Markers + reference

Dryopteris

4 species · Dryopteridaceae · Polypodiales

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Species 4
Genome length 149–150 kb
Candidate markers 267
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

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

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpl23 Genome 267 0.0169 1.00 49.7 yes View details
petB Genome 1451 0.0226 1.00 60.9 yes View details
psaJ-trnP-UGG Genome 374 0.0460 0.99 72.2 yes View details
psbJ-petA Genome 730 0.0495 1.00 80.0 yes View details
petN-psbM Genome 1203 0.0353 1.00 71.2 yes View details
psbI-psbK Genome 512 0.0446 1.00 74.3 yes View details
rps16-matK Genome 669 0.0411 0.99 73.3 yes View details
ndhB Genome 2309 0.0173 0.99 57.1 yes View details
ycf1 Genome 5136 0.0248 1.00 55.5 yes View details
psaC Genome 246 0.0102 1.00 44.6 yes View details
trnP-GGG-rpl32 Genome 619 0.0493 1.00 79.4 yes View details
ndhF Genome 1842 0.0283 1.00 63.4 yes View details
trnG-UCC-ycf12 Genome 171 0.0565 0.99 77.8 yes View details
trnP-UGG-trnW-CCA Genome 186 0.0739 0.99 77.2 yes View details
trnI-CAU-rpl23 Genome 165 0.0626 1.00 75.9 yes View details
trnS-UGA-psbI Genome 73 0.0479 1.00 75.8 yes View details
trnG-UCC-trnC-GCA Genome 497 0.0369 1.00 73.9 yes View details
trnL-UAG-trnP-GGG Genome 280 0.0452 1.00 73.9 yes View details
rpl23-rpl2 Genome 68 0.0907 1.00 73.1 yes View details
rpl22-rps3 Genome 107 0.0498 1.00 72.8 yes View details
atpH-atpF Genome 352 0.0442 0.99 71.5 yes View details
ndhE-psaC Genome 324 0.0454 0.98 71.4 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnI-CAU-rpl23_p1 trnI-CAU-rpl23 TAATTGGCGAATTCACGGGT TGGTTCTTCAATTTCTCCGT 224 1.000 61.0
trnI-CAU-rpl23_p2 trnI-CAU-rpl23 ATTCACGGGTTCAACTCCTG TGGTTCTTCAATTTCTCCGT 214 1.000 60.7
trnI-CAU-rpl23_p3 trnI-CAU-rpl23 TAATTGGCGAATTCACGGGT TTGGTTCTTCAATTTCTCCGT 225 1.000 59.5
trnI-CAU-rpl23_p4 trnI-CAU-rpl23 ATTCACGGGTTCAACTCCTG TTGGTTCTTCAATTTCTCCGT 215 1.000 59.3
trnI-CAU-rpl23_p5 trnI-CAU-rpl23 CGGTTAAAGCACCCAACTCA TGGTTCTTCAATTTCTCCGT 244 1.000 58.1
rpl23_p1 rpl23 TAATTGGCGAATTCACGGGT TTCCGTTGTTTCCCCGAATT 617 1.000 84.5
rpl23_p2 rpl23 TAATTGGCGAATTCACGGGT TCAGTTTGTCTCGCCGAAAA 756 1.000 83.6
rpl23_p3 rpl23 TAATTGGCGAATTCACGGGT TTCAGTTTGTCTCGCCGAAA 757 1.000 83.6
rpl23_p4 rpl23 TAATTGGCGAATTCACGGGT CTTCGGTATACGCATAGGGC 1204 1.000 83.3
rpl23_p5 rpl23 TAATTGGCGAATTCACGGGT GCCTTCGGTATACGCATAGG 1206 1.000 83.3
rpl23-rpl2_p1 rpl23-rpl2 TAATTGGCGAATTCACGGGT TTCCGTTGTTTCCCCGAATT 617 1.000 84.5
rpl23-rpl2_p2 rpl23-rpl2 TAATTGGCGAATTCACGGGT TCAGTTTGTCTCGCCGAAAA 756 1.000 83.6
rpl23-rpl2_p3 rpl23-rpl2 TAATTGGCGAATTCACGGGT CTTCGGTATACGCATAGGGC 1204 1.000 83.3
rpl23-rpl2_p4 rpl23-rpl2 TAATTGGCGAATTCACGGGT GCCTTCGGTATACGCATAGG 1206 1.000 83.3
rpl23-rpl2_p5 rpl23-rpl2 TAATTGGCGAATTCACGGGT CCCGACTGCCAAATCGAATA 1247 0.250 48.7
rpl22-rps3_p1 rpl22-rps3 TGTAACTGATCGCATGGTGG TGTCTGTGCGAACCGATAAG 676–677 1.000 83.3
rpl22-rps3_p2 rpl22-rps3 TGTAACTGATCGCATGGTGG TTGAGTCGTCCGGCTATTTG 1104–1105 1.000 82.6
rpl22-rps3_p3 rpl22-rps3 TGTAACTGATCGCATGGTGG GTTGAGTCGTCCGGCTATTT 1105–1106 1.000 82.6
rpl22-rps3_p4 rpl22-rps3 TGTAACTGATCGCATGGTGG CTTGTCTGTGCGAACCGATA 679 0.750 71.5
rpl22-rps3_p5 rpl22-rps3 TTCATAATGGCCGAGAGCAC TTGAGTCGTCCGGCTATTTG 1136 0.250 49.6
petB_p1 petB GTCACACACTCCCGTAATCC AATTGAGCAGGCTCTATGGC 2006–2014 1.000 83.9
petB_p2 petB CAACATGGCTTCTCATCCGA AATTGAGCAGGCTCTATGGC 2493–2501 1.000 83.3
petB_p3 petB GTTTCGCAACATGGCTTCTC AATTGAGCAGGCTCTATGGC 2499–2507 1.000 83.3
petB_p4 petB AGAAAGGTCGGAAAGGGAGA AATTGAGCAGGCTCTATGGC 2095 0.250 49.6
petB_p5 petB GTCACACACTCCCGTAATCC TCGAAGGAAGGTCCATCAGT 2244 0.250 49.5
psaJ-trnP-UGG_p1 psaJ-trnP-UGG GTAGGTGTGTTACGGCGATT GAACCTGCGGCATTTTGTAC 931–944 1.000 84.3
psaJ-trnP-UGG_p2 psaJ-trnP-UGG AACGTCTACGGAGAGATCGT GAACCTGCGGCATTTTGTAC 1114–1128 1.000 83.7
psaJ-trnP-UGG_p3 psaJ-trnP-UGG GTAGGTGTGTTACGGCGATT GAGTGAGGAGGAAGCGAAAG 1070–1073 0.500 63.0
psaJ-trnP-UGG_p4 psaJ-trnP-UGG AACGTCTACGGAGAGATCGT GAGTGAGGAGGAAGCGAAAG 1253–1257 0.500 62.6
psaJ-trnP-UGG_p5 psaJ-trnP-UGG GAGGAACGTCTACGGAGAGA GAGTGAGGAGGAAGCGAAAG 1257–1261 0.500 62.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Dryopteris fulgens NC_067596.1 149380 View on NCBI ↗
Dryopteris gaoligongensis NC_067598.1 149702 View on NCBI ↗
Dryopteris sparsa NC_067599.1 149420 View on NCBI ↗
Dryopteris yoroii NC_067601.1 148690 View on NCBI ↗