Markers + reference

Dontostemon

3 species · Brassicaceae · Brassicales

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Species 3
Genome length 154–155 kb
Candidate markers 270
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-AAA-rps16 LSC 641 0.0349 1.00 69.3 yes View details
psbK-psbI LSC 424 0.0489 1.00 78.1 yes View details
trnT-ACC-psbD LSC 1242 0.0301 0.98 75.9 yes View details
trnL-UUA-trnF-UUC LSC 341 0.0342 1.00 75.7 yes View details
ycf4-cemA LSC 422 0.0483 1.00 71.7 yes View details
rpl16 LSC 1561 0.0321 0.99 69.9 yes View details
ycf1 IRb 1050 0.0051 0.99 52.0 no View details
ndhF-rpl32 SSC 865 0.0518 0.98 81.2 yes View details
rpl32-trnL-CUA SSC 847 0.0921 0.98 87.5 yes View details
rps15-ycf1 SSC 321 0.0469 1.00 68.3 yes View details
ycf1 SSC 5373 0.0251 1.00 54.7 yes View details
ccsA-ndhD SSC 249 0.0601 0.98 78.9 yes View details
psbC-trnS-UCA LSC 192 0.0358 0.97 77.2 yes View details
trnF-UUC-ndhJ LSC 591 0.0319 0.99 76.3 yes View details
atpH-atpI LSC 491 0.0279 1.00 75.3 yes View details
rps16-trnQ-CAA LSC 472 0.0434 0.94 74.7 yes View details
trnP-CCA-psaJ LSC 363 0.0425 0.99 74.4 yes View details
psbG-ndhC LSC 84 0.0615 0.77 72.5 yes View details
trnR-AGA-atpA LSC 315 0.0472 0.99 72.2 yes View details
psaI-ycf4 LSC 415 0.0289 1.00 72.2 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
trnK-AAA-rps16_p1 trnK-AAA-rps16 CCTTTCAGGATCAGTCGTGG CCCAATGAGCCGTTTATCGA 1002–1047 1.000 84.9
trnK-AAA-rps16_p2 trnK-AAA-rps16 CCTTTCAGGATCAGTCGTGG TCCCAATGAGCCGTTTATCG 1003–1048 1.000 84.9
trnK-AAA-rps16_p3 trnK-AAA-rps16 CCAAACGGACTGGGGTTAAA CCCAATGAGCCGTTTATCGA 1343–1396 1.000 84.4
trnK-AAA-rps16_p4 trnK-AAA-rps16 CCAAACGGACTGGGGTTAAA TCCCAATGAGCCGTTTATCG 1344–1397 1.000 84.4
trnK-AAA-rps16_p5 trnK-AAA-rps16 AGCTAGACTGCTAACCGGAT CCCAATGAGCCGTTTATCGA 1523–1580 1.000 83.6
rps16-trnQ-CAA_p1 rps16-trnQ-CAA AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 440–545 1.000 86.7
rps16-trnQ-CAA_p2 rps16-trnQ-CAA AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 444–549 1.000 82.0
rps16-trnQ-CAA_p3 rps16-trnQ-CAA AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 470–575 1.000 81.7
rps16-trnQ-CAA_p4 rps16-trnQ-CAA CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 432–537 1.000 81.6
rps16-trnQ-CAA_p5 rps16-trnQ-CAA AGTCGCACGTTGCTTTCTAC GAGGTTCGAATCCTTCCGTC 439–544 1.000 81.0
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCAGCTGTAAG TTCTTCACGTCCCGGATTAC 524–610 1.000 82.1
psbK-psbI_p2 psbK-psbI TGGCAAGCAGCTGTAAGTTT TTCTTCACGTCCCGGATTAC 521–607 1.000 80.1
psbK-psbI_p3 psbK-psbI TTGGCAAGCAGCTGTAAGTT TTCTTCACGTCCCGGATTAC 522–608 1.000 80.1
psbK-psbI_p4 psbK-psbI TTTGGCAAGCAGCTGTAAGT TTCTTCACGTCCCGGATTAC 523–609 1.000 80.1
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCAGCTGTAAG CCGGATTACGTCCTGGATCA 513–599 1.000 79.7
trnR-AGA-atpA_p1 trnR-AGA-atpA AGCCTTCCAAGCTAACGATG AGGGCCGCTAAATTAAGCTC 1174–1212 1.000 85.5
trnR-AGA-atpA_p2 trnR-AGA-atpA AGCCTTCCAAGCTAACGATG GGGCCGCTAAATTAAGCTCT 1173–1211 1.000 85.5
trnR-AGA-atpA_p3 trnR-AGA-atpA ACCCTTAGCCTTCCAAGCTA AGGGCCGCTAAATTAAGCTC 1180–1218 1.000 85.4
trnR-AGA-atpA_p4 trnR-AGA-atpA ACCCTTAGCCTTCCAAGCTA GGGCCGCTAAATTAAGCTCT 1179–1217 1.000 85.4
trnR-AGA-atpA_p5 trnR-AGA-atpA CGACGTCGACTAAAACCCTT GGGCCGCTAAATTAAGCTCT 1193–1231 1.000 85.2
atpH-atpI_p1 atpH-atpI AACCGAAGCAGCAGAAATCA TACAAGCGGGATTCAAGCTC 586–608 1.000 83.8
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT TACAAGCGGGATTCAAGCTC 644–666 1.000 83.3
atpH-atpI_p3 atpH-atpI GTCCAATAGAAGCAAGCCCA TACAAGCGGGATTCAAGCTC 626–648 1.000 83.3
atpH-atpI_p4 atpH-atpI AACCGAAGCAGCAGAAATCA TTTTTGCCACTTTAGCTGCG 563–585 1.000 83.1
atpH-atpI_p5 atpH-atpI GCTGTACCTTGACCAACTCC TACAAGCGGGATTCAAGCTC 648–670 1.000 82.6
trnT-ACC-psbD_p1 trnT-ACC-psbD GTGGTAGAGTAACGCCATGG ACCTACAAAAACGAAGCGGT 1292–1396 1.000 86.2
trnT-ACC-psbD_p2 trnT-ACC-psbD TCAGTGGTAGAGTAACGCCA ACCTACAAAAACGAAGCGGT 1295–1399 1.000 86.0
trnT-ACC-psbD_p3 trnT-ACC-psbD CCAAGACGGCCCTTTTAACT ACCTACAAAAACGAAGCGGT 1314–1418 1.000 85.9
trnT-ACC-psbD_p4 trnT-ACC-psbD ACGGCCCTTTTAACTCAGTG ACCTACAAAAACGAAGCGGT 1309–1413 1.000 85.8
trnT-ACC-psbD_p5 trnT-ACC-psbD GACGGCCCTTTTAACTCAGT ACCTACAAAAACGAAGCGGT 1310–1414 1.000 85.3

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
Dontostemon elegans NC_081114.1 154535 View on NCBI ↗
Dontostemon glandulosus NC_081115.1 153628 View on NCBI ↗
Dontostemon micranthus NC_049628.1 154464 View on NCBI ↗