Markers + reference

Lessonia

4 species · Lessoniaceae · Laminariales

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Species 4
Genome length 130–130 kb
Candidate markers 340
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 340 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rnl SSC 2925 0.0055 0.00 34.1 yes View details
trnS-psaD LSC 199 0.0392 0.91 68.8 yes View details
ilvH LSC 597 0.0148 1.00 53.9 yes View details
psbK-ccsA LSC 328 0.0315 1.00 62.3 yes View details
psaJ-cp74 LSC 158 0.0462 0.94 72.1 yes View details
cp74 LSC 1578 0.0113 1.00 53.6 yes View details
psbA-cbbx LSC 634 0.0203 0.99 61.3 yes View details
rbcR-psbY LSC 415 0.0217 1.00 57.4 yes View details
rnl SSC 2929 0.0037 1.00 55.3 no View details
petF SSC 294 0.0159 1.00 49.1 yes View details
trnT-trnV SSC 293 0.0216 1.00 58.0 yes View details
trnY-cp30 LSC 62 0.0618 1.00 80.1 yes View details
petF-rpl12 SSC 153 0.0545 1.00 73.2 yes View details
trnH-trnT SSC 81 0.0370 1.00 70.8 yes View details
psbN-psbT SSC 54 0.0463 1.00 70.4 yes View details
trnS-trnM LSC 7 0.1667 1.00 70.2 yes View details
thiG-trnG LSC 133 0.0397 0.98 69.2 yes View details
ftsH-psbH SSC 90 0.0389 1.00 66.1 yes View details
psaM-chlI LSC 114 0.0322 1.00 65.4 yes View details
rps18-rpl33 LSC 10 0.0500 1.00 62.6 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rnl_p1 rnl TAAACACCAAGACAATATTTTT GGAGTTAATTTTTAAAGCTAGAA 3000 0.250 10.0
rnl_p2 rnl TAAACACCAAGACAATATTTTT GGAGTTAATTTTTAAAGCTAGAAA 3000 0.250 10.0
rnl_p3 rnl TAAACACCAAGACAATATTTTT GGAGTTAATTTTTAAAGCTAGAAAT 3000 0.250 10.0
rnl_p4 rnl TAAACACCAAGACAATATTTTT GGAGTTAATTTTTAAAGCTAGAAATA 3000 0.250 10.0
rnl_p5 rnl TAAACACCAAGACAATATTTTT GGAGTTAATTTTTAAAGCTAGAAATAA 3000 0.250 10.0
psaM-chlI_p1 psaM-chlI GGTTCCAAGCCTGTAAAGCT CGTAATTCCCCTTCTTCCGG 1174–1188 1.000 80.8
psaM-chlI_p2 psaM-chlI GGTTCCAAGCCTGTAAAGCT TTCGGCATGCATTCCAAAAC 1211–1225 1.000 80.6
psaM-chlI_p3 psaM-chlI GGTTCCAAGCCTGTAAAGCT TTCTCGTTCGACTGTGTTCC 1103–1117 1.000 80.3
psaM-chlI_p4 psaM-chlI GGTTCCAAGCCTGTAAAGCT CCTTCTCGTTCGACTGTGTT 1105–1119 1.000 80.3
psaM-chlI_p5 psaM-chlI GGTTCCAAGCCTGTAAAGCT TGTGCTGGGTGTCGTATAGA 1129–1143 1.000 80.1
trnS-psaD_p1 trnS-psaD ACGCGTAAACGTTCATCTGA ACCCAGCTTCTATAAAATGGA 273–285 1.000 49.6
trnS-psaD_p2 trnS-psaD AAATCAGACGCAATCGACCA ACCCAGCTTCTATAAAATGGA 249–261 1.000 49.6
trnS-psaD_p3 trnS-psaD ATCAGACGCAATCGACCATC ACCCAGCTTCTATAAAATGGA 247–259 1.000 49.2
trnS-psaD_p4 trnS-psaD ACGCGTAAACGTTCATCTGA CCTAACCCAGCTTCTATAAAATGG 277–289 1.000 48.2
trnS-psaD_p5 trnS-psaD ACGCGTAAACGTTCATCTGA ACCCAGCTTCTATAAAATGGAA 273–285 1.000 48.2
trnY-cp30_p1 trnY-cp30 AAGGGGGCGGATTGTAAATC GTCGAGATGGTCCGGATTTT 196 1.000 79.8
trnY-cp30_p2 trnY-cp30 AATCCGCTGGTTTTCCTACG GTCGAGATGGTCCGGATTTT 180 1.000 78.5
trnY-cp30_p3 trnY-cp30 TCATGGACTGTTAGGGTCGA GTCGAGATGGTCCGGATTTT 230 1.000 78.1
trnY-cp30_p4 trnY-cp30 GCTGGTTTTCCTACGTTGGT GTCGAGATGGTCCGGATTTT 175 1.000 77.5
trnY-cp30_p5 trnY-cp30 GTTAAAGGGGGCGGATTGTA GTCGAGATGGTCCGGATTTT 200 1.000 76.9
thiG-trnG_p1 thiG-trnG CTGGGAGATCCAATTCCTGC ATCGCTGGTTCTGTTAACCC 1259–1271 1.000 81.5
thiG-trnG_p2 thiG-trnG CAGTCCCAACAATAAGGCGA ATCGCTGGTTCTGTTAACCC 724–736 1.000 81.5
thiG-trnG_p3 thiG-trnG CGGGTCAGGGAGAAGATAGT ATCGCTGGTTCTGTTAACCC 1023–1035 1.000 81.4
thiG-trnG_p4 thiG-trnG TTGTCTACCTGCTTGCACAG ATCGCTGGTTCTGTTAACCC 1383–1395 1.000 80.7
thiG-trnG_p5 thiG-trnG ATTCTCGGCCTAAAAACGCT ATCGCTGGTTCTGTTAACCC 952 0.250 48.2
trnS-trnM_p1 trnS-trnM TCGAACCCTCGGTACAAAGA GACTCATAAGCCCTTGGTCG 126 1.000 77.8
trnS-trnM_p2 trnS-trnM TCGAACCCTCGGTACAAAGA AGTAGGGGACTCATAAGCCC 133 1.000 77.3
trnS-trnM_p3 trnS-trnM TCGAACCCTCGGTACAAAGA GTAGGGGACTCATAAGCCCT 132 1.000 77.3
trnS-trnM_p4 trnS-trnM CGAACCCTCGGTACAAAGAA GACTCATAAGCCCTTGGTCG 125 1.000 77.3
trnS-trnM_p5 trnS-trnM TTCGAACCCTCGGTACAAAG GACTCATAAGCCCTTGGTCG 127 1.000 77.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Lessonia flavicans NC_056288.1 130085 View on NCBI ↗
Lessonia nigrescens NC_084366.1 130317 View on NCBI ↗
Lessonia spicata NC_044182.1 130305 View on NCBI ↗
Lessonia trabeculata PV367283.1 130389 View on NCBI ↗