Markers + reference

Barringtonia

2 species · Lecythidaceae · Ericales

Back to catalogue

Species 2
Genome length 159–159 kb
Candidate markers 271
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-GCC LSC 698 0.0057 1.00 62.0 yes View details
rps2 LSC 711 0.0000 1.00 26.8 yes View details
rpoC2 LSC 4158 0.0002 1.00 53.9 yes View details
psbM-trnD-GUC LSC 1135 0.0000 1.00 26.1 yes View details
ndhJ LSC 477 0.0000 1.00 30.5 yes View details
trnM-CAU-atpE LSC 227 0.0088 1.00 57.6 yes View details
clpP LSC 2289 0.0009 1.00 57.7 yes View details
ycf1 SSC 5664 0.0005 1.00 52.8 yes View details
trnD-GUC LSC 74 0.0270 1.00 68.0 yes View details
petA-psbJ LSC 1129 0.0000 1.00 58.9 yes View details
rpoB-trnC-GCA LSC 1162 0.0000 1.00 58.8 yes View details
rps16-trnQ-UUG LSC 1548 0.0000 1.00 58.7 yes View details
rps12-trnV-GAC IRb 1869 0.0000 0.99 58.7 yes View details
trnV-GAC-rps12 IRa 1869 0.0000 0.99 58.7 yes View details
rps2-rpoC2 LSC 225 0.0089 1.00 57.6 yes View details
ndhJ-ndhK LSC 116 0.0086 1.00 57.5 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTTCTTCAAGTCGCACGTTG GAAATTGAAATGGGGCGTGG 1685–1686 1.000 79.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ACCACATCGTTTCAACCGAA GAAATTGAAATGGGGCGTGG 1659–1660 1.000 79.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GTTCTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 1627–1628 1.000 79.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ACCACATCGTTTCAACCGAA GAGGTTCGAATCCTTCCGTC 1601–1602 1.000 79.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 1678–1679 1.000 78.9
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AACCGAAAGACCCCTTAACT 804 1.000 67.3
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC AACCGAAAGACCCCTTAACT 803 1.000 67.3
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA AACCGAAAGACCCCTTAACT 858 1.000 66.1
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AAACCGAAAGACCCCTTAACT 805 1.000 65.4
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC AAACCGAAAGACCCCTTAACT 804 1.000 65.4
trnG-GCC_p1 trnG-GCC CGCACAATTCTCCTGTTCGA TGTAAATTACTATAGCGAGTCTGT 885–886 1.000 40.1
trnG-GCC_p2 trnG-GCC ACGCACAATTCTCCTGTTCG TGTAAATTACTATAGCGAGTCTGT 886–887 1.000 40.1
trnG-GCC_p3 trnG-GCC GCACAATTCTCCTGTTCGAC TGTAAATTACTATAGCGAGTCTGT 884–885 1.000 40.1
trnG-GCC_p4 trnG-GCC CGCACAATTCTCCTGTTCGA ATGTAAATTACTATAGCGAGTCTGT 886–887 1.000 40.1
trnG-GCC_p5 trnG-GCC CGCACAATTCTCCTGTTCGA TGTAAATTACTATAGCGAGTCTG 885–886 1.000 40.1
rps2_p1 rps2 TCTCTTGTTTGAGGTTCACA GGGGGAGTGTGGGGAAAA 816 1.000 40.0
rps2_p2 rps2 TCTCTTGTTTGAGGTTCACAA GGGGGAGTGTGGGGAAAA 816 1.000 40.0
rps2_p3 rps2 ATCTCTTGTTTGAGGTTCACA GGGGGAGTGTGGGGAAAA 817 1.000 40.0
rps2_p4 rps2 TCTCTTGTTTGAGGTTCACAAA GGGGGAGTGTGGGGAAAA 816 1.000 40.0
rps2_p5 rps2 ACCAATTCCAAAAATCTAGGGAGT GGGGGAGTGTGGGGAAAA 789 1.000 40.0
rps2-rpoC2_p1 rps2-rpoC2 CGAGGGTTCCATTTCTTGGT TCACGATACACCAGAACTTCT 354 1.000 58.2
rps2-rpoC2_p2 rps2-rpoC2 CGAGGGTTCCATTTCTTGGT TTCACGATACACCAGAACTTCT 355 1.000 55.9
rps2-rpoC2_p3 rps2-rpoC2 GCCATTCGAGGGTTCCATTT TCACGATACACCAGAACTTCT 360 1.000 55.6
rps2-rpoC2_p4 rps2-rpoC2 CGAGGGTTCCATTTCTTGGT ACGATACACCAGAACTTCTAGG 352 1.000 55.0
rps2-rpoC2_p5 rps2-rpoC2 TGGTACCATGGCCAAAATGA TCACGATACACCAGAACTTCT 338 1.000 54.9
rpoC2_p1 rpoC2 AACAAGTCTGCGCGTAAGAT GGGAGCTAGAGGAAATGCAT 220 1.000 72.1
rpoC2_p2 rpoC2 AACAAGTCTGCGCGTAAGAT TTAATGTCGGATCCCCAAGG 168 1.000 71.7
rpoC2_p3 rpoC2 AACAAGTCTGCGCGTAAGAT GTCTTTTTCGGGAGCTAGAGG 229 1.000 70.9
rpoC2_p4 rpoC2 GCCACAATCTGTTCGACGTA GGGAGCTAGAGGAAATGCAT 262 1.000 70.4
rpoC2_p5 rpoC2 AACAAGTCTGCGCGTAAGAT TCTTTTTCGGGAGCTAGAGGA 228 1.000 70.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Barringtonia fusicarpa NC_035701.1 158927 View on NCBI ↗
Barringtonia racemosa NC_035705.1 159002 View on NCBI ↗