Markers + reference

Lemna

2 species · Araceae · Alismatales

Back to catalogue

Species 2
Genome length 166–167 kb
Candidate markers 276
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 276 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-tRNA-Gln(UUG) LSC 980 0.0355 0.98 71.3 yes View details
tRNA-Ser(GCU)-tRNA-Gly(UCC) LSC 1614 0.0435 0.95 79.9 yes View details
rpoB-tRNA-Cys(GCA) LSC 1449 0.0247 0.95 69.1 yes View details
tRNA-Glu(UUC)-tRNA-Thr(GGU) LSC 875 0.0358 0.96 75.3 yes View details
tRNA-Thr(GGU)-psbD LSC 1140 0.0337 0.99 70.3 yes View details
rpl16 LSC 1714 0.0214 0.98 61.8 yes View details
rps15-ndhF IRb 314 0.0638 0.95 72.9 yes View details
ndhF SSC 2229 0.0188 1.00 53.3 yes View details
ndhF-rpl32 SSC 1070 0.0415 0.97 76.0 yes View details
psaC-ndhE SSC 840 0.0615 0.93 79.0 yes View details
rpl2-tRNA-His(GUG) LSC 295 0.1061 0.45 74.0 no View details
tRNA-Cys(GCA)-petN LSC 1042 0.0351 0.96 76.1 yes View details
petA-psbJ LSC 1123 0.0255 0.98 75.3 yes View details
tRNA-Arg(UCU)-atpA LSC 178 0.0417 0.94 73.5 yes View details
rpl36-rps8 LSC 228 0.0395 1.00 71.4 yes View details
ndhD-psaC SSC 139 0.0455 0.95 70.4 yes View details
tRNA-Leu(UAA)-tRNA-Phe(GAA) LSC 134 0.0448 1.00 69.7 yes View details
psbC-tRNA-Ser(UGA) LSC 112 0.0357 1.00 68.8 yes View details
psbE-petL LSC 1126 0.0194 0.96 68.5 yes View details
rps19-rpl2 LSC 52 0.0455 0.85 68.4 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-tRNA-Gln(UUG)_p1 rps16-tRNA-Gln(UUG) AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1053–1078 1.000 82.6
rps16-tRNA-Gln(UUG)_p2 rps16-tRNA-Gln(UUG) GGATCACGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1067–1092 1.000 80.7
rps16-tRNA-Gln(UUG)_p3 rps16-tRNA-Gln(UUG) AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1057–1082 1.000 77.8
rps16-tRNA-Gln(UUG)_p4 rps16-tRNA-Gln(UUG) AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1083–1108 1.000 77.6
rps16-tRNA-Gln(UUG)_p5 rps16-tRNA-Gln(UUG) CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1045–1070 1.000 77.4
tRNA-Ser(GCU)-tRNA-Gly(UCC)_p1 tRNA-Ser(GCU)-tRNA-Gly(UCC) ATTAGCAATCCGCCGCTTTA AGGACGAATCACACTTTTACCA 1691–1717 1.000 67.5
tRNA-Ser(GCU)-tRNA-Gly(UCC)_p2 tRNA-Ser(GCU)-tRNA-Gly(UCC) ATTAGCAATCCGCCGCTTTA GGACGAATCACACTTTTACCAC 1690–1716 1.000 67.1
tRNA-Ser(GCU)-tRNA-Gly(UCC)_p3 tRNA-Ser(GCU)-tRNA-Gly(UCC) CGGAGAGAGAGGGATTCGAA AGGACGAATCACACTTTTACCA 1739–1765 1.000 65.1
tRNA-Ser(GCU)-tRNA-Gly(UCC)_p4 tRNA-Ser(GCU)-tRNA-Gly(UCC) CGGAGAGAGAGGGATTCGAA GGACGAATCACACTTTTACCAC 1738–1764 1.000 64.6
tRNA-Ser(GCU)-tRNA-Gly(UCC)_p5 tRNA-Ser(GCU)-tRNA-Gly(UCC) GCTTTAGTCCACTCAGCCAT AGGACGAATCACACTTTTACCA 1677–1703 1.000 64.6
tRNA-Arg(UCU)-atpA_p1 tRNA-Arg(UCU)-atpA AAAAGCAGCGTCCATTGTCT TTCTACAACAGGAGCAAGCC 272–280 1.000 80.3
tRNA-Arg(UCU)-atpA_p2 tRNA-Arg(UCU)-atpA AAAGCAGCGTCCATTGTCTA TTCTACAACAGGAGCAAGCC 271–279 1.000 79.7
tRNA-Arg(UCU)-atpA_p3 tRNA-Arg(UCU)-atpA AAGCAGCGTCCATTGTCTAA TTCTACAACAGGAGCAAGCC 270–278 1.000 79.7
tRNA-Arg(UCU)-atpA_p4 tRNA-Arg(UCU)-atpA AAAAGCAGCGTCCATTGTCT TTCCACCAAGACATTCACCC 343–351 1.000 78.5
tRNA-Arg(UCU)-atpA_p5 tRNA-Arg(UCU)-atpA AAGCAGCGTCCATTGTCTAA TTCCACCAAGACATTCACCC 341–349 1.000 77.9
rpoB-tRNA-Cys(GCA)_p1 rpoB-tRNA-Cys(GCA) ATTCCCTCATTTCCATCGCG TTTCTTGATCAGGCGACACC 1514–1556 1.000 80.7
rpoB-tRNA-Cys(GCA)_p2 rpoB-tRNA-Cys(GCA) ATTCCCTCATTTCCATCGCG GCGACACCCAGATTTGAACT 1502–1544 1.000 78.5
rpoB-tRNA-Cys(GCA)_p3 rpoB-tRNA-Cys(GCA) ATTCCCTCATTTCCATCGCG TAAAGGATTTGCAGTCCCCC 1477–1519 1.000 78.2
rpoB-tRNA-Cys(GCA)_p4 rpoB-tRNA-Cys(GCA) ATTCCCTCATTTCCATCGCG CCTTACCACTTGGCCATGTC 1456–1498 1.000 78.2
rpoB-tRNA-Cys(GCA)_p5 rpoB-tRNA-Cys(GCA) CATTCCCTCATTTCCATCGC TTTCTTGATCAGGCGACACC 1515–1557 1.000 75.3
tRNA-Cys(GCA)-petN_p1 tRNA-Cys(GCA)-petN GGTGTCGCCTGATCAAGAAA AGCCCAAGCGAGACTTACTA 1048–1089 1.000 83.3
tRNA-Cys(GCA)-petN_p2 tRNA-Cys(GCA)-petN GGTGTCGCCTGATCAAGAAA CCACTCCTACCCCAGACTAC 1104–1145 1.000 82.5
tRNA-Cys(GCA)-petN_p3 tRNA-Cys(GCA)-petN GGTGTCGCCTGATCAAGAAA TCCACTCCTACCCCAGACTA 1105–1146 1.000 81.7
tRNA-Cys(GCA)-petN_p4 tRNA-Cys(GCA)-petN GGTGTCGCCTGATCAAGAAA AAAGTCCACTCCTACCCCAG 1109–1150 1.000 81.5
tRNA-Cys(GCA)-petN_p5 tRNA-Cys(GCA)-petN GGTGTCGCCTGATCAAGAAA CCGTACCCCTAAAGTCCACT 1160 0.500 55.0
tRNA-Glu(UUC)-tRNA-Thr(GGU)_p1 tRNA-Glu(UUC)-tRNA-Thr(GGU) ACTTTCCCAGTACCCTACCC GAACCGATGACTTACGCCTT 1018–1404 1.000 84.1
tRNA-Glu(UUC)-tRNA-Thr(GGU)_p2 tRNA-Glu(UUC)-tRNA-Thr(GGU) ACTTTCCCAGTACCCTACCC CCATGGCGTTACTCTACCAC 997–1383 1.000 83.8
tRNA-Glu(UUC)-tRNA-Thr(GGU)_p3 tRNA-Glu(UUC)-tRNA-Thr(GGU) ACTTTCCCAGTACCCTACCC TGGCGTTACTCTACCACTGA 994–1380 1.000 83.6
tRNA-Glu(UUC)-tRNA-Thr(GGU)_p4 tRNA-Glu(UUC)-tRNA-Thr(GGU) AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 962–1348 1.000 83.5
tRNA-Glu(UUC)-tRNA-Thr(GGU)_p5 tRNA-Glu(UUC)-tRNA-Thr(GGU) AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 960–1346 1.000 83.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Lemna minor NC_010109.1 165955 View on NCBI ↗
Lemna turionifera NC_072328.1 166606 View on NCBI ↗