| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| rps16-trnQ-UUG | LSC | 1012 | 0.0270 | 0.99 | 77.3 | yes | View details |
| trnG-UCC-trnT-GGU | LSC | 738 | 0.0338 | 0.99 | 77.5 | yes | View details |
| trnT-GGU-trnE-UUC | LSC | 515 | 0.0314 | 0.97 | 69.0 | yes | View details |
| trnD-GUC-psbM | LSC | 969 | 0.0240 | 0.99 | 64.6 | yes | View details |
| psbM-petN | LSC | 816 | 0.0226 | 0.97 | 69.8 | yes | View details |
| petN-trnC-GCA | LSC | 880 | 0.0266 | 0.97 | 72.2 | yes | View details |
| atpI-atpH | LSC | 820 | 0.0350 | 0.95 | 65.7 | yes | View details |
| trnT-UGU-trnL-UAA | LSC | 765 | 0.0280 | 1.00 | 78.3 | yes | View details |
| petA-psbJ | LSC | 780 | 0.0270 | 0.95 | 76.5 | yes | View details |
| rpl16 | LSC | 1474 | 0.0194 | 1.00 | 63.9 | yes | View details |
| ndhF-rpl32 | SSC | 986 | 0.0320 | 0.93 | 71.7 | yes | View details |
| rpl32-trnL-UAG | SSC | 339 | 0.0492 | 1.00 | 73.1 | yes | View details |
| trnC-GCA-rpoB | LSC | 1009 | 0.0225 | 1.00 | 72.6 | yes | View details |
| trnG-GCC-trnfM-CAU | LSC | 343 | 0.0315 | 0.99 | 72.1 | yes | View details |
| ycf3-trnS-GGA | LSC | 571 | 0.0213 | 0.99 | 71.2 | yes | View details |
| psbE-petL | LSC | 774 | 0.0195 | 0.98 | 70.0 | yes | View details |
| ccsA-ndhD | SSC | 193 | 0.0494 | 1.00 | 69.7 | yes | View details |
| psaA-ycf3 | LSC | 641 | 0.0211 | 0.99 | 68.2 | yes | View details |
| atpB-rbcL | LSC | 799 | 0.0165 | 0.94 | 67.9 | yes | View details |
| ndhC-trnV-UAC | LSC | 931 | 0.0228 | 0.99 | 67.3 | yes | View details |
| psaC-ndhE | SSC | 515 | 0.0225 | 0.96 | 67.1 | 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
19
Genome length
134–135 kb
Candidate markers
272
Primer pairs
105
Genome-wide nucleotide diversity
Candidate markers
12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 272 candidates).
Primer pairs
Showing the top 30 of 105 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 |
1021–1141 | 1.000 | 90.3 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | TCATGTCCTTCAAGTCGCAC |
GAGGTTCGAATCCTTCCGTC |
1032–1152 | 1.000 | 89.8 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
TTCGGAGGTTCGAATCCTTC |
1025–1145 | 1.000 | 85.5 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | ATCATGTCCTTCAAGTCGCA |
GAGGTTCGAATCCTTCCGTC |
1033–1153 | 1.000 | 85.2 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | CGTTGCTTTCTACCACATCG |
GAGGTTCGAATCCTTCCGTC |
1013–1133 | 1.000 | 85.1 |
| trnG-GCC-trnfM-CAU_p1 | trnG-GCC-trnfM-CAU | GCGAGCGTAGTTCAATGGTA |
AGTTTTTGGCCCTACAGAGC |
493–518 | 1.000 | 90.6 |
| trnG-GCC-trnfM-CAU_p2 | trnG-GCC-trnfM-CAU | TAGCGAGCGTAGTTCAATGG |
AGTTTTTGGCCCTACAGAGC |
495–520 | 1.000 | 89.7 |
| trnG-GCC-trnfM-CAU_p3 | trnG-GCC-trnfM-CAU | GCGAGCGTAGTTCAATGGTA |
CGAGGCTCATAACCTTGAGG |
449–474 | 1.000 | 89.5 |
| trnG-GCC-trnfM-CAU_p4 | trnG-GCC-trnfM-CAU | GCGAGCGTAGTTCAATGGTA |
CAGTTTGGTAGCTCACGAGG |
464–489 | 1.000 | 89.1 |
| trnG-GCC-trnfM-CAU_p5 | trnG-GCC-trnfM-CAU | GCGAGCGTAGTTCAATGGTA |
CCAGTTTTTGGCCCTACAGA |
495–520 | 1.000 | 89.0 |
| trnG-UCC-trnT-GGU_p1 | trnG-UCC-trnT-GGU | ACGAATCACACTTTTACCACT |
TGAACCGATGACTTATGCCT |
828–939 | 1.000 | 52.7 |
| trnG-UCC-trnT-GGU_p2 | trnG-UCC-trnT-GGU | ACGAATCACACTTTTACCACT |
CCGATGACTTATGCCTTACCA |
824–935 | 1.000 | 52.0 |
| trnG-UCC-trnT-GGU_p3 | trnG-UCC-trnT-GGU | ACGAATCACACTTTTACCACT |
ACCGATGACTTATGCCTTACC |
825–936 | 1.000 | 52.0 |
| trnG-UCC-trnT-GGU_p4 | trnG-UCC-trnT-GGU | AGAACGAATCACACTTTTACCAC |
TGAACCGATGACTTATGCCT |
831–942 | 1.000 | 52.0 |
| trnG-UCC-trnT-GGU_p5 | trnG-UCC-trnT-GGU | GAACGAATCACACTTTTACCACT |
TGAACCGATGACTTATGCCT |
830–941 | 1.000 | 52.0 |
| trnT-GGU-trnE-UUC_p1 | trnT-GGU-trnE-UUC | ATCGCGGGCCTTTACTTTAG |
GCATCGACCCAGGAAGAATT |
1343–1413 | 1.000 | 91.2 |
| trnT-GGU-trnE-UUC_p2 | trnT-GGU-trnE-UUC | ATCGCGGGCCTTTACTTTAG |
TTGAACTACAATCCCTGCGG |
1781–1848 | 1.000 | 90.7 |
| trnT-GGU-trnE-UUC_p3 | trnT-GGU-trnE-UUC | GAACATTCTGAGCACGGGAA |
GCATCGACCCAGGAAGAATT |
888–954 | 0.579 | 70.4 |
| trnT-GGU-trnE-UUC_p4 | trnT-GGU-trnE-UUC | ATCGCGGGCCTTTACTTTAG |
TGATATTGCCTTCTGCCCAC |
1960–1974 | 0.263 | 52.4 |
| trnT-GGU-trnE-UUC_p5 | trnT-GGU-trnE-UUC | GAACATTCTGAGCACGGGAA |
TGATATTGCCTTCTGCCCAC |
1506–1520 | 0.263 | 51.8 |
| trnD-GUC-psbM_p1 | trnD-GUC-psbM | TCAATTGGTTAGAGCACCGC |
TGCGAGAATATTTACTTCCA |
826–1077 | 1.000 | 52.0 |
| trnD-GUC-psbM_p2 | trnD-GUC-psbM | TAGGTATGCCATACACCCCG |
TGCGAGAATATTTACTTCCA |
859–1110 | 1.000 | 52.0 |
| trnD-GUC-psbM_p3 | trnD-GUC-psbM | TCAATTGGTTAGAGCACCGC |
ATGCGAGAATATTTACTTCCA |
827–1078 | 1.000 | 52.0 |
| trnD-GUC-psbM_p4 | trnD-GUC-psbM | TCAATTGGTTAGAGCACCGC |
TGCGAGAATATTTACTTCCAT |
826–1077 | 1.000 | 52.0 |
| trnD-GUC-psbM_p5 | trnD-GUC-psbM | TAGGTATGCCATACACCCCG |
TGCGAGAATATTTACTTCCAT |
859–1110 | 1.000 | 52.0 |
| psbM-petN_p1 | psbM-petN | AAAACTGCCAGCCAAAATGA |
AGTATGGGGGAGAAGTGGAC |
814–899 | 1.000 | 79.9 |
| psbM-petN_p2 | psbM-petN | AAAACTGCCAGCCAAAATGA |
GTATGGGGGAGAAGTGGACT |
813–898 | 1.000 | 79.9 |
| psbM-petN_p3 | psbM-petN | AAAACTGCCAGCCAAAATGA |
TATGGGGGAGAAGTGGACTC |
812–897 | 1.000 | 79.4 |
| psbM-petN_p4 | psbM-petN | AAAACTGCCAGCCAAAATGA |
TAGTAAGTCTCGCTTGGGCT |
872–957 | 1.000 | 79.2 |
| psbM-petN_p5 | psbM-petN | AAAACTGCCAGCCAAAATGA |
GGGGGAGAAGTGGACTCTAG |
809–894 | 1.000 | 79.1 |
Result downloads
Reference species (19)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Eragrostis atrovirens | NC_059727.1 | 134857 | View on NCBI ↗ |
| Eragrostis autumnalis | NC_059728.1 | 134556 | View on NCBI ↗ |
| Eragrostis brownii | NC_059729.1 | 134728 | View on NCBI ↗ |
| Eragrostis cilianensis | NC_059730.1 | 134654 | View on NCBI ↗ |
| Eragrostis cylindrica | NC_059731.1 | 133777 | View on NCBI ↗ |
| Eragrostis ferruginea | NC_059732.1 | 134380 | View on NCBI ↗ |
| Eragrostis fractus | NC_059733.1 | 134578 | View on NCBI ↗ |
| Eragrostis harpachnoides | NC_059742.1 | 133830 | View on NCBI ↗ |
| Eragrostis japonica | NC_059734.1 | 134126 | View on NCBI ↗ |
| Eragrostis minor | NC_029412.1 | 135023 | View on NCBI ↗ |
| Eragrostis nevinii | NC_059735.1 | 133776 | View on NCBI ↗ |
| Eragrostis nigra | NC_059736.1 | 134861 | View on NCBI ↗ |
| Eragrostis perennans | NC_059737.1 | 134663 | View on NCBI ↗ |
| Eragrostis pilosa | NC_059738.1 | 134737 | View on NCBI ↗ |
| Eragrostis rufinerva | NC_059739.1 | 134685 | View on NCBI ↗ |
| Eragrostis setifolia | NC_042832.1 | 134928 | View on NCBI ↗ |
| Eragrostis tef | NC_029413.1 | 134435 | View on NCBI ↗ |
| Eragrostis tenella | NC_059740.1 | 134550 | View on NCBI ↗ |
| Eragrostis unioloides | NC_059741.1 | 134711 | View on NCBI ↗ |