| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnG-GCC-psbZ | Genome | 902 | 0.0715 | 0.87 | 83.2 | yes | View details |
| trnQ-UUG-accD | Genome | 386 | 0.0697 | 0.98 | 79.2 | yes | View details |
| accD | Genome | 1170 | 0.0393 | 0.91 | 74.2 | yes | View details |
| clpP | Genome | 630 | 0.1048 | 0.89 | 80.7 | yes | View details |
| trnI-CAU-ycf2 | Genome | 2087 | 0.0531 | 0.90 | 83.7 | yes | View details |
| trnN-GUU-ycf1 | Genome | 658 | 0.0916 | 0.73 | 75.8 | yes | View details |
| trnY-GUA-trnD-GUC | Genome | 473 | 0.0370 | 0.99 | 82.8 | yes | View details |
| trnK-UUU-rbcL | Genome | 893 | 0.0265 | 0.99 | 80.2 | yes | View details |
| trnP-UGG-psaJ | Genome | 408 | 0.0340 | 0.94 | 79.3 | yes | View details |
| petN-trnC-GCA | Genome | 937 | 0.0257 | 0.94 | 77.0 | yes | View details |
| trnS-UGA-psbC | Genome | 205 | 0.0466 | 1.00 | 76.8 | yes | View details |
| psbA-trnK-UUU | Genome | 334 | 0.0424 | 0.95 | 76.2 | yes | View details |
| trnC-GCA-rpoB | Genome | 1199 | 0.0221 | 0.98 | 76.1 | yes | View details |
| rps12-trnV-GAC | Genome | 2114 | 0.0302 | 0.92 | 76.1 | yes | View details |
| trnG-UCC-trnS-GCU | Genome | 681 | 0.0301 | 1.00 | 75.1 | 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
25
Genome length
121–127 kb
Candidate markers
226
Primer pairs
75
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 226 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 |
|---|---|---|---|---|---|---|
| psbA-trnK-UUU_p1 | psbA-trnK-UUU | TCGCGTCTCTCTAAAATTGCA |
TGCAATGAAAAATGCACGCA |
434–534 | 1.000 | 82.5 |
| psbA-trnK-UUU_p2 | psbA-trnK-UUU | TCGCGTCTCTCTAAAATTGCA |
GCAATGAAAAATGCACGCAC |
433–533 | 1.000 | 81.9 |
| psbA-trnK-UUU_p3 | psbA-trnK-UUU | CGCGTCTCTCTAAAATTGCAG |
TGCAATGAAAAATGCACGCA |
433–533 | 1.000 | 80.5 |
| psbA-trnK-UUU_p4 | psbA-trnK-UUU | CGCGTCTCTCTAAAATTGCAG |
GCAATGAAAAATGCACGCAC |
432–532 | 1.000 | 79.9 |
| psbA-trnK-UUU_p5 | psbA-trnK-UUU | TCGCGTCTCTCTAAAATTGCA |
CAATGAAAAATGCACGCACG |
432–532 | 1.000 | 79.8 |
| trnK-UUU-rbcL_p1 | trnK-UUU-rbcL | TGGAGTCGCACTTAAAAGCC |
AGTCCTGAATTAGCTGCTGC |
1012–1198 | 1.000 | 87.9 |
| trnK-UUU-rbcL_p2 | trnK-UUU-rbcL | AACCCTACCGATGGTATGGA |
AGTCCTGAATTAGCTGCTGC |
1065–1251 | 1.000 | 87.9 |
| trnK-UUU-rbcL_p3 | trnK-UUU-rbcL | AGTCGTGGTCTTACAAACCC |
AGTCCTGAATTAGCTGCTGC |
1080–1266 | 1.000 | 87.4 |
| trnK-UUU-rbcL_p4 | trnK-UUU-rbcL | GTCGTGGTCTTACAAACCCT |
AGTCCTGAATTAGCTGCTGC |
1079–1265 | 1.000 | 87.4 |
| trnK-UUU-rbcL_p5 | trnK-UUU-rbcL | AGTCGCACTTAAAAGCCGAG |
AGTCCTGAATTAGCTGCTGC |
1009–1195 | 1.000 | 87.2 |
| trnG-GCC-psbZ_p1 | trnG-GCC-psbZ | CGGATAGCGGGAATCGAAC |
CTTCTCCTGATGGTTGGTCG |
531–1087 | 1.000 | 82.4 |
| trnG-GCC-psbZ_p2 | trnG-GCC-psbZ | GATAGCGGGAATCGAACCC |
CTTCTCCTGATGGTTGGTCG |
529–1085 | 1.000 | 82.2 |
| trnG-GCC-psbZ_p3 | trnG-GCC-psbZ | GGATAGCGGGAATCGAACC |
CTTCTCCTGATGGTTGGTCG |
530–1086 | 1.000 | 82.2 |
| trnG-GCC-psbZ_p4 | trnG-GCC-psbZ | CGGATAGCGGGAATCGAAC |
TTGCTTCTCCTGATGGTTGG |
534–1090 | 1.000 | 80.8 |
| trnG-GCC-psbZ_p5 | trnG-GCC-psbZ | CGGATAGCGGGAATCGAAC |
TCCTGATGGTTGGTCGAGTA |
527–1083 | 1.000 | 80.7 |
| trnS-UGA-psbC_p1 | trnS-UGA-psbC | GGTTCGAATCCCCCTCTCT |
ATTTATGGCACGCGGGAAG |
306–341 | 1.000 | 70.6 |
| trnS-UGA-psbC_p2 | trnS-UGA-psbC | TTCGAATCCCCCTCTCTCC |
ATTTATGGCACGCGGGAAG |
304–339 | 1.000 | 69.4 |
| trnS-UGA-psbC_p3 | trnS-UGA-psbC | GGTTCGAATCCCCCTCTCTC |
ATTTATGGCACGCGGGAAG |
306–341 | 1.000 | 69.3 |
| trnS-UGA-psbC_p4 | trnS-UGA-psbC | GTTCGAATCCCCCTCTCTCC |
ATTTATGGCACGCGGGAAG |
305–340 | 1.000 | 69.3 |
| trnS-UGA-psbC_p5 | trnS-UGA-psbC | TTCGAATCCCCCTCTCTCCT |
ATTTATGGCACGCGGGAAG |
304–339 | 1.000 | 68.3 |
| trnY-GUA-trnD-GUC_p1 | trnY-GUA-trnD-GUC | TGGCAATATGTCTACGCTGG |
CGGTGCTCTGACCAATTGAA |
499–580 | 1.000 | 86.3 |
| trnY-GUA-trnD-GUC_p2 | trnY-GUA-trnD-GUC | GGCAATATGTCTACGCTGGT |
CGGTGCTCTGACCAATTGAA |
498–579 | 1.000 | 86.3 |
| trnY-GUA-trnD-GUC_p3 | trnY-GUA-trnD-GUC | GGGGACGGACTGTAAATTCG |
CGGTGCTCTGACCAATTGAA |
520–601 | 1.000 | 85.4 |
| trnY-GUA-trnD-GUC_p4 | trnY-GUA-trnD-GUC | GGGACGGACTGTAAATTCGT |
CGGTGCTCTGACCAATTGAA |
519–600 | 1.000 | 85.2 |
| trnY-GUA-trnD-GUC_p5 | trnY-GUA-trnD-GUC | GATTCTTCCTGGGTCGATGC |
CGGTGCTCTGACCAATTGAA |
553–634 | 1.000 | 84.9 |
| petN-trnC-GCA_p1 | petN-trnC-GCA | TTAAAGCAGCCCAAGCAAGA |
TTTCCCCAGTTCAAATCCGG |
845–1063 | 1.000 | 91.3 |
| petN-trnC-GCA_p2 | petN-trnC-GCA | TTAAAGCAGCCCAAGCAAGA |
GGGGGACTGCAAATCCTTTT |
863–1081 | 1.000 | 89.1 |
| petN-trnC-GCA_p3 | petN-trnC-GCA | AGAGTCCACTTCTTCCCCAT |
TTTCCCCAGTTCAAATCCGG |
899–1117 | 1.000 | 88.5 |
| petN-trnC-GCA_p4 | petN-trnC-GCA | CAGCCCAAGCAAGACTTACT |
TTTCCCCAGTTCAAATCCGG |
908–1057 | 0.920 | 86.6 |
| petN-trnC-GCA_p5 | petN-trnC-GCA | CAGCCCAAGCAAGACTTACT |
GGGGGACTGCAAATCCTTTT |
926–1075 | 0.920 | 84.4 |
Result downloads
Reference species (25)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Hedysarum baldshuanicum | OQ736730.1 | 122603 | View on NCBI ↗ |
| Hedysarum bucharicum | OQ736741.1 | 122066 | View on NCBI ↗ |
| Hedysarum chaitocarpum | OQ736745.1 | 123126 | View on NCBI ↗ |
| Hedysarum cumuschtanicum | OQ736748.1 | 123005 | View on NCBI ↗ |
| Hedysarum daraut-kurganicum | OQ736735.1 | 121141 | View on NCBI ↗ |
| Hedysarum denticulatum | OQ736726.1 | 123522 | View on NCBI ↗ |
| Hedysarum drobovii | NC_087910.1 | 121176 | View on NCBI ↗ |
| Hedysarum flavescens | NC_087909.1 | 123126 | View on NCBI ↗ |
| Hedysarum gypsaceum | OQ736734.1 | 121614 | View on NCBI ↗ |
| Hedysarum hemithamnoides | OQ736729.1 | 122773 | View on NCBI ↗ |
| Hedysarum iomuticum | OQ736738.1 | 123032 | View on NCBI ↗ |
| Hedysarum jaxarticum | OQ736727.1 | 122365 | View on NCBI ↗ |
| Hedysarum lehmannianum | NC_087911.1 | 123586 | View on NCBI ↗ |
| Hedysarum mogianicum | OQ736736.1 | 122717 | View on NCBI ↗ |
| Hedysarum montanum | OQ736742.1 | 122963 | View on NCBI ↗ |
| Hedysarum nuratense | OQ736746.1 | 122682 | View on NCBI ↗ |
| Hedysarum olgae | OQ736744.1 | 122957 | View on NCBI ↗ |
| Hedysarum plumosum | OQ736749.1 | 121344 | View on NCBI ↗ |
| Hedysarum popovii | OQ736737.1 | 122450 | View on NCBI ↗ |
| Hedysarum pskemense | OQ736740.1 | 121428 | View on NCBI ↗ |
| Hedysarum sunhangii | OQ736733.1 | 120689 | View on NCBI ↗ |
| Hedysarum taipeicum | NC_046493.1 | 126699 | View on NCBI ↗ |
| Hedysarum talassicum | OQ736731.1 | 122800 | View on NCBI ↗ |
| Hedysarum taschkendicum | OQ736743.1 | 121220 | View on NCBI ↗ |
| Hedysarum turkestanicum | OQ736728.1 | 122367 | View on NCBI ↗ |