Markers + reference

Malcolmia

2 species · Brassicaceae · Brassicales

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Species 2
Genome length 155–155 kb
Candidate markers 270
Primer pairs 100

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 8 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1161 0.0017 1.00 59.7 yes View details
trnS-AGC-trnG-GGA LSC 651 0.0031 1.00 60.5 yes View details
rpoC2 LSC 4140 0.0007 1.00 54.3 yes View details
psbM-trnD-GAC LSC 990 0.0030 1.00 55.0 yes View details
trnT-ACC-psbD LSC 1123 0.0018 1.00 59.9 yes View details
ycf3-trnS-UCC LSC 1082 0.0018 1.00 59.8 yes View details
trnL-UUA-trnF-UUC LSC 598 0.0039 0.85 62.9 yes View details
trnP-CCA-psaJ LSC 364 0.0027 1.00 55.0 yes View details
psaJ-rpl33 LSC 448 0.0050 0.90 61.9 yes View details
clpP LSC 2050 0.0010 1.00 57.6 yes View details
ycf1 IRb 1032 0.0000 1.00 40.0 no View details
ycf1 SSC 5385 0.0011 1.00 53.1 yes View details
ndhJ-psbG LSC 102 0.0196 1.00 63.8 yes View details
ndhC-trnV-GUA LSC 846 0.0024 1.00 60.1 yes View details
psaA-ycf3 LSC 712 0.0014 1.00 59.8 yes View details
trnR-CGU-trnN-AAC IRb 635 0.0016 1.00 59.7 yes View details
trnN-AAC-trnR-CGU IRa 635 0.0016 1.00 59.7 yes View details
trnC-UGC-petN LSC 641 0.0016 1.00 59.6 yes View details
rbcL-accD LSC 672 0.0015 1.00 59.6 yes View details
cemA LSC 690 0.0014 1.00 59.6 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16_p1 rps16 ACGAGTCTTTCACATCCTCT ACCCGTAAATTCACTATTTCATTCA 1314–1315 1.000 40.1
rps16_p2 rps16 ACGAGTCTTTCACATCCTCT ACGATATACTGACTGAACTATGACT 1266–1267 1.000 40.1
rps16_p3 rps16 ACGAGTCTTTCACATCCTCT ACCCGTAAATTCACTATTTCA 1314–1315 1.000 40.1
rps16_p4 rps16 ACGAGTCTTTCACATCCTCTT ACCCGTAAATTCACTATTTCATTCA 1314–1315 1.000 40.1
rps16_p5 rps16 ACGAGTCTTTCACATCCTCTT ACGATATACTGACTGAACTATGACT 1266–1267 1.000 40.1
trnS-AGC-trnG-GGA_p1 trnS-AGC-trnG-GGA ACGCTTTAATCCACTCAGCC TGAATCAAACCGAGAGACCC 758–762 1.000 72.0
trnS-AGC-trnG-GGA_p2 trnS-AGC-trnG-GGA CGCTTTAATCCACTCAGCCA TGAATCAAACCGAGAGACCC 757–761 1.000 72.0
trnS-AGC-trnG-GGA_p3 trnS-AGC-trnG-GGA ACGCTTTAATCCACTCAGCC GAATCAAACCGAGAGACCCT 757–761 1.000 69.6
trnS-AGC-trnG-GGA_p4 trnS-AGC-trnG-GGA CGCTTTAATCCACTCAGCCA GAATCAAACCGAGAGACCCT 756–760 1.000 69.6
trnS-AGC-trnG-GGA_p5 trnS-AGC-trnG-GGA ATCCACTCAGCCATCTCTCC TGAATCAAACCGAGAGACCC 750–754 1.000 69.5
rpoC2_p1 rpoC2 ACAACGTTACTGTATGGATCGA AGAATGGGTCCATTTAATCATGT 278 1.000 40.3
rpoC2_p2 rpoC2 ACGTTACTGTATGGATCGAGA AGAATGGGTCCATTTAATCATGT 275 1.000 40.3
rpoC2_p3 rpoC2 AACAACGTTACTGTATGGATCGA AGAATGGGTCCATTTAATCATGT 279 1.000 40.3
rpoC2_p4 rpoC2 CAACGTTACTGTATGGATCGAGA AGAATGGGTCCATTTAATCATGT 277 1.000 40.3
rpoC2_p5 rpoC2 ACAACGTTACTGTATGGATCG AGAATGGGTCCATTTAATCATGT 278 1.000 40.3
trnC-UGC-petN_p1 trnC-UGC-petN TTTCCCCAGTTCAAATCCGG ACTTCTTCCCCACACTACGA 751 1.000 79.4
trnC-UGC-petN_p2 trnC-UGC-petN TTTCCCCAGTTCAAATCCGG CTACCATTAAAGCCGCCCAT 710 1.000 79.3
trnC-UGC-petN_p3 trnC-UGC-petN GTTTCTATCGTTTTGGCGGC ACTTCTTCCCCACACTACGA 807 1.000 79.2
trnC-UGC-petN_p4 trnC-UGC-petN GTTTCTATCGTTTTGGCGGC CTACCATTAAAGCCGCCCAT 766 1.000 79.1
trnC-UGC-petN_p5 trnC-UGC-petN TTTCCCCAGTTCAAATCCGG CACTTCTTCCCCACACTACG 752 1.000 78.8
psbM-trnD-GAC_p1 psbM-trnD-GAC AGGAACGAGAATGAAGAGTGC TTCAATTGGTCAGAGCACCG 1107–1108 1.000 68.2
psbM-trnD-GAC_p2 psbM-trnD-GAC ACGAGAATGAAGAGTGCAGT TTCAATTGGTCAGAGCACCG 1103–1104 1.000 67.5
psbM-trnD-GAC_p3 psbM-trnD-GAC GGAACGAGAATGAAGAGTGCA TTCAATTGGTCAGAGCACCG 1106–1107 1.000 66.0
psbM-trnD-GAC_p4 psbM-trnD-GAC AACGAGAATGAAGAGTGCAGT TTCAATTGGTCAGAGCACCG 1104–1105 1.000 65.3
psbM-trnD-GAC_p5 psbM-trnD-GAC GGAACGAGAATGAAGAGTGC TTCAATTGGTCAGAGCACCG 1106–1107 1.000 64.8
trnT-ACC-psbD_p1 trnT-ACC-psbD GTGGTAGAGTAACGCCATGG ACCTACAAAAACGAAGCGGT 1276–1277 1.000 79.3
trnT-ACC-psbD_p2 trnT-ACC-psbD TCAGTGGTAGAGTAACGCCA ACCTACAAAAACGAAGCGGT 1279–1280 1.000 79.2
trnT-ACC-psbD_p3 trnT-ACC-psbD CCAAGACGGCCCTTTTAACT ACCTACAAAAACGAAGCGGT 1298–1299 1.000 79.1
trnT-ACC-psbD_p4 trnT-ACC-psbD ACGGCCCTTTTAACTCAGTG ACCTACAAAAACGAAGCGGT 1293–1294 1.000 79.0
trnT-ACC-psbD_p5 trnT-ACC-psbD GACGGCCCTTTTAACTCAGT ACCTACAAAAACGAAGCGGT 1294–1295 1.000 78.4

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
Malcolmia bicolor MK637825.1 154858 View on NCBI ↗
Malcolmia maritima NC_049671.1 154766 View on NCBI ↗