Markers + reference

Vatica

6 species · Dipterocarpaceae · Malvales

Back to catalogue

Species 6
Genome length 151–152 kb
Candidate markers 250
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 250 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-trnQ-UUG LSC 1998 0.0092 0.95 64.6 yes View details
trnE-UUC-trnT-GGU LSC 958 0.0127 0.97 72.1 yes View details
accD LSC 1287 0.0092 0.99 54.2 yes View details
rps12-clpP LSC 376 0.0967 0.81 72.5 yes View details
trnN-GUU-rps15 SSC 6456 0.0075 0.99 60.3 yes View details
ndhD-ccsA SSC 252 0.0410 1.00 67.2 yes View details
ccsA SSC 963 0.0042 1.00 35.8 yes View details
trnL-UAG-ndhF SSC 2650 0.0114 0.95 58.1 yes View details
psbZ-trnG-GCC LSC 692 0.0116 0.96 68.0 yes View details
rps4-trnT-UGU LSC 558 0.0029 1.00 58.8 yes View details
rpl33-rps18 LSC 519 0.0132 1.00 58.8 yes View details
ndhC-trnV-UAC LSC 1031 0.0065 0.99 58.5 yes View details
trnP-UGG-psaJ LSC 419 0.0111 0.98 58.5 yes View details
trnF-GAA-ndhJ LSC 716 0.0055 0.98 58.4 yes View details
psaA-ycf3 LSC 836 0.0066 0.99 58.3 yes View details
petN-psbM LSC 772 0.0094 0.99 58.0 yes View details
trnT-UGU-trnL-UAA LSC 839 0.0030 0.97 57.9 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 85 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 CCGATGGTATGGACGAATCC TTTGGTCCCGGTGATCAAAG 2091–2162 0.833 77.3
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG CGATGGTATGGACGAATCCC TTTGGTCCCGGTGATCAAAG 2090–2161 0.833 77.3
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG GATGGTATGGACGAATCCCG TTTGGTCCCGGTGATCAAAG 2089–2160 0.833 77.3
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG CGATGGTATGGACGAATCCC CCGGTGATCAAAGGTTCGAA 2083–2154 0.833 76.5
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG GATGGTATGGACGAATCCCG CCGGTGATCAAAGGTTCGAA 2082–2153 0.833 76.5
petN-psbM_p1 petN-psbM GGCGGCATTAATGACAGTCT ATTGCTACTGCGCTGTTCAT 915–920 1.000 77.2
petN-psbM_p2 petN-psbM GGCGGCATTAATGACAGTCT TATTGCTACTGCGCTGTTCA 916–921 1.000 76.2
petN-psbM_p3 petN-psbM GGCGGCATTAATGACAGTCT TTGCTACTGCGCTGTTCATT 914–919 1.000 75.4
petN-psbM_p4 petN-psbM GGCGGCATTAATGACAGTCT TGCTTTTATTGCTACTGCGC 922–927 1.000 74.9
petN-psbM_p5 petN-psbM GGCGGCATTAATGACAGTCT GCTACTGCGCTGTTCATTCT 912–917 1.000 74.2
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTAGTATCCTACCCCCAGG GAACCGATGACTTACGCCTT 953–1096 1.000 85.1
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTAGTATCCTACCCCCAGG CCATGGCGTTACTCTACCAC 932–1075 1.000 84.6
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 902–1045 1.000 84.6
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 900–1043 1.000 84.6
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGTAGTATCCTACCCCCAGG TGGCGTTACTCTACCACTGA 929–1072 1.000 84.4
psbZ-trnG-GCC_p1 psbZ-trnG-GCC CTTCTCCTGATGGTTGGGTG CGTCTTCTCCTTGGCAAAGA 846–867 1.000 83.5
psbZ-trnG-GCC_p2 psbZ-trnG-GCC CCCGTTGTTTTTGCTTCTCC CGTCTTCTCCTTGGCAAAGA 859–880 1.000 83.3
psbZ-trnG-GCC_p3 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG CGTCTTCTCCTTGGCAAAGA 849–870 1.000 82.8
psbZ-trnG-GCC_p4 psbZ-trnG-GCC TTCTCCTGATGGTTGGGTGA CGTCTTCTCCTTGGCAAAGA 845–866 1.000 82.3
psbZ-trnG-GCC_p5 psbZ-trnG-GCC CTTCTCCTGATGGTTGGGTG TAAATACATTGCCTGGGCGG 885–906 1.000 82.2
psaA-ycf3_p1 psaA-ycf3 GCCCATTCCTCGAAAGAAGT ATCAAGCCGCTGAGTATTGG 1004–1039 1.000 81.5
psaA-ycf3_p2 psaA-ycf3 GCCCATTCCTCGAAAGAAGT GGAAACAGGCTATAGCGCTT 986–1021 1.000 81.5
psaA-ycf3_p3 psaA-ycf3 AGAAATGACCCGGTTTAGCC ATCAAGCCGCTGAGTATTGG 1021–1056 1.000 81.4
psaA-ycf3_p4 psaA-ycf3 AGAAATGACCCGGTTTAGCC GGAAACAGGCTATAGCGCTT 1003–1038 1.000 81.4
psaA-ycf3_p5 psaA-ycf3 GCCCATTCCTCGAAAGAAGT CAGAGGCTTGGTTCGATCAA 1019–1054 1.000 81.0
rps4-trnT-UGU_p1 rps4-trnT-UGU GATTGGTTTTTGCCGGCTTT CTCAGAGGTTAGAGCATCGC 717–719 1.000 78.6
rps4-trnT-UGU_p2 rps4-trnT-UGU GATTGGTTTTTGCCGGCTTT ATGGTCATCGGTTCGATTCC 685–687 1.000 77.8
rps4-trnT-UGU_p3 rps4-trnT-UGU GATTGGTTTTTGCCGGCTTT CAGAGGTTAGAGCATCGCAT 715–717 1.000 75.5
rps4-trnT-UGU_p4 rps4-trnT-UGU GATTGGTTTTTGCCGGCTTT TCAGAGGTTAGAGCATCGCA 716–718 1.000 75.5
rps4-trnT-UGU_p5 rps4-trnT-UGU TTGGTTTTTGCCGGCTTTAG CTCAGAGGTTAGAGCATCGC 715–717 1.000 75.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Vatica bantamensis NC_071231.1 151544 View on NCBI ↗
Vatica guangxiensis NC_051531.1 151010 View on NCBI ↗
Vatica javanica subsp. scaphifolia PV605346.1 151556 View on NCBI ↗
Vatica mangachapoi NC_041485.1 151538 View on NCBI ↗
Vatica odorata NC_054172.1 151553 View on NCBI ↗
Vatica rassak NC_058774.1 151394 View on NCBI ↗