Markers + reference

Athyrium

13 species · Athyriaceae · Polypodiales

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Species 13
Genome length 151–152 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

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnC-GCA-trnG-GCC LSC 447 0.0379 0.98 81.0 yes View details
petA-psbJ LSC 831 0.0351 1.00 72.3 yes View details
trnP-UGG-psaJ LSC 365 0.0398 1.00 68.6 yes View details
trnI-CAU-trnT-UGU IRb 1409 0.0073 1.00 46.1 yes View details
ndhF SSC 1590 0.0284 1.00 67.4 yes View details
rpl32-trnP-GGG SSC 685 0.0339 0.99 70.9 yes View details
trnP-GGG-trnL-UAG SSC 266 0.0436 1.00 71.8 yes View details
ndhA SSC 2078 0.0155 1.00 55.3 yes View details
ycf1 SSC 5109 0.0165 1.00 47.6 yes View details
ycf1-chlN SSC 376 0.0430 1.00 65.0 yes View details
psaJ-rpl33 LSC 233 0.0428 0.97 71.6 yes View details
psbK-psbI LSC 532 0.0287 0.99 71.1 yes View details
rpl23-trnI-CAU LSC 138 0.0561 1.00 70.7 yes View details
ccsA-ndhD SSC 401 0.0324 1.00 65.6 yes View details
rps4-trnL-UAA LSC 676 0.0205 1.00 65.5 yes View details
trnS-GCU-ycf12 LSC 558 0.0275 1.00 64.9 yes View details
rrn16-rps12 IRb 1931 0.0095 0.99 64.2 yes View details
rps12-rrn16 IRa 1931 0.0095 0.99 64.2 yes View details
matK-rps16 LSC 639 0.0232 1.00 64.1 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 GAAGGGATCCAGAAGTTGTCT GCCTGAACAAGTCGGAATCA 700–716 1.000 69.7
matK-rps16_p2 matK-rps16 GAAGGGATCCAGAAGTTGTCT TGCCTGAACAAGTCGGAATC 701–717 1.000 69.6
matK-rps16_p3 matK-rps16 AAGGGATCCAGAAGTTGTCT GCCTGAACAAGTCGGAATCA 699–715 1.000 67.5
matK-rps16_p4 matK-rps16 AGGGATCCAGAAGTTGTCTT GCCTGAACAAGTCGGAATCA 698–714 1.000 67.5
matK-rps16_p5 matK-rps16 AGGGATCCAGAAGTTGTCTT TGCCTGAACAAGTCGGAATC 699–715 1.000 67.5
psbK-psbI_p1 psbK-psbI CAAGCCGCAGTTAGTTTTCG TCCGGGATCGTTTGACAAAA 646–650 1.000 85.0
psbK-psbI_p2 psbK-psbI CAAGCCGCAGTTAGTTTTCG ATCTAATCCCTACGGCCAGG 672–676 1.000 83.9
psbK-psbI_p3 psbK-psbI AGCCGCAGTTAGTTTTCGAT TCCGGGATCGTTTGACAAAA 644–647 0.923 80.3
psbK-psbI_p4 psbK-psbI AAGCCGCAGTTAGTTTTCGA TCCGGGATCGTTTGACAAAA 645–648 0.923 80.0
psbK-psbI_p5 psbK-psbI AGCCGCAGTTAGTTTTCGAT ATCTAATCCCTACGGCCAGG 670–673 0.923 79.3
trnS-GCU-ycf12_p1 trnS-GCU-ycf12 GGGAGAGAGAGGGATTCGAA GCAAGTTGCGCAATTATTTCT 675–679 1.000 65.3
trnS-GCU-ycf12_p2 trnS-GCU-ycf12 AAGGGAGAGAGAGGGATTCG GCAAGTTGCGCAATTATTTCT 677–681 1.000 65.2
trnS-GCU-ycf12_p3 trnS-GCU-ycf12 AGCAATCCGACGCTTTAGAC GCAAGTTGCGCAATTATTTCT 624–628 1.000 63.6
trnS-GCU-ycf12_p4 trnS-GCU-ycf12 GGGAGAGAGAGGGATTCGAA GCAAGTTGCGCAATTATTTC 675–679 1.000 61.1
trnS-GCU-ycf12_p5 trnS-GCU-ycf12 AAGGGAGAGAGAGGGATTCG GCAAGTTGCGCAATTATTTC 677–681 1.000 61.1
trnC-GCA-trnG-GCC_p1 trnC-GCA-trnG-GCC GATTTGCAGTCCTCCGTCTT GTTCGATTCCCGCTATCCG 475–519 1.000 81.6
trnC-GCA-trnG-GCC_p2 trnC-GCA-trnG-GCC GATTTGCAGTCCTCCGTCTT GGGTTCGATTCCCGCTATC 477–521 1.000 81.4
trnC-GCA-trnG-GCC_p3 trnC-GCA-trnG-GCC GATTTGCAGTCCTCCGTCTT GGTTCGATTCCCGCTATCC 476–520 1.000 81.4
trnC-GCA-trnG-GCC_p4 trnC-GCA-trnG-GCC TCCGTCTTACCGCTTGACTA GTTCGATTCCCGCTATCCG 463–507 1.000 81.1
trnC-GCA-trnG-GCC_p5 trnC-GCA-trnG-GCC TCCGTCTTACCGCTTGACTA GGTTCGATTCCCGCTATCC 464–508 1.000 80.9
rps4-trnL-UAA_p1 rps4-trnL-UAA CGTAAGCCCCGGTAAATTCT ATTGCCCGATAAATGGTCCC 825–843 1.000 83.5
rps4-trnL-UAA_p2 rps4-trnL-UAA CGTAAGCCCCGGTAAATTCT CTGCCACTTGATACGTCTCC 784–802 1.000 83.3
rps4-trnL-UAA_p3 rps4-trnL-UAA CGTAAGCCCCGGTAAATTCT TCCATACCCAGGCTCAATCT 767–785 1.000 82.5
rps4-trnL-UAA_p4 rps4-trnL-UAA CGTAAGCCCCGGTAAATTCT TCTCCATACCCAGGCTCAAT 769–787 1.000 82.4
rps4-trnL-UAA_p5 rps4-trnL-UAA CGTAAGCCCCGGTAAATTCT CCATACCCAGGCTCAATCTG 766–784 1.000 81.9
trnV-UAC_p1 trnV-UAC TTCCCTGAAAGAAACAGCCC GCGATACTCTAACCGCTGAG 1653–1665 1.000 86.7
trnV-UAC_p2 trnV-UAC TTCCCTGAAAGAAACAGCCC GAGTCAAGTAGGCTGCCATC 1636–1648 1.000 86.7
trnV-UAC_p3 trnV-UAC TTCCCTGAAAGAAACAGCCC AGGCCAGACTAGAAGCTTCA 1874–1886 1.000 86.1
trnV-UAC_p4 trnV-UAC TTCCCTGAAAGAAACAGCCC CTGAGCCCAGAAGCACTAAG 1839–1844 0.692 71.6
trnV-UAC_p5 trnV-UAC CTTGCTATACTGCAACGGGT CTGAGCCCAGAAGCACTAAG 1485 0.231 48.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (13)

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

Species Accession Length (bp) Link
Athyrium acutipinnulum PV040735.1 151313 View on NCBI ↗
Athyrium anisopterum NC_035738.1 151284 View on NCBI ↗
Athyrium brevifrons NC_050007.1 151345 View on NCBI ↗
Athyrium clivicola NC_080875.1 151434 View on NCBI ↗
Athyrium deltoidofrons NC_080876.1 151315 View on NCBI ↗
Athyrium iseanum NC_080877.1 151392 View on NCBI ↗
Athyrium otophorum NC_080878.1 151472 View on NCBI ↗
Athyrium reflexipinnum NC_080879.1 151325 View on NCBI ↗
Athyrium sinense NC_035839.1 151319 View on NCBI ↗
Athyrium spinulosum NC_080880.1 151414 View on NCBI ↗
Athyrium vidalii NC_080881.1 151313 View on NCBI ↗
Athyrium wardii NC_080882.1 151345 View on NCBI ↗
Athyrium yokoscense NC_080883.1 151582 View on NCBI ↗