Markers + reference

Melastoma

6 species · Melastomataceae · Myrtales

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Species 6
Genome length 157–157 kb
Candidate markers 261
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 261 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1117 0.0053 0.98 55.4 yes View details
psbZ-trnG-UCC LSC 591 0.0079 1.00 51.9 yes View details
psaA-ycf3 LSC 606 0.0048 1.00 43.9 yes View details
ycf3 LSC 2063 0.0027 1.00 50.8 yes View details
atpB-rbcL LSC 797 0.0105 1.00 47.8 yes View details
petL-petG LSC 184 0.0217 1.00 44.1 yes View details
clpP LSC 2184 0.0027 1.00 42.2 yes View details
psbB-psbT LSC 194 0.0052 1.00 48.7 yes View details
rpl16 LSC 1444 0.0037 1.00 38.0 yes View details
ycf1 IRb 1833 0.0003 1.00 32.6 no View details
ndhE SSC 306 0.0000 1.00 20.7 yes View details
ycf1 SSC 5556 0.0019 1.00 34.8 yes View details
rpl2-trnH-GUG IRa 137 0.0000 1.00 67.3 no View details
psbT-psbN LSC 77 0.0433 1.00 66.0 yes View details
ndhE-ndhG SSC 241 0.0097 1.00 59.3 yes View details
atpF-atpH LSC 573 0.0034 0.99 55.5 yes View details
trnT-UGU-trnL-UAA LSC 875 0.0027 1.00 55.0 yes View details
rpl20-clpP LSC 1071 0.0017 1.00 53.9 yes View details
trnS-GCU-trnR-UCU LSC 1839 0.0016 1.00 53.7 yes View details
trnD-GUC-trnY-GUA LSC 456 0.0038 0.97 52.8 yes View details
trnP-UGG-psaJ LSC 483 0.0021 1.00 52.4 yes View details
psaJ-rpl33 LSC 547 0.0040 1.00 52.3 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGCCACACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1154–1190 1.000 82.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATCCACGAACGATCCTCTCT GAGGTTCGAATCCTTCCGTC 1177–1213 1.000 82.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GAACGATCCTCTCTGGCAAG GAGGTTCGAATCCTTCCGTC 1171–1207 1.000 82.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ACACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 1149–1185 1.000 80.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGCCACACGTTGCTTTCTA AACAGACTGACAAATGGGGC 1216–1252 1.000 80.2
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA CGAACTTGCGTCCAATAGGA 1944–1952 1.000 80.6
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC CGAACTTGCGTCCAATAGGA 1943–1951 1.000 80.6
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU ACGGAAAGAGAGGGATTCGA CGAACTTGCGTCCAATAGGA 1998–2006 1.000 79.4
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA ACGAACTTGCGTCCAATAGG 1945–1953 1.000 78.4
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC ACGAACTTGCGTCCAATAGG 1944–1952 1.000 78.4
atpF-atpH_p1 atpF-atpH TAAACCCAAAACTCCCAGCC GGATTGGTTGTCGCTTTAGC 687–695 1.000 76.9
atpF-atpH_p2 atpF-atpH GGCCCAAGGAAAGGAAAGAA GGATTGGTTGTCGCTTTAGC 657–665 1.000 76.9
atpF-atpH_p3 atpF-atpH GGCCCAAGGAAAGGAAAGAA CGGAGGGAAAAATACGAGGT 722–730 1.000 75.7
atpF-atpH_p4 atpF-atpH TAAACCCAAAACTCCCAGCC CGGAGGGAAAAATACGAGGT 752–760 1.000 75.6
atpF-atpH_p5 atpF-atpH TAAACCCAAAACTCCCAGCC GCGGAGGGAAAAATACGAGG 753–761 1.000 75.5
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA GCGGTGCTCTAACCAATTGA TGGCAATATGTCTACGCTGG 517–528 1.000 77.8
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA GCGGTGCTCTAACCAATTGA GGCAATATGTCTACGCTGGT 516–527 1.000 77.8
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA GCGGTGCTCTAACCAATTGA GGGGACGGACTGTAAATTCG 538–549 1.000 76.7
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA TTTATTCCGTCGGGACTGAC TGGCAATATGTCTACGCTGG 570–581 1.000 76.6
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA TTTATTCCGTCGGGACTGAC GGCAATATGTCTACGCTGGT 569–580 1.000 76.5
psbZ-trnG-UCC_p1 psbZ-trnG-UCC GACGGCTGGTCAAGTAACAA AATCGAACCCGCATCTTCTC 748–756 1.000 80.0
psbZ-trnG-UCC_p2 psbZ-trnG-UCC GACGGCTGGTCAAGTAACAA GAATCGAACCCGCATCTTCT 749–757 1.000 80.0
psbZ-trnG-UCC_p3 psbZ-trnG-UCC CCCGTTGTTTTTGCTTCTCC AATCGAACCCGCATCTTCTC 769–777 1.000 79.9
psbZ-trnG-UCC_p4 psbZ-trnG-UCC CCCGTTGTTTTTGCTTCTCC GAATCGAACCCGCATCTTCT 770–778 1.000 79.9
psbZ-trnG-UCC_p5 psbZ-trnG-UCC GACGGCTGGTCAAGTAACAA ACTTTAACTTAACCCGGGCG 777–785 1.000 78.9
psaA-ycf3_p1 psaA-ycf3 GCCCATTCCTCGAAAGAAGT TCACAAGGCGCTTCGAATAA 702–706 1.000 79.7
psaA-ycf3_p2 psaA-ycf3 GCCCATTCCTCGAAAGAAGT TTGAAGATCACAAGGCGCTT 709–713 1.000 79.6
psaA-ycf3_p3 psaA-ycf3 GCCCATTCCTCGAAAGAAGT ATCACAAGGCGCTTCGAATA 703–707 1.000 78.0
psaA-ycf3_p4 psaA-ycf3 TTTGGCCCATTCCTCGAAAG TCACAAGGCGCTTCGAATAA 706–710 1.000 77.0
psaA-ycf3_p5 psaA-ycf3 TTTGGCCCATTCCTCGAAAG TTGAAGATCACAAGGCGCTT 713–717 1.000 76.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Melastoma candidum NC_034716.1 156682 View on NCBI ↗
Melastoma dodecandrum NC_042821.1 156611 View on NCBI ↗
Melastoma malabathricum NC_077577.1 156606 View on NCBI ↗
Melastoma malabathricum subsp. normale OQ595236.1 156698 View on NCBI ↗
Melastoma penicillatum NC_077578.1 156695 View on NCBI ↗
Melastoma sanguineum NC_077579.1 156671 View on NCBI ↗