Markers + reference

Lagopsis

3 species · Lamiaceae · Lamiales

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Species 3
Genome length 152–152 kb
Candidate markers 267
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 9 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 914 0.0037 1.00 61.3 yes View details
rps16-trnQ-UUG LSC 675 0.0049 1.00 61.9 yes View details
atpF-atpH LSC 370 0.0072 0.99 59.2 yes View details
atpH-atpI LSC 934 0.0043 1.00 61.5 yes View details
trnE-UUC-trnT-GGU LSC 571 0.0035 1.00 47.7 yes View details
trnT-GGU-psbD LSC 1143 0.0029 1.00 61.6 yes View details
trnF-GAA-ndhJ LSC 671 0.0040 1.00 61.4 yes View details
petA-psbJ LSC 1058 0.0069 1.00 63.8 yes View details
petB LSC 1383 0.0024 1.00 46.8 yes View details
rpl32-trnL-UAG SSC 724 0.0060 1.00 60.5 yes View details
ccsA SSC 963 0.0042 1.00 38.2 yes View details
ndhG-ndhI SSC 372 0.0090 1.00 59.7 yes View details
ndhC-trnV-UAC LSC 1048 0.0020 0.94 64.1 yes View details
atpB-rbcL LSC 814 0.0033 0.99 61.5 yes View details
trnS-GCU-trnS-CGA LSC 682 0.0020 1.00 61.2 yes View details
psbE-petL LSC 925 0.0022 1.00 61.0 yes View details
petN-psbM LSC 784 0.0034 1.00 60.9 yes View details
rpoB-trnC-GCA LSC 1095 0.0012 1.00 60.7 yes View details
rps2 LSC 711 0.0028 1.00 60.5 yes View details
petD LSC 1225 0.0027 1.00 60.3 yes View details
rpl20-rps12 LSC 762 0.0018 1.00 60.0 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 GGTTACGGACGAATTGGTCA TTTCCTTGAAAGGGGTGCTC 1106–1108 1.000 79.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 TGTAAAAGATTCGAGCCGCA TTTCCTTGAAAGGGGTGCTC 1073–1075 1.000 79.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTTCCTTGAAAGGGGTGCTC 1049–1051 1.000 79.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTTCCTTGAAAGGGGTGCTC 1048–1050 1.000 79.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 ACGGACGAATTGGTCACTTC TTTCCTTGAAAGGGGTGCTC 1102–1104 1.000 78.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAAATTGAAATGGGGCGTGG 824–829 1.000 79.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 807–812 1.000 79.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 766–771 1.000 79.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 749–754 1.000 78.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAAATTGAAATGGGGCGTGG 825–830 1.000 78.7
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA CAATCCGACGCTTTAGTCCA ACCACTAAACTATACCCGCT 730–737 1.000 62.1
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA AATCCGACGCTTTAGTCCAC ACCACTAAACTATACCCGCT 729–736 1.000 62.1
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA ACGGAAAGAGAGGGATTCGA ACCACTAAACTATACCCGCT 784–791 1.000 60.9
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA AGCAATCCGACGCTTTAGTC ACCACTAAACTATACCCGCT 732–739 1.000 59.3
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA CGACGCTTTAGTCCACTCAG ACCACTAAACTATACCCGCT 725–732 1.000 59.1
atpF-atpH_p1 atpF-atpH TGGCCCAAAGAAACGAAAGA CGGAGGGAAAAATACGAGGT 518–521 1.000 75.1
atpF-atpH_p2 atpF-atpH TGGCCCAAAGAAACGAAAGA CGAGGCGGAGGGAAAAATAC 523–526 1.000 75.0
atpF-atpH_p3 atpF-atpH TGGCCCAAAGAAACGAAAGA GAGGCGGAGGGAAAAATACG 522–525 1.000 75.0
atpF-atpH_p4 atpF-atpH TGGCCCAAAGAAACGAAAGA GCGGAGGGAAAAATACGAGG 519–522 1.000 75.0
atpF-atpH_p5 atpF-atpH TGGCCCAAAGAAACGAAAGA GGCGGAGGGAAAAATACGAG 520–523 1.000 75.0
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT CCCGTCATGTTCCTTGGATT 1068 1.000 79.1
atpH-atpI_p2 atpH-atpI TCCGATAGAAGCAAGCCCTA CCCGTCATGTTCCTTGGATT 1105 1.000 78.7
atpH-atpI_p3 atpH-atpI TCCAGGTCCGATAGAAGCAA CCCGTCATGTTCCTTGGATT 1111 1.000 78.3
atpH-atpI_p4 atpH-atpI AGCCAATCCAGCAGCAATAA CCCGTCATGTTCCTTGGATT 1084 1.000 78.2
atpH-atpI_p5 atpH-atpI CCGATAGAAGCAAGCCCTAC CCCGTCATGTTCCTTGGATT 1104 1.000 78.2
rps2_p1 rps2 ATCACACAATATCCCCAGGT TAGTTCAGTTCGAGGGTCCT 884 1.000 58.4
rps2_p2 rps2 ATCACACAATATCCCCAGGT AGTTCAGTTCGAGGGTCCTC 883 1.000 57.3
rps2_p3 rps2 ATCACACAATATCCCCAGGT GTCCTCGTCGCTTTGTTTTT 869 1.000 57.2
rps2_p4 rps2 AATCACACAATATCCCCAGGT TAGTTCAGTTCGAGGGTCCT 885 1.000 56.8
rps2_p5 rps2 AATCACACAATATCCCCAGGT AGTTCAGTTCGAGGGTCCTC 884 1.000 55.7

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
Lagopsis darwiniana PX283822.1 151844 View on NCBI ↗
Lagopsis eriostachya PQ231082.1 151539 View on NCBI ↗
Lagopsis flava PQ231083.1 151700 View on NCBI ↗