Markers + reference

Nepeta

7 species · Lamiaceae · Lamiales

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Species 7
Genome length 152–152 kb
Candidate markers 265
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1059 0.0040 1.00 42.0 yes View details
rps16-trnQ-UUG LSC 1005 0.0388 0.96 78.0 yes View details
psbK-psbI LSC 385 0.0260 0.99 68.4 yes View details
psbI-trnS-GCU LSC 166 0.0827 0.91 77.2 yes View details
trnS-GCU-trnR-UCU LSC 1677 0.0212 0.99 72.5 yes View details
rps4-trnT-UGU LSC 386 0.0397 0.94 78.1 yes View details
ndhC-trnM-CAU LSC 1797 0.0190 0.99 61.7 yes View details
petA-psbJ LSC 1037 0.0347 0.99 78.2 yes View details
rpl32-trnL-UAG SSC 701 0.0425 0.96 80.1 yes View details
ycf1 SSC 5592 0.0241 0.99 58.6 yes View details
ccsA-ndhD SSC 253 0.0468 1.00 76.6 yes View details
trnE-UUC-trnT-GGU LSC 566 0.0258 0.98 76.1 yes View details
petG-trnW-CCA LSC 115 0.0469 1.00 74.5 yes View details
trnH-GUG-psbA LSC 257 0.0681 0.90 73.6 yes View details
trnD-GUC-trnY-GUA LSC 116 0.0277 0.95 72.2 yes View details
rps18-rpl20 LSC 225 0.0635 0.95 72.0 yes View details
trnG-GCC-trnM-CAU LSC 170 0.0381 0.97 71.6 yes View details
rps15-ycf1 SSC 377 0.0377 0.98 71.2 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CTGTTGCGTATTCAGCTCCT 885–1016 1.000 86.7
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GAGTGGGAGCTTAGTTTCCG 928–1059 1.000 86.6
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GAGTGGGAGCTTAGTTTCCG 942–1073 1.000 86.5
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GAGTGGGAGCTTAGTTTCCG 941–1072 1.000 86.5
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GAGTGGGAGCTTAGTTTCCG 943–1074 1.000 86.5
psbA_p1 psbA GATCCACTTGGCTACATCCG GAAAGCCGTGTGCAATGAAA 1682–1810 0.857 78.7
psbA_p2 psbA GATCCACTTGGCTACATCCG CCTCCCCAAAAGTCACTTCC 1985–2085 0.286 52.4
psbA_p3 psbA CAATCCACTGCCTTGATCCA CCTCCCCAAAAGTCACTTCC 1999–2099 0.286 52.4
psbA_p4 psbA AATCCACTGCCTTGATCCAC CCTCCCCAAAAGTCACTTCC 1998–2098 0.286 52.4
psbA_p5 psbA ACAATCCACTGCCTTGATCC CCTCCCCAAAAGTCACTTCC 2000–2100 0.286 52.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CCCTAGATCCTTGCCTCTGA GAGGTTCGAATCCTTCCGTC 1178–1306 1.000 90.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCGCACGTTGCTTTCTATCA GAGGTTCGAATCCTTCCGTC 1075 0.143 44.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AGTCGCACGTTGCTTTCTAT GAGGTTCGAATCCTTCCGTC 1077 0.143 44.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCGCACGTTGCTTTCTATCA GTCTCGCTATTCGGAGGTTC 1088 0.143 44.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGTCGCACGTTGCTTTCTAT GTCTCGCTATTCGGAGGTTC 1090 0.143 44.1
psbK-psbI_p1 psbK-psbI TAGCTTTTGTTTGGCAGGCT ACGAAGAGTTTCAGAGTAAGCA 434–449 1.000 65.1
psbK-psbI_p2 psbK-psbI GCAGGCTGCTGTAAGTTTTC ACGAAGAGTTTCAGAGTAAGCA 421–436 1.000 65.0
psbK-psbI_p3 psbK-psbI AGGCTGCTGTAAGTTTTCGA ACGAAGAGTTTCAGAGTAAGCA 419–434 1.000 63.4
psbK-psbI_p4 psbK-psbI TTAGCTTTTGTTTGGCAGGC ACGAAGAGTTTCAGAGTAAGCA 435–450 1.000 63.2
psbK-psbI_p5 psbK-psbI CAGGCTGCTGTAAGTTTTCG ACGAAGAGTTTCAGAGTAAGCA 420–435 1.000 62.9
psbI-trnS-GCU_p1 psbI-trnS-GCU GCGTAATCCTGGACGTGAAG TGGACTAAAGCGTCGGATTG 247–270 1.000 86.2
psbI-trnS-GCU_p2 psbI-trnS-GCU GCGTAATCCTGGACGTGAAG GTGGACTAAAGCGTCGGATT 248–271 1.000 86.2
psbI-trnS-GCU_p3 psbI-trnS-GCU GCGTAATCCTGGACGTGAAG ATTGGGAGAGATGGCTGAGT 266–289 1.000 85.4
psbI-trnS-GCU_p4 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TGGACTAAAGCGTCGGATTG 246–269 1.000 84.5
psbI-trnS-GCU_p5 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA GTGGACTAAAGCGTCGGATT 247–270 1.000 84.5
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGAAGACCTCTGTCCTATCCA 1728–1753 1.000 71.5
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGAAGACCTCTGTCCTATCCA 1727–1752 1.000 71.5
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGGTTTAGAAGACCTCTGTCCT 1734–1759 1.000 70.9
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGGTTTAGAAGACCTCTGTCCT 1733–1758 1.000 70.8
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU ACGGAAAGAGAGGGATTCGA AGAAGACCTCTGTCCTATCCA 1782–1807 1.000 70.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Nepeta bracteata NC_079688.1 151588 View on NCBI ↗
Nepeta dentata NC_071848.1 151893 View on NCBI ↗
Nepeta hemsleyana NC_058882.1 152171 View on NCBI ↗
Nepeta nuda PV930134.1 152195 View on NCBI ↗
Nepeta santoana PV837617.1 151822 View on NCBI ↗
Nepeta stewartiana NC_057283.1 152348 View on NCBI ↗
Nepeta thomsonii NC_071850.1 152210 View on NCBI ↗