Markers + reference

Dactyladenia

3 species · Chrysobalanaceae · Malpighiales

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Species 3
Genome length 162–162 kb
Candidate markers 268
Primer pairs 115

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnG-GCC-trnR-UCU LSC 672 0.0030 1.00 37.3 yes View details
rpoB-trnC-GCA LSC 1307 0.0020 1.00 35.2 yes View details
trnC-GCA-petN LSC 983 0.0054 1.00 47.1 yes View details
trnF-GAA-ndhJ LSC 792 0.0059 1.00 37.0 yes View details
petA-psbJ LSC 800 0.0067 1.00 58.3 yes View details
rpl20 LSC 354 0.0113 1.00 40.6 yes View details
psbH LSC 222 0.0030 1.00 27.1 yes View details
rpl16 LSC 1470 0.0054 1.00 63.5 yes View details
ycf1 IRb 1105 0.0006 1.00 42.8 no View details
rpl32-trnL-UAG SSC 1303 0.0031 1.00 38.8 yes View details
ndhA SSC 2306 0.0032 1.00 52.0 yes View details
ycf1 SSC 5721 0.0033 1.00 50.8 yes View details
ycf1-trnN-GUU IRa 377 0.0035 1.00 36.9 yes View details
atpA-atpF LSC 65 0.0308 1.00 70.4 yes View details
trnE-UUC-trnT-GGU LSC 679 0.0039 1.00 66.3 yes View details
ndhC-trnV-UAC LSC 1202 0.0046 0.95 66.3 yes View details
petL-petG LSC 214 0.0109 1.00 64.7 yes View details
petN-psbM LSC 1053 0.0038 1.00 61.3 yes View details
cemA LSC 720 0.0019 1.00 60.3 yes View details
psbC LSC 1422 0.0019 1.00 59.9 yes View details
ycf3 LSC 1950 0.0027 1.00 59.9 yes View details
petA LSC 963 0.0014 1.00 59.6 yes View details
clpP LSC 2072 0.0032 1.00 55.9 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 115 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TGAATGAATAAAGTTGAAGTGAGT TGGTTTGATTGTCTAGCGTGA 2801–2814 1.000 40.7
trnK-UUU_p2 trnK-UUU TGAATGAATAAAGTTGAAGTGAGTT TGGTTTGATTGTCTAGCGTGA 2801–2814 1.000 40.7
trnK-UUU_p3 trnK-UUU TTGAATGAATAAAGTTGAAGTGAGT TGGTTTGATTGTCTAGCGTGA 2802–2815 1.000 40.7
trnK-UUU_p4 trnK-UUU TGAATGAATAAAGTTGAAGTGAGT TGGTTTGATTGTCTAGCGTG 2801–2814 1.000 40.7
trnK-UUU_p5 trnK-UUU TTGAATGAATAAAGTTGAAGTGAGTT TGGTTTGATTGTCTAGCGTGA 2802–2815 1.000 40.7
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 752–820 1.000 63.7
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 755–823 1.000 63.4
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 758–826 1.000 63.0
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 761–829 1.000 62.8
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 756–824 1.000 61.2
atpA-atpF_p1 atpA-atpF CCGTCGCCTACTTGAAGTAC TATTGGCATGTTTGGAGCGA 218–220 1.000 79.4
atpA-atpF_p2 atpA-atpF GTCGCCTACTTGAAGTACGG TATTGGCATGTTTGGAGCGA 216–218 1.000 79.4
atpA-atpF_p3 atpA-atpF TACTAATCTCGTCGGCTCGA TATTGGCATGTTTGGAGCGA 136–138 1.000 78.9
atpA-atpF_p4 atpA-atpF TAATCTCGTCGGCTCGAATG TATTGGCATGTTTGGAGCGA 133–135 1.000 77.6
atpA-atpF_p5 atpA-atpF ACTTGAAGTACGGTACCGGT TATTGGCATGTTTGGAGCGA 209–211 1.000 77.1
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AAGACTAGATCCCCGCCTAC ACAAAGTATCTTCCGCGCTT 2389–2418 1.000 80.6
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TACCCTTCCTCCCCAATCTG ACAAAGTATCTTCCGCGCTT 2147–2176 1.000 79.9
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TGGCATTTTCCTTTGACCCA ACAAAGTATCTTCCGCGCTT 2340–2369 1.000 79.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AAGACTAGATCCCCGCCTAC TTGTTAATCAGGCGACACCC 2081–2103 1.000 79.6
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AAAAGACTAGATCCCCGCCT ACAAAGTATCTTCCGCGCTT 2391–2420 1.000 79.6
trnC-GCA-petN_p1 trnC-GCA-petN GGGTGTCGCCTGATTAACAA AGTCCACCTCTTCCCCATAC 1083–1090 1.000 78.7
trnC-GCA-petN_p2 trnC-GCA-petN GGGTGTCGCCTGATTAACAA AGCCCAAGCGAGACTTACTA 1024–1031 1.000 78.5
trnC-GCA-petN_p3 trnC-GCA-petN GGGTGTCGCCTGATTAACAA GAGTCCACCTCTTCCCCATA 1084–1091 1.000 78.2
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGTCCACCTCTTCCCCATAC 1119–1126 1.000 77.3
trnC-GCA-petN_p5 trnC-GCA-petN CTGCAAATCCTTTTTCCCCG AGTCCACCTCTTCCCCATAC 1113–1120 1.000 77.2
petN-psbM_p1 petN-psbM GTATGGGGAAGAGGTGGACT GCGCTGTTCATTCTTGTTCC 1148–1149 1.000 79.3
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT GCGCTGTTCATTCTTGTTCC 1207–1208 1.000 79.0
petN-psbM_p3 petN-psbM TATGGGGAAGAGGTGGACTC GCGCTGTTCATTCTTGTTCC 1147–1148 1.000 78.8
petN-psbM_p4 petN-psbM GTATGGGGAAGAGGTGGACT ATTGCTACTGCGCTGTTCAT 1157–1158 1.000 77.5
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT ATTGCTACTGCGCTGTTCAT 1216–1217 1.000 77.2

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
Dactyladenia bellayana NC_030555.1 162281 View on NCBI ↗
Dactyladenia buchneri NC_030556.1 162110 View on NCBI ↗
Dactyladenia floretii NC_030557.1 162288 View on NCBI ↗