Markers + reference

Clinopodium

8 species · Lamiaceae · Lamiales

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Species 8
Genome length 151–152 kb
Candidate markers 274
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ(UUG) LSC 962 0.0385 0.96 81.1 yes View details
psaA-ycf3 LSC 783 0.0261 0.98 72.8 yes View details
ycf1 IRb 1131 0.0080 1.00 51.7 no View details
ndhF SSC 2232 0.0160 1.00 56.9 yes View details
ndhF-rpl32 SSC 462 0.0260 0.99 69.1 yes View details
rpl32-trnL(UAG) SSC 702 0.0283 1.00 72.8 yes View details
ndhD SSC 1530 0.0077 1.00 51.1 yes View details
rps15-ycf1 SSC 411 0.0284 1.00 73.7 yes View details
ycf1 SSC 5451 0.0179 1.00 53.0 yes View details
psbI-trnS(GCU) LSC 86 0.0478 1.00 75.0 yes View details
ccsA-ndhD SSC 229 0.0368 1.00 72.9 yes View details
atpF-atpH LSC 267 0.0227 1.00 72.2 yes View details
petN-psbM LSC 948 0.0179 0.99 71.5 yes View details
trnH(GUG)-psbA LSC 322 0.0372 0.93 70.5 yes View details
trnT(UGU)-trnL(UAA) LSC 680 0.0176 0.99 69.0 yes View details
trnG(GCC)-trnfM(CAU) LSC 159 0.0310 1.00 67.7 yes View details
ycf3-trnS(GGA) LSC 823 0.0186 1.00 64.9 yes View details
trnT(GGU)-psbD LSC 1359 0.0148 0.99 64.7 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH(GUG)-psbA_p1 trnH(GUG)-psbA ATCCACTTGGCTACATCCG CTATCGAAGCTCCAACAAATG 349–376 1.000 50.0
trnH(GUG)-psbA_p2 trnH(GUG)-psbA ATCCACTTGGCTACATCCGC CTATCGAAGCTCCAACAAATG 349–376 1.000 50.0
trnH(GUG)-psbA_p3 trnH(GUG)-psbA CCACTTGGCTACATCCGC CTATCGAAGCTCCAACAAATG 347–374 1.000 50.0
trnH(GUG)-psbA_p4 trnH(GUG)-psbA ATCCACTTGGCTACATCCG TATCGAAGCTCCAACAAATG 348–375 1.000 50.0
trnH(GUG)-psbA_p5 trnH(GUG)-psbA ATCCACTTGGCTACATCCGC TATCGAAGCTCCAACAAATG 348–375 1.000 50.0
rps16-trnQ(UUG)_p1 rps16-trnQ(UUG) AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 999–1084 1.000 89.0
rps16-trnQ(UUG)_p2 rps16-trnQ(UUG) AAGTCGCACGTTGCTTTCTA GTCTCGCTATTCGGAGGTTC 1012–1097 1.000 88.5
rps16-trnQ(UUG)_p3 rps16-trnQ(UUG) AAGTCGCACGTTGCTTTCTA CGGGTTTTGGTCTCGCTATT 1021–1106 1.000 87.3
rps16-trnQ(UUG)_p4 rps16-trnQ(UUG) AAGTCGCACGTTGCTTTCTA TTTGGTCTCGCTATTCGGAG 1016–1101 1.000 84.8
rps16-trnQ(UUG)_p5 rps16-trnQ(UUG) AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1003–1088 1.000 84.2
psbI-trnS(GCU)_p1 psbI-trnS(GCU) ATCTAATGATCCGGGGCGTA TTCGAATCCCTCTCTTTCCG 146–221 1.000 78.2
psbI-trnS(GCU)_p2 psbI-trnS(GCU) TATCTAATGATCCGGGGCGT TTCGAATCCCTCTCTTTCCG 147–222 1.000 78.2
psbI-trnS(GCU)_p3 psbI-trnS(GCU) ATCTAATGATCCGGGGCGTA GGGTTCGAATCCCTCTCTTT 149–224 1.000 77.1
psbI-trnS(GCU)_p4 psbI-trnS(GCU) TATCTAATGATCCGGGGCGT GGGTTCGAATCCCTCTCTTT 150–225 1.000 77.1
psbI-trnS(GCU)_p5 psbI-trnS(GCU) ATCTAATGATCCGGGGCGTA GGTTCGAATCCCTCTCTTTCC 148–223 1.000 77.1
atpF-atpH_p1 atpF-atpH CCAGTAGCCCAAAGAAACGA CCGAGGCAGAGGGAAAAATA 427–439 1.000 77.3
atpF-atpH_p2 atpF-atpH TTAAATCCGAAACTCCCGGC CCGAGGCAGAGGGAAAAATA 453–465 1.000 76.4
atpF-atpH_p3 atpF-atpH CCAGTAGCCCAAAGAAACGA GGATTGGTTGTAGCACTAGCA 356–368 1.000 75.8
atpF-atpH_p4 atpF-atpH CCAGTAGCCCAAAGAAACGA TGGATTGGTTGTAGCACTAGC 357–369 1.000 75.8
atpF-atpH_p5 atpF-atpH CCAGTAGCCCAAAGAAACGA GCAGAGGGAAAAATACGAGGT 422–434 1.000 75.0
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT AGTTCCTACCGCTTTTCTACT 1089–1109 1.000 63.4
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TCATTCTAGTTCCTACCGCT 1096–1116 1.000 63.3
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT TCATTCTAGTTCCTACCGCTT 1096–1116 1.000 61.7
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT TTCATTCTAGTTCCTACCGCT 1097–1117 1.000 61.7
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT AGTTCCTACCGCTTTTCTACTT 1089–1109 1.000 61.2
trnT(GGU)-psbD_p1 trnT(GGU)-psbD GTGGTAGAGTAACGCCATGG GGACCAGCCTACAAAAACGA 1511–1535 1.000 83.1
trnT(GGU)-psbD_p2 trnT(GGU)-psbD TCAGTGGTAGAGTAACGCCA GGACCAGCCTACAAAAACGA 1514–1538 1.000 82.9
trnT(GGU)-psbD_p3 trnT(GGU)-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1501–1525 1.000 82.0
trnT(GGU)-psbD_p4 trnT(GGU)-psbD TCAGTGGTAGAGTAACGCCA ACAAAAACGAAACGGTCCCT 1504–1528 1.000 81.8
trnT(GGU)-psbD_p5 trnT(GGU)-psbD GGCGTAAGTCATCGGTTCAA GGACCAGCCTACAAAAACGA 1488–1512 1.000 81.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Clinopodium abyssinicum NC_058327.1 151513 View on NCBI ↗
Clinopodium acinos PP190943.1 151971 View on NCBI ↗
Clinopodium alpinum PP024531.1 151983 View on NCBI ↗
Clinopodium barosmum NC_085322.1 152261 View on NCBI ↗
Clinopodium chinense NC_050943.1 151989 View on NCBI ↗
Clinopodium euosmum NC_071895.1 151300 View on NCBI ↗
Clinopodium menthifolium subsp. ascendens ON641258.1 152114 View on NCBI ↗
Clinopodium vulgare subsp. vulgare PP190944.1 151999 View on NCBI ↗