| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| psbA | Genome | 1062 | 0.0006 | 1.00 | 39.4 | yes | View details |
| trnS-GCU-psbD | Genome | 1061 | 0.0020 | 1.00 | 40.1 | yes | View details |
| trnL-UAA-trnF-GAA | Genome | 360 | 0.0024 | 1.00 | 35.3 | yes | View details |
| rbcL-psaI | Genome | 1364 | 0.0019 | 1.00 | 46.7 | yes | View details |
| petA-psbJ | Genome | 828 | 0.0015 | 1.00 | 36.8 | yes | View details |
| ndhF-rpl32 | Genome | 914 | 0.0020 | 1.00 | 39.8 | yes | View details |
| ndhH-psbA | Genome | 74 | 0.0324 | 1.00 | 56.9 | no | View details |
| rps16 | Genome | 1062 | 0.0011 | 0.98 | 51.1 | yes | View details |
| atpF | Genome | 1383 | 0.0006 | 1.00 | 48.6 | yes | View details |
| rpl16-rps3 | Genome | 1180 | 0.0010 | 1.00 | 48.3 | yes | View details |
| matK-trnK-UUU | Genome | 685 | 0.0009 | 0.99 | 47.6 | yes | View details |
| ndhA | Genome | 2118 | 0.0011 | 1.00 | 47.5 | yes | View details |
| rps18-rps12 | Genome | 1205 | 0.0013 | 1.00 | 46.3 | yes | View details |
| matK | Genome | 1539 | 0.0002 | 1.00 | 46.0 | yes | View details |
| trnfM-CAU-trnT-GGU | Genome | 1974 | 0.0007 | 1.00 | 44.9 | 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
7
Genome length
115–137 kb
Candidate markers
229
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 229 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_p1 | psbA | TGGGTATTTCTGTCTTCAAAA |
AATACGTGTGCTTGGGAGTC |
1158 | 1.000 | 44.1 |
| psbA_p2 | psbA | TTGGGTATTTCTGTCTTCAAA |
AATACGTGTGCTTGGGAGTC |
1159 | 1.000 | 44.1 |
| psbA_p3 | psbA | TGGGTATTTCTGTCTTCAAAAA |
AATACGTGTGCTTGGGAGTC |
1158 | 1.000 | 44.1 |
| psbA_p4 | psbA | TTGGGTATTTCTGTCTTCAAAA |
AATACGTGTGCTTGGGAGTC |
1159 | 1.000 | 44.1 |
| psbA_p5 | psbA | ATTGGGTATTTCTGTCTTCAA |
AATACGTGTGCTTGGGAGTC |
1160 | 1.000 | 44.1 |
| trnK-UUU_p1 | trnK-UUU | CAACCAAGTCAGCCCAAAGA |
AATGTTTTGACAGAAGCGCG |
2750–2756 | 1.000 | 81.3 |
| trnK-UUU_p2 | trnK-UUU | TCAACCAAGTCAGCCCAAAG |
AATGTTTTGACAGAAGCGCG |
2751–2757 | 1.000 | 81.3 |
| trnK-UUU_p3 | trnK-UUU | AATGTCAACCAAGTCAGCCC |
AATGTTTTGACAGAAGCGCG |
2755–2761 | 1.000 | 80.7 |
| trnK-UUU_p4 | trnK-UUU | GTCAACCAAGTCAGCCCAAA |
AATGTTTTGACAGAAGCGCG |
2752–2758 | 1.000 | 79.0 |
| trnK-UUU_p5 | trnK-UUU | ACCAAGTCAGCCCAAAGATT |
AATGTTTTGACAGAAGCGCG |
2748–2754 | 1.000 | 78.3 |
| matK_p1 | matK | TCAACCCTTTCTTGTTTCTT |
CAACACCCTGTTCTGACCAT |
1663 | 1.000 | 44.0 |
| matK_p2 | matK | TCAACCCTTTCTTGTTTCTT |
AATGCAACACCCTGTTCTGA |
1667 | 1.000 | 44.0 |
| matK_p3 | matK | TCAACCCTTTCTTGTTTCTT |
ATGCAACACCCTGTTCTGAC |
1666 | 1.000 | 44.0 |
| matK_p4 | matK | ACCCTTTCTTGTTTCTTAATTTCGT |
CAACACCCTGTTCTGACCAT |
1660 | 1.000 | 44.0 |
| matK_p5 | matK | ACCCTTTCTTGTTTCTTAATTTCGT |
AATGCAACACCCTGTTCTGA |
1664 | 1.000 | 44.0 |
| matK-trnK-UUU_p1 | matK-trnK-UUU | CCATAATCGTGGGCAAATGC |
AATGTTTTGACAGAAGCGCG |
898–904 | 1.000 | 82.7 |
| matK-trnK-UUU_p2 | matK-trnK-UUU | CATAATCGTGGGCAAATGCA |
AATGTTTTGACAGAAGCGCG |
897–903 | 1.000 | 76.9 |
| matK-trnK-UUU_p3 | matK-trnK-UUU | CCATAATCGTGGGCAAATGC |
TGGGTTGCTAACTCAATGGT |
822–828 | 1.000 | 75.2 |
| matK-trnK-UUU_p4 | matK-trnK-UUU | CCATAATCGTGGGCAAATGC |
TCAATGTTTTGACAGAAGCGC |
900–906 | 1.000 | 75.0 |
| matK-trnK-UUU_p5 | matK-trnK-UUU | CCATAATCGTGGGCAAATGC |
TCTGGGTTGCTAACTCAATGG |
824–830 | 1.000 | 74.4 |
| rps16_p1 | rps16 | AGAAAGAGGTAAATTGTGTCT |
ACCACTTTGCAATGAAAAGAGG |
1169–1185 | 0.857 | 35.5 |
| rps16_p2 | rps16 | AAGAAAGAGGTAAATTGTGTCT |
ACCACTTTGCAATGAAAAGAGG |
1170–1186 | 0.857 | 35.5 |
| rps16_p3 | rps16 | TCCAAATAGGATTAAGAAAGAGGT |
ACCACTTTGCAATGAAAAGAGG |
1183–1199 | 0.857 | 35.5 |
| rps16_p4 | rps16 | AGAAAGAGGTAAATTGTGTCT |
CCACTTTGCAATGAAAAGAGGA |
1168–1184 | 0.857 | 35.5 |
| rps16_p5 | rps16 | AAGAAAGAGGTAAATTGTGTCT |
CCACTTTGCAATGAAAAGAGGA |
1169–1185 | 0.857 | 35.5 |
| trnS-GCU-psbD_p1 | trnS-GCU-psbD | ATTAGCAATCCGCCGCTTTA |
GAGCAATAGGCCAGACCATC |
1215–1218 | 1.000 | 79.2 |
| trnS-GCU-psbD_p2 | trnS-GCU-psbD | ATTAGCAATCCGCCGCTTTA |
ACAAAAACGAAACGGTCCCT |
1193–1196 | 1.000 | 78.1 |
| trnS-GCU-psbD_p3 | trnS-GCU-psbD | GAGCGGAAAGAGAGGGATTC |
GAGCAATAGGCCAGACCATC |
1266–1269 | 1.000 | 77.6 |
| trnS-GCU-psbD_p4 | trnS-GCU-psbD | ATTAGCAATCCGCCGCTTTA |
CCCTTCGTAACCAGTCATCC |
1177–1180 | 1.000 | 77.6 |
| trnS-GCU-psbD_p5 | trnS-GCU-psbD | ATTAGCAATCCGCCGCTTTA |
AGGCCAGACCATCCTACAAA |
1208–1211 | 1.000 | 77.4 |
Result downloads
Reference species (7)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Secale cereale | NC_021761.1 | 114843 | View on NCBI ↗ |
| Secale cereale subsp. segetale | OL688773.1 | 137042 | View on NCBI ↗ |
| Secale cereale subsp. vavilovii | OQ700975.1 | 137055 | View on NCBI ↗ |
| Secale strictum subsp. africanum | OQ700974.1 | 137068 | View on NCBI ↗ |
| Secale strictum subsp. anatolicum | OQ700976.1 | 137051 | View on NCBI ↗ |
| Secale strictum subsp. kuprijanovii | LC645210.1 | 137079 | View on NCBI ↗ |
| Secale strictum subsp. strictum | OL979486.1 | 137063 | View on NCBI ↗ |