Markers + reference

Melaleuca

3 species · Myrtaceae · Myrtales

Back to catalogue

Species 3
Genome length 159–160 kb
Candidate markers 269
Primer pairs 95

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 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 429 0.0452 1.00 74.1 yes View details
rps16-trnQ-UUG LSC 1432 0.0298 0.98 71.9 yes View details
trnC-GCA-petN LSC 879 0.0556 0.99 84.6 yes View details
trnD-GUC-trnY-GUA LSC 446 0.0867 0.93 83.2 yes View details
psbZ-trnG-GCC LSC 865 0.0841 0.91 84.6 yes View details
petA-psbJ LSC 1001 0.0400 0.98 76.8 yes View details
psbE-petL LSC 1230 0.0398 0.98 75.0 yes View details
rpl32-trnL-UAG SSC 1005 0.0423 0.64 67.1 yes View details
rps15-ycf1 SSC 440 0.0439 1.00 73.5 yes View details
rps18-rpl20 LSC 274 0.0487 1.00 82.0 yes View details
rrn5-trnR-ACG IRb 246 0.0328 0.99 76.9 yes View details
trnR-ACG-rrn5 IRa 246 0.0328 0.99 76.9 yes View details
psbI-trnS-GCU LSC 153 0.0544 0.96 74.3 yes View details
trnE-UUC-trnT-GGU LSC 886 0.0283 1.00 72.2 yes View details
trnS-GCU-trnG-UCC LSC 731 0.0276 0.99 70.1 yes View details
atpH-atpI LSC 1102 0.0224 0.97 70.1 yes View details
trnR-UCU-atpA LSC 342 0.0374 0.81 69.3 yes View details
psbT-psbN LSC 65 0.0308 1.00 69.0 yes View details
trnT-GGU-psbD LSC 1405 0.0182 0.94 67.3 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 TTCCCTCTAGACCTAGCTGC 498–560 1.000 83.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 512–574 1.000 83.6
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 511–573 1.000 83.6
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 513–575 1.000 83.5
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC TTCCCTCTAGACCTAGCTGC 527–589 1.000 80.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1480–1505 1.000 85.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GGGTGGGTGTAAGAATCCAC GAGGTTCGAATCCTTCCGTC 1517–1542 1.000 85.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1491–1516 1.000 85.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GGGTGGGTGTAAGAATCCAC TTCGGAGGTTCGAATCCTTC 1521–1546 1.000 80.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGGTGGGTGTAAGAATCCAC TAAGGCAACGGGTTTTGGTC 1547–1572 1.000 80.5
psbI-trnS-GCU_p1 psbI-trnS-GCU GTTTGGCAAGCTGCTGTAAG TGGACTAAAGCGTCGGATTG 749–768 1.000 85.5
psbI-trnS-GCU_p2 psbI-trnS-GCU GTTTGGCAAGCTGCTGTAAG GTGGACTAAAGCGTCGGATT 750–769 1.000 85.5
psbI-trnS-GCU_p3 psbI-trnS-GCU GTTTGGCAAGCTGCTGTAAG ATTGGGAGAGATGGCTGAGT 768–787 1.000 84.5
psbI-trnS-GCU_p4 psbI-trnS-GCU GTTTGGCAAGCTGCTGTAAG TTTTTCGTACCGAGGGTTCG 712–731 1.000 84.1
psbI-trnS-GCU_p5 psbI-trnS-GCU TGGCAAGCTGCTGTAAGTTT TGGACTAAAGCGTCGGATTG 746–765 1.000 83.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AAATCAAACCGAGGGATCCC 841–902 1.000 80.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AAATCAAACCGAGGGATCCC 840–901 1.000 80.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AAATCAAACCGAGGGATCCC 895–956 1.000 79.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TGGAAACGGAAAGAGAGGGA AAATCAAACCGAGGGATCCC 900–961 1.000 78.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGCAATCCGACGCTTTAGTC AAATCAAACCGAGGGATCCC 843–904 1.000 77.7
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GAGGAAGCAGAAGCCCTTTT 353–439 1.000 72.8
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CAGGAACAGAAGGAACGCTT 320–406 1.000 72.8
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TTCACTGAGGAAGCAGAAGC 359–445 1.000 72.0
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGGAAGCAGAAGCCCTTTTG 352–438 1.000 70.5
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GGAAGCAGAAGCCCTTTTGA 351–437 1.000 70.4
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT CGAATCCATGGAGGGTCATC 1113–1159 1.000 84.1
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT CGAATCCATGGAGGGTCATC 1169–1215 1.000 83.2
atpH-atpI_p3 atpH-atpI GTCCAATAGAAGCAAGCCCA CGAATCCATGGAGGGTCATC 1151–1197 1.000 83.2
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA CGAATCCATGGAGGGTCATC 1114–1160 1.000 82.9
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC CGAATCCATGGAGGGTCATC 1173–1219 1.000 82.6

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
Melaleuca alternifolia MN310606.1 160104 View on NCBI ↗
Melaleuca cajuputi NC_052729.1 158855 View on NCBI ↗
Melaleuca leucadendra NC_053326.1 160317 View on NCBI ↗