Markers + reference

Begonia

113 species · Begoniaceae · Cucurbitales

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Species 113
Genome length 133–175 kb
Candidate markers 289
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 289 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnE-UUC-trnT-GGU LSC 1191 0.0425 0.98 83.6 yes View details
psbZ-trnG-GCC LSC 583 0.0556 0.98 82.2 yes View details
trnT-UGU-trnL-UAA LSC 1264 0.0513 0.97 79.3 yes View details
psbE-petL LSC 1290 0.0404 0.84 72.9 yes View details
ycf1 IRb 1390 0.0085 1.00 61.6 no View details
ndhF-rpl32 SSC 981 0.0752 0.98 82.3 yes View details
rpl32-trnL-UAG SSC 1120 0.0582 0.98 80.3 yes View details
ycf1 SSC 5349 0.0392 1.00 73.3 yes View details
ndhC-trnV-UAC LSC 664 0.0441 0.99 81.2 yes View details
trnC-GCA-petN LSC 743 0.0414 1.00 80.2 yes View details
trnT-GGU-psbD LSC 1547 0.0345 0.98 80.2 yes View details
psbM-trnD-GUC LSC 905 0.0431 0.99 79.9 yes View details
rpoB-trnC-GCA LSC 1152 0.0442 0.95 79.4 yes View details
rbcL-accD LSC 708 0.0411 0.99 79.2 yes View details
clpP-psbB LSC 479 0.0284 0.99 78.7 yes View details
ycf1-ndhF SSC 1027 0.0401 1.00 78.6 yes View details
trnD-GUC-trnY-GUA LSC 479 0.0441 0.98 78.1 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT CCGGATTTGAACTGGGGAAA 1341–1874 0.973 90.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT TCTTCCACTTGCTTCTGCTG 1432–1965 0.779 82.0
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT TTCAGGCACAACACCATTCA 2000–2492 0.504 71.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT ATTCCATTCGTGACTGTGGG 1786–2211 0.142 56.4
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT GCAGCAGCCACTACATTAGT 1605–2059 0.097 54.4
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 503–1027 1.000 88.5
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 442–966 0.956 88.4
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGAGTCCACTTCTTCCCCAT 521–1045 1.000 86.3
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 460–984 0.956 86.2
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 441–965 0.956 82.4
psbM-trnD-GUC_p1 psbM-trnD-GUC AGGAACTAGAATGAACAGTGT GTTCGAGCCCCGTCAGTC 759–1007 1.000 52.0
psbM-trnD-GUC_p2 psbM-trnD-GUC GCAGTAGGAACTAGAATGAACAGT GTTCGAGCCCCGTCAGTC 764–1012 0.982 51.3
psbM-trnD-GUC_p3 psbM-trnD-GUC GCAGTAGGAACTAGAATGAACAG GTTCGAGCCCCGTCAGTC 764–1012 0.982 51.3
psbM-trnD-GUC_p4 psbM-trnD-GUC GCAGTAGGAACTAGAATGAACA GTTCGAGCCCCGTCAGTC 764–1012 0.982 51.3
psbM-trnD-GUC_p5 psbM-trnD-GUC AGAATGAACAGTGTAGTAGCA GTTCGAGCCCCGTCAGTC 752–1000 0.965 50.6
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA ATTCTTCTTGGGTCGATGCC 387–635 0.982 87.1
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TGGCAATATGTCTACGCTGG 334–582 0.982 85.6
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGCAATATGTCTACGCTGGT 333–581 0.982 85.5
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGGACGGACTGTAAATTCG 355–603 0.973 84.3
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGACGGACTGTAAATTCGT 354–602 0.973 84.1
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 677–1348 0.991 90.3
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 639–1310 0.991 89.5
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 618–1289 0.991 89.3
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCATGGCGTTACTCTACCAC 656–1327 0.947 88.1
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TGGCGTTACTCTACCACTGA 653–1324 0.947 87.9
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG TCCCTCCGTAACCAGTCATC 1373–1762 0.982 86.6
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA TCCCTCCGTAACCAGTCATC 1376–1765 0.973 86.1
trnT-GGU-psbD_p3 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA TCCCTCCGTAACCAGTCATC 1350–1739 1.000 85.6
trnT-GGU-psbD_p4 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GTCCCTCCGTAACCAGTCAT 1374–1763 0.982 84.3
trnT-GGU-psbD_p5 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CCTCCGTAACCAGTCATCCA 1371–1760 0.982 84.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (113)

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

Species Accession Length (bp) Link
Begonia aconitifolia NC_070304.1 170032 View on NCBI ↗
Begonia amoeboides NC_070305.1 168978 View on NCBI ↗
Begonia ampla PZ316381.1 169473 View on NCBI ↗
Begonia anemoniflora NC_070306.1 169158 View on NCBI ↗
Begonia anisosepala NC_070307.1 169555 View on NCBI ↗
Begonia ankaranensis PZ316382.1 169998 View on NCBI ↗
Begonia austroguangxiensis PZ316383.1 175154 View on NCBI ↗
Begonia baccata NC_070308.1 169961 View on NCBI ↗
Begonia balansana PZ316385.1 167758 View on NCBI ↗
Begonia biflora PZ316386.1 170131 View on NCBI ↗
Begonia bogneri NC_070309.1 170250 View on NCBI ↗
Begonia boliviensis PZ316388.1 170136 View on NCBI ↗
Begonia bowerae PZ316389.1 169361 View on NCBI ↗
Begonia bracteata NC_070310.1 169797 View on NCBI ↗
Begonia buddleiifolia NC_070311.1 168997 View on NCBI ↗
Begonia bullatifolia PZ316390.1 169235 View on NCBI ↗
Begonia cathayana NC_073119.1 169164 View on NCBI ↗
Begonia cavaleriei NC_073117.1 168857 View on NCBI ↗
Begonia chingipengii PZ316391.1 169425 View on NCBI ↗
Begonia chloroneura OQ091927.1 169870 View on NCBI ↗
Begonia cleopatrae PZ316392.1 169764 View on NCBI ↗
Begonia conchifolia PZ316393.1 169957 View on NCBI ↗
Begonia convolvulacea NC_070312.1 168493 View on NCBI ↗
Begonia coptidifolia NC_056110.1 169412 View on NCBI ↗
Begonia cubensis NC_070313.1 169672 View on NCBI ↗
Begonia cucullata PZ316395.1 169288 View on NCBI ↗
Begonia cylindrica PZ316396.1 169458 View on NCBI ↗
Begonia darthvaderiana PZ316397.1 170507 View on NCBI ↗
Begonia daxinensis OQ029585.1 169121 View on NCBI ↗
Begonia depauperata NC_070314.1 169210 View on NCBI ↗
Begonia dipetala NC_070315.1 170852 View on NCBI ↗
Begonia egregia NC_070317.1 168626 View on NCBI ↗
Begonia emeiensis NC_061410.1 169079 View on NCBI ↗
Begonia fagifolia PZ258588.1 168800 View on NCBI ↗
Begonia fangii PZ316401.1 170037 View on NCBI ↗
Begonia fenicis PZ316402.1 170105 View on NCBI ↗
Begonia ferox NC_067030.1 169114 View on NCBI ↗
Begonia filiformis PQ675783.1 169020 View on NCBI ↗
Begonia fimbristipula PZ316403.1 168574 View on NCBI ↗
Begonia fissistyla NC_070318.1 169526 View on NCBI ↗
Begonia foliosa NC_070319.1 169263 View on NCBI ↗
Begonia formosana PZ258589.1 169582 View on NCBI ↗
Begonia gironellae OQ091929.1 169444 View on NCBI ↗
Begonia glabra PZ258590.1 168980 View on NCBI ↗
Begonia goegoensis PZ316405.1 169084 View on NCBI ↗
Begonia guangdongensis OQ091930.1 169866 View on NCBI ↗
Begonia hainanensis PZ316407.1 170423 View on NCBI ↗
Begonia henrilaportei NC_070320.1 170355 View on NCBI ↗
Begonia henryi NC_070321.1 168124 View on NCBI ↗
Begonia heracleifolia OQ029586.1 169957 View on NCBI ↗
Begonia herbacea PZ316408.1 168723 View on NCBI ↗
Begonia heydei NC_070322.1 170025 View on NCBI ↗
Begonia incarnata PZ258591.1 169092 View on NCBI ↗
Begonia jinyunensis NC_068748.1 169578 View on NCBI ↗
Begonia karwinskyana NC_070323.1 169815 View on NCBI ↗
Begonia kingiana PZ316409.1 170426 View on NCBI ↗
Begonia lanceolata PZ316411.1 169618 View on NCBI ↗
Begonia lanternaria PZ316412.1 169921 View on NCBI ↗
Begonia leprosa NC_073118.1 168908 View on NCBI ↗
Begonia listada PZ258592.1 168779 View on NCBI ↗
Begonia liuyanii PZ316414.1 169075 View on NCBI ↗
Begonia longiciliata PZ316415.1 169559 View on NCBI ↗
Begonia lubbersii PZ316417.1 170095 View on NCBI ↗
Begonia ludwigii NC_070324.1 170355 View on NCBI ↗
Begonia luochengensis PQ675781.1 169473 View on NCBI ↗
Begonia luzonensis PZ316418.1 168804 View on NCBI ↗
Begonia lyallii PZ316419.1 170361 View on NCBI ↗
Begonia maculata PZ316420.1 169445 View on NCBI ↗
Begonia majungaensis PZ316421.1 170378 View on NCBI ↗
Begonia mannii PZ316422.1 167874 View on NCBI ↗
Begonia masoniana PZ316423.1 169009 View on NCBI ↗
Begonia megalophyllaria PZ316424.1 169070 View on NCBI ↗
Begonia meyeri-johannis NC_070325.1 167123 View on NCBI ↗
Begonia microsperma NC_070326.1 169651 View on NCBI ↗
Begonia nantoensis PZ258593.1 169754 View on NCBI ↗
Begonia natunaensis PZ316427.1 169259 View on NCBI ↗
Begonia oaxacana NC_070327.1 169783 View on NCBI ↗
Begonia oxyloba NC_070328.1 169003 View on NCBI ↗
Begonia peltatifolia PZ316429.1 170434 View on NCBI ↗
Begonia plebeja OQ091925.1 169986 View on NCBI ↗
Begonia polilloensis PZ316430.1 170385 View on NCBI ↗
Begonia polygonoides PZ316431.1 167968 View on NCBI ↗
Begonia pustulata PZ316432.1 169835 View on NCBI ↗
Begonia radicans PZ316433.1 170150 View on NCBI ↗
Begonia rajah PZ316434.1 170072 View on NCBI ↗
Begonia ravenii PZ316435.1 169026 View on NCBI ↗
Begonia retinervia NC_088496.1 169145 View on NCBI ↗
Begonia rossmanniae NC_070329.1 169232 View on NCBI ↗
Begonia rufipila PZ316437.1 170769 View on NCBI ↗
Begonia salaziensis PZ316438.1 171027 View on NCBI ↗
Begonia samhaensis NC_070330.1 169413 View on NCBI ↗
Begonia sanguinea NC_070331.1 168106 View on NCBI ↗
Begonia santos-limae NC_070332.1 169746 View on NCBI ↗
Begonia scapigera PZ258594.1 169270 View on NCBI ↗
Begonia silletensis subsp. mengyangensis OQ091926.1 169372 View on NCBI ↗
Begonia sinofloribunda PZ258595.1 168998 View on NCBI ↗
Begonia smithiana NC_073123.1 169694 View on NCBI ↗
Begonia soli-mutata PZ316440.1 170381 View on NCBI ↗
Begonia subcoriacea PQ619425.1 168614 View on NCBI ↗
Begonia sublongipes PZ316441.1 170192 View on NCBI ↗
Begonia sudjanae PZ316442.1 133127 View on NCBI ↗
Begonia susaniae PZ316443.1 169582 View on NCBI ↗
Begonia taiwaniana PZ316444.1 169770 View on NCBI ↗
Begonia thelmae OQ029584.1 169477 View on NCBI ↗
Begonia thiemei PZ258596.1 168961 View on NCBI ↗
Begonia ulmifolia NC_070333.1 168935 View on NCBI ↗
Begonia undulata NC_070334.1 169710 View on NCBI ↗
Begonia vankerckhovenii PZ316447.1 169952 View on NCBI ↗
Begonia variabilis PZ316448.1 169886 View on NCBI ↗
Begonia variifolia PZ258597.1 169630 View on NCBI ↗
Begonia vittariifolia PZ316449.1 169704 View on NCBI ↗
Begonia wallichiana PZ316450.1 168895 View on NCBI ↗
Begonia wangii PQ675782.1 169371 View on NCBI ↗