| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnS-GCU-trnC-GCA | LSC | 781 | 0.0115 | 0.99 | 68.1 | yes | View details |
| ycf3-trnS-GGA | LSC | 921 | 0.0083 | 1.00 | 64.8 | yes | View details |
| rbcL | LSC | 1428 | 0.0037 | 1.00 | 47.9 | yes | View details |
| ndhF-rpl32 | SSC | 1050 | 0.0061 | 1.00 | 61.4 | yes | View details |
| rpl32-trnL-UAG | SSC | 864 | 0.0140 | 1.00 | 73.6 | yes | View details |
| rps15-trnN-GUU | SSC | 5985 | 0.0056 | 1.00 | 59.1 | yes | View details |
| psbE-petL | LSC | 1287 | 0.0066 | 1.00 | 70.4 | yes | View details |
| petA-psbJ | LSC | 821 | 0.0046 | 0.99 | 68.4 | yes | View details |
| psbI-trnS-GCU | LSC | 136 | 0.0161 | 1.00 | 67.3 | yes | View details |
| trnT-UGU-trnF-GAA | LSC | 1436 | 0.0045 | 1.00 | 65.3 | yes | View details |
| rps16-trnQ-UUG | LSC | 949 | 0.0078 | 1.00 | 64.7 | yes | View details |
| ndhC-trnM-CAU | LSC | 1985 | 0.0040 | 1.00 | 64.5 | yes | View details |
| trnE-UUC-rpoB | LSC | 785 | 0.0049 | 1.00 | 61.6 | yes | View details |
| atpI-atpH | LSC | 1120 | 0.0038 | 1.00 | 60.3 | yes | View details |
| atpB-rbcL | LSC | 758 | 0.0023 | 1.00 | 59.1 | 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
24
Genome length
152–153 kb
Candidate markers
257
Primer pairs
80
Genome-wide nucleotide diversity
Candidate markers
6 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 257 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 |
|---|---|---|---|---|---|---|
| trnK-UUU_p1 | trnK-UUU | CCAAGCGCACGAATTTTCAA |
GGGTTCGTCGGATTAGCTTT |
2955–2976 | 1.000 | 81.0 |
| trnK-UUU_p2 | trnK-UUU | GCCCGTGTCAACCAATATCT |
GGGTTCGTCGGATTAGCTTT |
2888–2909 | 0.917 | 79.2 |
| trnK-UUU_p3 | trnK-UUU | TGCCCGTGTCAACCAATATC |
GGGTTCGTCGGATTAGCTTT |
2889–2910 | 0.917 | 77.4 |
| trnK-UUU_p4 | trnK-UUU | GCCCGTGTCAACCAATATCT |
CAAATGATGGGTTCGTCGGA |
2896–2917 | 0.875 | 75.3 |
| trnK-UUU_p5 | trnK-UUU | GCCCGTGTCAACCAATATCT |
TCAAATGATGGGTTCGTCGG |
2897–2918 | 0.875 | 75.3 |
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
GAGGTTCGAATCCTTCCGTC |
1021–1047 | 1.000 | 83.0 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | CGGATCGTGTCCTTCAAGTC |
GAGGTTCGAATCCTTCCGTC |
1036–1062 | 1.000 | 81.1 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | GGATCGTGTCCTTCAAGTCG |
GAGGTTCGAATCCTTCCGTC |
1035–1061 | 1.000 | 81.1 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | CCAAGAGCACCTTCATTCCT |
GAGGTTCGAATCCTTCCGTC |
1092–1118 | 1.000 | 79.9 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
TTCGGAGGTTCGAATCCTTC |
1025–1051 | 1.000 | 78.3 |
| psbI-trnS-GCU_p1 | psbI-trnS-GCU | CGTAATCCTGGACGTGAAGA |
ATTGGGAGAGATGGCTGAGT |
251–258 | 1.000 | 78.3 |
| psbI-trnS-GCU_p2 | psbI-trnS-GCU | CGTAATCCTGGACGTGAAGA |
CGAGTTATTCGTACCGAGGG |
199–206 | 1.000 | 77.7 |
| psbI-trnS-GCU_p3 | psbI-trnS-GCU | CGTAATCCTGGACGTGAAGAA |
ATTGGGAGAGATGGCTGAGT |
251–258 | 1.000 | 75.9 |
| psbI-trnS-GCU_p4 | psbI-trnS-GCU | CCTATCCAATGATCCAGGACG |
ATTGGGAGAGATGGCTGAGT |
270–277 | 1.000 | 74.7 |
| psbI-trnS-GCU_p5 | psbI-trnS-GCU | CGTAATCCTGGACGTGAAGA |
GATGGCTGAGTGGACGAAAG |
242–249 | 1.000 | 74.3 |
| trnS-GCU-trnC-GCA_p1 | trnS-GCU-trnC-GCA | ACGGAAAGAGAGGGATTCGA |
CCGGATTTGAACTGGGGAAA |
903–944 | 1.000 | 89.0 |
| trnS-GCU-trnC-GCA_p2 | trnS-GCU-trnC-GCA | ACGGAAAGAGAGGGATTCGA |
AAAAGGATTTGCAGTCCCCC |
885–926 | 1.000 | 87.0 |
| trnS-GCU-trnC-GCA_p3 | trnS-GCU-trnC-GCA | CTTTCGTCCACTCAGCCATC |
CCGGATTTGAACTGGGGAAA |
839–880 | 1.000 | 85.7 |
| trnS-GCU-trnC-GCA_p4 | trnS-GCU-trnC-GCA | AACGGAAAGAGAGGGATTCG |
CCGGATTTGAACTGGGGAAA |
904–945 | 1.000 | 84.9 |
| trnS-GCU-trnC-GCA_p5 | trnS-GCU-trnC-GCA | ACGGAAAGAGAGGGATTCGA |
ATTCGATTCGTGATGAGGCG |
937–956 | 0.375 | 51.7 |
| trnE-UUC-rpoB_p1 | trnE-UUC-rpoB | GCATGATTTACCCCCAGAGG |
CATTGCGTCTATCCCGGATT |
903–983 | 1.000 | 85.3 |
| trnE-UUC-rpoB_p2 | trnE-UUC-rpoB | GGCATGATTTACCCCCAGAG |
CATTGCGTCTATCCCGGATT |
904–984 | 1.000 | 85.3 |
| trnE-UUC-rpoB_p3 | trnE-UUC-rpoB | ACCCTCGTTATCTCCGTGAA |
CATTGCGTCTATCCCGGATT |
876–956 | 1.000 | 84.2 |
| trnE-UUC-rpoB_p4 | trnE-UUC-rpoB | GCATGATTTACCCCCAGAGG |
TGTGGACATTGCGTCTATCC |
909–989 | 1.000 | 84.1 |
| trnE-UUC-rpoB_p5 | trnE-UUC-rpoB | GGCATGATTTACCCCCAGAG |
TGTGGACATTGCGTCTATCC |
910–990 | 1.000 | 84.1 |
| atpI-atpH_p1 | atpI-atpH | TCCCTGTCATGTTCCTTGGA |
GGCAGAAACCAGTGGATTCA |
1232–1302 | 1.000 | 81.6 |
| atpI-atpH_p2 | atpI-atpH | TCCCTGTCATGTTCCTTGGA |
TACCTTGACCAACTCCAGGT |
1299–1369 | 1.000 | 81.3 |
| atpI-atpH_p3 | atpI-atpH | TCCCTGTCATGTTCCTTGGA |
AGCCAATCCAGCAGCAATAA |
1259–1329 | 1.000 | 81.1 |
| atpI-atpH_p4 | atpI-atpH | TCCCTGTCATGTTCCTTGGA |
AATAACGGAAGCGGCAGAAA |
1244–1314 | 1.000 | 80.8 |
| atpI-atpH_p5 | atpI-atpH | TCCCTGTCATGTTCCTTGGA |
GCAGTACCTTGACCAACTCC |
1303–1373 | 0.958 | 78.9 |
Result downloads
Reference species (24)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Saussurea bogedaensis | NC_083144.1 | 152513 | View on NCBI ↗ |
| Saussurea chabyoungsanica | NC_036677.1 | 152446 | View on NCBI ↗ |
| Saussurea delavayi | NC_044733.1 | 152254 | View on NCBI ↗ |
| Saussurea dorogostaiskii | NC_083143.1 | 152624 | View on NCBI ↗ |
| Saussurea durgae | NC_044735.1 | 152506 | View on NCBI ↗ |
| Saussurea hookeri | NC_044739.1 | 152461 | View on NCBI ↗ |
| Saussurea japonica | NC_044738.1 | 152612 | View on NCBI ↗ |
| Saussurea katochaete | NC_072928.1 | 152586 | View on NCBI ↗ |
| Saussurea kingii | NC_044736.1 | 152444 | View on NCBI ↗ |
| Saussurea leontodontoides | NC_044734.1 | 152387 | View on NCBI ↗ |
| Saussurea lhozhagensis | NC_044729.1 | 152527 | View on NCBI ↗ |
| Saussurea obvallata | NC_044726.1 | 152540 | View on NCBI ↗ |
| Saussurea oligocephala | NC_067031.1 | 152567 | View on NCBI ↗ |
| Saussurea orgaadayi | NC_083146.1 | 152594 | View on NCBI ↗ |
| Saussurea polylepis | NC_036490.1 | 152488 | View on NCBI ↗ |
| Saussurea przewalskii | NC_044732.1 | 152658 | View on NCBI ↗ |
| Saussurea pseudoleucoma | NC_044728.1 | 152412 | View on NCBI ↗ |
| Saussurea pubifolia | NC_044727.1 | 152622 | View on NCBI ↗ |
| Saussurea salicifolia | NC_057621.1 | 152584 | View on NCBI ↗ |
| Saussurea salwinensis | NC_044731.1 | 152382 | View on NCBI ↗ |
| Saussurea stella | NC_072930.1 | 152442 | View on NCBI ↗ |
| Saussurea talungensis | NC_058276.1 | 152355 | View on NCBI ↗ |
| Saussurea tsoongii | NC_044737.1 | 152501 | View on NCBI ↗ |
| Saussurea wettsteiniana | NC_057001.1 | 152631 | View on NCBI ↗ |