Markers + reference

Sisymbriopsis

3 species · Brassicaceae · Brassicales

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Species 3
Genome length 154–155 kb
Candidate markers 266
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-AGC-trnG-GGA LSC 784 0.0127 0.87 67.4 yes View details
trnC-UGC-petN LSC 660 0.0071 1.00 61.3 yes View details
psbM-trnD-GAC LSC 1023 0.0052 1.00 62.3 yes View details
trnE-GAA-trnT-ACC LSC 842 0.0060 0.99 59.3 yes View details
trnT-ACC-psbD LSC 1256 0.0053 1.00 62.1 yes View details
trnL-UUA-trnF-UUC LSC 565 0.0083 1.00 54.6 yes View details
ndhC-trnV-GUA LSC 887 0.0045 0.99 49.9 yes View details
rpl16 LSC 1520 0.0040 1.00 47.9 yes View details
ycf1 IRb 1035 0.0000 1.00 40.0 no View details
ndhF-rpl32 SSC 819 0.0057 0.99 63.2 yes View details
ccsA-ndhD SSC 215 0.0279 1.00 69.7 yes View details
ycf1 SSC 5271 0.0044 1.00 55.3 yes View details
psbE-petL LSC 1308 0.0049 1.00 65.8 yes View details
rpl32-trnL-CUA SSC 666 0.0060 1.00 62.3 yes View details
petA-psbJ LSC 925 0.0036 0.99 61.8 yes View details
psaA-ycf3 LSC 715 0.0037 1.00 61.7 yes View details
accD-psaI LSC 668 0.0030 1.00 60.7 yes View details
atpB-rbcL LSC 795 0.0025 1.00 60.5 yes View details
rpl20-rps12 LSC 760 0.0018 1.00 59.9 yes View details
ndhH SSC 1182 0.0011 1.00 59.5 yes View details
ndhF SSC 2241 0.0018 1.00 58.3 yes View details
ndhG-ndhI SSC 325 0.0082 1.00 58.3 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-AGC-trnG-GGA_p1 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA TGAATCAAACCGAGAGACCC 750–894 1.000 77.7
trnS-AGC-trnG-GGA_p2 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC TGAATCAAACCGAGAGACCC 748–892 1.000 77.4
trnS-AGC-trnG-GGA_p3 trnS-AGC-trnG-GGA GCTTTAGTCCACTCAGCCAT TGAATCAAACCGAGAGACCC 745–889 1.000 75.7
trnS-AGC-trnG-GGA_p4 trnS-AGC-trnG-GGA TCCAACGCTTTAGTCCACTC TGAATCAAACCGAGAGACCC 751–895 1.000 75.4
trnS-AGC-trnG-GGA_p5 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA GAATCAAACCGAGAGACCCT 749–893 1.000 75.3
trnC-UGC-petN_p1 trnC-UGC-petN TTTCCCCAGTTCAAATCCGG CTTCCCCACACTACGAGAGA 763–766 1.000 79.1
trnC-UGC-petN_p2 trnC-UGC-petN TTTCCCCAGTTCAAATCCGG TTCCCCACACTACGAGAGAG 762–765 1.000 79.1
trnC-UGC-petN_p3 trnC-UGC-petN GTTTCTATCGTTTTGGCGGC CTTCCCCACACTACGAGAGA 819–822 1.000 78.8
trnC-UGC-petN_p4 trnC-UGC-petN GTTTCTATCGTTTTGGCGGC TTCCCCACACTACGAGAGAG 818–821 1.000 78.8
trnC-UGC-petN_p5 trnC-UGC-petN TTTCCCCAGTTCAAATCCGG CTAGAGTCCACTCCTTCCCC 776–779 1.000 78.6
psbM-trnD-GAC_p1 psbM-trnD-GAC TGAGAATGAAGAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 1136–1139 1.000 59.7
psbM-trnD-GAC_p2 psbM-trnD-GAC GAGAATGAAGAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 1135–1138 1.000 56.4
psbM-trnD-GAC_p3 psbM-trnD-GAC AGGAATGAGAATGAAGAGTGCA TTCAATTGGTCAGAGCACCG 1141–1144 1.000 56.4
psbM-trnD-GAC_p4 psbM-trnD-GAC TGAGAATGAAGAGTGCAGTAGC GTTCAATTGGTCAGAGCACC 1137–1140 1.000 55.6
psbM-trnD-GAC_p5 psbM-trnD-GAC AGAATGAAGAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 1134–1137 1.000 54.3
trnE-GAA-trnT-ACC_p1 trnE-GAA-trnT-ACC TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 716–983 1.000 83.2
trnE-GAA-trnT-ACC_p2 trnE-GAA-trnT-ACC TTTCGTAGTACCCTACCCCC CCATGGCGTTACTCTACCAC 695–962 1.000 82.8
trnE-GAA-trnT-ACC_p3 trnE-GAA-trnT-ACC TTTCGTAGTACCCTACCCCC TGGCGTTACTCTACCACTGA 692–959 1.000 82.6
trnE-GAA-trnT-ACC_p4 trnE-GAA-trnT-ACC GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 678–945 1.000 82.4
trnE-GAA-trnT-ACC_p5 trnE-GAA-trnT-ACC TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 657–924 1.000 82.3
trnT-ACC-psbD_p1 trnT-ACC-psbD GTGGTAGAGTAACGCCATGG CAAAAACAAAGCGGTCCCTC 1405 1.000 79.0
trnT-ACC-psbD_p2 trnT-ACC-psbD TCAGTGGTAGAGTAACGCCA CAAAAACAAAGCGGTCCCTC 1408 1.000 78.8
trnT-ACC-psbD_p3 trnT-ACC-psbD GGCGTAAGTCATCGGTTCAA CAAAAACAAAGCGGTCCCTC 1382 1.000 77.2
trnT-ACC-psbD_p4 trnT-ACC-psbD TGGCCCTTTTAACTCAGTGG CAAAAACAAAGCGGTCCCTC 1421 1.000 77.2
trnT-ACC-psbD_p5 trnT-ACC-psbD GGCCCTTTTAACTCAGTGGT CAAAAACAAAGCGGTCCCTC 1420 1.000 77.2
psaA-ycf3_p1 psaA-ycf3 GCCCATTCCTCGAAAGAAGT GCTATAACGCTTACTCCCGG 863–867 1.000 79.3
psaA-ycf3_p2 psaA-ycf3 GCCCATTCCTCGAAAGAAGT GGCTATAACGCTTACTCCCG 864–868 1.000 79.3
psaA-ycf3_p3 psaA-ycf3 AGAAATGACCGGGTTTAGCC GCTATAACGCTTACTCCCGG 880–884 1.000 79.2
psaA-ycf3_p4 psaA-ycf3 AGAAATGACCGGGTTTAGCC GGCTATAACGCTTACTCCCG 881–885 1.000 79.2
psaA-ycf3_p5 psaA-ycf3 GCCCATTCCTCGAAAGAAGT ATTGGTTGACCATCACGAGG 823–827 1.000 78.9

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
Sisymbriopsis mollipila NC_050806.1 154682 View on NCBI ↗
Sisymbriopsis pamirica NC_053338.1 154457 View on NCBI ↗
Sisymbriopsis schugnana NC_053339.1 154423 View on NCBI ↗