Markers + reference

Sphenostylis

2 species · Fabaceae · Fabales

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Species 2
Genome length 150–150 kb
Candidate markers 262
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpl16 LSC 1419 0.0035 1.00 46.3 yes View details
trnG-GCC-psbZ LSC 640 0.0063 1.00 62.3 yes View details
petN-trnC-GCA LSC 708 0.0043 0.99 58.0 yes View details
rpoC2 LSC 4086 0.0024 1.00 40.4 yes View details
accD LSC 1506 0.0046 1.00 46.4 yes View details
clpP LSC 2104 0.0039 0.99 46.3 yes View details
ndhI-ndhG SSC 278 0.0144 1.00 61.1 yes View details
psaJ-rps18 LSC 865 0.0046 1.00 61.4 yes View details
trnT-GGU-trnE-UUC LSC 728 0.0028 0.99 61.0 yes View details
trnL-UAA-trnT-UGU LSC 789 0.0025 1.00 60.3 yes View details
trnQ-UUG-accD LSC 675 0.0015 0.99 60.3 yes View details
ycf4-cemA LSC 502 0.0079 0.75 60.3 yes View details
ndhJ-trnF-GAA LSC 794 0.0025 1.00 60.2 yes View details
petA-psbJ LSC 644 0.0031 1.00 60.2 yes View details
psbD-trnT-GGU LSC 996 0.0020 1.00 60.1 yes View details
trnD-GUC-psbM LSC 387 0.0079 0.99 60.1 yes View details
atpI-atpH LSC 1045 0.0019 1.00 60.0 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rpl16_p1 rpl16 ATTGCGCGTGTAGAATGGAT GTCTCAATTCTCGGGCGATT 2168–2171 1.000 79.4
rpl16_p2 rpl16 ATTGCGCGTGTAGAATGGAT TCTCAATTCTCGGGCGATTG 2167–2170 1.000 79.4
rpl16_p3 rpl16 ATTGCGCGTGTAGAATGGAT AACTGTCTCAATTCTCGGGC 2172–2175 1.000 79.1
rpl16_p4 rpl16 ATTGCGCGTGTAGAATGGAT ACCTCGGGTGCTAATGAAAC 2208–2211 1.000 79.0
rpl16_p5 rpl16 ATTGCGCGTGTAGAATGGAT GCGCAAAAGATTCGAGTTCC 2148–2151 1.000 79.0
ndhJ-trnF-GAA_p1 ndhJ-trnF-GAA ATAGTCATCCGCGTCTGAGA GCTTCAAGAATGGTCGGGAT 989 1.000 79.6
ndhJ-trnF-GAA_p2 ndhJ-trnF-GAA ATAGTCATCCGCGTCTGAGA CCTCGTGTCACCAGTTCAAA 938 1.000 79.5
ndhJ-trnF-GAA_p3 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC GCTTCAAGAATGGTCGGGAT 949 1.000 79.2
ndhJ-trnF-GAA_p4 ndhJ-trnF-GAA ATAGTCATCCGCGTCTGAGA AGAATGGTCGGGATAGCTCA 983 1.000 79.2
ndhJ-trnF-GAA_p5 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC CCTCGTGTCACCAGTTCAAA 898 1.000 79.2
trnL-UAA-trnT-UGU_p1 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GCGATGCTCTAACCTCTGAG 839–840 1.000 79.2
trnL-UAA-trnT-UGU_p2 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GCGATGCTCTAACCTCTGAG 847–848 1.000 78.7
trnL-UAA-trnT-UGU_p3 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GGATTCGAACCGATGACCAT 871–872 1.000 78.3
trnL-UAA-trnT-UGU_p4 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GGATTCGAACCGATGACCAT 879–880 1.000 77.8
trnL-UAA-trnT-UGU_p5 trnL-UAA-trnT-UGU CCCATTGTGAATTCCAGGGT GCGATGCTCTAACCTCTGAG 932–933 1.000 77.3
trnG-GCC-psbZ_p1 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA CTTCTCCTGAAGGTTGGTCA 794 1.000 69.2
trnG-GCC-psbZ_p2 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA CTTCTCCTGAAGGTTGGTCAA 794 1.000 67.1
trnG-GCC-psbZ_p3 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA TCTCCTGAAGGTTGGTCAAA 792 1.000 65.3
trnG-GCC-psbZ_p4 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA TTCTCCTGAAGGTTGGTCAA 793 1.000 65.3
trnG-GCC-psbZ_p5 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA TTCTCCTGAAGGTTGGTCAAA 793 1.000 63.5
psbD-trnT-GGU_p1 psbD-trnT-GGU CCGCAACCAGTCATCCATAA GTGGTAGAGTAACGCCATGG 1125–1126 1.000 79.5
psbD-trnT-GGU_p2 psbD-trnT-GGU CCGCAACCAGTCATCCATAA TCAGTGGTAGAGTAACGCCA 1128–1129 1.000 79.3
psbD-trnT-GGU_p3 psbD-trnT-GGU CCAACCCACAAAAACGAACC GTGGTAGAGTAACGCCATGG 1152–1153 1.000 79.2
psbD-trnT-GGU_p4 psbD-trnT-GGU CCAACCCACAAAAACGAACC TCAGTGGTAGAGTAACGCCA 1155–1156 1.000 79.0
psbD-trnT-GGU_p5 psbD-trnT-GGU AAAAACGAACCGGTCTCTCC GTGGTAGAGTAACGCCATGG 1143–1144 1.000 78.8
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC CCATGGCGTTACTCTACCAC GCTGCCTCCTTGAAAGAGAG 805–810 1.000 78.1
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC CCATGGCGTTACTCTACCAC TGTCCTGAACCACTAGACGA 784–789 1.000 77.9
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC TGGCGTTACTCTACCACTGA GCTGCCTCCTTGAAAGAGAG 802–807 1.000 77.9
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC ACACCTTACCATGGCGTTAC GCTGCCTCCTTGAAAGAGAG 813–818 1.000 77.8
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC TGGCGTTACTCTACCACTGA TGTCCTGAACCACTAGACGA 781–786 1.000 77.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Sphenostylis angustifolia PV870736.1 149636 View on NCBI ↗
Sphenostylis stenocarpa PP920094.1 149622 View on NCBI ↗