Markers + reference

Burmannia

3 species · Burmanniaceae · Dioscoreales

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Species 3
Genome length 108–156 kb
Candidate markers 271
Primer pairs 100

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 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 664 0.1264 0.96 80.3 yes View details
psbM-trnD-GUC LSC 646 0.1261 0.87 80.7 yes View details
trnT-UGU-trnL-UAA LSC 627 0.1202 0.98 82.8 yes View details
rbcL-accD LSC 931 0.1096 0.94 82.9 yes View details
ycf4-cemA LSC 901 0.1158 0.79 78.4 yes View details
psbE-petL LSC 1150 0.1073 0.46 68.9 yes View details
ycf1 SSC 5472 0.0617 0.99 69.9 yes View details
rps15-ycf1 SSC 416 0.1792 0.96 78.5 yes View details
ycf1 SSC 5694 0.0880 0.94 76.7 no View details
atpF LSC 1379 0.0716 0.96 83.0 yes View details
rpl16 LSC 1499 0.0627 0.98 82.6 yes View details
ndhI SSC 483 0.0697 1.00 82.6 yes View details
trnE-UUC-trnT-GGU LSC 751 0.0978 0.93 82.5 yes View details
clpP LSC 2146 0.0743 0.96 81.9 yes View details
trnF-GAA-ndhJ LSC 488 0.0975 0.97 81.8 yes View details
ycf3-trnS-GGA LSC 693 0.1073 0.96 81.6 yes View details
atpB-rbcL LSC 861 0.0808 0.95 81.6 yes View details
psaB LSC 2205 0.0602 1.00 81.4 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU GCGGAAATAGGAGCTTCCAT AAGACCACGACTGATCCTGA 932–1094 0.667 73.7
trnK-UUU_p2 trnK-UUU GCGGAAATAGGAGCTTCCAT AGACCACGACTGATCCTGAA 931–1093 0.667 73.7
trnK-UUU_p3 trnK-UUU GCGGAAATAGGAGCTTCCAT TACCTGATGGGGAAAGGGTT 784 0.333 50.7
trnK-UUU_p4 trnK-UUU AAGCGGAAATAGGAGCTTCC TACCTGATGGGGAAAGGGTT 786 0.333 50.1
trnK-UUU_p5 trnK-UUU AAGCGGAAATAGGAGCTTCC AGACCACGACTGATCCTGAA 1095 0.333 50.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC TACCACTAAACTATACCCGC 548–883 1.000 52.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC TTACCACTAAACTATACCCGC 549–884 1.000 52.0
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC TTTACCACTAAACTATACCCGC 550–885 1.000 52.0
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC CTTTTACCACTAAACTATACCCGC 552–887 1.000 52.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC TTTTACCACTAAACTATACCCGC 551–886 1.000 52.0
trnG-UCC_p1 trnG-UCC TCAGTTTAATGCTGTCCGGG TTCAATGAGGAGGCAGAAGC 1608–1735 0.667 73.4
trnG-UCC_p2 trnG-UCC TAGCAATCTGCCGCTTTCAT TTCAATGAGGAGGCAGAAGC 1917 0.333 52.0
trnG-UCC_p3 trnG-UCC TAGCAATCTGCCGCTTTCAT GGAGGCAGAAGCTCTTTTGA 1909 0.333 51.5
trnG-UCC_p4 trnG-UCC TAGCAATCTGCCGCTTTCAT AGGAGGCAGAAGCTCTTTTG 1910 0.333 51.4
trnG-UCC_p5 trnG-UCC TAGCAATCTGCCGCTTTCAT GAGTTAGAAGCCTTTGCCCA 2187 0.333 51.4
atpF_p1 atpF CCATTAGTACGACGCCAACA TATTGCGAGACAACCCGAAG 2066–2269 1.000 92.0
atpF_p2 atpF CCATTAGTACGACGCCAACA ATTTCTGCCGCTTCCGTTAT 2167–2370 1.000 91.7
atpF_p3 atpF TTACCCGTCTGTCTATCCCC TATTGCGAGACAACCCGAAG 2361–2564 1.000 91.3
atpF_p4 atpF CACGACCCAAATAAGCCTCA TATTGCGAGACAACCCGAAG 2156–2359 1.000 91.1
atpF_p5 atpF CCATTAGTACGACGCCAACA ATCCATTGATTTCTGCCGCT 2175–2378 0.667 73.7
psbM-trnD-GUC_p1 psbM-trnD-GUC TTGACTCACTGTTTTCACGT GTTCGAGCCCCGTCAATC 558–763 0.667 37.9
psbM-trnD-GUC_p2 psbM-trnD-GUC TGACTCACTGTTTTCACGTAGA GTTCGAGCCCCGTCAATC 557–762 0.667 37.0
psbM-trnD-GUC_p3 psbM-trnD-GUC TTTGACTCACTGTTTTCACGT GTTCGAGCCCCGTCAATC 559–764 0.667 36.2
psbM-trnD-GUC_p4 psbM-trnD-GUC TTGACTCACTGTTTTCACGTAGA GTTCGAGCCCCGTCAATC 558–763 0.667 35.8
psbM-trnD-GUC_p5 psbM-trnD-GUC TTTTGACTCACTGTTTTCACGT GTTCGAGCCCCGTCAATC 560–765 0.667 35.7
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 855–893 1.000 90.6
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU GTGCTCTGACCGATTGAACT GAACCGATGACTTACGCCTT 1469–1478 0.667 75.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GTGCTCTGACCGATTGAACT ATTGTCGCCAATGTGGAAGT 1893 0.333 51.9
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GTGCTCTGACCGATTGAACT TGTCGCCAATGTGGAAGTAG 1891 0.333 51.9
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GTGCTCTGACCGATTGAACT GTCGCCAATGTGGAAGTAGT 1890 0.333 51.9

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
Burmannia coelestis NC_036660.1 156223 View on NCBI ↗
Burmannia cryptopetala NC_036662.1 107771 View on NCBI ↗
Burmannia disticha NC_036661.1 156422 View on NCBI ↗