Markers + reference

Sonerila

10 species · Melastomataceae · Myrtales

Back to catalogue

Species 10
Genome length 154–155 kb
Candidate markers 262
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-trnQ-UUG LSC 2490 0.0313 0.93 75.9 yes View details
ndhC-trnV-UAC LSC 655 0.0389 0.97 83.0 yes View details
rbcL-accD LSC 523 0.0448 1.00 83.5 yes View details
petA-psbJ LSC 898 0.0355 0.99 80.1 yes View details
rps8-rpl14 LSC 304 0.0641 0.99 81.7 yes View details
ycf1 IRb 1899 0.0049 1.00 48.5 no View details
ndhF-rpl32 SSC 567 0.0425 0.91 77.7 yes View details
ndhG-ndhI SSC 399 0.0458 1.00 79.3 yes View details
rps15 SSC 264 0.0125 1.00 44.9 yes View details
rps15-ycf1 SSC 335 0.0602 0.99 79.8 yes View details
ycf1 SSC 5469 0.0267 1.00 69.7 yes View details
trnE-UUC-trnT-GGU LSC 646 0.0377 1.00 85.6 yes View details
trnS-GCU-trnR-UCU LSC 1776 0.0346 0.99 84.6 yes View details
trnC-GCA-petN LSC 834 0.0287 0.98 83.7 yes View details
trnD-GUC-trnY-GUA LSC 455 0.0350 1.00 82.1 yes View details
psbE-petL LSC 1136 0.0309 0.99 82.1 yes View details
ndhD-psaC SSC 144 0.0511 0.98 81.6 yes View details
trnT-UGU-trnL-UAA LSC 813 0.0311 0.99 80.5 yes View details
trnQ-UUG-psbK LSC 328 0.0415 1.00 79.3 yes View details
psbM-trnD-GUC LSC 699 0.0279 1.00 79.3 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
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG AAGCCGAGTACTCTACCGTT TTCGGAGGTTCGAATCCTTC 2389–2554 1.000 85.3
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG AAAGCCGAGTACTCTACCGT GAGGTTCGAATCCTTCCGTC 2386–2551 0.900 85.0
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG AAGCCGAGTACTCTACCGTT GAGGTTCGAATCCTTCCGTC 2385–2550 0.900 85.0
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG CCGCACTTAAAAGCCGAGTA GAGGTTCGAATCCTTCCGTC 2395–2560 0.900 84.1
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG TACCGTTGAGTTAGCAACCC GAGGTTCGAATCCTTCCGTC 2372–2537 0.900 82.7
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA AGGGTGAAATGAAAACAGAAGT 385–417 1.000 55.3
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GAATAGCGGGACCAAAACCC AGGGTGAAATGAAAACAGAAGT 394–426 1.000 53.6
trnQ-UUG-psbK_p3 trnQ-UUG-psbK AAAACCCGTTGCCTTACCAC AGGGTGAAATGAAAACAGAAGT 381–413 1.000 53.0
trnQ-UUG-psbK_p4 trnQ-UUG-psbK ACCAAAACCCGTTGCCTTAC AGGGTGAAATGAAAACAGAAGT 384–416 1.000 53.0
trnQ-UUG-psbK_p5 trnQ-UUG-psbK AAAAGGTATTCCCTGGGACG AGGGTGAAATGAAAACAGAAGT 458–463 0.800 40.6
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGAACTTGCGTCCAATAGGA 1880–1960 1.000 79.7
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGAACTTGCGTCCAATAGGA 1879–1959 1.000 79.7
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AAGAACTTGCGTCCAATAGGA 1881–1961 1.000 77.7
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA ACATAGAAGAACTTGCGTCCA 1891–1967 0.900 71.9
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC ACATAGAAGAACTTGCGTCCA 1890–1966 0.900 71.9
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAAAGCAGCCCAAGCAAGA 874–919 1.000 91.3
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CCTTTAGAGTCCACTTCGCC 933–978 0.900 86.9
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CTTTAGAGTCCACTTCGCCC 932–977 0.900 86.9
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCAAGACTTACT 868–913 0.900 85.5
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GTGGTGCCTTTAGAGTCCAC 939–984 0.900 85.2
psbM-trnD-GUC_p1 psbM-trnD-GUC TCACTTTGACTCACGGTTTT TCAATTGGTTAGAGCACCGC 689–888 1.000 65.8
psbM-trnD-GUC_p2 psbM-trnD-GUC TCACTTTGACTCACGGTTTTT TCAATTGGTTAGAGCACCGC 689–888 1.000 64.1
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAAGAGTGCAGTAGC TCAATTGGTTAGAGCACCGC 635–834 1.000 64.0
psbM-trnD-GUC_p4 psbM-trnD-GUC AATCACTTTGACTCACGGTT TCAATTGGTTAGAGCACCGC 691–890 1.000 63.9
psbM-trnD-GUC_p5 psbM-trnD-GUC ATCACTTTGACTCACGGTTT TCAATTGGTTAGAGCACCGC 690–889 1.000 63.9
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA TTTTATTCCGTCGGGACTGG TGGCAATATGTCTACGCTGG 580 0.100 39.0
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA TTTTATTCCGTCGGGACTGG GGCAATATGTCTACGCTGGT 579 0.100 39.0
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA TTTTATTCCGTCGGGACTGG GAATGGCTTCTTCCTGGGTC 639 0.100 38.9
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA TTTTATTCCGTCGGGACTGG GGGGACGGACTGTAAATTCG 601 0.100 38.1
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA TTTTATTCCGTCGGGACTGG GGGACGGACTGTAAATTCGT 600 0.100 37.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Sonerila annamica NC_068164.1 155271 View on NCBI ↗
Sonerila borneensis MK994893.1 154804 View on NCBI ↗
Sonerila cantonensis NC_068144.1 154858 View on NCBI ↗
Sonerila nervulosa NC_068173.1 154260 View on NCBI ↗
Sonerila obliqua NC_068149.1 154978 View on NCBI ↗
Sonerila parviflora MK994900.1 154752 View on NCBI ↗
Sonerila plagiocardia MK994789.1 153922 View on NCBI ↗
Sonerila pulchella MK994884.1 154862 View on NCBI ↗
Sonerila velutina MK994892.1 154682 View on NCBI ↗
Sonerila yunnanensis MK994862.1 154964 View on NCBI ↗