Markers + reference

Pelatantheria

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 146–147 kb
Candidate markers 267
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnE-UUC-trnT-GGU LSC 780 0.0413 0.96 78.4 yes View details
ndhC-trnV-UAC LSC 637 0.0640 0.98 78.8 yes View details
rpl16 LSC 1649 0.0245 0.99 61.6 yes View details
trnL-CAA-ndhB IRb 746 0.0483 0.80 71.3 yes View details
ndhB IRb 764 0.0656 0.94 78.4 yes View details
ycf1 IRb 65 0.0159 0.97 49.7 no View details
ycf1-rpl32 SSC 563 0.0969 0.86 80.4 yes View details
ycf1 SSC 5370 0.0204 1.00 51.3 yes View details
ndhB IRa 974 0.0951 0.81 91.8 yes View details
psbM-trnD-GUC LSC 1156 0.0213 0.98 73.3 yes View details
atpB-rbcL LSC 988 0.0149 0.95 72.0 yes View details
psbA-trnK-UUU LSC 252 0.0324 0.98 70.3 yes View details
rpl32-trnL-UAG SSC 512 0.0339 0.98 69.8 yes View details
cemA-petA LSC 246 0.0213 0.96 68.5 yes View details
trnR-UCU-atpA LSC 147 0.0479 0.99 68.1 yes View details
trnT-UGU-trnL-UAA LSC 622 0.0152 0.95 67.2 yes View details
matK-trnK-UUU LSC 1128 0.0261 0.82 67.0 yes View details
rpoA-rps11 LSC 76 0.0263 1.00 66.8 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK-UUU_p1 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC TCGTGTGCAATGAAAACTGC 403–408 1.000 81.5
psbA-trnK-UUU_p2 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC AAACTGCAAGCACGATTTGG 390–395 1.000 81.4
psbA-trnK-UUU_p3 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC CGTGTGCAATGAAAACTGCA 402–407 1.000 81.2
psbA-trnK-UUU_p4 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC ACGATTTGGGGAGGGATCTT 379–384 1.000 79.4
psbA-trnK-UUU_p5 psbA-trnK-UUU AACACCAAACCATCCGATGT TCGTGTGCAATGAAAACTGC 469–474 1.000 79.0
matK-trnK-UUU_p1 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA TCCGGGTTGCTAACTCAATG 1078–1275 1.000 76.4
matK-trnK-UUU_p2 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA CGGGTTGCTAACTCAATGGT 1076–1273 1.000 75.8
matK-trnK-UUU_p3 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA GATCCGGGTTGCTAACTCAA 1080–1277 1.000 74.1
matK-trnK-UUU_p4 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA TTGATCCGGGTTGCTAACTC 1082–1279 1.000 74.1
matK-trnK-UUU_p5 matK-trnK-UUU TCCTGAAGGAGTAGCGGATAT TCCGGGTTGCTAACTCAATG 1078–1275 1.000 72.5
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CCGAAGAAGCTGAAACCCTT 236–246 1.000 71.3
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TCACCGAAGAAGCTGAAACC 239–249 1.000 71.1
trnR-UCU-atpA_p3 trnR-UCU-atpA GTTCAAATCCTATTGGACGCA CCGAAGAAGCTGAAACCCTT 235–245 1.000 65.7
trnR-UCU-atpA_p4 trnR-UCU-atpA GTTCAAATCCTATTGGACGCA TCACCGAAGAAGCTGAAACC 238–248 1.000 65.5
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CACCGAAGAAGCTGAAACCC 238–248 1.000 63.1
psbM-trnD-GUC_p1 psbM-trnD-GUC CAGCGCAGTAGCAATAAACG CCATGCATATGGCTGGGATT 1283–1303 1.000 82.1
psbM-trnD-GUC_p2 psbM-trnD-GUC CAGCGCAGTAGCAATAAACG AGTTCAATCGGTCAGAGCAC 1261–1281 1.000 82.0
psbM-trnD-GUC_p3 psbM-trnD-GUC ATGAACAGCGCAGTAGCAAT CCATGCATATGGCTGGGATT 1288–1308 1.000 80.6
psbM-trnD-GUC_p4 psbM-trnD-GUC TTGGCTGACTGTTTTGACGT CCATGCATATGGCTGGGATT 1340–1360 1.000 80.5
psbM-trnD-GUC_p5 psbM-trnD-GUC TTGGCTGACTGTTTTGACGT AGTTCAATCGGTCAGAGCAC 1318–1338 1.000 80.4
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 884–1062 1.000 83.5
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCATGGCGTTACTCTACCAC 863–1041 1.000 83.2
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TGGCGTTACTCTACCACTGA 860–1038 1.000 83.0
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 862–1040 1.000 82.7
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCGATGACTTACGCCTTACC 881–1059 1.000 82.4
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 656–672 1.000 83.4
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 664–680 1.000 82.8
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 688–704 1.000 82.3
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 696–712 1.000 81.7
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ATCCAATCAAGTCCGTAGCG 679–695 1.000 81.4

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
Pelatantheria rivesii MN124412.1 146094 View on NCBI ↗
Pelatantheria scolopendrifolia NC_035829.1 146860 View on NCBI ↗