| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnG-UCC-trnT-GGU | LSC | 1720 | 0.0099 | 1.00 | 67.9 | yes | View details |
| trnT-GGU-trnE-UUC | LSC | 536 | 0.0165 | 0.98 | 68.8 | yes | View details |
| trnC-GCA-rpoB | LSC | 1234 | 0.0084 | 0.97 | 63.1 | yes | View details |
| petA-psbJ | LSC | 896 | 0.0086 | 0.97 | 63.7 | yes | View details |
| psaJ-rpl33 | LSC | 366 | 0.0125 | 0.98 | 61.0 | yes | View details |
| rpl16 | LSC | 1447 | 0.0109 | 0.99 | 55.3 | yes | View details |
| ndhF-rpl32 | SSC | 862 | 0.0095 | 1.00 | 67.7 | yes | View details |
| rpl32-trnL-UAG | SSC | 538 | 0.0167 | 0.99 | 71.0 | yes | View details |
| ccsA | SSC | 966 | 0.0051 | 1.00 | 42.5 | yes | View details |
| psbM-petN | LSC | 612 | 0.0086 | 1.00 | 64.5 | yes | View details |
| trnF-GAA-ndhJ | LSC | 618 | 0.0100 | 0.99 | 63.0 | yes | View details |
| psbE-petL | LSC | 1267 | 0.0055 | 1.00 | 59.7 | yes | View details |
| trnD-GUC-psbM | LSC | 685 | 0.0051 | 1.00 | 59.1 | yes | View details |
| rpl14-rpl16 | LSC | 109 | 0.0181 | 1.00 | 59.1 | yes | View details |
| trnS-GCU-psbD | LSC | 952 | 0.0067 | 1.00 | 59.0 | yes | View details |
| petB | LSC | 1403 | 0.0044 | 1.00 | 59.0 | yes | View details |
| atpI-atpH | LSC | 822 | 0.0043 | 0.99 | 58.6 | yes | View details |
| petN-trnC-GCA | LSC | 464 | 0.0063 | 1.00 | 57.8 | yes | View details |
| ndhC-trnV-UAC | LSC | 939 | 0.0071 | 0.99 | 57.2 | 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
37
Genome length
138–139 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 |
|---|---|---|---|---|---|---|
| trnS-GCU-psbD_p1 | trnS-GCU-psbD | ATTAGCAATCCGCCGCTTTA |
ATAAGCCGGACCATCCTACA |
974–1156 | 1.000 | 85.6 |
| trnS-GCU-psbD_p2 | trnS-GCU-psbD | ATTAGCAATCCGCCGCTTTA |
TAAGCCGGACCATCCTACAA |
973–1155 | 1.000 | 85.4 |
| trnS-GCU-psbD_p3 | trnS-GCU-psbD | ATTAGCAATCCGCCGCTTTA |
GCCGGACCATCCTACAAAAA |
970–1152 | 1.000 | 85.0 |
| trnS-GCU-psbD_p4 | trnS-GCU-psbD | ATTAGCAATCCGCCGCTTTA |
ACAAAAACGAAACGGTCCCT |
957–1139 | 1.000 | 84.5 |
| trnS-GCU-psbD_p5 | trnS-GCU-psbD | GCTTTAGTCCACTCAGCCAT |
ATAAGCCGGACCATCCTACA |
960–1142 | 1.000 | 82.7 |
| trnG-UCC-trnT-GGU_p1 | trnG-UCC-trnT-GGU | ACGAATCACACTTTTACCACT |
ACCACTAAGTGAAAAGCCCT |
1698–2090 | 1.000 | 50.1 |
| trnG-UCC-trnT-GGU_p2 | trnG-UCC-trnT-GGU | ACGAATCACACTTTTACCACT |
TGAACCGATGACTTATGCCT |
1668–2060 | 1.000 | 50.0 |
| trnG-UCC-trnT-GGU_p3 | trnG-UCC-trnT-GGU | ACGAATCACACTTTTACCACT |
GACTTCTGTCTTACCAAGGCA |
1726–2118 | 1.000 | 49.7 |
| trnG-UCC-trnT-GGU_p4 | trnG-UCC-trnT-GGU | ACGAATCACACTTTTACCACT |
TGACTTCTGTCTTACCAAGGC |
1727–2119 | 1.000 | 49.7 |
| trnG-UCC-trnT-GGU_p5 | trnG-UCC-trnT-GGU | ACGAATCACACTTTTACCACT |
CCGATGACTTATGCCTTACCA |
1664–2056 | 1.000 | 49.3 |
| trnT-GGU-trnE-UUC_p1 | trnT-GGU-trnE-UUC | AGGCATAAGTCATCGGTTCA |
TGTCCTGAACCACTAGACGA |
405–669 | 1.000 | 77.9 |
| trnT-GGU-trnE-UUC_p2 | trnT-GGU-trnE-UUC | AGGCATAAGTCATCGGTTCA |
GCTGCCTCCTTGAAAGAGAG |
426–690 | 1.000 | 77.7 |
| trnT-GGU-trnE-UUC_p3 | trnT-GGU-trnE-UUC | AGCCCTTTTAACTCAGTGGT |
TGTCCTGAACCACTAGACGA |
442–706 | 1.000 | 77.6 |
| trnT-GGU-trnE-UUC_p4 | trnT-GGU-trnE-UUC | AGCCCTTTTAACTCAGTGGT |
GCTGCCTCCTTGAAAGAGAG |
463–727 | 1.000 | 77.5 |
| trnT-GGU-trnE-UUC_p5 | trnT-GGU-trnE-UUC | TGGTAAGGCATAAGTCATCGG |
GCTGCCTCCTTGAAAGAGAG |
431–695 | 1.000 | 76.9 |
| trnD-GUC-psbM_p1 | trnD-GUC-psbM | AATAGGCATGCCATACACCC |
GGCAGTAGGAACTAGAATGAACA |
829–1222 | 1.000 | 60.5 |
| trnD-GUC-psbM_p2 | trnD-GUC-psbM | TTCAATTGGTCAGAGCACCG |
GGCAGTAGGAACTAGAATGAACA |
795–1188 | 1.000 | 59.3 |
| trnD-GUC-psbM_p3 | trnD-GUC-psbM | AATAGGCATGCCATACACCC |
AGGCAGTAGGAACTAGAATGAAC |
830–1223 | 1.000 | 58.4 |
| trnD-GUC-psbM_p4 | trnD-GUC-psbM | AATAGGCATGCCATACACCC |
TGCGAGAATATTGACTTCCA |
790–1183 | 1.000 | 57.3 |
| trnD-GUC-psbM_p5 | trnD-GUC-psbM | AATAGGCATGCCATACACCC |
AGGCAGTAGGAACTAGAATGA |
830–1223 | 1.000 | 57.1 |
| psbM-petN_p1 | psbM-petN | TGTTCATTCTAGTTCCTACTGCC |
TAGTAAGTCTCGCTTGGGCT |
700–782 | 0.973 | 59.9 |
| psbM-petN_p2 | psbM-petN | TGTTCATTCTAGTTCCTACTGCC |
GTAGTATGGGGGAGGAGTGG |
644–726 | 0.973 | 59.1 |
| psbM-petN_p3 | psbM-petN | TGTTCATTCTAGTTCCTACTGCC |
TAGTATGGGGGAGGAGTGGA |
643–725 | 0.973 | 58.4 |
| psbM-petN_p4 | psbM-petN | GTTCATTCTAGTTCCTACTGCCT |
TAGTAAGTCTCGCTTGGGCT |
699–781 | 0.973 | 57.9 |
| psbM-petN_p5 | psbM-petN | TGTTCATTCTAGTTCCTACTGCC |
CGCTAGTAGTATGGGGGAGG |
649–731 | 0.946 | 56.4 |
| petN-trnC-GCA_p1 | petN-trnC-GCA | AGCCCAAGCGAGACTTACTA |
CTGCAAATCCTTTACCCCCA |
524–533 | 1.000 | 83.3 |
| petN-trnC-GCA_p2 | petN-trnC-GCA | AGCCCAAGCGAGACTTACTA |
TGCAAATCCTTTACCCCCAG |
523–532 | 1.000 | 83.3 |
| petN-trnC-GCA_p3 | petN-trnC-GCA | AGCCCAAGCGAGACTTACTA |
GCAAATCCTTTACCCCCAGT |
522–531 | 1.000 | 83.3 |
| petN-trnC-GCA_p4 | petN-trnC-GCA | AGCCCAAGCGAGACTTACTA |
ACTGCAAATCCTTTACCCCC |
525–534 | 1.000 | 83.2 |
| petN-trnC-GCA_p5 | petN-trnC-GCA | CCACTCCTCCCCCATACTAC |
TGCAAATCCTTTACCCCCAG |
579–588 | 1.000 | 81.8 |
Result downloads
Reference species (37)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Hyparrhenia anamesa | NC_087669.1 | 139452 | View on NCBI ↗ |
| Hyparrhenia anemopaegma | MH181199.1 | 138502 | View on NCBI ↗ |
| Hyparrhenia arrhenobasis | NC_087670.1 | 139333 | View on NCBI ↗ |
| Hyparrhenia bagirmica | MH181190.1 | 138737 | View on NCBI ↗ |
| Hyparrhenia bracteata | NC_087671.1 | 139001 | View on NCBI ↗ |
| Hyparrhenia collina | NC_087697.1 | 139323 | View on NCBI ↗ |
| Hyparrhenia confinis | NC_087672.1 | 139056 | View on NCBI ↗ |
| Hyparrhenia confinis var. nudiglumis | OQ518200.1 | 139252 | View on NCBI ↗ |
| Hyparrhenia cyanescens | NC_087673.1 | 139396 | View on NCBI ↗ |
| Hyparrhenia cymbaria | NC_087674.1 | 139252 | View on NCBI ↗ |
| Hyparrhenia dichroa | NC_087675.1 | 138673 | View on NCBI ↗ |
| Hyparrhenia diplandra | NC_035037.1 | 139175 | View on NCBI ↗ |
| Hyparrhenia dregeana | NC_087676.1 | 139330 | View on NCBI ↗ |
| Hyparrhenia figariana | NC_087677.1 | 138650 | View on NCBI ↗ |
| Hyparrhenia filipendula | NC_087678.1 | 139276 | View on NCBI ↗ |
| Hyparrhenia finitima | NC_087679.1 | 139204 | View on NCBI ↗ |
| Hyparrhenia gazensis | NC_087680.1 | 139261 | View on NCBI ↗ |
| Hyparrhenia hirta | NC_087681.1 | 139331 | View on NCBI ↗ |
| Hyparrhenia involucrata | NC_087682.1 | 139321 | View on NCBI ↗ |
| Hyparrhenia lithophila | NC_087683.1 | 138427 | View on NCBI ↗ |
| Hyparrhenia madaropoda | NC_087684.1 | 139163 | View on NCBI ↗ |
| Hyparrhenia mobukensis | NC_087685.1 | 139113 | View on NCBI ↗ |
| Hyparrhenia multiplex | NC_087686.1 | 139411 | View on NCBI ↗ |
| Hyparrhenia newtonii | NC_087687.1 | 139469 | View on NCBI ↗ |
| Hyparrhenia niariensis | NC_087688.1 | 139134 | View on NCBI ↗ |
| Hyparrhenia papillipes | MH181179.1 | 139151 | View on NCBI ↗ |
| Hyparrhenia pilgeriana | NC_087689.1 | 139161 | View on NCBI ↗ |
| Hyparrhenia poecilotricha | NC_087690.1 | 139403 | View on NCBI ↗ |
| Hyparrhenia rudis | NC_087691.1 | 139384 | View on NCBI ↗ |
| Hyparrhenia rufa | NC_035011.1 | 139269 | View on NCBI ↗ |
| Hyparrhenia schimperi | NC_087692.1 | 139317 | View on NCBI ↗ |
| Hyparrhenia smithiana | NC_087693.1 | 139311 | View on NCBI ↗ |
| Hyparrhenia subplumosa | NC_030625.1 | 139174 | View on NCBI ↗ |
| Hyparrhenia tuberculata | NC_087695.1 | 139431 | View on NCBI ↗ |
| Hyparrhenia umbrosa | NC_087696.1 | 139451 | View on NCBI ↗ |
| Hyparrhenia variabilis | NC_040112.1 | 139481 | View on NCBI ↗ |
| Hyparrhenia violascens | MH181167.1 | 138684 | View on NCBI ↗ |