Markers + reference

Pothos

2 species · Araceae · Alismatales

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Species 2
Genome length 165–165 kb
Candidate markers 267
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 877 0.0233 0.98 63.3 yes View details
rps16 LSC 1211 0.0138 0.90 57.8 yes View details
trnS-GCU-trnR-UCU LSC 2037 0.0208 0.99 62.9 yes View details
atpF-atpH LSC 499 0.0294 0.96 66.2 yes View details
psbZ-trnG-GCC LSC 458 0.0334 0.85 71.3 yes View details
rps4-trnT-UGU LSC 965 0.0234 0.84 58.8 yes View details
trnF-GAA-ndhJ LSC 939 0.0145 0.81 61.9 yes View details
accD-psaI LSC 1069 0.0216 1.00 62.5 yes View details
trnL-CAA-ndhB LSC 755 0.0328 0.97 68.7 yes View details
rps15-ndhH SSC 6639 0.0222 0.98 52.7 yes View details
trnM-CAU-atpE LSC 159 0.0629 1.00 82.8 yes View details
petD-rpoA LSC 211 0.0569 1.00 78.1 yes View details
ndhH-rps15 IRb 103 0.0638 0.91 71.4 yes View details
psbA-trnK-UUU LSC 231 0.0223 0.97 68.2 yes View details
petN-psbM LSC 1177 0.0146 0.99 68.0 yes View details
petA-psbJ LSC 1100 0.0111 0.99 66.5 yes View details
psbE-petL LSC 1171 0.0086 0.99 64.8 yes View details
psaC-ndhE IRb 1028 0.0060 0.98 64.4 yes View details
ndhE-psaC IRa 1028 0.0060 0.98 64.4 yes View details
trnQ-UUG-psbK LSC 389 0.0286 0.99 64.3 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
psbA-trnK-UUU_p1 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC AATTGCAAGCACGATTTGGG 358–365 1.000 81.9
psbA-trnK-UUU_p2 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC CATAGGGAAAGTCGTGTGCA 383–390 1.000 81.6
psbA-trnK-UUU_p3 psbA-trnK-UUU ATGTAAAGGCGGTTTTCGGT AATTGCAAGCACGATTTGGG 408–415 1.000 80.9
psbA-trnK-UUU_p4 psbA-trnK-UUU ATGTAAAGGCGGTTTTCGGT CATAGGGAAAGTCGTGTGCA 433–440 1.000 80.7
psbA-trnK-UUU_p5 psbA-trnK-UUU CCATCCAATGTAAAGGCGGT AATTGCAAGCACGATTTGGG 415–422 1.000 79.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAGGAGCTCAACCCACAAG 975–1058 1.000 81.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAGGAGCTCAACCCACAAG 974–1057 1.000 81.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGCTCAACCCACAAGAACTG 970–1053 1.000 81.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGCTCAACCCACAAGAACTG 969–1052 1.000 81.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAAGGAGCTCAACCCACAAG 984–1067 1.000 80.5
rps16_p1 rps16 TTGTGTTGAATTGGCACGAC CGTTCCGACCAATCTGTTGA 1648–1775 1.000 79.5
rps16_p2 rps16 TTGTGTTGAATTGGCACGAC TCGTTCCGACCAATCTGTTG 1649–1776 1.000 79.5
rps16_p3 rps16 GGATGGGGATAAACGGATCC CGTTCCGACCAATCTGTTGA 1775–1905 1.000 79.5
rps16_p4 rps16 ACTTGTGTTGAATTGGCACG CGTTCCGACCAATCTGTTGA 1650–1777 1.000 79.4
rps16_p5 rps16 ACTTGTGTTGAATTGGCACG TCGTTCCGACCAATCTGTTG 1651–1778 1.000 79.4
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA CTCAGGCAATTTCCCGAAGA 514–516 1.000 76.0
trnQ-UUG-psbK_p2 trnQ-UUG-psbK CGAATAACGGGACCAAAACC CTCAGGCAATTTCCCGAAGA 524–526 1.000 74.1
trnQ-UUG-psbK_p3 trnQ-UUG-psbK ACCAAAACCCGTTGCCTTAC CTCAGGCAATTTCCCGAAGA 513–515 1.000 73.7
trnQ-UUG-psbK_p4 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA TCAGGCAATTTCCCGAAGAA 513–515 1.000 72.3
trnQ-UUG-psbK_p5 trnQ-UUG-psbK TGAAGAATTGATCTGGGACGG CTCAGGCAATTTCCCGAAGA 560–562 1.000 71.1
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU AGTGACCAGAGAAACGGAGA AGAAGACCTCTGTCCTATCCA 2175–2236 1.000 65.6
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU ATTAGCAATCCGCCGCTTTA AGAAGACCTCTGTCCTATCCA 2113–2174 1.000 65.4
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU AGTGACCAGAGAAACGGAGA AGGTTTAGAAGACCTCTGTCCT 2181–2242 1.000 65.0
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU ATTAGCAATCCGCCGCTTTA AGGTTTAGAAGACCTCTGTCCT 2119–2180 1.000 64.7
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU GAGAAACGGAGAGAGAGGGA AGAAGACCTCTGTCCTATCCA 2167–2228 1.000 64.6
atpF-atpH_p1 atpF-atpH GGCCAGGGAAACGAAAGAAT AATTTACGGACTGGTCGTGG 590–599 1.000 80.5
atpF-atpH_p2 atpF-atpH GCCAGGGAAACGAAAGAATC AATTTACGGACTGGTCGTGG 589–598 1.000 76.8
atpF-atpH_p3 atpF-atpH GGCCAGGGAAACGAAAGAA AATTTACGGACTGGTCGTGG 590–599 1.000 75.9
atpF-atpH_p4 atpF-atpH GGCCAGGGAAACGAAAGAAT ACAATTTACGGACTGGTCGT 592–601 1.000 74.6
atpF-atpH_p5 atpF-atpH GGCCAGGGAAACGAAAGAAT GGTCGTGGCATTAGCACTTT 578–587 1.000 74.6

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
Pothos chinensis PV938952.1 165165 View on NCBI ↗
Pothos scandens MN046891.1 164719 View on NCBI ↗