Markers + reference

Sonneratia

7 species · Lythraceae · Myrtales

Back to catalogue

Species 7
Genome length 153–153 kb
Candidate markers 265
Primer pairs 95

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 314 0.0126 1.00 55.6 yes View details
rps16-trnQ-UUG LSC 575 0.0060 1.00 46.8 yes View details
trnG-GCC-trnR-UCU LSC 311 0.0101 0.99 42.4 yes View details
atpH-atpI LSC 889 0.0050 1.00 43.4 yes View details
trnE-UUC-trnM-CAU LSC 981 0.0043 1.00 54.1 yes View details
lhbA-trnG-UCC LSC 340 0.0097 0.99 40.4 yes View details
rpl33-rps18 LSC 309 0.0305 1.00 67.1 yes View details
ycf1 IRb 1077 0.0000 1.00 25.4 no View details
rpl32-trnL-UAG SSC 674 0.0077 1.00 54.2 yes View details
ycf1 SSC 5592 0.0032 1.00 45.5 yes View details
trnC-GCA-petN LSC 878 0.0026 1.00 58.6 yes View details
trnL-UAG-ccsA SSC 94 0.0208 1.00 56.1 yes View details
trnF-GAA-ndhJ LSC 763 0.0026 1.00 53.3 yes View details
psaA-ycf3 LSC 693 0.0027 1.00 53.2 yes View details
psbE-petL LSC 1390 0.0010 1.00 52.0 yes View details
petB LSC 1440 0.0014 1.00 52.0 yes View details
ndhC-trnV-UAC LSC 1754 0.0018 1.00 51.6 yes View details
rbcL LSC 1449 0.0012 1.00 51.6 yes View details
psbM-trnD-GUC LSC 910 0.0031 1.00 50.2 yes View details
accD-psaI LSC 2116 0.0020 1.00 48.9 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 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 GCGCTAACCTTGGTATGGAA 429–440 1.000 81.1
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 379–390 1.000 81.1
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 443–454 1.000 81.0
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 442–453 1.000 81.0
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 444–455 1.000 81.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TATGTCTGTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 653–658 1.000 81.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA GAGGTTCGAATCCTTCCGTC 638–643 1.000 79.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AGTCGCACGTTGCTTTTTAC GAGGTTCGAATCCTTCCGTC 642–647 1.000 78.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CAAGTCGCACGTTGCTTTTT GAGGTTCGAATCCTTCCGTC 644–649 1.000 77.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TATGTCTGTCAAGTCGCACG GGGTTTTGGTCCCGGTATTC 674–679 1.000 77.3
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU TCAAAAATGCGAAAAAGCGGA CAGGAACAGAAGGAACGCTT 463 0.143 36.1
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU TCAAAAATGCGAAAAAGCGGA TTCAGGAACAGAAGGAACGC 465 0.143 36.1
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU CTCAAAAATGCGAAAAAGCGG CAGGAACAGAAGGAACGCTT 464 0.143 33.4
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU CTCAAAAATGCGAAAAAGCGG TTCAGGAACAGAAGGAACGC 466 0.143 33.4
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU CAAAAATGCGAAAAAGCGGA CAGGAACAGAAGGAACGCTT 462 0.143 32.2
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATTTTTGCAACCTTAGCCGC 974–981 1.000 80.5
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT CGAATCCATGGAGGGTCATC 942–949 1.000 79.7
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA ATTTTTGCAACCTTAGCCGC 975–982 1.000 79.3
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA CGAATCCATGGAGGGTCATC 943–950 1.000 78.6
atpH-atpI_p5 atpH-atpI TAACGGAAGCGGCAGAAATC ATTTTTGCAACCTTAGCCGC 973–980 1.000 75.7
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAAAGCAGCCCAAGCAAGA 867–950 1.000 83.8
trnC-GCA-petN_p2 trnC-GCA-petN GGTATCATTTTGGCGGCATG TTAAAGCAGCCCAAGCAAGA 920–1003 1.000 83.3
trnC-GCA-petN_p3 trnC-GCA-petN GTATCATTTTGGCGGCATGG TTAAAGCAGCCCAAGCAAGA 919–1002 1.000 83.3
trnC-GCA-petN_p4 trnC-GCA-petN GGGTGTCGCCTGATTAACAA TTAAAGCAGCCCAAGCAAGA 849–932 1.000 83.0
trnC-GCA-petN_p5 trnC-GCA-petN TGGTATCATTTTGGCGGCAT TTAAAGCAGCCCAAGCAAGA 921–1004 1.000 82.6
psbM-trnD-GUC_p1 psbM-trnD-GUC AGGCAGTAGGAACTAGAATGA TTCAATTGGTCAGAGCACCG 1026–1037 1.000 49.4
psbM-trnD-GUC_p2 psbM-trnD-GUC AAGGCAGTAGGAACTAGAATGA TTCAATTGGTCAGAGCACCG 1027–1038 1.000 47.6
psbM-trnD-GUC_p3 psbM-trnD-GUC AGGCAGTAGGAACTAGAATGAA TTCAATTGGTCAGAGCACCG 1026–1037 1.000 47.6
psbM-trnD-GUC_p4 psbM-trnD-GUC TCAATCACTTTGACTGACTGT TTCAATTGGTCAGAGCACCG 1070–1081 1.000 46.2
psbM-trnD-GUC_p5 psbM-trnD-GUC GGAACTAGAATGAAAAGTGCAGT TTCAATTGGTCAGAGCACCG 1018–1029 1.000 45.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Sonneratia apetala MH986669.1 153052 View on NCBI ↗
Sonneratia caseolaris NC_062074.1 153038 View on NCBI ↗
Sonneratia griffithii NC_061007.1 152730 View on NCBI ↗
Sonneratia ovata MN990685.1 153247 View on NCBI ↗
Sonneratia x gulngai NC_062075.1 153121 View on NCBI ↗
Sonneratia x hainanensis NC_062073.1 153122 View on NCBI ↗
Sonneratia x zhongcairongii NC_062167.1 153045 View on NCBI ↗