| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| rps16-trnQ-UUG | LSC | 1305 | 0.0169 | 0.98 | 67.8 | yes | View details |
| trnG-GCC-trnfM-CAU | LSC | 290 | 0.0326 | 0.92 | 65.3 | yes | View details |
| trnG-UCC-trnT-GGU | LSC | 1769 | 0.0194 | 0.99 | 72.4 | yes | View details |
| trnC-GCA-rpoB | LSC | 763 | 0.0163 | 0.98 | 72.0 | yes | View details |
| trnF-GAA-ndhJ | LSC | 591 | 0.0189 | 1.00 | 66.9 | yes | View details |
| petL-petG | LSC | 167 | 0.0298 | 1.00 | 54.0 | yes | View details |
| rpl16 | LSC | 1503 | 0.0116 | 0.99 | 63.8 | yes | View details |
| ndhF-rpl32 | SSC | 865 | 0.0166 | 0.99 | 76.4 | yes | View details |
| rpl32-trnL-UAG | SSC | 544 | 0.0293 | 0.97 | 71.9 | yes | View details |
| petA-psbJ | LSC | 911 | 0.0127 | 0.99 | 79.4 | yes | View details |
| psbM-petN | LSC | 614 | 0.0161 | 1.00 | 78.9 | yes | View details |
| rbcL-psaI | LSC | 928 | 0.0132 | 0.99 | 75.7 | yes | View details |
| trnT-UGU-trnL-UAA | LSC | 820 | 0.0137 | 0.96 | 73.8 | yes | View details |
| trnD-GUC-psbM | LSC | 677 | 0.0134 | 1.00 | 72.6 | yes | View details |
| ccsA-ndhD | SSC | 180 | 0.0388 | 1.00 | 68.9 | yes | View details |
| psaI-ycf4 | LSC | 382 | 0.0115 | 0.99 | 67.3 | yes | View details |
| trnS-GCU-psbD | LSC | 964 | 0.0084 | 0.98 | 65.9 | yes | View details |
| trnY-GUA-trnD-GUC | LSC | 349 | 0.0167 | 1.00 | 65.6 | yes | View details |
| ndhA | SSC | 2111 | 0.0060 | 1.00 | 65.1 | 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
38
Genome length
139–141 kb
Candidate markers
265
Primer pairs
95
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 265 candidates).
Primer pairs
Showing the top 30 of 95 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 |
931–1641 | 1.000 | 89.7 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | TCATGTCCTTCAAGTCGCAC |
GAGGTTCGAATCCTTCCGTC |
942–1652 | 1.000 | 89.2 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
CTCGGAGGTTCGAATCCTTC |
935–1645 | 1.000 | 88.6 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | TCATGTCCTTCAAGTCGCAC |
CTCGGAGGTTCGAATCCTTC |
946–1656 | 1.000 | 88.1 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
TACTCGGAGGTTCGAATCCT |
937–1647 | 1.000 | 86.8 |
| trnS-GCU-psbD_p1 | trnS-GCU-psbD | ATTAGCAATCCGCCGCTTTA |
ACTCTACCAACGGCTATAGTCA |
1005–1045 | 0.974 | 71.7 |
| trnS-GCU-psbD_p2 | trnS-GCU-psbD | GCTTTAGTCCACTCAGCCAT |
ACTCTACCAACGGCTATAGTCA |
991–1031 | 0.974 | 68.8 |
| trnS-GCU-psbD_p3 | trnS-GCU-psbD | AGTCCACTCAGCCATCTCTC |
ACTCTACCAACGGCTATAGTCA |
986–1026 | 0.974 | 68.0 |
| trnS-GCU-psbD_p4 | trnS-GCU-psbD | ATTAGCAATCCGCCGCTTTA |
CTCTACCAACGGCTATAGTCA |
1004–1044 | 0.974 | 67.5 |
| trnS-GCU-psbD_p5 | trnS-GCU-psbD | ATTAGCAATCCGCCGCTTTA |
ACTCTACCAACGGCTATAGTC |
1005–1045 | 0.974 | 67.5 |
| trnG-GCC-trnfM-CAU_p1 | trnG-GCC-trnfM-CAU | AGGAGAAGATACGGGTTCGA |
CGAGGCTCATAACCTTGAGG |
314–571 | 1.000 | 86.7 |
| trnG-GCC-trnfM-CAU_p2 | trnG-GCC-trnfM-CAU | GTAGCGAGCGTAGTTCAGTG |
CGAGGCTCATAACCTTGAGG |
353–610 | 1.000 | 86.4 |
| trnG-GCC-trnfM-CAU_p3 | trnG-GCC-trnfM-CAU | ATGTAGCGAGCGTAGTTCAG |
CGAGGCTCATAACCTTGAGG |
355–612 | 1.000 | 86.3 |
| trnG-GCC-trnfM-CAU_p4 | trnG-GCC-trnfM-CAU | AGGAGAAGATACGGGTTCGA |
CAGTTTGGTAGCTCACGAGG |
329–586 | 1.000 | 86.3 |
| trnG-GCC-trnfM-CAU_p5 | trnG-GCC-trnfM-CAU | GTAGCGAGCGTAGTTCAGTG |
CAGTTTGGTAGCTCACGAGG |
368–625 | 1.000 | 85.8 |
| trnG-UCC-trnT-GGU_p1 | trnG-UCC-trnT-GGU | ACGAATCACACTTTTACCACT |
TGAACCGATGACTTATGCCT |
1340–2101 | 1.000 | 52.7 |
| trnG-UCC-trnT-GGU_p2 | trnG-UCC-trnT-GGU | ACGAATCACACTTTTACCACT |
CCGATGACTTATGCCTTACCA |
1336–2097 | 1.000 | 52.0 |
| trnG-UCC-trnT-GGU_p3 | trnG-UCC-trnT-GGU | ACGAATCACACTTTTACCACT |
ACCGATGACTTATGCCTTACC |
1337–2098 | 1.000 | 52.0 |
| trnG-UCC-trnT-GGU_p4 | trnG-UCC-trnT-GGU | ACGAATCACACTTTTACCACT |
ACCACTAAGTGAAAAGCCCT |
1370–2131 | 0.895 | 48.7 |
| trnG-UCC-trnT-GGU_p5 | trnG-UCC-trnT-GGU | GAACGAATCACACTTTTACCACT |
ACCACTAAGTGAAAAGCCCT |
1372–2133 | 0.895 | 47.8 |
| trnY-GUA-trnD-GUC_p1 | trnY-GUA-trnD-GUC | AATTCTTCCTGGGTCGATGC |
CGGTGCTCTGACCAATTGAA |
396–504 | 1.000 | 87.6 |
| trnY-GUA-trnD-GUC_p2 | trnY-GUA-trnD-GUC | GGGGACGGACTGTAAATTCG |
CGGTGCTCTGACCAATTGAA |
363–471 | 1.000 | 85.4 |
| trnY-GUA-trnD-GUC_p3 | trnY-GUA-trnD-GUC | GGGACGGACTGTAAATTCGT |
CGGTGCTCTGACCAATTGAA |
362–470 | 1.000 | 85.2 |
| trnY-GUA-trnD-GUC_p4 | trnY-GUA-trnD-GUC | AATTCTTCCTGGGTCGATGC |
GGTGCTCTGACCAATTGAAC |
395–503 | 1.000 | 83.5 |
| trnY-GUA-trnD-GUC_p5 | trnY-GUA-trnD-GUC | TGGGGACGGACTGTAAATTC |
CGGTGCTCTGACCAATTGAA |
364–472 | 1.000 | 82.0 |
| trnD-GUC-psbM_p1 | trnD-GUC-psbM | AATAGGCATGCCATACACCC |
GGCAGTAGGAACTAGAATGAACA |
831–1246 | 1.000 | 63.2 |
| trnD-GUC-psbM_p2 | trnD-GUC-psbM | TTCAATTGGTCAGAGCACCG |
GGCAGTAGGAACTAGAATGAACA |
797–1212 | 1.000 | 61.8 |
| trnD-GUC-psbM_p3 | trnD-GUC-psbM | AATAGGCATGCCATACACCC |
AGGCAGTAGGAACTAGAATGAAC |
832–1247 | 1.000 | 61.1 |
| trnD-GUC-psbM_p4 | trnD-GUC-psbM | AATAGGCATGCCATACACCC |
AGGCAGTAGGAACTAGAATGA |
832–1247 | 1.000 | 59.9 |
| trnD-GUC-psbM_p5 | trnD-GUC-psbM | AATAGGCATGCCATACACCC |
TGCGAGAATATTGACTTCCA |
792–1207 | 1.000 | 59.8 |
Result downloads
Reference species (38)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Andropogon abyssinicus | NC_035030.1 | 138738 | View on NCBI ↗ |
| Andropogon amethystinus | NC_087653.1 | 139083 | View on NCBI ↗ |
| Andropogon andringitrensis | NC_087651.1 | 139089 | View on NCBI ↗ |
| Andropogon angustatus | NC_087652.1 | 138820 | View on NCBI ↗ |
| Andropogon appendiculatus | MH181173.1 | 140579 | View on NCBI ↗ |
| Andropogon ascinodis | NC_040129.1 | 138841 | View on NCBI ↗ |
| Andropogon brazzae | MH181212.1 | 139840 | View on NCBI ↗ |
| Andropogon burmanicus | NC_035038.1 | 140898 | View on NCBI ↗ |
| Andropogon canaliculatus | MH181224.1 | 138817 | View on NCBI ↗ |
| Andropogon chevalieri | NC_087654.1 | 139160 | View on NCBI ↗ |
| Andropogon chinensis | NC_035012.1 | 138817 | View on NCBI ↗ |
| Andropogon chrysostachyus | MH181181.1 | 139459 | View on NCBI ↗ |
| Andropogon crossotos | MH181194.1 | 139792 | View on NCBI ↗ |
| Andropogon distachyos | NC_035041.1 | 139098 | View on NCBI ↗ |
| Andropogon festuciformis | NC_087656.1 | 139673 | View on NCBI ↗ |
| Andropogon gayanus | NC_040127.1 | 138675 | View on NCBI ↗ |
| Andropogon gayanus var. bisquamulatus | OQ518181.1 | 138784 | View on NCBI ↗ |
| Andropogon gayanus var. polycladus | OQ518180.1 | 138653 | View on NCBI ↗ |
| Andropogon gerardi | NC_040111.1 | 139712 | View on NCBI ↗ |
| Andropogon greenwayi | NC_040128.1 | 138831 | View on NCBI ↗ |
| Andropogon heterantherus | MH181186.1 | 139205 | View on NCBI ↗ |
| Andropogon ingratus | MH181172.1 | 139764 | View on NCBI ↗ |
| Andropogon itremoensis | NC_087657.1 | 139784 | View on NCBI ↗ |
| Andropogon ivorensis | MH660710.1 | 139857 | View on NCBI ↗ |
| Andropogon kelleri | NC_087658.1 | 139540 | View on NCBI ↗ |
| Andropogon laxatus | MH181182.1 | 140838 | View on NCBI ↗ |
| Andropogon leprodes | NC_087659.1 | 138928 | View on NCBI ↗ |
| Andropogon lima | NC_087660.1 | 139132 | View on NCBI ↗ |
| Andropogon macrophyllus | NC_087661.1 | 139426 | View on NCBI ↗ |
| Andropogon mannii | MH181231.1 | 139015 | View on NCBI ↗ |
| Andropogon munroi | MH181215.1 | 140230 | View on NCBI ↗ |
| Andropogon pseudapricus | NC_087663.1 | 138668 | View on NCBI ↗ |
| Andropogon pteropholis | NC_087664.1 | 138823 | View on NCBI ↗ |
| Andropogon pusillus | MH181175.1 | 138986 | View on NCBI ↗ |
| Andropogon schirensis | MH181168.1 | 139840 | View on NCBI ↗ |
| Andropogon tenuiberbis | NC_086841.1 | 140300 | View on NCBI ↗ |
| Andropogon textilis | NC_087666.1 | 138777 | View on NCBI ↗ |
| Andropogon virgatus | MH181223.1 | 139727 | View on NCBI ↗ |