Markers + reference

Wolffia

4 species · Araceae · Alismatales

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Species 4
Genome length 169–170 kb
Candidate markers 272
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhH SSC 1188 0.3091 0.89 77.3 yes View details
ndhI-ndhG SSC 231 0.3391 0.97 72.1 yes View details
ndhE-psaC SSC 823 0.3904 0.89 77.5 yes View details
trnL-UAG-rpl32 SSC 579 0.4021 0.84 76.3 yes View details
rpl32-ndhF SSC 1041 0.3248 0.66 74.7 yes View details
ndhF SSC 2214 0.3142 0.84 75.3 yes View details
trnT-GGU-psbD LSC 1199 0.0705 0.98 90.4 yes View details
psbM-trnD-GUC LSC 944 0.0903 0.99 86.6 yes View details
trnE-UUC-trnT-GGU LSC 1425 0.1302 0.90 86.5 yes View details
pafI-trnS-GGA LSC 833 0.1025 0.99 85.4 yes View details
trnC-GCA-petN LSC 1005 0.1046 0.97 85.2 yes View details
psbK-psbI LSC 586 0.1210 0.95 85.0 yes View details
psbE-petL LSC 1192 0.0985 0.97 84.6 yes View details
rbcL-accD LSC 919 0.0862 0.99 84.4 yes View details
rps16-trnQ-UUG LSC 1475 0.1256 0.97 84.3 yes View details
rps16 LSC 1265 0.0783 0.97 84.2 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16_p1 rps16 CCTTTCAGGATCAGTCGTGG TGGTTTTCTTGCCGATCCTT 1972–1981 0.500 60.3
rps16_p2 rps16 CCTTTCAGGATCAGTCGTGG TTGGTTTTCTTGCCGATCCT 1973–1982 0.500 60.3
rps16_p3 rps16 CCTTTCAGGATCAGTCGTGG CCGATCCTTGGCAGCATAAA 1961–1970 0.500 60.0
rps16_p4 rps16 TCAGGATCAGTCGTGGTCTT TGGTTTTCTTGCCGATCCTT 1968–1977 0.500 59.8
rps16_p5 rps16 TCAGGATCAGTCGTGGTCTT TTGGTTTTCTTGCCGATCCT 1969–1978 0.500 59.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GAACGAACCATGTCGAGACA CTTACAGCAGCTTGCCAAAC 2264–2291 0.750 81.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ACGAACCATGTCGAGACAAG CTTACAGCAGCTTGCCAAAC 2262–2289 0.750 81.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GAACGAACCATGTCGAGACA GAGGTTCGAATCCTTCCGTC 1625–1632 0.750 80.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ACGGATTCCAACACGTTTGA CTTACAGCAGCTTGCCAAAC 2497–2538 0.500 63.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ACGGATTCCAACACGTTTGA GAGGTTCGAATCCTTCCGTC 1864–1879 0.500 63.8
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGAAAAGTTTGAGAGTAAGCA 573–639 1.000 61.5
psbK-psbI_p2 psbK-psbI AGCATTTGTTTGGCAAGCTG ACGAAAAGTTTGAGAGTAAGCA 580–646 1.000 61.0
psbK-psbI_p3 psbK-psbI ATTTGTTTGGCAAGCTGCTG ACGAAAAGTTTGAGAGTAAGCA 577–643 1.000 61.0
psbK-psbI_p4 psbK-psbI CATTTGTTTGGCAAGCTGCT ACGAAAAGTTTGAGAGTAAGCA 578–644 1.000 61.0
psbK-psbI_p5 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACGAAAAGTTTGAGAGTAAGCA 570–636 1.000 59.5
trnC-GCA-petN_p1 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC AGCCCAAGCGAGACTTACTA 776–1116 1.000 87.0
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTA AGCCCAAGCGAGACTTACTA 801–1141 1.000 86.6
trnC-GCA-petN_p3 trnC-GCA-petN GACATGGCCAAGTGGTAAGG AGCCCAAGCGAGACTTACTA 822–1162 1.000 86.5
trnC-GCA-petN_p4 trnC-GCA-petN CGACATGGCCAAGTGGTAAG AGCCCAAGCGAGACTTACTA 823–1163 1.000 83.5
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTAT AGCCCAAGCGAGACTTACTA 801–1141 1.000 82.5
psbM-trnD-GUC_p1 psbM-trnD-GUC TGCGAGAATATTTACTTCCA TTCAATTGGTCAGAGCACCG 958–1055 1.000 52.0
psbM-trnD-GUC_p2 psbM-trnD-GUC ATGCGAGAATATTTACTTCCA TTCAATTGGTCAGAGCACCG 959–1056 1.000 52.0
psbM-trnD-GUC_p3 psbM-trnD-GUC TGCGAGAATATTTACTTCCAT TTCAATTGGTCAGAGCACCG 958–1055 1.000 52.0
psbM-trnD-GUC_p4 psbM-trnD-GUC AATGCGAGAATATTTACTTCCA TTCAATTGGTCAGAGCACCG 960–1057 1.000 52.0
psbM-trnD-GUC_p5 psbM-trnD-GUC TGCGAGAATATTTACTTCCA GTTCAATTGGTCAGAGCACC 959–1056 1.000 52.0
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU ACTTTCCCAGTACCCTACCC GAACCGATGACTTACGCCTT 1382–1645 1.000 91.7
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU ACTTTCCCAGTACCCTACCC CCATGGCGTTACTCTACCAC 1361–1624 1.000 91.2
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU ACTTTCCCAGTACCCTACCC TGGCGTTACTCTACCACTGA 1358–1621 1.000 91.0
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 1326–1589 1.000 90.8
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 1324–1587 1.000 90.8

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
Wolffia arrhiza NC_072708.1 169602 View on NCBI ↗
Wolffia australiana NC_015899.1 168704 View on NCBI ↗
Wolffia brasiliensis NC_047280.1 168514 View on NCBI ↗
Wolffia globosa NC_048463.1 169405 View on NCBI ↗