Markers + reference

Lumnitzera

2 species · Combretaceae · Myrtales

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Species 2
Genome length 159–160 kb
Candidate markers 264
Primer pairs 100

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 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 582 0.0261 0.92 65.8 yes View details
trnK-UUU-rps16 LSC 905 0.0134 0.99 67.2 yes View details
trnS-GCU-trnG-UCC LSC 780 0.0196 0.98 62.0 yes View details
trnR-UCU-atpA LSC 547 0.0238 1.00 67.4 yes View details
atpH-atpI LSC 1239 0.0127 0.95 57.0 yes View details
petN-psbM LSC 899 0.0111 1.00 63.4 yes View details
psbZ-trnG-UCC LSC 687 0.0169 0.95 68.3 yes View details
trnM-CAU-atpE LSC 222 0.0452 1.00 78.9 yes View details
ndhF-rpl32 SSC 830 0.0607 0.95 79.3 yes View details
rpl32-trnL-UAG SSC 1244 0.0089 0.99 51.2 yes View details
rpoC1-rpoB LSC 26 0.0385 1.00 74.6 yes View details
ndhK-ndhC LSC 56 0.0357 1.00 73.0 yes View details
trnT-GGU-psbD LSC 1269 0.0100 0.94 69.1 yes View details
ndhC-trnV-UAC LSC 1499 0.0093 0.94 67.3 yes View details
trnC-GCA-ndhJ LSC 789 0.0089 1.00 63.3 yes View details
trnD-GUC-trnY-GUA LSC 469 0.0108 0.99 63.2 yes View details
rps12-clpP LSC 161 0.0186 1.00 63.2 yes View details
rpl14-rps3 LSC 1737 0.0070 0.99 62.9 yes View details
trnT-UGU-trnL-UAA LSC 1033 0.0039 0.99 62.0 yes View details
psbE-petL LSC 1131 0.0083 0.96 61.8 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 605–649 1.000 84.2
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 619–663 1.000 84.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 618–662 1.000 84.1
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 620–664 1.000 84.1
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 608–652 1.000 84.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 TACCGAGGGTCTGAACGAAT AAAAAGGCGCTCAACCTACA 1099–1100 1.000 79.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACTCTACCGAGGGTCTGAAC AAAAAGGCGCTCAACCTACA 1103–1104 1.000 79.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 CGAGGGTCTGAACGAATCTC AAAAAGGCGCTCAACCTACA 1096–1097 1.000 79.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 ACAAACTCTACCGAGGGTCT AAAAAGGCGCTCAACCTACA 1107–1108 1.000 78.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 TACCGAGGGTCTGAACGAAT CTTGAAAAAGGCGCTCAACC 1103–1104 1.000 78.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGATCCCTTAACTAGAGAAGCG 881–933 1.000 64.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GGATCCCTTAACTAGAGAAGCG 880–932 1.000 64.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA GGATCCCTTAACTAGAGAAGCG 935–987 1.000 63.3
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAGAAGCGATCAGTAAAACGA 868–920 1.000 63.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AGAGAAGCGATCAGTAAAACGA 867–919 1.000 63.1
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GAGGAAGCAGAAGCCCTTTT 644–681 1.000 67.5
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TTCACTGAGGAAGCAGAAGC 650–687 1.000 66.7
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CAGGAACAGATGGAACGCTT 611–648 1.000 66.7
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TTCAGGAACAGATGGAACGC 613–650 1.000 66.7
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGGAAGCAGAAGCCCTTTTG 643–680 1.000 65.2
atpH-atpI_p1 atpH-atpI AATAGAAGCAAGCCCGACAG CCTTGAATTCATTCGCGACG 1766–1825 1.000 82.6
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT CCTTGAATTCATTCGCGACG 1732–1791 1.000 82.6
atpH-atpI_p3 atpH-atpI AATAGAAGCAAGCCCGACAG TGTTTCGAATTGGTCAGGGG 1673–1732 1.000 82.6
atpH-atpI_p4 atpH-atpI AAGCGAATCGGTATGCCAAT CCTTGAATTCATTCGCGACG 2120–2181 1.000 82.1
atpH-atpI_p5 atpH-atpI AGCGAATCGGTATGCCAATT CCTTGAATTCATTCGCGACG 2119–2180 1.000 82.1
rpoC1-rpoB_p1 rpoC1-rpoB GGGTTTTGTCACCTCTCCAA TTGCTCGTTCGAGAACTACG 239 1.000 77.1
rpoC1-rpoB_p2 rpoC1-rpoB GGGTTTTGTCACCTCTCCAA ACGATCTTTGGCTCTGGAAC 222 1.000 76.7
rpoC1-rpoB_p3 rpoC1-rpoB GGGTTTTGTCACCTCTCCAA TTCGATTGCTCGTTCGAGAA 244 1.000 74.7
rpoC1-rpoB_p4 rpoC1-rpoB GGGTTTTGTCACCTCTCCAA TTTCGATTGCTCGTTCGAGA 245 1.000 74.7
rpoC1-rpoB_p5 rpoC1-rpoB GGGTTTTGTCACCTCTCCAA CGATTGCTCGTTCGAGAACT 242 1.000 74.4

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
Lumnitzera littorea NC_039752.1 159687 View on NCBI ↗
Lumnitzera racemosa NC_042408.1 159473 View on NCBI ↗