Markers + reference

Aquilaria

11 species · Thymelaeaceae · Malvales

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Species 11
Genome length 175–175 kb
Candidate markers 287
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 9 remaining regions by MarkerSeek score (out of 287 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 705 0.0094 0.99 54.7 yes View details
psbM-trnD-GUC LSC 754 0.0089 1.00 46.1 yes View details
psaA-ycf3 LSC 973 0.0097 1.00 61.0 yes View details
rps4-trnT-UGU LSC 516 0.0180 1.00 66.4 yes View details
trnF-GAA-ndhJ LSC 517 0.0059 1.00 44.7 yes View details
ndhC-trnV-UAC LSC 505 0.0215 1.00 64.2 yes View details
psbJ-petA LSC 777 0.0109 1.00 57.1 yes View details
cemA-ycf4 LSC 952 0.0072 1.00 53.3 yes View details
ndhF-rpl32 SSC 807 0.0148 1.00 64.7 yes View details
trnG-UCC-trnfM-CAU LSC 208 0.0119 1.00 57.8 yes View details
rpl2-rpl23 IRb 18 0.0505 1.00 57.0 yes View details
rpl23-rpl2 IRa 18 0.0505 1.00 57.0 yes View details
petN-psbM LSC 1105 0.0047 1.00 56.7 yes View details
trnE-UUC-trnT-GGU LSC 684 0.0030 1.00 55.4 yes View details
rps16-trnQ-UUG LSC 1184 0.0042 1.00 55.2 yes View details
rpoC1-rpoB LSC 29 0.0213 1.00 53.7 yes View details
atpF-atpH LSC 533 0.0036 1.00 53.5 yes View details
rps16 LSC 1141 0.0036 0.99 52.4 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TATTTCCTTGAAAGGGGCGC 806–816 1.000 77.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GCGGGGTTTTACGGAACTTA 755–760 0.909 75.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCGGGGTTTTACGGAACTTA 754–759 0.909 75.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GCGGGGTTTTACGGAACTTA 764–769 0.909 74.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC GCGGGGTTTTACGGAACTTA 741–746 0.909 73.4
rps16_p1 rps16 TGAGTCATCCACACCTCTTT CTACGCACAGACTGAACCAA 1293–1299 1.000 65.0
rps16_p2 rps16 TGAGTCATCCACACCTCTTTT CTACGCACAGACTGAACCAA 1293–1299 1.000 63.3
rps16_p3 rps16 ATGAGTCATCCACACCTCTT CTACGCACAGACTGAACCAA 1294–1300 1.000 63.1
rps16_p4 rps16 TGAGTCATCCACACCTCTTT CGCACAGACTGAACCAATGA 1290–1296 1.000 62.3
rps16_p5 rps16 ATGAGTCATCCACACCTCTTT CTACGCACAGACTGAACCAA 1294–1300 1.000 61.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTTGGTCCCGCTATTCGAAG 1272–1446 1.000 80.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC TTTGGTCCCGCTATTCGAAG 1283–1457 1.000 79.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTTTTGGTCCCGCTATTCGA 1274–1448 1.000 78.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATCAAAATGGGGCGTGG 1313–1487 0.909 76.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAAATCAAAATGGGGCGTGG 1324–1498 0.909 76.0
trnS-CGA_p1 trnS-CGA GACGCCAGAGTCCTTTGTTT CATGAATTCATGCATCATTGA 919–923 1.000 41.0
trnS-CGA_p2 trnS-CGA CGCCAGAGTCCTTTGTTTGA CATGAATTCATGCATCATTGA 917–921 1.000 41.0
trnS-CGA_p3 trnS-CGA GACGCCAGAGTCCTTTGTTT CATGAATTCATGCATCATTGAA 919–923 1.000 41.0
trnS-CGA_p4 trnS-CGA TATCTTGAGGACGCCAGAGT CATGAATTCATGCATCATTGA 928–932 1.000 40.9
trnS-CGA_p5 trnS-CGA TATCTTGAGGACGCCAGAGT CATGAATTCATGCATCATTGAA 928–932 1.000 40.9
atpF-atpH_p1 atpF-atpH ATTTAACCCGAAACTCCCGG TGGTCTGGTTGTAGCATTGG 649–657 1.000 79.2
atpF-atpH_p2 atpF-atpH GGCCAGTGACCTAAGGAAAC TGGTCTGGTTGTAGCATTGG 624–632 1.000 78.6
atpF-atpH_p3 atpF-atpH ATGGCCAGTGACCTAAGGAA TGGTCTGGTTGTAGCATTGG 626–634 1.000 77.4
atpF-atpH_p4 atpF-atpH TGGCCAGTGACCTAAGGAAA TGGTCTGGTTGTAGCATTGG 625–633 1.000 75.6
atpF-atpH_p5 atpF-atpH GCCAGTGACCTAAGGAAACG TGGTCTGGTTGTAGCATTGG 623–631 1.000 75.6
rpoC1-rpoB_p1 rpoC1-rpoB GGGTTTTGTCACCTCTCCAA TTGGCTTTGGAACTGAACCA 218–222 1.000 76.7
rpoC1-rpoB_p2 rpoC1-rpoB ATTTGTTGAGGCGAAACCGA TTGGCTTTGGAACTGAACCA 157–161 1.000 76.6
rpoC1-rpoB_p3 rpoC1-rpoB TTTGTTGAGGCGAAACCGAT TTGGCTTTGGAACTGAACCA 156–160 1.000 76.6
rpoC1-rpoB_p4 rpoC1-rpoB GAGGCGAAACCGATCCTATT TTGGCTTTGGAACTGAACCA 150–154 1.000 75.6
rpoC1-rpoB_p5 rpoC1-rpoB GGGTTTTGTCACCTCTCCAA TGGCTTTGGAACTGAACCAT 217–221 1.000 74.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Aquilaria agallochum NC_065040.1 174866 View on NCBI ↗
Aquilaria beccariana NC_052855.1 174831 View on NCBI ↗
Aquilaria crassna NC_043844.1 174830 View on NCBI ↗
Aquilaria cumingiana NC_065041.1 174834 View on NCBI ↗
Aquilaria hirta NC_052856.1 174761 View on NCBI ↗
Aquilaria khasiana PQ576418.2 174770 View on NCBI ↗
Aquilaria microcarpa NC_052857.1 174819 View on NCBI ↗
Aquilaria rostrata NC_052858.1 174693 View on NCBI ↗
Aquilaria rugosa NC_065042.1 174893 View on NCBI ↗
Aquilaria subintegra NC_052859.1 174828 View on NCBI ↗
Aquilaria yunnanensis NC_036940.1 174885 View on NCBI ↗