Markers + reference

Bunias

2 species · Brassicaceae · Brassicales

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Species 2
Genome length 154–154 kb
Candidate markers 280
Primer pairs 95

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 10 remaining regions by MarkerSeek score (out of 280 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI LSC 395 0.0329 1.00 62.4 yes View details
rpoB-trnC LSC 978 0.0297 1.00 67.4 yes View details
psbM-trnD LSC 1008 0.0238 1.00 61.4 yes View details
trnE-trnT LSC 814 0.0298 0.99 67.6 yes View details
psbE-ORF31 LSC 1097 0.0253 0.72 60.3 yes View details
rpl16-rpl16 LSC 1115 0.0292 0.98 63.7 yes View details
ycf1 IRb 1035 0.0019 1.00 45.3 no View details
ndhF-rpl32 SSC 829 0.0411 1.00 71.5 yes View details
rpl32-trnL SSC 699 0.0378 0.98 73.7 yes View details
ycf1 SSC 5289 0.0218 1.00 56.3 yes View details
atpA-atpF LSC 66 0.0462 0.98 76.6 yes View details
psbI-trnS LSC 97 0.0667 0.93 76.2 yes View details
psbG-ndhC LSC 61 0.0656 1.00 76.1 yes View details
ndhD-psaC SSC 135 0.0519 1.00 75.9 yes View details
psbL-psbF LSC 21 0.0476 1.00 74.8 yes View details
rps15-ycf1 SSC 317 0.0413 0.99 72.4 yes View details
trnR-atpA LSC 276 0.0435 1.00 71.8 yes View details
trnF-ndhJ LSC 579 0.0295 1.00 70.6 yes View details
atpH-atpI LSC 498 0.0186 0.97 69.8 yes View details
trnfM-rps14 LSC 158 0.0380 1.00 69.8 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
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCAGCTGTAAG ACAAAAAGTTTGAGAGTAAGCA 448–475 1.000 42.3
psbK-psbI_p2 psbK-psbI TGGCAAGCAGCTGTAAGTTT ACAAAAAGTTTGAGAGTAAGCA 445–472 1.000 42.3
psbK-psbI_p3 psbK-psbI TTGGCAAGCAGCTGTAAGTT ACAAAAAGTTTGAGAGTAAGCA 446–473 1.000 42.3
psbK-psbI_p4 psbK-psbI TTTGGCAAGCAGCTGTAAGT ACAAAAAGTTTGAGAGTAAGCA 447–474 1.000 42.3
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCAGCTGTAAG ACAAAAAGTTTGAGAGTAAGCAT 448–475 1.000 42.3
psbI-trnS_p1 psbI-trnS TCCTATCTAATGATCCAGGACGT TAGGAGAGATGGCTGAGTGG 225–231 1.000 59.9
psbI-trnS_p2 psbI-trnS TCCTATCTAATGATCCAGGACGT TGAGTGGACTAAAGCGTTGG 212–218 1.000 59.5
psbI-trnS_p3 psbI-trnS TCCTATCTAATGATCCAGGACGT GCTGAGTGGACTAAAGCGTT 214–220 1.000 59.2
psbI-trnS_p4 psbI-trnS TCCTATCTAATGATCCAGGACGT CGAGTTAATCGTACCGAGGG 175–181 1.000 58.7
psbI-trnS_p5 psbI-trnS TCCTATCTAATGATCCAGGACGT ATGGCTGAGTGGACTAAAGC 217–223 1.000 57.4
trnR-atpA_p1 trnR-atpA GCGAAAAGCGTCCATTGTC ACATTAACCGCTGAAGCAGA 445–458 1.000 70.3
trnR-atpA_p2 trnR-atpA GCGAAAAGCGTCCATTGTC AGACATTAACCGCTGAAGCA 447–460 1.000 70.3
trnR-atpA_p3 trnR-atpA GCGAAAAGCGTCCATTGTC GACATTAACCGCTGAAGCAG 446–459 1.000 67.6
trnR-atpA_p4 trnR-atpA GCGAAAAGCGTCCATTGTC TAACCGCTGAAGCAGAAAGC 441–454 1.000 67.4
trnR-atpA_p5 trnR-atpA GCGAAAAGCGTCCATTGTC ACCAAGACATTAACCGCTGA 451–464 1.000 67.3
atpA-atpF_p1 atpA-atpF GCCCACTTGAAGTACGGTAC ACAAGGAGCTATAGGAACCCT 282–283 1.000 67.5
atpA-atpF_p2 atpA-atpF CCCACTTGAAGTACGGTACC ACAAGGAGCTATAGGAACCCT 281–282 1.000 66.8
atpA-atpF_p3 atpA-atpF CCATCGCCCACTTGAAGTAC ACAAGGAGCTATAGGAACCCT 287–288 1.000 64.7
atpA-atpF_p4 atpA-atpF GCCCACTTGAAGTACGGTAC ACAAGGAGCTATAGGAACCC 282–283 1.000 62.9
atpA-atpF_p5 atpA-atpF CCCACTTGAAGTACGGTACC ACAAGGAGCTATAGGAACCC 281–282 1.000 62.1
atpH-atpI_p1 atpH-atpI AACCGAAGCAGCAGAAATCA TACAAGCGGGATTCAAGCTC 594–607 1.000 81.9
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT TACAAGCGGGATTCAAGCTC 652–665 1.000 81.6
atpH-atpI_p3 atpH-atpI GTCCAATAGAAGCAAGCCCA TACAAGCGGGATTCAAGCTC 634–647 1.000 81.5
atpH-atpI_p4 atpH-atpI GCTGTACCTTGACCAACTCC TACAAGCGGGATTCAAGCTC 656–669 1.000 80.9
atpH-atpI_p5 atpH-atpI AACCGAAGCAGCAGAAATCA GCGGGATTCAAGCTCTCATT 589–602 1.000 79.5
rpoB-trnC_p1 rpoB-trnC GTTCCCTCTTTTCCATCCCC CCGGATTTGAACTGGGGAAA 1066 1.000 80.6
rpoB-trnC_p2 rpoB-trnC GTTCCCTCTTTTCCATCCCC AAAAGGATTTGCAGTCCCCC 1048 1.000 78.4
rpoB-trnC_p3 rpoB-trnC TGTTCCCTCTTTTCCATCCC CCGGATTTGAACTGGGGAAA 1067 1.000 74.5
rpoB-trnC_p4 rpoB-trnC GTTCCCTCTTTTCCATCCCC AAGTCTGTTGTTGAGGCGG 1088 1.000 73.1
rpoB-trnC_p5 rpoB-trnC TCTTTTCCATCCCCGAGCAT CCGGATTTGAACTGGGGAAA 1060 1.000 73.1

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
Bunias erucago NC_036110.1 153742 View on NCBI ↗
Bunias orientalis NC_036111.1 154012 View on NCBI ↗