Markers + reference

Lepisorus

4 species · Polypodiaceae · Polypodiales

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Species 4
Genome length 152–158 kb
Candidate markers 272
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 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rrn16-rps12 IRb 4419 0.1176 0.43 77.4 yes View details
rps12-rrn16 IRa 4419 0.1196 0.43 77.6 yes View details
rpoB-trnD-GUC LSC 705 0.0579 0.96 85.2 yes View details
matK-rps16 LSC 668 0.0626 0.96 83.7 yes View details
rps16 LSC 1062 0.0788 0.97 83.7 yes View details
trnT-GGU-trnfM-CAU LSC 479 0.0699 0.99 83.2 yes View details
psbD-trnT-GGU LSC 1393 0.0636 1.00 83.1 yes View details
trnR-UCG-accD LSC 320 0.0672 1.00 82.3 yes View details
atpH-atpI LSC 722 0.0594 0.99 81.5 yes View details
petN-trnC-GCA LSC 457 0.0496 1.00 81.2 yes View details
trnC-GCA-trnG-GCC LSC 485 0.0671 0.99 81.2 yes View details
psbZ-trnS-UGA LSC 401 0.0590 1.00 80.9 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-rps16_p1 matK-rps16 ACGCTATCGATTGAACGCTT ATTTCGAAAGGGGCAAGGTT 914–949 0.750 79.0
matK-rps16_p2 matK-rps16 TCGATTGAACGCTTTGTTGC ATTTCGAAAGGGGCAAGGTT 908–943 0.500 66.8
matK-rps16_p3 matK-rps16 TCGATTGAACGCTTTGTTGC AGTAGCTCAATCAACAGCGG 939–974 0.500 66.8
matK-rps16_p4 matK-rps16 AGCTAGTTGACGCAGACAAG ATTTCGAAAGGGGCAAGGTT 1067–1091 0.500 64.7
matK-rps16_p5 matK-rps16 AGCTAGTTGACGCAGACAAG AGTAGCTCAATCAACAGCGG 1122 0.250 49.3
rps16_p1 rps16 GCTTGCTTAGCCGCATATTG ATGCGACGTATGCAGCTAAA 1022–1531 0.500 66.8
rps16_p2 rps16 CCCCTGCTTTTCCAACTTCT ATGCGACGTATGCAGCTAAA 1453 0.250 49.5
rps16_p3 rps16 CCCCTGCTTTTCCAACTTCT TCTAGGTTACGAAGGCACCA 1719 0.250 49.4
rps16_p4 rps16 CCCCTGCTTTTCCAACTTCT GAGCGTCATATTGGCAAACG 1811 0.250 49.3
rps16_p5 rps16 CCCCTGCTTTTCCAACTTCT CCCTAGGATACCGACCCTTT 1738 0.250 49.2
atpH-atpI_p1 atpH-atpI TCCCTCCTGGAAAGTTTTGC CATTCAGTTACCCCACGGAG 1690–1729 1.000 87.9
atpH-atpI_p2 atpH-atpI TCCCTCCTGGAAAGTTTTGC AGGTGCCAGAAATCTGCAAA 1882–1921 0.750 75.2
atpH-atpI_p3 atpH-atpI GAGGGAGTAGCGATCTCACT AGGTGCCAGAAATCTGCAAA 1921–1960 0.750 75.0
atpH-atpI_p4 atpH-atpI ACACCCCCTTTCCGTAGTAA AGGTGCCAGAAATCTGCAAA 2034–2073 0.750 74.8
atpH-atpI_p5 atpH-atpI TCCCTCCTGGAAAGTTTTGC GCAAGTAGGGGTCTTCGAAG 1973 0.250 49.9
rpoB-trnD-GUC_p1 rpoB-trnD-GUC CAAGTTCTGGTAGTACGGGC GAGTTCATCGGGATTGACGG 773–809 1.000 88.2
rpoB-trnD-GUC_p2 rpoB-trnD-GUC CAAGTTCTGGTAGTACGGGC GGAGTTCATCGGGATTGACG 774–810 1.000 88.2
rpoB-trnD-GUC_p3 rpoB-trnD-GUC GCAAGTTCTGGTAGTACGGG GAGTTCATCGGGATTGACGG 774–810 1.000 88.2
rpoB-trnD-GUC_p4 rpoB-trnD-GUC GCAAGTTCTGGTAGTACGGG GGAGTTCATCGGGATTGACG 775–811 1.000 88.2
rpoB-trnD-GUC_p5 rpoB-trnD-GUC AGTTCTGGTAGTACGGGCAT GAGTTCATCGGGATTGACGG 771–807 1.000 87.1
petN-trnC-GCA_p1 petN-trnC-GCA GAGCTCCCCCAGATAATTGC TGCAGGCGAAGACCTATCTA 1354–1379 0.750 77.0
petN-trnC-GCA_p2 petN-trnC-GCA GTTTTTCATTCCGGGTGCAG TGCAGGCGAAGACCTATCTA 1562–1569 0.500 64.3
petN-trnC-GCA_p3 petN-trnC-GCA CTGTTTTTCATTCCGGGTGC TGCAGGCGAAGACCTATCTA 1571 0.250 48.9
petN-trnC-GCA_p4 petN-trnC-GCA GAGTTAACGGAGGTGTGACC TGCAGGCGAAGACCTATCTA 1519 0.250 48.9
petN-trnC-GCA_p5 petN-trnC-GCA TCCCTGTTTTTCATTCCGGG TGCAGGCGAAGACCTATCTA 1574 0.250 48.8
trnC-GCA-trnG-GCC_p1 trnC-GCA-trnG-GCC GATTTGCAGTCCTCCGTCTT GTTCGATTCCCGCTATCCG 540–563 1.000 78.8
trnC-GCA-trnG-GCC_p2 trnC-GCA-trnG-GCC GATTTGCAGTCCTCCGTCTT GGGTTCGATTCCCGCTATC 542–565 1.000 78.7
trnC-GCA-trnG-GCC_p3 trnC-GCA-trnG-GCC GATTTGCAGTCCTCCGTCTT GGTTCGATTCCCGCTATCC 541–564 1.000 78.7
trnC-GCA-trnG-GCC_p4 trnC-GCA-trnG-GCC TCCGTCTTACCGCTTGACTA GTTCGATTCCCGCTATCCG 528–551 1.000 78.3
trnC-GCA-trnG-GCC_p5 trnC-GCA-trnG-GCC TCCGTCTTACCGCTTGACTA GGTTCGATTCCCGCTATCC 529–552 1.000 78.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Lepisorus clathratus NC_035739.1 156998 View on NCBI ↗
Lepisorus fortuni NC_056109.1 151915 View on NCBI ↗
Lepisorus hederaceus MN623364.1 152337 View on NCBI ↗
Lepisorus microphyllus MN623356.1 158029 View on NCBI ↗