Markers + reference

Kernera

2 species · Brassicaceae · Brassicales

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Species 2
Genome length 155–155 kb
Candidate markers 270
Primer pairs 90

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 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-CAC-psbA LSC 333 0.0032 0.95 59.8 yes View details
atpF LSC 1279 0.0000 1.00 30.9 yes View details
atpF-atpH LSC 479 0.0084 1.00 61.0 yes View details
atpH-atpI LSC 500 0.0020 1.00 48.2 yes View details
rpoB LSC 3219 0.0006 1.00 55.6 yes View details
trnP-CCA-psaJ LSC 342 0.0000 1.00 47.4 yes View details
clpP LSC 2080 0.0010 1.00 58.3 yes View details
rpl16 LSC 1528 0.0013 1.00 59.4 yes View details
ycf1 IRb 1041 0.0000 1.00 40.0 no View details
ycf1 SSC 5331 0.0013 1.00 53.3 yes View details
ndhF-rpl32 SSC 750 0.0013 1.00 59.8 yes View details
matK-trnK-AAA LSC 673 0.0015 1.00 59.6 yes View details
atpI LSC 750 0.0013 1.00 59.5 yes View details
psaA-ycf3 LSC 723 0.0014 1.00 59.5 yes View details
trnT-ACA-trnL-UUA LSC 802 0.0012 1.00 59.5 yes View details
trnT-ACC-psbD LSC 1252 0.0008 1.00 59.4 yes View details
ndhC-trnV-GUA LSC 901 0.0011 1.00 59.4 yes View details
ycf3-trnS-UCC LSC 1087 0.0009 1.00 59.3 yes View details
accD LSC 1470 0.0007 1.00 59.1 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-CAC-psbA_p1 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT GACCTAGCTTCTGTTGAGGC 388–400 1.000 82.4
trnH-CAC-psbA_p2 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC GACCTAGCTTCTGTTGAGGC 389–401 1.000 82.2
trnH-CAC-psbA_p3 trnH-CAC-psbA AATCCACTTGGCTACATCCG GACCTAGCTTCTGTTGAGGC 381–393 1.000 80.9
trnH-CAC-psbA_p4 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT CCGTGCTAACCTTGGTATGG 446–458 1.000 79.4
trnH-CAC-psbA_p5 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC CCGTGCTAACCTTGGTATGG 447–459 1.000 79.2
matK-trnK-AAA_p1 matK-trnK-AAA CCGAGCTCCATCGAACTCTA AACGGTAGAGTACTCGGCTT 805 1.000 73.2
matK-trnK-AAA_p2 matK-trnK-AAA CCGAGCTCCATCGAACTCTA ACGGTAGAGTACTCGGCTTT 804 1.000 73.2
matK-trnK-AAA_p3 matK-trnK-AAA AAAACTCTGTTGCCGAGCTC AACGGTAGAGTACTCGGCTT 817 1.000 72.6
matK-trnK-AAA_p4 matK-trnK-AAA AAAACTCTGTTGCCGAGCTC ACGGTAGAGTACTCGGCTTT 816 1.000 72.6
matK-trnK-AAA_p5 matK-trnK-AAA CCGAGCTCCATCGAACTCTA GGGTTGCTAACTCAACGGTA 818 1.000 71.0
atpF_p1 atpF CGTCGGCTTTAATGGTTACC AGTTTAGCTAGAAGAGGAGA 1398 1.000 40.0
atpF_p2 atpF CGTCGGCTTTAATGGTTACC AGTTTAGCTAGAAGAGGAGAT 1398 1.000 40.0
atpF_p3 atpF TCGTCGGCTTTAATGGTTACC AGTTTAGCTAGAAGAGGAGA 1399 1.000 40.0
atpF_p4 atpF CGTCGGCTTTAATGGTTACC AGTTTAGCTAGAAGAGGAGATT 1398 1.000 40.0
atpF_p5 atpF TCGTCGGCTTTAATGGTTACC AGTTTAGCTAGAAGAGGAGAT 1399 1.000 40.0
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG TGGCCTGGTTGTAGCATTAG 597–598 1.000 76.2
atpF-atpH_p2 atpF-atpH CCAGTGACCCAAGTAAACGA TGGCCTGGTTGTAGCATTAG 570–571 1.000 72.9
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG TTTATGGCCTGGTTGTAGCA 601–602 1.000 72.5
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG GGCCTGGTTGTAGCATTAGC 596–597 1.000 71.8
atpF-atpH_p5 atpF-atpH GGCCAGTGACCCAAGTAAAC TGGCCTGGTTGTAGCATTAG 572–573 1.000 71.2
atpH-atpI_p1 atpH-atpI TACCTTGACCAACTCCAGGT TTTTTGCCACTTTAGCTGCG 644 1.000 78.2
atpH-atpI_p2 atpH-atpI GTCCAATAGAAGCAAGCCCA TTTTTGCCACTTTAGCTGCG 626 1.000 78.0
atpH-atpI_p3 atpH-atpI GCTGTACCTTGACCAACTCC TTTTTGCCACTTTAGCTGCG 648 1.000 77.5
atpH-atpI_p4 atpH-atpI AGGTCCAATAGAAGCAAGCC TTTTTGCCACTTTAGCTGCG 628 1.000 75.7
atpH-atpI_p5 atpH-atpI GTACCTTGACCAACTCCAGG TTTTTGCCACTTTAGCTGCG 645 1.000 75.3
atpI_p1 atpI TGGGCTAACCTAAAAACGAA TCTTATTTCTGTCAGAGGGCA 812 1.000 40.1
atpI_p2 atpI TTGGGCTAACCTAAAAACGA TCTTATTTCTGTCAGAGGGCA 813 1.000 40.1
atpI_p3 atpI TTGGGCTAACCTAAAAACGAA TCTTATTTCTGTCAGAGGGCA 813 1.000 40.1
atpI_p4 atpI TGGGCTAACCTAAAAACGAA TCTTATTTCTGTCAGAGGGCAA 812 1.000 40.1
atpI_p5 atpI TGGGCTAACCTAAAAACGAA TTCTTATTTCTGTCAGAGGGCA 813 1.000 40.1

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
Kernera saxatilis NC_049658.1 154610 View on NCBI ↗
Kernera saxatilis subsp. saxatilis PP165050.1 154799 View on NCBI ↗