Markers + reference

Genlisea

7 species · Lentibulariaceae · Lamiales

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Species 7
Genome length 140–143 kb
Candidate markers 275
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpH-atpI LSC 1060 0.0938 0.95 80.4 yes View details
psaA-ycf3 LSC 967 0.0942 0.94 76.6 yes View details
ndhK LSC 425 0.1664 1.00 71.1 yes View details
ycf1 IRb 375 0.0537 1.00 71.0 no View details
rpl32-trnL-UAG SSC 516 0.1624 0.98 81.1 yes View details
ccsA-psaC SSC 788 0.1531 0.98 83.0 yes View details
psaC-rps15 SSC 958 0.1107 0.98 82.9 yes View details
rps15-ycf1 SSC 382 0.1357 0.96 77.2 yes View details
ycf1 SSC 5187 0.0851 0.99 78.4 yes View details
rpl20-rps12 LSC 812 0.0484 0.99 85.6 yes View details
atpB-rbcL LSC 802 0.0594 0.99 85.5 yes View details
psbE-petL LSC 821 0.0734 0.98 85.4 yes View details
trnS-GCU-trnG-UCC LSC 708 0.0896 0.99 84.4 yes View details
trnT-GGU-psbD LSC 1237 0.0680 1.00 84.3 yes View details
rbcL-accD LSC 721 0.0656 0.99 84.2 yes View details
petA-psbJ LSC 972 0.0721 0.96 83.9 yes View details
rpl16 LSC 1276 0.0650 0.97 83.9 yes View details
trnK-UUU-rps16 LSC 825 0.1015 0.99 83.8 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 GTGTTGTTGAAATCGCTCGG GCAATTGATGTTCGAGCTCG 1770–1795 0.714 74.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTGTTGTTGAAATCGCTCGG TTTTCTTGAGCCGTACGAGG 1866–1891 0.714 74.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 TGAAATCGCTCGGGCTTTAA TTTTCTTGAGCCGTACGAGG 1859–1879 0.286 50.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 TTGAAATCGCTCGGGCTTTA TTTTCTTGAGCCGTACGAGG 1860–1880 0.286 50.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 TGAAATCGCTCGGGCTTTAA GCAATTGATGTTCGAGCTCG 1763–1782 0.286 50.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC ACCACTAAACTATACCCGCT 614–773 1.000 64.4
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC GTCCACTCAGCCATCTCTCC ACCACTAAACTATACCCGCT 615–774 1.000 60.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GTCCACTCAGCCATCTCTC ACCACTAAACTATACCCGCT 615–774 1.000 56.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC TACCACTAAACTATACCCGCT 615–774 1.000 56.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC ACGAATCACACTTTTACCACT 629–788 1.000 55.0
trnG-UCC_p1 trnG-UCC ATTAGCAATCCGGCGCTTTA TTCAGGAGCAAATGGATCGG 1800–1946 0.857 85.6
trnG-UCC_p2 trnG-UCC ATTAGCAATCCGGCGCTTTA ATTGGAACTGGCGCAATTTG 2129–2275 0.857 84.9
trnG-UCC_p3 trnG-UCC TGAGTGTTTTTGGCCACGTA TTCAGGAGCAAATGGATCGG 1341–1400 0.714 76.4
trnG-UCC_p4 trnG-UCC CCACTCAGCCATCTCTCCTA TTCAGGAGCAAATGGATCGG 1863–1924 0.714 75.7
trnG-UCC_p5 trnG-UCC TGAGTGTTTTTGGCCACGTA ATTGGAACTGGCGCAATTTG 1670–1729 0.714 74.7
atpH-atpI_p1 atpH-atpI GGATGGCCAGTAGTCCAAAG CACCTCAGGCGCATATTTCT 1726–2074 0.857 84.3
atpH-atpI_p2 atpH-atpI GGATGGCCAGTAGTCCAAAG CTCACCTCAGGCGCATATTT 1728–2076 0.857 84.3
atpH-atpI_p3 atpH-atpI GGATGGCCAGTAGTCCAAAG TCACCTCAGGCGCATATTTC 1727–2075 0.857 84.3
atpH-atpI_p4 atpH-atpI GGATGGCCAGTAGTCCAAAG TACGACAGTTGCTTTGGCTT 1750–2098 0.857 84.2
atpH-atpI_p5 atpH-atpI GGATGGCCAGTAGTCCAAAG TTTCCAAGTCCACGGACAAG 2059–2407 0.857 83.8
trnT-GGU-psbD_p1 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA AAAGGTTGTACCCGTGAACC 1475–1498 0.857 83.8
trnT-GGU-psbD_p2 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA TGGACCAGAGAATGCGATTG 1760–1783 0.857 82.4
trnT-GGU-psbD_p3 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA AAAAGGGTTCAGCGTCCAAT 1901–1924 0.857 82.0
trnT-GGU-psbD_p4 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA AAAGGGTTCAGCGTCCAATT 1900–1923 0.857 82.0
trnT-GGU-psbD_p5 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA GCGGTGACCATGGAATAAGT 2059–2082 0.714 70.1
psaA-ycf3_p1 psaA-ycf3 TGCGAGTTGGATCACTTAGC CGCGGAAGTTTGGTTTGATC 1241–1405 1.000 91.6
psaA-ycf3_p2 psaA-ycf3 TGCGAGTTGGATCACTTAGC ATCAAGCCGCTCAGTATTGG 1224–1388 1.000 91.6
psaA-ycf3_p3 psaA-ycf3 ACATGTACTTGATGACCCGC CGCGGAAGTTTGGTTTGATC 1569–1732 0.857 85.8
psaA-ycf3_p4 psaA-ycf3 ACATGTACTTGATGACCCGC ATCAAGCCGCTCAGTATTGG 1552–1715 0.857 85.8
psaA-ycf3_p5 psaA-ycf3 TGCGAGTTGGATCACTTAGC CAATTTGCGAGGTTTGGGTC 1871–1953 0.714 74.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Genlisea aurea NC_037078.1 140010 View on NCBI ↗
Genlisea filiformis NC_037079.1 140308 View on NCBI ↗
Genlisea margaretae NC_025652.1 141255 View on NCBI ↗
Genlisea pygmaea NC_037080.1 140466 View on NCBI ↗
Genlisea repens NC_037081.1 140432 View on NCBI ↗
Genlisea tuberosa NC_037082.1 140677 View on NCBI ↗
Genlisea violacea NC_037083.1 143416 View on NCBI ↗