Markers + reference

Diplazium

4 species · Athyriaceae · Polypodiales

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Species 4
Genome length 150–152 kb
Candidate markers 273
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
matK-rps16 Genome 620 0.0874 1.00 79.1 yes View details
psbM-petN Genome 865 0.0948 1.00 83.1 yes View details
trnC-GCA-trnG-GCC Genome 435 0.1384 0.96 84.4 yes View details
psbD-trnT-GGU Genome 1418 0.0962 0.97 84.2 yes View details
petA-psbJ Genome 895 0.1032 0.95 83.1 yes View details
rpl23-trnI-CAU Genome 178 0.1891 0.96 76.7 yes View details
ndhF Genome 2232 0.0721 1.00 78.9 yes View details
rpl32-trnP-GGG Genome 710 0.1511 0.96 83.4 yes View details
trnP-GGG-trnL-UAG Genome 278 0.1286 0.97 81.3 yes View details
ccsA-ndhD Genome 405 0.1322 0.97 77.7 yes View details
trnT-UGU-trnR-ACG Genome 774 0.0480 0.95 83.0 yes View details
trnR-ACG-trnT-UGU Genome 774 0.0480 0.95 83.0 yes View details
psbK-psbI Genome 540 0.1117 1.00 82.5 yes View details
trnS-GCU-ycf12 Genome 560 0.0923 0.99 81.7 yes View details
rps4-trnL-UAA Genome 645 0.0987 1.00 81.7 yes View details
psbE-petL Genome 758 0.0727 0.98 81.5 yes View details
rpoB-trnD-GUC Genome 768 0.0948 0.84 80.6 yes View details
petB Genome 1452 0.0578 1.00 80.5 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-rps16_p1 matK-rps16 CGAGACTGAGGCTGAGTAGA CTGCGAACGAGGGGATTTTA 1772 0.250 49.6
matK-rps16_p2 matK-rps16 CGAGACTGAGGCTGAGTAGA TGCGAACGAGGGGATTTTAG 1771 0.250 49.6
matK-rps16_p3 matK-rps16 CGAGACTGAGGCTGAGTAGA GGAGCGCAATCAACAGAAAC 1315 0.250 49.5
matK-rps16_p4 matK-rps16 CGAGACTGAGGCTGAGTAGA CTTCGGGGTTAGGCCTAAAC 1813 0.250 49.5
matK-rps16_p5 matK-rps16 CGAGACTGAGGCTGAGTAGA TTTTAGGGGTCGGTGAGGAT 1868 0.250 49.4
psbK-psbI_p1 psbK-psbI ACTTCGGGTTTCCTGTCAAC TTCGTCCGGGATCATTTGAC 1105–1142 0.500 67.2
psbK-psbI_p2 psbK-psbI CACTTCGGGTTTCCTGTCAA TTCGTCCGGGATCATTTGAC 1106–1143 0.500 67.2
psbK-psbI_p3 psbK-psbI GCGAGAAGAGTTTGGGGTAG TTCGTCCGGGATCATTTGAC 1045 0.250 49.8
psbK-psbI_p4 psbK-psbI GTAGCGAGAAGAGTTTGGGG TTCGTCCGGGATCATTTGAC 1048 0.250 49.8
psbK-psbI_p5 psbK-psbI AATCTTCGATCCCGTTGTGG TTCGTCCGGGATCATTTGAC 725 0.250 49.7
trnS-GCU-ycf12_p1 trnS-GCU-ycf12 GTCAAATGATCCCGGACGAA CACAGATTACCCTTCCGAGC 855–859 0.500 66.7
trnS-GCU-ycf12_p2 trnS-GCU-ycf12 GTCAAATGATCCCGGACGAA TAGGTATTCGGTTGTGCTGC 885 0.250 49.7
trnS-GCU-ycf12_p3 trnS-GCU-ycf12 GTCAAATGATCCCGGACGAA TACGACTTCCGAAGCACAAG 1218 0.250 49.4
trnS-GCU-ycf12_p4 trnS-GCU-ycf12 GGGAGAGAGAGGGATTCGAA TAGGTATTCGGTTGTGCTGC 775 0.250 49.3
trnS-GCU-ycf12_p5 trnS-GCU-ycf12 GTCAAATGATCCCGGACGAA CGTCACAGATTACCCTTCCG 862 0.250 49.2
trnG-UCC_p1 trnG-UCC GCAGCACAACCGAATACCTA CTTCAGTTTGTTCACGACGC 1221 0.250 49.8
trnG-UCC_p2 trnG-UCC GCAGCACAACCGAATACCTA CTAGGGCTCCGGGATTCTTA 1174 0.250 49.8
trnG-UCC_p3 trnG-UCC GCAGCACAACCGAATACCTA TAGGGCTCCGGGATTCTTAG 1173 0.250 49.8
trnG-UCC_p4 trnG-UCC GCAGCACAACCGAATACCTA GATTGTACCCGGGGAATCAC 1455 0.250 49.6
trnG-UCC_p5 trnG-UCC GCAGCACAACCGAATACCTA ACAGAACAAGCGGAAACACT 1544 0.250 49.5
rpoB-trnD-GUC_p1 rpoB-trnD-GUC CAACCCCCTCTTGCTTCTTT CGGTAACTCGATGAGGCAAA 1643 0.250 50.0
rpoB-trnD-GUC_p2 rpoB-trnD-GUC CAAGTTCTGGTAGTACGGGC CGGTAACTCGATGAGGCAAA 1046 0.250 49.9
rpoB-trnD-GUC_p3 rpoB-trnD-GUC GCAAGTTCTGGTAGTACGGG CGGTAACTCGATGAGGCAAA 1047 0.250 49.9
rpoB-trnD-GUC_p4 rpoB-trnD-GUC CAACCCCCTCTTGCTTCTTT AGCGCATCTCATTCGAGTTT 1483 0.250 49.9
rpoB-trnD-GUC_p5 rpoB-trnD-GUC CAACCCCCTCTTGCTTCTTT ATGAGGCAAAACCGAAGTGT 1633 0.250 49.8
psbM-petN_p1 psbM-petN TTTGCCTCATCGAGTTACCG ACTTGTAGTTCGGGGAAGGA 1633 0.250 49.8
psbM-petN_p2 psbM-petN GCCACCGCACTTTTTATTCC ACTTGTAGTTCGGGGAAGGA 974 0.250 49.8
psbM-petN_p3 psbM-petN ACACTTCGGTTTTGCCTCAT ACTTGTAGTTCGGGGAAGGA 1643 0.250 49.7
psbM-petN_p4 psbM-petN GCCACTCGAGCTATTTTCCA ACTTGTAGTTCGGGGAAGGA 1043 0.250 49.6
psbM-petN_p5 psbM-petN TCTTAGCCACCGCACTTTTT ACTTGTAGTTCGGGGAAGGA 979 0.250 49.6

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
Diplazium bellum NC_035849.1 151601 View on NCBI ↗
Diplazium dilatatum NC_035850.1 151114 View on NCBI ↗
Diplazium dushanense NC_035851.1 150179 View on NCBI ↗
Diplazium striatum NC_035852.1 150779 View on NCBI ↗