Markers + reference

Salvia

105 species · Lamiaceae · Lamiales

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Species 105
Genome length 151–152 kb
Candidate markers 274
Primer pairs 90

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 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 318 0.0636 0.95 76.5 yes View details
ycf1 IRb 1050 0.0059 1.00 49.2 no View details
ndhF SSC 2232 0.0258 1.00 66.5 yes View details
ndhF-rpl32 SSC 458 0.0450 0.98 73.2 yes View details
rpl32-trnL-UAG SSC 648 0.0549 0.98 78.0 yes View details
ccsA-ndhD SSC 237 0.0710 0.97 68.9 yes View details
ndhG-ndhI SSC 363 0.0551 1.00 73.0 yes View details
rps15-ycf1 SSC 406 0.0573 1.00 70.8 yes View details
ycf1 SSC 5526 0.0321 1.00 70.3 yes View details
trnT-GGU-psbD LSC 1372 0.0269 1.00 74.8 yes View details
trnK-UUU-rps16 LSC 570 0.0413 0.99 74.2 yes View details
trnE-UUC-trnT-GGU LSC 541 0.0355 0.99 72.5 yes View details
petA-psbJ LSC 1009 0.0318 1.00 72.0 yes View details
petN-psbM LSC 987 0.0321 0.99 71.7 yes View details
rps16-trnQ-UUG LSC 754 0.0343 0.99 70.6 yes View details
atpH-atpI LSC 1011 0.0315 0.97 70.5 yes View details
psbK-psbI LSC 392 0.0430 0.99 70.1 yes View details
trnS-GCU-trnG-UCC LSC 704 0.0313 0.98 70.1 yes View details
ndhC-trnV-UAC LSC 804 0.0270 1.00 70.1 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 CAACCGTGCTAACCTTGGTA 370–457 1.000 89.6
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 318–405 0.971 89.2
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 332–419 0.971 89.2
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 331–418 0.971 89.2
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 333–420 0.933 87.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC CTTTTAAAGAAGGCGGGAGT 627–655 0.914 67.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA CTTTTAAAGAAGGCGGGAGT 622–650 0.914 67.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC AGAAGGCGGGAGTTTTTAAA 487–648 0.990 66.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC CTTTTAAAGAAGGCGGGAGTT 627–655 0.914 65.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA CTTTTAAAGAAGGCGGGAGTT 622–650 0.914 65.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 262–1146 1.000 90.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 254–1138 1.000 85.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AGTCGCACGTTGCTTTCTAC GAGGTTCGAATCCTTCCGTC 261–1145 1.000 84.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GCACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 257–1141 1.000 82.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTTCGAATCCTTCCGTCCC 261–1143 1.000 82.4
psbK-psbI_p1 psbK-psbI TAGCTTTTGTTTGGCAGGCT ACGAAGAGTTTCAGAGTAAGCA 434–1855 1.000 68.9
psbK-psbI_p2 psbK-psbI GCAGGCTGCTGTAAGTTTTC ACGAAGAGTTTCAGAGTAAGCA 421–1856 1.000 68.6
psbK-psbI_p3 psbK-psbI TTAGCTTTTGTTTGGCAGGC ACGAAGAGTTTCAGAGTAAGCA 435–1853 1.000 67.1
psbK-psbI_p4 psbK-psbI AGGCTGCTGTAAGTTTTCGA ACGAAGAGTTTCAGAGTAAGCA 419–1854 1.000 67.0
psbK-psbI_p5 psbK-psbI CAGGCTGCTGTAAGTTTTCG ACGAAGAGTTTCAGAGTAAGCA 420–1855 1.000 66.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TACCACTAAACTATACCCGC 659–2895 1.000 59.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TACCACTAAACTATACCCGC 658–2894 1.000 59.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TTACCACTAAACTATACCCGC 660–2896 1.000 58.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TTACCACTAAACTATACCCGC 659–2895 1.000 58.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TACCACTAAACTATACCCGC 713–2896 1.000 58.7
atpH-atpI_p1 atpH-atpI AACAACTCACACACACTCCC TTCGGAACCCACAAACCATT 2156–2305 0.971 90.0
atpH-atpI_p2 atpH-atpI AACAACTCACACACACTCCC GCAGATAGGGGGTTTCCAAG 2245–2394 0.543 72.9
atpH-atpI_p3 atpH-atpI CACACACACTCCCTTTCCAA GCAGATAGGGGGTTTCCAAG 2238–2387 0.543 72.8
atpH-atpI_p4 atpH-atpI AACAACTCACACACACTCCC TGCTTTGGCTTTACTCACGT 2003–2041 0.333 61.9
atpH-atpI_p5 atpH-atpI CACACACACTCCCTTTCCAA TGCTTTGGCTTTACTCACGT 1996–2034 0.333 61.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (105)

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

Species Accession Length (bp) Link
Salvia adenophora MT156363.1 151072 View on NCBI ↗
Salvia aerea NC_067739.1 151492 View on NCBI ↗
Salvia aethiopis PV870855.1 151252 View on NCBI ↗
Salvia amarissima PV870856.1 151039 View on NCBI ↗
Salvia apiana NC_084049.1 151550 View on NCBI ↗
Salvia azurea MT156371.1 150959 View on NCBI ↗
Salvia bowleyana NC_063911.1 151508 View on NCBI ↗
Salvia brachyloma NC_053372.1 151329 View on NCBI ↗
Salvia brandegeei PX971244.1 151340 View on NCBI ↗
Salvia bucharica PV601297.1 151184 View on NCBI ↗
Salvia bulleyana NC_041092.1 151547 View on NCBI ↗
Salvia campanulata NC_057284.1 151658 View on NCBI ↗
Salvia castanea NC_067740.1 151469 View on NCBI ↗
Salvia castanea f. tomentosa MW387501.1 151590 View on NCBI ↗
Salvia cavaleriei NC_053375.1 151432 View on NCBI ↗
Salvia chienii NC_064053.1 151386 View on NCBI ↗
Salvia chinensis PV591959.1 151458 View on NCBI ↗
Salvia clevelandii PX971245.1 151384 View on NCBI ↗
Salvia columbariae PX971246.1 151338 View on NCBI ↗
Salvia curviflora MT156364.1 150986 View on NCBI ↗
Salvia cyclostegia NC_053379.1 151644 View on NCBI ↗
Salvia dabieshanensis NC_063912.1 151330 View on NCBI ↗
Salvia daiguii NC_059718.1 151434 View on NCBI ↗
Salvia deserta NC_084045.1 151326 View on NCBI ↗
Salvia dorrii PV870857.1 151727 View on NCBI ↗
Salvia dorystaechas NC_084050.1 151994 View on NCBI ↗
Salvia eremostachya PV870858.1 151720 View on NCBI ↗
Salvia farinacea PQ359435.1 150919 View on NCBI ↗
Salvia flava NC_053376.1 151489 View on NCBI ↗
Salvia forsskaolei NC_084047.1 151745 View on NCBI ↗
Salvia fruticosa PV870859.1 151105 View on NCBI ↗
Salvia glabrescens NC_067735.1 151476 View on NCBI ↗
Salvia glutinosa NC_067736.1 151662 View on NCBI ↗
Salvia grandifolia NC_084046.1 151268 View on NCBI ↗
Salvia guidongensis OR767373.1 151223 View on NCBI ↗
Salvia hispanica NC_046838.1 150980 View on NCBI ↗
Salvia honania NC_058852.1 151559 View on NCBI ↗
Salvia huberi PV870860.1 151048 View on NCBI ↗
Salvia insignis PV972776.1 151286 View on NCBI ↗
Salvia iodantha MT156366.1 150814 View on NCBI ↗
Salvia karwinskii MT156372.1 150907 View on NCBI ↗
Salvia korolkovii PV601298.1 150970 View on NCBI ↗
Salvia kronenburgii PV870861.1 151078 View on NCBI ↗
Salvia leucantha NC_084044.1 151038 View on NCBI ↗
Salvia liguliloba NC_067742.1 151387 View on NCBI ↗
Salvia lilacinocoerulea PV991053.1 151653 View on NCBI ↗
Salvia limbata PV870862.1 151174 View on NCBI ↗
Salvia luteistriata NC_067741.1 151583 View on NCBI ↗
Salvia lyrata NC_084048.1 151228 View on NCBI ↗
Salvia madrensis MT156373.1 151091 View on NCBI ↗
Salvia mairei NC_053378.1 151629 View on NCBI ↗
Salvia meiliensis NC_050896.1 151614 View on NCBI ↗
Salvia mekongensis NC_053380.1 151746 View on NCBI ↗
Salvia merjamie NC_050897.1 151286 View on NCBI ↗
Salvia microphylla MT156365.1 150873 View on NCBI ↗
Salvia miltiorrhiza NC_020431.1 151328 View on NCBI ↗
Salvia mohavensis PV870863.1 151672 View on NCBI ↗
Salvia multicaulis OR684571.1 151373 View on NCBI ↗
Salvia munzii PX971247.1 151311 View on NCBI ↗
Salvia nanchuanensis NC_058851.1 151568 View on NCBI ↗
Salvia nanchuanensis var. pteridifolia MW435408.1 151455 View on NCBI ↗
Salvia nilotica NC_050898.1 151450 View on NCBI ↗
Salvia nipponica MT156377.1 151484 View on NCBI ↗
Salvia nubicola NC_067737.1 151632 View on NCBI ↗
Salvia officinalis NC_038165.1 151089 View on NCBI ↗
Salvia officinalis subsp. gallica PV870864.1 151133 View on NCBI ↗
Salvia omeiana PX971248.1 151218 View on NCBI ↗
Salvia oxyphora MT156374.1 151014 View on NCBI ↗
Salvia pachyphylla PV870865.1 151269 View on NCBI ↗
Salvia pansamalensis MT156368.1 150988 View on NCBI ↗
Salvia petrophila NC_050899.1 151688 View on NCBI ↗
Salvia plebeia NC_050929.1 151062 View on NCBI ↗
Salvia plectranthoides NC_053374.1 151416 View on NCBI ↗
Salvia pratensis PP272175.1 151417 View on NCBI ↗
Salvia prattii MK944407.1 151690 View on NCBI ↗
Salvia prionitis NC_065866.1 151493 View on NCBI ↗
Salvia przewalskii NC_041091.1 151319 View on NCBI ↗
Salvia roborowskii NC_064050.1 151649 View on NCBI ↗
Salvia rosmarinus NC_027259.1 152462 View on NCBI ↗
Salvia saccardiana PV870867.1 151353 View on NCBI ↗
Salvia scapiformis NC_067743.1 151407 View on NCBI ↗
Salvia sclarea NC_050900.1 151268 View on NCBI ↗
Salvia semiatrata MT156370.1 151036 View on NCBI ↗
Salvia sikkimensis NC_071851.1 151104 View on NCBI ↗
Salvia sonchifolia NC_064054.1 151230 View on NCBI ↗
Salvia sonomensis PV870868.1 151317 View on NCBI ↗
Salvia spathacea PV870869.1 151727 View on NCBI ↗
Salvia splendens NC_050901.1 150604 View on NCBI ↗
Salvia subbipinnata NC_063913.1 151388 View on NCBI ↗
Salvia submutica PV601299.1 151319 View on NCBI ↗
Salvia subpalmatinervis NC_053373.1 151385 View on NCBI ↗
Salvia substolonifera NC_061230.1 151378 View on NCBI ↗
Salvia tianschanica PV995245.1 151626 View on NCBI ↗
Salvia tiliifolia NC_050053.1 150836 View on NCBI ↗
Salvia tricuspis NC_067738.1 151633 View on NCBI ↗
Salvia trijuga NC_061229.1 151392 View on NCBI ↗
Salvia tubifera MT156369.1 150977 View on NCBI ↗
Salvia tuerckheimii PX971249.1 151058 View on NCBI ↗
Salvia umbratica NC_053377.1 151606 View on NCBI ↗
Salvia verbenaca PP272176.1 151216 View on NCBI ↗
Salvia verticillata subsp. verticillata PP272177.1 151367 View on NCBI ↗
Salvia wardii NC_064051.1 151485 View on NCBI ↗
Salvia xanthocheila PV870871.1 151257 View on NCBI ↗
Salvia yangii NC_050902.1 151466 View on NCBI ↗
Salvia yunnanensis NC_050903.1 151413 View on NCBI ↗