| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| rpl23 | LSC | 279 | 0.0050 | 1.00 | 26.5 | yes | View details |
| petA-psbJ | LSC | 693 | 0.0056 | 1.00 | 50.3 | yes | View details |
| petL-petG | LSC | 176 | 0.0052 | 1.00 | 33.6 | yes | View details |
| rpl16 | LSC | 1459 | 0.0037 | 1.00 | 33.5 | yes | View details |
| rpl23 | IRb | 282 | 0.0003 | 1.00 | 23.5 | no | View details |
| ndhF-rpl32 | SSC | 848 | 0.0056 | 1.00 | 42.5 | yes | View details |
| rpl32-trnL-UAG | SSC | 631 | 0.0106 | 1.00 | 44.2 | yes | View details |
| ccsA | SSC | 960 | 0.0025 | 1.00 | 29.8 | yes | View details |
| rpl23 | IRa | 282 | 0.0003 | 1.00 | 23.5 | no | View details |
| trnG-UCC-trnI | LSC | 682 | 0.0043 | 1.00 | 53.1 | yes | View details |
| trnD-GUC-psbM | LSC | 700 | 0.0043 | 1.00 | 50.1 | yes | View details |
| rps16-trnQ-UUG | LSC | 790 | 0.0042 | 1.00 | 49.3 | yes | View details |
| psaA-ycf3 | LSC | 643 | 0.0037 | 1.00 | 48.2 | yes | View details |
| trnT-UGU-trnL-UAA | LSC | 814 | 0.0038 | 1.00 | 47.9 | yes | View details |
| psbE-petL | LSC | 1272 | 0.0023 | 1.00 | 47.5 | yes | View details |
| rps12a-trnT-GGU | LSC | 378 | 0.0046 | 1.00 | 46.5 | yes | View details |
| trnR-UCU-trnfM | LSC | 114 | 0.0121 | 1.00 | 46.4 | yes | View details |
| psbK-psbI | LSC | 408 | 0.0056 | 1.00 | 46.3 | yes | View details |
| trnY-GUA-trnD-GUC | LSC | 315 | 0.0053 | 1.00 | 44.8 | 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
27
Genome length
135–136 kb
Candidate markers
277
Primer pairs
85
Genome-wide nucleotide diversity
Candidate markers
9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 277 candidates).
Primer pairs
Showing the top 30 of 85 primer pairs (ranked by primer score).
| Primer ID | Label | Forward | Reverse | Amplicon (bp) | Cross-species rate | Score |
|---|---|---|---|---|---|---|
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
GAGGTTCGAATCCTTCCGTC |
852–890 | 1.000 | 81.2 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | TCATGTCCTTCAAGTCGCAC |
GAGGTTCGAATCCTTCCGTC |
863–901 | 1.000 | 80.6 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
AGTGTCGCATAAAACCCGAA |
921–959 | 1.000 | 80.2 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
CTCGGAGGTTCGAATCCTTC |
856–894 | 1.000 | 80.1 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | TCATGTCCTTCAAGTCGCAC |
AGTGTCGCATAAAACCCGAA |
932–970 | 1.000 | 79.7 |
| psbK-psbI_p1 | psbK-psbI | GTTTGGCAAGCTGCTGTAAG |
GATTCCGTCCTGGGTCATTG |
521–533 | 1.000 | 80.4 |
| psbK-psbI_p2 | psbK-psbI | CGTGGATGTTATGCCTGTCA |
GATTCCGTCCTGGGTCATTG |
570–582 | 1.000 | 80.3 |
| psbK-psbI_p3 | psbK-psbI | CGTGGATGTTATGCCTGTCA |
GAATTTTTACTCCTCGCGCC |
593–605 | 1.000 | 79.2 |
| psbK-psbI_p4 | psbK-psbI | CGTGGATGTTATGCCTGTCA |
GGAATTTTTACTCCTCGCGC |
594–606 | 1.000 | 79.2 |
| psbK-psbI_p5 | psbK-psbI | GTTTGGCAAGCTGCTGTAAG |
GAATTTTTACTCCTCGCGCC |
544–556 | 1.000 | 79.2 |
| trnG-UCC-trnI_p1 | trnG-UCC-trnI | ACGAATCACACTTTTACCACT |
GCGGATTCTGGAACCCTAAG |
832–840 | 0.926 | 51.0 |
| trnG-UCC-trnI_p2 | trnG-UCC-trnI | AGAACGAATCACACTTTTACCAC |
GCGGATTCTGGAACCCTAAG |
835–843 | 0.926 | 49.9 |
| trnG-UCC-trnI_p3 | trnG-UCC-trnI | GAACGAATCACACTTTTACCACT |
GCGGATTCTGGAACCCTAAG |
834–842 | 0.926 | 49.9 |
| trnG-UCC-trnI_p4 | trnG-UCC-trnI | AACGAATCACACTTTTACCACT |
GCGGATTCTGGAACCCTAAG |
833–841 | 0.926 | 49.1 |
| trnG-UCC-trnI_p5 | trnG-UCC-trnI | TACCACTAAACTATACCCGC |
GCGGATTCTGGAACCCTAAG |
818–826 | 0.926 | 47.2 |
| rps12a-trnT-GGU_p1 | rps12a-trnT-GGU | ACCAAATGTTCCTTCCACGA |
CGTCTTAGCACGGCATTACT |
543 | 0.926 | 72.5 |
| rps12a-trnT-GGU_p2 | rps12a-trnT-GGU | ACCAAATGTTCCTTCCACGA |
CTTACGTCTTAGCACGGCAT |
547 | 0.926 | 72.5 |
| rps12a-trnT-GGU_p3 | rps12a-trnT-GGU | ACCAAATGTTCCTTCCACGA |
ACGTCTTAGCACGGCATTAC |
544 | 0.926 | 70.3 |
| rps12a-trnT-GGU_p4 | rps12a-trnT-GGU | ACCAAATGTTCCTTCCACGA |
TTACGTCTTAGCACGGCATT |
546 | 0.926 | 70.2 |
| rps12a-trnT-GGU_p5 | rps12a-trnT-GGU | ACCAAATGTTCCTTCCACGAA |
CGTCTTAGCACGGCATTACT |
543 | 0.926 | 69.3 |
| trnY-GUA-trnD-GUC_p1 | trnY-GUA-trnD-GUC | AATTCTTCCTGGGTCGATGC |
CGGTGCTCTGACCAATTGAA |
434–439 | 1.000 | 78.7 |
| trnY-GUA-trnD-GUC_p2 | trnY-GUA-trnD-GUC | GGGGACGGACTGTAAATTCG |
CGGTGCTCTGACCAATTGAA |
401–406 | 1.000 | 76.5 |
| trnY-GUA-trnD-GUC_p3 | trnY-GUA-trnD-GUC | GGGACGGACTGTAAATTCGT |
CGGTGCTCTGACCAATTGAA |
400–405 | 1.000 | 76.3 |
| trnY-GUA-trnD-GUC_p4 | trnY-GUA-trnD-GUC | AATTCTTCCTGGGTCGATGC |
GGTGCTCTGACCAATTGAAC |
433–438 | 1.000 | 74.6 |
| trnY-GUA-trnD-GUC_p5 | trnY-GUA-trnD-GUC | TGGGGACGGACTGTAAATTC |
CGGTGCTCTGACCAATTGAA |
402–407 | 1.000 | 73.1 |
| trnD-GUC-psbM_p1 | trnD-GUC-psbM | TTCAATTGGTCAGAGCACCG |
AGAATGAACAGTGCAGTAGC |
611–827 | 1.000 | 63.9 |
| trnD-GUC-psbM_p2 | trnD-GUC-psbM | TTCAATTGGTCAGAGCACCG |
AGGAACTAGAATGAACAGTGCA |
618–834 | 1.000 | 60.8 |
| trnD-GUC-psbM_p3 | trnD-GUC-psbM | GTTCAATTGGTCAGAGCACC |
AGAATGAACAGTGCAGTAGC |
612–828 | 1.000 | 59.8 |
| trnD-GUC-psbM_p4 | trnD-GUC-psbM | CGCGGGGATTGTAGTTCAA |
AGAATGAACAGTGCAGTAGC |
625–841 | 1.000 | 58.6 |
| trnD-GUC-psbM_p5 | trnD-GUC-psbM | GGTATGCCATACATCCCGC |
AGAATGAACAGTGCAGTAGC |
641–857 | 1.000 | 58.5 |
Result downloads
Reference species (27)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Avena abyssinica | NC_044158.1 | 135942 | View on NCBI ↗ |
| Avena agadiriana | NC_044159.1 | 135945 | View on NCBI ↗ |
| Avena atlantica | NC_044163.1 | 136006 | View on NCBI ↗ |
| Avena barbata | NC_044173.1 | 135946 | View on NCBI ↗ |
| Avena brevis | NC_044172.1 | 135939 | View on NCBI ↗ |
| Avena canariensis | NC_044161.1 | 135955 | View on NCBI ↗ |
| Avena clauda | NC_044167.1 | 135557 | View on NCBI ↗ |
| Avena damascena | NC_044166.1 | 135925 | View on NCBI ↗ |
| Avena eriantha | NC_044157.1 | 135560 | View on NCBI ↗ |
| Avena fatua | NC_044170.1 | 135889 | View on NCBI ↗ |
| Avena hirtula | NC_050395.1 | 135937 | View on NCBI ↗ |
| Avena hispanica | NC_044164.1 | 135935 | View on NCBI ↗ |
| Avena hybrida | NC_044148.1 | 135900 | View on NCBI ↗ |
| Avena insularis | MG674209.1 | 135967 | View on NCBI ↗ |
| Avena longiglumis | OP805352.1 | 135378 | View on NCBI ↗ |
| Avena lusitanica | NC_044149.1 | 135879 | View on NCBI ↗ |
| Avena maroccana | NC_044162.1 | 135887 | View on NCBI ↗ |
| Avena murphyi | NC_044174.1 | 135892 | View on NCBI ↗ |
| Avena nuda | NC_044147.1 | 135934 | View on NCBI ↗ |
| Avena occidentalis | NC_044175.1 | 135893 | View on NCBI ↗ |
| Avena sativa | NC_027468.1 | 135890 | View on NCBI ↗ |
| Avena sterilis | NC_031650.1 | 135887 | View on NCBI ↗ |
| Avena sterilis subsp. ludoviciana | PP328777.1 | 135899 | View on NCBI ↗ |
| Avena strigosa | NC_044171.1 | 135938 | View on NCBI ↗ |
| Avena vaviloviana | NC_044168.1 | 135946 | View on NCBI ↗ |
| Avena ventricosa | NC_044165.1 | 135681 | View on NCBI ↗ |
| Avena wiestii | NC_044160.1 | 135944 | View on NCBI ↗ |