Markers + reference

Nervilia

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 158–163 kb
Candidate markers 271
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 859 0.2275 0.85 85.3 yes View details
trnS-GCU-trnG-UCC LSC 1073 0.1511 0.70 76.9 yes View details
rpoB-trnC-GCA LSC 1028 0.1699 0.94 85.6 yes View details
petN-psbM LSC 893 0.1739 0.85 80.8 yes View details
trnE-UUC-trnT-GGU LSC 1263 0.1810 0.91 87.9 yes View details
ndhC-trnV-UAC LSC 1381 0.1563 0.92 84.8 yes View details
clpP1 LSC 2203 0.0950 0.99 77.9 yes View details
psbB-psbT LSC 548 0.2839 0.98 79.9 yes View details
ndhE-psaC SSC 753 0.2140 0.95 84.3 yes View details
psbE-petL LSC 1442 0.1018 0.94 84.5 yes View details
rrn4.5-rrn5 IRb 213 0.0788 0.95 84.4 yes View details
rrn5-rrn4.5 IRa 213 0.0788 0.95 84.4 yes View details
matK-trnK-UUU LSC 1213 0.1534 0.92 84.1 yes View details
psaA-pafI LSC 761 0.1151 0.91 83.5 yes View details
accD-psaI LSC 822 0.0985 0.95 83.0 yes View details
clpP1-psbB LSC 833 0.1378 0.91 83.0 yes View details
trnK-UUU-rps16 LSC 554 0.1062 0.94 82.3 yes View details
petA-psbJ LSC 892 0.0855 0.93 82.1 yes View details
psbK-psbI LSC 431 0.1449 0.96 81.9 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_p1 trnK-UUU GTCAGAACGGCGTATGTGTA AGTGCCTGATGTGGGAAAAG 763–818 1.000 89.2
trnK-UUU_p2 trnK-UUU GAAAGGGAGGCACTTCTTGT AGTGCCTGATGTGGGAAAAG 811–866 1.000 89.1
trnK-UUU_p3 trnK-UUU GTCAGAACGGCGTATGTGTA CTGTCTCCGGGGTATATGGT 467 0.500 57.8
trnK-UUU_p4 trnK-UUU GAAAGGGAGGCACTTCTTGT CTGTCTCCGGGGTATATGGT 515 0.500 57.7
trnK-UUU_p5 trnK-UUU AGTGCAATACGGTCAGAACG CTGTCTCCGGGGTATATGGT 478 0.500 57.6
matK-trnK-UUU_p1 matK-trnK-UUU GGATGGGGTGGGGTATTAGT TACGGGTTGCTAACTCAACG 1737–1826 1.000 90.1
matK-trnK-UUU_p2 matK-trnK-UUU TGGATGGGGTGGGGTATTAG TACGGGTTGCTAACTCAACG 1738–1827 1.000 90.1
matK-trnK-UUU_p3 matK-trnK-UUU GGATGGGGTGGGGTATTAGT AACGGTAGAGTACTCGGCTT 1721–1810 1.000 89.3
matK-trnK-UUU_p4 matK-trnK-UUU GGATGGGGTGGGGTATTAGT ACGGTAGAGTACTCGGCTTT 1720–1809 1.000 89.3
matK-trnK-UUU_p5 matK-trnK-UUU CATATGGATGGGGTGGGGTA TACGGGTTGCTAACTCAACG 1742 0.500 57.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 CTTTTCCCACATCAGGCACT TCGATCCCGAAGAGAAGGAA 1168–1193 1.000 88.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACCATATACCCCGGAGACAG TCGATCCCGAAGAGAAGGAA 1464 0.500 58.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 ACCATATACCCCGGAGACAG TCGTTGCAATTGATGGTCGA 1480 0.500 58.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 ACCATATACCCCGGAGACAG CCTTGAAAAAGGCGCTCAAC 1368 0.500 58.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 ACCATATACCCCGGAGACAG CTTGAAAAAGGCGCTCAACC 1367 0.500 58.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 919–932 1.000 90.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 923–936 1.000 89.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 925–938 1.000 87.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA ACTCGGAGGTTCGAATCCTT 924–937 1.000 87.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAGACCAAAAGAATGGGGCG 993 0.500 57.9
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACTACTGTGTAAACGAAGAGT 496–569 1.000 52.5
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGAAGAGTTTAAGAGTAAGCA 484–557 1.000 51.6
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACTACTGTGTAAACGAAGAGTT 496–569 1.000 51.0
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACTACTGTGTAAACGAAGAGT 493–566 1.000 50.6
psbK-psbI_p5 psbK-psbI TTGGCAAGCTGCTGTAAGTT ACTACTGTGTAAACGAAGAGT 494–567 1.000 50.6
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA CCGAGCTGAGACAAGAAGAC 1280–1535 1.000 91.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC CCGAGCTGAGACAAGAAGAC 1279–1534 1.000 91.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATCTAATGATCCGGGGCGTA CCGAGCTGAGACAAGAAGAC 1524–1788 1.000 90.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TATCTAATGATCCGGGGCGT CCGAGCTGAGACAAGAAGAC 1525–1789 1.000 90.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ATCGGAGAGAGAGGGATTCG CCGAGCTGAGACAAGAAGAC 1335–1590 1.000 90.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Nervilia aragoana NC_066070.1 158174 View on NCBI ↗
Nervilia fordii NC_066071.1 162651 View on NCBI ↗