Markers + reference

Deparia

4 species · Athyriaceae · Polypodiales

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Species 4
Genome length 151–151 kb
Candidate markers 275
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpH-atpI Genome 746 0.0481 0.99 76.9 yes View details
psbM-petN Genome 878 0.0565 0.98 83.1 yes View details
trnC-GCA-trnG-GCC Genome 462 0.0663 0.94 85.6 yes View details
psbD-trnT-GGU Genome 1411 0.0513 1.00 83.8 yes View details
trnT-GGU-trnfM-CAU Genome 499 0.0568 0.99 78.3 yes View details
petA-psbJ Genome 845 0.0521 0.99 81.4 yes View details
petG-trnW-CCA Genome 260 0.0724 1.00 75.8 yes View details
ndhF Genome 2244 0.0402 1.00 76.9 yes View details
rpl32-trnP-GGG Genome 694 0.0817 1.00 82.9 yes View details
trnP-GGG-trnL-UAG Genome 294 0.0913 1.00 83.1 yes View details
ccsA-ndhD Genome 418 0.0758 0.99 80.4 yes View details
ndhB-ndhB Genome 867 0.0412 1.00 73.2 no View details
trnF-GAA-ndhJ Genome 228 0.0541 1.00 82.8 yes View details
trnS-GCU-ycf12 Genome 560 0.0601 1.00 82.4 yes View details
rpoB-trnD-GUC Genome 758 0.0418 0.99 79.4 yes View details
trnS-UGA-psbC Genome 296 0.0541 0.96 78.3 yes View details
ndhC-trnV-UAC Genome 488 0.0502 0.98 77.7 yes View details
ycf12-trnG-UCC Genome 173 0.0614 0.98 77.6 yes View details
petN-trnC-GCA Genome 499 0.0407 0.98 77.3 yes View details
rps4-trnL-UAA Genome 668 0.0452 1.00 76.7 yes View details
infA-rps8 Genome 136 0.0502 1.00 76.7 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-GCU-ycf12_p1 trnS-GCU-ycf12 CAGGTTCATCGATCCACCAG ACGCCAAAATAGCAAGTTGC 712–736 1.000 88.3
trnS-GCU-ycf12_p2 trnS-GCU-ycf12 TTTGTCGAATGATCCCGGAC ACGCCAAAATAGCAAGTTGC 788–817 1.000 87.8
trnS-GCU-ycf12_p3 trnS-GCU-ycf12 GACAGGTTCATCGATCCACC ACGCCAAAATAGCAAGTTGC 714–738 0.750 77.9
trnS-GCU-ycf12_p4 trnS-GCU-ycf12 GAGGGGAGAGAGAGGGATTC ACGCCAAAATAGCAAGTTGC 675–691 0.750 76.1
trnS-GCU-ycf12_p5 trnS-GCU-ycf12 CCTACACCCACGGCTAGATA ACGCCAAAATAGCAAGTTGC 1226–1254 0.750 73.8
ycf12-trnG-UCC_p1 ycf12-trnG-UCC ATGGAGCCAAATTCCGGATC TCTCTCCTCTTTCCACCGTT 1352–1370 0.750 75.5
ycf12-trnG-UCC_p2 ycf12-trnG-UCC ATGGAGCCAAATTCCGGATC TTCTCTCCTCTTTCCACCGT 1353–1371 0.750 75.5
ycf12-trnG-UCC_p3 ycf12-trnG-UCC GATGGAGCCAAATTCCGGAT TCTCTCCTCTTTCCACCGTT 1353–1371 0.750 75.5
ycf12-trnG-UCC_p4 ycf12-trnG-UCC GATGGAGCCAAATTCCGGAT TTCTCTCCTCTTTCCACCGT 1354–1372 0.750 75.5
ycf12-trnG-UCC_p5 ycf12-trnG-UCC GAGCCAAATTCCGGATCACT TCTCTCCTCTTTCCACCGTT 1349–1367 0.750 75.3
atpH-atpI_p1 atpH-atpI GTCAAAGGAAAATCGCGGTG GTTGGTAGTAGCTGTTCCCG 1397–1419 0.750 73.7
atpH-atpI_p2 atpH-atpI TCGAAAACAGTTTGGGGGAG GTTGGTAGTAGCTGTTCCCG 1202 0.500 60.4
atpH-atpI_p3 atpH-atpI TCGAAAACAGTTTGGGGGAG GGCGAATCGTTCAGTTACCT 1446 0.500 60.3
atpH-atpI_p4 atpH-atpI TCGAAAACAGTTTGGGGGAG TACCTATCGTAGCCACCAGG 1641 0.500 60.3
atpH-atpI_p5 atpH-atpI TCGAAAACAGTTTGGGGGAG ATTACGCACATCGAGCAACT 1801 0.500 60.3
rpoB-trnD-GUC_p1 rpoB-trnD-GUC CAAGTTCTGGTAGTACGGGC GCGGTGCTCTAACCAATTGA 803–811 1.000 82.5
rpoB-trnD-GUC_p2 rpoB-trnD-GUC GCAAGTTCTGGTAGTACGGG GCGGTGCTCTAACCAATTGA 804–812 1.000 82.5
rpoB-trnD-GUC_p3 rpoB-trnD-GUC AGTTCTGGTAGTACGGGCAT GCGGTGCTCTAACCAATTGA 801–809 1.000 81.4
rpoB-trnD-GUC_p4 rpoB-trnD-GUC AAGTTCTGGTAGTACGGGCA GCGGTGCTCTAACCAATTGA 802–810 1.000 79.6
rpoB-trnD-GUC_p5 rpoB-trnD-GUC CAAGTTCTGGTAGTACGGGC GGATTGACGGGTCTCGAAC 844–852 1.000 78.2
psbM-petN_p1 psbM-petN GCCACCGCACTTTTTATTCC TCACGCAGAAACAATCCCAA 1346–1373 1.000 89.1
psbM-petN_p2 psbM-petN GCCACCGCACTTTTTATTCC ATTGATAACCCGAACGTCCG 1311–1338 1.000 89.0
psbM-petN_p3 psbM-petN GCCACCGCACTTTTTATTCC TTTCATGTGTCTCGATGCGT 1365–1392 1.000 88.6
psbM-petN_p4 psbM-petN GCCACCGCACTTTTTATTCC CCTCAAGCTTTGCCTCGTAT 1122–1130 0.750 75.4
psbM-petN_p5 psbM-petN GCCACCGCACTTTTTATTCC GTCGCCTAACGGGAAAATCT 1544–1552 0.500 61.1
petN-trnC-GCA_p1 petN-trnC-GCA CGTTTGTCACAATCCGCTTC AAGACGGAGGACTGCAAATC 638–648 1.000 84.4
petN-trnC-GCA_p2 petN-trnC-GCA CGTTTGTCACAATCCGCTTC TAGTCAAGCGGTAAGACGGA 650–660 1.000 83.7
petN-trnC-GCA_p3 petN-trnC-GCA TGTCACAATCCGCTTCTTCC AAGACGGAGGACTGCAAATC 634–644 1.000 83.3
petN-trnC-GCA_p4 petN-trnC-GCA CGTTTGTCACAATCCGCTTC CCAGTTCGAATCTGGGTGTC 609–619 1.000 83.3
petN-trnC-GCA_p5 petN-trnC-GCA TGTCACAATCCGCTTCTTCC TAGTCAAGCGGTAAGACGGA 646–656 1.000 82.6

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
Deparia giraldii PQ742175.1 151298 View on NCBI ↗
Deparia lancea NC_035844.1 151011 View on NCBI ↗
Deparia pycnosora NC_035845.1 151126 View on NCBI ↗
Deparia viridifrons NC_035846.1 150939 View on NCBI ↗