Markers + reference

Ecklonia

3 species · Lessoniaceae · Laminariales

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Species 3
Genome length 131–131 kb
Candidate markers 354
Primer pairs 105

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 354 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps20 LSC 306 0.0196 1.00 52.4 yes View details
secA LSC 2634 0.0086 1.00 46.9 yes View details
trnM-trnD LSC 157 0.0170 1.00 56.5 yes View details
ycf34 LSC 285 0.0140 1.00 48.1 yes View details
rbcL-rbcS LSC 280 0.0238 1.00 53.2 yes View details
cp74 LSC 1569 0.0127 1.00 52.0 yes View details
psbA-cbbx LSC 711 0.0206 1.00 61.2 yes View details
psaL LSC 438 0.0183 1.00 52.1 yes View details
psbY-rpl32 LSC 339 0.0308 0.96 66.5 yes View details
petF SSC 294 0.0510 1.00 75.7 yes View details
ycf16-trnN SSC 271 0.0517 1.00 75.8 yes View details
psaL-rbcR LSC 52 0.0641 1.00 75.8 yes View details
ftsH-psbH SSC 112 0.0833 1.00 75.6 yes View details
dnaK-trnS LSC 134 0.0498 1.00 72.5 yes View details
chlN-psaF LSC 124 0.0437 0.98 70.8 yes View details
rpoC2-rpoC1 LSC 13 0.0513 1.00 70.6 yes View details
thiG-trnG LSC 129 0.0362 1.00 67.5 yes View details
rbcS-trnR LSC 368 0.0199 1.00 66.2 yes View details
psaJ-cp74 LSC 191 0.0392 0.89 65.7 yes View details
rpl20-ilvH LSC 87 0.0230 1.00 65.1 yes View details
rps14-petG LSC 47 0.0284 1.00 64.6 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rpoC2-rpoC1_p1 rpoC2-rpoC1 GGCAGCTTTTCTCTGACCAT TCGAACTACACCTGGTCGTA 179 1.000 77.6
rpoC2-rpoC1_p2 rpoC2-rpoC1 GGCAGCTTTTCTCTGACCAT ATTCGAACTACACCTGGTCG 181 1.000 73.9
rpoC2-rpoC1_p3 rpoC2-rpoC1 GGCAGCTTTTCTCTGACCAT TTCGAACTACACCTGGTCGT 180 1.000 73.7
rpoC2-rpoC1_p4 rpoC2-rpoC1 TAGGCAGCTTTTCTCTGACC TCGAACTACACCTGGTCGTA 181 1.000 72.8
rpoC2-rpoC1_p5 rpoC2-rpoC1 GGCAGCTTTTCTCTGACCATA TCGAACTACACCTGGTCGTA 179 1.000 70.9
rps20_p1 rps20 TATCGAACCGTTCTTCACCG TGGTCGATTGCGTCTGATTT 901–908 1.000 79.8
rps20_p2 rps20 TATCGAACCGTTCTTCACCG GATGGTCGATTGCGTCTGAT 903–910 1.000 79.4
rps20_p3 rps20 AACCGTTCTTCACCGTTTCT TGGTCGATTGCGTCTGATTT 896–903 1.000 79.3
rps20_p4 rps20 ACCGTTCTTCACCGTTTCTT TGGTCGATTGCGTCTGATTT 895–902 1.000 79.3
rps20_p5 rps20 TATCGAACCGTTCTTCACCG AGAACAATGCCTTGCCCTAG 1327–1334 1.000 79.1
secA_p1 secA GCACGAAAACCAGAAACAGC TTACACACTATTAAAGAATCACTT 2999 0.667 27.3
secA_p2 secA GCACGAAAACCAGAAACAGC TTTACACACTATTAAAGAATCACT 3000 0.667 27.3
secA_p3 secA AGCACGAAAACCAGAAACAG TTACACACTATTAAAGAATCACTT 3000 0.667 27.3
secA_p4 secA CACGAAAACCAGAAACAGCT TTACACACTATTAAAGAATCACTT 2998 0.667 27.3
secA_p5 secA CACGAAAACCAGAAACAGCT TTTACACACTATTAAAGAATCACT 2999 0.667 27.3
thiG-trnG_p1 thiG-trnG CAGTCCCAACAATAAGGCGA AACTTGCGAGTGTAGCTCAG 273 1.000 80.6
thiG-trnG_p2 thiG-trnG GTCCCAACAATAAGGCGAGA AACTTGCGAGTGTAGCTCAG 271 1.000 78.3
thiG-trnG_p3 thiG-trnG AGTCCCAACAATAAGGCGAG AACTTGCGAGTGTAGCTCAG 272 1.000 78.3
thiG-trnG_p4 thiG-trnG TCCAGTCCCAACAATAAGGC AACTTGCGAGTGTAGCTCAG 275 1.000 77.4
thiG-trnG_p5 thiG-trnG CAGTCCCAACAATAAGGCGA CTTGCGAGTGTAGCTCAGTG 271 1.000 76.0
dnaK-trnS_p1 dnaK-trnS CTCCAAATATTTTACTTATATTAGCCA TGAGATGGCTGAGTGGCTTA 249–250 1.000 43.5
dnaK-trnS_p2 dnaK-trnS CTCCAAATATTTTACTTATATTAGCCA TTAGGGTGAGATGGCTGAGT 255–256 1.000 43.4
dnaK-trnS_p3 dnaK-trnS ACTCCAAATATTTTACTTATATTAGCC TTAGGGTGAGATGGCTGAGT 256–257 1.000 43.4
dnaK-trnS_p4 dnaK-trnS CTCCAAATATTTTACTTATATTAGCCA GGTTCAAATCCAGCCAGAGT 280–281 1.000 43.1
dnaK-trnS_p5 dnaK-trnS ACTCCAAATATTTTACTTATATTAGCC GGTTCAAATCCAGCCAGAGT 281–282 1.000 43.1
trnM-trnD_p1 trnM-trnD CGACCAAGGGCTTATGAGTC GAATTTCGGGATTGACGGGA 287 1.000 80.4
trnM-trnD_p2 trnM-trnD GGGCTTATGAGTCCCCTACT GAATTTCGGGATTGACGGGA 280 1.000 80.0
trnM-trnD_p3 trnM-trnD TCTGGCTGGATTTGAACCTG GAATTTCGGGATTGACGGGA 307 1.000 79.1
trnM-trnD_p4 trnM-trnD ACTCTGGCTGGATTTGAACC GAATTTCGGGATTGACGGGA 309 1.000 79.1
trnM-trnD_p5 trnM-trnD ACTCAGCCATCTCACCCTAA GAATTTCGGGATTGACGGGA 334 1.000 78.7

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
Ecklonia arborea MZ156038.1 130965 View on NCBI ↗
Ecklonia radiata NC_070408.1 130955 View on NCBI ↗
Ecklonia radicosa MZ156040.1 130860 View on NCBI ↗