Markers + reference

Platanthera

6 species · Orchidaceae · Asparagales

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Species 6
Genome length 154–155 kb
Candidate markers 273
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 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 647 0.0304 1.00 64.0 yes View details
rps16 LSC 1201 0.0247 0.98 65.9 yes View details
psbK-psbI LSC 456 0.0291 1.00 54.9 yes View details
rpoB-trnC-GCA LSC 1246 0.0198 0.98 62.8 yes View details
trnT-GGU-psbD LSC 1018 0.0238 0.99 61.4 yes View details
trnT-UGU-trnL-UAA LSC 955 0.0265 0.98 76.6 yes View details
rpoA LSC 987 0.0101 1.00 45.3 yes View details
ycf1 IRb 1017 0.0050 1.00 37.4 no View details
ndhF-rpl32 SSC 762 0.0361 0.98 70.3 yes View details
rpl32-trnL-UAG SSC 653 0.0390 0.98 70.9 yes View details
ycf1 SSC 5460 0.0192 1.00 51.7 yes View details
petD-rpoA LSC 227 0.0536 0.99 74.3 yes View details
rps3-rpl22 LSC 86 0.0512 1.00 71.5 yes View details
rrn4.5-rrn5 IRb 213 0.0354 1.00 71.0 yes View details
rrn5-rrn4.5 IRa 213 0.0354 1.00 71.0 yes View details
trnR-UCU-atpA LSC 140 0.0531 1.00 70.3 yes View details
trnE-UUC-trnT-GGU LSC 902 0.0225 0.99 70.2 yes View details
trnS-GCU-trnG-GCC LSC 615 0.0259 1.00 69.7 yes View details
psaA-ycf3 LSC 668 0.0194 0.99 67.0 yes View details
psbB-psbT LSC 442 0.0286 0.99 66.4 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 95 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 TCGATCCCGAAGAGAAGGAA 830–863 1.000 84.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCGATCCCGAAGAGAAGGAA 829–862 1.000 84.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 CAGGATCAGTCGCGGTATTC TCGATCCCGAAGAGAAGGAA 916–949 1.000 83.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CCTTGAAAAAGGCGCTCAAC 733–755 0.667 68.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTTGAAAAAGGCGCTCAACC 732–754 0.667 68.5
rps16_p1 rps16 TATTTGTTCGAGACGCCGTT CAAGCGGTAAGGCAATAGGT 1889–1973 1.000 87.1
rps16_p2 rps16 TATTTGTTCGAGACGCCGTT GAGGTTCGAATCCTTCCGTC 1852–1936 1.000 87.0
rps16_p3 rps16 GCACAACTGCGTCAAAACAT CAAGCGGTAAGGCAATAGGT 2141–2231 1.000 86.1
rps16_p4 rps16 GTTGAGTTAGCAACCCGGAT CAAGCGGTAAGGCAATAGGT 2219–2293 0.833 78.7
rps16_p5 rps16 GTTGAGTTAGCAACCCGGAT GAGGTTCGAATCCTTCCGTC 2182–2256 0.833 78.5
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TGGACTAAAGCGTCGGATTG 820–826 1.000 85.4
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG GTGGACTAAAGCGTCGGATT 821–827 1.000 85.4
psbK-psbI_p3 psbK-psbI ACCTATTGCCTTACCGCTTG TGGACTAAAGCGTCGGATTG 1362–1379 1.000 84.7
psbK-psbI_p4 psbK-psbI ACCTATTGCCTTACCGCTTG GTGGACTAAAGCGTCGGATT 1363–1380 1.000 84.7
psbK-psbI_p5 psbK-psbI ACCTATTGCCTTACCGCTTG ACGCCCCGGATCATTAGATA 1116–1135 1.000 83.6
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 682–719 1.000 57.5
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 681–718 1.000 57.5
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 685–722 1.000 56.5
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 684–721 1.000 56.5
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 683–720 1.000 56.5
trnR-UCU-atpA_p1 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG GCCGGCAAATCAAAATTGGA 750–759 1.000 86.0
trnR-UCU-atpA_p2 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG GGGTCGTGAAGCTTATCCAG 1042–1051 1.000 84.5
trnR-UCU-atpA_p3 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG GGTCGTGAAGCTTATCCAGG 1041–1050 1.000 84.4
trnR-UCU-atpA_p4 trnR-UCU-atpA CCTAGCCTTCCAAGCTAACG GGGTCGTGAAGCTTATCCAG 1045–1054 1.000 84.2
trnR-UCU-atpA_p5 trnR-UCU-atpA CCTAGCCTTCCAAGCTAACG GGTCGTGAAGCTTATCCAGG 1044–1053 1.000 84.2
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCAAATTAAGACCGCGGGTA TTGGTACCTGTTTGAGCCAC 1733–1765 1.000 85.2
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCAAATTAAGACCGCGGGTA GCCACACGAATAACCCAGAT 1718–1750 1.000 85.0
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCCCTACACAGGCAAATTGT TTGGTACCTGTTTGAGCCAC 2172–2204 1.000 83.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCCCTACACAGGCAAATTGT GCCACACGAATAACCCAGAT 2157–2189 1.000 83.7
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCAAATTAAGACCGCGGGTA CCTTACCACTTGGCCATACC 1533–1534 0.500 59.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Platanthera bifolia PP541859.1 154235 View on NCBI ↗
Platanthera bifolia subsp. osca PX897272.1 154223 View on NCBI ↗
Platanthera chlorantha NC_044626.1 154260 View on NCBI ↗
Platanthera japonica NC_037440.2 155014 View on NCBI ↗
Platanthera mandarinorum NC_046805.1 154162 View on NCBI ↗
Platanthera ussuriensis MN686021.1 155016 View on NCBI ↗