Markers + reference

Cabomba

3 species · Cabombaceae · Nymphaeales

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Species 3
Genome length 159–164 kb
Candidate markers 279
Primer pairs 95

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 10 remaining regions by MarkerSeek score (out of 279 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-TTT-rps16 LSC 783 0.0423 1.00 76.4 yes View details
trnS-GCT-trnG-TCC LSC 1056 0.0643 0.88 79.9 yes View details
petN-psbM LSC 1292 0.0301 0.99 67.7 yes View details
ycf3-trnS-GGA LSC 855 0.0346 0.99 71.7 yes View details
accD-trnH-ATG LSC 695 0.0284 0.95 63.6 yes View details
petD-rpoA LSC 412 0.0977 0.86 77.7 yes View details
rpl32-trnL-TAG SSC 377 0.0674 1.00 79.5 yes View details
psaC-ndhE SSC 447 0.0641 1.00 80.4 yes View details
ycf1 SSC 5664 0.0314 1.00 61.0 yes View details
rpl16-rps3 LSC 163 0.0695 1.00 80.4 yes View details
psbZ-trnG-GCC LSC 276 0.0428 0.96 80.0 yes View details
trnT-TGT-trnL-TAA LSC 519 0.0394 0.98 79.0 yes View details
rps16-trnQ-TTG LSC 1595 0.0309 0.96 77.0 yes View details
trnH-GTG-psbA LSC 233 0.0690 1.00 73.5 yes View details
trnE-TTC-trnT-GGT LSC 714 0.0341 0.96 73.0 yes View details
ndhC-trnV-TAC LSC 1948 0.0274 0.97 72.8 yes View details
rpl14-rpl16 LSC 136 0.0343 1.00 72.8 yes View details
psaA-ycf3 LSC 682 0.0305 0.99 71.7 yes View details
psbE-petL LSC 1266 0.0241 0.98 71.2 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GTG-psbA_p1 trnH-GTG-psbA AATCCACTTGGCTACATCCG GTTGACAGTCAAGGTCGTGT 397–398 1.000 81.9
trnH-GTG-psbA_p2 trnH-GTG-psbA AATCCACTTGGCTACATCCG TGCATGGTTCCTTGGTAACC 675–676 1.000 79.9
trnH-GTG-psbA_p3 trnH-GTG-psbA AATCCACTTGGCTACATCCG CGTATTCAGCTCCTGTTGCT 879–880 1.000 79.8
trnH-GTG-psbA_p4 trnH-GTG-psbA AATCCACTTGGCTACATCCG CTGTTGCGTATTCAGCTCCT 885–886 1.000 79.7
trnH-GTG-psbA_p5 trnH-GTG-psbA AATCCACTTGGCTACATCCG GTGAGTGGGAGCTTAGCTTC 930–931 1.000 79.6
trnK-TTT-rps16_p1 trnK-TTT-rps16 CCTTTCAGGATCAGTCGTGG GGAAAAAGGAGCTCAACCCA 954–1000 0.667 73.0
trnK-TTT-rps16_p2 trnK-TTT-rps16 CCTTTCAGGATCAGTCGTGG TGGAAAAAGGAGCTCAACCC 955–1001 0.667 73.0
trnK-TTT-rps16_p3 trnK-TTT-rps16 TCAGGATCAGTCGTGGTCTT GGAAAAAGGAGCTCAACCCA 950–996 0.667 72.5
trnK-TTT-rps16_p4 trnK-TTT-rps16 TCAGGATCAGTCGTGGTCTT TGGAAAAAGGAGCTCAACCC 951–997 0.667 72.5
trnK-TTT-rps16_p5 trnK-TTT-rps16 TTCAGGATCAGTCGTGGTCT GGAAAAAGGAGCTCAACCCA 951–997 0.667 72.5
rps16-trnQ-TTG_p1 rps16-trnQ-TTG AATCCACAGCCGATCATGTC ACGGGTTTTGGTCCTGTTAC 1646–1715 1.000 86.6
rps16-trnQ-TTG_p2 rps16-trnQ-TTG GTCATTCAAGTCGCACGTTG ACGGGTTTTGGTCCTGTTAC 1629–1698 1.000 86.5
rps16-trnQ-TTG_p3 rps16-trnQ-TTG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 1623–1692 1.000 86.3
rps16-trnQ-TTG_p4 rps16-trnQ-TTG ACGTTGCCTTCTACCACATC ACGGGTTTTGGTCCTGTTAC 1615–1684 1.000 86.3
rps16-trnQ-TTG_p5 rps16-trnQ-TTG GTTGCCTTCTACCACATCGT ACGGGTTTTGGTCCTGTTAC 1613–1682 1.000 86.3
trnS-GCT-trnG-TCC_p1 trnS-GCT-trnG-TCC ACGGAGAAAGAGGGATTCGA AACCGAAAGAACCCTTAACT 971–1217 1.000 59.7
trnS-GCT-trnG-TCC_p2 trnS-GCT-trnG-TCC ACGGAGAAAGAGGGATTCGA ACGAATCACACTTTTACCACT 933–1179 1.000 59.7
trnS-GCT-trnG-TCC_p3 trnS-GCT-trnG-TCC GGGTACGGAGAAAGAGGGAT AACCGAAAGAACCCTTAACT 975–1221 1.000 59.2
trnS-GCT-trnG-TCC_p4 trnS-GCT-trnG-TCC GGGTACGGAGAAAGAGGGAT ACGAATCACACTTTTACCACT 937–1183 1.000 59.2
trnS-GCT-trnG-TCC_p5 trnS-GCT-trnG-TCC AATCTGCCGCTTTAGTCCAC AACCGAAAGAACCCTTAACT 916–1162 1.000 59.1
petN-psbM_p1 petN-psbM ACGTTTTCCCTTTCACTCGT ACGTAAAAACAGTAAGTCAAAACGA 1106–1422 1.000 47.1
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT ACGTAAAAACAGTAAGTCAAAACGA 1083–1399 1.000 47.1
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT ACGTAAAAACAGTAAGTCAAAACGA 1144–1460 1.000 47.0
petN-psbM_p4 petN-psbM GGGGGCATAATTCACATGGA ACGTAAAAACAGTAAGTCAAAACGA 1166–1482 1.000 46.9
petN-psbM_p5 petN-psbM AGGGGGCATAATTCACATGG ACGTAAAAACAGTAAGTCAAAACGA 1167–1483 1.000 46.9
trnE-TTC-trnT-GGT_p1 trnE-TTC-trnT-GGT AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 537–852 1.000 86.0
trnE-TTC-trnT-GGT_p2 trnE-TTC-trnT-GGT AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 535–850 1.000 86.0
trnE-TTC-trnT-GGT_p3 trnE-TTC-trnT-GGT AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 516–831 1.000 85.6
trnE-TTC-trnT-GGT_p4 trnE-TTC-trnT-GGT AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 514–829 1.000 85.6
trnE-TTC-trnT-GGT_p5 trnE-TTC-trnT-GGT GATGTCCTGAACCGCTAGAC GAACCGATGACTTACGCCTT 534–849 1.000 85.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Cabomba aquatica NC_039434.1 159487 View on NCBI ↗
Cabomba caroliniana NC_031505.1 164057 View on NCBI ↗
Cabomba furcata NC_039435.1 160271 View on NCBI ↗