Markers + reference

Parashorea

2 species · Dipterocarpaceae · Malvales

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Species 2
Genome length 151–152 kb
Candidate markers 243
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 243 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1767 0.0445 0.83 79.2 yes View details
psbZ-trnG-UCC LSC 670 0.0419 1.00 79.2 yes View details
ycf4-cemA LSC 792 0.0871 0.96 81.7 yes View details
psbE-petL LSC 1109 0.0250 0.98 68.5 yes View details
clpP LSC 1388 0.0570 1.00 73.5 yes View details
rpl23-trnI-CAU IRb 345 0.0421 0.55 65.3 yes View details
ycf1 SSC 5559 0.0205 0.99 51.3 yes View details
ycf1-trnN-GUU IRa 512 0.0631 0.87 75.3 yes View details
trnI-CAU-rpl23 IRa 345 0.0421 0.55 65.3 yes View details
trnL-UAG-ccsA SSC 89 0.1628 0.97 82.6 yes View details
rpoC1-rpoB LSC 26 0.0385 1.00 74.6 yes View details
rps12-clpP LSC 172 0.0872 1.00 73.5 yes View details
psbN-psbH LSC 98 0.0408 1.00 72.4 yes View details
trnN-GUU-trnR-ACG IRa 648 0.0149 0.94 71.6 yes View details
trnE-UUC-psbD LSC 2344 0.0202 0.97 71.2 yes View details
trnI-CAU-ycf2 IRb 82 0.1786 0.68 70.8 yes View details
ycf2-trnI-CAU IRa 82 0.1786 0.68 70.8 yes View details
rpl33-rps18 LSC 568 0.0374 0.89 69.9 yes View details
rps15-ycf1 SSC 398 0.0286 0.97 68.4 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 AAGTCGCACGTTGCTTTCTA TTTGGTCCCGGTGATCAAAG 1579–1857 1.000 85.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCCACAGTCGATCATGTCCT TTTGGTCCCGGTGATCAAAG 1601–1879 1.000 85.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC TTTGGTCCCGGTGATCAAAG 1590–1868 1.000 84.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CCGGTGATCAAAGGTTCGAA 1572–1850 1.000 84.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCCACAGTCGATCATGTCCT CCGGTGATCAAAGGTTCGAA 1594–1872 1.000 84.2
rpoC1-rpoB_p1 rpoC1-rpoB GGGTTTTGTCACCTCTCCAA ACGATCTTTGGCTCTGGAAC 222 1.000 76.7
rpoC1-rpoB_p2 rpoC1-rpoB GGGTTTTGTCACCTCTCCAA TTCGATTGCTCGTTCGAGAA 244 1.000 74.7
rpoC1-rpoB_p3 rpoC1-rpoB GGGTTTTGTCACCTCTCCAA TTTCGATTGCTCGTTCGAGA 245 1.000 74.7
rpoC1-rpoB_p4 rpoC1-rpoB GGGTTTTGTCACCTCTCCAA CGATCTTTGGCTCTGGAACT 221 1.000 74.3
rpoC1-rpoB_p5 rpoC1-rpoB GGGTTTTGTCACCTCTCCAA TCGATTGCTCGTTCGAGAAT 243 1.000 73.0
trnE-UUC-psbD_p1 trnE-UUC-psbD CGTAGTATCCTACCCCCAGG GAAACGGTCCCTACGTAACC 2511–2601 1.000 82.8
trnE-UUC-psbD_p2 trnE-UUC-psbD GCTGCCTCCTTGAAAGAGAG GAAACGGTCCCTACGTAACC 2476–2566 1.000 81.4
trnE-UUC-psbD_p3 trnE-UUC-psbD TGTCCTGAACCACTAGACGA GAAACGGTCCCTACGTAACC 2455–2545 1.000 81.2
trnE-UUC-psbD_p4 trnE-UUC-psbD CGTAGTATCCTACCCCCAGG ACAAAAACGAAACGGTCCCT 2519–2609 1.000 80.8
trnE-UUC-psbD_p5 trnE-UUC-psbD CGTAGTATCCTACCCCCAGG GACCGGACCAACCTACAAAA 2533–2623 1.000 80.7
psbZ-trnG-UCC_p1 psbZ-trnG-UCC CTTCTCCTGATGGTTGGGTG CGTCTTCTCCTTGGCAAAGA 824–884 1.000 80.5
psbZ-trnG-UCC_p2 psbZ-trnG-UCC TTGCTTCTCCTGATGGTTGG CGTCTTCTCCTTGGCAAAGA 827–887 1.000 79.8
psbZ-trnG-UCC_p3 psbZ-trnG-UCC TTCTCCTGATGGTTGGGTGA CGTCTTCTCCTTGGCAAAGA 823–883 1.000 79.4
psbZ-trnG-UCC_p4 psbZ-trnG-UCC CTTCTCCTGATGGTTGGGTG TAAATACATTGCCTGGGCGG 863–923 1.000 79.2
psbZ-trnG-UCC_p5 psbZ-trnG-UCC TCCTGATGGTTGGGTGAGTA CGTCTTCTCCTTGGCAAAGA 820–880 1.000 78.8
ycf4-cemA_p1 ycf4-cemA GTCGCATCCTCCTACGATTC CGTATCGATACAACCCGCAT 1325–1371 1.000 85.3
ycf4-cemA_p2 ycf4-cemA GTCGCATCCTCCTACGATTC CGGAAGGGTGGAAACAAGAA 1601–1647 1.000 84.6
ycf4-cemA_p3 ycf4-cemA ATAGCGGGGTCTCGAAAAAC TTGTGCGCCTTTAGCAATTG 1610–1656 1.000 84.6
ycf4-cemA_p4 ycf4-cemA ATAGCGGGGTCTCGAAAAAC CGTATCGATACAACCCGCAT 1629–1675 1.000 84.5
ycf4-cemA_p5 ycf4-cemA ATAGCGGGGTCTCGAAAAAC CGGAAGGGTGGAAACAAGAA 1905–1951 1.000 84.1
psbE-petL_p1 psbE-petL AGAACGTTCTCCTGTGCTTC GTCGTATCTTGCTCAGACCG 1224–1227 1.000 80.9
psbE-petL_p2 psbE-petL ACGAATAACCAACCCGCAAT GTCGTATCTTGCTCAGACCG 1310–1313 1.000 80.6
psbE-petL_p3 psbE-petL GTTCTCCTGTGCTTCCAGAC GTCGTATCTTGCTCAGACCG 1219–1222 1.000 80.6
psbE-petL_p4 psbE-petL TGCTGACGAATAACCAACCC GTCGTATCTTGCTCAGACCG 1315–1318 1.000 80.4
psbE-petL_p5 psbE-petL CGAATAACCAACCCGCAATG GTCGTATCTTGCTCAGACCG 1309–1312 1.000 80.4

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
Parashorea chinensis NC_046579.1 152002 View on NCBI ↗
Parashorea macrophylla MH791330.1 151001 View on NCBI ↗