Markers + reference

Eutrema

8 species · Brassicaceae · Brassicales

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Species 8
Genome length 153–154 kb
Candidate markers 247
Primer pairs 115

Genome-wide nucleotide diversity

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

Candidate markers

14 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 247 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
matK-rps16 LSC 1453 0.0230 0.96 65.5 yes View details
psbK-psbI LSC 436 0.0453 0.99 85.9 yes View details
trnS-GCT-trnR-TCT LSC 1506 0.0265 0.96 66.1 yes View details
rpoB-trnC-GCA LSC 1112 0.0314 1.00 74.0 yes View details
trnE-TTC-trnT-GGT LSC 817 0.0324 0.99 79.4 yes View details
trnT-TGT-trnL-CAA LSC 1543 0.0212 0.95 64.3 yes View details
ndhC-trnM-CAT LSC 1756 0.0228 0.99 71.8 yes View details
petA-psbJ LSC 943 0.0291 1.00 66.4 yes View details
psaJ-rpl33 LSC 435 0.0457 0.99 72.5 yes View details
rpl36-rps8 LSC 466 0.0437 1.00 82.3 yes View details
ycf1 IRb 1035 0.0023 1.00 35.7 no View details
ndhF-rpl32 SSC 689 0.0345 0.99 67.4 yes View details
rpl32-trnL-TAG SSC 737 0.0442 0.94 80.6 yes View details
ycf1 SSC 5313 0.0211 1.00 56.0 yes View details
trnR-TCT-atpA LSC 305 0.0468 0.99 79.1 yes View details
trnH-GTG-psbA LSC 300 0.0595 0.94 78.4 yes View details
ccsA-ndhD SSC 226 0.0491 0.96 72.0 yes View details
petN-psbM LSC 547 0.0288 0.99 71.3 yes View details
trnF-GAA-ndhJ LSC 481 0.0321 0.97 71.3 yes View details
psbM-trnD-GTC LSC 1031 0.0273 0.99 71.1 yes View details
trnP-TGG-psaJ LSC 338 0.0302 1.00 70.2 yes View details
rpl20-rps12 LSC 784 0.0180 0.96 67.6 yes View details
psbE-petL LSC 1358 0.0285 1.00 66.8 yes View details
petG-trnW-CCA LSC 129 0.0543 1.00 66.8 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 115 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GTG-psbA_p1 trnH-GTG-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 329–374 1.000 90.4
trnH-GTG-psbA_p2 trnH-GTG-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 332–377 1.000 90.3
trnH-GTG-psbA_p3 trnH-GTG-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 330–375 1.000 90.2
trnH-GTG-psbA_p4 trnH-GTG-psbA ACTGCCTTAATCCACTTGGC TTCCCTCTAGACCTAGCTGC 333–378 1.000 90.1
trnH-GTG-psbA_p5 trnH-GTG-psbA AATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 322–367 1.000 88.8
matK-rps16_p1 matK-rps16 CGAGCCCCATCGAACTTTAA CCCAATGAGCCGTTTATCGA 1525–1774 0.875 82.5
matK-rps16_p2 matK-rps16 CGAGCCCCATCGAACTTTAA TCCCAATGAGCCGTTTATCG 1526–1775 0.875 82.5
matK-rps16_p3 matK-rps16 CGAGCCCCATCGAACTTTAA ATGCGTGAATCAAGCGTTTG 2070–2316 0.875 82.4
matK-rps16_p4 matK-rps16 CGAGCCCCATCGAACTTTAA CATGCGTGAATCAAGCGTTT 2071–2317 0.875 82.4
matK-rps16_p5 matK-rps16 CGAGCCCCATCGAACTTTAA TCGATCCCGAAGAGAAGGAA 1488–1737 0.875 81.9
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCAGCTGTAAG TTCTTCACGTCCCGGATTAC 569–587 1.000 83.0
psbK-psbI_p2 psbK-psbI TGGCAAGCAGCTGTAAGTTT TTCTTCACGTCCCGGATTAC 566–584 1.000 81.1
psbK-psbI_p3 psbK-psbI TTGGCAAGCAGCTGTAAGTT TTCTTCACGTCCCGGATTAC 567–585 1.000 81.0
psbK-psbI_p4 psbK-psbI TTTGGCAAGCAGCTGTAAGT TTCTTCACGTCCCGGATTAC 568–586 1.000 81.0
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCAGCTGTAAG CCGGATTACGTCCTGGATCA 558–576 1.000 80.8
trnS-GCT-trnR-TCT_p1 trnS-GCT-trnR-TCT GCTTTAGTCCACTCAGCCAT TGATATTGCGTCCAATAGGA 1610–1765 1.000 52.8
trnS-GCT-trnR-TCT_p2 trnS-GCT-trnR-TCT AGTCCACTCAGCCATCTCTC TGATATTGCGTCCAATAGGA 1605–1760 1.000 51.9
trnS-GCT-trnR-TCT_p3 trnS-GCT-trnR-TCT GCTTTAGTCCACTCAGCCAT TTGATATTGCGTCCAATAGGA 1611–1766 1.000 51.8
trnS-GCT-trnR-TCT_p4 trnS-GCT-trnR-TCT AGTCCACTCAGCCATCTCTC TTGATATTGCGTCCAATAGGA 1606–1761 1.000 50.9
trnS-GCT-trnR-TCT_p5 trnS-GCT-trnR-TCT GCTTTAGTCCACTCAGCCAT AGGTTTAGAAGACCTATGTCCT 1574–1729 1.000 50.5
trnR-TCT-atpA_p1 trnR-TCT-atpA GCGAAAAGCGTCCATTGTC TCAAGAGCAACTGGAACGTT 422–454 1.000 77.2
trnR-TCT-atpA_p2 trnR-TCT-atpA GCGAAAAGCGTCCATTGTC TTCAAGAGCAACTGGAACGT 423–455 1.000 77.2
trnR-TCT-atpA_p3 trnR-TCT-atpA GCGAAAAGCGTCCATTGTCT TCAAGAGCAACTGGAACGTT 422–454 1.000 73.3
trnR-TCT-atpA_p4 trnR-TCT-atpA GCGAAAAGCGTCCATTGTCT TTCAAGAGCAACTGGAACGT 423–455 1.000 73.3
trnR-TCT-atpA_p5 trnR-TCT-atpA GGTTCAAATCCTATTGGACGC TCAAGAGCAACTGGAACGTT 365–397 1.000 72.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CACGAGCCCATATTCTTGCT ATGTCTGTGCATTCCGAGAC 1969–2001 0.750 74.6
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ATTGGATCCCCACCTACACA ATGTCTGTGCATTCCGAGAC 2168–2200 0.750 74.4
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ATTGGATCCCCACCTACACA CTCCAAGGAATCTGCCTCAC 2283 0.375 54.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ATTGGATCCCCACCTACACA AGTCTCCAAGGAATCTGCCT 2286 0.375 54.8
rpoB-trnC-GCA_p5 rpoB-trnC-GCA ATTGGATCCCCACCTACACA TCTCCAAGGAATCTGCCTCA 2284 0.375 54.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Eutrema botschantzevii NC_029379.1 153279 View on NCBI ↗
Eutrema deltoideum NC_073149.1 154051 View on NCBI ↗
Eutrema halophilum NC_029378.1 153311 View on NCBI ↗
Eutrema heterophyllum NC_028728.1 153876 View on NCBI ↗
Eutrema nepalense NC_081126.1 153647 View on NCBI ↗
Eutrema salsugineum NC_028170.1 153407 View on NCBI ↗
Eutrema tenue LC500907.1 153875 View on NCBI ↗
Eutrema yunnanense NC_028727.1 153948 View on NCBI ↗