Markers + reference

Bolbitis

9 species · Dryopteridaceae · Polypodiales

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Species 9
Genome length 152–157 kb
Candidate markers 239
Primer pairs 95

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 9 remaining regions by MarkerSeek score (out of 239 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-ycf12 LSC 537 0.0733 0.99 78.9 yes View details
rpoC2-trnD-GUC LSC 7170 0.0278 1.00 64.2 yes View details
psbM-trnC-GCA LSC 2545 0.0796 0.96 80.7 yes View details
trnC-GCA-trnG-GCC LSC 503 0.0778 0.99 81.2 yes View details
cemA-psbJ LSC 1985 0.0420 0.98 80.4 yes View details
trnN-GUU-rpl32 SSC 3527 0.0498 1.00 76.1 yes View details
rpl32-trnP-GGG SSC 382 0.0909 0.99 75.5 yes View details
ycf1 SSC 4002 0.0493 1.00 69.8 yes View details
ycf1-chlN SSC 1479 0.0619 0.99 80.2 yes View details
rpl20-rps12 LSC 914 0.0494 1.00 82.5 yes View details
matK-rps16 LSC 1148 0.0567 0.98 81.7 yes View details
psbD-trnT-GGU LSC 1374 0.0540 0.99 79.7 yes View details
ndhE-ndhG SSC 161 0.0569 1.00 79.5 yes View details
trnW-CCA-trnP-UGG LSC 183 0.0741 1.00 79.2 yes View details
rps4-trnL-UAA LSC 678 0.0568 1.00 79.1 yes View details
trnE-UUC-psbM LSC 465 0.0439 0.95 77.4 yes View details
rpl14-rpl16 LSC 281 0.0688 1.00 77.3 yes View details
trnF-GAA-ndhJ LSC 226 0.0644 0.97 77.0 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-rps16_p1 matK-rps16 CGCGGAATTTCCCTTTTTCC CGAACGAGGGGATTTTCGAT 2354–2376 0.778 80.3
matK-rps16_p2 matK-rps16 GCACAAACTTCGAATGAGGC ACTTGCTATTGCTGCCCTAC 1602–1609 0.333 57.6
matK-rps16_p3 matK-rps16 CGCGGAATTTCCCTTTTTCC ACTTGCTATTGCTGCCCTAC 1927–1934 0.333 57.2
matK-rps16_p4 matK-rps16 CGCGGAATTTCCCTTTTTCC TTCCTACAACCCCAGGAGAG 1966 0.111 44.0
matK-rps16_p5 matK-rps16 GCACAAACTTCGAATGAGGC TTCCTACAACCCCAGGAGAG 1641 0.111 43.8
trnS-GCU-ycf12_p1 trnS-GCU-ycf12 CAATCCGACGCTTTAGACCA CCCACCCACTCCTCGTATAT 762–797 0.667 77.6
trnS-GCU-ycf12_p2 trnS-GCU-ycf12 AATCCGACGCTTTAGACCAC CCCACCCACTCCTCGTATAT 761–796 0.667 77.6
trnS-GCU-ycf12_p3 trnS-GCU-ycf12 CGAGGGTCGCTACAATTCAA CCCACCCACTCCTCGTATAT 1303–1348 0.667 77.2
trnS-GCU-ycf12_p4 trnS-GCU-ycf12 CAATCCGACGCTTTAGACCA TCTTTTTGGGATCGTGCCAA 1098 0.111 44.3
trnS-GCU-ycf12_p5 trnS-GCU-ycf12 CGAGGGTCGCTACAATTCAA TCTTTTTGGGATCGTGCCAA 1649 0.111 44.3
rpoC2-trnD-GUC_p1 rpoC2-trnD-GUC ATCCGAAGTTGCAGTGCTAG ATTGCTATCGATGGGAGGGA 951 0.111 44.1
rpoC2-trnD-GUC_p2 rpoC2-trnD-GUC ATCCGAAGTTGCAGTGCTAG TTGCTATCGATGGGAGGGAT 950 0.111 44.1
rpoC2-trnD-GUC_p3 rpoC2-trnD-GUC GTGATGCATTGATACGCAGC ATTGCTATCGATGGGAGGGA 716 0.111 44.0
rpoC2-trnD-GUC_p4 rpoC2-trnD-GUC GTGATGCATTGATACGCAGC TTGCTATCGATGGGAGGGAT 715 0.111 44.0
rpoC2-trnD-GUC_p5 rpoC2-trnD-GUC TGCATTGATACGCAGCATCT TTGCTATCGATGGGAGGGAT 711 0.111 43.9
trnE-UUC-psbM_p1 trnE-UUC-psbM ATCCCTCCCATCGATAGCAA TTGAATCATCCCCTGCGAAG 1478 0.111 43.9
trnE-UUC-psbM_p2 trnE-UUC-psbM TCCCTCCCATCGATAGCAAT TTGAATCATCCCCTGCGAAG 1477 0.111 43.9
trnE-UUC-psbM_p3 trnE-UUC-psbM TCTATCCTCGGACTTGGGTC TTGAATCATCCCCTGCGAAG 1212 0.111 43.6
trnE-UUC-psbM_p4 trnE-UUC-psbM CTCATCGTTGACTCTGAGGC TTGAATCATCCCCTGCGAAG 1378 0.111 43.5
trnE-UUC-psbM_p5 trnE-UUC-psbM CATCGTTGACTCTGAGGCAA TTGAATCATCCCCTGCGAAG 1376 0.111 43.4
psbM-trnC-GCA_p1 psbM-trnC-GCA GATGAAGATTCGGTCGACCC ACGTGGACACCATACCTGTA 2457–2959 0.556 72.5
psbM-trnC-GCA_p2 psbM-trnC-GCA GATGAAGATTCGGTCGACCC CCGGATCGACGTTGTTTACT 2383–2885 0.333 61.3
psbM-trnC-GCA_p3 psbM-trnC-GCA GGATGAAGATTCGGTCGACC CCGGATCGACGTTGTTTACT 2384–2886 0.333 61.3
psbM-trnC-GCA_p4 psbM-trnC-GCA GATGAAGATTCGGTCGACCC TCCGGATCGACGTTGTTTAC 2384–2886 0.333 61.2
psbM-trnC-GCA_p5 psbM-trnC-GCA GGATGAAGATTCGGTCGACC TCCGGATCGACGTTGTTTAC 2385–2887 0.333 61.2
trnC-GCA-trnG-GCC_p1 trnC-GCA-trnG-GCC CCTACGTCTTACCGCTTGAC GTTCGATTCCCGCTATCCG 550–598 1.000 81.1
trnC-GCA-trnG-GCC_p2 trnC-GCA-trnG-GCC GTCCTACGTCTTACCGCTTG GTTCGATTCCCGCTATCCG 552–600 1.000 81.1
trnC-GCA-trnG-GCC_p3 trnC-GCA-trnG-GCC CCTACGTCTTACCGCTTGAC GGGTTCGATTCCCGCTATC 552–600 1.000 80.9
trnC-GCA-trnG-GCC_p4 trnC-GCA-trnG-GCC CCTACGTCTTACCGCTTGAC GGTTCGATTCCCGCTATCC 551–599 1.000 80.9
trnC-GCA-trnG-GCC_p5 trnC-GCA-trnG-GCC GTCCTACGTCTTACCGCTTG GGTTCGATTCCCGCTATCC 553–601 1.000 80.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Bolbitis aliena NC_071960.1 152833 View on NCBI ↗
Bolbitis angustipinna NC_087872.1 152562 View on NCBI ↗
Bolbitis deltigera NC_071959.1 156843 View on NCBI ↗
Bolbitis hekouensis NC_071934.1 153120 View on NCBI ↗
Bolbitis laxireticulata NC_061668.1 153093 View on NCBI ↗
Bolbitis sinensis NC_071924.1 152711 View on NCBI ↗
Bolbitis subcordata MN623358.1 153428 View on NCBI ↗
Bolbitis tonkinensis NC_071958.1 152773 View on NCBI ↗
Bolbitis x multipinna NC_064057.1 152437 View on NCBI ↗