Markers + reference

Stachys

10 species · Lamiaceae · Lamiales

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Species 10
Genome length 150–151 kb
Candidate markers 273
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 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoB-trnC-GCA LSC 1101 0.0179 1.00 54.6 yes View details
rpl20-rps12 LSC 733 0.0199 1.00 55.2 yes View details
ycf1 IRb 1059 0.0071 1.00 38.2 no View details
ndhF SSC 2229 0.0152 1.00 50.3 yes View details
rpl32-trnL-UAG SSC 502 0.0252 0.99 61.8 yes View details
ndhD SSC 1521 0.0095 1.00 47.8 yes View details
ndhG-ndhI SSC 375 0.0296 1.00 62.4 yes View details
rps15-ycf1 SSC 389 0.0371 1.00 60.3 yes View details
ycf1 SSC 5322 0.0187 1.00 56.1 yes View details
psbT-psbN LSC 73 0.0460 1.00 71.7 yes View details
ccsA-ndhD SSC 181 0.0418 1.00 67.3 yes View details
ndhD-psaC SSC 103 0.0624 1.00 67.0 yes View details
rpl2-trnH-GUG LSC 94 0.0201 1.00 67.0 no View details
rps16-trnQ-UUG LSC 747 0.0197 1.00 64.7 yes View details
trnG-UCC-trnR-UCU LSC 163 0.0494 0.98 64.4 yes View details
trnC-GCA-petN LSC 834 0.0175 1.00 64.3 yes View details
trnE-UUC-trnT-GGU LSC 570 0.0160 1.00 63.7 yes View details
petN-psbM LSC 508 0.0190 0.99 63.0 yes View details
psaA-ycf3 LSC 749 0.0138 0.98 60.4 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
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAAATTGAAATGGGGCGTGG 80–976 1.000 86.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 80–918 1.000 86.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 80–959 1.000 86.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 80–901 1.000 86.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAAATTGAAATGGGGCGTGG 80–977 1.000 85.8
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 80–266 1.000 70.6
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 80–269 1.000 70.3
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 80–272 1.000 69.8
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 80–275 1.000 69.5
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 80–270 1.000 68.1
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT AACGGGGCTTCACAATCTTT 80–1846 1.000 84.3
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT ACGGGGCTTCACAATCTTTT 80–1845 1.000 84.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG AACGGGGCTTCACAATCTTT 80–2038 1.000 84.1
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG ACGGGGCTTCACAATCTTTT 80–2037 1.000 84.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG GAAGGGAATCGCGAAGTCTT 80–2112 1.000 83.9
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ACTTCTTCCCCACACTACGA 80–949 1.000 85.5
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTCTTCCCCACACTACGAGT 80–947 1.000 85.5
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CACTTCTTCCCCACACTACG 80–950 1.000 84.8
trnC-GCA-petN_p4 trnC-GCA-petN GTATCATTTTGGCGGCATGG ACTTCTTCCCCACACTACGA 80–1001 1.000 84.7
trnC-GCA-petN_p5 trnC-GCA-petN GTATCATTTTGGCGGCATGG TTCTTCCCCACACTACGAGT 80–999 1.000 84.7
petN-psbM_p1 petN-psbM ACTCGTAGTGTGGGGAAGAA TCCTACCGCCTTTCTGCTTA 80–595 1.000 83.6
petN-psbM_p2 petN-psbM TCGTAGTGTGGGGAAGAAGT TCCTACCGCCTTTCTGCTTA 80–593 1.000 83.6
petN-psbM_p3 petN-psbM CGTAGTGTGGGGAAGAAGTG TCCTACCGCCTTTCTGCTTA 80–592 1.000 83.1
petN-psbM_p4 petN-psbM TCGTAGTGTGGGGAAGAAGT CCTACCGCCTTTCTGCTTAT 80–592 1.000 82.2
petN-psbM_p5 petN-psbM ACTCGTAGTGTGGGGAAGAA CCTACCGCCTTTCTGCTTAT 80–594 1.000 82.1
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 80–727 1.000 80.9
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCATGGCGTTACTCTACCAC 80–706 1.000 80.6
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TGGCGTTACTCTACCACTGA 80–703 1.000 80.4
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCGATGACTTACGCCTTACC 80–724 1.000 79.8
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TTGAACCGATGACTTACGCC 80–729 1.000 78.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Stachys affinis NC_062803.1 149521 View on NCBI ↗
Stachys byzantina NC_029825.1 149749 View on NCBI ↗
Stachys chamissonis NC_029822.1 150254 View on NCBI ↗
Stachys coccinea NC_029823.1 150275 View on NCBI ↗
Stachys geobombycis NC_082543.1 150566 View on NCBI ↗
Stachys germanica PX260186.1 150238 View on NCBI ↗
Stachys japonica MT554703.1 150599 View on NCBI ↗
Stachys recta subsp. labiosa PP272178.1 150280 View on NCBI ↗
Stachys recta subsp. recta PP272180.1 150312 View on NCBI ↗
Stachys sylvatica NC_029824.1 150167 View on NCBI ↗