Markers + reference

Lepanthes

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 156–157 kb
Candidate markers 272
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 552 0.0280 0.97 62.0 yes View details
psbK-psbI LSC 360 0.0284 0.98 66.4 yes View details
trnS-GCU-trnG-UCC LSC 921 0.0255 0.98 70.7 yes View details
atpA LSC 1524 0.0026 1.00 46.3 yes View details
rpoB-trnC-GCA LSC 1338 0.0233 0.96 67.4 yes View details
trnT-GGU-psbD LSC 643 0.0300 0.93 68.5 yes View details
atpB-rbcL LSC 1031 0.0191 0.97 64.8 yes View details
accD-psaI LSC 807 0.0496 1.00 84.3 yes View details
petA-psbJ LSC 876 0.0284 0.97 73.7 yes View details
psbE-petL LSC 1123 0.0208 0.98 66.8 yes View details
ycf1 IRb 1080 0.0046 1.00 50.2 no View details
ycf1 SSC 5439 0.0120 1.00 46.3 yes View details
ndhF-rpl32 SSC 816 0.0253 0.97 76.0 yes View details
psaB-psaA LSC 25 0.0400 1.00 75.5 yes View details
atpA-atpF LSC 72 0.1250 1.00 74.5 yes View details
trnT-UGU-trnL-UAA LSC 612 0.0212 1.00 71.0 yes View details
psbB-psbT LSC 508 0.0142 0.97 67.8 yes View details
psbI-trnS-GCU LSC 138 0.0362 1.00 67.3 yes View details
trnF-GAA-ndhJ LSC 145 0.0414 1.00 67.1 yes View details
petN-psbM LSC 760 0.0212 0.99 66.8 yes View details
rpl22-rps19 IRb 188 0.0167 0.96 66.1 yes View details
rps15-ycf1 SSC 331 0.0185 0.98 64.8 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TGGAATGACCAAACCTATCAGA CCCTCTTGGCTCTTTCCTTC 2993 0.500 33.5
trnK-UUU_p2 trnK-UUU TGGAATGACCAAACCTATCAGA TCCCTCTTGGCTCTTTCCTT 2994 0.500 32.4
trnK-UUU_p3 trnK-UUU TGGAATGACCAAACCTATCAGA TTCCCTCTTGGCTCTTTCCT 2995 0.500 32.4
trnK-UUU_p4 trnK-UUU TGGAATGACCAAACCTATCAGAA CCCTCTTGGCTCTTTCCTTC 2993 0.500 30.9
trnK-UUU_p5 trnK-UUU TGGAATGACCAAACCTATCAGA CCATTCCCTCTTGGCTCTTT 2998 0.500 30.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TCGATCCCGAAGAGAAGGAA 787–800 1.000 81.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCGATCCCGAAGAGAAGGAA 786–799 1.000 81.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TCTATCCCAATGGGCCATCT 829–842 1.000 80.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCTATCCCAATGGGCCATCT 828–841 1.000 80.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCAGGATCAGTCGCAG TCTATCCCAATGGGCCATCT 920–933 1.000 79.1
psbK-psbI_p1 psbK-psbI CTTTGTTTGGCAAGCTGCTT ACGCCCCGGATCATTAGATA 478–484 1.000 82.0
psbK-psbI_p2 psbK-psbI CTTTGTTTGGCAAGCTGCTT TACGCCCCGGATCATTAGAT 479–485 1.000 82.0
psbK-psbI_p3 psbK-psbI AATCGTAGACGTTATGCCGG ACGCCCCGGATCATTAGATA 526–532 1.000 81.1
psbK-psbI_p4 psbK-psbI AATCGTAGACGTTATGCCGG TACGCCCCGGATCATTAGAT 527–533 1.000 81.1
psbK-psbI_p5 psbK-psbI CGTTATGCCGGTTATCCCTT ACGCCCCGGATCATTAGATA 517–523 1.000 80.2
psbI-trnS-GCU_p1 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA TGGACTAAAGCGTCGGATTG 251 1.000 81.0
psbI-trnS-GCU_p2 psbI-trnS-GCU TATCTAATGATCCGGGGCGT TGGACTAAAGCGTCGGATTG 252 1.000 81.0
psbI-trnS-GCU_p3 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA GTGGACTAAAGCGTCGGATT 252 1.000 81.0
psbI-trnS-GCU_p4 psbI-trnS-GCU TATCTAATGATCCGGGGCGT GTGGACTAAAGCGTCGGATT 253 1.000 81.0
psbI-trnS-GCU_p5 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA GGGTTCGAATCCCTCTCTCT 201 1.000 79.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AATGGCAAGACCCCTTAACT 1028–1038 1.000 72.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AATGGCAAGACCCCTTAACT 1027–1037 1.000 72.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AATTGCAAGTGATCAGGGGG AATGGCAAGACCCCTTAACT 1102–1112 1.000 71.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AAATGGCAAGACCCCTTAACT 1029–1039 1.000 70.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AAATGGCAAGACCCCTTAACT 1028–1038 1.000 70.9
atpA_p1 atpA AGCCTTCCAAGCTAACGATG ATTGATATCCTCGGGTCCGT 2063–2068 1.000 80.8
atpA_p2 atpA CCTAGCCTTCCAAGCTAACG ATTGATATCCTCGGGTCCGT 2066–2071 1.000 80.6
atpA_p3 atpA ATTCCCGCTACCCGCTATAT ATTGATATCCTCGGGTCCGT 2035–2040 1.000 80.0
atpA_p4 atpA AGCCTTCCAAGCTAACGATG AATTGAGCGTGAGAGCCAAA 2531–2536 1.000 79.9
atpA_p5 atpA AGCCTTCCAAGCTAACGATG AGCCATTGAACAGCTCGAAA 2361–2366 1.000 79.9

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
Lepanthes clareae PX828354.1 156557 View on NCBI ↗
Lepanthes cloesii PX828355.1 156112 View on NCBI ↗