Markers + reference

Pteridium

2 species · Dennstaedtiaceae · Polypodiales

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Species 2
Genome length 152–152 kb
Candidate markers 272
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

9 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
matK Genome 1494 0.0060 1.00 55.2 yes View details
psbM-petN Genome 1366 0.0059 1.00 62.3 yes View details
ndhC-trnV-UAC Genome 2324 0.0065 1.00 60.8 yes View details
petA-psbJ Genome 989 0.0051 1.00 61.7 yes View details
infA Genome 243 0.0082 1.00 45.7 yes View details
rps8 Genome 399 0.0100 1.00 56.7 yes View details
rpl14-rpl16 Genome 403 0.0249 1.00 54.4 yes View details
trnL-UAG-ccsA Genome 273 0.0037 0.98 41.8 yes View details
ycf1 Genome 5064 0.0045 1.00 48.3 yes View details
trnG-UCC-trnR-TCT Genome 146 0.0274 1.00 68.3 yes View details
rpl33-rps18 Genome 72 0.0278 1.00 64.9 yes View details
trnS-GCU-ycf12 Genome 685 0.0058 1.00 62.1 yes View details
rps4 Genome 588 0.0068 1.00 62.0 yes View details
ccsA Genome 951 0.0053 1.00 61.8 yes View details
psbK-psbI Genome 506 0.0079 1.00 61.5 yes View details
ycf2-trnN-GUU Genome 579 0.0052 1.00 61.3 yes View details
trnN-GUU-ycf2 Genome 579 0.0052 1.00 61.3 yes View details
petD Genome 1121 0.0036 1.00 60.8 yes View details
chlL Genome 882 0.0034 1.00 60.7 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK_p1 matK TCTCTTTGCAAGGAGATCAA AATGCTTGGGAGTTACTGCA 1534 1.000 46.0
matK_p2 matK TTCTCTTTGCAAGGAGATCA AATGCTTGGGAGTTACTGCA 1535 1.000 46.0
matK_p3 matK TTCTCTTTGCAAGGAGATCAA AATGCTTGGGAGTTACTGCA 1535 1.000 44.9
matK_p4 matK TTTCTCTTTGCAAGGAGATCA AATGCTTGGGAGTTACTGCA 1536 1.000 44.9
matK_p5 matK TCTCTTTGCAAGGAGATCAA CAATGCTTGGGAGTTACTGC 1535 1.000 43.2
psbK-psbI_p1 psbK-psbI TGCCAAATTACCCGAAGCTT GGATTTCGTCCGGGATCATT 718–719 1.000 77.9
psbK-psbI_p2 psbK-psbI TTGCCAAATTACCCGAAGCT GGATTTCGTCCGGGATCATT 719–720 1.000 77.8
psbK-psbI_p3 psbK-psbI ACCCGAAGCTTATGCCATTT GGATTTCGTCCGGGATCATT 709–710 1.000 77.4
psbK-psbI_p4 psbK-psbI TAGCTTTTGTTTGGCAAGCC GGATTTCGTCCGGGATCATT 638–639 1.000 74.4
psbK-psbI_p5 psbK-psbI TGCCAAATTACCCGAAGCTT TTTCGTCCGGGATCATTTGA 715–716 1.000 73.7
trnS-GCU-ycf12_p1 trnS-GCU-ycf12 TTTAGACCTCTCGGCCATCT TGCCAAAACAGCAAGTTGTG 748–752 1.000 79.1
trnS-GCU-ycf12_p2 trnS-GCU-ycf12 TTTAGACCTCTCGGCCATCT ATGCCACTACCAATGCCAAA 761–765 1.000 78.6
trnS-GCU-ycf12_p3 trnS-GCU-ycf12 TTTAGACCTCTCGGCCATCT GCCACTACCAATGCCAAAAC 759–763 1.000 78.5
trnS-GCU-ycf12_p4 trnS-GCU-ycf12 ATCCGACGCTTTAGACCTCT TGCCAAAACAGCAAGTTGTG 757–761 1.000 78.5
trnS-GCU-ycf12_p5 trnS-GCU-ycf12 TTTAGACCTCTCGGCCATCT CGGGGATGAGGTCACAAATT 822–826 1.000 78.1
trnG-UCC_p1 trnG-UCC AGGAGGAATGGAGAGATGGG TAGTCGGTGGGGGCTAATTC 1128–1132 1.000 72.6
trnG-UCC_p2 trnG-UCC AGGAGGAATGGAGAGATGGG GCAGGGCTCCGATATTTCTAG 1101–1105 1.000 71.3
trnG-UCC_p3 trnG-UCC GAGGGCTCCTCCTATACCAG TAGTCGGTGGGGGCTAATTC 1107 0.500 52.5
trnG-UCC_p4 trnG-UCC GAGGGCTCCTCCTATACCAG GCAGGGCTCCGATATTTCTAG 1080 0.500 51.2
trnG-UCC_p5 trnG-UCC GAGGGCTCCTCCTATACCAG GGCAGGGCTCCGATATTTC 1081 0.500 50.9
trnG-UCC-trnR-TCT_p1 trnG-UCC-trnR-TCT TGGGTTCCCGTCGACTATAA GCTTAGTCGCCTCAAAGACA 311 1.000 79.2
trnG-UCC-trnR-TCT_p2 trnG-UCC-trnR-TCT TACTGATGCGGGTTCGATTC GCTTAGTCGCCTCAAAGACA 274 1.000 78.8
trnG-UCC-trnR-TCT_p3 trnG-UCC-trnR-TCT CTACTGATGCGGGTTCGATT GCTTAGTCGCCTCAAAGACA 275 1.000 78.7
trnG-UCC-trnR-TCT_p4 trnG-UCC-trnR-TCT TTCTGAATTAGCGGCGTCAT GCTTAGTCGCCTCAAAGACA 336 1.000 77.8
trnG-UCC-trnR-TCT_p5 trnG-UCC-trnR-TCT AATTAGCGGCGTCATAACCA GCTTAGTCGCCTCAAAGACA 331 1.000 77.8
psbM-petN_p1 psbM-petN GCCACCGCACTTTTTATTCC CCCCGACGGTGATTTTTACA 1504–1506 1.000 79.0
psbM-petN_p2 psbM-petN ATATTCTCGCGTTCGTAGCC CCCCGACGGTGATTTTTACA 1521–1523 1.000 78.7
psbM-petN_p3 psbM-petN GCCACCGCACTTTTTATTCC GTAGTTCGGGGAAGAAGTGG 1469–1471 1.000 77.5
psbM-petN_p4 psbM-petN CGGCCGCTCAGAATAACTAG CCCCGACGGTGATTTTTACA 1446–1448 1.000 77.3
psbM-petN_p5 psbM-petN ATATTCTCGCGTTCGTAGCC GTAGTTCGGGGAAGAAGTGG 1486–1488 1.000 77.2

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
Pteridium aquilinum subsp. aquilinum NC_014348.1 152362 View on NCBI ↗
Pteridium aquilinum subsp. japonicum MT747831.1 152489 View on NCBI ↗