1502 | 0.0019 | 1.00 | 36.1 | yes | View details |
| ndhF-rpl32 | SSC | 900 | 0.0035 | 1.00 | 51.9 | yes | View details |
| rpl32-trnL-UAG | SSC | 715 | 0.0067 | 1.00 | 41.0 | yes | View details |
| trnK-UUU | LSC | 38 | 0.0083 | 1.00 | 56.7 | yes | View details |
| ndhC-trnV-UAC | LSC | 930 | 0.0016 | 1.00 | 52.5 | yes | View details |
| psbT-psbN | LSC | 48 | 0.0056 | 1.00 | 49.3 | yes | View details |
| trnS-GCU-psbD | LSC | 997 | 0.0022 | 1.00 | 48.1 | yes | View details |
| rpl14-rpl16 | LSC | 109 | 0.0074 | 1.00 | 47.9 | yes | View details |
| ycf3-trnS-GGA | LSC | 595 | 0.0018 | 1.00 | 47.8 | yes | View details |
| petN-trnC-GCA | LSC | 907 | 0.0017 | 1.00 | 47.7 | yes | View details |
| petG-trnW-CCA | LSC | 122 | 0.0139 | 1.00 | 47.7 | yes | View details |
| trnF-GAA-ndhJ | LSC | 581 | 0.0035 | 1.00 | 47.6 | yes | View details |
| ycf3 | LSC | 1977 | 0.0013 | 1.00 | 46.9 | 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
37
Genome length
139–140 kb
Candidate markers
266
Primer pairs
90
Genome-wide nucleotide diversity
Candidate markers
8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 266 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_p1 | trnK-UUU | TGAGGATCAGTCGTGGTCTT |
CGTGCGGTGTAATTCCATTG |
180–185 | 1.000 | 82.3 |
| trnK-UUU_p2 | trnK-UUU | AGGATCAGTCGTGGTCTTCT |
CGTGCGGTGTAATTCCATTG |
178–183 | 1.000 | 81.2 |
| trnK-UUU_p3 | trnK-UUU | GAGGATCAGTCGTGGTCTTC |
CGTGCGGTGTAATTCCATTG |
179–184 | 1.000 | 78.4 |
| trnK-UUU_p4 | trnK-UUU | TGAGGATCAGTCGTGGTCTT |
AATGTTTTGACAGGAGCGTG |
196–201 | 1.000 | 74.9 |
| trnK-UUU_p5 | trnK-UUU | TGAGGATCAGTCGTGGTCTT |
CAATGTTTTGACAGGAGCGT |
197–202 | 1.000 | 74.8 |
| trnS-GCU-psbD_p1 | trnS-GCU-psbD | ATTAGCAATCCGCCGCTTTA |
GCCGGACCATCCTACAAAAA |
1124–1159 | 1.000 | 80.4 |
| trnS-GCU-psbD_p2 | trnS-GCU-psbD | ATTAGCAATCCGCCGCTTTA |
ACAAAAACGAAACGGTCCCT |
1111–1146 | 1.000 | 79.8 |
| trnS-GCU-psbD_p3 | trnS-GCU-psbD | GCTTTAGTCCACTCAGCCAT |
GCCGGACCATCCTACAAAAA |
1110–1145 | 1.000 | 77.4 |
| trnS-GCU-psbD_p4 | trnS-GCU-psbD | ATTAGCAATCCGCCGCTTTA |
GAAACGGTCCCTTCGTAACC |
1103–1138 | 1.000 | 77.2 |
| trnS-GCU-psbD_p5 | trnS-GCU-psbD | GCTTTAGTCCACTCAGCCAT |
ACAAAAACGAAACGGTCCCT |
1097–1132 | 1.000 | 76.8 |
| trnG-UCC-trnT-GGU_p1 | trnG-UCC-trnT-GGU | ACGAATCACACTTTTACCACT |
CCATGGCATTACTCTACCACC |
2022–2228 | 1.000 | 48.7 |
| trnG-UCC-trnT-GGU_p2 | trnG-UCC-trnT-GGU | ACGAATCACACTTTTACCACT |
GACTTACGTCTTACCATGGCA |
2035–2241 | 1.000 | 48.0 |
| trnG-UCC-trnT-GGU_p3 | trnG-UCC-trnT-GGU | ACGAATCACACTTTTACCACT |
TGACTTACGTCTTACCATGGC |
2036–2242 | 1.000 | 48.0 |
| trnG-UCC-trnT-GGU_p4 | trnG-UCC-trnT-GGU | AGAACGAATCACACTTTTACCAC |
CCATGGCATTACTCTACCACC |
2025–2231 | 1.000 | 47.7 |
| trnG-UCC-trnT-GGU_p5 | trnG-UCC-trnT-GGU | GAACGAATCACACTTTTACCACT |
CCATGGCATTACTCTACCACC |
2024–2230 | 1.000 | 47.7 |
| trnD-GUC-psbM_p1 | trnD-GUC-psbM | TAGGTATGCCATACACCCCG |
AGAATGAACAGTGCAGTAGC |
1199–1206 | 1.000 | 59.3 |
| trnD-GUC-psbM_p2 | trnD-GUC-psbM | TTCAATTGGTCAGAGCACCG |
AGAATGAACAGTGCAGTAGC |
1167–1168 | 0.973 | 58.0 |
| trnD-GUC-psbM_p3 | trnD-GUC-psbM | TAGGTATGCCATACACCCCG |
AGGAACTAGAATGAACAGTGCA |
1206–1213 | 1.000 | 56.1 |
| trnD-GUC-psbM_p4 | trnD-GUC-psbM | TTCAATTGGTCAGAGCACCG |
AGGAACTAGAATGAACAGTGCA |
1174–1175 | 0.973 | 54.8 |
| trnD-GUC-psbM_p5 | trnD-GUC-psbM | GTTCAATTGGTCAGAGCACC |
AGAATGAACAGTGCAGTAGC |
1168–1169 | 0.973 | 53.8 |
| petN-trnC-GCA_p1 | petN-trnC-GCA | AGCCCAAGCGAGACTTACTA |
AGTTCAAATCTGGGTGCCG |
949–975 | 1.000 | 71.9 |
| petN-trnC-GCA_p2 | petN-trnC-GCA | AGCCCAAGCGAGACTTACTA |
CCAGTTCAAATCTGGGTGCC |
951–977 | 1.000 | 71.4 |
| petN-trnC-GCA_p3 | petN-trnC-GCA | CCACTCCTCCCCCATACTAC |
AGTTCAAATCTGGGTGCCG |
1005–1031 | 1.000 | 70.8 |
| petN-trnC-GCA_p4 | petN-trnC-GCA | CCACTCCTCCCCCATACTAC |
CCAGTTCAAATCTGGGTGCC |
1007–1033 | 1.000 | 70.4 |
| petN-trnC-GCA_p5 | petN-trnC-GCA | TCCACTCCTCCCCCATACTA |
AGTTCAAATCTGGGTGCCG |
1006–1032 | 1.000 | 70.1 |
| rpoC2_p1 | rpoC2 | TTCGCTCCACAAGGATCAAG |
TTGTTCTCTGGGCTCCCATA |
519–720 | 1.000 | 84.3 |
| rpoC2_p2 | rpoC2 | AATCATGTCCAACGGCCATT |
TTGTTCTCTGGGCTCCCATA |
357–558 | 1.000 | 84.1 |
| rpoC2_p3 | rpoC2 | TTACCATGCGCCCGAATATC |
TTGTTCTCTGGGCTCCCATA |
624–825 | 1.000 | 83.3 |
| rpoC2_p4 | rpoC2 | TTCGCTCCACAAGGATCAAG |
GGGCTCCCATATTCGTCTTC |
585–786 | 1.000 | 83.0 |
| rpoC2_p5 | rpoC2 | GGGGAAATGCACTGGAGTAC |
TTGTTCTCTGGGCTCCCATA |
650–851 | 1.000 | 82.9 |
Result downloads
Reference species (37)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Bambusa albolineata | MW557324.1 | 139326 | View on NCBI ↗ |
| Bambusa arnhemica | NC_026958.1 | 139289 | View on NCBI ↗ |
| Bambusa bambos | NC_026957.1 | 139606 | View on NCBI ↗ |
| Bambusa basihirsuta | NC_050773.1 | 139377 | View on NCBI ↗ |
| Bambusa bicicatricata | NC_050772.1 | 139398 | View on NCBI ↗ |
| Bambusa boniopsis | NC_050754.1 | 139343 | View on NCBI ↗ |
| Bambusa contracta | NC_059751.1 | 139470 | View on NCBI ↗ |
| Bambusa cornigera | NC_050770.1 | 139394 | View on NCBI ↗ |
| Bambusa dolichoclada | NC_063133.1 | 139473 | View on NCBI ↗ |
| Bambusa dolichomerithalla | NC_063131.1 | 139478 | View on NCBI ↗ |
| Bambusa emeiensis | NC_015830.1 | 139493 | View on NCBI ↗ |
| Bambusa emeiensis f. viridiflava | PQ472912.1 | 139393 | View on NCBI ↗ |
| Bambusa flexuosa | NC_050774.1 | 139355 | View on NCBI ↗ |
| Bambusa grandis | NC_068816.1 | 139443 | View on NCBI ↗ |
| Bambusa intermedia | MW463057.1 | 139446 | View on NCBI ↗ |
| Bambusa lapidea | NC_059750.1 | 139525 | View on NCBI ↗ |
| Bambusa multiplex | NC_024668.1 | 139394 | View on NCBI ↗ |
| Bambusa odashimae | NC_050771.1 | 139376 | View on NCBI ↗ |
| Bambusa oldhamii | NC_012927.1 | 139350 | View on NCBI ↗ |
| Bambusa oliveriana | NC_050768.1 | 139446 | View on NCBI ↗ |
| Bambusa ooh | OR069396.1 | 139350 | View on NCBI ↗ |
| Bambusa pachinensis | NC_063132.1 | 139471 | View on NCBI ↗ |
| Bambusa pachinensis var. hirsutissima | OM001093.1 | 139491 | View on NCBI ↗ |
| Bambusa rigida | NC_050300.1 | 139500 | View on NCBI ↗ |
| Bambusa rutila | NC_050775.1 | 139361 | View on NCBI ↗ |
| Bambusa sinospinosa | NC_050781.1 | 139548 | View on NCBI ↗ |
| Bambusa stenoaurita | NC_058217.1 | 139451 | View on NCBI ↗ |
| Bambusa stenostachya | NC_063134.1 | 139517 | View on NCBI ↗ |
| Bambusa teres | NC_050751.1 | 139535 | View on NCBI ↗ |
| Bambusa textilis | NC_071780.1 | 139354 | View on NCBI ↗ |
| Bambusa tuldoides | NC_071779.1 | 139359 | View on NCBI ↗ |
| Bambusa tuldoides f. swolleninternode | OM687229.1 | 139460 | View on NCBI ↗ |
| Bambusa utilis | NC_063148.1 | 139491 | View on NCBI ↗ |
| Bambusa variostriata | NC_063090.1 | 139448 | View on NCBI ↗ |
| Bambusa ventricosa | NC_042671.1 | 139460 | View on NCBI ↗ |
| Bambusa vulgaris | NC_050780.1 | 139528 | View on NCBI ↗ |
| Bambusa x changningensis | NC_068060.1 | 139505 | View on NCBI ↗ |