Markers + reference

Pleurothallis

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 156–158 kb
Candidate markers 268
Primer pairs 120

Genome-wide nucleotide diversity

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

Candidate markers

14 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI LSC 530 0.0517 0.95 84.1 yes View details
trnS-GCU-trnG-UCC LSC 900 0.0302 0.92 71.9 yes View details
atpF LSC 1495 0.0228 1.00 58.7 yes View details
trnE-UUC-trnT-GGU LSC 653 0.0448 0.99 72.5 yes View details
atpB-rbcL LSC 1025 0.0243 0.92 66.0 yes View details
rbcL-accD LSC 869 0.0444 0.96 73.7 yes View details
psbE-petL LSC 1130 0.0230 1.00 66.5 yes View details
psaJ-rpl33 LSC 611 0.0459 1.00 79.1 yes View details
clpP1 LSC 2193 0.0147 0.99 53.5 yes View details
clpP1-psbB LSC 825 0.0308 0.79 66.9 yes View details
rpl16 LSC 1644 0.0251 0.97 62.0 yes View details
rps12-trnV-GAC IRb 1911 0.0148 0.95 70.7 yes View details
ycf1 IRb 1071 0.0047 1.00 61.4 no View details
ycf1 SSC 5367 0.0186 1.00 48.9 yes View details
rpl2-rpl23 IRb 18 0.1111 1.00 87.5 yes View details
psbC-trnS-UGA LSC 141 0.0500 0.99 81.9 yes View details
cemA-petA LSC 242 0.0426 0.97 79.2 yes View details
psbI-trnS-GCU LSC 129 0.0775 1.00 76.8 yes View details
rpoB-trnC-GCA LSC 1403 0.0211 0.94 75.4 yes View details
psaC-ndhE SSC 543 0.0231 0.96 75.0 yes View details
trnK-UUU-rps16 LSC 581 0.0314 0.99 73.1 yes View details
rpl16-rps3 LSC 187 0.0608 0.97 71.1 yes View details
ndhC-trnV-UAC LSC 688 0.0330 0.97 71.0 yes View details
matK-trnK-UUU LSC 882 0.0336 0.98 70.9 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 120 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TCGATTGAAATGACCAAACCT ATCCCCATTCCCTATTGGCT 2993 0.500 33.1
trnK-UUU_p2 trnK-UUU TGACCAAACCTATCAGAACAAGA ATCCCCATTCCCTATTGGCT 2983 0.500 30.3
trnK-UUU_p3 trnK-UUU TCGATTGAAATGACCAAACCT TCCCCATTCCCTATTGGCTA 2992 0.500 30.1
trnK-UUU_p4 trnK-UUU ATCGATTGAAATGACCAAACCT ATCCCCATTCCCTATTGGCT 2994 0.500 29.4
trnK-UUU_p5 trnK-UUU TCGATTGAAATGACCAAACC ATCCCCATTCCCTATTGGCT 2993 0.500 28.4
matK-trnK-UUU_p1 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA ATCCGGGTTGCTAACTCAAC 1015–1203 1.000 74.2
matK-trnK-UUU_p2 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA AACGGTAGAGTACTCGGCTT 998–1186 1.000 73.7
matK-trnK-UUU_p3 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA ACGGTAGAGTACTCGGCTTT 997–1185 1.000 73.7
matK-trnK-UUU_p4 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA GATCCGGGTTGCTAACTCAA 1016–1204 1.000 71.9
matK-trnK-UUU_p5 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA TTGATCCGGGTTGCTAACTC 1018–1206 1.000 71.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GTGCTCAACCCACAGGAAC 674–679 1.000 68.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GTGCTCAACCCACAGGAAC 673–678 1.000 68.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TGCTCAACCCACAGGAACT 673–678 1.000 67.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TGCTCAACCCACAGGAACT 672–677 1.000 67.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC GTGCTCAACCCACAGGAAC 660–665 1.000 66.0
psbK-psbI_p1 psbK-psbI CTTTGTTTGGCAAGCTGCTT ACGCCCCGGATCATTAGATA 645–654 1.000 85.5
psbK-psbI_p2 psbK-psbI CTTTGTTTGGCAAGCTGCTT TACGCCCCGGATCATTAGAT 646–655 1.000 85.5
psbK-psbI_p3 psbK-psbI AATCGTAGACGTTATGCCGG ACGCCCCGGATCATTAGATA 693–702 1.000 84.5
psbK-psbI_p4 psbK-psbI AATCGTAGACGTTATGCCGG TACGCCCCGGATCATTAGAT 694–703 1.000 84.5
psbK-psbI_p5 psbK-psbI CGTTATGCCGGTTATCCCTT ACGCCCCGGATCATTAGATA 684–693 1.000 83.6
psbI-trnS-GCU_p1 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA TGGACTAAAGCGTCGGATTG 242 1.000 82.7
psbI-trnS-GCU_p2 psbI-trnS-GCU TATCTAATGATCCGGGGCGT TGGACTAAAGCGTCGGATTG 243 1.000 82.7
psbI-trnS-GCU_p3 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA GTGGACTAAAGCGTCGGATT 243 1.000 82.7
psbI-trnS-GCU_p4 psbI-trnS-GCU TATCTAATGATCCGGGGCGT GTGGACTAAAGCGTCGGATT 244 1.000 82.7
psbI-trnS-GCU_p5 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA GGGTTCGAATCCCTCTCTCT 192 1.000 81.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 969–989 1.000 57.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 968–988 1.000 57.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 972–992 1.000 56.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 971–991 1.000 56.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 970–990 1.000 56.6

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
Pleurothallis lindenii PX828359.1 157622 View on NCBI ↗
Pleurothallis matudana NC_085594.1 156494 View on NCBI ↗