Markers + reference

Chamaegastrodia

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 116–131 kb
Candidate markers 224
Primer pairs 65

Genome-wide nucleotide diversity

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

Candidate markers

4 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 224 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoC2 LSC 1575 0.0468 0.99 71.4 yes View details
rpoC2-trnC-GCA LSC 2000 0.4058 0.99 79.1 yes View details
psbB LSC 1081 0.1866 0.97 82.0 yes View details
ndhD-rpl32 SSC 370 0.1956 0.61 69.3 yes View details
accD-psaI LSC 730 0.1071 0.95 83.6 yes View details
rpl32-trnL-UAG SSC 603 0.0507 0.95 77.4 yes View details
trnW-CCA-trnP-UGG LSC 160 0.0592 0.95 75.5 yes View details
psaI-ycf4 LSC 310 0.1184 0.98 74.7 yes View details
trnY-GUA-trnE-UUC LSC 59 0.0847 1.00 71.8 yes View details
trnD-GUC-trnY-GUA LSC 295 0.0461 0.96 70.7 yes View details
psaI LSC 105 0.0645 0.89 70.5 yes View details
trnT-UGU-trnL-UAA LSC 753 0.0310 0.99 70.3 yes View details
rps16-trnQ-UUG LSC 231 0.0696 1.00 69.2 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 65 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 304–323 1.000 82.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGGCAATTTGGCGAAGAAAA 778–821 1.000 82.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GTGTTTCCTTGTTCCGGGAT GAGGTTCGAATCCTTCCGTC 688 0.500 58.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GTGTTTCCTTGTTCCGGGAT GGGCAATTTGGCGAAGAAAA 1162 0.500 57.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GTGTTTCCTTGTTCCGGGAT TCGCTTTTTGAATCGAGGGT 1395 0.500 57.8
rpoC2_p1 rpoC2 GAGCCCTTATTGCTGCTGAT GCCTGGGTCAGTGATTTGAA 2452 0.500 59.1
rpoC2_p2 rpoC2 TGACTTCGAGCCCTTATTGC GCCTGGGTCAGTGATTTGAA 2459 0.500 59.1
rpoC2_p3 rpoC2 GAGCCCTTATTGCTGCTGAT GATGCATTTCCTCTAGCCCC 2924 0.500 59.1
rpoC2_p4 rpoC2 ACTTCGAGCCCTTATTGCTG GCCTGGGTCAGTGATTTGAA 2457 0.500 59.0
rpoC2_p5 rpoC2 TGACTTCGAGCCCTTATTGC GATGCATTTCCTCTAGCCCC 2931 0.500 59.0
rpoC2-trnC-GCA_p1 rpoC2-trnC-GCA GTTTTGGCAGGCCTACTCAT TTGGTACCTGTTTGAGCCAC 2248 0.500 58.5
rpoC2-trnC-GCA_p2 rpoC2-trnC-GCA GTTTTGGCAGGCCTACTCAT CAGAGCCTCTCGTGAGTCTA 2642 0.500 58.5
rpoC2-trnC-GCA_p3 rpoC2-trnC-GCA GTTTTGGCAGGCCTACTCAT TACTCAGAGCCTCTCGTGAG 2646 0.500 58.5
rpoC2-trnC-GCA_p4 rpoC2-trnC-GCA GTTTTGGCAGGCCTACTCAT TGAGTACTCAGAGCCTCTCG 2650 0.500 58.5
rpoC2-trnC-GCA_p5 rpoC2-trnC-GCA GTTTTGGCAGGCCTACTCAT GAGTACTCAGAGCCTCTCGT 2649 0.500 58.5
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA GGTGCTCTAACCGATTGAACT CTGGTTCAAATCCAGCTCGG 335–348 1.000 70.6
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA GGTGCTCTAACCGATTGAACT GAGATGTCTACGCTGGTTCA 347–360 1.000 70.1
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA GGTGCTCTAACCGATTGAACT TCTACGCTGGTTCAAATCCA 341–354 1.000 68.6
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA GGTGCTCTAACCGATTGAACT TGGTTCAAATCCAGCTCGG 334–347 1.000 67.9
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA GGTGCTCTAACCGATTGAACT GAGATGTCTACGCTGGTTCAA 347–360 1.000 67.8
trnY-GUA-trnE-UUC_p1 trnY-GUA-trnE-UUC TCTTGCTTGGGCTGCTTTAA CCATGGCGTTACTCTACCAC 1004–1248 1.000 82.8
trnY-GUA-trnE-UUC_p2 trnY-GUA-trnE-UUC TCTTGCTTGGGCTGCTTTAA TGGCGTTACTCTACCACTGA 1001–1245 1.000 82.7
trnY-GUA-trnE-UUC_p3 trnY-GUA-trnE-UUC GGACTTGAGTAAGAGTGGCG CCATGGCGTTACTCTACCAC 559 0.500 59.5
trnY-GUA-trnE-UUC_p4 trnY-GUA-trnE-UUC GGACTTGAGTAAGAGTGGCG TGGCGTTACTCTACCACTGA 556 0.500 59.3
trnY-GUA-trnE-UUC_p5 trnY-GUA-trnE-UUC GGACTTGAGTAAGAGTGGCG CCATTGGAACGGAACCAGAA 992 0.500 59.2
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA TCGGAATCGAACCAATGACC ACCAATTTCGCCATATCCCC 837–1076 1.000 82.7
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA TCGGAATCGAACCAATGACC TAGCGTCTACCAATTTCGCC 845–1084 1.000 82.2
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 803–1042 1.000 81.9
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 811–1050 1.000 81.4
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA TCGGAATCGAACCAATGACC ATCCAATCAAGTCCGTAGCG 860–1099 1.000 80.9

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
Chamaegastrodia inverta MW589502.1 116220 View on NCBI ↗
Chamaegastrodia shikokiana NC_046802.1 130934 View on NCBI ↗