Markers + reference

Brassica

15 species · Brassicaceae · Brassicales

Back to catalogue

Species 15
Genome length 153–154 kb
Candidate markers 268
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0030 1.00 28.4 yes View details
trnK-UUU-rps16 LSC 648 0.0243 0.96 54.1 yes View details
trnS-GCU-trnG-UCC LSC 664 0.0186 0.96 58.6 yes View details
ndhC-trnV-UAC LSC 867 0.0631 0.76 69.7 yes View details
psaJ-rpl33 LSC 435 0.0221 0.98 54.8 yes View details
rpl20-rps12 LSC 765 0.0132 1.00 47.1 yes View details
rpl32-trnL-UAG SSC 596 0.0210 0.99 55.2 yes View details
rps15-trnN-GUU SSC 5972 0.0117 1.00 42.1 yes View details
trnH-GUG-psbA LSC 183 0.0645 0.99 76.7 yes View details
rps16-trnQ-UUG LSC 456 0.0201 0.96 55.6 yes View details
ndhF-rpl32 SSC 829 0.0159 0.96 53.2 yes View details
trnF-GAA-ndhJ LSC 589 0.0114 0.98 51.7 yes View details
ycf4-cemA LSC 526 0.0111 0.89 48.1 yes View details
psbE-petL LSC 1366 0.0106 0.99 47.9 yes View details
cemA-petA LSC 225 0.0142 1.00 47.5 yes View details
petA-psbJ LSC 989 0.0133 0.96 47.4 yes View details
trnR-UCU-atpA LSC 218 0.0252 0.99 46.5 yes View details
matK-trnK-UUU LSC 679 0.0140 0.99 46.2 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-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 256–330 1.000 90.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 259–333 1.000 90.3
trnH-GUG-psbA_p3 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 257–331 1.000 90.2
trnH-GUG-psbA_p4 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TTCCCTCTAGACCTAGCTGC 260–334 1.000 90.1
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 249–323 1.000 88.8
psbA_p1 psbA CTGCCTTAATCCACTTGGCT CTTTACGGGGGAAGACCAAG 2020–2086 1.000 82.8
psbA_p2 psbA ACTGCCTTAATCCACTTGGC CTTTACGGGGGAAGACCAAG 2021–2087 1.000 82.6
psbA_p3 psbA CTGCCTTAATCCACTTGGCT TGCGGGTTTGGTATTTGGAT 1946–2012 1.000 82.0
psbA_p4 psbA ACTGCCTTAATCCACTTGGC TGCGGGTTTGGTATTTGGAT 1947–2013 1.000 81.8
psbA_p5 psbA CTGCCTTAATCCACTTGGCT TCTTTACGGGGGAAGACCAA 2021–2087 1.000 81.5
matK-trnK-UUU_p1 matK-trnK-UUU TCTTGAGTTCTGAAATGACACA ACGGTAGAGTACTCGGCTTT 721–725 1.000 49.9
matK-trnK-UUU_p2 matK-trnK-UUU TCTTGAGTTCTGAAATGACACA AACGGTAGAGTACTCGGCTT 722–726 1.000 49.8
matK-trnK-UUU_p3 matK-trnK-UUU TTCTTGAGTTCTGAAATGACACA AACGGTAGAGTACTCGGCTT 723–727 1.000 47.6
matK-trnK-UUU_p4 matK-trnK-UUU TTCTTGAGTTCTGAAATGACACA ACGGTAGAGTACTCGGCTTT 722–726 1.000 47.6
matK-trnK-UUU_p5 matK-trnK-UUU TCTTGAGTTCTGAAATGACACA GGGTTGCTAACTCAACGGTA 735–739 1.000 47.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CCCAATGAGCCGTTTATCGA 967–1010 1.000 88.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TCCCAATGAGCCGTTTATCG 968–1011 1.000 88.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT CCCAATGAGCCGTTTATCGA 963–1006 1.000 88.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCGACACCGAAAACAAGGTT CCCAATGAGCCGTTTATCGA 1101–1102 0.133 44.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCGACACCGAAAACAAGGTT TCCCAATGAGCCGTTTATCG 1102–1103 0.133 44.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 529–534 1.000 86.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGGTGGCGGATCAAAACAT GAGGTTCGAATCCTTCCGTC 575–580 1.000 86.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCTTCAATTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 539–544 1.000 85.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAAGGTGGCGGATCAAAACA GAGGTTCGAATCCTTCCGTC 576–581 1.000 84.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCACAGCAGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 555–560 1.000 84.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CCAACGCTTTAGTCCACTCA AATCAAACCGAGAGACCCTT 750–789 1.000 75.1
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CCAACGCTTTAGTCCACTCA ATCAAACCGAGAGACCCTTT 749–788 1.000 75.1
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AACGCTTTAGTCCACTCAGC AATCAAACCGAGAGACCCTT 748–787 1.000 74.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AACGCTTTAGTCCACTCAGC ATCAAACCGAGAGACCCTTT 747–786 1.000 74.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CCAACGCTTTAGTCCACTCA AATCAAACCGAGAGACCCTTT 750–789 1.000 73.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (15)

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

Species Accession Length (bp) Link
Brassica carinata NC_059807.1 153641 View on NCBI ↗
Brassica juncea NC_028272.1 153483 View on NCBI ↗
Brassica juncea var. multiceps PX240752.1 153483 View on NCBI ↗
Brassica napus NC_016734.1 152860 View on NCBI ↗
Brassica nigra NC_030450.1 153633 View on NCBI ↗
Brassica oleracea NC_041167.1 153364 View on NCBI ↗
Brassica oleracea var. botrytis MT499334.1 153364 View on NCBI ↗
Brassica oleracea var. capitata MN629887.1 153363 View on NCBI ↗
Brassica rapa NC_040849.1 153483 View on NCBI ↗
Brassica rapa subsp. chinensis PV995099.1 153481 View on NCBI ↗
Brassica rapa subsp. narinosa PV995108.1 153482 View on NCBI ↗
Brassica rapa subsp. rapa NC_049891.1 153621 View on NCBI ↗
Brassica rapa var. parachinensis PX244600.1 153482 View on NCBI ↗
Brassica rapa var. purpuraria PP191173.1 153483 View on NCBI ↗
Brassica rapa x Raphanus sativus NC_058844.1 153482 View on NCBI ↗