Markers + reference

Cymatocarpus

3 species · Brassicaceae · Brassicales

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Species 3
Genome length 155–155 kb
Candidate markers 266
Primer pairs 120

Genome-wide nucleotide diversity

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

Candidate markers

15 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
trnH-CAC-psbA LSC 291 0.0550 1.00 80.3 yes View details
trnK-AAA-rps16 LSC 603 0.0357 0.99 69.9 yes View details
rps16 LSC 1120 0.0190 1.00 63.8 yes View details
trnS-AGC-trnG-GGA LSC 660 0.0291 0.97 73.3 yes View details
trnR-AGA-atpA LSC 309 0.0261 0.99 62.2 yes View details
trnE-GAA-trnT-ACC LSC 815 0.0221 1.00 61.2 yes View details
trnL-UUA-trnF-UUC LSC 944 0.0954 0.95 91.7 yes View details
ndhC-trnV-GUA LSC 911 0.0206 0.98 64.6 yes View details
petA-psbJ LSC 900 0.0282 1.00 76.3 yes View details
psbE-petL LSC 1285 0.0200 0.98 66.3 yes View details
clpP LSC 2040 0.0152 1.00 53.1 yes View details
ycf1 IRb 1035 0.0019 1.00 37.7 no View details
ndhF-rpl32 SSC 829 0.0282 1.00 66.5 yes View details
rpl32-trnL-CUA SSC 789 0.0364 1.00 79.2 yes View details
ycf1 SSC 5352 0.0153 1.00 49.1 yes View details
trnG-GGA-trnR-AGA LSC 162 0.0658 1.00 85.7 yes View details
ndhE-ndhG SSC 261 0.0471 0.98 73.5 yes View details
rps15-ycf1 SSC 356 0.0338 0.97 67.4 yes View details
trnT-ACA-trnL-UUA LSC 610 0.0251 1.00 66.6 yes View details
psbC-trnS-UCA LSC 182 0.0258 0.99 64.8 yes View details
psbM-trnD-GAC LSC 1032 0.0188 1.00 64.7 yes View details
trnD-GAC-trnY-UAC LSC 461 0.0181 1.00 64.5 yes View details
psaI-ycf4 LSC 406 0.0197 1.00 64.4 yes View details
petD-rpoA LSC 193 0.0415 1.00 64.3 yes View details
rps14-psaB LSC 129 0.0207 1.00 64.2 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 120 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-CAC-psbA_p1 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 349–367 1.000 87.1
trnH-CAC-psbA_p2 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 350–368 1.000 86.9
trnH-CAC-psbA_p3 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 364–382 1.000 86.7
trnH-CAC-psbA_p4 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 367–385 1.000 86.6
trnH-CAC-psbA_p5 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 365–383 1.000 86.5
trnK-AAA-rps16_p1 trnK-AAA-rps16 CCTTTCAGGATCAGTCGTGG CCCAATGAGCCGTTTATCGA 965–1057 1.000 83.6
trnK-AAA-rps16_p2 trnK-AAA-rps16 CCTTTCAGGATCAGTCGTGG TCCCAATGAGCCGTTTATCG 966–1058 1.000 83.6
trnK-AAA-rps16_p3 trnK-AAA-rps16 TCAGGATCAGTCGTGGTCTT CCCAATGAGCCGTTTATCGA 961–1053 1.000 83.2
trnK-AAA-rps16_p4 trnK-AAA-rps16 TCAGGATCAGTCGTGGTCTT TCCCAATGAGCCGTTTATCG 962–1054 1.000 83.2
trnK-AAA-rps16_p5 trnK-AAA-rps16 TTCAGGATCAGTCGTGGTCT CCCAATGAGCCGTTTATCGA 962–1054 1.000 83.2
rps16_p1 rps16 GATGGAAGCGAAAGAGGAGG ACTGACTGAACTATGACTATTCATGA 1276–1285 1.000 42.6
rps16_p2 rps16 ATGGAAGCGAAAGAGGAGGA ACGATATACTGACTGAACTATGACT 1282–1291 1.000 42.6
rps16_p3 rps16 GATGGAAGCGAAAGAGGAGG ACTGACTGAACTATGACTATTCA 1276–1285 1.000 42.6
rps16_p4 rps16 GATGGAAGCGAAAGAGGAGG ACGATATACTGACTGAACTATGACT 1283–1292 1.000 42.5
rps16_p5 rps16 GATGGAAGCGAAAGAGGAGG ACGATATACTGACTGAACTATGAC 1283–1292 1.000 42.5
trnS-AGC-trnG-GGA_p1 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA TGAATCAAACCGAGAGACCC 757–801 1.000 77.9
trnS-AGC-trnG-GGA_p2 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC TGAATCAAACCGAGAGACCC 755–799 1.000 77.7
trnS-AGC-trnG-GGA_p3 trnS-AGC-trnG-GGA GCTTTAGTCCACTCAGCCAT TGAATCAAACCGAGAGACCC 752–796 1.000 76.0
trnS-AGC-trnG-GGA_p4 trnS-AGC-trnG-GGA TCCAACGCTTTAGTCCACTC TGAATCAAACCGAGAGACCC 758–802 1.000 75.6
trnS-AGC-trnG-GGA_p5 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA GAATCAAACCGAGAGACCCT 756–800 1.000 75.6
trnG-GGA-trnR-AGA_p1 trnG-GGA-trnR-AGA AGCCTTCCAAGCTAACGATG TGATATTGCGTCCAATAGGA 266–309 1.000 55.1
trnG-GGA-trnR-AGA_p2 trnG-GGA-trnR-AGA ACCCTTAGCCTTCCAAGCTA TGATATTGCGTCCAATAGGA 272–315 1.000 55.0
trnG-GGA-trnR-AGA_p3 trnG-GGA-trnR-AGA CGACGTCGACTAAAACCCTT TGATATTGCGTCCAATAGGA 286–329 1.000 54.6
trnG-GGA-trnR-AGA_p4 trnG-GGA-trnR-AGA AAACCCTTAGCCTTCCAAGC TGATATTGCGTCCAATAGGA 274–317 1.000 54.6
trnG-GGA-trnR-AGA_p5 trnG-GGA-trnR-AGA AGCCTTCCAAGCTAACGATG TTGATATTGCGTCCAATAGGA 267–310 1.000 54.1
trnR-AGA-atpA_p1 trnR-AGA-atpA GGTTCAAATCCTATTGGACGC ACATTAACCGCTGAAGCAGA 410–415 1.000 66.2
trnR-AGA-atpA_p2 trnR-AGA-atpA GGTTCAAATCCTATTGGACGC AGACATTAACCGCTGAAGCA 412–417 1.000 66.1
trnR-AGA-atpA_p3 trnR-AGA-atpA CGAAAAGCGTCCATTGTCTA ACATTAACCGCTGAAGCAGA 466–471 1.000 64.8
trnR-AGA-atpA_p4 trnR-AGA-atpA CGAAAAGCGTCCATTGTCTA AGACATTAACCGCTGAAGCA 468–473 1.000 64.7
trnR-AGA-atpA_p5 trnR-AGA-atpA GGTTCAAATCCTATTGGACGC GACATTAACCGCTGAAGCAG 411–416 1.000 63.4

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
Cymatocarpus grossheimii NC_053334.1 154793 View on NCBI ↗
Cymatocarpus heterophyllus NC_053335.1 154954 View on NCBI ↗
Cymatocarpus pilosissimus NC_050792.1 154874 View on NCBI ↗