Markers + reference

Anoectochilus

10 species · Orchidaceae · Asparagales

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Species 10
Genome length 151–153 kb
Candidate markers 271
Primer pairs 90

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
trnK-UUU-rps16 LSC 693 0.0132 1.00 60.8 yes View details
atpF LSC 1360 0.0077 1.00 58.3 yes View details
atpF-atpH LSC 428 0.0170 1.00 62.7 yes View details
trnT-UGU-trnL-UAA LSC 963 0.0408 0.98 82.1 yes View details
accD-psaI LSC 605 0.0100 1.00 51.1 yes View details
rpl16 LSC 1642 0.0056 1.00 51.2 yes View details
ycf1 IRb 1116 0.0034 1.00 52.3 no View details
rpl32-trnL-UAG SSC 416 0.0178 0.82 58.5 yes View details
ycf1 SSC 5769 0.0105 0.98 54.1 yes View details
clpP-psbB LSC 485 0.0090 0.99 69.7 yes View details
psbM-trnD-GUC LSC 1015 0.0103 0.96 67.0 yes View details
petA-psbJ LSC 967 0.0094 0.98 65.2 yes View details
trnT-GGU-psbD LSC 728 0.0059 1.00 63.4 yes View details
atpH-atpI LSC 547 0.0075 1.00 62.7 yes View details
rpl16-rps3 LSC 178 0.0283 1.00 62.2 yes View details
rpoB-trnC-GCA LSC 1208 0.0077 0.98 59.7 yes View details
psbK-psbI LSC 461 0.0146 0.98 59.5 yes View details
ycf4-cemA LSC 725 0.0046 1.00 57.8 yes View details
petD-rpoA LSC 180 0.0174 1.00 57.5 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GCAAAGACAACGAATTCCGG 1294–1335 1.000 83.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCAAAGACAACGAATTCCGG 1293–1334 1.000 83.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TCGATCCCGAAGAGAAGGAA 880–903 1.000 82.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCGATCCCGAAGAGAAGGAA 879–902 1.000 82.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGGATCAGTCGCGGTCTTAT GCAAAGACAACGAATTCCGG 1379–1420 1.000 81.8
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCTTCACGCCCAGGATTAC 591–606 1.000 81.2
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT TTCTTCACGCCCAGGATTAC 588–603 1.000 79.2
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT TTCTTCACGCCCAGGATTAC 589–604 1.000 79.2
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT TTCTTCACGCCCAGGATTAC 590–605 1.000 79.2
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG GGATTACGTCCCGGATCATT 578–593 1.000 77.8
atpF_p1 atpF GCTCGAAGGGTTCCCATTAG GCGGGTGGAGTGATACAAAA 1505–1515 1.000 80.9
atpF_p2 atpF AGCTCGAAGGGTTCCCATTA GCGGGTGGAGTGATACAAAA 1506–1516 1.000 77.9
atpF_p3 atpF CTCGAAGGGTTCCCATTAGT GCGGGTGGAGTGATACAAAA 1504–1514 1.000 70.2
atpF_p4 atpF GCTCGAAGGGTTCCCATTAG GCGGGTGGAGTGATACAAA 1505–1515 1.000 70.0
atpF_p5 atpF AGCTCGAAGGGTTCCCATT GCGGGTGGAGTGATACAAAA 1506–1516 1.000 68.3
atpF-atpH_p1 atpF-atpH GCCCCACGGAAACAAAAGAA ATTTATGGACTGGTCGTGGC 519–533 1.000 72.7
atpF-atpH_p2 atpF-atpH GCCCCACGGAAACAAAAGAA GGTCGTGGCATTAGCTCTTT 508–522 1.000 71.0
atpF-atpH_p3 atpF-atpH CCCCACGGAAACAAAAGAAT ATTTATGGACTGGTCGTGGC 518–532 1.000 70.8
atpF-atpH_p4 atpF-atpH GCCCCACGGAAACAAAAGA ATTTATGGACTGGTCGTGGC 519–533 1.000 70.1
atpF-atpH_p5 atpF-atpH GCCCCACGGAAACAAAAGAA CAGAGGGCAAAATACGAGGT 578–592 1.000 69.6
atpH-atpI_p1 atpH-atpI AGCCAATCCAGCAGCAATAA AACTTTGGCTGCGGCTTATA 642–653 1.000 80.8
atpH-atpI_p2 atpH-atpI GCCAATCCAGCAGCAATAAC AACTTTGGCTGCGGCTTATA 641–652 1.000 80.3
atpH-atpI_p3 atpH-atpI TCCAGCAGCAATAACGGAAG AACTTTGGCTGCGGCTTATA 636–647 1.000 79.9
atpH-atpI_p4 atpH-atpI AGCCAATCCAGCAGCAATAA GGCTGCGGCTTATATAGGTG 636–647 1.000 79.6
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC GGCTGCGGCTTATATAGGTG 635–646 1.000 79.1
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGTCAAGCCCCGATTAATGA TAAAGGATTTGCAGTCCCCC 1328–1363 1.000 78.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CGTCAAGCCCCGATTAATGA CGACACCCAGATTCGAACTG 1352–1387 1.000 77.4
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CGTCAAGCCCCGATTAATGA TTTGTTGATCAGGCGACACC 1365–1400 1.000 76.5
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CGTCAAGCCCCGATTAATGA ATAAAGGATTTGCAGTCCCCC 1329–1364 1.000 74.4
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CGTCAAGCCCCGATTAATGA TTTTGTTGATCAGGCGACAC 1366–1401 1.000 74.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Anoectochilus brevilabris PQ591845.1 152261 View on NCBI ↗
Anoectochilus burmannicus NC_066958.1 152868 View on NCBI ↗
Anoectochilus chapaensis PX648172.1 152393 View on NCBI ↗
Anoectochilus emeiensis NC_033895.1 152650 View on NCBI ↗
Anoectochilus formosanus NC_061756.1 151414 View on NCBI ↗
Anoectochilus hainanensis MW589501.1 152645 View on NCBI ↗
Anoectochilus lylei PQ604654.1 152976 View on NCBI ↗
Anoectochilus nandanensis PX648173.1 152418 View on NCBI ↗
Anoectochilus roxburghii NC_061758.1 152821 View on NCBI ↗
Anoectochilus zhejiangensis NC_054353.1 152509 View on NCBI ↗