Markers + reference

Hemionitis

2 species · Pteridaceae · Polypodiales

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Species 2
Genome length 151–157 kb
Candidate markers 268
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhB LSC 1109 0.2042 1.00 79.2 yes View details
matK-chlB LSC 1777 0.2371 0.97 81.3 yes View details
rpoB-trnD-GUC LSC 846 0.2659 0.97 82.1 yes View details
psbM-petN LSC 933 0.2540 0.93 83.1 yes View details
rps4-trnL-UAA LSC 745 0.2414 0.97 84.5 yes View details
petA-psbJ LSC 1006 0.2513 0.94 83.3 yes View details
rpl14-rpl16 LSC 494 0.3005 0.88 79.6 yes View details
ndhF SSC 2214 0.1787 1.00 78.2 yes View details
rpl32-trnP-GGG SSC 628 0.3393 0.90 82.2 yes View details
ccsA-ndhD SSC 400 0.2838 0.93 78.8 yes View details
ycf1 SSC 5097 0.1830 1.00 72.9 yes View details
psbD-trnT-GGU LSC 1241 0.2272 0.93 86.4 yes View details
psbE-petL LSC 752 0.2163 0.90 82.4 yes View details
atpH-atpI LSC 754 0.2208 0.97 82.0 yes View details
atpF LSC 1287 0.1025 0.98 81.1 yes View details
atpF-atpH LSC 402 0.2283 0.95 81.1 yes View details
trnS-GGA-rps4 LSC 492 0.2589 0.92 80.8 yes View details
rpl20-rps12 LSC 946 0.1645 0.98 80.5 yes View details
ndhC-trnV-UAC LSC 416 0.2000 0.96 80.4 yes View details
rpl16 LSC 898 0.1563 0.98 80.4 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ndhB_p1 ndhB GTGTCTCTACGTTAGGAATCGT TATCGATGAGTGGAGCGAGT 604 0.500 38.8
ndhB_p2 ndhB GTGTCTCTACGTTAGGAATCGT GGTATCCATGGCAGTCAGTG 951 0.500 38.8
ndhB_p3 ndhB GTGTCTCTACGTTAGGAATCGT TGGAGCAGCTTTCAAACTGT 447 0.500 38.6
ndhB_p4 ndhB GTGTCTCTACGTTAGGAATCGT GGATGGTTCTTAGCTGTGCA 736 0.500 38.2
ndhB_p5 ndhB GTGTCTCTACGTTAGGAATCGT TTCCATCGCTTCTGAACGTT 903 0.500 37.8
matK-chlB_p1 matK-chlB GTCAGCGGAAGTGAATCGAT CCGGATTCGTAAGGGGAAAG 2582 0.500 59.0
matK-chlB_p2 matK-chlB GTCAGCGGAAGTGAATCGAT ACGTATGCGGCTAAGGAAAG 2499 0.500 58.9
matK-chlB_p3 matK-chlB GTCAGCGGAAGTGAATCGAT CCTGAAGCTGAGTCGGAATC 2613 0.500 58.9
matK-chlB_p4 matK-chlB GTCAGCGGAAGTGAATCGAT GCCCTCTGCCATATTTGGAA 2890 0.500 58.8
matK-chlB_p5 matK-chlB GTCAGCGGAAGTGAATCGAT CCTTTCCTGGGTTACGAAGG 2775 0.500 58.5
atpF_p1 atpF AGTACGGTGCCGATGTTAAC GCAAAACCTTCAAGGAGGGA 1491–1496 1.000 89.3
atpF_p2 atpF TTTGCTTGCGAATGATGCTG GCAAAACCTTCAAGGAGGGA 1442–1447 1.000 89.3
atpF_p3 atpF AGTACGGTGCCGATGTTAAC TTGCCGAAGTGGATAACTCG 1605 0.500 60.0
atpF_p4 atpF TTTGCTTGCGAATGATGCTG TTGCCGAAGTGGATAACTCG 1556 0.500 59.8
atpF_p5 atpF AGTACGGTGCCGATGTTAAC AAATCCGCCTGTCTAAGCTG 1887 0.500 59.8
atpF-atpH_p1 atpF-atpH GACGATCTCACTTATACTTCTCGT TTGCAAATCCGCCTGTCTAA 446–451 1.000 55.9
atpF-atpH_p2 atpF-atpH GACGATCTCACTTATACTTCTCGT TTTGCAAATCCGCCTGTCTA 447–452 1.000 55.9
atpF-atpH_p3 atpF-atpH ACGATCTCACTTATACTTCTCGT TTGCAAATCCGCCTGTCTAA 445–450 1.000 55.6
atpF-atpH_p4 atpF-atpH ACGATCTCACTTATACTTCTCGT TTTGCAAATCCGCCTGTCTA 446–451 1.000 55.6
atpF-atpH_p5 atpF-atpH GACGATCTCACTTATACTTCTCGT ATTTGCAAATCCGCCTGTCT 448–453 1.000 53.8
atpH-atpI_p1 atpH-atpI CGAGTTATCCACTTCGGCAA ACTTCTCGGGTTGTTATCGC 1910 0.500 59.9
atpH-atpI_p2 atpH-atpI TCCCTCCTTGAAGGTTTTGC ACTTCTCGGGTTGTTATCGC 2019 0.500 59.9
atpH-atpI_p3 atpH-atpI CGAGTTATCCACTTCGGCAA ATTTTGGCTGACGAGTTGGT 1451 0.500 59.8
atpH-atpI_p4 atpH-atpI TCCCTCCTTGAAGGTTTTGC ATTTTGGCTGACGAGTTGGT 1560 0.500 59.8
atpH-atpI_p5 atpH-atpI CGAGTTATCCACTTCGGCAA CAGCCAGAAATTTGCAGTCG 1864 0.500 59.7
rpoB-trnD-GUC_p1 rpoB-trnD-GUC TAAATCTCCCTCCCCGATCC CTTCCCTAATCCCCCGAGAT 1895 0.500 59.5
rpoB-trnD-GUC_p2 rpoB-trnD-GUC TAAATCTCCCTCCCCGATCC GAATCCAGCTCGACCCAATT 1507 0.500 59.4
rpoB-trnD-GUC_p3 rpoB-trnD-GUC GGCATCTCTGTCTTCGACTG CTTCCCTAATCCCCCGAGAT 1627 0.500 59.1
rpoB-trnD-GUC_p4 rpoB-trnD-GUC TAAATCTCCCTCCCCGATCC AATAACTCCGACCCAACGTG 1411 0.500 59.1
rpoB-trnD-GUC_p5 rpoB-trnD-GUC GGCATCTCTGTCTTCGACTG GAATCCAGCTCGACCCAATT 1239 0.500 59.0

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
Hemionitis ludens NC_040214.1 157068 View on NCBI ↗
Hemionitis truncata NC_040202.1 150713 View on NCBI ↗