Markers + reference

Ammannia

3 species · Lythraceae · Myrtales

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Species 3
Genome length 157–158 kb
Candidate markers 271
Primer pairs 105

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 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 845 0.0401 0.99 75.1 yes View details
rps16-trnQ-UUG LSC 1367 0.0355 0.98 72.2 yes View details
trnR-UCU-atpA LSC 317 0.0597 0.93 72.1 yes View details
atpH-atpI LSC 974 0.0295 0.98 70.5 yes View details
trnC-GCA-petN LSC 816 0.0306 1.00 69.7 yes View details
petN-psbM LSC 945 0.0289 0.98 66.3 yes View details
trnE-UUC-trnT-GGU LSC 917 0.0420 0.99 77.1 yes View details
trnT-GGU-psbD LSC 1441 0.0286 0.98 68.0 yes View details
trnF-GAA-ndhJ LSC 785 0.0256 0.98 70.4 yes View details
petA-psbJ LSC 887 0.0334 0.99 66.3 yes View details
ndhF-rpl32 SSC 852 0.0347 0.99 71.2 yes View details
trnT-UGU-trnL-UAA LSC 694 0.0330 0.99 77.2 yes View details
trnL-UAG-ccsA SSC 93 0.0932 1.00 74.2 yes View details
trnG-UCC-trnR-UCU LSC 171 0.0394 0.99 72.9 yes View details
ndhK-ndhC LSC 55 0.0364 1.00 72.9 yes View details
psaC-ndhE SSC 290 0.0415 1.00 72.2 yes View details
petD-rpoA LSC 215 0.0496 1.00 71.3 yes View details
accD-psaI LSC 659 0.0269 1.00 70.6 yes View details
trnQ-UUG-psbK LSC 392 0.0341 0.97 70.3 yes View details
rpl36-infA LSC 155 0.0516 1.00 70.1 yes View details
trnH-GUG-psbA LSC 258 0.0413 0.94 69.9 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 105 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 CTGTCGAAGCTCCATCTACA 308–324 1.000 76.9
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CTGTCGAAGCTCCATCTACA 322–338 1.000 76.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CTGTCGAAGCTCCATCTACA 321–337 1.000 76.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CTGTCGAAGCTCCATCTACA 323–339 1.000 76.7
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CTGTCGAAGCTCCATCTACAA 308–324 1.000 74.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT ACAGAATTTCATTTTAATCAAACG 910–934 1.000 46.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ACAGAATTTCATTTTAATCAAACG 909–933 1.000 46.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CAGAATTTCATTTTAATCAAACGA 909–933 1.000 46.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CAGAATTTCATTTTAATCAAACGA 908–932 1.000 46.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA ACAGAATTTCATTTTAATCAAACG 919–943 1.000 46.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA GAGGTTCGAATCCTTCCGTC 974–1435 1.000 85.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCTGTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 990–1451 1.000 85.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AGTCGCACGTTGCTTTTTAC GAGGTTCGAATCCTTCCGTC 978–1439 1.000 84.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CAAGTCGCACGTTGCTTTTT GAGGTTCGAATCCTTCCGTC 980–1441 1.000 83.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GTCGCACGTTGCTTTTTACC GAGGTTCGAATCCTTCCGTC 977–1438 1.000 82.3
trnQ-UUG-psbK_p1 trnQ-UUG-psbK AGGTATTTCCTGGGACGGAA ACTACTCGAATAAAGGGCGG 522–533 1.000 77.3
trnQ-UUG-psbK_p2 trnQ-UUG-psbK AGGTATTTCCTGGGACGGAA ACTCGAATAAAGGGCGGAAT 519–530 1.000 76.4
trnQ-UUG-psbK_p3 trnQ-UUG-psbK TATTTCCTGGGACGGAAGGA ACTACTCGAATAAAGGGCGG 519–530 1.000 75.6
trnQ-UUG-psbK_p4 trnQ-UUG-psbK AGGTATTTCCTGGGACGGAA CTACTCGAATAAAGGGCGGA 521–532 1.000 75.0
trnQ-UUG-psbK_p5 trnQ-UUG-psbK GTATTTCCTGGGACGGAAGG ACTACTCGAATAAAGGGCGG 520–531 1.000 75.0
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 251–270 1.000 68.9
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU ACCCTTAGCCTTCCAAGCTA AGAAGACCTCTGTCCTATCCA 257–276 1.000 68.8
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 257–276 1.000 68.1
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU ACCCTTAGCCTTCCAAGCTA AGGTTTAGAAGACCTCTGTCCT 263–282 1.000 68.0
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CTAACGATGCGGGTTCGATT AGAAGACCTCTGTCCTATCCA 240–259 1.000 66.0
trnR-UCU-atpA_p1 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG CTCTCACGGTGGAAGAACAG 789–846 1.000 86.8
trnR-UCU-atpA_p2 trnR-UCU-atpA ACCCTTAGCCTTCCAAGCTA CTCTCACGGTGGAAGAACAG 795–852 1.000 86.7
trnR-UCU-atpA_p3 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG CGAAGCTTATCCGGGAGATG 1220–1277 1.000 85.7
trnR-UCU-atpA_p4 trnR-UCU-atpA ACCCTTAGCCTTCCAAGCTA CGAAGCTTATCCGGGAGATG 1226–1283 1.000 85.7
trnR-UCU-atpA_p5 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG ATCCCTCCAAACAAGCACAG 1284–1341 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
Ammannia baccifera PP056263.1 157799 View on NCBI ↗
Ammannia maritima NC_081998.1 157292 View on NCBI ↗
Ammannia robusta NC_082008.1 157730 View on NCBI ↗