Markers + reference

Scutellaria

178 species · Lamiaceae · Lamiales

Back to catalogue

Species 178
Genome length 151–153 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

7 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
trnK-UUU-rps16 LSC 901 0.0335 1.00 72.7 yes View details
petN-psbM LSC 1016 0.0248 0.97 65.6 yes View details
rbcL-accD LSC 713 0.0205 0.99 62.1 yes View details
petA-psbJ LSC 1007 0.0284 1.00 72.2 yes View details
ndhF SSC 2262 0.0207 1.00 64.1 yes View details
rpl32-trnL-UAG SSC 446 0.0422 0.98 73.6 yes View details
ycf1 SSC 5637 0.0233 1.00 66.0 yes View details
trnT-UGU-trnL-UAA LSC 680 0.0263 0.99 71.2 yes View details
trnS-GCU-trnG-UCC LSC 700 0.0207 0.99 70.8 yes View details
trnG-GCC-trnfM-CAU LSC 147 0.0418 0.97 70.3 yes View details
trnT-GGU-psbD LSC 1305 0.0163 1.00 69.3 yes View details
rps16-trnQ-UUG LSC 745 0.0191 0.97 68.1 yes View details
rpoB-trnC-GCA LSC 1160 0.0183 1.00 68.0 yes View details
rpl20-rps12 LSC 794 0.0130 1.00 67.8 yes View details
psaC-ndhE SSC 255 0.0325 1.00 67.8 yes View details
ndhC-trnV-UAC LSC 985 0.0217 1.00 67.6 yes View details
ycf3-trnS-GGA LSC 883 0.0166 1.00 67.5 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG AAAAGGGTATGTTGCTGCCA 1392–1866 0.927 88.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAAGGGTATGTTGCTGCCA 1391–1865 0.927 88.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG CCCAATGAGCCGTTTATCGA 882–1285 0.854 85.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CCCAATGAGCCGTTTATCGA 881–1284 0.854 85.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TCCCAATGAGCCGTTTATCG 882–1285 0.854 85.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 723–1275 1.000 90.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 706–1258 1.000 90.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 724–1276 1.000 89.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AGCACCCTCATTCCTAGACA GAGGTTCGAATCCTTCCGTC 772–1324 1.000 89.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 720–1272 1.000 88.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AACCGAAAGACCCTTTAACT 665–887 1.000 63.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AACCGAAAGACCCTTTAACT 664–886 1.000 63.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 629–851 1.000 63.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 628–850 1.000 63.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AACCGAAAGACCCTTTAACT 719–941 1.000 62.7
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TTGTCTCATTTGCATCCCCG CCGGATTTGAACTGGGGAAA 1044–1269 0.989 86.6
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TTGTCTCATTTGCATCCCCG AAAAGGATTTGCAGTCCCCC 1026–1251 0.989 84.4
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GTCTCATTTGCATCCCCGAG CCGGATTTGAACTGGGGAAA 1042–1267 0.966 84.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CAAACCCTGATCGATGAACCT CCGGATTTGAACTGGGGAAA 1112–1337 1.000 83.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GTCTCATTTGCATCCCCGAG AAAAGGATTTGCAGTCCCCC 1024–1249 0.966 82.2
petN-psbM_p1 petN-psbM ACTCGTAGTGTGGGGAAGAA CAGTCCCGACGGATCAAAAT 1505–1810 1.000 91.8
petN-psbM_p2 petN-psbM TCGTAGTGTGGGGAAGAAGT CAGTCCCGACGGATCAAAAT 1503–1808 1.000 91.8
petN-psbM_p3 petN-psbM ACTCGTAGTGTGGGGAAGAA GTCCCGACGGATCAAAATCA 1503–1808 0.994 91.6
petN-psbM_p4 petN-psbM TCGTAGTGTGGGGAAGAAGT GTCCCGACGGATCAAAATCA 1501–1806 0.994 91.6
petN-psbM_p5 petN-psbM TCGTAGTGTGGGGAAGAAGT AATTTTCTGCTCGATCCCCC 1602–1907 0.618 76.2
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CCGCAACCAGTCATCCATAA 1234–1583 1.000 91.2
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA CCGCAACCAGTCATCCATAA 1237–1586 1.000 91.0
trnT-GGU-psbD_p3 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GACAAAAACGAAACGGTCCC 1255–1604 1.000 90.6
trnT-GGU-psbD_p4 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GACAAAAACGAAACGGTCCC 1258–1607 1.000 90.4
trnT-GGU-psbD_p5 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1254–1603 1.000 89.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (178)

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

Species Accession Length (bp) Link
Scutellaria adenostegia PQ058237.1 151773 View on NCBI ↗
Scutellaria adsurgens PQ058240.1 151844 View on NCBI ↗
Scutellaria agrestis PQ058275.1 151670 View on NCBI ↗
Scutellaria albida PQ059215.1 151946 View on NCBI ↗
Scutellaria albida subsp. condensata MW420937.1 151908 View on NCBI ↗
Scutellaria albida subsp. velenovskyi PQ059241.1 151882 View on NCBI ↗
Scutellaria alpina PQ059196.1 151828 View on NCBI ↗
Scutellaria altaica PQ075892.1 151716 View on NCBI ↗
Scutellaria altissima PQ059199.1 151998 View on NCBI ↗
Scutellaria amabilis PQ075894.1 151879 View on NCBI ↗
Scutellaria amoena NC_057255.1 151569 View on NCBI ↗
Scutellaria angustifolia MW420978.1 152539 View on NCBI ↗
Scutellaria antirrhinoides PQ075899.1 152477 View on NCBI ↗
Scutellaria arabica PQ059208.1 152002 View on NCBI ↗
Scutellaria aurata PQ058277.1 151855 View on NCBI ↗
Scutellaria austrotaiwanensis PQ075900.1 151922 View on NCBI ↗
Scutellaria axilliflora PQ075901.1 152231 View on NCBI ↗
Scutellaria axilliflora var. medullifera PQ075902.1 152141 View on NCBI ↗
Scutellaria baicalensis NC_027262.1 152731 View on NCBI ↗
Scutellaria barbata NC_059814.1 152050 View on NCBI ↗
Scutellaria brachyspica PQ075905.1 151831 View on NCBI ↗
Scutellaria brevibracteata PQ059216.1 151992 View on NCBI ↗
Scutellaria brevibracteata subsp. subvelutina PQ059224.1 151952 View on NCBI ↗
Scutellaria calcarata MN128385.1 152033 View on NCBI ↗
Scutellaria californica PQ075909.1 152418 View on NCBI ↗
Scutellaria caryopteroides NC_072112.1 152073 View on NCBI ↗
Scutellaria caudifolia PQ075911.1 152329 View on NCBI ↗
Scutellaria caudifolia var. obliquifolia PQ075908.1 152006 View on NCBI ↗
Scutellaria chungtienensis PQ075912.1 151840 View on NCBI ↗
Scutellaria colpodea PZ169282.1 151885 View on NCBI ↗
Scutellaria columnae PQ059198.1 151919 View on NCBI ↗
Scutellaria comosa PQ058241.1 151798 View on NCBI ↗
Scutellaria cordifrons PQ058242.1 152207 View on NCBI ↗
Scutellaria cristata PZ130072.1 151638 View on NCBI ↗
Scutellaria cypria PQ059220.1 151785 View on NCBI ↗
Scutellaria delavayi PQ075918.1 152020 View on NCBI ↗
Scutellaria diffusa PQ059212.1 152407 View on NCBI ↗
Scutellaria edelbergii PQ059226.1 152252 View on NCBI ↗
Scutellaria elliptica var. hirsuta PQ059304.1 151591 View on NCBI ↗
Scutellaria eplingii PQ058279.1 151780 View on NCBI ↗
Scutellaria farsistanica PQ059227.1 152132 View on NCBI ↗
Scutellaria flocculosa PQ058280.1 151663 View on NCBI ↗
Scutellaria forrestii NC_072113.1 151759 View on NCBI ↗
Scutellaria franchetiana NC_059813.1 151852 View on NCBI ↗
Scutellaria galericulata PQ059292.1 152562 View on NCBI ↗
Scutellaria gardoquioides MW413436.1 151763 View on NCBI ↗
Scutellaria glabrata PZ130067.1 151771 View on NCBI ↗
Scutellaria grandiflora PQ058243.1 151836 View on NCBI ↗
Scutellaria grossa PQ059197.1 151967 View on NCBI ↗
Scutellaria grossheimiana PQ059204.1 151785 View on NCBI ↗
Scutellaria hainanensis PQ075885.1 152189 View on NCBI ↗
Scutellaria helenae PQ059306.1 152278 View on NCBI ↗
Scutellaria hintoniana MW420959.1 151030 View on NCBI ↗
Scutellaria holosericea PZ169285.1 151891 View on NCBI ↗
Scutellaria humilis PQ058251.1 152406 View on NCBI ↗
Scutellaria hypericifolia MW286270.1 151574 View on NCBI ↗
Scutellaria immaculata MW420944.1 152008 View on NCBI ↗
Scutellaria indica NC_072111.1 152003 View on NCBI ↗
Scutellaria indica var. coccinea MN047312.1 151956 View on NCBI ↗
Scutellaria indica var. elliptica PQ059294.1 152055 View on NCBI ↗
Scutellaria indica var. parvifolia PQ059312.1 151888 View on NCBI ↗
Scutellaria indica var. subacaulis PQ059311.1 152025 View on NCBI ↗
Scutellaria insignis NC_028533.1 151908 View on NCBI ↗
Scutellaria integrifolia PQ059295.1 151669 View on NCBI ↗
Scutellaria intermedia PZ169286.1 151765 View on NCBI ↗
Scutellaria isocheila PQ058270.1 151979 View on NCBI ↗
Scutellaria javanica PQ059314.1 152070 View on NCBI ↗
Scutellaria javanica var. luzonica PQ058285.1 151925 View on NCBI ↗
Scutellaria karjaginii PQ059195.1 151821 View on NCBI ↗
Scutellaria kingiana MN128389.1 152395 View on NCBI ↗
Scutellaria kotkaiensis PQ059229.1 152279 View on NCBI ↗
Scutellaria kuramensis PZ169287.1 152274 View on NCBI ↗
Scutellaria laeteviolacea PQ075890.1 151831 View on NCBI ↗
Scutellaria laeteviolacea var. maekawae PQ059359.1 151889 View on NCBI ↗
Scutellaria lanipes PQ058244.1 151880 View on NCBI ↗
Scutellaria lateriflora NC_034693.1 152283 View on NCBI ↗
Scutellaria laxa PQ059296.1 152481 View on NCBI ↗
Scutellaria likiangensis NC_061416.1 151761 View on NCBI ↗
Scutellaria linarioides PQ059316.1 152025 View on NCBI ↗
Scutellaria litwinowii PQ059317.1 152194 View on NCBI ↗
Scutellaria longifolia MW420966.1 151742 View on NCBI ↗
Scutellaria macrosiphon PQ059318.1 152049 View on NCBI ↗
Scutellaria meehanioides NC_057189.1 152484 View on NCBI ↗
Scutellaria megalaspis PQ059231.1 151945 View on NCBI ↗
Scutellaria mesostegia PQ075922.1 151839 View on NCBI ↗
Scutellaria microdasys PQ059319.1 151846 View on NCBI ↗
Scutellaria microviolacea PQ059320.1 151865 View on NCBI ↗
Scutellaria minor PQ059203.1 152601 View on NCBI ↗
Scutellaria mollifolia MN128384.1 152417 View on NCBI ↗
Scutellaria multicaulis PZ169284.1 151765 View on NCBI ↗
Scutellaria muramatsui PQ059322.1 152059 View on NCBI ↗
Scutellaria nervosa PQ058257.1 152637 View on NCBI ↗
Scutellaria nuristanica PQ059232.1 151907 View on NCBI ↗
Scutellaria oligodonta PQ059323.1 151715 View on NCBI ↗
Scutellaria omeiensis var. serratifolia PQ059324.1 152055 View on NCBI ↗
Scutellaria orientalis subsp. bornmuelleri PQ059223.1 151798 View on NCBI ↗
Scutellaria orientalis subsp. orientalis PQ059307.1 151776 View on NCBI ↗
Scutellaria ossethica PQ059233.1 151992 View on NCBI ↗
Scutellaria ovata subsp. ovata PQ059327.1 151639 View on NCBI ↗
Scutellaria pacifica PQ059298.1 152521 View on NCBI ↗
Scutellaria parvula var. australis PQ059330.1 152571 View on NCBI ↗
Scutellaria parvula var. leonardi PQ058258.1 152559 View on NCBI ↗
Scutellaria paulsenii PQ058238.1 151751 View on NCBI ↗
Scutellaria pekinensis var. pekinensis PQ059333.1 151972 View on NCBI ↗
Scutellaria pekinensis var. purpureicaulis PQ059331.1 152536 View on NCBI ↗
Scutellaria pekinensis var. transitra PQ059299.1 152465 View on NCBI ↗
Scutellaria pekinensis var. ussuriensis PQ059194.1 152525 View on NCBI ↗
Scutellaria peregrina PQ059200.1 152024 View on NCBI ↗
Scutellaria phyllostachya PZ169288.1 151810 View on NCBI ↗
Scutellaria pinnatifida PQ059326.1 151802 View on NCBI ↗
Scutellaria pinnatifida subsp. alpina PQ059206.1 151861 View on NCBI ↗
Scutellaria pinnatifida subsp. pichleri MW420935.1 151551 View on NCBI ↗
Scutellaria platystegia PQ059235.1 151792 View on NCBI ↗
Scutellaria polyadenia PQ058256.1 152418 View on NCBI ↗
Scutellaria pontica PQ059211.1 152291 View on NCBI ↗
Scutellaria porphyrantha PQ059236.1 151945 View on NCBI ↗
Scutellaria prostrata PQ059300.1 151805 View on NCBI ↗
Scutellaria przewalskii PQ059325.1 152202 View on NCBI ↗
Scutellaria purpurascens PQ058276.1 151944 View on NCBI ↗
Scutellaria purpurascens subsp. purpurascens PQ058269.1 151693 View on NCBI ↗
Scutellaria pycnoclada PZ169294.1 151781 View on NCBI ↗
Scutellaria quadrilobulata PQ059301.1 152080 View on NCBI ↗
Scutellaria racemosa PQ059336.1 152586 View on NCBI ↗
Scutellaria raddeana PQ059237.1 151891 View on NCBI ↗
Scutellaria ramosissima PQ059244.1 151830 View on NCBI ↗
Scutellaria rehderiana MT982397.1 151827 View on NCBI ↗
Scutellaria resinosa PQ058263.1 152308 View on NCBI ↗
Scutellaria rubicunda MW420939.1 152016 View on NCBI ↗
Scutellaria rubropunctata PQ059337.1 152080 View on NCBI ↗
Scutellaria salviifolia PQ059210.1 152351 View on NCBI ↗
Scutellaria scandens PQ059338.1 152624 View on NCBI ↗
Scutellaria schachristanica PZ169289.1 151772 View on NCBI ↗
Scutellaria schweinfurthii PQ058254.1 152504 View on NCBI ↗
Scutellaria schweinfurthii subsp. paucifolia PQ058255.1 152460 View on NCBI ↗
Scutellaria scordifolia NC_052883.1 152366 View on NCBI ↗
Scutellaria scordiifolia var. ammophila PQ059339.1 152574 View on NCBI ↗
Scutellaria scordiifolia var. puberula PQ059189.1 152566 View on NCBI ↗
Scutellaria seleriana MW420962.1 151744 View on NCBI ↗
Scutellaria serrata PQ059340.1 151523 View on NCBI ↗
Scutellaria sessilifolia PQ059344.1 152445 View on NCBI ↗
Scutellaria shikokiana PQ059190.1 152554 View on NCBI ↗
Scutellaria sibthorpii PQ059217.1 151990 View on NCBI ↗
Scutellaria sieberi PQ059201.1 151983 View on NCBI ↗
Scutellaria sieversii PQ058246.1 151483 View on NCBI ↗
Scutellaria sosnowskyi PQ075921.1 152149 View on NCBI ↗
Scutellaria splendens MW420963.1 151861 View on NCBI ↗
Scutellaria stocksii PQ059207.1 152182 View on NCBI ↗
Scutellaria striatella PZ169290.1 152162 View on NCBI ↗
Scutellaria subcaespitosa PQ058249.1 152066 View on NCBI ↗
Scutellaria supina PZ169291.1 151780 View on NCBI ↗
Scutellaria tashiroi PQ059348.1 152071 View on NCBI ↗
Scutellaria tayloriana PQ059349.1 151977 View on NCBI ↗
Scutellaria tenera PQ059191.1 152031 View on NCBI ↗
Scutellaria teucriifolia PQ059238.1 151738 View on NCBI ↗
Scutellaria theobromina PQ059239.1 151809 View on NCBI ↗
Scutellaria tienchuanensis PQ059351.1 152496 View on NCBI ↗
Scutellaria tournefortii PQ059214.1 151923 View on NCBI ↗
Scutellaria tsinyunensis NC_050161.1 152089 View on NCBI ↗
Scutellaria tuberifera NC_059812.1 152332 View on NCBI ↗
Scutellaria tuberosa PQ059352.1 152229 View on NCBI ↗
Scutellaria tuminensis PQ059353.1 152576 View on NCBI ↗
Scutellaria tuvensis PQ059303.1 151820 View on NCBI ↗
Scutellaria uliginosa PQ058274.1 151732 View on NCBI ↗
Scutellaria urticifolia PZ169292.1 151777 View on NCBI ↗
Scutellaria utriculata PQ059221.1 151986 View on NCBI ↗
Scutellaria velutina PQ058248.1 152070 View on NCBI ↗
Scutellaria ventenatii PQ058273.1 152058 View on NCBI ↗
Scutellaria veronicifolia var. patentipilosa PQ059350.1 152040 View on NCBI ↗
Scutellaria villosissima PZ169293.1 151940 View on NCBI ↗
Scutellaria violacea var. violacea PQ075913.1 152041 View on NCBI ↗
Scutellaria violascens PQ058253.1 152473 View on NCBI ↗
Scutellaria woodii PQ058281.1 151856 View on NCBI ↗
Scutellaria wrightii PQ058264.1 152280 View on NCBI ↗
Scutellaria wulingshanensis PQ059355.1 152565 View on NCBI ↗
Scutellaria x churchilliana PQ058261.1 152348 View on NCBI ↗
Scutellaria yezoensis PQ058247.1 152585 View on NCBI ↗
Scutellaria yingtakensis PQ059356.1 151985 View on NCBI ↗
Scutellaria yunnanensis var. salicifolia PQ059357.1 151910 View on NCBI ↗