Markers + reference

Diplaziopsis

2 species · Diplaziopsidaceae · Polypodiales

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Species 2
Genome length 151–152 kb
Candidate markers 268
Primer pairs 95

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 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoB-trnD-GUC Genome 785 0.0744 0.99 78.5 yes View details
psbM-petN Genome 1279 0.0454 0.98 71.7 yes View details
trnC-GCA-trnG-GCC Genome 430 0.0896 0.99 78.2 yes View details
trnS-UGA-psbC Genome 287 0.0523 1.00 68.3 yes View details
ndhC-trnM-CAU Genome 1255 0.0606 0.99 78.3 yes View details
petA-psbJ Genome 853 0.0610 1.00 77.2 yes View details
rpl23 Genome 270 0.0333 1.00 56.7 yes View details
ndhF Genome 2220 0.0423 1.00 69.3 yes View details
rpl32-trnP-GGG Genome 640 0.0549 1.00 74.6 yes View details
trnP-GGG-trnL-UAG Genome 261 0.1012 0.98 78.2 yes View details
rps4-trnL-UAA Genome 704 0.0512 0.97 78.1 yes View details
psbE-petL Genome 760 0.0490 0.99 77.6 yes View details
trnF-GAA-ndhJ Genome 253 0.0576 0.96 76.8 yes View details
rpl23-trnI-CAU Genome 162 0.0864 1.00 76.4 yes View details
trnL-UAA-trnF-GAA Genome 319 0.0579 0.97 76.3 yes View details
psbK-psbI Genome 545 0.0516 1.00 75.6 yes View details
trnY-GUA-trnE-UUC Genome 140 0.0571 1.00 75.0 yes View details
trnR-ACG-rrn5 Genome 273 0.0476 1.00 73.9 yes View details
rrn5-trnR-ACG Genome 273 0.0476 1.00 73.9 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 ACGAAGAATATCACTACTGCGT 616–637 1.000 62.4
psbK-psbI_p2 psbK-psbI CAAGCCGCAGTTAGTTTTCG GCGTAGACAAATAGTTTGAGGG 598–619 1.000 60.7
psbK-psbI_p3 psbK-psbI GCAAGCCGCAGTTAGTTTTC ACGAAGAATATCACTACTGCGT 617–638 1.000 60.2
psbK-psbI_p4 psbK-psbI TTCTTCTGGCCTTCGTTTGG ACGAAGAATATCACTACTGCGT 636–657 1.000 59.5
psbK-psbI_p5 psbK-psbI TGCCTGTAATACCGGTGTTC ACGAAGAATATCACTACTGCGT 660–681 1.000 59.4
rpoB-trnD-GUC_p1 rpoB-trnD-GUC CAAGTTCTGGTAGTACGGGC TTATCGGGATTGACGGGTCT 885–903 1.000 83.9
rpoB-trnD-GUC_p2 rpoB-trnD-GUC GCAAGTTCTGGTAGTACGGG TTATCGGGATTGACGGGTCT 886–904 1.000 83.9
rpoB-trnD-GUC_p3 rpoB-trnD-GUC AGTTCTGGTAGTACGGGCAT TTATCGGGATTGACGGGTCT 883–901 1.000 82.8
rpoB-trnD-GUC_p4 rpoB-trnD-GUC CAAGTTCTGGTAGTACGGGC GCGGTGCTCTAACCAATTGA 838–856 1.000 81.5
rpoB-trnD-GUC_p5 rpoB-trnD-GUC GCAAGTTCTGGTAGTACGGG GCGGTGCTCTAACCAATTGA 839–857 1.000 81.5
trnY-GUA-trnE-UUC_p1 trnY-GUA-trnE-UUC GTCCCCATTAACCACTCGAG ATAAAAGGTAATCGGGCCCC 257 1.000 74.6
trnY-GUA-trnE-UUC_p2 trnY-GUA-trnE-UUC CCCATTAACCACTCGAGCAT ATAAAAGGTAATCGGGCCCC 254 1.000 74.5
trnY-GUA-trnE-UUC_p3 trnY-GUA-trnE-UUC CTGGATTCGAACCAGCGTAG ATAAAAGGTAATCGGGCCCC 301 1.000 73.3
trnY-GUA-trnE-UUC_p4 trnY-GUA-trnE-UUC TTGCCAGCGGATTTACAGTC ATAAAAGGTAATCGGGCCCC 278 1.000 72.5
trnY-GUA-trnE-UUC_p5 trnY-GUA-trnE-UUC TATCAACCTACAGCCTCGGG ATAAAAGGTAATCGGGCCCC 332 1.000 71.8
psbM-petN_p1 psbM-petN GCCACCGCACTTTTTATTCC TCAAGCTTTGTCTTGTGCCT 1519–1529 1.000 83.9
psbM-petN_p2 psbM-petN GCCACCGCACTTTTTATTCC AGGTTGAGGTGCTCCATAGT 1776–1786 1.000 83.8
psbM-petN_p3 psbM-petN GCCACCGCACTTTTTATTCC TTTCATGTGTCTCGATGCGT 1738–1748 1.000 83.6
psbM-petN_p4 psbM-petN GCCACCGCACTTTTTATTCC CTACACGTCGACGACATACC 2071–2079 1.000 83.4
psbM-petN_p5 psbM-petN ATTGGGTAGGAATCGCCAAC AGGTTGAGGTGCTCCATAGT 2413–2416 1.000 83.2
trnC-GCA-trnG-GCC_p1 trnC-GCA-trnG-GCC GATTTGCAGTCCTCCGTCTT GTTCGATTCCCGCTATCCG 490–497 1.000 76.8
trnC-GCA-trnG-GCC_p2 trnC-GCA-trnG-GCC GATTTGCAGTCCTCCGTCTT GGGTTCGATTCCCGCTATC 492–499 1.000 76.6
trnC-GCA-trnG-GCC_p3 trnC-GCA-trnG-GCC GATTTGCAGTCCTCCGTCTT GGTTCGATTCCCGCTATCC 491–498 1.000 76.6
trnC-GCA-trnG-GCC_p4 trnC-GCA-trnG-GCC TCCGTCTTACCGCTTGACTA GTTCGATTCCCGCTATCCG 478–485 1.000 76.4
trnC-GCA-trnG-GCC_p5 trnC-GCA-trnG-GCC TCCGTCTTACCGCTTGACTA GGTTCGATTCCCGCTATCC 479–486 1.000 76.2
trnS-UGA-psbC_p1 trnS-UGA-psbC GGGTTCGAATCCCTCTCTCT TGTCTATGACACCCCTTAATTGA 333–354 1.000 49.5
trnS-UGA-psbC_p2 trnS-UGA-psbC GGGTTCGAATCCCTCTCTCT TGTCTATGACACCCCTTAATTG 333–354 1.000 45.9
trnS-UGA-psbC_p3 trnS-UGA-psbC GGGTTCGAATCCCTCTCTCT GTCTATGACACCCCTTAATTGA 332–353 1.000 43.8
trnS-UGA-psbC_p4 trnS-UGA-psbC TTCGAATCCCTCTCTCTCCT TGTCTATGACACCCCTTAATTGA 330–351 1.000 43.5
trnS-UGA-psbC_p5 trnS-UGA-psbC GTTCGAATCCCTCTCTCTCC TGTCTATGACACCCCTTAATTGA 331–352 1.000 43.5

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
Diplaziopsis cavaleriana NC_035847.1 151934 View on NCBI ↗
Diplaziopsis javanica NC_035848.1 151496 View on NCBI ↗