Markers + reference

Oberonia

3 species · Orchidaceae · Asparagales

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Species 3
Genome length 143–147 kb
Candidate markers 259
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 259 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-GCC LSC 923 0.0595 0.97 83.0 yes View details
rpoC1 LSC 2803 0.0107 1.00 47.9 yes View details
trnE-UUC-trnT-GGU LSC 1323 0.0601 0.95 79.8 yes View details
atpB-rbcL LSC 986 0.0519 0.99 79.6 yes View details
clpP-psbB LSC 639 0.0735 0.99 81.4 yes View details
ndhB IRb 1746 0.0100 0.71 47.2 yes View details
trnN-GUU-rpl32 SSC 1263 0.1017 0.97 89.0 yes View details
ndhB IRa 1746 0.0100 0.71 47.2 no View details
psaI-ycf4 LSC 425 0.0566 1.00 79.5 yes View details
trnW-CCA-trnP-UGG LSC 166 0.0462 1.00 79.4 yes View details
petN-psbM LSC 788 0.0429 0.97 78.9 yes View details
psbE-petL LSC 1237 0.0402 0.98 78.3 yes View details
psbB-psbT LSC 594 0.0484 0.98 77.8 yes View details
trnK-UUU-rps16 LSC 435 0.0450 0.99 77.3 yes View details
trnC-GCA-petN LSC 665 0.0331 1.00 77.2 yes View details
petA-psbJ LSC 1058 0.0414 0.99 76.9 yes View details
psbM-trnD-GUC LSC 969 0.0415 0.99 76.2 yes View details
ccsA-psaC SSC 573 0.0445 0.99 76.1 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-rps16_p1 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC AGAGAATTTCAAGTTTCTTTGGA 491–538 1.000 47.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGAGAATTTCAAGTTTCTTTGGA 505–552 1.000 47.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGAGAATTTCAAGTTTCTTTGGA 504–551 1.000 47.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGAGAATTTCAAGTTTCTTTGGAT 504–551 1.000 47.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGGATCAGTCGCGGTCTTAT AGAGAATTTCAAGTTTCTTTGGA 590–637 1.000 46.6
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 875–1098 1.000 61.7
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 874–1097 1.000 61.7
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 878–1101 1.000 60.6
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 877–1100 1.000 60.6
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 876–1099 1.000 60.6
rpoC1_p1 rpoC1 AGTATAGCATGAGTTAGCTAGC TCCAGATGAATAGGAAGGAAGT 2877–2883 0.667 27.4
rpoC1_p2 rpoC1 AGTATAGCATGAGTTAGCTAGC AGGAAGGAAGTTTGATCTCAATGA 2866–2872 0.667 27.4
rpoC1_p3 rpoC1 AGTATAGCATGAGTTAGCTAGC TCCAGATGAATAGGAAGGAAGTT 2877–2883 0.667 27.4
rpoC1_p4 rpoC1 AGTATAGCATGAGTTAGCTAGC TTCCAGATGAATAGGAAGGAAGT 2878–2884 0.667 27.4
rpoC1_p5 rpoC1 AGTATAGCATGAGTTAGCTAGC AGGAAGGAAGTTTGATCTCA 2866–2872 0.667 27.4
trnC-GCA-petN_p1 trnC-GCA-petN TTTGGATGAAATTTGGCGGC AGCCCAAGCGAGACTTACTA 760–788 1.000 84.9
trnC-GCA-petN_p2 trnC-GCA-petN CCAGTTCGAATCTGGGTGTC AGCCCAAGCGAGACTTACTA 699–727 1.000 84.0
trnC-GCA-petN_p3 trnC-GCA-petN GATGAAATTTGGCGGCATGG AGCCCAAGCGAGACTTACTA 756–784 1.000 82.2
trnC-GCA-petN_p4 trnC-GCA-petN GGATGAAATTTGGCGGCATG AGCCCAAGCGAGACTTACTA 757–785 1.000 82.2
trnC-GCA-petN_p5 trnC-GCA-petN TTTGGATGAAATTTGGCGGC CCCACTCCTTCCCCATACTA 817–845 1.000 81.7
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT ACGTCAAAACAGTCAGCCAA 848–936 1.000 84.9
petN-psbM_p2 petN-psbM TAGTATGGGGAAGGAGTGGG ACGTCAAAACAGTCAGCCAA 791–879 1.000 82.4
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT TACGTCAAAACAGTCAGCCA 849–937 1.000 82.1
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT CGTCAAAACAGTCAGCCAAA 847–935 1.000 80.2
petN-psbM_p5 petN-psbM TAGTATGGGGAAGGAGTGGG TACGTCAAAACAGTCAGCCA 792–880 1.000 79.6
psbM-trnD-GUC_p1 psbM-trnD-GUC CAGCGCAGTAGCAATAAACG TTCGTCGCTCCATGAAGAAG 1306–1337 0.667 70.4
psbM-trnD-GUC_p2 psbM-trnD-GUC CAGCGCAGTAGCAATAAACG CCATGCATATGGCTGGGATT 1073–1096 0.667 69.9
psbM-trnD-GUC_p3 psbM-trnD-GUC ATGAATCTTTTCGAGGGGCC TTCGTCGCTCCATGAAGAAG 1851 0.333 52.8
psbM-trnD-GUC_p4 psbM-trnD-GUC ATGAATCTTTTCGAGGGGCC CCATGCATATGGCTGGGATT 1610 0.333 52.3
psbM-trnD-GUC_p5 psbM-trnD-GUC ATGAATCTTTTCGAGGGGCC AGTTCAATCGGTCAGAGCAC 1588 0.333 52.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Oberonia integerrima NC_084378.1 146620 View on NCBI ↗
Oberonia japonica NC_035832.1 142996 View on NCBI ↗
Oberonia seidenfadenii NC_056165.1 143062 View on NCBI ↗