Markers + reference

Phegopteris

2 species · Thelypteridaceae · Polypodiales

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Species 2
Genome length 150–151 kb
Candidate markers 271
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-ycf12 Genome 560 0.1196 1.00 78.2 yes View details
trnC-GCA-trnG-GCC Genome 440 0.1179 0.89 81.5 yes View details
psbD-trnT-GGU Genome 1268 0.0886 0.99 81.0 yes View details
ndhC-trnV-UAC Genome 516 0.1028 0.98 80.3 yes View details
petG-trnW-CCA Genome 279 0.0919 0.97 73.7 yes View details
ndhF Genome 2247 0.0685 1.00 75.7 yes View details
trnP-GGG-trnL-UAG Genome 295 0.1358 0.90 81.6 yes View details
ycf1-chlN Genome 422 0.1327 0.93 79.5 yes View details
trnT-GGU-trnfM-CAU Genome 477 0.1078 0.91 85.7 yes View details
psbM-petN Genome 919 0.0931 0.96 84.9 yes View details
trnT-UGU-trnR-ACG Genome 653 0.0611 0.98 82.4 yes View details
petA-psbJ Genome 852 0.0777 0.98 82.0 yes View details
rps4-trnL-UAA Genome 637 0.0795 0.97 81.9 yes View details
psbE-petL Genome 771 0.0844 0.94 81.3 yes View details
trnL-UAA-trnF-GAA Genome 322 0.1026 0.97 79.9 yes View details
psbZ-trnS-UGA Genome 432 0.1148 0.91 79.7 yes View details
rps16 Genome 1090 0.0741 0.97 79.6 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16_p1 rps16 CGCTAAAGTGCTGAGCTACA GGGGCATGATACCAAAGGAG 1826–1849 1.000 87.3
rps16_p2 rps16 CTTGAACTACCTGCGTCTCC GGGGCATGATACCAAAGGAG 1672–1695 1.000 87.1
rps16_p3 rps16 CGCTAAAGTGCTGAGCTACA TGGGCATGGAAGATCATTCG 1860–1883 1.000 87.1
rps16_p4 rps16 CTTGAACTACCTGCGTCTCC TGGGCATGGAAGATCATTCG 1706–1729 1.000 86.9
rps16_p5 rps16 CTGTAAGCTGGGCCCATTAG GGGGCATGATACCAAAGGAG 1490 0.500 59.7
trnS-GCU-ycf12_p1 trnS-GCU-ycf12 TAATGTCTCACGAAAGCCGG TTACCAACGCCAAGATAGCC 1040 0.500 59.7
trnS-GCU-ycf12_p2 trnS-GCU-ycf12 TAATGTCTCACGAAAGCCGG GAATGGCGCATTCTTTTCCC 1438 0.500 59.4
trnS-GCU-ycf12_p3 trnS-GCU-ycf12 TAATGTCTCACGAAAGCCGG GGAATGGCGCATTCTTTTCC 1439 0.500 59.4
trnS-GCU-ycf12_p4 trnS-GCU-ycf12 GGGAGAGAGAGGGATTCGAA TTACCAACGCCAAGATAGCC 694 0.500 59.1
trnS-GCU-ycf12_p5 trnS-GCU-ycf12 AAGGGAGAGAGAGGGATTCG TTACCAACGCCAAGATAGCC 696 0.500 59.1
psbM-petN_p1 psbM-petN TCCCAACAGCTTTTCTGCTT TCTCACTTGTAGTTCGGGGA 977–1010 1.000 86.7
psbM-petN_p2 psbM-petN CGGCCGCTCAGAATAACTAG TCTCACTTGTAGTTCGGGGA 941–974 1.000 85.8
psbM-petN_p3 psbM-petN TCCCAACAGCTTTTCTGCTT TTGTAGTTCGGGGAAGAAGC 971–1004 1.000 85.4
psbM-petN_p4 psbM-petN ATCCCAACAGCTTTTCTGCT TCTCACTTGTAGTTCGGGGA 978–1011 1.000 84.9
psbM-petN_p5 psbM-petN CGGCCGCTCAGAATAACTAG TTGTAGTTCGGGGAAGAAGC 935–968 1.000 84.5
trnC-GCA-trnG-GCC_p1 trnC-GCA-trnG-GCC GATTTGCAGTCCTCCGTCTT GTTCGATTCCCGCTATCCG 472–500 1.000 81.3
trnC-GCA-trnG-GCC_p2 trnC-GCA-trnG-GCC GATTTGCAGTCCTCCGTCTT GGTTCGATTCCCGCTATCC 473–501 1.000 81.1
trnC-GCA-trnG-GCC_p3 trnC-GCA-trnG-GCC TTAGGCGACACCCAGATTTG GTTCGATTCCCGCTATCCG 507–535 1.000 80.7
trnC-GCA-trnG-GCC_p4 trnC-GCA-trnG-GCC GTTAGGCGACACCCAGATTT GTTCGATTCCCGCTATCCG 508–536 1.000 80.7
trnC-GCA-trnG-GCC_p5 trnC-GCA-trnG-GCC TTTCTTGTTAGGCGACACCC GTTCGATTCCCGCTATCCG 514–542 1.000 80.5
psbZ-trnS-UGA_p1 psbZ-trnS-UGA TTTCTACGGGATAGGCGGAT CGATACCGAACCCGTTCTTT 1347–1372 1.000 89.1
psbZ-trnS-UGA_p2 psbZ-trnS-UGA TTTCTACGGGATAGGCGGAT AGATCAACGCCGTGAACTAC 1492–1517 1.000 88.3
psbZ-trnS-UGA_p3 psbZ-trnS-UGA TTGCCCCTCCTTTTTCCTTC CGATACCGAACCCGTTCTTT 1501 0.500 59.9
psbZ-trnS-UGA_p4 psbZ-trnS-UGA CTTGCCCCTCCTTTTTCCTT CGATACCGAACCCGTTCTTT 1502 0.500 59.9
psbZ-trnS-UGA_p5 psbZ-trnS-UGA TTGCCCCTCCTTTTTCCTTC AGATCAACGCCGTGAACTAC 1646 0.500 59.9
psbD-trnT-GGU_p1 psbD-trnT-GGU TTTTCCAATGGCAATGGTCA TTCAAATCCGACAAAGGGCT 1301–1309 1.000 70.2
psbD-trnT-GGU_p2 psbD-trnT-GGU TTTTCCAATGGCAATGGTCA CCCCTTTAACTCAGCGGTAG 1352–1360 1.000 69.7
psbD-trnT-GGU_p3 psbD-trnT-GGU TTTTCCAATGGCAATGGTCA GTTCAAATCCGACAAAGGGC 1302–1310 1.000 69.7
psbD-trnT-GGU_p4 psbD-trnT-GGU TTTCCAATGGCAATGGTCAT TTCAAATCCGACAAAGGGCT 1300–1308 1.000 68.3
psbD-trnT-GGU_p5 psbD-trnT-GGU TTTCCAATGGCAATGGTCAT CCCCTTTAACTCAGCGGTAG 1351–1359 1.000 67.8

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
Phegopteris aurita NC_035861.1 149917 View on NCBI ↗
Phegopteris decursive-pinnata MN623353.1 150995 View on NCBI ↗