Markers + reference

Prunella

2 species · Lamiaceae · Lamiales

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Species 2
Genome length 151–151 kb
Candidate markers 270
Primer pairs 115

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 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 791 0.0064 0.99 58.6 yes View details
atpH-atpI LSC 1035 0.0039 1.00 61.0 yes View details
petN-psbM LSC 1020 0.0039 1.00 61.0 yes View details
ycf3-trnS-GGA LSC 842 0.0036 1.00 56.7 yes View details
trnS-GGA-rps4 LSC 281 0.0071 1.00 56.6 yes View details
rbcL-accD LSC 665 0.0045 1.00 52.9 yes View details
petL-petG LSC 185 0.0000 1.00 26.8 yes View details
ycf1 IRb 1131 0.0009 1.00 52.2 no View details
ndhF SSC 2232 0.0031 1.00 50.1 yes View details
rpl32-trnL-UAG SSC 494 0.0061 1.00 60.0 yes View details
rps15-ycf1 SSC 436 0.0069 1.00 55.5 yes View details
ycf1 SSC 5547 0.0025 1.00 39.6 yes View details
trnG-GCC-trnfM-CAU LSC 164 0.0124 0.98 61.4 yes View details
trnT-GGU-psbD LSC 1335 0.0030 1.00 60.5 yes View details
matK LSC 1527 0.0026 1.00 60.2 yes View details
rbcL LSC 1434 0.0021 1.00 60.0 yes View details
ccsA SSC 978 0.0020 1.00 59.9 yes View details
trnS-GCU-trnG-UCC LSC 675 0.0030 1.00 59.8 yes View details
rpoB-trnC-GCA LSC 1168 0.0017 1.00 59.7 yes View details
trnF-GAA-ndhJ LSC 637 0.0016 1.00 59.7 yes View details
ndhK LSC 678 0.0015 1.00 59.6 yes View details
rpl20-rps12 LSC 787 0.0013 1.00 59.5 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 115 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU AATCAAGTGGATTACAAAATTTGT CCATGTCCATACACCCTTTGT 2683 1.000 40.1
trnK-UUU_p2 trnK-UUU AATCAAGTGGATTACAAAATTTGT TCCATGTCCATACACCCTTTG 2684 1.000 40.1
trnK-UUU_p3 trnK-UUU TCAAGTGGATTACAAAATTTGTA CCATGTCCATACACCCTTTGT 2681 1.000 40.1
trnK-UUU_p4 trnK-UUU TCTAACTAAATCAAGTGGATTACA CCATGTCCATACACCCTTTGT 2691 1.000 40.1
trnK-UUU_p5 trnK-UUU TCAAGTGGATTACAAAATTTGTA TCCATGTCCATACACCCTTTG 2682 1.000 40.1
matK_p1 matK TCTCTTCATCCATTTTCTTTACGA AGTTTACTTGTCCCCGAGGT 1679 1.000 40.2
matK_p2 matK TCTCTTCATCCATTTTCTTTACGA CCCCCGAATCTTCTACCCTT 1601 1.000 40.2
matK_p3 matK TCTCTTCATCCATTTTCTTTACGAA AGTTTACTTGTCCCCGAGGT 1679 1.000 40.2
matK_p4 matK CTCTTCATCCATTTTCTTTACGA AGTTTACTTGTCCCCGAGGT 1678 1.000 40.2
matK_p5 matK TCTCTTCATCCATTTTCTTTACG AGTTTACTTGTCCCCGAGGT 1679 1.000 40.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTCCTGTCATTCGGAGGTTC 871–877 1.000 79.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 858–864 1.000 79.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAAAATCCACAACGGGTCGT GTCCTGTCATTCGGAGGTTC 897–903 1.000 78.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAAAATCCACAACGGGTCGT GAGGTTCGAATCCTTCCGTC 884–890 1.000 77.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CGGGTTTTGGTCCTGTCATT 880–886 1.000 76.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AACCGAAAGACCCTTTAACT 780 1.000 52.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AACCGAAAGACCCTTTAACT 779 1.000 52.0
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 744 1.000 51.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 743 1.000 51.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AACCGAAAGACCCTTTAACT 834 1.000 50.9
trnG-UCC_p1 trnG-UCC AGCACGCTCGGTTTAATGAT TGGGAATTGTATATTCAACGATTGA 965–966 1.000 40.2
trnG-UCC_p2 trnG-UCC TTCAGCACGCTCGGTTTAAT TGGGAATTGTATATTCAACGATTGA 968–969 1.000 40.2
trnG-UCC_p3 trnG-UCC TGCTCGACAAAAGGTCCATT TGGGAATTGTATATTCAACGATTGA 908–909 1.000 40.2
trnG-UCC_p4 trnG-UCC TTGCTCGACAAAAGGTCCAT TGGGAATTGTATATTCAACGATTGA 909–910 1.000 40.2
trnG-UCC_p5 trnG-UCC AGCACGCTCGGTTTAATGAT TGGGAATTGTATATTCAACGA 965–966 1.000 40.2
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA TCCCTGTCATGTTCCTTGGA 1169 1.000 77.4
atpH-atpI_p2 atpH-atpI AGCCAATCCAGCAGCAATAA TCCCTGTCATGTTCCTTGGA 1187 1.000 77.0
atpH-atpI_p3 atpH-atpI GCCAATCCAGCAGCAATAAC TCCCTGTCATGTTCCTTGGA 1186 1.000 76.5
atpH-atpI_p4 atpH-atpI TCCAGCAGCAATAACGGAAG TCCCTGTCATGTTCCTTGGA 1181 1.000 76.1
atpH-atpI_p5 atpH-atpI AACGGAAGCAGCAGAAATCA TTTTTGCAACTTTAGCCGCG 1121 1.000 75.3

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
Prunella vulgaris NC_039654.1 151342 View on NCBI ↗
Prunella vulgaris subsp. vulgaris PP272174.1 151370 View on NCBI ↗