| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnH-GUG-psbA | LSC | 251 | 0.0237 | 1.00 | 58.9 | yes | View details |
| trnR-UCU-atpA | LSC | 525 | 0.0130 | 0.96 | 50.0 | yes | View details |
| petN-psbM | LSC | 596 | 0.0180 | 1.00 | 58.1 | yes | View details |
| trnT-GGU-psbD | LSC | 1321 | 0.0086 | 1.00 | 58.0 | yes | View details |
| trnT-UGU-trnL-UAA | LSC | 943 | 0.0116 | 1.00 | 65.6 | yes | View details |
| ndhC-trnV-UAC | LSC | 506 | 0.0123 | 1.00 | 56.9 | yes | View details |
| rpl16 | LSC | 1363 | 0.0075 | 1.00 | 46.6 | yes | View details |
| ndhF | SSC | 2232 | 0.0067 | 1.00 | 40.7 | yes | View details |
| ndhF-rpl32 | SSC | 1065 | 0.0126 | 1.00 | 59.5 | yes | View details |
| rpl32-trnL-UAG | SSC | 1123 | 0.0125 | 0.95 | 57.4 | yes | View details |
| ycf1 | SSC | 5610 | 0.0076 | 1.00 | 46.5 | yes | View details |
| rps16-trnQ-UUG | LSC | 846 | 0.0085 | 1.00 | 61.6 | yes | View details |
| rpoB-trnC-GCA | LSC | 1070 | 0.0081 | 1.00 | 60.5 | yes | View details |
| ycf4-cemA | LSC | 340 | 0.0125 | 1.00 | 59.2 | yes | View details |
| psbM-trnD-GUC | LSC | 1189 | 0.0071 | 1.00 | 57.2 | yes | View details |
| atpF-atpH | LSC | 455 | 0.0047 | 0.97 | 56.1 | yes | View details |
| trnF-GAA-ndhJ | LSC | 507 | 0.0058 | 1.00 | 55.8 | yes | View details |
| trnE-UUC-trnT-GGU | LSC | 503 | 0.0047 | 0.98 | 54.9 | yes | View details |
| psbL-psbF | LSC | 22 | 0.0215 | 1.00 | 54.8 | yes | View details |
| psbE-petL | LSC | 1302 | 0.0055 | 1.00 | 53.2 | 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
32
Genome length
156–156 kb
Candidate markers
267
Primer pairs
100
Genome-wide nucleotide diversity
Candidate markers
11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 267 candidates).
Primer pairs
Showing the top 30 of 100 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 |
AGCTGCTGTTGAAGTTCCAT |
306–342 | 1.000 | 86.3 |
| trnH-GUG-psbA_p2 | trnH-GUG-psbA | CAATCCACTGCCTTGATCCA |
AGCTGCTGTTGAAGTTCCAT |
320–356 | 1.000 | 85.9 |
| trnH-GUG-psbA_p3 | trnH-GUG-psbA | AATCCACTGCCTTGATCCAC |
AGCTGCTGTTGAAGTTCCAT |
319–355 | 1.000 | 85.9 |
| trnH-GUG-psbA_p4 | trnH-GUG-psbA | ACAATCCACTGCCTTGATCC |
AGCTGCTGTTGAAGTTCCAT |
321–357 | 1.000 | 85.8 |
| trnH-GUG-psbA_p5 | trnH-GUG-psbA | GATCCACTTGGCTACATCCG |
GCTGCTGTTGAAGTTCCATC |
305–341 | 1.000 | 83.6 |
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
GAGGTTCGAATCCTTCCGTC |
875–925 | 1.000 | 86.0 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | TCATGTCCTTCAAGTCGCAC |
GAGGTTCGAATCCTTCCGTC |
886–936 | 1.000 | 85.4 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | CCACAGCTGATCATGTCCTT |
GAGGTTCGAATCCTTCCGTC |
896–946 | 1.000 | 83.7 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
GTGTCGACTAGAAATGGGGC |
937–987 | 1.000 | 83.6 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | TCCACAGCTGATCATGTCCT |
GAGGTTCGAATCCTTCCGTC |
897–947 | 1.000 | 83.6 |
| trnR-UCU-atpA_p1 | trnR-UCU-atpA | TGGAATGAAAAGCGTCCATTG |
ACGTTTTCTACTTCAGGAACA |
510–649 | 1.000 | 48.5 |
| trnR-UCU-atpA_p2 | trnR-UCU-atpA | GGAATGAAAAGCGTCCATTGT |
ACGTTTTCTACTTCAGGAACA |
509–648 | 1.000 | 48.5 |
| trnR-UCU-atpA_p3 | trnR-UCU-atpA | GGAATGAAAAGCGTCCATTGT |
GAACGTTTTCTACTTCAGGAACA |
511–650 | 1.000 | 48.5 |
| trnR-UCU-atpA_p4 | trnR-UCU-atpA | TGGAATGAAAAGCGTCCATTG |
CGTTTTCTACTTCAGGAACAAGT |
509–648 | 1.000 | 48.5 |
| trnR-UCU-atpA_p5 | trnR-UCU-atpA | TGGAATGAAAAGCGTCCATTG |
GAACGTTTTCTACTTCAGGAACA |
512–651 | 1.000 | 48.4 |
| atpF-atpH_p1 | atpF-atpH | ATTAAACCCGAAACTCCCGG |
CGGAGGGAAAAATACGAGGT |
620–637 | 1.000 | 79.7 |
| atpF-atpH_p2 | atpF-atpH | ATTAAACCCGAAACTCCCGG |
GAGGCGGAGGGAAAAATACG |
624–641 | 1.000 | 79.5 |
| atpF-atpH_p3 | atpF-atpH | ATTAAACCCGAAACTCCCGG |
GCGGAGGGAAAAATACGAGG |
621–638 | 1.000 | 79.5 |
| atpF-atpH_p4 | atpF-atpH | ATTAAACCCGAAACTCCCGG |
GGCGGAGGGAAAAATACGAG |
622–639 | 1.000 | 79.5 |
| atpF-atpH_p5 | atpF-atpH | ATTAAACCCGAAACTCCCGG |
CAGAGGCGGAGGGAAAAATA |
626–643 | 1.000 | 79.4 |
| rpoB-trnC-GCA_p1 | rpoB-trnC-GCA | ATTGCTTCATTTCCACCCCC |
CCGGATTTGAACTGGGGAAA |
1146–1181 | 1.000 | 80.3 |
| rpoB-trnC-GCA_p2 | rpoB-trnC-GCA | CTCTGTTAAGCCCTGCTCAA |
CCGGATTTGAACTGGGGAAA |
1219–1254 | 1.000 | 79.6 |
| rpoB-trnC-GCA_p3 | rpoB-trnC-GCA | ATTGCTTCATTTCCACCCCC |
TCTTTTGGTGATCAGGCGAC |
1168–1203 | 1.000 | 79.4 |
| rpoB-trnC-GCA_p4 | rpoB-trnC-GCA | GTTCCTCTGTTAAGCCCTGC |
CCGGATTTGAACTGGGGAAA |
1223–1258 | 1.000 | 79.0 |
| rpoB-trnC-GCA_p5 | rpoB-trnC-GCA | CTCTGTTAAGCCCTGCTCAA |
TCTTTTGGTGATCAGGCGAC |
1241–1276 | 1.000 | 78.7 |
| petN-psbM_p1 | petN-psbM | TCTTGCTTGGGCTGCTTTAA |
GTGGAAAGGTGGTTCGATGA |
1111–1142 | 1.000 | 87.2 |
| petN-psbM_p2 | petN-psbM | TCTTGCTTGGGCTGCTTTAA |
AGTGGAAAGGTGGTTCGATG |
1112–1143 | 1.000 | 87.1 |
| petN-psbM_p3 | petN-psbM | TCTTGCTTGGGCTGCTTTAA |
GGTTGGGTGGGGTTTGTTTA |
1144–1175 | 1.000 | 86.8 |
| petN-psbM_p4 | petN-psbM | ATCTTGCTTGGGCTGCTTTA |
GTGGAAAGGTGGTTCGATGA |
1112–1143 | 1.000 | 85.5 |
| petN-psbM_p5 | petN-psbM | TAAATCTTGCTTGGGCTGCT |
GTGGAAAGGTGGTTCGATGA |
1115–1146 | 1.000 | 85.4 |
Result downloads
Reference species (32)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Spiraea alpina | OR601530.1 | 155950 | View on NCBI ↗ |
| Spiraea aquilegiifolia | NC_067996.1 | 155927 | View on NCBI ↗ |
| Spiraea cantoniensis | NC_085722.1 | 155925 | View on NCBI ↗ |
| Spiraea chamaedryfolia | PX591894.1 | 156149 | View on NCBI ↗ |
| Spiraea chinensis | NC_067997.1 | 155913 | View on NCBI ↗ |
| Spiraea dasyantha | NC_085725.1 | 156068 | View on NCBI ↗ |
| Spiraea elegans | NC_067998.1 | 155975 | View on NCBI ↗ |
| Spiraea fritschiana | NC_085726.1 | 156068 | View on NCBI ↗ |
| Spiraea henryi | NC_068000.1 | 155931 | View on NCBI ↗ |
| Spiraea hirsuta | NC_067999.1 | 155953 | View on NCBI ↗ |
| Spiraea hypericifolia | NC_085718.1 | 155992 | View on NCBI ↗ |
| Spiraea japonica | NC_068004.1 | 156167 | View on NCBI ↗ |
| Spiraea japonica var. glabra | OR513066.1 | 156187 | View on NCBI ↗ |
| Spiraea laeta | NC_085723.1 | 156033 | View on NCBI ↗ |
| Spiraea longigemmis | NC_085720.1 | 155977 | View on NCBI ↗ |
| Spiraea media | NC_084454.1 | 155916 | View on NCBI ↗ |
| Spiraea microgyna | PZ148117.1 | 156044 | View on NCBI ↗ |
| Spiraea mongolica | NC_051992.1 | 155949 | View on NCBI ↗ |
| Spiraea nipponica | NC_085728.1 | 155961 | View on NCBI ↗ |
| Spiraea ovalis | NC_085721.1 | 155994 | View on NCBI ↗ |
| Spiraea prunifolia | NC_085727.1 | 155948 | View on NCBI ↗ |
| Spiraea prunifolia var. simpliciflora | OR513072.1 | 155969 | View on NCBI ↗ |
| Spiraea pubescens | NC_084453.1 | 155942 | View on NCBI ↗ |
| Spiraea purpurea | NC_068003.1 | 156156 | View on NCBI ↗ |
| Spiraea salicifolia | NC_067995.1 | 155904 | View on NCBI ↗ |
| Spiraea thunbergii | NC_064734.1 | 155922 | View on NCBI ↗ |
| Spiraea tianschanica | NC_068001.1 | 155965 | View on NCBI ↗ |
| Spiraea tomentosa | NC_068002.1 | 155915 | View on NCBI ↗ |
| Spiraea trichocarpa | NC_085729.1 | 155907 | View on NCBI ↗ |
| Spiraea trilobata | MW822176.1 | 155981 | View on NCBI ↗ |
| Spiraea veitchii | NC_085719.1 | 156001 | View on NCBI ↗ |
| Spiraea x vanhouttei | NC_085724.1 | 155953 | View on NCBI ↗ |