Markers + reference

Onoclea

2 species · Onocleaceae · Polypodiales

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Species 2
Genome length 148–149 kb
Candidate markers 264
Primer pairs 90

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 7 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
matK Genome 1500 0.0000 1.00 40.0 yes View details
matK-rps16 Genome 616 0.0065 1.00 62.5 yes View details
atpF-atpH Genome 353 0.0142 1.00 53.6 yes View details
atpH Genome 246 0.0041 1.00 43.5 yes View details
psbM-petN Genome 866 0.0000 1.00 29.3 yes View details
atpB Genome 1482 0.0007 1.00 59.1 yes View details
psbE-petL Genome 759 0.0013 1.00 59.5 yes View details
petB Genome 1463 0.0014 1.00 59.5 yes View details
trnT-UGU-trnR-ACG Genome 718 0.0028 1.00 60.4 yes View details
trnR-ACG-trnT-UGU Genome 718 0.0028 1.00 60.4 yes View details
rps16 Genome 1081 0.0000 0.97 61.3 yes View details
ndhD Genome 1509 0.0007 1.00 59.1 yes View details
petN Genome 90 0.0111 1.00 58.9 yes View details
ndhF Genome 2241 0.0004 1.00 57.5 yes View details
rpoC1 Genome 2802 0.0000 1.00 56.2 yes View details
ycf1 Genome 5100 0.0004 1.00 52.7 yes View details
ndhB Genome 1207 0.0000 1.00 40.0 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
ndhB_p1 ndhB CGCTGTTGGTCGAACAATTC AAATCCGTGTGGCAGAAAGT 963 1.000 79.5
ndhB_p2 ndhB CGCTGTTGGTCGAACAATTC AATCCGTGTGGCAGAAAGTT 962 1.000 79.5
ndhB_p3 ndhB CGCTGTTGGTCGAACAATTC GTGTGGCAGAAAGTTACCCA 957 1.000 79.4
ndhB_p4 ndhB CGCTGTTGGTCGAACAATTC TGTGGCAGAAAGTTACCCAC 956 1.000 79.4
ndhB_p5 ndhB CGCTGTTGGTCGAACAATTC TCCGTGTGGCAGAAAGTTAC 960 1.000 78.6
matK_p1 matK TGAATTGCGTTGGAAAGGGA CCCCCACCTGATTTGCATAA 1642 1.000 78.6
matK_p2 matK AAAGGGAGAAGAGGCAGACT CCCCCACCTGATTTGCATAA 1629 1.000 78.4
matK_p3 matK AAGGGAGAAGAGGCAGACTT CCCCCACCTGATTTGCATAA 1628 1.000 78.4
matK_p4 matK GTGAATTGCGTTGGAAAGGG CCCCCACCTGATTTGCATAA 1643 1.000 78.2
matK_p5 matK CGTTGGAAAGGGAGAAGAGG CCCCCACCTGATTTGCATAA 1635 1.000 77.9
matK-rps16_p1 matK-rps16 CGCTAAGTCCTTCTTCCTGG ATTTTGAGACGGGCGAAGTT 743–811 1.000 77.1
matK-rps16_p2 matK-rps16 CGCTAAGTCCTTCTTCCTGG GGGCGCAATCAACAAAAACT 772–840 1.000 76.9
matK-rps16_p3 matK-rps16 CGCTAAGTCCTTCTTCCTGG TGAACAAGTCGGGATCAACC 720–788 1.000 76.6
matK-rps16_p4 matK-rps16 CGCTAAGTCCTTCTTCCTGG TAAGAAAGGGGCGCAATCAA 780–848 1.000 76.3
matK-rps16_p5 matK-rps16 CGCTAAGTCCTTCTTCCTGG TTAAGAAAGGGGCGCAATCA 781–849 1.000 76.3
rps16_p1 rps16 CTGTAAGCTGGGCCCATTAG ATGCGTCAGAAGGTTCGTAC 1171–1198 1.000 81.6
rps16_p2 rps16 GCTGGGCCCATTAGATTCTC ATGCGTCAGAAGGTTCGTAC 1165–1192 1.000 81.1
rps16_p3 rps16 CTGTAAGCTGGGCCCATTAG AGGAATGCGTCAGAAGGTTC 1175–1202 1.000 80.9
rps16_p4 rps16 GCTGGGCCCATTAGATTCTC AGGAATGCGTCAGAAGGTTC 1169–1196 1.000 80.3
rps16_p5 rps16 AAGCTGGGCCCATTAGATTC ATGCGTCAGAAGGTTCGTAC 1167–1194 1.000 78.9
trnG-UCC_p1 trnG-UCC GGGGGACTCCTCCTATAACC CCCAAATCGTGAACAAACGG 1175 1.000 79.4
trnG-UCC_p2 trnG-UCC GGGGGACTCCTCCTATAACC CCCCAAATCGTGAACAAACG 1176 1.000 79.4
trnG-UCC_p3 trnG-UCC GGGGGACTCCTCCTATAACC TTGTTCACGACACAATCCGT 1145 1.000 79.3
trnG-UCC_p4 trnG-UCC GGGGGACTCCTCCTATAACC ACTGGGGGCTCCAATATTCT 1106 1.000 79.1
trnG-UCC_p5 trnG-UCC GGGGGACTCCTCCTATAACC TTAGCCCCCAAATCGTGAAC 1181 1.000 78.4
atpF-atpH_p1 atpF-atpH GGAGCAGCGATCTCACTTAC GGATCAGTTGTAGCTCCAGC 430–444 1.000 79.4
atpF-atpH_p2 atpF-atpH CGGCAAGAGTCCAATCACTT GGATCAGTTGTAGCTCCAGC 453–467 1.000 79.1
atpF-atpH_p3 atpF-atpH AATACTTGCGGCAAGAGTCC GGATCAGTTGTAGCTCCAGC 461–475 1.000 78.5
atpF-atpH_p4 atpF-atpH AGCAGCGATCTCACTTACAC GGATCAGTTGTAGCTCCAGC 428–442 1.000 78.4
atpF-atpH_p5 atpF-atpH GCAGCGATCTCACTTACACT GGATCAGTTGTAGCTCCAGC 427–441 1.000 78.4

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
Onoclea sensibilis NC_035860.1 148395 View on NCBI ↗
Onoclea sensibilis var. interrupta PQ742174.1 148731 View on NCBI ↗