Markers + reference

Thelypteris

3 species · Thelypteridaceae · Polypodiales

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Species 3
Genome length 152–152 kb
Candidate markers 233
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 233 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
matK-rps16 LSC 958 0.0202 1.00 57.7 yes View details
psbK-psbI LSC 534 0.0262 1.00 63.8 yes View details
rpoC2-trnD-GUC LSC 7315 0.0079 1.00 45.8 yes View details
trnC-GCA-trnG-GCC LSC 445 0.0232 1.00 68.4 yes View details
trnS-UGA-psbC LSC 298 0.0382 1.00 71.7 yes View details
cemA-psbJ LSC 2039 0.0150 1.00 67.8 yes View details
petB LSC 1494 0.0129 1.00 52.3 yes View details
trnN-GUU-rpl21 SSC 3019 0.0148 1.00 56.5 yes View details
trnP-GGG-trnL-UAG SSC 266 0.0451 1.00 73.6 yes View details
ycf1-chlN SSC 1479 0.0183 1.00 57.1 yes View details
ndhB-matK LSC 1791 0.0175 1.00 62.1 no View details
trnG-GCC-psbZ LSC 267 0.0331 0.98 73.9 yes View details
ycf4-cemA LSC 183 0.0437 1.00 70.6 yes View details
ndhJ-ndhK LSC 70 0.0381 1.00 70.5 yes View details
trnD-GUC-trnY-GUA LSC 57 0.0351 1.00 66.9 yes View details
atpF-atpH LSC 190 0.0351 1.00 65.3 yes View details
trnF-GAA-ndhJ LSC 227 0.0294 1.00 64.8 yes View details
trnP-UGG-psaJ LSC 354 0.0235 1.00 63.3 yes View details
psbZ-trnS-UGA LSC 433 0.0200 1.00 62.4 yes View details
rpl23-trnI-CAU LSC 180 0.0296 1.00 61.7 yes View details
clpP-psbB LSC 530 0.0151 1.00 61.1 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-rps16_p1 matK-rps16 AGTGGATGCACAAACTTCGT GTTTTACCCCGTCTACGACC 2211–2216 1.000 81.9
matK-rps16_p2 matK-rps16 AGTGGATGCACAAACTTCGT TAATTGCGATCGACAGCCAA 1709–1711 1.000 81.7
matK-rps16_p3 matK-rps16 AGTGGATGCACAAACTTCGT AAGCTATCAGGGAGGTTGGT 1673–1675 1.000 81.6
matK-rps16_p4 matK-rps16 AGTGGATGCACAAACTTCGT AGCTATCAGGGAGGTTGGTT 1672–1674 1.000 81.6
matK-rps16_p5 matK-rps16 AGTGGATGCACAAACTTCGT GTGGTATTTTGAAACGGGCG 1562–1564 1.000 81.6
psbK-psbI_p1 psbK-psbI CAAGCCGCAGTTAGTTTTCG AGGGTTTCGTCCAGGATCAT 654–666 1.000 78.8
psbK-psbI_p2 psbK-psbI CAAGCCGCAGTTAGTTTTCG GGGTTTCGTCCAGGATCATT 653–665 1.000 78.8
psbK-psbI_p3 psbK-psbI CAAGCCGCAGTTAGTTTTCG TTTTACCTAATCCCCACGGC 675–687 1.000 78.7
psbK-psbI_p4 psbK-psbI CGGTGTTCTTTCTCCTCCTG AGGGTTTCGTCCAGGATCAT 686–698 1.000 78.4
psbK-psbI_p5 psbK-psbI CGGTGTTCTTTCTCCTCCTG GGGTTTCGTCCAGGATCATT 685–697 1.000 78.4
atpF-atpH_p1 atpF-atpH GAAAATTGCGATGCGGACAA GCTTCGTCATTTGCCAATCC 255–260 1.000 82.2
atpF-atpH_p2 atpF-atpH GAAAATTGCGATGCGGACAA GCTTTCACGGAAGCTTTGAC 300–305 1.000 82.1
atpF-atpH_p3 atpF-atpH GAAAATTGCGATGCGGACAA GAAGGCAAGACACGAGGTAC 336–341 1.000 79.9
atpF-atpH_p4 atpF-atpH GAAAATTGCGATGCGGACAA GGCAAGACACGAGGTACTTC 333–338 1.000 79.9
atpF-atpH_p5 atpF-atpH GAAAATTGCGATGCGGACAA AGAAGGCAAGACACGAGGTA 337–342 1.000 79.2
rpoC2-trnD-GUC_p1 rpoC2-trnD-GUC CAATCCACCCCTAGCCTCTA TTTCCTTTACAGCCTGCGAG 162 1.000 83.1
rpoC2-trnD-GUC_p2 rpoC2-trnD-GUC GAAACAATCCACCCCTAGCC TTTCCTTTACAGCCTGCGAG 166 1.000 81.9
rpoC2-trnD-GUC_p3 rpoC2-trnD-GUC CAATCCACCCCTAGCCTCTA ATTTCCTTTACAGCCTGCGA 163 1.000 80.7
rpoC2-trnD-GUC_p4 rpoC2-trnD-GUC TGAAACAATCCACCCCTAGC TTTCCTTTACAGCCTGCGAG 167 1.000 79.7
rpoC2-trnD-GUC_p5 rpoC2-trnD-GUC GAAACAATCCACCCCTAGCC ATTTCCTTTACAGCCTGCGA 167 1.000 79.5
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA AATTGGTTAGAGCACCGACC GATGCTCGAGTGGCTAATGG 195–206 1.000 76.4
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA AATTGGTTAGAGCACCGACC GACTGTAAATCCGCTGGCAA 170–181 1.000 76.1
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA ACCTGTCAAGTCGGAAGTTG GATGCTCGAGTGGCTAATGG 178–189 1.000 75.4
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA ACCTGTCAAGTCGGAAGTTG GACTGTAAATCCGCTGGCAA 153–164 1.000 75.2
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA AATTGGTTAGAGCACCGACC ACTGTAAATCCGCTGGCAAC 169–180 1.000 73.8
trnC-GCA-trnG-GCC_p1 trnC-GCA-trnG-GCC GATTTGCAGTCCTCCGTCTT GTTCGATTCCCGCTATCCG 487–505 1.000 76.1
trnC-GCA-trnG-GCC_p2 trnC-GCA-trnG-GCC GATTTGCAGTCCTCCGTCTT GGTTCGATTCCCGCTATCC 488–506 1.000 75.9
trnC-GCA-trnG-GCC_p3 trnC-GCA-trnG-GCC TTAGGCGACACCCAGATTTG GTTCGATTCCCGCTATCCG 522–540 1.000 75.6
trnC-GCA-trnG-GCC_p4 trnC-GCA-trnG-GCC GTTAGGCGACACCCAGATTT GTTCGATTCCCGCTATCCG 523–541 1.000 75.6
trnC-GCA-trnG-GCC_p5 trnC-GCA-trnG-GCC TTTCTTGTTAGGCGACACCC GTTCGATTCCCGCTATCCG 529–547 1.000 75.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Thelypteris arida NC_070302.1 151513 View on NCBI ↗
Thelypteris latipinna NC_070300.1 151588 View on NCBI ↗
Thelypteris parasitica NC_070301.1 151573 View on NCBI ↗