Markers + reference

Davallia

2 species · Davalliaceae · Polypodiales

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Species 2
Genome length 152–154 kb
Candidate markers 272
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhB Genome 1224 0.2105 0.03 55.6 yes View details
rps16 Genome 1052 0.1965 0.93 83.2 yes View details
psbK-psbI Genome 553 0.2445 0.91 84.1 yes View details
rpoB-trnD-GUC Genome 683 0.2305 0.94 84.0 yes View details
psbM-petN Genome 1167 0.2020 0.95 83.7 yes View details
ycf2-ndhF Genome 3582 0.2210 0.15 56.6 yes View details
trnL-UAG-ccsA Genome 275 0.2920 1.00 73.0 yes View details
psbD-trnT-GGU Genome 1360 0.1696 0.95 85.7 yes View details
rpl20-rps12 Genome 846 0.1219 0.96 84.0 yes View details
atpH-atpI Genome 748 0.1649 0.90 83.4 yes View details
trnT-GGU-trnfM-CAU Genome 501 0.2030 0.94 83.2 yes View details
trnC-GCA-trnG-GCC Genome 529 0.2070 0.87 82.9 yes View details
trnN-GUU-ycf2 Genome 518 0.1202 0.95 82.8 yes View details
psbE-petL Genome 748 0.1512 0.96 82.6 yes View details
petB Genome 1457 0.1021 0.97 81.4 yes View details
petA-psbJ Genome 413 0.2531 0.97 81.3 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ndhB_p1 ndhB TCTTGGGGCGACTTATCAAA ACCAATTTTGCTTTCTCGGA 1179 0.500 33.5
ndhB_p2 ndhB TGGGGCGACTTATCAAATTGA ACCAATTTTGCTTTCTCGGA 1176 0.500 31.9
ndhB_p3 ndhB ATCTTGGGGCGACTTATCAA ACCAATTTTGCTTTCTCGGA 1180 0.500 31.6
ndhB_p4 ndhB TCTTGGGGCGACTTATCAAA ACCAATTTTGCTTTCTCGGAT 1179 0.500 30.0
ndhB_p5 ndhB TCTTGGGGCGACTTATCAAAT ACCAATTTTGCTTTCTCGGA 1179 0.500 29.6
rps16_p1 rps16 GCCTTCCCCTCCTTTTTCAA GACTTCTGAAGCTGAGTCGG 1592 0.500 59.8
rps16_p2 rps16 GCCTTCCCCTCCTTTTTCAA GGACTTCTGAAGCTGAGTCG 1593 0.500 59.8
rps16_p3 rps16 GCCTTCCCCTCCTTTTTCAA AGGGGATAAGCACCAAGTCT 1641 0.500 59.7
rps16_p4 rps16 GCCTTCCCCTCCTTTTTCAA CTTTGTGAGGGGGAAAACCA 1553 0.500 59.3
rps16_p5 rps16 GCCTTCCCCTCCTTTTTCAA TTGTGAGGGGGAAAACCAAG 1551 0.500 59.3
psbK-psbI_p1 psbK-psbI GCCGCAGTTAGCTTTCGATA AGACAAATAGTTTGAGGGTAAGCA 555–599 1.000 55.6
psbK-psbI_p2 psbK-psbI GCCGCAGTTAGCTTTCGATA TGCATAGACAAATAGTTTGAGGGT 560–604 1.000 55.1
psbK-psbI_p3 psbK-psbI GCCGCAGTTAGCTTTCGATA GACAAATAGTTTGAGGGTAAGCA 554–598 1.000 54.8
psbK-psbI_p4 psbK-psbI TAGCTTTTGTTTGGCAAGCC AGACAAATAGTTTGAGGGTAAGCA 572–616 1.000 54.8
psbK-psbI_p5 psbK-psbI TAGCTTTTGTTTGGCAAGCC TGCATAGACAAATAGTTTGAGGGT 577–621 1.000 54.3
atpH-atpI_p1 atpH-atpI TTCTGGCTGTCTCGCAATAC AGGTGCCAGAAATCTGCAAA 1460 0.500 59.9
atpH-atpI_p2 atpH-atpI TTCTGGCTGTCTCGCAATAC TCGTCATCGCCTTGTTAGTG 1494 0.500 59.8
atpH-atpI_p3 atpH-atpI AATTACTTGAGGGAGCAGCG AGGTGCCAGAAATCTGCAAA 1981 0.500 59.8
atpH-atpI_p4 atpH-atpI AATTGAAGCGAGGCCTACAG AGGTGCCAGAAATCTGCAAA 1394 0.500 59.8
atpH-atpI_p5 atpH-atpI GGGAAAGGAGGGGTAGAGTT AGGTGCCAGAAATCTGCAAA 1623 0.500 59.7
rpoB-trnD-GUC_p1 rpoB-trnD-GUC CAAGTTCTGGTAGTACGGGC CGAGCGGTTTTGTCGAAAAA 1412 0.500 59.2
rpoB-trnD-GUC_p2 rpoB-trnD-GUC GCAAGTTCTGGTAGTACGGG CGAGCGGTTTTGTCGAAAAA 1413 0.500 59.2
rpoB-trnD-GUC_p3 rpoB-trnD-GUC CAAGTTCTGGTAGTACGGGC GACGCACCCTTTTCAGGTTA 1211 0.500 59.0
rpoB-trnD-GUC_p4 rpoB-trnD-GUC GCAAGTTCTGGTAGTACGGG GACGCACCCTTTTCAGGTTA 1212 0.500 59.0
rpoB-trnD-GUC_p5 rpoB-trnD-GUC GATATCCGCGTCTGTAGCAG CGAGCGGTTTTGTCGAAAAA 2077 0.500 59.0
psbM-petN_p1 psbM-petN TTCTCGCGTTTGTAGCTACC AAGACGGAGGACTGCAAATC 1819–1849 1.000 90.2
psbM-petN_p2 psbM-petN TTCTCGCGTTTGTAGCTACC TGTTGTTTCTGCCCGAATCA 1919 0.500 59.7
psbM-petN_p3 psbM-petN TTCTCGCGTTTGTAGCTACC TTTATTGCGCCAAGATCGGA 1692 0.500 59.6
psbM-petN_p4 psbM-petN TTCTCGCGTTTGTAGCTACC CCTTTGAATAGGGAGCCGTC 1546 0.500 59.5
psbM-petN_p5 psbM-petN TTCTCGCGTTTGTAGCTACC TTTCATGTGTCTCGATGCGT 1631 0.500 59.3

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
Davallia solida var. fejeensis NC_044688.1 152479 View on NCBI ↗
Davallia trichomanoides PX170254.1 154217 View on NCBI ↗