Markers + reference

Lunaria

2 species · Brassicaceae · Brassicales

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Species 2
Genome length 155–155 kb
Candidate markers 270
Primer pairs 95

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 8 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-AAA-rps16 LSC 679 0.0162 1.00 58.9 yes View details
psbK-psbI LSC 402 0.0175 1.00 55.7 yes View details
petA-psbJ LSC 1028 0.0119 0.98 67.5 yes View details
psbE-petL LSC 1356 0.0134 0.99 67.5 yes View details
trnP-CCA-psaJ LSC 334 0.0269 1.00 65.9 yes View details
psaJ-rpl33 LSC 423 0.0336 0.99 75.5 yes View details
rpl36-rps8 LSC 463 0.0195 1.00 55.9 yes View details
ycf1 IRb 1200 0.0042 1.00 46.3 no View details
ndhF-rpl32 SSC 820 0.0209 0.99 71.1 yes View details
rpl32-trnL-CUA SSC 901 0.0247 0.99 69.2 yes View details
ycf1 SSC 5382 0.0100 1.00 57.0 yes View details
rps4-trnT-ACA LSC 385 0.0234 1.00 67.7 yes View details
ccsA-ndhD SSC 217 0.0230 1.00 65.7 yes View details
atpB-rbcL LSC 808 0.0075 1.00 63.4 yes View details
psaI-ycf4 LSC 443 0.0092 0.99 61.8 yes View details
ndhA SSC 2161 0.0074 1.00 61.6 yes View details
trnI-AUC-trnA-GCA IRb 64 0.0156 1.00 61.5 yes View details
trnA-GCA-trnI-AUC IRa 64 0.0156 1.00 61.5 yes View details
accD-psaI LSC 644 0.0047 1.00 61.4 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
trnK-AAA_p1 trnK-AAA GGACTCCCAAGCACACAAAT TTATCCCTGACGCACACATG 2958–2961 1.000 77.7
trnK-AAA_p2 trnK-AAA GGACTCCCAAGCACACAAAT CCATTTATCCCTGACGCACA 2962–2965 1.000 77.6
trnK-AAA_p3 trnK-AAA GGACTCCCAAGCACACAAAT TCCATTTATCCCTGACGCAC 2963–2966 1.000 75.3
trnK-AAA_p4 trnK-AAA GGACTCCCAAGCACACAAAT GCACACATGCCTGGATTTTT 2947–2950 1.000 74.2
trnK-AAA_p5 trnK-AAA ACTCCCAAGCACACAAATTCT TTATCCCTGACGCACACATG 2956–2959 1.000 72.4
trnK-AAA-rps16_p1 trnK-AAA-rps16 AACTCTACCGCAGATCTGGA CGCTCAACCAACAAGAACAG 842–844 1.000 76.8
trnK-AAA-rps16_p2 trnK-AAA-rps16 AAAGCCGAGTACTCTACCGT CGCTCAACCAACAAGAACAG 774–776 1.000 76.7
trnK-AAA-rps16_p3 trnK-AAA-rps16 AAGCCGAGTACTCTACCGTT CGCTCAACCAACAAGAACAG 773–775 1.000 76.7
trnK-AAA-rps16_p4 trnK-AAA-rps16 TACCGTTGAGTTAGCAACCC CGCTCAACCAACAAGAACAG 760–762 1.000 74.4
trnK-AAA-rps16_p5 trnK-AAA-rps16 AGTCGCACTTAAAAGCCGAG CGCTCAACCAACAAGAACAG 785–787 1.000 73.4
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCAGCTGTAAG ACAAAAAGTTTGAGAGTAAGCA 455–474 1.000 41.4
psbK-psbI_p2 psbK-psbI TGGCAAGCAGCTGTAAGTTT ACAAAAAGTTTGAGAGTAAGCA 452–471 1.000 41.4
psbK-psbI_p3 psbK-psbI TTGGCAAGCAGCTGTAAGTT ACAAAAAGTTTGAGAGTAAGCA 453–472 1.000 41.4
psbK-psbI_p4 psbK-psbI TTTGGCAAGCAGCTGTAAGT ACAAAAAGTTTGAGAGTAAGCA 454–473 1.000 41.4
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCAGCTGTAAG ACAAAAAGTTTGAGAGTAAGCAT 455–474 1.000 41.4
rps4-trnT-ACA_p1 rps4-trnT-ACA CGGAGCGTGATTGGTTTCTA CTCAGAGGTTAGAGCATCGC 563 1.000 80.2
rps4-trnT-ACA_p2 rps4-trnT-ACA CGGAGCGTGATTGGTTTCTA ATGGTCATCGGTTCGATTCC 531 1.000 79.4
rps4-trnT-ACA_p3 rps4-trnT-ACA TCTAAGATCGCTTCCTGCCT CTCAGAGGTTAGAGCATCGC 547 1.000 78.5
rps4-trnT-ACA_p4 rps4-trnT-ACA TCTAAGATCGCTTCCTGCCT ATGGTCATCGGTTCGATTCC 515 1.000 77.7
rps4-trnT-ACA_p5 rps4-trnT-ACA CGGAGCGTGATTGGTTTCTA CCGCTTAGCTCAGAGGTTAG 571 1.000 77.2
atpB-rbcL_p1 atpB-rbcL CATCCAGTACCGGACCAATG CACCAGCTTTGAATCCAACAC 954–959 1.000 72.2
atpB-rbcL_p2 atpB-rbcL CATCCAGTACCGGACCAATG ACCAGCTTTGAATCCAACACT 953–958 1.000 72.0
atpB-rbcL_p3 atpB-rbcL ATCCAGTACCGGACCAATGA CACCAGCTTTGAATCCAACAC 953–958 1.000 71.6
atpB-rbcL_p4 atpB-rbcL TCCAGTACCGGACCAATGAT CACCAGCTTTGAATCCAACAC 952–957 1.000 71.6
atpB-rbcL_p5 atpB-rbcL TCCAGTACCGGACCAATGAT ACCAGCTTTGAATCCAACACT 951–956 1.000 71.3
accD-psaI_p1 accD-psaI TGGATGCAATTGTACCACGT AAAGAAGCCATTGCAAGTGC 813–822 1.000 77.5
accD-psaI_p2 accD-psaI TGGATGCAATTGTACCACGT CCGGAAAGACTAGGCCTACT 794–803 1.000 77.0
accD-psaI_p3 accD-psaI TGGATGCAATTGTACCACGT CAAGTGCCGGAAAGACTAGG 800–809 1.000 76.6
accD-psaI_p4 accD-psaI TGGATGCAATTGTACCACGT GCAAGTGCCGGAAAGACTAG 801–810 1.000 71.4
accD-psaI_p5 accD-psaI TGGATGCAATTGTACCACGT ATTGCAAGTGCCGGAAAGA 804–813 1.000 70.5

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
Lunaria annua NC_049659.1 154603 View on NCBI ↗
Lunaria rediviva NC_039955.1 154546 View on NCBI ↗