Markers + reference

Cakile

12 species · Brassicaceae · Brassicales

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Species 12
Genome length 153–154 kb
Candidate markers 269
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 690 0.0036 1.00 59.2 yes View details
rps16-trnQ-UUG LSC 453 0.0042 1.00 50.8 yes View details
rpoB-trnC-GCA LSC 1089 0.0033 1.00 47.9 yes View details
trnT-GGU-psbD LSC 1148 0.0023 1.00 52.6 yes View details
trnL-UAA-trnF-GAA LSC 686 0.0061 0.89 53.6 yes View details
psbE-petL LSC 1363 0.0022 1.00 53.5 yes View details
trnP-GGG-psaJ LSC 334 0.0043 1.00 30.9 yes View details
ycf1 SSC 1029 0.0008 1.00 43.5 no View details
ndhF-rpl32 SSC 789 0.0024 1.00 48.3 yes View details
rpl32-trnL-UAG SSC 616 0.0040 1.00 51.8 yes View details
ycf1 SSC 5313 0.0016 1.00 47.7 yes View details
trnS-GCU-trnG LSC 570 0.0031 1.00 59.1 yes View details
ycf3 LSC 2037 0.0009 1.00 58.6 yes View details
ccsA-ndhD SSC 208 0.0056 1.00 49.8 yes View details
ndhC-trnV-UAC LSC 883 0.0011 1.00 49.2 yes View details
petA-psbJ LSC 981 0.0007 1.00 48.8 yes View details
rpl16 LSC 1507 0.0012 0.99 48.5 yes View details
psbM-trnD-GUC LSC 1012 0.0022 1.00 48.2 yes View details
ycf4-cemA LSC 473 0.0032 1.00 48.2 yes View details
atpB-rbcL LSC 782 0.0016 1.00 47.9 yes View details
psbZ-trnG-UCC LSC 499 0.0025 1.00 47.4 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TAAAAAGGGCGCTCAACCAA 398–830 1.000 78.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTAAAAAGGGCGCTCAACCA 399–831 1.000 78.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TAAAAAGGGCGCTCAACCAA 397–829 1.000 78.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTAAAAAGGGCGCTCAACCA 398–830 1.000 78.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTTAAAAAGGGCGCTCAACC 399–831 1.000 77.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 522–1966 1.000 79.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 533–1967 1.000 79.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ATAAAAGGCGGCGGATCAAA GAGGTTCGAATCCTTCCGTC 567–1967 1.000 78.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAGCAGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 543–1966 1.000 77.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCCACAGCAGATCATGTCCT GAGGTTCGAATCCTTCCGTC 544–1967 1.000 77.3
trnS-GCU-trnG_p1 trnS-GCU-trnG CCAACGCTTTAGTCCACTCA AATCAAACCGAGAGACCCTT 191–780 1.000 68.4
trnS-GCU-trnG_p2 trnS-GCU-trnG CCAACGCTTTAGTCCACTCA ATCAAACCGAGAGACCCTTT 191–779 1.000 68.4
trnS-GCU-trnG_p3 trnS-GCU-trnG AACGCTTTAGTCCACTCAGC AATCAAACCGAGAGACCCTT 189–778 1.000 68.1
trnS-GCU-trnG_p4 trnS-GCU-trnG AACGCTTTAGTCCACTCAGC ATCAAACCGAGAGACCCTTT 189–777 1.000 68.1
trnS-GCU-trnG_p5 trnS-GCU-trnG CCAACGCTTTAGTCCACTCA AATCAAACCGAGAGACCCTTT 192–780 1.000 66.4
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GTTCCCTCTTTTCCATCCCC CCGGATTTGAACTGGGGAAA 80–1178 1.000 79.4
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GTTCCCTCTTTTCCATCCCC AAAAGGATTTGCAGTCCCCC 80–1160 1.000 77.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GTTCCCTCTTTTCCATCCCC TTCAAGTCTCCTGTTGAGGC 80–1203 1.000 75.6
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TGTTCCCTCTTTTCCATCCC CCGGATTTGAACTGGGGAAA 80–1179 1.000 73.4
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TCTTTTCCATCCCCGAGCAT CCGGATTTGAACTGGGGAAA 80–1172 1.000 71.9
psbM-trnD-GUC_p1 psbM-trnD-GUC AGGAACGAGAATGAAGAGTGC TACCCGCTTGATTTCCATGG 80–1159 1.000 72.0
psbM-trnD-GUC_p2 psbM-trnD-GUC ACGAGAATGAAGAGTGCAGT TACCCGCTTGATTTCCATGG 80–1155 1.000 71.3
psbM-trnD-GUC_p3 psbM-trnD-GUC AGGAACGAGAATGAAGAGTGC CCGCTTGATTTCCATGGGAT 80–1156 1.000 70.0
psbM-trnD-GUC_p4 psbM-trnD-GUC AGGAACGAGAATGAAGAGTGC GCTACCCGCTTGATTTCCAT 80–1161 1.000 69.8
psbM-trnD-GUC_p5 psbM-trnD-GUC GGAACGAGAATGAAGAGTGCA TACCCGCTTGATTTCCATGG 80–1158 1.000 69.8
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACCTACAAAAACGAAGCGGT 80–1322 1.000 80.8
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA ACCTACAAAAACGAAGCGGT 80–1325 1.000 80.5
trnT-GGU-psbD_p3 trnT-GGU-psbD ACGGCCCTTTTAACTCAGTG ACCTACAAAAACGAAGCGGT 80–1339 1.000 80.5
trnT-GGU-psbD_p4 trnT-GGU-psbD GACGGCCCTTTTAACTCAGT ACCTACAAAAACGAAGCGGT 80–1340 1.000 79.7
trnT-GGU-psbD_p5 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA ACCTACAAAAACGAAGCGGT 80–1299 1.000 79.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (12)

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

Species Accession Length (bp) Link
Cakile arabica NC_030775.1 153378 View on NCBI ↗
Cakile arctica NC_056081.1 153732 View on NCBI ↗
Cakile edentula NC_056082.1 153655 View on NCBI ↗
Cakile edentula subsp. harperi NC_056083.1 153651 View on NCBI ↗
Cakile edentula subsp. lacustris NC_056084.1 153652 View on NCBI ↗
Cakile lanceolata NC_056085.1 153656 View on NCBI ↗
Cakile lanceolata subsp. fusiformis NC_056087.1 153460 View on NCBI ↗
Cakile lanceolata subsp. lanceolata NC_056086.1 153463 View on NCBI ↗
Cakile maritima NC_049614.1 153587 View on NCBI ↗
Cakile maritima subsp. baltica NC_056090.1 153698 View on NCBI ↗
Cakile maritima subsp. euxina NC_056089.1 153492 View on NCBI ↗
Cakile maritima subsp. islandica NC_056088.1 153658 View on NCBI ↗