Markers + reference

Leonurus

3 species · Lamiaceae · Lamiales

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Species 3
Genome length 151–152 kb
Candidate markers 259
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 259 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-TGA-psbZ LSC 326 0.0020 1.00 41.8 yes View details
rbcL-accD LSC 689 0.0068 1.00 63.1 yes View details
psaJ-rpl33 LSC 460 0.0015 1.00 45.8 yes View details
ycf1 IRb 1119 0.0000 1.00 28.1 no View details
rpl32-trnL-TAG SSC 727 0.0055 1.00 62.6 yes View details
ndhD SSC 1410 0.0033 1.00 60.9 yes View details
ndhH SSC 1182 0.0023 1.00 60.2 yes View details
ycf1 SSC 5535 0.0012 1.00 53.3 yes View details
ndhC-trnM-CAT LSC 1799 0.0019 1.00 60.8 yes View details
atpH-atpI LSC 804 0.0025 1.00 60.6 yes View details
atpB-rbcL LSC 803 0.0025 1.00 60.5 yes View details
rps16-trnQ-TTG LSC 1016 0.0026 1.00 60.4 yes View details
matK LSC 1536 0.0017 1.00 60.1 yes View details
psaA-ycf3 LSC 721 0.0009 1.00 60.0 yes View details
petA-psbJ LSC 1036 0.0019 1.00 60.0 yes View details
trnK-TTT-rps16 LSC 720 0.0019 1.00 59.9 yes View details
petD-rps11 LSC 1253 0.0016 1.00 59.8 yes View details
ycf4-cemA LSC 559 0.0012 1.00 59.7 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-TTT_p1 trnK-TTT TTCGTGTCAACCAATCCGAA ACATCCTTTGTTGAAGTTTTGT 2723–2729 1.000 40.3
trnK-TTT_p2 trnK-TTT TCGTGTCAACCAATCCGAAT ACATCCTTTGTTGAAGTTTTGT 2722–2728 1.000 40.3
trnK-TTT_p3 trnK-TTT TTCGTGTCAACCAATCCGAA ACATCCTTTGTTGAAGTTTTGTT 2723–2729 1.000 40.3
trnK-TTT_p4 trnK-TTT GTTCGTGTCAACCAATCCGA ACATCCTTTGTTGAAGTTTTGT 2724–2730 1.000 40.3
trnK-TTT_p5 trnK-TTT TCGTGTCAACCAATCCGAAT ACATCCTTTGTTGAAGTTTTGTT 2722–2728 1.000 40.3
matK_p1 matK GGATCTTTTTATCTCTCGATCCA AGTTTATCTGTCCCCGAGGT 1706–1712 1.000 40.5
matK_p2 matK TGGATCTTTTTATCTCTCGATCC AGTTTATCTGTCCCCGAGGT 1707–1713 1.000 40.5
matK_p3 matK ACATCAACATTTCAGAATAGTGGA AGTTTATCTGTCCCCGAGGT 1740–1746 1.000 40.5
matK_p4 matK TTGGATCTTTTTATCTCTCGATCC AGTTTATCTGTCCCCGAGGT 1708–1714 1.000 40.5
matK_p5 matK GGATCTTTTTATCTCTCGATCCAT AGTTTATCTGTCCCCGAGGT 1706–1712 1.000 40.5
trnK-TTT-rps16_p1 trnK-TTT-rps16 CCCTTTCAGGATCAGTCGTG TTTCCTTGAAAGGGGTGCTC 942–945 1.000 80.0
trnK-TTT-rps16_p2 trnK-TTT-rps16 CCTTTCAGGATCAGTCGTGG TTTCCTTGAAAGGGGTGCTC 941–944 1.000 80.0
trnK-TTT-rps16_p3 trnK-TTT-rps16 TCCCTTTCAGGATCAGTCGT TTTCCTTGAAAGGGGTGCTC 943–946 1.000 79.6
trnK-TTT-rps16_p4 trnK-TTT-rps16 TCAGGATCAGTCGTGGTCTT TTTCCTTGAAAGGGGTGCTC 937–940 1.000 79.5
trnK-TTT-rps16_p5 trnK-TTT-rps16 TTCAGGATCAGTCGTGGTCT TTTCCTTGAAAGGGGTGCTC 938–941 1.000 79.5
rps16-trnQ-TTG_p1 rps16-trnQ-TTG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 1147 1.000 79.1
rps16-trnQ-TTG_p2 rps16-trnQ-TTG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1089 1.000 78.6
rps16-trnQ-TTG_p3 rps16-trnQ-TTG GGATCGTGTCCTTCAAGTCG GAAATTGAAATGGGGCGTGG 1161 1.000 77.2
rps16-trnQ-TTG_p4 rps16-trnQ-TTG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1103 1.000 76.7
rps16-trnQ-TTG_p5 rps16-trnQ-TTG CGTTGCTTTCTACCACATCG GAAATTGAAATGGGGCGTGG 1139 1.000 73.9
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT CCCGTCATGTTCCTTGGATT 936–941 1.000 79.1
atpH-atpI_p2 atpH-atpI AGCCAATCCAGCAGCAATAA CCCGTCATGTTCCTTGGATT 952–957 1.000 78.2
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA CCCGTCATGTTCCTTGGATT 937–942 1.000 77.9
atpH-atpI_p4 atpH-atpI GCCAATCCAGCAGCAATAAC CCCGTCATGTTCCTTGGATT 951–956 1.000 77.7
atpH-atpI_p5 atpH-atpI TCCAGCAGCAATAACGGAAG CCCGTCATGTTCCTTGGATT 946–951 1.000 77.3
trnS-TGA-psbZ_p1 trnS-TGA-psbZ CAACCACTCAGCCATCTCTC TACTTGACCAACCGTCTGGA 453 1.000 77.7
trnS-TGA-psbZ_p2 trnS-TGA-psbZ CAACCACTCAGCCATCTCTC AGCAAATACGACAGGTACGC 431 1.000 77.1
trnS-TGA-psbZ_p3 trnS-TGA-psbZ CAACCACTCAGCCATCTCTC GCAAATACGACAGGTACGCT 430 1.000 77.1
trnS-TGA-psbZ_p4 trnS-TGA-psbZ GTTTTCAAGACCGGGGCTAT TACTTGACCAACCGTCTGGA 473 1.000 76.8
trnS-TGA-psbZ_p5 trnS-TGA-psbZ CAACCACTCAGCCATCTCTC CAACCGTCTGGAGAAGCAAA 445 1.000 76.8

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
Leonurus cardiaca NC_058592.1 151236 View on NCBI ↗
Leonurus panzerioides PQ231095.1 151819 View on NCBI ↗
Leonurus turkestanicus PQ231098.1 151746 View on NCBI ↗