Markers + reference

Goniophlebium

2 species · Polypodiaceae · Polypodiales

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Species 2
Genome length 152–153 kb
Candidate markers 269
Primer pairs 95

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 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 Genome 1028 0.1547 0.99 81.0 yes View details
psbK-psbI Genome 550 0.1618 0.94 82.8 yes View details
trnS-GCU-ycf12 Genome 559 0.1441 0.99 79.4 yes View details
psbM-petN Genome 1185 0.1360 0.98 82.0 yes View details
trnP-UGG-psaJ Genome 357 0.1709 1.00 75.9 yes View details
rpl23 Genome 267 0.0824 1.00 70.3 yes View details
ycf2-ndhF Genome 1060 0.1471 0.98 82.6 yes View details
rpl32-trnP-GGG Genome 619 0.1729 1.00 79.1 yes View details
chlL-ycf2 Genome 1046 0.1636 0.98 82.5 yes View details
rpoB-trnD-GUC Genome 668 0.1169 0.97 86.7 yes View details
trnC-GCA-trnG-GCC Genome 500 0.1390 0.96 83.2 yes View details
atpH-atpI Genome 736 0.1122 0.97 82.5 yes View details
rps12-rrn16 Genome 1912 0.0403 0.99 82.3 yes View details
rrn16-rps12 Genome 1913 0.0403 0.99 82.2 yes View details
psbD-trnT-GGU Genome 1354 0.1069 0.99 82.1 yes View details
rps4-trnL-UAA Genome 638 0.1075 0.98 81.9 yes View details
rpl20-rps12 Genome 953 0.0973 0.98 81.8 yes View details
trnT-GGU-trnfM-CAU Genome 483 0.1326 0.98 81.7 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16_p1 rps16 AACGCTTGCTTAACCACAGA TTGGAGATACGATAGCCCGT 1906 0.500 59.6
rps16_p2 rps16 CTCCCCCTGCTTTTCCAATT TTGGAGATACGATAGCCCGT 1829 0.500 59.5
rps16_p3 rps16 AACGCTTGCTTAACCACAGA TTACGAAGGCACCAACCAAA 1755 0.500 59.3
rps16_p4 rps16 AACGCTTGCTTAACCACAGA TCTAGGTTACGAAGGCACCA 1761 0.500 59.1
rps16_p5 rps16 CTCCCCCTGCTTTTCCAATT TTACGAAGGCACCAACCAAA 1678 0.500 59.1
psbK-psbI_p1 psbK-psbI TTGGGTTTCCTGTCAACCAG CTAATCTCTACGTCCGGGGT 1132 0.500 59.3
psbK-psbI_p2 psbK-psbI TGCCAAATTACCCGAAGCTT CTAATCTCTACGTCCGGGGT 779 0.500 59.2
psbK-psbI_p3 psbK-psbI TTGCCAAATTACCCGAAGCT CTAATCTCTACGTCCGGGGT 780 0.500 59.2
psbK-psbI_p4 psbK-psbI TTGGGTTTCCTGTCAACCAG TCGTCCAGGATCGTTCGATA 1111 0.500 59.1
psbK-psbI_p5 psbK-psbI ATCGAGTCTATTGAGGGGCA CTAATCTCTACGTCCGGGGT 1353 0.500 59.1
trnS-GCU-ycf12_p1 trnS-GCU-ycf12 AAAAGGTGTTGGATCCCCAC CCGAAGTACAAGAGTGACGG 1613 0.500 59.8
trnS-GCU-ycf12_p2 trnS-GCU-ycf12 AAAAGGTGTTGGATCCCCAC CGAAGTACAAGAGTGACGGG 1612 0.500 59.8
trnS-GCU-ycf12_p3 trnS-GCU-ycf12 ACCCCGGACGTAGAGATTAG CCGAAGTACAAGAGTGACGG 1206 0.500 59.7
trnS-GCU-ycf12_p4 trnS-GCU-ycf12 ACCCCGGACGTAGAGATTAG CGAAGTACAAGAGTGACGGG 1205 0.500 59.7
trnS-GCU-ycf12_p5 trnS-GCU-ycf12 AAAAGGTGTTGGATCCCCAC ACCTACTCCCCATTTTCGGA 1324 0.500 59.6
trnG-UCC_p1 trnG-UCC CTGGCAGCTCAAAAGGGTAA ATTAGCTAGGGGTCAGCGAT 1754–1800 1.000 89.2
trnG-UCC_p2 trnG-UCC TCCGAAAATGGGGAGTAGGT ACACTGCAGGAGAAGTAGGT 1444 0.500 59.6
trnG-UCC_p3 trnG-UCC TCCGAAAATGGGGAGTAGGT ATTAGCTAGGGGTCAGCGAT 1718 0.500 59.6
trnG-UCC_p4 trnG-UCC CTGGCAGCTCAAAAGGGTAA ACACTGCAGGAGAAGTAGGT 1526 0.500 59.1
trnG-UCC_p5 trnG-UCC TCGCCAATATGCAGATAGCC ACACTGCAGGAGAAGTAGGT 1362 0.500 59.1
atpH-atpI_p1 atpH-atpI GTAGGAAGTGACAAGCCTCG CATTCAGTTACCCCACGGAG 1644–1665 1.000 88.2
atpH-atpI_p2 atpH-atpI GTAGGAAGTGACAAGCCTCG AGGTGCCAGAAATCTGCAAA 1836–1857 1.000 87.7
atpH-atpI_p3 atpH-atpI TTCTGGCTGTCTCGCAATAC AGGTGCCAGAAATCTGCAAA 1430–1448 1.000 87.5
atpH-atpI_p4 atpH-atpI GAGGGAGTAGCGATCTCACT AGGTGCCAGAAATCTGCAAA 1924–1945 1.000 87.2
atpH-atpI_p5 atpH-atpI GGAGGGGTAAAAGTGCAACA AGGTGCCAGAAATCTGCAAA 1605 0.500 59.9
rpoB-trnD-GUC_p1 rpoB-trnD-GUC CAAGTTCTGGTAGTACGGGC GGTGCTCTAACCGATTGAACT 719–768 1.000 81.7
rpoB-trnD-GUC_p2 rpoB-trnD-GUC GCAAGTTCTGGTAGTACGGG GGTGCTCTAACCGATTGAACT 720–769 1.000 81.7
rpoB-trnD-GUC_p3 rpoB-trnD-GUC CAAGTTCTGGTAGTACGGGC GGATTGACGGGTCTCGAAC 762–811 1.000 81.1
rpoB-trnD-GUC_p4 rpoB-trnD-GUC GCAAGTTCTGGTAGTACGGG GGATTGACGGGTCTCGAAC 763–812 1.000 81.1
rpoB-trnD-GUC_p5 rpoB-trnD-GUC AGTTCTGGTAGTACGGGCAT GGTGCTCTAACCGATTGAACT 717–766 1.000 80.6

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
Goniophlebium amoenum MN017598.1 152067 View on NCBI ↗
Goniophlebium niponicum NC_040221.1 152551 View on NCBI ↗