Markers + reference

Nymphoides

6 species · Menyanthaceae · Asterales

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Species 6
Genome length 152–152 kb
Candidate markers 267
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 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 483 0.0423 0.98 78.7 yes View details
trnS-GCU-trnG-UCC LSC 665 0.0232 0.98 67.9 yes View details
trnG-UCC-trnR-UCU LSC 343 0.0874 0.85 77.5 yes View details
petA-psbJ LSC 1012 0.0311 1.00 71.7 yes View details
rpl16-rps3 LSC 1255 0.0166 0.98 66.6 yes View details
rpl22 LSC 492 0.0419 1.00 79.2 yes View details
ycf1 IRb 1146 0.0062 1.00 54.7 no View details
ndhF-rpl32 SSC 704 0.0327 0.97 73.7 yes View details
rpl32-trnL-UAG SSC 754 0.0275 1.00 73.1 yes View details
ccsA-ndhD SSC 270 0.0427 0.92 72.1 yes View details
ycf1 SSC 5478 0.0159 1.00 51.3 yes View details
atpA-atpF LSC 68 0.0456 1.00 75.1 yes View details
trnG-GCC-trnfM-CAU LSC 185 0.0346 1.00 72.8 yes View details
psbK-psbI LSC 445 0.0149 1.00 68.1 yes View details
ndhC-trnV-UAC LSC 755 0.0168 0.99 67.1 yes View details
rpoB-trnC-GCA LSC 1299 0.0163 0.99 66.7 yes View details
rps16-trnQ-UUG LSC 713 0.0156 0.99 66.3 yes View details
psbM-trnD-GUC LSC 989 0.0141 1.00 65.3 yes View details
accD-psaI LSC 698 0.0186 1.00 65.3 yes View details
trnT-UGU-trnL-UAA LSC 576 0.0193 0.99 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCGAAGCTCCATCTACAAATGG 508–539 1.000 72.1
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCGAAGCTCCATCTACAAATGG 522–553 1.000 71.9
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TCGAAGCTCCATCTACAAATGG 521–552 1.000 71.9
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG CGAAGCTCCATCTACAAATGG 507–538 1.000 71.9
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TCGAAGCTCCATCTACAAATGG 523–554 1.000 71.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 771–786 1.000 83.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 786–801 1.000 81.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 785–800 1.000 81.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 775–790 1.000 78.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 801–816 1.000 78.1
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGTCCCGGATCATTGGATA 531–565 1.000 83.5
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TACGTCCCGGATCATTGGAT 532–566 1.000 83.5
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG CGTCCCGGATCATTGGATAG 530–564 1.000 82.9
psbK-psbI_p4 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTACGTCCCGGATCATTGGA 533–567 1.000 81.7
psbK-psbI_p5 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACGTCCCGGATCATTGGATA 528–562 1.000 81.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC TACCACTAAACTATACCCGC 706–762 1.000 50.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC TTACCACTAAACTATACCCGC 707–763 1.000 49.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC TACCACTAAACTATACCCGC 700–756 1.000 47.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC TTTACCACTAAACTATACCCGC 708–764 1.000 47.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TTTCGTCCACTCAGCCATCT TACCACTAAACTATACCCGC 705–761 1.000 47.6
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 292–422 1.000 75.3
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 295–425 1.000 75.1
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 298–428 1.000 74.7
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 301–431 1.000 74.5
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 296–426 1.000 72.9
atpA-atpF_p1 atpA-atpF TTTCGTCTGCTCGAATGGTT ATTGGGGGCGATGAAAGAAA 123–135 1.000 82.0
atpA-atpF_p2 atpA-atpF TTTCGTCTGCTCGAATGGTT TTGGGGGCGATGAAAGAAAT 122–134 1.000 82.0
atpA-atpF_p3 atpA-atpF TCGTCTGCTCGAATGGTTAC ATTGGGGGCGATGAAAGAAA 121–133 1.000 81.2
atpA-atpF_p4 atpA-atpF TCGTCTGCTCGAATGGTTAC TTGGGGGCGATGAAAGAAAT 120–132 1.000 81.2
atpA-atpF_p5 atpA-atpF GTCTGCTCGAATGGTTACCA TTGGGGGCGATGAAAGAAAT 118–130 1.000 80.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Nymphoides coreana NC_041481.1 152104 View on NCBI ↗
Nymphoides coronata NC_041484.1 151985 View on NCBI ↗
Nymphoides crenata NC_041483.1 152225 View on NCBI ↗
Nymphoides hydrophylla NC_041482.1 152111 View on NCBI ↗
Nymphoides peltata NC_061690.1 152198 View on NCBI ↗
Nymphoides simulans NC_041480.1 152031 View on NCBI ↗