Markers + reference

Leptochilus

2 species · Polypodiaceae · Polypodiales

Back to catalogue

Species 2
Genome length 154–156 kb
Candidate markers 265
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhB Genome 2371 0.0732 0.02 55.2 yes View details
atpH-atpI Genome 817 0.0477 0.98 73.8 yes View details
psbM-petN Genome 1144 0.0502 0.99 73.3 yes View details
rpl32-trnP-GGG Genome 682 0.0784 0.90 81.0 yes View details
rps15-ycf1 Genome 4523 0.0499 0.88 69.2 yes View details
trnL-UAG-ccsA Genome 351 0.0661 0.95 79.8 yes View details
psaI-ycf4 Genome 432 0.0425 0.98 77.8 yes View details
chlN-chlL Genome 80 0.1000 1.00 75.6 yes View details
rpoB-trnD-GUC Genome 636 0.0397 0.99 74.3 yes View details
trnW-CCA-trnP-UGG Genome 199 0.0553 1.00 73.7 yes View details
rpl2-rpl23 Genome 69 0.1159 1.00 73.6 yes View details
trnP-GGG-trnL-UAG Genome 237 0.0506 1.00 73.2 yes View details
trnG-UCC-trnR-UCU Genome 167 0.0479 1.00 73.1 yes View details
rps4-trnL-UAA Genome 630 0.0397 1.00 71.9 yes View details
atpA-atpF Genome 86 0.0581 1.00 71.5 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ndhB_p1 ndhB TCGCGTCACAAGAAGAGAAG TCAATCTCAAATATTACTCCGA 2426 0.500 20.0
ndhB_p2 ndhB TGCGGAGACAAACTAGTTGG TCAATCTCAAATATTACTCCGA 2492 0.500 20.0
ndhB_p3 ndhB TCGCGTCACAAGAAGAGAAG TTCAATCTCAAATATTACTCCGA 2427 0.500 20.0
ndhB_p4 ndhB AGTTCGCGTCACAAGAAGAG TCAATCTCAAATATTACTCCGA 2429 0.500 20.0
ndhB_p5 ndhB CGCGTCACAAGAAGAGAAGT TCAATCTCAAATATTACTCCGA 2425 0.500 20.0
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU ACGTTCGGTTCTGGATTAGC AACACGGAATTACGCCCAAT 351 1.000 80.4
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU ACGTTCGGTTCTGGATTAGC ACGGAATTACGCCCAATAGG 348 1.000 79.8
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU TACTGATGCGGGTTCGATTC AACACGGAATTACGCCCAAT 281 1.000 79.2
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CGCCGTCGACTATAACCTTT AACACGGAATTACGCCCAAT 313 1.000 79.1
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CTACTGATGCGGGTTCGATT AACACGGAATTACGCCCAAT 282 1.000 79.1
atpA-atpF_p1 atpA-atpF TTTGCTTGCGAATGATGCTG GAGCCATGGATAGCAAGTCC 164 1.000 81.4
atpA-atpF_p2 atpA-atpF TTTGCTTGCGAATGATGCTG CCATGGATAGCAAGTCCGAC 161 1.000 81.3
atpA-atpF_p3 atpA-atpF TTTGCTTGCGAATGATGCTG TCAACTGCACTTGCGAATGA 208 1.000 78.5
atpA-atpF_p4 atpA-atpF TGCTGCTAATTTCGTCAGGT GAGCCATGGATAGCAAGTCC 149 1.000 78.0
atpA-atpF_p5 atpA-atpF TGCTGCTAATTTCGTCAGGT CCATGGATAGCAAGTCCGAC 146 1.000 77.9
atpH-atpI_p1 atpH-atpI GCCTTCTACTTCTGGCTGTC TATTTCAGCCGACGAGTTGG 1108–1124 1.000 84.5
atpH-atpI_p2 atpH-atpI GCCTTCTACTTCTGGCTGTC AGGTGCCAGAAATCTGCAAA 1522–1538 1.000 83.7
atpH-atpI_p3 atpH-atpI GAGGGAGTAGCGATCTCACT AGGTGCCAGAAATCTGCAAA 2026–2031 1.000 83.2
atpH-atpI_p4 atpH-atpI GAGGGGTAAAGGTGCAACAA AGGTGCCAGAAATCTGCAAA 1685 0.500 59.9
atpH-atpI_p5 atpH-atpI GAGGGGTAAAGGTGCAACAA TATTTCAGCCGACGAGTTGG 1271 0.500 59.9
rpoB-trnD-GUC_p1 rpoB-trnD-GUC CAAGTTCTGGTAATACGGGCA GAGTTCATCGGGATTGACGG 735–740 1.000 71.8
rpoB-trnD-GUC_p2 rpoB-trnD-GUC CAAGTTCTGGTAATACGGGCA GGAGTTCATCGGGATTGACG 736–741 1.000 71.8
rpoB-trnD-GUC_p3 rpoB-trnD-GUC TGCAAGTTCTGGTAATACGGG GAGTTCATCGGGATTGACGG 737–742 1.000 71.8
rpoB-trnD-GUC_p4 rpoB-trnD-GUC TGCAAGTTCTGGTAATACGGG GGAGTTCATCGGGATTGACG 738–743 1.000 71.8
rpoB-trnD-GUC_p5 rpoB-trnD-GUC CAAGTTCTGGTAATACGGGCA CAACTTCCGTCTTGACAGGG 703–708 1.000 71.5
psbM-petN_p1 psbM-petN CCACTTACATGCCCCAAACT ATTGGATGTTGTTTCCGCCT 2216 0.500 58.8
psbM-petN_p2 psbM-petN CCACTTACATGCCCCAAACT AAGACGGAGGACTGCAAATC 2145 0.500 58.6
psbM-petN_p3 psbM-petN CCACTTACATGCCCCAAACT TGTTGTTTCCGCCTGGATAG 2210 0.500 58.5
psbM-petN_p4 psbM-petN CCACTTACATGCCCCAAACT TTGTAGTTTGGGGACGAAGC 1579 0.500 58.5
psbM-petN_p5 psbM-petN CCACTTACATGCCCCAAACT CATTTCATGTGCCTCGATGC 1942 0.500 58.5

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
Leptochilus decurrens NC_058826.1 153753 View on NCBI ↗
Leptochilus hemionitideus NC_040177.1 156083 View on NCBI ↗