| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnD-GUC-trnY-GUA | LSC | 453 | 0.0187 | 1.00 | 53.4 | yes | View details |
| petA-psbJ | LSC | 617 | 0.0274 | 1.00 | 60.8 | yes | View details |
| ycf1 | IRb | 2265 | 0.0040 | 1.00 | 33.5 | no | View details |
| ndhF-rpl32 | SSC | 755 | 0.0226 | 1.00 | 63.0 | yes | View details |
| rpl32-trnL-UAG | SSC | 668 | 0.0262 | 1.00 | 71.5 | yes | View details |
| ycf1 | SSC | 5619 | 0.0126 | 1.00 | 47.6 | yes | View details |
| trnH-GUG-psbA | LSC | 130 | 0.0636 | 1.00 | 64.9 | yes | View details |
| trnI-GAU-rrn16 | IRa | 244 | 0.0445 | 1.00 | 63.3 | yes | View details |
| rrn16-trnI-GAU | IRb | 246 | 0.0445 | 1.00 | 63.0 | yes | View details |
| rpl2-trnH-GUG | IRa | 139 | 0.0029 | 1.00 | 59.3 | no | View details |
| rbcL-accD | LSC | 756 | 0.0138 | 1.00 | 57.1 | yes | View details |
| rps16-trnQ-UUG | LSC | 516 | 0.0169 | 1.00 | 57.0 | yes | View details |
| trnT-UGU-trnL-UAA | LSC | 601 | 0.0097 | 0.99 | 55.0 | yes | View details |
| ndhD-psaC | SSC | 150 | 0.0516 | 1.00 | 54.6 | yes | View details |
| trnS-GCU-trnG-GCC | LSC | 677 | 0.0189 | 1.00 | 54.5 | yes | View details |
| trnK-UUU-rps16 | LSC | 698 | 0.0151 | 0.99 | 53.9 | 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
19
Genome length
152–153 kb
Candidate markers
271
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 271 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 |
CCTCTAGACCTAGCTGCTGT |
197–205 | 1.000 | 85.3 |
| trnH-GUG-psbA_p2 | trnH-GUG-psbA | GATCCACTTGGCTACATCCG |
GCGCTAACCTTGGTATGGAA |
247–255 | 1.000 | 84.2 |
| trnH-GUG-psbA_p3 | trnH-GUG-psbA | AATCCACTGCCTTGATCCAC |
GCGCTAACCTTGGTATGGAA |
260–268 | 1.000 | 83.9 |
| trnH-GUG-psbA_p4 | trnH-GUG-psbA | CAATCCACTGCCTTGATCCA |
GCGCTAACCTTGGTATGGAA |
261–269 | 1.000 | 83.8 |
| trnH-GUG-psbA_p5 | trnH-GUG-psbA | ACAATCCACTGCCTTGATCC |
GCGCTAACCTTGGTATGGAA |
262–270 | 1.000 | 83.8 |
| trnK-UUU-rps16_p1 | trnK-UUU-rps16 | CCTTTCAGGATCAGTCGTGG |
GCAATTGATGTGCGATCTCG |
982–1042 | 1.000 | 86.9 |
| trnK-UUU-rps16_p2 | trnK-UUU-rps16 | ATTCATTCGACCCAACTCGG |
GCAATTGATGTGCGATCTCG |
1119–1179 | 1.000 | 86.5 |
| trnK-UUU-rps16_p3 | trnK-UUU-rps16 | CATTCGACCCAACTCGGAAT |
GCAATTGATGTGCGATCTCG |
1116–1176 | 1.000 | 86.5 |
| trnK-UUU-rps16_p4 | trnK-UUU-rps16 | TCAGGATCAGTCGTGGTCTT |
GCAATTGATGTGCGATCTCG |
978–1038 | 1.000 | 86.4 |
| trnK-UUU-rps16_p5 | trnK-UUU-rps16 | TTCAGGATCAGTCGTGGTCT |
GCAATTGATGTGCGATCTCG |
979–1039 | 1.000 | 86.4 |
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | TATGTCTGTCAAGTCGCACG |
GAGGTTCGAATCCTTCCGTC |
557–677 | 1.000 | 86.4 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | GCACGTTGCTTTTTACCACA |
GAGGTTCGAATCCTTCCGTC |
542–662 | 1.000 | 85.1 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | AGTCGCACGTTGCTTTTTAC |
GAGGTTCGAATCCTTCCGTC |
546–666 | 1.000 | 83.6 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | CAAGTCGCACGTTGCTTTTT |
GAGGTTCGAATCCTTCCGTC |
548–668 | 1.000 | 83.0 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | TATGTCTGTCAAGTCGCACG |
GGGTTTTGGTCCCGGTATTC |
578–698 | 1.000 | 82.6 |
| trnS-GCU-trnG-GCC_p1 | trnS-GCU-trnG-GCC | CAATCCGACGCTTTAGTCCA |
ACGAATCACACTTTTACCACT |
738–753 | 1.000 | 57.1 |
| trnS-GCU-trnG-GCC_p2 | trnS-GCU-trnG-GCC | AATCCGACGCTTTAGTCCAC |
ACGAATCACACTTTTACCACT |
737–752 | 1.000 | 57.1 |
| trnS-GCU-trnG-GCC_p3 | trnS-GCU-trnG-GCC | GAAAGGCTCGTACAACGGAT |
ACGAATCACACTTTTACCACT |
761–776 | 1.000 | 57.0 |
| trnS-GCU-trnG-GCC_p4 | trnS-GCU-trnG-GCC | GCTCGTACAACGGATTAGCA |
ACGAATCACACTTTTACCACT |
756–771 | 1.000 | 56.4 |
| trnS-GCU-trnG-GCC_p5 | trnS-GCU-trnG-GCC | ACGGAAAGAGAGGGATTCGA |
ACGAATCACACTTTTACCACT |
792–807 | 1.000 | 55.6 |
| trnD-GUC-trnY-GUA_p1 | trnD-GUC-trnY-GUA | ATTTGATTCCGTCGGGACTG |
TGGCAATATGTCTACGCTGG |
564–579 | 1.000 | 82.8 |
| trnD-GUC-trnY-GUA_p2 | trnD-GUC-trnY-GUA | ATTTGATTCCGTCGGGACTG |
GGCAATATGTCTACGCTGGT |
563–578 | 1.000 | 82.8 |
| trnD-GUC-trnY-GUA_p3 | trnD-GUC-trnY-GUA | ATTTGATTCCGTCGGGACTG |
GGGGACGGACTGTAAATTCG |
585–600 | 1.000 | 81.7 |
| trnD-GUC-trnY-GUA_p4 | trnD-GUC-trnY-GUA | ATTTGATTCCGTCGGGACTG |
GGGACGGACTGTAAATTCGT |
584–599 | 1.000 | 81.5 |
| trnD-GUC-trnY-GUA_p5 | trnD-GUC-trnY-GUA | ATTTGATTCCGTCGGGACTG |
GATTCTTCCTGGGTCGATGC |
618–633 | 1.000 | 81.0 |
| trnT-UGU-trnL-UAA_p1 | trnT-UGU-trnL-UAA | GGAATCGAACCGATGACCAT |
ACCAATTTCGCCATATCCCC |
679–686 | 1.000 | 81.4 |
| trnT-UGU-trnL-UAA_p2 | trnT-UGU-trnL-UAA | AAATGCGGTGCTCTAACCTC |
ACCAATTTCGCCATATCCCC |
651–658 | 1.000 | 81.4 |
| trnT-UGU-trnL-UAA_p3 | trnT-UGU-trnL-UAA | GGAATCGAACCGATGACCAT |
TAGCGTCTACCAATTTCGCC |
687–694 | 1.000 | 80.9 |
| trnT-UGU-trnL-UAA_p4 | trnT-UGU-trnL-UAA | AAATGCGGTGCTCTAACCTC |
TAGCGTCTACCAATTTCGCC |
659–666 | 1.000 | 80.9 |
| trnT-UGU-trnL-UAA_p5 | trnT-UGU-trnL-UAA | GCATTACAAATGCGGTGCTC |
ACCAATTTCGCCATATCCCC |
658–665 | 1.000 | 79.9 |
Result downloads
Reference species (19)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Lagerstroemia anhuiensis | MT019856.1 | 152049 | View on NCBI ↗ |
| Lagerstroemia calyculata | NC_042897.1 | 152294 | View on NCBI ↗ |
| Lagerstroemia caudata | MT019857.1 | 152194 | View on NCBI ↗ |
| Lagerstroemia excelsa | NC_042896.1 | 152214 | View on NCBI ↗ |
| Lagerstroemia fauriei | NC_029808.1 | 152440 | View on NCBI ↗ |
| Lagerstroemia glabra | MT019859.1 | 152005 | View on NCBI ↗ |
| Lagerstroemia guilinensis | NC_029885.1 | 152193 | View on NCBI ↗ |
| Lagerstroemia indica | NC_030484.1 | 152205 | View on NCBI ↗ |
| Lagerstroemia intermedia | NC_034662.1 | 152330 | View on NCBI ↗ |
| Lagerstroemia lecomtei | PV276194.1 | 152265 | View on NCBI ↗ |
| Lagerstroemia limii | NC_042889.1 | 152153 | View on NCBI ↗ |
| Lagerstroemia loudonii | NC_061954.1 | 152372 | View on NCBI ↗ |
| Lagerstroemia minuticarpa | PZ011249.1 | 152183 | View on NCBI ↗ |
| Lagerstroemia siamica | NC_042890.1 | 152519 | View on NCBI ↗ |
| Lagerstroemia speciosa | NC_031414.1 | 152476 | View on NCBI ↗ |
| Lagerstroemia subcostata | NC_034952.1 | 152049 | View on NCBI ↗ |
| Lagerstroemia suprareticulata | NC_071782.1 | 152196 | View on NCBI ↗ |
| Lagerstroemia tomentosa | NC_042893.1 | 152294 | View on NCBI ↗ |
| Lagerstroemia venusta | NC_042892.1 | 152521 | View on NCBI ↗ |