Markers + reference

Ceriops

3 species · Rhizophoraceae · Malpighiales

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Species 3
Genome length 164–167 kb
Candidate markers 265
Primer pairs 85

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 9 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-trnQ-UUG LSC 1628 0.0532 0.95 86.2 yes View details
trnQ-UUG-psbK LSC 590 0.0654 0.91 83.7 yes View details
trnS-GCU-trnT-CGU LSC 2029 0.0779 0.94 82.1 yes View details
trnT-CGU-trnR-UCU LSC 341 0.0993 0.96 84.1 yes View details
trnR-UCU-atpA LSC 643 0.1327 0.88 80.8 yes View details
trnT-GGU-psbD LSC 2180 0.0441 0.93 73.2 yes View details
psbZ-trnG-GCC LSC 1434 0.0508 0.93 75.7 yes View details
ndhC-trnV LSC 1696 0.0373 0.90 72.2 yes View details
rpl16 LSC 1641 0.0433 1.00 76.0 yes View details
accD-psaI LSC 878 0.0525 0.97 80.4 yes View details
trnS-UGA-psbZ LSC 456 0.0526 1.00 79.8 yes View details
trnP-UGG-psaJ LSC 485 0.0466 0.99 79.5 yes View details
rps19 LSC 81 0.1646 1.00 78.4 no View details
trnE-UUC-trnT-GGU LSC 1264 0.0360 0.97 76.1 yes View details
trnC-GCA-petN LSC 1079 0.0298 0.99 74.4 yes View details
psbI-trnS-GCU LSC 171 0.0429 1.00 72.2 yes View details
ycf3-trnS-GGA LSC 464 0.0189 0.99 71.1 yes View details
rpl14-rpl16 LSC 133 0.0530 0.99 70.9 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG AAAGCCGAGTACTCTACCGT GAGGTTCGAATCCTTCCGTC 1491–1952 1.000 87.3
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG AAGCCGAGTACTCTACCGTT GAGGTTCGAATCCTTCCGTC 1490–1951 1.000 87.3
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG TACCGTTGAGTTAGCAACCC GAGGTTCGAATCCTTCCGTC 1477–1938 1.000 85.0
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG AGTCGCACTTAAAAGCCGAG GAGGTTCGAATCCTTCCGTC 1502–1963 1.000 84.0
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG TCGCACTTAAAAGCCGAGTA GAGGTTCGAATCCTTCCGTC 1500–1961 1.000 82.8
trnQ-UUG-psbK_p1 trnQ-UUG-psbK ATAGGTATGCTCTGGGACGG TAGGCTTCGGGCAATTTTGT 627–770 1.000 85.4
trnQ-UUG-psbK_p2 trnQ-UUG-psbK ATAGGTATGCTCTGGGACGG GCTTCGGGCAATTTTGTGAA 624–767 1.000 84.9
trnQ-UUG-psbK_p3 trnQ-UUG-psbK ATAGGTATGCTCTGGGACGG GTAGGCTTCGGGCAATTTTG 628–771 1.000 83.8
trnQ-UUG-psbK_p4 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA TAGGCTTCGGGCAATTTTGT 582–725 1.000 83.2
trnQ-UUG-psbK_p5 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA GCTTCGGGCAATTTTGTGAA 579–722 1.000 82.7
psbI-trnS-GCU_p1 psbI-trnS-GCU AATGATCCGGGGCGCAAT TGGACTAAAGCGTCGGATTG 280–483 1.000 55.0
psbI-trnS-GCU_p2 psbI-trnS-GCU AATGATCCGGGGCGCAAT GTGGACTAAAGCGTCGGATT 281–484 1.000 54.9
psbI-trnS-GCU_p3 psbI-trnS-GCU AATGATCCGGGGCGCAATC TGGACTAAAGCGTCGGATTG 280–483 1.000 54.2
psbI-trnS-GCU_p4 psbI-trnS-GCU AATGATCCGGGGCGCAATC GTGGACTAAAGCGTCGGATT 281–484 1.000 54.2
psbI-trnS-GCU_p5 psbI-trnS-GCU AATGATCCGGGGCGCAAT ATTGGGAGAGATGGCTGAGT 299–502 1.000 53.8
trnS-GCU-trnT-CGU_p1 trnS-GCU-trnT-CGU CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCACT 1669–2493 1.000 80.8
trnS-GCU-trnT-CGU_p2 trnS-GCU-trnT-CGU AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCACT 1668–2492 1.000 80.8
trnS-GCU-trnT-CGU_p3 trnS-GCU-trnT-CGU CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCAC 1669–2493 1.000 80.8
trnS-GCU-trnT-CGU_p4 trnS-GCU-trnT-CGU AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCAC 1668–2492 1.000 80.7
trnS-GCU-trnT-CGU_p5 trnS-GCU-trnT-CGU AGAACCGGAAAGAGAGGGAT ACGAATCGCACTTTTACCACT 1727–2551 1.000 78.6
trnT-CGU-trnR-UCU_p1 trnT-CGU-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 423–919 1.000 73.3
trnT-CGU-trnR-UCU_p2 trnT-CGU-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 426–922 1.000 73.0
trnT-CGU-trnR-UCU_p3 trnT-CGU-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 429–925 1.000 72.6
trnT-CGU-trnR-UCU_p4 trnT-CGU-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 432–928 1.000 72.3
trnT-CGU-trnR-UCU_p5 trnT-CGU-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 427–923 1.000 70.8
trnR-UCU-atpA_p1 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG GCGAGTTGCTCAAACAATCC 1374–1762 1.000 91.5
trnR-UCU-atpA_p2 trnR-UCU-atpA CCTAGCCTTCCAAGCTAACG GCGAGTTGCTCAAACAATCC 1377–1765 1.000 91.3
trnR-UCU-atpA_p3 trnR-UCU-atpA CCCCTCTCTCTCGTGTCTAG GCGAGTTGCTCAAACAATCC 1603–1992 1.000 90.5
trnR-UCU-atpA_p4 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG CTTTCTAAACAAGCGCAGGC 1837–2225 1.000 90.0
trnR-UCU-atpA_p5 trnR-UCU-atpA CCCCTCTCTCTCGTGTCTAG CTTTCTAAACAAGCGCAGGC 2066–2455 1.000 89.3

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
Ceriops decandra NC_061406.1 166650 View on NCBI ↗
Ceriops tagal NC_061404.1 164432 View on NCBI ↗
Ceriops zippeliana NC_061405.1 166083 View on NCBI ↗