Markers + reference

Canarium

3 species · Burseraceae · Sapindales

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Species 3
Genome length 159–163 kb
Candidate markers 265
Primer pairs 60

Genome-wide nucleotide diversity

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

Candidate markers

3 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 IRb 5277 0.0728 0.20 56.8 yes View details
ndhF-rpl32 SSC 1070 0.0810 0.72 77.5 yes View details
ycf1 IRa 5277 0.0453 0.95 70.8 yes View details
trnH-GUG-psbA LSC 597 0.0512 0.99 87.3 yes View details
atpA-atpF LSC 56 0.0606 0.98 75.3 yes View details
trnR-UCU-atpA LSC 186 0.0352 0.97 73.0 yes View details
trnK-UUU-rps16 LSC 1088 0.0159 1.00 68.3 yes View details
clpP LSC 2196 0.0326 0.90 66.0 yes View details
psbE-petL LSC 1428 0.0082 1.00 64.3 yes View details
trnT-UGU-trnL-UAA LSC 1047 0.0139 0.98 63.8 yes View details
rps12-clpP LSC 260 0.0576 0.73 63.4 yes View details
ndhC-trnV-UAC LSC 926 0.0058 0.98 63.1 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 60 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 647–666 1.000 87.5
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 661–680 1.000 87.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 660–679 1.000 87.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 662–681 1.000 87.3
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 696–715 1.000 85.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCGATGGTATGGACGAATC AAAAAGGCGCTCAACCTACA 1261–1288 1.000 81.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC AAAAAGGCGCTCAACCTACA 1260–1287 1.000 81.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAAGGCGCTCAACCTACA 1199–1226 1.000 81.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGCGCTCAACCTACA 1198–1225 1.000 81.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAAAAGGCGCTCAACCTACA 1208–1235 1.000 80.2
trnR-UCU-atpA_p1 trnR-UCU-atpA ATTCGGAATGAAAGCGTCCA AAGACATTCACCGAGGAAGC 311–358 1.000 84.4
trnR-UCU-atpA_p2 trnR-UCU-atpA TCGGAATGAAAGCGTCCATT AAGACATTCACCGAGGAAGC 309–356 1.000 84.4
trnR-UCU-atpA_p3 trnR-UCU-atpA TTCGGAATGAAAGCGTCCAT AAGACATTCACCGAGGAAGC 310–357 1.000 84.4
trnR-UCU-atpA_p4 trnR-UCU-atpA CGGAATGAAAGCGTCCATTG AAGACATTCACCGAGGAAGC 308–355 1.000 83.9
trnR-UCU-atpA_p5 trnR-UCU-atpA TCGGAATGAAAGCGTCCATT TCAGGAACAATTGGAACGCT 265–312 1.000 83.4
atpA-atpF_p1 atpA-atpF CCGTCGCCTACTTGAAGTAC TGTTTGGGTCGCTGAAAGAA 200–201 1.000 81.3
atpA-atpF_p2 atpA-atpF GTCGCCTACTTGAAGTACGG TGTTTGGGTCGCTGAAAGAA 198–199 1.000 81.3
atpA-atpF_p3 atpA-atpF CCGTCGCCTACTTGAAGTAC ATGTTTGGGTCGCTGAAAGA 201–202 1.000 79.5
atpA-atpF_p4 atpA-atpF GTCGCCTACTTGAAGTACGG ATGTTTGGGTCGCTGAAAGA 199–200 1.000 79.5
atpA-atpF_p5 atpA-atpF GTCGCCTACTTGAAGTACGG CATGTTTGGGTCGCTGAAAG 200–201 1.000 78.9
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 1087–1106 1.000 83.1
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 1095–1114 1.000 82.5
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 1119–1138 1.000 82.1
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 1127–1146 1.000 81.5
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG AGTCCGTAGCGTCTACCAAT 1101–1120 1.000 81.1
ndhC-trnV-UAC_p1 ndhC-trnV-UAC TCTGGCCCTTTGCTAATTGG GCACGTTGGGTCTTTGAAAG 1065–1139 1.000 82.4
ndhC-trnV-UAC_p2 ndhC-trnV-UAC TCTGGCCCTTTGCTAATTGG AGAAGGTCTACGGTTCGAGT 1001–1075 1.000 81.8
ndhC-trnV-UAC_p3 ndhC-trnV-UAC TCTGGCCCTTTGCTAATTGG AATGCACGTTGGGTCTTTGA 1068–1142 1.000 80.9
ndhC-trnV-UAC_p4 ndhC-trnV-UAC TCTGGCCCTTTGCTAATTGG ATGCACGTTGGGTCTTTGAA 1067–1141 1.000 80.9
ndhC-trnV-UAC_p5 ndhC-trnV-UAC CCCTTTGCTAATTGGGGCTA GCACGTTGGGTCTTTGAAAG 1060–1134 1.000 80.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Canarium album NC_048982.1 163347 View on NCBI ↗
Canarium odontophyllum NC_073520.1 159433 View on NCBI ↗
Canarium ovatum PQ768873.1 159632 View on NCBI ↗