Markers + reference

Aethionema

4 species · Brassicaceae · Brassicales

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Species 4
Genome length 154–154 kb
Candidate markers 255
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 255 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-psbA LSC 264 0.0721 0.77 73.3 yes View details
trnK-trnQ LSC 2112 0.0326 0.98 73.7 yes View details
psbK-psbI LSC 421 0.0416 1.00 72.7 yes View details
ycf1 IRb 1095 0.0064 1.00 39.2 no View details
ndhF-rpl32 SSC 862 0.0343 0.96 74.4 yes View details
rpl32-trnL SSC 524 0.0478 0.97 84.0 yes View details
ycf1 SSC 5259 0.0322 1.00 60.1 yes View details
trnE-trnT LSC 808 0.0330 1.00 77.4 yes View details
trnG-trnR LSC 199 0.0471 0.88 74.6 yes View details
ndhE-ndhG SSC 296 0.0389 1.00 73.3 yes View details
rps15-ycf1 SSC 413 0.0417 0.99 72.8 yes View details
petA-psbJ LSC 960 0.0277 0.99 71.6 yes View details
rpl36-rps8 LSC 490 0.0299 1.00 70.1 yes View details
ndhG-ndhI SSC 357 0.0383 0.94 69.2 yes View details
psbI-trnS LSC 93 0.0562 0.99 69.0 yes View details
trnT-trnL LSC 806 0.0261 1.00 68.7 yes View details
psbM-trnD LSC 958 0.0301 1.00 68.1 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-psbA_p1 trnH-psbA GATCCACTTGGCTACATCCG GTTGATAGTCAAGGGCGTGT 376–439 1.000 88.3
trnH-psbA_p2 trnH-psbA GATCCACTTGGCTACATCCG GGTGTAGCTGGTGTATTCGG 694–757 1.000 86.5
trnH-psbA_p3 trnH-psbA CAATCCACTGCCTTGATCCA GGTGTAGCTGGTGTATTCGG 708–761 0.750 74.8
trnH-psbA_p4 trnH-psbA AATCCACTGCCTTGATCCAC GGTGTAGCTGGTGTATTCGG 707–760 0.750 74.8
trnH-psbA_p5 trnH-psbA ACAATCCACTGCCTTGATCC GGTGTAGCTGGTGTATTCGG 709–762 0.750 74.8
trnK-trnQ_p1 trnK-trnQ AAAGCCGAGTACTCTACCGT GAGGTTCGAATCCTTCCGTC 2170–2277 1.000 85.4
trnK-trnQ_p2 trnK-trnQ AAGCCGAGTACTCTACCGTT GAGGTTCGAATCCTTCCGTC 2169–2276 1.000 85.4
trnK-trnQ_p3 trnK-trnQ TACCGTTGAGTTAGCAACCC GAGGTTCGAATCCTTCCGTC 2156–2263 1.000 83.1
trnK-trnQ_p4 trnK-trnQ AGTCGCACTTAAAAGCCGAG GAGGTTCGAATCCTTCCGTC 2181–2288 1.000 82.1
trnK-trnQ_p5 trnK-trnQ TCGCACTTAAAAGCCGAGTA GAGGTTCGAATCCTTCCGTC 2179–2286 1.000 80.9
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCAGCTGTAAG AGACAAAAAGTTTGAGAGTAAGCA 474–477 1.000 46.4
psbK-psbI_p2 psbK-psbI TGGCAAGCAGCTGTAAGTTT AGACAAAAAGTTTGAGAGTAAGCA 471–474 1.000 46.4
psbK-psbI_p3 psbK-psbI TTGGCAAGCAGCTGTAAGTT AGACAAAAAGTTTGAGAGTAAGCA 472–475 1.000 46.4
psbK-psbI_p4 psbK-psbI TTTGGCAAGCAGCTGTAAGT AGACAAAAAGTTTGAGAGTAAGCA 473–476 1.000 46.4
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCAGCTGTAAG ACAGTGTAGACAAAAAGTTTGAGA 481–484 1.000 46.3
psbI-trnS_p1 psbI-trnS TCCTATCTAATGATCCAGGACGT CGAGTTAATCGTACCGAGGG 176–177 1.000 57.8
psbI-trnS_p2 psbI-trnS CCTATCTAATGATCCAGGACGT CGAGTTAATCGTACCGAGGG 175–176 1.000 54.5
psbI-trnS_p3 psbI-trnS TCCTATCTAATGATCCAGGACGT TTAATCGTACCGAGGGTTCG 172–173 1.000 54.3
psbI-trnS_p4 psbI-trnS TCCTATCTAATGATCCAGGACGT GGGTTCGAATCCCTCTCTTT 159–160 1.000 52.9
psbI-trnS_p5 psbI-trnS TCCTATCTAATGATCCAGGACG CGAGTTAATCGTACCGAGGG 176–177 1.000 52.4
trnG-trnR_p1 trnG-trnR AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTATGTCCT 251–285 1.000 53.6
trnG-trnR_p2 trnG-trnR ACCCTTAGCCTTCCAAGCTA AGGTTTAGAAGACCTATGTCCT 257–291 1.000 53.4
trnG-trnR_p3 trnG-trnR AGCCTTCCAAGCTAACGATG AGAAGACCTATGTCCTATCCA 245–279 1.000 53.4
trnG-trnR_p4 trnG-trnR ACCCTTAGCCTTCCAAGCTA AGAAGACCTATGTCCTATCCA 251–285 1.000 53.3
trnG-trnR_p5 trnG-trnR AAACCCTTAGCCTTCCAAGC AGGTTTAGAAGACCTATGTCCT 259–293 1.000 53.1
psbM-trnD_p1 psbM-trnD TCGTAGTGTGGGGAAGAAGT AAGTATGCCCCCATCGTCTA 2367–2371 1.000 84.6
psbM-trnD_p2 psbM-trnD CGTAGTGTGGGGAAGAAGTG AAGTATGCCCCCATCGTCTA 2366–2370 1.000 84.0
psbM-trnD_p3 psbM-trnD TCGTAGTGTGGGGAAGAAGT TGGCAATATGTCTACGCTGG 2185–2189 1.000 83.9
psbM-trnD_p4 psbM-trnD TCGTAGTGTGGGGAAGAAGT GGCAATATGTCTACGCTGGT 2184–2188 1.000 83.9
psbM-trnD_p5 psbM-trnD TTTCCCTCTCCCTCGTAGTG AAGTATGCCCCCATCGTCTA 2379–2383 1.000 83.4

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
Aethionema arabicum NC_034367.1 154234 View on NCBI ↗
Aethionema cordifolium NC_009265.1 154168 View on NCBI ↗
Aethionema grandiflorum NC_009266.1 154243 View on NCBI ↗
Aethionema saxatile NC_049587.1 154022 View on NCBI ↗