Markers + reference

Goodyera

11 species · Orchidaceae · Asparagales

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Species 11
Genome length 152–156 kb
Candidate markers 273
Primer pairs 100

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
rps16-trnQ-UUG LSC 438 0.0560 0.55 74.5 yes View details
trnQ-UUG-psbK LSC 385 0.0497 0.93 81.2 yes View details
trnT-UGU-trnL-UAA LSC 771 0.0538 0.99 89.3 yes View details
trnL-UAA-trnF-GAA LSC 418 0.0605 0.95 84.7 yes View details
ndhC-trnV-UAC LSC 630 0.0538 1.00 88.0 yes View details
accD LSC 1716 0.0471 0.87 78.2 yes View details
petA-psbJ LSC 955 0.0461 1.00 83.4 yes View details
clpP-psbB LSC 647 0.0647 0.96 86.7 yes View details
ycf1 IRb 1069 0.0082 1.00 57.3 no View details
rpl32-trnL-UAG SSC 745 0.0505 0.91 84.1 yes View details
ycf1 SSC 5364 0.0357 1.00 72.8 yes View details
trnF-GAA-ndhJ LSC 516 0.0433 1.00 85.7 yes View details
rpl36-infA LSC 121 0.0479 1.00 82.7 yes View details
matK-trnK-UUU LSC 1075 0.0461 0.98 82.5 yes View details
trnE-UUC-trnT-GGU LSC 411 0.0408 0.97 82.3 yes View details
rps18-rpl20 LSC 263 0.0598 1.00 82.2 yes View details
psaA-ycf3 LSC 627 0.0311 1.00 82.0 yes View details
trnS-GCU-trnG-UCC LSC 487 0.0380 1.00 81.3 yes View details
trnK-UUU-rps16 LSC 558 0.0454 0.98 80.9 yes View details
rpl16-rps3 LSC 170 0.0453 0.99 80.4 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU GATTCTTTTTAATTTTAACTTTGGT AGATCATATCTACACTTCATCT 2974–2991 0.364 20.9
trnK-UUU_p2 trnK-UUU AATTTTAACTTTGGTATAGATTGA AGATCATATCTACACTTCATCT 2964–2981 0.273 14.9
trnK-UUU_p3 trnK-UUU AATTTTAACTTTGGTATAGATTGA GCAGTACAATTCCCTTATTTT 2988–3000 0.182 9.7
trnK-UUU_p4 trnK-UUU AATTTTAACTTTGGTATAGATTGA GCAGTACAATTCCCTTATTT 2988–3000 0.182 9.7
trnK-UUU_p5 trnK-UUU AATTTTAACTTTGGTATAGATTGA GCAGTACAATTCCCTTATTTTT 2988–3000 0.182 9.7
matK-trnK-UUU_p1 matK-trnK-UUU CTAGATGGATGGGATGGGGT ATCCGGGTTGCTAACTCAAC 1476–1622 1.000 90.7
matK-trnK-UUU_p2 matK-trnK-UUU CTAGATGGATGGGATGGGGT AACGGTAGAGTACTCGGCTT 1459–1605 1.000 90.2
matK-trnK-UUU_p3 matK-trnK-UUU CTAGATGGATGGGATGGGGT ACGGTAGAGTACTCGGCTTT 1458–1604 1.000 90.2
matK-trnK-UUU_p4 matK-trnK-UUU TCTAGATGGATGGGATGGGG ATCCGGGTTGCTAACTCAAC 1477–1623 1.000 88.3
matK-trnK-UUU_p5 matK-trnK-UUU CTAGATGGATGGGATGGGGT GGGTTGCTAACTCAACGGTA 1472–1618 1.000 87.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GCAAAGACAACGAATTCCGG 1233–1292 0.909 86.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCAAAGACAACGAATTCCGG 1232–1291 0.909 86.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 CTTTTCCCACATCAGGCACT GCAAAGACAACGAATTCCGG 1624–1679 0.818 83.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 CTTTTCCCACATCAGGCACT TCGATCCCGAAGAGAAGGAA 1209–1273 0.818 82.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 CTTTTCCCACATCAGGCACT GTGCAAAGCAAAGACAACGA 1631–1686 0.636 72.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 335–693 1.000 89.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 402–682 0.909 86.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC AAAAGAAAAATGGGGCGTGG 393–751 0.909 82.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 406–686 0.909 81.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AAAAGAAAAATGGGGCGTGG 460–740 0.818 79.3
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA AGGGTAGAATTAAGACAGATACAGA 405–470 1.000 52.0
trnQ-UUG-psbK_p2 trnQ-UUG-psbK CGAATAACGGGACCAAAACC AGGGTAGAATTAAGACAGATACAGA 415–480 1.000 52.0
trnQ-UUG-psbK_p3 trnQ-UUG-psbK ACCAAAACCCGTTGCCTTAC AGGGTAGAATTAAGACAGATACAGA 404–469 1.000 52.0
trnQ-UUG-psbK_p4 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA GGGTAGAATTAAGACAGATACAGA 404–469 1.000 52.0
trnQ-UUG-psbK_p5 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA AGGGTAGAATTAAGACAGATACAG 405–470 1.000 52.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 406–599 1.000 63.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 405–598 1.000 63.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 408–601 1.000 62.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GTTATCAGGGGAGTCGGAGA ACGAATCACACTTTTACCACT 473–666 0.909 59.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGTTATCAGGGGAGTCGGAG ACGAATCACACTTTTACCACT 474–667 0.909 59.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Goodyera biflora NC_064114.1 154375 View on NCBI ↗
Goodyera fumata NC_026773.1 155643 View on NCBI ↗
Goodyera henryi NC_064115.1 154292 View on NCBI ↗
Goodyera malipoensis MW589514.1 154687 View on NCBI ↗
Goodyera marginata MW589515.1 152680 View on NCBI ↗
Goodyera nankoensis MW589516.1 152566 View on NCBI ↗
Goodyera procera NC_029363.1 153240 View on NCBI ↗
Goodyera pubescens NC_064116.1 152417 View on NCBI ↗
Goodyera repens MW589518.1 152538 View on NCBI ↗
Goodyera striata NC_064117.1 152742 View on NCBI ↗
Goodyera yangmeishanensis MW589522.1 153926 View on NCBI ↗