Markers + reference

Tectaria

2 species · Tectariaceae · Polypodiales

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Species 2
Genome length 148–159 kb
Candidate markers 267
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhB Genome 1223 0.0823 0.98 81.0 yes View details
psbK-psbI Genome 528 0.1257 0.99 83.0 yes View details
atpH-atpI Genome 790 0.1053 0.77 79.0 yes View details
psbM-petN Genome 1147 0.0947 0.99 84.0 yes View details
trnC-GCA-trnG-GCC Genome 492 0.1242 1.00 79.8 yes View details
psbD-trnT-GGU Genome 1426 0.0819 0.99 79.0 yes View details
rrn16-rps12 Genome 1906 0.1048 1.00 93.3 yes View details
rpl21-ndhD Genome 392 0.1637 1.00 75.4 yes View details
rps12-rrn16 Genome 1900 0.1052 1.00 93.3 yes View details
rps4-trnL-UAA Genome 611 0.0869 1.00 83.3 yes View details
psbF-psbE Genome 15 0.0667 1.00 83.3 yes View details
trnD-GUC-trnY-GUA Genome 52 0.1154 1.00 82.0 yes View details
petA-psbJ Genome 737 0.0954 0.98 81.3 yes View details
ndhC-trnV-UAC Genome 502 0.0828 0.96 81.1 yes View details
trnS-GCU-ycf12 Genome 563 0.1030 1.00 80.1 yes View details
psaC-ndhE Genome 322 0.0946 0.98 80.1 yes View details
trnT-GGU-trnfM-CAU Genome 439 0.0963 0.99 79.9 yes View details
rpoB-trnD-GUC Genome 654 0.0896 0.99 79.8 yes View details
trnS-GGA-rps4 Genome 457 0.0544 0.96 78.6 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ndhB_p1 ndhB TGGGGAAAAAGAGGGAGCTA GACCGCTTCTGAAAATTGGC 916 0.500 59.4
ndhB_p2 ndhB TGGGGAAAAAGAGGGAGCTA TATTAACTGCAGGTTCGGGC 773 0.500 59.3
ndhB_p3 ndhB CCAACAGGTGGGGAAAAAGA GACCGCTTCTGAAAATTGGC 924 0.500 59.2
ndhB_p4 ndhB CCAACAGGTGGGGAAAAAGA TATTAACTGCAGGTTCGGGC 781 0.500 59.1
ndhB_p5 ndhB TGGGGAAAAAGAGGGAGCTA TTTCTATTGATGGCTGGGGC 624 0.500 59.0
psbK-psbI_p1 psbK-psbI ACCGGTGTTTTTCCTTCTCC CCGAAGACGAAGAGAGATACG 651–662 1.000 78.2
psbK-psbI_p2 psbK-psbI CCGCAGTTAGCTTCCGATAA CCGAAGACGAAGAGAGATACG 613–624 1.000 76.7
psbK-psbI_p3 psbK-psbI CCGGTGTTTTTCCTTCTCCT CCGAAGACGAAGAGAGATACG 650–661 1.000 76.3
psbK-psbI_p4 psbK-psbI TAGCTTTTGTTTGGCAAGCC CCGAAGACGAAGAGAGATACG 631–642 1.000 74.2
psbK-psbI_p5 psbK-psbI ACCGGTGTTTTTCCTTCTCC CGAAGACGAAGAGAGATACGA 650–661 1.000 70.6
trnS-GCU-ycf12_p1 trnS-GCU-ycf12 GCAATCCGACGCTTTAAACC CAAGTTGCGCAATTGTTTCT 627–660 1.000 70.8
trnS-GCU-ycf12_p2 trnS-GCU-ycf12 CAATCCGACGCTTTAAACCC CAAGTTGCGCAATTGTTTCT 626–659 1.000 67.4
trnS-GCU-ycf12_p3 trnS-GCU-ycf12 AATCCGACGCTTTAAACCCC CAAGTTGCGCAATTGTTTCT 625–658 1.000 67.3
trnS-GCU-ycf12_p4 trnS-GCU-ycf12 CTTTAAACCCCTCGGCCATC CAAGTTGCGCAATTGTTTCT 616–649 1.000 66.9
trnS-GCU-ycf12_p5 trnS-GCU-ycf12 GCAATCCGACGCTTTAAACC AGTTGCGCAATTGTTTCTAGA 625–658 1.000 66.1
atpH-atpI_p1 atpH-atpI GCAGCAATAACAGAAGCAGC GCTGCAGCTTATATTGGGGA 690–870 1.000 87.6
atpH-atpI_p2 atpH-atpI AGCAATAACAGAAGCAGCAGA GCTGCAGCTTATATTGGGGA 688–868 1.000 79.9
atpH-atpI_p3 atpH-atpI CAGCAATAACAGAAGCAGCAG GCTGCAGCTTATATTGGGGA 689–869 1.000 79.3
atpH-atpI_p4 atpH-atpI GCAGCAATAACAGAAGCAGC GCTGCAGCTTATATTGGGGAA 690–870 1.000 78.5
atpH-atpI_p5 atpH-atpI CAGCAATAACAGAAGCAGCA GCTGCAGCTTATATTGGGGA 689–869 1.000 78.1
rpoB-trnD-GUC_p1 rpoB-trnD-GUC GTTCTGGTAGTACGGGCAT TTATCGGGATTGACGGGTCT 746–751 1.000 65.5
rpoB-trnD-GUC_p2 rpoB-trnD-GUC GTTCTGGTAGTACGGGCAT GTTTATCGGGATTGACGGGT 748–753 1.000 64.7
rpoB-trnD-GUC_p3 rpoB-trnD-GUC GTTCTGGTAGTACGGGCAT TTTATCGGGATTGACGGGTC 747–752 1.000 62.4
rpoB-trnD-GUC_p4 rpoB-trnD-GUC GTTCTGGTAGTACGGGCAT AGTTTATCGGGATTGACGGG 749–754 1.000 62.3
rpoB-trnD-GUC_p5 rpoB-trnD-GUC GTTCTGGTAGTACGGGCAT TATCGGGATTGACGGGTCTC 745–750 1.000 61.9
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA GTTCGAGACCCGTCAATCC ACTTCTCACTTCTGGGTCGA 168 1.000 74.5
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA GGTTCGAGACCCGTCAATC ACTTCTCACTTCTGGGTCGA 169 1.000 74.4
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA AGTTCAATCGGTTAGAGCACC ACTTCTCACTTCTGGGTCGA 213 1.000 74.0
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA GTTCGAGACCCGTCAATCC CACTTCTCACTTCTGGGTCG 169 1.000 73.9
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA AGTTCAATCGGTTAGAGCACC CACTTCTCACTTCTGGGTCG 214 1.000 73.5

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
Tectaria coadunata NC_086772.1 148333 View on NCBI ↗
Tectaria panamensis NC_044687.1 158656 View on NCBI ↗