Markers + reference

Neottia

5 species · Orchidaceae · Asparagales

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Species 5
Genome length 106–157 kb
Candidate markers 230
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 230 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 696 0.0967 0.86 78.9 yes View details
rps16-trnQ-UUG LSC 836 0.1268 0.98 83.5 yes View details
trnC-GCA-trnD-GUC LSC 788 0.0763 0.97 78.8 yes View details
trnT-UGU-trnL-UAA LSC 848 0.1017 0.97 81.4 yes View details
atpB-rbcL LSC 715 0.0718 1.00 84.2 yes View details
clpP-psbB LSC 630 0.0960 1.00 88.0 yes View details
trnE-UUC-trnT-GGU LSC 1046 0.0598 0.99 86.2 yes View details
rps16 LSC 1181 0.0499 0.99 84.4 yes View details
matK-trnK-UUU LSC 836 0.0724 0.97 84.3 yes View details
rpoB-trnC-GCA LSC 539 0.0578 0.99 83.3 yes View details
trnS-GCU-trnG-GCC LSC 542 0.0605 0.96 82.7 yes View details
trnL-UAG-rpl32 SSC 576 0.0739 0.97 82.3 yes View details
accD-psaI LSC 494 0.0599 0.98 82.2 yes View details
ndhG-ccsA SSC 546 0.0710 0.95 81.7 yes View details
trnD-GUC-trnY-GUA LSC 287 0.0578 1.00 81.3 yes View details
trnF-GAA-ndhJ LSC 564 0.0674 1.00 81.3 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TTAGTTTTATTTGAACTTTGGT GACTCAGTTCTGCAGTGCAA 2808–2934 0.600 32.2
trnK-UUU_p2 trnK-UUU TTAGTTTTATTTGAACTTTGGT TTGACTCAGTTCTGCAGTGC 2810–2936 0.600 32.2
trnK-UUU_p3 trnK-UUU TTTAGTTTTATTTGAACTTTGGT GACTCAGTTCTGCAGTGCAA 2809–2935 0.600 32.2
trnK-UUU_p4 trnK-UUU TTTAGTTTTATTTGAACTTTGGT TTGACTCAGTTCTGCAGTGC 2811–2937 0.600 32.2
trnK-UUU_p5 trnK-UUU TTTTAGTTTTATTTGAACTTTGGT GACTCAGTTCTGCAGTGCAA 2810–2936 0.600 32.2
matK-trnK-UUU_p1 matK-trnK-UUU TCGCGACGAGAATGGAATTT ATCCGGGTTGCTAACTCAAC 1204–1349 1.000 90.2
matK-trnK-UUU_p2 matK-trnK-UUU TCGCGACGAGAATGGAATTT AACGGTAGAGTACTCGGCTT 1187–1332 1.000 89.8
matK-trnK-UUU_p3 matK-trnK-UUU TCGCGACGAGAATGGAATTT ACGGTAGAGTACTCGGCTTT 1186–1331 1.000 89.8
matK-trnK-UUU_p4 matK-trnK-UUU TCGCGACGAGAATGGAATTT ATTGACAATGGCGTCTCGAA 1550–1705 0.600 72.7
matK-trnK-UUU_p5 matK-trnK-UUU ACTAATCGCGACGAGAATGG ATTGACAATGGCGTCTCGAA 1555–1710 0.600 71.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 GCGCAAAAGATCATAGTCGC CGCAAAGCAAAGACAACGAA 1224–1380 0.800 82.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCAAAGACAACGAATTCCGG 1151–1348 0.800 82.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 GCGCAAAAGATCATAGTCGC GCAAAGACAACGAATTCCGG 1218–1374 0.600 75.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 TACCTCATCCAAATGCGCAA GCAAAGACAACGAATTCCGG 1388 0.200 46.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 TTACCTCATCCAAATGCGCA GCAAAGACAACGAATTCCGG 1389 0.200 46.7
rps16_p1 rps16 TTCGAGACGCCATTGTCAAT ACGAGACTTTTTCTACGCCC 2141 0.200 46.6
rps16_p2 rps16 GTTGAGTTAGCAACCCGGAT ACGAGACTTTTTCTACGCCC 2487 0.200 46.5
rps16_p3 rps16 AAAGCCGAGTACTCTACCGT ACGAGACTTTTTCTACGCCC 2505 0.200 46.0
rps16_p4 rps16 AAGCCGAGTACTCTACCGTT ACGAGACTTTTTCTACGCCC 2504 0.200 46.0
rps16_p5 rps16 TTCGAGACGCCATTGTCAAT CGAGACTTTTTCTACGCCCT 2140 0.200 44.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CCGGAATTCGTTGTCTTTGC GAGGTTCGAATCCTTCCGTC 1443–1627 1.000 91.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC GAGGTTCGAATCCTTCCGTC 933–1129 1.000 90.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGCTCGAGCTCCATCATATG GAGGTTCGAATCCTTCCGTC 1094–1282 0.600 75.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCGGAATTCGTTGTCTTTGC CCAGGGATAACCGGCATAAC 2009–2117 0.600 74.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGCTCGAGCTCCATCATATG CCAGGGATAACCGGCATAAC 1659–1660 0.400 65.6
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC TTAGTCCCCTCAGCCATCTC ACGAATCACACTTTTACCACT 599–862 1.000 61.3
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC TTTAGTCCCCTCAGCCATCT ACGAATCACACTTTTACCACT 600–863 1.000 60.8
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC TTAGTCCCCTCAGCCATCTC AGAACGAATCACACTTTTACCAC 602–865 1.000 60.2
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC TTAGTCCCCTCAGCCATCTC GAACGAATCACACTTTTACCACT 601–864 1.000 60.2
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC TTTAGTCCCCTCAGCCATCT GAACGAATCACACTTTTACCACT 602–865 1.000 59.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Neottia camtschatea NC_030707.1 106385 View on NCBI ↗
Neottia cordata NC_041189.1 147034 View on NCBI ↗
Neottia fugongensis NC_030711.1 156536 View on NCBI ↗
Neottia ovata NC_030712.1 156978 View on NCBI ↗
Neottia pinetorum NC_030710.1 155959 View on NCBI ↗