Markers + reference

Menkea

3 species · Brassicaceae · Brassicales

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Species 3
Genome length 155–155 kb
Candidate markers 258
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 258 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-rps16 LSC 676 0.0421 1.00 80.2 yes View details
trnS-atpA LSC 1974 0.0303 0.97 65.5 yes View details
trnT-trnL LSC 786 0.0388 0.97 77.0 yes View details
trnL-trnF LSC 822 0.0949 0.96 84.8 yes View details
trnF-ndhJ LSC 583 0.0427 0.99 74.1 yes View details
petA-psbJ LSC 945 0.0406 0.99 78.8 yes View details
psbE-ORF31 LSC 1346 0.0374 0.99 73.0 yes View details
rpl16 LSC 1510 0.0267 1.00 61.5 yes View details
ycf1 IRb 1032 0.0071 1.00 55.0 no View details
ndhF-rpl32 SSC 857 0.0459 0.98 76.8 yes View details
rpl32-trnL SSC 790 0.0790 1.00 84.0 yes View details
ycf1 SSC 5328 0.0296 1.00 59.2 yes View details
trnH-psbA LSC 274 0.0745 1.00 81.0 yes View details
ndhC-trnV LSC 866 0.0384 0.97 75.5 yes View details
rps16-trnQ LSC 431 0.0444 0.97 75.1 yes View details
psbI-trnS LSC 89 0.0449 1.00 74.5 yes View details
rps19-rpl2 IRb 55 0.0494 0.98 73.2 yes View details
ndhJ-psbG LSC 102 0.0523 1.00 72.0 yes View details
atpH-atpI LSC 500 0.0327 0.98 70.9 yes View details
trnS-rps4 LSC 316 0.0316 1.00 70.2 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-psbA_p1 trnH-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 332–358 1.000 86.8
trnH-psbA_p2 trnH-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 333–359 1.000 86.6
trnH-psbA_p3 trnH-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 347–373 1.000 86.4
trnH-psbA_p4 trnH-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 350–376 1.000 86.3
trnH-psbA_p5 trnH-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 348–374 1.000 86.2
trnK-rps16_p1 trnK-rps16 AAAGCCGAGTACTCTACCGT CGCTCAACCAACAAGAACAG 731–765 1.000 83.8
trnK-rps16_p2 trnK-rps16 AAGCCGAGTACTCTACCGTT CGCTCAACCAACAAGAACAG 730–764 1.000 83.8
trnK-rps16_p3 trnK-rps16 TACCGTTGAGTTAGCAACCC CGCTCAACCAACAAGAACAG 717–751 1.000 81.5
trnK-rps16_p4 trnK-rps16 AGTCGCACTTAAAAGCCGAG CGCTCAACCAACAAGAACAG 742–776 1.000 80.5
trnK-rps16_p5 trnK-rps16 TCGCACTTAAAAGCCGAGTA CGCTCAACCAACAAGAACAG 740–774 1.000 79.3
rps16-trnQ_p1 rps16-trnQ AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 493–504 1.000 84.4
rps16-trnQ_p2 rps16-trnQ CCTTCAATTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 503–514 1.000 83.5
rps16-trnQ_p3 rps16-trnQ TCAATTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 500–511 1.000 80.1
rps16-trnQ_p4 rps16-trnQ AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 497–508 1.000 79.6
rps16-trnQ_p5 rps16-trnQ AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 523–534 1.000 79.2
psbI-trnS_p1 psbI-trnS TCCTATCTAATGATCCAGGACGT TAGGAGAGATGGCTGAGTGG 224–231 1.000 57.8
psbI-trnS_p2 psbI-trnS TCCTATCTAATGATCCAGGACGT TGAGTGGACTAAAGCGTTGG 211–218 1.000 57.3
psbI-trnS_p3 psbI-trnS TCCTATCTAATGATCCAGGACGT GCTGAGTGGACTAAAGCGTT 213–220 1.000 56.9
psbI-trnS_p4 psbI-trnS TCCTATCTAATGATCCAGGACGT CGAGTTAATCGTACCGAGGG 174–181 1.000 56.0
psbI-trnS_p5 psbI-trnS TCCTATCTAATGATCCAGGACGT ATGGCTGAGTGGACTAAAGC 216–223 1.000 55.3
trnS-atpA_p1 trnS-atpA CCAACGCTTTAGTCCACTCA GGGTCGTGAAGCTTATCCAG 2636–2684 1.000 83.2
trnS-atpA_p2 trnS-atpA CCAACGCTTTAGTCCACTCA GGTCGTGAAGCTTATCCAGG 2635–2683 1.000 83.2
trnS-atpA_p3 trnS-atpA AACGCTTTAGTCCACTCAGC GGGTCGTGAAGCTTATCCAG 2634–2682 1.000 82.9
trnS-atpA_p4 trnS-atpA AACGCTTTAGTCCACTCAGC GGTCGTGAAGCTTATCCAGG 2633–2681 1.000 82.9
trnS-atpA_p5 trnS-atpA CCAACGCTTTAGTCCACTCA GTTTCGAGAGTAGGATCCGC 2440 0.333 51.0
atpH-atpI_p1 atpH-atpI TACCTTGACCAACTCCAGGT TTTTTGCCACTTTAGCTGCG 638–644 1.000 82.9
atpH-atpI_p2 atpH-atpI GTCCAATAGAAGCAAGCCCA TTTTTGCCACTTTAGCTGCG 620–626 1.000 82.9
atpH-atpI_p3 atpH-atpI GCTGTACCTTGACCAACTCC TTTTTGCCACTTTAGCTGCG 642–648 1.000 82.3
atpH-atpI_p4 atpH-atpI TACCTTGACCAACTCCAGGT GCGGGATTCAAGCTCTCATT 656–662 1.000 81.2
atpH-atpI_p5 atpH-atpI GTCCAATAGAAGCAAGCCCA GCGGGATTCAAGCTCTCATT 638–644 1.000 81.2

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
Menkea crassa NC_069347.1 154744 View on NCBI ↗
Menkea sphaerocarpa NC_069343.1 155229 View on NCBI ↗
Menkea villosula NC_069355.1 155291 View on NCBI ↗