Markers + reference

Lemmaphyllum

2 species · Polypodiaceae · Polypodiales

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Species 2
Genome length 158–158 kb
Candidate markers 267
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 7 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1045 0.0019 1.00 53.2 yes View details
psbK-psbI LSC 521 0.0038 1.00 59.5 yes View details
trnS-GCU-ycf12 LSC 558 0.0054 1.00 61.1 yes View details
psbD-trnT-GGU LSC 1418 0.0014 1.00 59.6 yes View details
rbcL LSC 1428 0.0014 1.00 59.6 yes View details
cemA LSC 1500 0.0013 1.00 47.2 yes View details
petA-psbJ LSC 686 0.0015 1.00 59.7 yes View details
petB LSC 1463 0.0014 1.00 59.7 yes View details
ccsA-ndhD SSC 417 0.0024 0.99 50.2 yes View details
ycf1 SSC 5103 0.0008 1.00 53.0 yes View details
trnD-GUC-trnY-GUA LSC 52 0.0192 1.00 63.6 yes View details
rps4-trnL-UAA LSC 632 0.0016 1.00 59.7 yes View details
matK-rps16 LSC 648 0.0015 1.00 59.6 yes View details
trnT-UGU-trnR-ACG IRb 736 0.0014 1.00 59.5 yes View details
trnR-ACG-trnT-UGU IRa 736 0.0014 1.00 59.5 yes View details
atpA LSC 1524 0.0007 1.00 59.1 yes View details
atpF LSC 1284 0.0000 1.00 59.1 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-rps16_p1 matK-rps16 TGCATCAAATCTAAGAGAGGACC TATCTCGAAAGGGGCAAGGT 754 1.000 52.5
matK-rps16_p2 matK-rps16 GAGGACCCATAAGTTATTCTCGT TATCTCGAAAGGGGCAAGGT 738 1.000 48.5
matK-rps16_p3 matK-rps16 TGCATCAAATCTAAGAGAGGACC ATATCTCGAAAGGGGCAAGG 755 1.000 48.4
matK-rps16_p4 matK-rps16 TCAAATCTAAGAGAGGACCCA TATCTCGAAAGGGGCAAGGT 750 1.000 48.0
matK-rps16_p5 matK-rps16 GCATCAAATCTAAGAGAGGACCC TATCTCGAAAGGGGCAAGGT 753 1.000 47.8
rps16_p1 rps16 GAATCTGTAAACTGGGCCCA TTTCGCGTCAGAAAGTTTGC 1161–1163 1.000 75.3
rps16_p2 rps16 GAATCTGTAAACTGGGCCCA GCGTCAGAAAGTTTGCACAA 1157–1159 1.000 74.6
rps16_p3 rps16 GGAACGACAGATACGGCATA TTTCGCGTCAGAAAGTTTGC 1229–1231 1.000 73.0
rps16_p4 rps16 AGAATCTGTAAACTGGGCCC TTTCGCGTCAGAAAGTTTGC 1162–1164 1.000 72.9
rps16_p5 rps16 GGAACGACAGATACGGCATA GCGTCAGAAAGTTTGCACAA 1225–1227 1.000 72.3
psbK-psbI_p1 psbK-psbI TGCCAAATTACCCGAAGCTT ATCTAATCCCTACGTCCGGG 752–754 1.000 79.0
psbK-psbI_p2 psbK-psbI TTGCCAAATTACCCGAAGCT ATCTAATCCCTACGTCCGGG 753–755 1.000 79.0
psbK-psbI_p3 psbK-psbI TGCCAAATTACCCGAAGCTT GGGTTTCGTCCAGGATCATT 734–736 1.000 76.3
psbK-psbI_p4 psbK-psbI TTGCCAAATTACCCGAAGCT GGGTTTCGTCCAGGATCATT 735–737 1.000 76.3
psbK-psbI_p5 psbK-psbI GCCGCAGTTAGCTTTCGATA ATCTAATCCCTACGTCCGGG 655–657 1.000 76.3
trnS-GCU-ycf12_p1 trnS-GCU-ycf12 GGGAGAGAGAGGGATTCGAA AACGGTCCTGATGCAACTAC 707–708 1.000 79.1
trnS-GCU-ycf12_p2 trnS-GCU-ycf12 GGGAGAGAGAGGGATTCGAA ACTAACGGTCCTGATGCAAC 710–711 1.000 79.1
trnS-GCU-ycf12_p3 trnS-GCU-ycf12 AAGGGAGAGAGAGGGATTCG AACGGTCCTGATGCAACTAC 709–710 1.000 79.0
trnS-GCU-ycf12_p4 trnS-GCU-ycf12 AAGGGAGAGAGAGGGATTCG ACTAACGGTCCTGATGCAAC 712–713 1.000 79.0
trnS-GCU-ycf12_p5 trnS-GCU-ycf12 GCAATCCGACGCTTTAAACC AACGGTCCTGATGCAACTAC 655–656 1.000 78.9
atpA_p1 atpA TGGATAAGGCACGAGGGTTA TTTTCATCTCATCACGCGGG 1644 1.000 73.9
atpA_p2 atpA ATTGGGCGTAATTCCGTGTT TTTTCATCTCATCACGCGGG 1702 1.000 73.6
atpA_p3 atpA TGGATAAGGCACGAGGGTTA ATCTCATCACGCGGGTTTTA 1639 1.000 73.5
atpA_p4 atpA TGGATAAGGCACGAGGGTTA TCTCATCACGCGGGTTTTAT 1638 1.000 73.5
atpA_p5 atpA ATTGGGCGTAATTCCGTGTT TCTCATCACGCGGGTTTTAT 1696 1.000 73.2
atpF_p1 atpF TGCTGCTAATTTCGTCAGGT GCAAAACTTTCCAGGAGGGA 1427–1431 1.000 76.4
atpF_p2 atpF TGCTGCTAATTTCGTCAGGT CGGACCAGAGGTTGTTCAAA 1451–1455 1.000 76.1
atpF_p3 atpF CCCGCGTGATGAGATGAAAA GCAAAACTTTCCAGGAGGGA 1345–1349 1.000 75.1
atpF_p4 atpF CCCGCGTGATGAGATGAAAA CGGACCAGAGGTTGTTCAAA 1369–1373 1.000 74.9
atpF_p5 atpF TAAAACCCGCGTGATGAGAT GCAAAACTTTCCAGGAGGGA 1350–1354 1.000 74.7

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
Lemmaphyllum drymoglossoides OP369280.1 157571 View on NCBI ↗
Lemmaphyllum intermedium NC_053788.1 157795 View on NCBI ↗