Markers + reference

Heteranthera

11 species · Pontederiaceae · Commelinales

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Species 11
Genome length 160–162 kb
Candidate markers 270
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1438 0.0388 1.00 90.8 yes View details
trnS-GCU-trnG-UCC LSC 1211 0.0617 0.98 88.7 yes View details
atpH-atpI LSC 1509 0.0329 0.97 78.4 yes View details
trnT-UGU-trnL-UAA LSC 1025 0.0422 1.00 89.7 yes View details
rbcL-accD LSC 759 0.0371 1.00 82.7 yes View details
accD-psaI LSC 1308 0.0319 1.00 75.7 yes View details
petA-psbJ LSC 1127 0.0327 0.99 81.0 yes View details
ycf1 IRb 1155 0.0119 1.00 53.0 no View details
rpl32-trnL-UAG SSC 600 0.0500 0.99 87.5 yes View details
psaC-ndhE SSC 639 0.0383 0.96 81.8 yes View details
ycf1 SSC 5589 0.0277 1.00 65.4 yes View details
psaI-ycf4 LSC 386 0.0469 1.00 82.3 yes View details
rps15-ycf1 SSC 403 0.0431 1.00 81.4 yes View details
trnE-UUC-trnT-GGU LSC 783 0.0292 1.00 81.2 yes View details
trnS-GGA-rps4 LSC 292 0.0327 1.00 79.8 yes View details
trnF-GAA-ndhJ LSC 696 0.0267 1.00 79.6 yes View details
rpoC2-rpoC1 LSC 197 0.0487 1.00 78.6 yes View details
trnS-UGA-psbZ LSC 347 0.0279 0.99 78.2 yes View details
psbC-trnS-UGA LSC 123 0.0349 1.00 78.0 yes View details
petD-rpoA LSC 197 0.0554 0.94 77.7 yes View details
rpoB-trnC-GCA LSC 1194 0.0229 1.00 76.9 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CCACAACCGATCATGTCCTT GAAATCAAAATGGGGCGTGG 1584–1653 1.000 91.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATCAAAATGGGGCGTGG 1563–1632 1.000 90.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAACCGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1526–1595 1.000 90.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAAATCAAAATGGGGCGTGG 1574–1643 1.000 90.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1505–1574 1.000 90.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 931–1600 1.000 63.4
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 934–1603 1.000 62.3
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 933–1602 1.000 62.3
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 932–1601 1.000 61.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT ACGAATCACACTTTTACCACT 917–1586 1.000 60.4
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA TAGGTGAATCCATGGAGGGT 1493–1629 0.909 82.8
atpH-atpI_p2 atpH-atpI GCCAATCCAGCAGCAATAAC TAGGTGAATCCATGGAGGGT 1510–1646 0.909 81.9
atpH-atpI_p3 atpH-atpI TCCAGCAGCAATAACGGAAG TAGGTGAATCCATGGAGGGT 1505–1641 0.909 81.6
atpH-atpI_p4 atpH-atpI AACGGAAGCAGCAGAAATCA AGGTGAATCCATGGAGGGTC 1492–1628 0.909 81.3
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC AGGTGAATCCATGGAGGGTC 1509–1645 0.909 80.4
rpoC2-rpoC1_p1 rpoC2-rpoC1 TTGTGAAAGACCAGATCGGC AGAGGAAGCCGTACAAGGAT 272–285 1.000 89.4
rpoC2-rpoC1_p2 rpoC2-rpoC1 GTGAAAGACCAGATCGGCTC AGAGGAAGCCGTACAAGGAT 270–283 1.000 88.1
rpoC2-rpoC1_p3 rpoC2-rpoC1 TTGTGAAAGACCAGATCGGC TAGAGGAAGCCGTACAAGGA 273–286 1.000 86.3
rpoC2-rpoC1_p4 rpoC2-rpoC1 TTGTGAAAGACCAGATCGGC GCCGTACAAGGATTTTGTCG 265–278 1.000 86.3
rpoC2-rpoC1_p5 rpoC2-rpoC1 TTGTGAAAGACCAGATCGGC TCGAGCCTACTCATACGCTA 248–261 0.909 82.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA ATTTCCATCATTCCGGAGCA GCGACACCCAGATTTGAACT 1276–1318 0.909 76.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TTTCCATCATTCCGGAGCAT GCGACACCCAGATTTGAACT 1275–1317 0.909 76.1
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TTTCCATCATTCCGGAGCAT CCTTACCACTTGGCCATGTC 1229–1271 0.909 76.0
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ATTTCCATCATTCCGGAGCA TAAAGGATTTGCAGTCCCCC 1251–1293 0.909 75.9
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TTTCCATCATTCCGGAGCAT TAAAGGATTTGCAGTCCCCC 1250–1292 0.909 75.9
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 851–928 1.000 89.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 830–907 1.000 89.7
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCATGGCGTTACTCTACCAC 830–907 1.000 89.4
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA CCATGGCGTTACTCTACCAC 809–886 1.000 89.2
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TGGCGTTACTCTACCACTGA 827–904 1.000 89.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Heteranthera callifolia NC_063306.1 161221 View on NCBI ↗
Heteranthera dubia PQ010082.1 161342 View on NCBI ↗
Heteranthera limosa PQ010083.1 161601 View on NCBI ↗
Heteranthera lutea PQ010103.1 161069 View on NCBI ↗
Heteranthera mexicana PQ010084.1 160427 View on NCBI ↗
Heteranthera multiflora PQ010085.1 160982 View on NCBI ↗
Heteranthera oblongifolia PQ010086.1 160552 View on NCBI ↗
Heteranthera reniformis PQ010087.1 161373 View on NCBI ↗
Heteranthera rotundifolia PQ010088.1 160897 View on NCBI ↗
Heteranthera seubertiana PQ010089.1 160347 View on NCBI ↗
Heteranthera zosterifolia PQ010090.1 160470 View on NCBI ↗