Markers + reference

Ceratopteris

3 species · Pteridaceae · Polypodiales

Back to catalogue

Species 3
Genome length 149–154 kb
Candidate markers 270
Primer pairs 95

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 7 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI LSC 536 0.2833 0.90 67.8 yes View details
trnS-GCU; trnS-GGA; trnS-UGA-ycf12 LSC 719 0.2652 0.64 62.2 yes View details
rpoB-trnD-GUC LSC 826 0.2669 0.88 81.9 yes View details
psbM-petN LSC 1943 0.2653 0.32 69.3 yes View details
rps4-trnL-UAA LSC 769 0.2338 0.91 82.6 yes View details
petA-psbJ LSC 1023 0.2710 0.86 80.4 yes View details
trnI-CAU-trnT-UGU IRb 1937 0.2094 0.23 52.5 yes View details
ycf1 SSC 5082 0.2208 0.97 75.3 yes View details
petB LSC 1501 0.1357 0.95 83.3 yes View details
rpl2 LSC 1576 0.1599 0.94 82.9 yes View details
ycf3 LSC 1976 0.1398 0.94 82.1 yes View details
ndhA SSC 2017 0.1633 0.94 82.0 yes View details
matK-rps16 LSC 707 0.2431 0.90 81.8 yes View details
clpP LSC 1894 0.1539 0.96 81.6 yes View details
clpP-psbB LSC 552 0.2044 0.90 80.9 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 TAAGTTCGCGCACGTTATCA CGAATAGTCGCAATTGACGC 1128 0.333 53.1
matK-rps16_p2 matK-rps16 TAAGTTCGCGCACGTTATCA GAGTATAGGGCGCTGATTCG 1377 0.333 53.0
matK-rps16_p3 matK-rps16 TAAGTTCGCGCACGTTATCA GGAAGGTCACTAGGGAGGTT 1091 0.333 52.8
matK-rps16_p4 matK-rps16 TAAGTTCGCGCACGTTATCA GGGGTTAATCTCTGCATGCA 1170 0.333 52.7
matK-rps16_p5 matK-rps16 TAAGTTCGCGCACGTTATCA TTGGGTTTTACAATCCCCGG 1073 0.333 52.6
psbK-psbI_p1 psbK-psbI GTTACCCGAAGCTTATGCCA AGAGGACGATAGAAGGGAGC 1123 0.333 53.0
psbK-psbI_p2 psbK-psbI GTTACCCGAAGCTTATGCCA GAGGACGATAGAAGGGAGCT 1122 0.333 53.0
psbK-psbI_p3 psbK-psbI GTTACCCGAAGCTTATGCCA CTAGCGTTCCCAAGCAGATT 1355 0.333 52.8
psbK-psbI_p4 psbK-psbI GTTACCCGAAGCTTATGCCA GACTCAATCCTTACGGCCAG 762 0.333 52.6
psbK-psbI_p5 psbK-psbI TAACCGCGTCGAGGAAAAAT GAGGACGATAGAAGGGAGCT 1234 0.333 52.6
trnS-GCU; trnS-GGA; trnS-UGA-ycf12_p1 trnS-GCU; trnS-GGA; trnS-UGA-ycf12 TCGATGCAACGGCGTATTAA GAGTCGTTGAAGCACTGGAT 2005 0.333 52.0
trnS-GCU; trnS-GGA; trnS-UGA-ycf12_p2 trnS-GCU; trnS-GGA; trnS-UGA-ycf12 TCGATGCAACGGCGTATTAA AAAGCCTCAGAAATTGCGGA 1441 0.333 52.0
trnS-GCU; trnS-GGA; trnS-UGA-ycf12_p3 trnS-GCU; trnS-GGA; trnS-UGA-ycf12 TCGATGCAACGGCGTATTAA AAGCCTCAGAAATTGCGGAA 1440 0.333 52.0
trnS-GCU; trnS-GGA; trnS-UGA-ycf12_p4 trnS-GCU; trnS-GGA; trnS-UGA-ycf12 TAGCAATCCGTCGCTTTCAA GAGTCGTTGAAGCACTGGAT 1449 0.333 51.9
trnS-GCU; trnS-GGA; trnS-UGA-ycf12_p5 trnS-GCU; trnS-GGA; trnS-UGA-ycf12 TTAGCAATCCGTCGCTTTCA GAGTCGTTGAAGCACTGGAT 1450 0.333 51.9
trnG-UCC_p1 trnG-UCC AATCTGCTTGGGAACGCTAG CCAACCAGTTATCCCGACTG 1697 0.333 52.9
trnG-UCC_p2 trnG-UCC AATCTGCTTGGGAACGCTAG GCCCTATCCATTAGGCGATG 1613 0.333 52.9
trnG-UCC_p3 trnG-UCC AATCTGCTTGGGAACGCTAG TCTTGGTTCAGTTGCGTGAA 1889 0.333 52.8
trnG-UCC_p4 trnG-UCC AATCTGCTTGGGAACGCTAG TTCTTGGTTCAGTTGCGTGA 1890 0.333 52.8
trnG-UCC_p5 trnG-UCC AACACCAGTCCATAGGAGCT CCAACCAGTTATCCCGACTG 1583 0.333 52.8
rpoB-trnD-GUC_p1 rpoB-trnD-GUC TCTCCGACTGAAGGTTCTGT CATTGAGTAATCCAGCCCCC 1522 0.333 53.2
rpoB-trnD-GUC_p2 rpoB-trnD-GUC CTGGTACATATGGATCGGCG CATTGAGTAATCCAGCCCCC 1575 0.333 53.2
rpoB-trnD-GUC_p3 rpoB-trnD-GUC CAAGTTCTGGTAGTACGGGC CATTGAGTAATCCAGCCCCC 1371 0.333 53.2
rpoB-trnD-GUC_p4 rpoB-trnD-GUC GCAAGTTCTGGTAGTACGGG CATTGAGTAATCCAGCCCCC 1372 0.333 53.2
rpoB-trnD-GUC_p5 rpoB-trnD-GUC GCATCCTCCGGTGATTCAAT CATTGAGTAATCCAGCCCCC 1987 0.333 53.0
psbM-petN_p1 psbM-petN TTACATTCAGACAGCCGCTC TCTTTCGCTTGTAGTTCGGG 2014 0.333 52.7
psbM-petN_p2 psbM-petN GGGGGCTGGATTACTCAATG TCTTTCGCTTGTAGTTCGGG 2518 0.333 52.6
psbM-petN_p3 psbM-petN CAGCCGCTCAGAGTAACAAT TCTTTCGCTTGTAGTTCGGG 2003 0.333 52.6
psbM-petN_p4 psbM-petN TTCTTGCGTTTGTAGCCACT TCTTTCGCTTGTAGTTCGGG 2075 0.333 52.4
psbM-petN_p5 psbM-petN TTACATTCAGACAGCCGCTC AGGAAAAGGCGTGAATCTCC 2278 0.333 52.3

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
Ceratopteris cornuta NC_040212.1 154106 View on NCBI ↗
Ceratopteris pteridoides NC_066508.1 149426 View on NCBI ↗
Ceratopteris thalictroides NC_062137.1 149399 View on NCBI ↗