Markers + reference

Hymenophyllum

5 species · Hymenophyllaceae · Hymenophyllales

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Species 5
Genome length 140–161 kb
Candidate markers 261
Primer pairs 55

Genome-wide nucleotide diversity

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

Candidate markers

1 hotspot label from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 261 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnV-GAC-rrn16 Genome 5727 0.2774 0.82 76.0 yes View details
psbE-petL Genome 669 0.0528 0.96 87.3 yes View details
atpH-atpI Genome 608 0.0497 1.00 86.7 yes View details
psbD-trnT-GGT Genome 1523 0.0629 0.87 86.6 yes View details
psbM-trnD-GTC Genome 655 0.0589 0.84 86.0 yes View details
rps4-trnL-TAA Genome 883 0.0717 0.95 85.7 yes View details
trnE-TTC-trnG-GCC Genome 597 0.1081 1.00 84.4 yes View details
psbK-psbI Genome 805 0.0655 0.99 83.9 yes View details
atpF-atpH Genome 347 0.0547 0.97 83.3 yes View details
trnS-TGA-psbC Genome 767 0.0706 0.91 83.0 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 55 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbK-psbI_p1 psbK-psbI CCATCCAGAGCTGAAAAGGG TTCGAATCCCTCTCTCTCCC 1582–1719 0.800 80.3
psbK-psbI_p2 psbK-psbI CCATCCAGAGCTGAAAAGGG GGTTGGCCTTGAATTGAACG 2207–2210 0.400 56.0
psbK-psbI_p3 psbK-psbI TGGAAGATCCATCCAGAGCT GGTTGGCCTTGAATTGAACG 2215 0.200 46.0
psbK-psbI_p4 psbK-psbI TGGAAGATCCATCCAGAGCT TTCGAATCCCTCTCTCTCCC 1676 0.200 45.9
psbK-psbI_p5 psbK-psbI TGGAAGATCCATCCAGAGCT GGGTTCGAATCCCTCTCTCT 1679 0.200 44.8
trnG-TCC_p1 trnG-TCC GTCTCCGGAAACAGGCTAAG GGTCAGCGTCTACGTGAATT 1846–1875 1.000 90.7
trnG-TCC_p2 trnG-TCC GTCTCCGGAAACAGGCTAAG GACAATGGACGCTCCTTCAT 1383–1410 0.800 82.4
trnG-TCC_p3 trnG-TCC GAGTTCCGGAGATCAACACC TGTTTACGGAACAAGCGGAA 1608–1638 0.600 73.1
trnG-TCC_p4 trnG-TCC GAGTTCCGGAGATCAACACC GGTCAGCGTCTACGTGAATT 1810–1840 0.600 72.5
trnG-TCC_p5 trnG-TCC GAGTTCCGGAGATCAACACC GACAATGGACGCTCCTTCAT 1348–1375 0.400 59.6
atpF-atpH_p1 atpF-atpH CAAAACCCGCAGCAAGAATC AGCATCATCATTTGCAAATCCC 428–439 1.000 71.9
atpF-atpH_p2 atpF-atpH CAAAACCCGCAGCAAGAATC GCATCATCATTTGCAAATCCCT 427–438 1.000 71.9
atpF-atpH_p3 atpF-atpH CCCGCAGCAAGAATCCAATA AGCATCATCATTTGCAAATCCC 423–434 1.000 71.8
atpF-atpH_p4 atpF-atpH CCCGCAGCAAGAATCCAATA GCATCATCATTTGCAAATCCCT 422–433 1.000 71.8
atpF-atpH_p5 atpF-atpH CGCAGCAAGAATCCAATAGC GCATCATCATTTGCAAATCCCT 420–431 1.000 71.3
atpH-atpI_p1 atpH-atpI GCAGCAATAACAGAAGCAGC GGAGAATCTATGGAAGGTCATCA 670–711 1.000 58.9
atpH-atpI_p2 atpH-atpI GCAGCAATAACAGAAGCAGC AGGAGAATCTATGGAAGGTCA 671–712 1.000 58.8
atpH-atpI_p3 atpH-atpI GCAGCAATAACAGAAGCAGC GCTGCAGCTTATATAGGAGA 685–726 1.000 58.2
atpH-atpI_p4 atpH-atpI CCGATAGAAGCAAGGCCTAC GGAGAATCTATGGAAGGTCATCA 700–741 1.000 58.0
atpH-atpI_p5 atpH-atpI CCGATAGAAGCAAGGCCTAC AGGAGAATCTATGGAAGGTCA 701–742 1.000 57.9
psbM-trnD-GTC_p1 psbM-trnD-GTC TGCAGTAGCTATGAATGCGA GGTGCTCTAACCGATTGAACT 618–720 1.000 76.7
psbM-trnD-GTC_p2 psbM-trnD-GTC GTGCAGTAGCTATGAATGCG GGTGCTCTAACCGATTGAACT 619–721 1.000 76.3
psbM-trnD-GTC_p3 psbM-trnD-GTC GCAGTAGCTATGAATGCGAGA GGTGCTCTAACCGATTGAACT 617–719 1.000 75.6
psbM-trnD-GTC_p4 psbM-trnD-GTC TGCAGTAGCTATGAATGCGA GGGATTGACGGGTTTCGAAC 662–764 1.000 75.3
psbM-trnD-GTC_p5 psbM-trnD-GTC TGCAGTAGCTATGAATGCGA GGGATTGACGGGTTTCGAA 662–764 1.000 75.0
trnE-TTC-trnG-GCC_p1 trnE-TTC-trnG-GCC GTCGCCTCCTTGAAAGAGAG GTTCGATTCCCGCTATCCG 666–1030 1.000 80.5
trnE-TTC-trnG-GCC_p2 trnE-TTC-trnG-GCC GTCGCCTCCTTGAAAGAGAG GGGTTCGATTCCCGCTATC 668–1032 1.000 80.3
trnE-TTC-trnG-GCC_p3 trnE-TTC-trnG-GCC GTCGCCTCCTTGAAAGAGAG GGTTCGATTCCCGCTATCC 667–1031 1.000 80.3
trnE-TTC-trnG-GCC_p4 trnE-TTC-trnG-GCC TCGCCTCCTTGAAAGAGAGA GTTCGATTCCCGCTATCCG 665–1029 1.000 79.9
trnE-TTC-trnG-GCC_p5 trnE-TTC-trnG-GCC TCGCCTCCTTGAAAGAGAGA GGTTCGATTCCCGCTATCC 666–1030 1.000 79.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Hymenophyllum barbatum MN583334.1 144112 View on NCBI ↗
Hymenophyllum coreanum MN583335.1 157967 View on NCBI ↗
Hymenophyllum exsertum PX673994.1 139868 View on NCBI ↗
Hymenophyllum polyanthos MN583336.1 160865 View on NCBI ↗
Hymenophyllum wrightii MN583337.1 149309 View on NCBI ↗