| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| psbA | LSC | 1062 | 0.0004 | 1.00 | 32.2 | yes | View details |
| trnG-UCC-trnT-GGU | LSC | 2052 | 0.0028 | 0.99 | 56.7 | yes | View details |
| trnY-GUA-trnD-GUC | LSC | 352 | 0.0017 | 1.00 | 38.9 | yes | View details |
| ndhK | LSC | 741 | 0.0027 | 1.00 | 47.7 | yes | View details |
| rbcL-psaI | LSC | 1247 | 0.0040 | 1.00 | 54.9 | yes | View details |
| ycf4-cemA | LSC | 442 | 0.0035 | 1.00 | 48.8 | yes | View details |
| rpl14 | LSC | 372 | 0.0018 | 1.00 | 30.1 | yes | View details |
| rpl16 | LSC | 1509 | 0.0022 | 1.00 | 35.8 | yes | View details |
| rpl32-trnL-UAG | SSC | 718 | 0.0045 | 1.00 | 41.1 | yes | View details |
| ndhD | SSC | 1503 | 0.0008 | 1.00 | 30.2 | yes | View details |
| psbT-psbN | LSC | 48 | 0.0199 | 1.00 | 56.0 | yes | View details |
| rps19-psbA | LSC | 136 | 0.0143 | 1.00 | 55.9 | no | View details |
| trnT-UGU-trnL-UAA | LSC | 807 | 0.0023 | 1.00 | 52.3 | yes | View details |
| trnC-GCA-rpoB | LSC | 1170 | 0.0011 | 1.00 | 50.4 | yes | View details |
| psbZ-trnfM-CAU | LSC | 790 | 0.0008 | 1.00 | 48.9 | yes | View details |
| trnT-GGU-trnE-UUC | LSC | 554 | 0.0009 | 1.00 | 48.3 | yes | View details |
| psaA-ycf3 | LSC | 614 | 0.0012 | 1.00 | 48.3 | yes | View details |
| petD | LSC | 1231 | 0.0020 | 1.00 | 48.3 | yes | View details |
| infA-rps8 | LSC | 112 | 0.0069 | 1.00 | 48.2 | yes | View details |
| rpl22-rps19 | LSC | 71 | 0.0037 | 1.00 | 48.2 | 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
23
Genome length
139–140 kb
Candidate markers
263
Primer pairs
95
Genome-wide nucleotide diversity
Candidate markers
10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 263 candidates).
Primer pairs
Showing the top 30 of 95 primer pairs (ranked by primer score).
| Primer ID | Label | Forward | Reverse | Amplicon (bp) | Cross-species rate | Score |
|---|---|---|---|---|---|---|
| psbA_p1 | psbA | TCTGGCTTTCCTTCCTTCAA |
AATACGTGTGCTTGGGAGTC |
1159 | 1.000 | 68.9 |
| psbA_p2 | psbA | TTCTGGCTTTCCTTCCTTCA |
AATACGTGTGCTTGGGAGTC |
1160 | 1.000 | 68.9 |
| psbA_p3 | psbA | TCTGGCTTTCCTTCCTTCAAA |
AATACGTGTGCTTGGGAGTC |
1159 | 1.000 | 66.9 |
| psbA_p4 | psbA | TTCTGGCTTTCCTTCCTTCAA |
AATACGTGTGCTTGGGAGTC |
1160 | 1.000 | 66.9 |
| psbA_p5 | psbA | TTTCTGGCTTTCCTTCCTTCA |
AATACGTGTGCTTGGGAGTC |
1161 | 1.000 | 66.9 |
| psbZ-trnfM-CAU_p1 | psbZ-trnfM-CAU | TTGCTTCTCCTGATGGTTGG |
CGAGGCTCATAACCTTGAGG |
919–948 | 1.000 | 79.4 |
| psbZ-trnfM-CAU_p2 | psbZ-trnfM-CAU | GCTTCTCCTGATGGTTGGTC |
CGAGGCTCATAACCTTGAGG |
917–946 | 1.000 | 79.0 |
| psbZ-trnfM-CAU_p3 | psbZ-trnfM-CAU | TTGCTTCTCCTGATGGTTGG |
CAGTTTGGTAGCTCACGAGG |
934–963 | 1.000 | 78.9 |
| psbZ-trnfM-CAU_p4 | psbZ-trnfM-CAU | GCTTCTCCTGATGGTTGGTC |
CAGTTTGGTAGCTCACGAGG |
932–961 | 1.000 | 78.5 |
| psbZ-trnfM-CAU_p5 | psbZ-trnfM-CAU | TTGCTTCTCCTGATGGTTGG |
GAGCGGAGTAGAGCAGTTTG |
947–976 | 1.000 | 78.2 |
| trnG-UCC-trnT-GGU_p1 | trnG-UCC-trnT-GGU | ACGAATCACACTTTTACCACT |
CCATGGCATTACTCTACCACC |
2119–2223 | 1.000 | 48.2 |
| trnG-UCC-trnT-GGU_p2 | trnG-UCC-trnT-GGU | ACGAATCACACTTTTACCACT |
GACTTACGTCTTACCATGGCA |
2132–2236 | 1.000 | 47.4 |
| trnG-UCC-trnT-GGU_p3 | trnG-UCC-trnT-GGU | ACGAATCACACTTTTACCACT |
TGACTTACGTCTTACCATGGC |
2133–2237 | 1.000 | 47.4 |
| trnG-UCC-trnT-GGU_p4 | trnG-UCC-trnT-GGU | AGAACGAATCACACTTTTACCAC |
CCATGGCATTACTCTACCACC |
2122–2226 | 1.000 | 47.1 |
| trnG-UCC-trnT-GGU_p5 | trnG-UCC-trnT-GGU | GAACGAATCACACTTTTACCACT |
CCATGGCATTACTCTACCACC |
2121–2225 | 1.000 | 47.1 |
| trnT-GGU-trnE-UUC_p1 | trnT-GGU-trnE-UUC | AGCCCTTTTAACTCAGTGGT |
GCTGCCTCCTTGAAAGAGAG |
653–675 | 1.000 | 70.3 |
| trnT-GGU-trnE-UUC_p2 | trnT-GGU-trnE-UUC | AGCCCTTTTAACTCAGTGGT |
TGTCCTGAACCACTAGACGA |
632–654 | 1.000 | 70.3 |
| trnT-GGU-trnE-UUC_p3 | trnT-GGU-trnE-UUC | AGGCATAAGTCATCGGTTCA |
GCTGCCTCCTTGAAAGAGAG |
616–638 | 1.000 | 70.3 |
| trnT-GGU-trnE-UUC_p4 | trnT-GGU-trnE-UUC | AGGCATAAGTCATCGGTTCA |
TGTCCTGAACCACTAGACGA |
595–617 | 1.000 | 70.3 |
| trnT-GGU-trnE-UUC_p5 | trnT-GGU-trnE-UUC | TGGTAAGGCATAAGTCATCGG |
GCTGCCTCCTTGAAAGAGAG |
621–643 | 1.000 | 69.5 |
| trnY-GUA-trnD-GUC_p1 | trnY-GUA-trnD-GUC | AATTCTTCCTGGGTCGATGC |
CGGTGCTCTGACCAATTGAA |
476–477 | 1.000 | 76.8 |
| trnY-GUA-trnD-GUC_p2 | trnY-GUA-trnD-GUC | GGGGACGGACTGTAAATTCG |
CGGTGCTCTGACCAATTGAA |
443–444 | 1.000 | 74.5 |
| trnY-GUA-trnD-GUC_p3 | trnY-GUA-trnD-GUC | GGGACGGACTGTAAATTCGT |
CGGTGCTCTGACCAATTGAA |
442–443 | 1.000 | 74.3 |
| trnY-GUA-trnD-GUC_p4 | trnY-GUA-trnD-GUC | AATTCTTCCTGGGTCGATGC |
GGTGCTCTGACCAATTGAAC |
475–476 | 1.000 | 72.7 |
| trnY-GUA-trnD-GUC_p5 | trnY-GUA-trnD-GUC | TGGGGACGGACTGTAAATTC |
CGGTGCTCTGACCAATTGAA |
444–445 | 1.000 | 71.1 |
| trnC-GCA-rpoB_p1 | trnC-GCA-rpoB | AAAGGATTTGCAGTCCCCTG |
CCGGGTATTGTGGACATTCC |
1232–1267 | 1.000 | 79.4 |
| trnC-GCA-rpoB_p2 | trnC-GCA-rpoB | AAAGGATTTGCAGTCCCCTG |
CGGGTATTGTGGACATTCCC |
1231–1266 | 1.000 | 79.4 |
| trnC-GCA-rpoB_p3 | trnC-GCA-rpoB | AAAGGATTTGCAGTCCCCTG |
AAGTTCTTCTGCCAAGCCTT |
1296–1331 | 1.000 | 78.9 |
| trnC-GCA-rpoB_p4 | trnC-GCA-rpoB | AAAGGATTTGCAGTCCCCTG |
AGTTCTTCTGCCAAGCCTTG |
1295–1330 | 1.000 | 78.8 |
| trnC-GCA-rpoB_p5 | trnC-GCA-rpoB | AAAGGATTTGCAGTCCCCTG |
CAAGTTCTTCTGCCAAGCCT |
1297–1332 | 1.000 | 78.8 |
Result downloads
Reference species (23)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Dendrocalamus bambusoides | NC_050762.1 | 139523 | View on NCBI ↗ |
| Dendrocalamus barbatus | NC_050747.1 | 139423 | View on NCBI ↗ |
| Dendrocalamus barbatus var. internodiiradicatus | MK679778.1 | 139423 | View on NCBI ↗ |
| Dendrocalamus birmanicus | NC_050750.1 | 139465 | View on NCBI ↗ |
| Dendrocalamus brandisii | NC_050763.1 | 139422 | View on NCBI ↗ |
| Dendrocalamus farinosus | NC_063702.1 | 139458 | View on NCBI ↗ |
| Dendrocalamus fugongensis | NC_050764.1 | 139439 | View on NCBI ↗ |
| Dendrocalamus giganteus | NC_050752.1 | 139440 | View on NCBI ↗ |
| Dendrocalamus hamiltonii | NC_050746.1 | 139395 | View on NCBI ↗ |
| Dendrocalamus latiflorus | NC_013088.1 | 139394 | View on NCBI ↗ |
| Dendrocalamus liboensis | NC_081047.1 | 139483 | View on NCBI ↗ |
| Dendrocalamus membranaceus | NC_050766.1 | 139482 | View on NCBI ↗ |
| Dendrocalamus minor | NC_050755.1 | 139451 | View on NCBI ↗ |
| Dendrocalamus minor var. amoenus | MK679791.1 | 139458 | View on NCBI ↗ |
| Dendrocalamus ovatus | NC_050759.1 | 139458 | View on NCBI ↗ |
| Dendrocalamus pachystachyus | NC_050753.1 | 139502 | View on NCBI ↗ |
| Dendrocalamus pulverulentus | NC_050758.1 | 139455 | View on NCBI ↗ |
| Dendrocalamus sapidus | NC_050757.1 | 139511 | View on NCBI ↗ |
| Dendrocalamus semiscandens | NC_050748.1 | 139458 | View on NCBI ↗ |
| Dendrocalamus sikkimensis | NC_050760.1 | 139436 | View on NCBI ↗ |
| Dendrocalamus sinicus | NC_045941.1 | 139441 | View on NCBI ↗ |
| Dendrocalamus strictus | NC_050776.1 | 139404 | View on NCBI ↗ |
| Dendrocalamus yunnanicus | NC_050761.1 | 139432 | View on NCBI ↗ |