Markers + reference

Speranskia

3 species · Euphorbiaceae · Malpighiales

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Species 3
Genome length 170–190 kb
Candidate markers 267
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-GCC LSC 1955 0.2094 0.99 83.8 yes View details
atpF-atpH LSC 1686 0.1680 0.97 78.3 yes View details
psbZ-trnG-UCC LSC 1516 0.1487 0.90 80.8 yes View details
ndhC-trnV-UAC LSC 2236 0.1888 0.83 79.0 yes View details
rpl16-rps3 LSC 2552 0.1206 0.95 81.2 yes View details
trnT-UGU-trnL-UAA LSC 506 0.0534 1.00 89.2 yes View details
trnE-UUC-trnT-GGU LSC 1809 0.0753 0.99 88.1 yes View details
petA-psbJ LSC 1257 0.0528 0.99 87.3 yes View details
rps3-rps19 LSC 752 0.0623 0.99 86.3 yes View details
accD-psaI LSC 1719 0.0766 0.99 85.9 yes View details
psbI-trnS-GCU LSC 245 0.1456 1.00 84.5 yes View details
clpP-psbB LSC 866 0.0804 0.99 84.5 yes View details
rps19-trnH-GUG IRa 535 0.1308 0.93 84.0 no View details
trnG-GCC-trnR-UCU LSC 696 0.1067 0.97 83.2 yes View details
rpl33-rps18 LSC 537 0.0800 0.99 81.3 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbI-trnS-GCU_p1 psbI-trnS-GCU GTAATCCTGGGCGTGAAGAA CGAATTATCCGTACCGAGGG 308–632 0.667 72.8
psbI-trnS-GCU_p2 psbI-trnS-GCU GTAATCCTGGGCGTGAAGAA GATGGCTGAGTGGACGAAAG 351–675 0.667 70.4
psbI-trnS-GCU_p3 psbI-trnS-GCU GTAATCCTGGGCGTGAAGAA TTCGAATCCCTCTCTTTCCG 288–612 0.667 67.8
psbI-trnS-GCU_p4 psbI-trnS-GCU GTAATCCTGGGCGTGAAGAA TTATCCGTACCGAGGGTTCG 304–628 0.667 67.7
psbI-trnS-GCU_p5 psbI-trnS-GCU GTAATCCTGGGCGTGAAGAA CGAAAGCGTCGGATTGCTAA 337–661 0.667 67.5
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC AATTCCAAGTCATTGCCGGA ACGAATCACACTTTTACCACT 1703–2099 0.667 48.7
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC ATTCCAAGTCATTGCCGGAA ACGAATCACACTTTTACCACT 1702–2098 0.667 48.7
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC AATTCCAAGTCATTGCCGGA GAACGAATCACACTTTTACCACT 1705–2101 0.667 47.6
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC ATTCCAAGTCATTGCCGGAA AGAACGAATCACACTTTTACCAC 1705–2101 0.667 47.6
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC ATTCCAAGTCATTGCCGGAA GAACGAATCACACTTTTACCACT 1704–2100 0.667 47.6
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG GCGAGTTGCTCAAACAATCC 1378–2735 1.000 89.5
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG GCGAGTTGCTCAAACAATCC 1381–2738 1.000 89.3
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU TTTCGCTCACGTCTTCTAGC GCGAGTTGCTCAAACAATCC 1506–2863 1.000 89.1
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU AAGGGATCATCGGCTCCATA GCGAGTTGCTCAAACAATCC 2048 0.333 52.8
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU TAAGGGATCATCGGCTCCAT GCGAGTTGCTCAAACAATCC 2049 0.333 52.8
atpF-atpH_p1 atpF-atpH CAGTGACCCAAGGAAACGAA CCGTTATTGCTGCTGGTTTG 887–2053 1.000 91.5
atpF-atpH_p2 atpF-atpH CAGTGACCCAAGGAAACGAA CGTTATTGCTGCTGGTTTGG 886–2052 1.000 91.5
atpF-atpH_p3 atpF-atpH CAGTGACCCAAGGAAACGAA ATTTCTGCCGCTTCCGTTAT 900–2066 1.000 91.4
atpF-atpH_p4 atpF-atpH CAGTGACCCAAGGAAACGAA AGGCCAAGCTGTAGAAGGTA 817–1983 1.000 91.3
atpF-atpH_p5 atpF-atpH CAGTGACCCAAGGAAACGAA ATCCATTGATTTCTGCCGCT 908–2074 1.000 91.2
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 1912 0.333 51.2
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 1891 0.333 51.0
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCATGGCGTTACTCTACCAC 1891 0.333 50.7
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA CCATGGCGTTACTCTACCAC 1870 0.333 50.6
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TGGCGTTACTCTACCACTGA 1888 0.333 50.5
psbZ-trnG-UCC_p1 psbZ-trnG-UCC TCCTTAATTCTCTCATCTCTTGA CGTCTTCTCCTTGGCAAAGA 1247–2086 1.000 52.0
psbZ-trnG-UCC_p2 psbZ-trnG-UCC GGTATCCTTAATTCTCTCATCTCT CGTCTTCTCCTTGGCAAAGA 1251–2090 1.000 52.0
psbZ-trnG-UCC_p3 psbZ-trnG-UCC GGTATCCTTAATTCTCTCATCTCTTG CGTCTTCTCCTTGGCAAAGA 1251–2090 1.000 52.0
psbZ-trnG-UCC_p4 psbZ-trnG-UCC GGTATCCTTAATTCTCTCATCTCTTGA CGTCTTCTCCTTGGCAAAGA 1251–2090 1.000 52.0
psbZ-trnG-UCC_p5 psbZ-trnG-UCC ATCCTTAATTCTCTCATCTCTTGA CGTCTTCTCCTTGGCAAAGA 1248–2087 1.000 52.0

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
Speranskia cantonensis PP941956.1 172459 View on NCBI ↗
Speranskia tuberculata PP941955.1 190093 View on NCBI ↗
Speranskia yunnanensis PP941957.1 170054 View on NCBI ↗