Markers + reference

Biscutella

4 species · Brassicaceae · Brassicales

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Species 4
Genome length 154–154 kb
Candidate markers 263
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0085 1.00 50.2 yes View details
trnK-trnQ LSC 2218 0.0356 0.97 74.8 yes View details
ycf1 IRb 963 0.0114 0.99 53.5 no View details
ndhF-rpl32 SSC 911 0.0475 0.93 79.4 yes View details
rpl32-trnL SSC 957 0.0507 0.98 82.5 yes View details
ycf1 SSC 5199 0.0594 0.99 74.0 yes View details
trnW-trnP LSC 198 0.0532 0.96 81.7 yes View details
atpH-atpI LSC 528 0.0414 0.94 81.0 yes View details
trnH-psbA LSC 256 0.0964 0.98 79.2 yes View details
rpl36-rps8 LSC 482 0.0430 0.96 78.7 yes View details
trnR-atpA LSC 313 0.0598 0.93 78.2 yes View details
trnT-trnR LSC 161 0.0549 1.00 77.4 yes View details
trnS-trnT LSC 617 0.0404 1.00 75.0 yes View details
ndhC-trnV LSC 753 0.0413 0.98 75.0 yes View details
petB-petD LSC 197 0.0415 0.93 73.1 yes View details
rpl22-rps19 LSC 60 0.0472 0.97 73.1 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-psbA_p1 trnH-psbA CCACTTGGCTACATCCGC GAGGCTCCATCTACAAATGG 298–345 1.000 55.2
trnH-psbA_p2 trnH-psbA TCCACTTGGCTACATCCGC GAGGCTCCATCTACAAATGG 299–346 1.000 52.0
trnH-psbA_p3 trnH-psbA TCCACTTGGCTACATCCG GAGGCTCCATCTACAAATGG 299–346 1.000 52.0
trnH-psbA_p4 trnH-psbA CCACTTGGCTACATCCGC AGGCTCCATCTACAAATGG 297–344 1.000 52.0
trnH-psbA_p5 trnH-psbA TCCACTTGGCTACATCCGC AGGCTCCATCTACAAATGG 298–345 1.000 52.0
psbA_p1 psbA CTGCCTTAATCCACTTGGCT ATTTGTGTGCTTGGGAGTCC 1396–1408 0.500 59.3
psbA_p2 psbA ACTGCCTTAATCCACTTGGC ATTTGTGTGCTTGGGAGTCC 1397–1409 0.500 59.1
psbA_p3 psbA CTGCCTTAATCCACTTGGCT AAAATGCAAGCACGGTTTGG 1727–1733 0.500 58.9
psbA_p4 psbA ACTGCCTTAATCCACTTGGC AAAATGCAAGCACGGTTTGG 1728–1734 0.500 58.6
psbA_p5 psbA CTGCCTTAATCCACTTGGCT TTACGGGGGAAGACCAAGTT 2076–2082 0.500 58.4
trnK-trnQ_p1 trnK-trnQ AAAGCCGAGTACTCTACCGT GAGGTTCGAATCCTTCCGTC 2255–2351 1.000 86.8
trnK-trnQ_p2 trnK-trnQ AAGCCGAGTACTCTACCGTT GAGGTTCGAATCCTTCCGTC 2254–2350 1.000 86.8
trnK-trnQ_p3 trnK-trnQ TACCGTTGAGTTAGCAACCC GAGGTTCGAATCCTTCCGTC 2241–2337 1.000 84.5
trnK-trnQ_p4 trnK-trnQ AGTCGCACTTAAAAGCCGAG GAGGTTCGAATCCTTCCGTC 2266–2362 1.000 83.6
trnK-trnQ_p5 trnK-trnQ TCGCACTTAAAAGCCGAGTA GAGGTTCGAATCCTTCCGTC 2264–2360 1.000 82.3
trnS-trnT_p1 trnS-trnT CCAACGCTTTAGTCCACTCA ACGAATCACACTTTTACCACT 682–785 1.000 56.3
trnS-trnT_p2 trnS-trnT AACGCTTTAGTCCACTCAGC ACGAATCACACTTTTACCACT 680–783 1.000 56.0
trnS-trnT_p3 trnS-trnT GCTTTAGTCCACTCAGCCAT ACGAATCACACTTTTACCACT 677–780 1.000 54.4
trnS-trnT_p4 trnS-trnT TCCAACGCTTTAGTCCACTC ACGAATCACACTTTTACCACT 683–786 1.000 54.0
trnS-trnT_p5 trnS-trnT AGTCCACTCAGCCATCTCTC ACGAATCACACTTTTACCACT 672–775 1.000 53.6
trnT-trnR_p1 trnT-trnR AGCCTTCCAAGCTAACGATG TGATATTGCGTCCAATAGGA 283–290 0.750 40.8
trnT-trnR_p2 trnT-trnR ACCCTTAGCCTTCCAAGCTA TGATATTGCGTCCAATAGGA 289–296 0.750 40.7
trnT-trnR_p3 trnT-trnR CGACGTCGACTAAAACCCTT TGATATTGCGTCCAATAGGA 303–310 0.750 40.3
trnT-trnR_p4 trnT-trnR AAACCCTTAGCCTTCCAAGC TGATATTGCGTCCAATAGGA 291–298 0.750 40.3
trnT-trnR_p5 trnT-trnR AGCCTTCCAAGCTAACGATG TTGATATTGCGTCCAATAGGA 284–291 0.750 39.8
trnR-atpA_p1 trnR-atpA GCGAAAAGCGTCCATTGTC GAACGTTTTCTACTTCAAGAGA 397–422 1.000 49.9
trnR-atpA_p2 trnR-atpA GCGAAAAGCGTCCATTGTC GAACGTTTTCTACTTCAAGAGAA 397–422 1.000 49.9
trnR-atpA_p3 trnR-atpA GCGAAAAGCGTCCATTGTC AACGTTTTCTACTTCAAGAGA 396–421 1.000 49.9
trnR-atpA_p4 trnR-atpA GCGAAAAGCGTCCATTGTC ACGTTTTCTACTTCAAGAGAA 395–420 1.000 49.9
trnR-atpA_p5 trnR-atpA GCGAAAAGCGTCCATTGTC ACGTTTTCTACTTCAAGAGAAA 395–420 1.000 49.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Biscutella baetica NC_039952.1 154138 View on NCBI ↗
Biscutella laevigata NC_049595.1 154217 View on NCBI ↗
Biscutella lyrata NC_039953.1 153720 View on NCBI ↗
Biscutella sempervirens subsp. vicentina NC_049601.1 154226 View on NCBI ↗