Markers + reference

Pugionium

3 species · Brassicaceae · Brassicales

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Species 3
Genome length 155–155 kb
Candidate markers 258
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 258 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-psbA LSC 275 0.0145 1.00 59.1 yes View details
rps16 LSC 1132 0.0018 1.00 33.2 yes View details
trnD-trnY LSC 438 0.0061 1.00 39.9 yes View details
psbC LSC 1422 0.0000 1.00 31.9 yes View details
ndhC-trnV LSC 870 0.0031 1.00 48.2 yes View details
petA-psbJ LSC 966 0.0028 1.00 48.0 yes View details
petD LSC 1208 0.0017 1.00 46.6 yes View details
rpl16 LSC 1520 0.0018 1.00 38.9 yes View details
ycf1 IRb 1041 0.0006 1.00 46.7 no View details
rpl32-trnL SSC 922 0.0036 1.00 48.1 yes View details
ycf1 SSC 5343 0.0030 1.00 43.9 yes View details
trnK-rps16 LSC 732 0.0046 1.00 61.7 yes View details
rbcL-accD LSC 715 0.0019 1.00 60.5 yes View details
petB LSC 1443 0.0018 1.00 60.3 yes View details
trnR-atpA LSC 297 0.0067 1.00 59.1 yes View details
rpoA LSC 984 0.0027 1.00 58.1 yes View details
atpE LSC 399 0.0033 1.00 56.7 yes View details
psbC-trnS LSC 180 0.0259 1.00 56.5 yes View details
rpl20 LSC 354 0.0038 1.00 56.0 yes View details
atpA LSC 1524 0.0013 1.00 55.6 yes View details
rpoC2 LSC 4092 0.0015 1.00 54.9 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-psbA_p1 trnH-psbA CTGCCTTAATCCACTTGGCT GCGCTAACCTTGGTATGGAA 398–403 1.000 79.9
trnH-psbA_p2 trnH-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 333–338 1.000 79.9
trnH-psbA_p3 trnH-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 348–353 1.000 79.8
trnH-psbA_p4 trnH-psbA ACTGCCTTAATCCACTTGGC GCGCTAACCTTGGTATGGAA 399–404 1.000 79.7
trnH-psbA_p5 trnH-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 351–356 1.000 79.7
trnK_p1 trnK TGCTCTAGGAATATTATTTCCA CTGGTTGTATCTACATATTTGCAGT 2727–2733 1.000 40.4
trnK_p2 trnK TGCTCTAGGAATATTATTTCCA TGGTTGTATCTACATATTTGCAGT 2726–2732 1.000 40.4
trnK_p3 trnK TGCTCTAGGAATATTATTTCCAA CTGGTTGTATCTACATATTTGCAGT 2727–2733 1.000 40.4
trnK_p4 trnK TTGCTCTAGGAATATTATTTCCA CTGGTTGTATCTACATATTTGCAGT 2728–2734 1.000 40.4
trnK_p5 trnK TGCTCTAGGAATATTATTTCCAA TGGTTGTATCTACATATTTGCAGT 2726–2732 1.000 40.4
trnK-rps16_p1 trnK-rps16 AACTCTACCGCAGATCTGGA CGCTCAACCAACAAGAACAG 904–905 1.000 76.2
trnK-rps16_p2 trnK-rps16 AGTCGCACTTAAAAGCCGAG CGCTCAACCAACAAGAACAG 847–848 1.000 72.8
trnK-rps16_p3 trnK-rps16 TACCGCAGATCTGGACGAAT CGCTCAACCAACAAGAACAG 899–900 1.000 72.5
trnK-rps16_p4 trnK-rps16 ACTCTACCGCAGATCTGGAC CGCTCAACCAACAAGAACAG 903–904 1.000 72.5
trnK-rps16_p5 trnK-rps16 GCAGATCTGGACGAATCCTT CGCTCAACCAACAAGAACAG 895–896 1.000 72.4
rps16_p1 rps16 CATGTGTGCGTCAGGGATAA GAGGTTCGAATCCTTCCGTC 2189 1.000 79.6
rps16_p2 rps16 GATGGAAGCGAAAGAGGAGG GAGGTTCGAATCCTTCCGTC 1635–1636 1.000 79.4
rps16_p3 rps16 AAATCCAGTCATGTGTGCGT GAGGTTCGAATCCTTCCGTC 2198 1.000 79.0
rps16_p4 rps16 CATGTGTGCGTCAGGGATAA ATCCTTCCGTCCCAGAGTAC 2180 1.000 78.4
rps16_p5 rps16 CATGTGTGCGTCAGGGATAA TGACTGAACCTTTTACGCGT 1929 1.000 78.4
trnR-atpA_p1 trnR-atpA GCGAAAAGCGTCCATTGTC TCAAGAGCAACTGGAACGTT 417–423 1.000 71.1
trnR-atpA_p2 trnR-atpA GCGAAAAGCGTCCATTGTC TTCAAGAGCAACTGGAACGT 418–424 1.000 71.1
trnR-atpA_p3 trnR-atpA GCGAAAAGCGTCCATTGTC ACATTAACCGCTGAAGCAGA 458–464 1.000 69.8
trnR-atpA_p4 trnR-atpA GCGAAAAGCGTCCATTGTC AGACATTAACCGCTGAAGCA 460–466 1.000 69.8
trnR-atpA_p5 trnR-atpA GCGAAAAGCGTCCATTGTCT TCAAGAGCAACTGGAACGTT 417–423 1.000 67.2
atpA_p1 atpA AAGAATGATCCATTTCTTTTCTT TGGTATGTTTGGTACGATGA 1652 1.000 40.1
atpA_p2 atpA AGAATGATCCATTTCTTTTCTTT TGGTATGTTTGGTACGATGA 1651 1.000 40.1
atpA_p3 atpA AAGAATGATCCATTTCTTTTCTT TGGTATGTTTGGTACGATGAA 1652 1.000 40.1
atpA_p4 atpA AGAATGATCCATTTCTTTTCTTT TGGTATGTTTGGTACGATGAA 1651 1.000 40.1
atpA_p5 atpA AGAATGATCCATTTCTTTTCTTT TTGGTATGTTTGGTACGATGA 1652 1.000 40.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Pugionium cornutum NC_030516.1 154992 View on NCBI ↗
Pugionium dolabratum NC_030515.1 155002 View on NCBI ↗
Pugionium pterocarpum MK637779.1 154534 View on NCBI ↗