Markers + reference

Barbarea

3 species · Brassicaceae · Brassicales

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Species 3
Genome length 155–155 kb
Candidate markers 274
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 292 0.0297 1.00 71.4 yes View details
trnS-GCU-trnG LSC 656 0.0251 0.99 67.2 yes View details
rpoC2 LSC 4140 0.0045 1.00 43.4 yes View details
rpoB-trnC-GCA LSC 1101 0.0085 1.00 53.0 yes View details
ndhC-trnV-UAC LSC 907 0.0096 0.99 59.1 yes View details
petA-psbJ LSC 1010 0.0126 1.00 53.9 yes View details
psbE-petL LSC 951 0.0081 0.99 57.3 yes View details
trnP-UGG-psaJ LSC 373 0.0089 1.00 52.6 yes View details
ycf1 IRb 1029 0.0013 1.00 56.2 no View details
rpl32-trnL-UAG SSC 907 0.0140 1.00 56.9 yes View details
ycf1 SSC 5382 0.0071 1.00 50.0 yes View details
ndhF-rpl32 SSC 860 0.0094 0.99 68.6 yes View details
trnF-GAA-ndhJ LSC 583 0.0120 1.00 66.1 yes View details
petD-rpoA LSC 201 0.0166 1.00 64.7 yes View details
rbcL-accD LSC 653 0.0092 1.00 64.6 yes View details
accD-psaI LSC 657 0.0020 0.99 64.4 yes View details
psaA-ycf3 LSC 671 0.0080 1.00 64.1 yes View details
trnE-UUC-trnT-GGU LSC 771 0.0039 0.99 63.8 yes View details
atpB-rbcL LSC 803 0.0066 1.00 63.0 yes View details
trnR-UCU-atpA LSC 299 0.0119 0.94 61.2 yes View details
trnT-GGU-psbD LSC 1241 0.0054 1.00 60.7 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
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 350–352 1.000 81.5
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 351–353 1.000 81.2
trnH-GUG-psbA_p3 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT GTAACGCTCACAACTTCCCA 382–384 1.000 80.6
trnH-GUG-psbA_p4 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TAACGCTCACAACTTCCCAC 381–383 1.000 80.6
trnH-GUG-psbA_p5 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TAACGCTCACAACTTCCCAC 382–384 1.000 80.4
trnS-GCU-trnG_p1 trnS-GCU-trnG CCAACGCTTTAGTCCACTCA GGAACGAATCACACTTTTACCA 718–726 1.000 57.8
trnS-GCU-trnG_p2 trnS-GCU-trnG AACGCTTTAGTCCACTCAGC GGAACGAATCACACTTTTACCA 716–724 1.000 57.5
trnS-GCU-trnG_p3 trnS-GCU-trnG CCAACGCTTTAGTCCACTCA AGGGATTAAAGGAACGAATCACA 728–736 1.000 57.0
trnS-GCU-trnG_p4 trnS-GCU-trnG AACGCTTTAGTCCACTCAGC AGGGATTAAAGGAACGAATCACA 726–734 1.000 56.7
trnS-GCU-trnG_p5 trnS-GCU-trnG CCAACGCTTTAGTCCACTCA GGAACGAATCACACTTTTACCAC 718–726 1.000 56.7
trnR-UCU-atpA_p1 trnR-UCU-atpA GCGAAAAGCGTCCATTGTC TCAAGAGCAACTGGAACGTT 405–421 1.000 73.8
trnR-UCU-atpA_p2 trnR-UCU-atpA GCGAAAAGCGTCCATTGTC TTCAAGAGCAACTGGAACGT 406–422 1.000 73.8
trnR-UCU-atpA_p3 trnR-UCU-atpA GCGAAAAGCGTCCATTGTC ACCGCAGTTCCAAGAAATCA 480–496 1.000 73.6
trnR-UCU-atpA_p4 trnR-UCU-atpA GCGAAAAGCGTCCATTGTC ACATTAACCGCTGAAGCAGA 446–462 1.000 72.3
trnR-UCU-atpA_p5 trnR-UCU-atpA GCGAAAAGCGTCCATTGTC AGACATTAACCGCTGAAGCA 448–464 1.000 72.2
rpoC2_p1 rpoC2 GTTCCAACCCTTAATCCGCT AAGGCTGGCATTCTTCAACA 792 0.667 66.4
rpoC2_p2 rpoC2 GTTCCAACCCTTAATCCGCT AGGCTGGCATTCTTCAACAA 791 0.667 66.4
rpoC2_p3 rpoC2 TATTGAATCAATCGCGCGGA AAGGCTGGCATTCTTCAACA 756 0.667 66.2
rpoC2_p4 rpoC2 TATTGAATCAATCGCGCGGA AGGCTGGCATTCTTCAACAA 755 0.667 66.2
rpoC2_p5 rpoC2 GCACCAATCAAGAATCCCCA AGGCTGGCATTCTTCAACAA 841 0.667 66.1
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GTTCCCTCTTTTCCATCCCC CTTACCACTCGGCCATGC 1145–1149 1.000 63.0
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GTTCCCTCTTTTCCATCCCC CCTTACCACTCGGCCATG 1146–1150 1.000 60.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TGTTCCCTCTTTTCCATCCC CTTACCACTCGGCCATGC 1146–1150 1.000 57.0
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TCTTTTCCATCCCCGAGCAT CTTACCACTCGGCCATGC 1139–1143 1.000 55.5
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CTCTTTTCCATCCCCGAGC CTTACCACTCGGCCATGC 1140–1144 1.000 55.5
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 901–914 1.000 80.7
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCATGGCGTTACTCTACCAC 880–893 1.000 80.3
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TGGCGTTACTCTACCACTGA 877–890 1.000 80.1
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 863–876 1.000 80.0
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 842–855 1.000 79.9

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
Barbarea bracteosa PP103298.1 154889 View on NCBI ↗
Barbarea verna NC_009269.1 154532 View on NCBI ↗
Barbarea vulgaris NC_081109.1 154958 View on NCBI ↗