Markers + reference

Rubroshorea

2 species · Dipterocarpaceae · Malvales

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Species 2
Genome length 151–151 kb
Candidate markers 263
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 9 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1571 0.1002 0.57 72.4 yes View details
trnT-GGU-psbD LSC 1546 0.0288 0.99 67.8 yes View details
psbZ-trnG-GCC LSC 609 0.0741 0.95 94.7 yes View details
psbE-petL LSC 1102 0.0306 0.98 68.3 yes View details
rpl33-rps18 LSC 539 0.0342 0.87 65.2 yes View details
rps12-psbB LSC 2012 0.0234 0.98 66.3 yes View details
trnN-GUU-ycf1 IRb 439 0.0520 0.96 74.3 yes View details
ycf1 SSC 5574 0.0273 1.00 53.2 yes View details
trnL-UAG-rpl32 SSC 1322 0.0351 0.88 66.8 yes View details
rpl32-ndhF SSC 901 0.0415 0.99 70.5 yes View details
trnI-CAU-ycf2 IRb 62 0.1786 0.90 85.9 yes View details
ycf2-trnI-CAU IRa 62 0.1786 0.90 85.9 yes View details
atpF-atpH LSC 587 0.0363 0.98 80.8 yes View details
trnS-GCU-trnG-UCC LSC 592 0.0451 0.97 80.4 yes View details
psbC-trnS-UGA LSC 239 0.0669 1.00 75.9 yes View details
psbL-psbF LSC 26 0.0769 1.00 75.6 yes View details
trnT-UGU-trnL-UAA LSC 806 0.0262 0.99 74.2 yes View details
trnH-GUG-psbA LSC 188 0.0372 1.00 73.9 yes View details
trnM-CAU-rps14 LSC 168 0.0440 0.95 73.6 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 258–275 1.000 80.5
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 272–289 1.000 80.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 271–288 1.000 80.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 273–290 1.000 80.3
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACAATCCACTGCCTT TTCCCTCTAGACCTAGCTGC 278–295 1.000 80.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTTGGTCCCGGTGATCAAAG 1236–1661 1.000 87.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC TTTGGTCCCGGTGATCAAAG 1247–1672 1.000 86.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CCGGTGATCAAAGGTTCGAA 1229–1654 1.000 86.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CCGGTGATCAAAGGTTCGAA 1240–1665 1.000 85.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AATAGACAGAATGGGGCGTG 1278–1703 1.000 85.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC AGCAAAACGGAAAGAGAGGG CGAAGGACCCCTTAACTATCA 756–768 1.000 63.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC GCAAAACGGAAAGAGAGGGA CGAAGGACCCCTTAACTATCA 755–767 1.000 63.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA CGAAGGACCCCTTAACTATCA 750–762 1.000 63.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGCAAAACGGAAAGAGAGGG CGAAGGACCCCTTAACTATCAA 756–768 1.000 61.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GCAAAACGGAAAGAGAGGGA CGAAGGACCCCTTAACTATCAA 755–767 1.000 61.6
atpF-atpH_p1 atpF-atpH CCAGTGACCCAAAGAAACGA CCCAGGCGGATGGAAAAATA 748–779 1.000 82.3
atpF-atpH_p2 atpF-atpH CCAGTGACCCAAAGAAACGA TGGTTATCGCATTGGCACTT 673–704 1.000 81.8
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG CCCAGGCGGATGGAAAAATA 775–806 1.000 81.6
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG TGGTTATCGCATTGGCACTT 700–731 1.000 81.1
atpF-atpH_p5 atpF-atpH CCAGTGACCCAAAGAAACGA CTGGTTATCGCATTGGCACT 674–705 1.000 78.2
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GAAACGGTCCCTACGTAACC 1688–1704 1.000 82.4
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GAAACGGTCCCTACGTAACC 1691–1707 1.000 82.2
trnT-GGU-psbD_p3 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA GAAACGGTCCCTACGTAACC 1665–1681 1.000 80.7
trnT-GGU-psbD_p4 trnT-GGU-psbD TGGTAGAGTAACGCCATGGT GAAACGGTCCCTACGTAACC 1687–1703 1.000 79.5
trnT-GGU-psbD_p5 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CGAAACGGTCCCTACGTAAC 1689–1705 1.000 79.4
psbC-trnS-UGA_p1 psbC-trnS-UGA TCGTGGGTCATTTATGGCAC GGTTGATAGCTCCGGTCTTG 421–435 1.000 80.5
psbC-trnS-UGA_p2 psbC-trnS-UGA AGCGGGATTTGAAAAGGGAA GGTTGATAGCTCCGGTCTTG 378–392 1.000 80.4
psbC-trnS-UGA_p3 psbC-trnS-UGA TCGTGGGTCATTTATGGCAC ACCGGCATAGTTCGAAGAAC 398 0.500 57.9
psbC-trnS-UGA_p4 psbC-trnS-UGA AGCGGGATTTGAAAAGGGAA ACCGGCATAGTTCGAAGAAC 355 0.500 57.5
psbC-trnS-UGA_p5 psbC-trnS-UGA TCGTGATCTTGAGCCTGTTC ACCGGCATAGTTCGAAGAAC 331 0.500 57.0

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
Rubroshorea johorensis PX570610.1 151409 View on NCBI ↗
Rubroshorea palembanica PQ412302.1 150558 View on NCBI ↗