Markers + reference

Setaria

4 species · Poaceae · Poales

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Species 4
Genome length 138–139 kb
Candidate markers 273
Primer pairs 100

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 543 0.0145 0.99 55.4 yes View details
rps16-trnQ-UUG LSC 1260 0.0111 0.68 52.9 yes View details
trnG-UCC-trnM-CAU LSC 1940 0.0126 0.97 60.4 yes View details
trnY-GUA-trnD-GUC LSC 370 0.0187 0.94 63.4 yes View details
trnD-GUC-psbM LSC 1046 0.0121 0.99 61.6 yes View details
psbM-petN LSC 801 0.0132 0.97 70.1 yes View details
trnT-UGU-trnL-UAA LSC 824 0.0162 0.90 65.0 yes View details
rbcL-psaI LSC 879 0.0177 0.99 62.3 yes View details
petA-psbJ LSC 900 0.0116 0.98 68.1 yes View details
rpl32-trnL-UAG SSC 390 0.0120 1.00 51.4 yes View details
psbK-psbI LSC 402 0.0150 1.00 62.7 yes View details
ndhA SSC 2107 0.0078 1.00 61.8 yes View details
trnM-CAU-trnT-GGU LSC 5 0.1000 1.00 60.3 yes View details
trnN-GUU-rps15 IRb 1576 0.0011 1.00 60.2 yes View details
rps15-trnN-GUU IRa 1576 0.0011 1.00 60.2 yes View details
rps12-trnV-GAC IRb 1707 0.0019 1.00 60.0 yes View details
ycf3-trnS-GGA LSC 580 0.0061 1.00 59.9 yes View details
trnV-GAC-rps12 IRa 1707 0.0019 1.00 59.9 yes View details
trnF-GAA-ndhJ LSC 596 0.0122 0.94 59.2 yes View details
ndhC-trnV-UAC LSC 613 0.0155 1.00 59.2 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.

Primer pairs

Showing the top 30 of 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 TGAGGATCAGTCGTGGTCTT ATTTCCTTGAAACGGGTGCT 760–773 1.000 82.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AGGATCAGTCGTGGTCTTCT ATTTCCTTGAAACGGGTGCT 758–771 1.000 81.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 TGAGGATCAGTCGTGGTCTT ATACGTTTCTAGGGGAGGGG 927–940 1.000 80.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 TGAGGATCAGTCGTGGTCTT TTCTAGGGGAGGGGTTGTTT 921–934 1.000 80.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 TGAGGATCAGTCGTGGTCTT TTTCTAGGGGAGGGGTTGTT 922–935 1.000 80.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 745–1334 1.000 83.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 756–1345 1.000 83.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 749–1338 1.000 82.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 760–1349 1.000 82.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 751–1340 1.000 80.8
psbK-psbI_p1 psbK-psbI CGTGGATGTTATGCCTGTCA GGATTACGTCCTGGGTCATT 537–581 1.000 77.2
psbK-psbI_p2 psbK-psbI CAAGCCGCTGTAAGTTTTCG GGATTACGTCCTGGGTCATT 482–526 1.000 77.1
psbK-psbI_p3 psbK-psbI AGCCGCTGTAAGTTTTCGAT GGATTACGTCCTGGGTCATT 480–524 1.000 76.8
psbK-psbI_p4 psbK-psbI AAGCCGCTGTAAGTTTTCGA GGATTACGTCCTGGGTCATT 481–525 1.000 76.5
psbK-psbI_p5 psbK-psbI ACCCGAAGCTTATGCCATTT GGATTACGTCCTGGGTCATT 567–611 1.000 76.2
trnG-UCC-trnM-CAU_p1 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1832–2041 1.000 46.5
trnG-UCC-trnM-CAU_p2 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 1828–2037 1.000 45.8
trnG-UCC-trnM-CAU_p3 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT ACCGATGACTTATGCCTTACC 1829–2038 1.000 45.8
trnG-UCC-trnM-CAU_p4 trnG-UCC-trnM-CAU AGAACGAATCACACTTTTACCAC TGAACCGATGACTTATGCCT 1835–2044 1.000 45.8
trnG-UCC-trnM-CAU_p5 trnG-UCC-trnM-CAU GAACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1834–2043 1.000 45.8
trnM-CAU-trnT-GGU_p1 trnM-CAU-trnT-GGU CTCAGTGGTAGAGTAATGCCA ACTCTACCACTAAGTGAAAAG 81 1.000 41.0
trnM-CAU-trnT-GGU_p2 trnM-CAU-trnT-GGU ACTCAGTGGTAGAGTAATGCC ACTCTACCACTAAGTGAAAAG 82 1.000 41.0
trnM-CAU-trnT-GGU_p3 trnM-CAU-trnT-GGU AGCCCTTTTAACTCAGTGGT ACTCTACCACTAAGTGAAAAG 92 1.000 40.9
trnM-CAU-trnT-GGU_p4 trnM-CAU-trnT-GGU AAGCCCTTTTAACTCAGTGGT ACTCTACCACTAAGTGAAAAG 93 1.000 40.9
trnM-CAU-trnT-GGU_p5 trnM-CAU-trnT-GGU AAAGCCCTTTTAACTCAGTGGT ACTCTACCACTAAGTGAAAAG 94 1.000 40.9
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC CGGTGCTCTGACCAATTGAA 471–494 1.000 81.8
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG CGGTGCTCTGACCAATTGAA 438–461 1.000 79.5
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT CGGTGCTCTGACCAATTGAA 437–460 1.000 79.3
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC GGTGCTCTGACCAATTGAAC 470–493 1.000 77.7
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC TGGGGACGGACTGTAAATTC CGGTGCTCTGACCAATTGAA 439–462 1.000 76.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Setaria geminata NC_030494.1 139142 View on NCBI ↗
Setaria parviflora PX369354.1 139153 View on NCBI ↗
Setaria verticillata NC_086645.1 138946 View on NCBI ↗
Setaria viridis NC_028075.1 138102 View on NCBI ↗