Markers + reference

Osbeckia

2 species · Melastomataceae · Myrtales

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Species 2
Genome length 156–157 kb
Candidate markers 261
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 261 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1076 0.0523 0.99 80.8 yes View details
trnS-GCU-trnR-UCU LSC 1872 0.0307 0.99 70.6 yes View details
trnR-UCU-atpA LSC 419 0.0569 0.96 80.9 yes View details
trnE-UUC-trnT-GGU LSC 774 0.0483 0.99 80.4 yes View details
psbE-petL LSC 1167 0.0328 0.99 72.3 yes View details
rps8-rpl14 LSC 345 0.0814 1.00 72.3 yes View details
ycf1 IRb 1893 0.0053 1.00 47.8 no View details
ndhF-rpl32 SSC 971 0.0474 1.00 75.8 yes View details
rps15 SSC 264 0.0341 1.00 57.9 yes View details
ycf1 SSC 5577 0.0309 1.00 57.5 yes View details
psbT-psbN LSC 77 0.1299 1.00 83.4 yes View details
psbZ-trnG-UCC LSC 611 0.0362 0.95 77.2 yes View details
trnL-UAG-ccsA SSC 164 0.0580 0.84 75.7 yes View details
atpH-atpI LSC 897 0.0325 0.96 74.7 yes View details
ndhG-ndhI SSC 452 0.0356 0.93 74.5 yes View details
petD-rpoA LSC 199 0.0410 0.98 74.2 yes View details
psaA-ycf3 LSC 633 0.0182 0.95 73.7 yes View details
ndhE-ndhG SSC 227 0.0283 0.93 72.9 yes View details
trnD-GUC-trnY-GUA LSC 438 0.0374 0.98 71.9 yes View details
ndhH-rps15 SSC 123 0.0813 1.00 71.9 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
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGCCACACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1149–1166 1.000 83.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATCCACGAACGATCCTCTCT GAGGTTCGAATCCTTCCGTC 1172–1189 1.000 83.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GAACGATCCTCTCTGGCAAG GAGGTTCGAATCCTTCCGTC 1166–1183 1.000 83.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ACACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 1144–1161 1.000 81.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGCCACACGTTGCTTTCTA AACAGACTGACAAATGGGGC 1211–1228 1.000 80.7
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA CGAACTTGCGTCCAATAGGA 1971–1985 1.000 83.0
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC CGAACTTGCGTCCAATAGGA 1970–1984 1.000 83.0
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU ACGGAAAGAGAGGGATTCGA CGAACTTGCGTCCAATAGGA 2025–2039 1.000 81.7
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA ACGAACTTGCGTCCAATAGG 1972–1986 1.000 80.8
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC ACGAACTTGCGTCCAATAGG 1971–1985 1.000 80.8
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CATTCACCGAGGAAGCAGAA 512–516 1.000 71.6
trnR-UCU-atpA_p2 trnR-UCU-atpA ACAAAGAAAGCGTCCATTGTC CATTCACCGAGGAAGCAGAA 571–575 1.000 71.5
trnR-UCU-atpA_p3 trnR-UCU-atpA ACAAAGAAAGCGTCCATTGTC AAGACATTCACCGAGGAAGC 575–579 1.000 71.5
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AAGACATTCACCGAGGAAGC 516–520 1.000 71.5
trnR-UCU-atpA_p5 trnR-UCU-atpA ACAAAGAAAGCGTCCATTGT CATTCACCGAGGAAGCAGAA 571–575 1.000 69.8
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TAGCCGCCGCTTATATAGGA 950–973 1.000 83.9
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCC 962–985 1.000 83.7
atpH-atpI_p3 atpH-atpI GAAGCAAGTCCGACAGCTAA TAGCCGCCGCTTATATAGGA 980–1003 1.000 83.4
atpH-atpI_p4 atpH-atpI GAAGCAAGTCCGACAGCTAA TTTTTGCAACTTTAGCCGCC 992–1015 1.000 83.3
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA TAGCCGCCGCTTATATAGGA 951–974 1.000 82.7
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA GCGGTGCTCTAACCAATTGA TGGCAATATGTCTACGCTGG 499–509 1.000 77.8
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA GCGGTGCTCTAACCAATTGA GGCAATATGTCTACGCTGGT 498–508 1.000 77.8
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA GCGGTGCTCTAACCAATTGA GGGGACGGACTGTAAATTCG 520–530 1.000 76.7
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA TTTATTCCGTCGGGACTGAC TGGCAATATGTCTACGCTGG 552–562 1.000 76.5
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA TTTATTCCGTCGGGACTGAC GGCAATATGTCTACGCTGGT 551–561 1.000 76.5
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 915–951 1.000 82.5
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCATGGCGTTACTCTACCAC 894–930 1.000 82.2
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TGGCGTTACTCTACCACTGA 891–927 1.000 82.0
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 877–913 1.000 81.9
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 856–892 1.000 81.8

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
Osbeckia octandra NC_077580.1 156684 View on NCBI ↗
Osbeckia stellata NC_046486.1 156372 View on NCBI ↗