Markers + reference

Mallotus

3 species · Euphorbiaceae · Malpighiales

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Species 3
Genome length 163–165 kb
Candidate markers 268
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 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 956 0.2162 0.90 82.2 yes View details
atpH-atpI LSC 999 0.0755 0.95 98.3 yes View details
petN-psbM LSC 1025 0.0847 0.99 79.7 yes View details
trnE-UUC-trnT-GGU LSC 1770 0.0783 0.61 69.7 yes View details
trnT-GGU-psbD LSC 1815 0.0586 0.99 82.3 yes View details
psbZ-trnG-UCC LSC 625 0.1086 0.99 91.8 yes View details
psbE-petL LSC 1585 0.1005 0.97 85.2 yes View details
rpl22-rps19 IRb 1181 0.1123 0.39 65.1 yes View details
ndhF SSC 3580 0.0318 0.96 63.4 yes View details
rps19-trnH-GUG IRa 814 0.3243 0.98 84.6 no View details
trnK-UUU-rps16 LSC 547 0.0652 1.00 86.7 yes View details
trnH-GUG-psbA LSC 590 0.0805 0.95 85.3 yes View details
rps16-trnQ-UUG LSC 1083 0.0803 0.97 84.6 yes View details
atpF-atpH LSC 382 0.0444 0.90 83.5 yes View details
trnD-GUC-trnY-GUA LSC 382 0.0532 1.00 83.5 yes View details
atpA-atpF LSC 67 0.0601 0.91 82.7 yes View details
psbM-trnD-GUC LSC 922 0.0540 0.98 82.5 yes View details
accD-psaI LSC 1166 0.0808 0.94 82.4 yes View details
trnG-UCC-trnfM-CAU LSC 173 0.0694 1.00 81.9 yes View details
psbC-trnS-UGA LSC 197 0.0863 1.00 80.8 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 644–744 1.000 90.1
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 647–747 1.000 90.0
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 658–758 1.000 89.9
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 657–757 1.000 89.9
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 659–759 1.000 89.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGGGGTTACAGAACTTCTTCTC 656–1187 1.000 68.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGGGGTTACAGAACTTCTTCT 656–1187 1.000 68.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC GGGGGTTACAGAACTTCTTCTC 655–1186 1.000 64.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC GGGGGTTACAGAACTTCTTCT 655–1186 1.000 64.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA ACTATCCCCCTTCTCTTGTTCT 633 0.333 34.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TGGACTTGAAATTTGCCCGA GAAATTCAAATGGGGCGTGG 1491–1646 1.000 90.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCCGAATTGGATCCTTTCT GAAATTCAAATGGGGCGTGG 1477–1632 1.000 90.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TGGACTTGAAATTTGCCCGA GAGGTTCGAATCCTTCCGTC 1433–1588 1.000 90.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TGGACTTGAAATTTGCCCGA CTTACAGCAGCTTGCCAAAC 2033–2221 1.000 88.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TGGACTTGAAATTTGCCCGA TAGGCTTCGGGCAATTTTGT 1946–2134 1.000 88.8
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG CGTTTCAAGAGTAGGGTCCG 1548–1711 1.000 91.7
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG GCGAGTTGCTCAAACAATCC 1384–1547 1.000 91.5
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG CGTTTCAAGAGTAGGGTCCG 1551–1714 1.000 91.5
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG GCGAGTTGCTCAAACAATCC 1387–1550 1.000 91.3
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU TTTCGCCCACGTCTTATAGC CGTTTCAAGAGTAGGGTCCG 1676–1839 0.667 77.2
atpA-atpF_p1 atpA-atpF CCGTCGCCTACTTGAAGTAC GCTTGACCGACGAGTTACAT 248–260 1.000 84.8
atpA-atpF_p2 atpA-atpF GTCGCCTACTTGAAGTACGG GCTTGACCGACGAGTTACAT 246–258 1.000 84.8
atpA-atpF_p3 atpA-atpF TACTAATCTCGTCGGCTCGA GCTTGACCGACGAGTTACAT 166–178 1.000 84.4
atpA-atpF_p4 atpA-atpF CCGTCGCCTACTTGAAGTAC AGCCTTACAGGGAGCTCTAG 283–295 1.000 83.9
atpA-atpF_p5 atpA-atpF GTCGCCTACTTGAAGTACGG AGCCTTACAGGGAGCTCTAG 281–293 1.000 83.9
atpF-atpH_p1 atpF-atpH CCAGTGACCCAAAGAAACGA CGGAGGGAAAAATACGAGGT 520–558 1.000 81.3
atpF-atpH_p2 atpF-atpH CCAGTGACCCAAAGAAACGA CGAGGCGGAGGGAAAAATAC 525–563 1.000 81.2
atpF-atpH_p3 atpF-atpH CCAGTGACCCAAAGAAACGA GAGGCGGAGGGAAAAATACG 524–562 1.000 81.2
atpF-atpH_p4 atpF-atpH CCAGTGACCCAAAGAAACGA GCGGAGGGAAAAATACGAGG 521–559 1.000 81.2
atpF-atpH_p5 atpF-atpH CCAGTGACCCAAAGAAACGA GGCGGAGGGAAAAATACGAG 522–560 1.000 81.2

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
Mallotus japonicus NC_057003.1 164912 View on NCBI ↗
Mallotus paniculatus NC_058595.1 164455 View on NCBI ↗
Mallotus peltatus NC_047284.1 163303 View on NCBI ↗