Markers + reference

Draba

9 species · Brassicaceae · Brassicales

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Species 9
Genome length 153–154 kb
Candidate markers 268
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 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-CAC-psbA LSC 331 0.0533 0.98 77.8 yes View details
trnK-AAA-trnQ-CAA LSC 1462 0.0216 1.00 73.0 yes View details
rpoB-trnC-UGC LSC 942 0.0209 1.00 64.7 yes View details
trnC-UGC-petN LSC 630 0.0168 0.97 67.6 yes View details
psbM-trnD-GAC LSC 1038 0.0231 0.99 69.5 yes View details
trnE-GAA-trnT-ACC LSC 691 0.0267 0.99 70.7 yes View details
petA-psbJ LSC 856 0.0237 0.99 68.4 yes View details
rpl16 LSC 1529 0.0142 1.00 56.0 yes View details
ycf1 IRb 1035 0.0026 1.00 39.1 no View details
ndhF-rpl32 SSC 837 0.0323 0.92 75.7 yes View details
rpl32-trnL-CUA SSC 454 0.0369 1.00 74.8 yes View details
ycf1 SSC 5343 0.0138 1.00 51.3 yes View details
atpH-atpI LSC 445 0.0234 0.99 76.1 yes View details
trnF-UUC-ndhJ LSC 621 0.0225 1.00 70.5 yes View details
trnR-AGA-atpA LSC 268 0.0366 1.00 68.7 yes View details
psbK-psbI LSC 442 0.0258 0.96 68.4 yes View details
ndhC-trnV-GUA LSC 833 0.0176 1.00 67.7 yes View details
trnS-AGC-trnG-GGA LSC 632 0.0207 1.00 66.1 yes View details
psaA-ycf3 LSC 738 0.0145 0.99 65.3 yes View details
trnM-AUG-atpE LSC 128 0.0309 0.99 64.1 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-CAC-psbA_p1 trnH-CAC-psbA AATCCACTTGGCTACATCCG GCTGTTGAGGCTCCATCTAC 382–451 1.000 86.8
trnH-CAC-psbA_p2 trnH-CAC-psbA AATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 397–466 1.000 86.6
trnH-CAC-psbA_p3 trnH-CAC-psbA AATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 400–469 1.000 86.6
trnH-CAC-psbA_p4 trnH-CAC-psbA AATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 449–518 1.000 84.3
trnH-CAC-psbA_p5 trnH-CAC-psbA AATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 450–519 1.000 83.8
trnK-AAA-trnQ-CAA_p1 trnK-AAA-trnQ-CAA AAAGCCGAGTACTCTACCGT GAGGTTCGAATCCTTCCGTC 977–1564 1.000 87.6
trnK-AAA-trnQ-CAA_p2 trnK-AAA-trnQ-CAA AAGCCGAGTACTCTACCGTT GAGGTTCGAATCCTTCCGTC 976–1563 1.000 87.6
trnK-AAA-trnQ-CAA_p3 trnK-AAA-trnQ-CAA TACCGTTGAGTTAGCAACCC GAGGTTCGAATCCTTCCGTC 963–1550 1.000 85.3
trnK-AAA-trnQ-CAA_p4 trnK-AAA-trnQ-CAA AGTCGCACTTAAAAGCCGAG GAGGTTCGAATCCTTCCGTC 988–1575 1.000 84.3
trnK-AAA-trnQ-CAA_p5 trnK-AAA-trnQ-CAA TCGCACTTAAAAGCCGAGTA GAGGTTCGAATCCTTCCGTC 986–1573 1.000 83.1
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCAGCTGTAAG ACAAAAAGTTTGAGAGTAAGCA 475–495 1.000 48.7
psbK-psbI_p2 psbK-psbI TGGCAAGCAGCTGTAAGTTT ACAAAAAGTTTGAGAGTAAGCA 472–492 1.000 48.7
psbK-psbI_p3 psbK-psbI TTGGCAAGCAGCTGTAAGTT ACAAAAAGTTTGAGAGTAAGCA 473–493 1.000 48.7
psbK-psbI_p4 psbK-psbI TTTGGCAAGCAGCTGTAAGT ACAAAAAGTTTGAGAGTAAGCA 474–494 1.000 48.7
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCAGCTGTAAG ACAAAAAGTTTGAGAGTAAGCAT 475–495 1.000 48.7
trnS-AGC-trnG-GGA_p1 trnS-AGC-trnG-GGA CTTTAGTCCGCTCAGCCATC AATCAAACCGAGAGACCCTT 734–818 1.000 68.9
trnS-AGC-trnG-GGA_p2 trnS-AGC-trnG-GGA CTTTAGTCCGCTCAGCCATC ATCAAACCGAGAGACCCTTT 733–817 1.000 68.9
trnS-AGC-trnG-GGA_p3 trnS-AGC-trnG-GGA GCAATCCAACGCTTTAGTCC AATCAAACCGAGAGACCCTT 745–829 1.000 67.8
trnS-AGC-trnG-GGA_p4 trnS-AGC-trnG-GGA GCAATCCAACGCTTTAGTCC ATCAAACCGAGAGACCCTTT 744–828 1.000 67.8
trnS-AGC-trnG-GGA_p5 trnS-AGC-trnG-GGA CTTTAGTCCGCTCAGCCATC AATCAAACCGAGAGACCCTTT 734–818 1.000 66.9
trnR-AGA-atpA_p1 trnR-AGA-atpA AGCCTTCCAAGCTAACGATG AGCCCCTCTCACAGTAGAAG 778–852 1.000 86.4
trnR-AGA-atpA_p2 trnR-AGA-atpA AGCCTTCCAAGCTAACGATG TGACTGCCTTACCAATCGTG 1124 0.111 43.5
trnR-AGA-atpA_p3 trnR-AGA-atpA TTCTGTGAAAGCACCCAGAC TGACTGCCTTACCAATCGTG 1320 0.111 43.4
trnR-AGA-atpA_p4 trnR-AGA-atpA ACCCTTAGCCTTCCAAGCTA TGACTGCCTTACCAATCGTG 1130 0.111 43.4
trnR-AGA-atpA_p5 trnR-AGA-atpA AAACCCTTAGCCTTCCAAGC TGACTGCCTTACCAATCGTG 1132 0.111 43.1
atpH-atpI_p1 atpH-atpI GTCCAATAGAAGCAAGCCCA TACAAGCGGGATTCAAGCTC 594–627 1.000 84.0
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT TACAAGCGGGATTCAAGCTC 612–645 1.000 83.9
atpH-atpI_p3 atpH-atpI GCTGTACCTTGACCAACTCC TACAAGCGGGATTCAAGCTC 616–649 1.000 83.3
atpH-atpI_p4 atpH-atpI TACCTTGACCAACTCCAGGT TTTTTGCCACTTTAGCTGCG 589–622 1.000 83.3
atpH-atpI_p5 atpH-atpI GTCCAATAGAAGCAAGCCCA TTTTTGCCACTTTAGCTGCG 571–604 1.000 83.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Draba aizoides NC_049623.1 152795 View on NCBI ↗
Draba alpina NC_081116.1 152549 View on NCBI ↗
Draba fladnizensis NC_081117.1 153853 View on NCBI ↗
Draba incana NC_049627.1 153588 View on NCBI ↗
Draba melanopus NC_081118.1 153799 View on NCBI ↗
Draba nemorosa NC_009272.1 153289 View on NCBI ↗
Draba oligosperma NC_049629.1 153566 View on NCBI ↗
Draba oreades NC_037760.1 153503 View on NCBI ↗
Draba rockii NC_081119.1 153930 View on NCBI ↗