Markers + reference

Christella

2 species · Thelypteridaceae · Polypodiales

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Species 2
Genome length 152–152 kb
Candidate markers 233
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 10 remaining regions by MarkerSeek score (out of 233 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoC2-trnD-GUC LSC 7310 0.0073 1.00 48.2 yes View details
trnC-GCA-trnG-GCC LSC 447 0.0248 0.99 63.3 yes View details
trnS-UGA-psbC LSC 298 0.0346 0.97 67.2 yes View details
trnS-GGA-trnL-UAA LSC 1743 0.0144 1.00 55.4 yes View details
trnN-GUU-rpl21 SSC 3019 0.0162 1.00 61.3 yes View details
trnP-GGG-trnL-UAG SSC 258 0.0388 1.00 65.4 yes View details
ycf1-chlN SSC 1495 0.0156 0.99 54.9 yes View details
ndhB-matK LSC 1795 0.0207 1.00 63.1 no View details
trnD-GUC-trnY-GUA LSC 57 0.0526 1.00 73.6 yes View details
psbM-petN LSC 871 0.0161 1.00 68.0 yes View details
trnG-GCC-psbZ LSC 263 0.0311 0.98 67.8 yes View details
psbK-psbI LSC 534 0.0169 1.00 67.1 yes View details
atpH-atpI LSC 754 0.0120 1.00 65.5 yes View details
rps19-rpl23 LSC 1713 0.0117 1.00 65.0 yes View details
ycf4-cemA LSC 183 0.0383 1.00 64.7 yes View details
trnM-CAU-atpE LSC 145 0.0207 1.00 64.4 yes View details
psaC-ndhE SSC 311 0.0225 1.00 64.1 yes View details
trnF-GAA-ndhJ LSC 227 0.0264 1.00 63.6 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbK-psbI_p1 psbK-psbI CAAGCCGCAGTTAGTTTTCG AGGGTTTCGTCCAGGATCAT 654–665 1.000 77.4
psbK-psbI_p2 psbK-psbI CAAGCCGCAGTTAGTTTTCG GGGTTTCGTCCAGGATCATT 653–664 1.000 77.3
psbK-psbI_p3 psbK-psbI CAAGCCGCAGTTAGTTTTCG TTTTACCTAATCCCCACGGC 675–686 1.000 77.3
psbK-psbI_p4 psbK-psbI CGGTGTTCTTTCTCCTCCTG AGGGTTTCGTCCAGGATCAT 686–697 1.000 77.0
psbK-psbI_p5 psbK-psbI CGGTGTTCTTTCTCCTCCTG GGGTTTCGTCCAGGATCATT 685–696 1.000 77.0
atpH-atpI_p1 atpH-atpI CTAACCCAGCAGCAATGACA AGCTCATATCGGGGAATCCA 826–828 1.000 79.4
atpH-atpI_p2 atpH-atpI TAACCCAGCAGCAATGACAG AGCTCATATCGGGGAATCCA 825–827 1.000 79.4
atpH-atpI_p3 atpH-atpI CTAACCCAGCAGCAATGACA GTACCCACGATGCCTTTAGG 894–896 1.000 79.2
atpH-atpI_p4 atpH-atpI TAACCCAGCAGCAATGACAG GTACCCACGATGCCTTTAGG 893–895 1.000 79.2
atpH-atpI_p5 atpH-atpI TAACCCAGCAGCAATGACAG GCTCATATCGGGGAATCCAC 824–826 1.000 78.9
rpoC2-trnD-GUC_p1 rpoC2-trnD-GUC GCTACAAAAAGAAGTTACTCGGT ACCCTGAGTCAGCAATCTCT 188 1.000 51.6
rpoC2-trnD-GUC_p2 rpoC2-trnD-GUC GCTACAAAAAGAAGTTACTCGGT GTCAACCCTGAGTCAGCAAT 192 1.000 50.5
rpoC2-trnD-GUC_p3 rpoC2-trnD-GUC AGCTACAAAAAGAAGTTACTCGG ACCCTGAGTCAGCAATCTCT 189 1.000 49.6
rpoC2-trnD-GUC_p4 rpoC2-trnD-GUC AGCTACAAAAAGAAGTTACTCGG GTCAACCCTGAGTCAGCAAT 193 1.000 48.4
rpoC2-trnD-GUC_p5 rpoC2-trnD-GUC GCTACAAAAAGAAGTTACTCGGT TCAACCCTGAGTCAGCAATC 191 1.000 48.2
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
psbM-petN_p1 psbM-petN GCCACCGCACTTTTTATTCC TCTCACTTGTAGTTCGGGGA 992–993 1.000 78.7
psbM-petN_p2 psbM-petN GCCACCGCACTTTTTATTCC TTGTAGTTCGGGGAAGAAGC 986–987 1.000 77.3
psbM-petN_p3 psbM-petN GCCACCGCACTTTTTATTCC CCCTCTCACTTGTAGTTCGG 995–996 1.000 75.8
psbM-petN_p4 psbM-petN GCCACCGCACTTTTTATTCC CCTCTCACTTGTAGTTCGGG 994–995 1.000 75.8
psbM-petN_p5 psbM-petN GCCACCGCACTTTTTATTCC CTCTCACTTGTAGTTCGGGG 993–994 1.000 75.8
trnC-GCA-trnG-GCC_p1 trnC-GCA-trnG-GCC GATTTGCAGTCCTCCGTCTT GTTCGATTCCCGCTATCCG 504–507 1.000 72.1
trnC-GCA-trnG-GCC_p2 trnC-GCA-trnG-GCC GATTTGCAGTCCTCCGTCTT GGTTCGATTCCCGCTATCC 505–508 1.000 71.9
trnC-GCA-trnG-GCC_p3 trnC-GCA-trnG-GCC TTAGGCGACACCCAGATTTG GTTCGATTCCCGCTATCCG 539–542 1.000 71.8
trnC-GCA-trnG-GCC_p4 trnC-GCA-trnG-GCC GTTAGGCGACACCCAGATTT GTTCGATTCCCGCTATCCG 540–543 1.000 71.8
trnC-GCA-trnG-GCC_p5 trnC-GCA-trnG-GCC TTTCTTGTTAGGCGACACCC GTTCGATTCCCGCTATCCG 546–549 1.000 71.8

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
Christella acuminata NC_070299.1 151533 View on NCBI ↗
Christella appendiculata NC_035842.1 151571 View on NCBI ↗