Markers + reference

Platycerium

2 species · Polypodiaceae · Polypodiales

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Species 2
Genome length 158–160 kb
Candidate markers 263
Primer pairs 60

Genome-wide nucleotide diversity

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

Candidate markers

2 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rrn16-rps12 IRb 6746 0.3538 0.58 67.4 yes View details
rps12-rrn16 IRa 6746 0.3538 0.58 67.4 yes View details
psbD-trnT-GGU LSC 1360 0.0880 0.97 85.5 yes View details
petA-psbJ LSC 681 0.1232 0.94 85.4 yes View details
trnP-GGG-trnL-UAG SSC 251 0.1625 0.96 82.9 yes View details
psbM-petN LSC 978 0.0930 0.96 82.3 yes View details
rpoB-trnD-GUC LSC 644 0.0778 0.96 80.8 yes View details
matK-chlB LSC 1439 0.1142 0.99 80.5 yes View details
psbK-psbI LSC 422 0.1257 0.91 80.4 yes View details
atpH-atpI LSC 679 0.0905 0.98 80.4 yes View details
psbI-ycf12 LSC 722 0.0878 0.98 79.7 yes View details
trnC-GCA-trnG-GCC LSC 486 0.1242 0.98 79.7 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 60 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-chlB_p1 matK-chlB ATTTTGGTAACGGGCGCTAT GACTTCCGAAGCTGAGTCAG 1818–1827 1.000 87.9
matK-chlB_p2 matK-chlB CTCTAAAACGCGGCTACACT GACTTCCGAAGCTGAGTCAG 2043 0.500 59.9
matK-chlB_p3 matK-chlB TCTCTAAAACGCGGCTACAC GACTTCCGAAGCTGAGTCAG 2044 0.500 59.8
matK-chlB_p4 matK-chlB CTCTAAAACGCGGCTACACT CGATACAACTCATGCAGCCT 2502 0.500 59.5
matK-chlB_p5 matK-chlB CTCTAAAACGCGGCTACACT TGTTTCTCAAGCAGCTTGGT 2577 0.500 59.5
psbK-psbI_p1 psbK-psbI GCTGCAGTTAGCTTTCGCTA ACAAATAGTTTGAGGGTAAGCA 429–466 1.000 52.0
psbK-psbI_p2 psbK-psbI GCTGCAGTTAGCTTTCGCTA ACAAATAGTTTGAGGGTAAGCAT 429–466 1.000 52.0
psbK-psbI_p3 psbK-psbI TCTCCTAGCTTTTGTTTGGCA ACAAATAGTTTGAGGGTAAGCA 451–488 1.000 52.0
psbK-psbI_p4 psbK-psbI GCTGCAGTTAGCTTTCGCTA CAAATAGTTTGAGGGTAAGCA 428–465 1.000 52.0
psbK-psbI_p5 psbK-psbI GCTGCAGTTAGCTTTCGCTA ACAAATAGTTTGAGGGTAAGC 429–466 1.000 52.0
psbI-ycf12_p1 psbI-ycf12 TGCCAAATTACCCGAAGCTT CGTTACTAAGCAGTGCGACT 1856 0.500 59.2
psbI-ycf12_p2 psbI-ycf12 TTGCCAAATTACCCGAAGCT CGTTACTAAGCAGTGCGACT 1857 0.500 59.2
psbI-ycf12_p3 psbI-ycf12 TGCCAAATTACCCGAAGCTT TCGTTACTAAGCAGTGCGAC 1857 0.500 59.1
psbI-ycf12_p4 psbI-ycf12 TTGCCAAATTACCCGAAGCT TCGTTACTAAGCAGTGCGAC 1858 0.500 59.1
psbI-ycf12_p5 psbI-ycf12 GTTTCGGACTGCCTCATCTT CGTTACTAAGCAGTGCGACT 1718 0.500 59.0
atpH-atpI_p1 atpH-atpI TCCCTCCTGGAAAGTTTTGC AGGTGCCAGAAATCTGCAAA 1827–1831 1.000 85.3
atpH-atpI_p2 atpH-atpI TCCCTCCTGGAAAGTTTTGC GAATACCGTTCCTGGGTTCC 1724–1728 1.000 85.3
atpH-atpI_p3 atpH-atpI GAGGGAGTAGCGATCTCACT AGGTGCCAGAAATCTGCAAA 1866–1870 1.000 85.0
atpH-atpI_p4 atpH-atpI TCCCTCCTGGAAAGTTTTGC TGGCAAGTAGGAGTCTTCCA 1913–1917 1.000 85.0
atpH-atpI_p5 atpH-atpI TCCCTCCTGGAAAGTTTTGC TGGGGGAAGAAGAATACCGT 1735 0.500 59.7
rpoB-trnD-GUC_p1 rpoB-trnD-GUC CAAGTTCTGGTAGTACGGGC AATGTCAGCCTAACGTGTCC 1217 0.500 59.2
rpoB-trnD-GUC_p2 rpoB-trnD-GUC GCAAGTTCTGGTAGTACGGG AATGTCAGCCTAACGTGTCC 1218 0.500 59.2
rpoB-trnD-GUC_p3 rpoB-trnD-GUC CCCCTTCGAATTCATCCAGG AATGTCAGCCTAACGTGTCC 1504 0.500 59.0
rpoB-trnD-GUC_p4 rpoB-trnD-GUC CCCTTCGAATTCATCCAGGG AATGTCAGCCTAACGTGTCC 1503 0.500 59.0
rpoB-trnD-GUC_p5 rpoB-trnD-GUC GTAGCATCCTCCGACGATTC AATGTCAGCCTAACGTGTCC 1836 0.500 58.8
psbM-petN_p1 psbM-petN TCTTTACATTCAGACGGCCG TTTCATGTGTCTCGATGCGT 1364–1402 1.000 87.9
psbM-petN_p2 psbM-petN TCTTTACATTCAGACGGCCG AAGACGGAGGACTGCAAATC 1568–1607 1.000 87.2
psbM-petN_p3 psbM-petN TCTTTACATTCAGACGGCCG CCTTAATGCCCCAGTTCGAA 1549–1588 1.000 87.1
psbM-petN_p4 psbM-petN TCTTTACATTCAGACGGCCG GGTGTCGCCTAAAAGGAGAG 1564 0.500 59.9
psbM-petN_p5 psbM-petN GGACACGTTAGGCTGACATT GGTGTCGCCTAAAAGGAGAG 1872 0.500 59.1

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
Platycerium bifurcatum NC_054302.1 160442 View on NCBI ↗
Platycerium wallichii NC_057599.1 158286 View on NCBI ↗