Markers + reference

Woodwardia

3 species · Blechnaceae · Polypodiales

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Species 3
Genome length 153–155 kb
Candidate markers 269
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

5 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
matK-rps16 LSC 621 0.0683 1.00 80.0 yes View details
trnC-GCA-trnG-UCC LSC 402 0.1219 1.00 80.8 yes View details
trnR-UCU-rps12 IRb 2923 0.0893 0.99 82.2 yes View details
rpl32-trnP-GGG SSC 537 0.1024 0.99 80.0 yes View details
rps12-ICG91_pgr003 IRa 2923 0.0890 0.99 82.2 yes View details
rpoB-trnD-GUC LSC 791 0.0489 1.00 84.9 yes View details
rps4-trnL-UAA LSC 656 0.0487 0.98 82.3 yes View details
psbM-petN LSC 869 0.0622 0.99 82.0 yes View details
atpH-atpI LSC 753 0.0514 0.99 81.0 yes View details
petN-trnC-GCA LSC 483 0.0605 0.98 80.6 yes View details
petA-psbJ LSC 832 0.0603 0.99 80.4 yes View details
rpl21-rpl32 SSC 180 0.0685 1.00 80.0 yes View details
trnS-GGA-rps4 LSC 435 0.0544 1.00 79.8 yes View details
ccsA-ndhD SSC 413 0.0675 0.96 79.0 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-rps16_p1 matK-rps16 TCGTGTCCATGAAGCTAACG ATCCCCTCGCTACTATTGCT 1439 0.333 53.1
matK-rps16_p2 matK-rps16 GGCGAACCAGAGTTTCTAGG ATCCCCTCGCTACTATTGCT 1245 0.333 53.1
matK-rps16_p3 matK-rps16 TGCTAAGTCCTTCGCTGTTC ATCCCCTCGCTACTATTGCT 813 0.333 52.6
matK-rps16_p4 matK-rps16 TCGTGTCCATGAAGCTAACG AGTGAAAAGAAGGAAGGCGG 1822 0.333 52.4
matK-rps16_p5 matK-rps16 TACTTCTTCGCCCTTCTTGC ATCCCCTCGCTACTATTGCT 1371 0.333 52.4
atpH-atpI_p1 atpH-atpI AGATAGATGCGGCAGGTACT GTTGGTAGTAGCTGTTCCCG 1286–1294 1.000 86.8
atpH-atpI_p2 atpH-atpI AGATAGATGCGGCAGGTACT GTACCCATGACGCCTTTAGG 1240–1248 1.000 86.5
atpH-atpI_p3 atpH-atpI AGATAGATGCGGCAGGTACT TCTACCAAACCCCCATCACT 1342–1350 1.000 86.2
atpH-atpI_p4 atpH-atpI AGATAGATGCGGCAGGTACT GGCGAATCGTTCAGTTACCT 1530–1538 0.667 71.6
atpH-atpI_p5 atpH-atpI AGATAGATGCGGCAGGTACT ATCAACACTACTGTCGCGTC 1488 0.333 53.1
rpoB-trnD-GUC_p1 rpoB-trnD-GUC CAAGTTCTGGTAGTACGGGC GCGGTGCTCTAACCAATTGA 829–911 1.000 83.4
rpoB-trnD-GUC_p2 rpoB-trnD-GUC GCAAGTTCTGGTAGTACGGG GCGGTGCTCTAACCAATTGA 830–912 1.000 83.4
rpoB-trnD-GUC_p3 rpoB-trnD-GUC AGTTCTGGTAGTACGGGCAT GCGGTGCTCTAACCAATTGA 827–909 1.000 82.4
rpoB-trnD-GUC_p4 rpoB-trnD-GUC AAGTTCTGGTAGTACGGGCA GCGGTGCTCTAACCAATTGA 828–910 1.000 80.6
rpoB-trnD-GUC_p5 rpoB-trnD-GUC CAAGTTCTGGTAGTACGGGC GGATTGACGGGTCTCGAAC 870–952 1.000 79.1
psbM-petN_p1 psbM-petN ATTCAAACGGCTGCTCAGAA TCTCACTTGTAGTTCGGGGA 922–931 1.000 84.9
psbM-petN_p2 psbM-petN TTCAAACGGCTGCTCAGAAT TCTCACTTGTAGTTCGGGGA 921–930 1.000 84.9
psbM-petN_p3 psbM-petN TACATTCAAACGGCTGCTCA TCTCACTTGTAGTTCGGGGA 925–934 1.000 84.3
psbM-petN_p4 psbM-petN ATTCAAACGGCTGCTCAGAA TTGTAGTTCGGGGAAGAAGC 916–925 1.000 83.6
psbM-petN_p5 psbM-petN TTCAAACGGCTGCTCAGAAT TTGTAGTTCGGGGAAGAAGC 915–924 1.000 83.6
petN-trnC-GCA_p1 petN-trnC-GCA GCCCAAGCTATAGTAACTAGATCC AAGACGGAGGACTGCAAATC 557–565 1.000 55.3
petN-trnC-GCA_p2 petN-trnC-GCA GCCCAAGCTATAGTAACTAGATCC CCAGTTCGAATCTGGGTGTC 528–536 1.000 54.4
petN-trnC-GCA_p3 petN-trnC-GCA CCCAAGCTATAGTAACTAGATCCG AAGACGGAGGACTGCAAATC 556–564 1.000 54.0
petN-trnC-GCA_p4 petN-trnC-GCA GCCCAAGCTATAGTAACTAGATCC TCAAGTGGTAAGACGGAGGA 566–574 1.000 53.6
petN-trnC-GCA_p5 petN-trnC-GCA GCCCAAGCTATAGTAACTAGATCC AAGTGGTAAGACGGAGGACT 564–572 1.000 53.6
trnC-GCA-trnG-UCC_p1 trnC-GCA-trnG-UCC CAACCGTTTGTCACAATCCG AACTAAATACGTGCGCGAGT 1193–1233 1.000 89.8
trnC-GCA-trnG-UCC_p2 trnC-GCA-trnG-UCC CAACCGTTTGTCACAATCCG ACTAAATACGTGCGCGAGTT 1192–1232 1.000 89.8
trnC-GCA-trnG-UCC_p3 trnC-GCA-trnG-UCC CGTTTGTCACAATCCGCTTC AACTAAATACGTGCGCGAGT 1189–1229 1.000 89.7
trnC-GCA-trnG-UCC_p4 trnC-GCA-trnG-UCC CGTTTGTCACAATCCGCTTC ACTAAATACGTGCGCGAGTT 1188–1228 1.000 89.7
trnC-GCA-trnG-UCC_p5 trnC-GCA-trnG-UCC CAACCGTTTGTCACAATCCG ACGCCGAGGCAGAAATATTT 1316–1360 1.000 89.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Woodwardia japonica NC_050356.1 153224 View on NCBI ↗
Woodwardia prolifera PQ300107.1 155328 View on NCBI ↗
Woodwardia unigemmata NC_028543.1 153717 View on NCBI ↗