Markers + reference

Clausia

2 species · Brassicaceae · Brassicales

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Species 2
Genome length 156–158 kb
Candidate markers 270
Primer pairs 70

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 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
accD LSC 1464 0.0802 1.00 76.6 yes View details
clpP LSC 2076 0.2493 0.36 69.2 yes View details
ycf1 IRb 2859 0.0604 0.98 74.3 yes View details
rps15-ycf1 SSC 2561 0.0730 0.97 78.6 yes View details
ycf1 IRa 3108 0.0640 0.97 75.6 no View details
trnH-CAC-psbA LSC 244 0.1250 0.98 79.6 yes View details
trnS-AGC-trnG-GGA LSC 581 0.0520 0.96 77.9 yes View details
petA-psbJ LSC 1012 0.0379 0.97 77.0 yes View details
trnF-UUC-ndhJ LSC 602 0.0361 0.97 76.8 yes View details
rpl32-trnL-CUA SSC 548 0.0762 0.98 76.7 yes View details
psbC-trnS-UCA LSC 185 0.0444 0.97 76.4 yes View details
ndhC-trnV-GUA LSC 876 0.0440 0.99 76.0 yes View details
trnI-CAU-ycf2 IRb 88 0.0976 0.93 75.9 yes View details
ycf2-trnI-CAU IRa 88 0.0976 0.93 75.9 yes View details
psaJ-rpl33 LSC 425 0.0463 0.96 75.6 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 70 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 GCTGTTGAGGCTCCATCTAC 302–303 1.000 87.5
trnH-CAC-psbA_p2 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 303–304 1.000 87.3
trnH-CAC-psbA_p3 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 317–318 1.000 87.0
trnH-CAC-psbA_p4 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 320–321 1.000 86.8
trnH-CAC-psbA_p5 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 318–319 1.000 86.7
trnS-AGC-trnG-GGA_p1 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA TACCACTAAACTATACCCGC 627–632 1.000 53.2
trnS-AGC-trnG-GGA_p2 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC TACCACTAAACTATACCCGC 625–630 1.000 52.9
trnS-AGC-trnG-GGA_p3 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA TTACCACTAAACTATACCCGC 628–633 1.000 52.1
trnS-AGC-trnG-GGA_p4 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC TTACCACTAAACTATACCCGC 626–631 1.000 51.8
trnS-AGC-trnG-GGA_p5 trnS-AGC-trnG-GGA GCTTTAGTCCACTCAGCCAT TACCACTAAACTATACCCGC 622–627 1.000 51.3
psbC-trnS-UCA_p1 psbC-trnS-UCA TCGTGGGTCATTTATGGCAC GGGTTCGAATCCCTCTCTCT 315–318 1.000 79.8
psbC-trnS-UCA_p2 psbC-trnS-UCA TCGTGGGTCATTTATGGCAC GATGGCTCCGGTCTTGAAAA 365–368 1.000 79.6
psbC-trnS-UCA_p3 psbC-trnS-UCA CGGCAGCAGGATTTGAAAAA GGGTTCGAATCCCTCTCTCT 276–279 1.000 78.8
psbC-trnS-UCA_p4 psbC-trnS-UCA CGGCAGCAGGATTTGAAAAA GATGGCTCCGGTCTTGAAAA 326–329 1.000 78.5
psbC-trnS-UCA_p5 psbC-trnS-UCA TTCGTGGGTCATTTATGGCA GATGGCTCCGGTCTTGAAAA 366–369 1.000 77.6
trnF-UUC-ndhJ_p1 trnF-UUC-ndhJ CCTCGTGTCACCAGTTCAAA CATCCACGACTGAAACGGAT 732–741 1.000 84.0
trnF-UUC-ndhJ_p2 trnF-UUC-ndhJ CCTCGTGTCACCAGTTCAAA CCCGAAAGTTGGATAGGGTG 705–714 1.000 83.9
trnF-UUC-ndhJ_p3 trnF-UUC-ndhJ CCTCGTGTCACCAGTTCAAA CCGAAAGTTGGATAGGGTGG 704–713 1.000 83.9
trnF-UUC-ndhJ_p4 trnF-UUC-ndhJ CCTCGTGTCACCAGTTCAAA CCACGACTGAAACGGATCTT 729–738 1.000 83.4
trnF-UUC-ndhJ_p5 trnF-UUC-ndhJ CCTCGTGTCACCAGTTCAAA TGATAGCCATCCACGACTGA 739–748 1.000 82.2
ndhC-trnV-GUA_p1 ndhC-trnV-GUA TGCCAAAACAGGAATAGCACT TCGAACTGTTTTACCGAGCA 993–997 1.000 71.0
ndhC-trnV-GUA_p2 ndhC-trnV-GUA TGCCAAAACAGGAATAGCACT GTTCGAGTCCGTATAGCCCT 965–969 1.000 69.8
ndhC-trnV-GUA_p3 ndhC-trnV-GUA TGCCAAAACAGGAATAGCAC TCGAACTGTTTTACCGAGCA 993–997 1.000 68.8
ndhC-trnV-GUA_p4 ndhC-trnV-GUA TGCCAAAACAGGAATAGCACT CGAACTGTTTTACCGAGCAG 992–996 1.000 68.3
ndhC-trnV-GUA_p5 ndhC-trnV-GUA TGCCAAAACAGGAATAGCACT TTCGAGTCCGTATAGCCCTA 964–968 1.000 67.7
accD_p1 accD TCATGTAAATATAGGCCAGAAGCT AGGGTTTTCGTTTAATTCTGA 1524–1962 1.000 45.7
accD_p2 accD TGTAAATATAGGCCAGAAGCTCT AGGGTTTTCGTTTAATTCTGA 1521 0.500 20.0
accD_p3 accD TGTAAATATAGGCCAGAAGCTCT AAGGGTTTTCGTTTAATTCTGA 1522 0.500 20.0
accD_p4 accD TGTAAATATAGGCCAGAAGCTCT AGGGTTTTCGTTTAATTCTGAT 1521 0.500 20.0
accD_p5 accD AAATATAGGCCAGAAGCTCT AGGGTTTTCGTTTAATTCTGA 1518 0.500 20.0

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
Clausia aprica NC_049602.1 155653 View on NCBI ↗
Clausia trichosepala MK637698.1 158444 View on NCBI ↗