Markers + reference

Helianthus

37 species · Asteraceae · Asterales

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Species 37
Genome length 151–151 kb
Candidate markers 266
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psaA-pafI LSC 762 0.0033 0.95 59.7 yes View details
atpB-rbcL LSC 753 0.0033 1.00 58.9 yes View details
rbcL LSC 1458 0.0038 1.00 44.4 yes View details
petA-psbJ LSC 803 0.0035 0.97 58.1 yes View details
trnP-UGG-psaJ LSC 319 0.0031 1.00 33.3 yes View details
clpP1 LSC 1996 0.0015 0.98 51.5 yes View details
petB LSC 1417 0.0021 1.00 41.1 yes View details
psaC SSC 246 0.0004 1.00 23.5 yes View details
ndhD SSC 1503 0.0008 1.00 33.1 yes View details
ndhD-ccsA SSC 265 0.0204 0.98 59.7 yes View details
trnL-UAG-rpl32 SSC 763 0.0038 1.00 56.9 yes View details
rpl32-ndhF SSC 849 0.0023 1.00 49.8 yes View details
trnR-ACG-rrn5 IRa 276 0.0083 1.00 55.4 yes View details
rpl2-trnH-GUG IRa 157 0.0003 1.00 65.5 no View details
rps16 LSC 1135 0.0022 0.99 61.2 yes View details
rrn5-trnR-ACG IRb 276 0.0080 0.99 59.9 yes View details
atpI-atpH LSC 1172 0.0022 1.00 59.5 yes View details
ndhC-trnV-UAC LSC 942 0.0029 0.97 59.2 yes View details
rpl14-rpl16 LSC 106 0.0112 0.98 59.2 yes View details
trnT-UGU-trnL-UAA LSC 540 0.0021 1.00 55.5 yes View details
accD-psaI LSC 698 0.0018 1.00 54.2 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU AACGGTTTGCAAAAATTTCT TCGTAGATGTAGATTAATGCTTTGA 2739–2772 1.000 42.3
trnK-UUU_p2 trnK-UUU AAACGGTTTGCAAAAATTTCT TCGTAGATGTAGATTAATGCTTTGA 2740–2773 1.000 42.3
trnK-UUU_p3 trnK-UUU AAAACGGTTTGCAAAAATTTCT TCGTAGATGTAGATTAATGCTTTGA 2741–2774 1.000 42.3
trnK-UUU_p4 trnK-UUU AACGGTTTGCAAAAATTTCT CGTAGATGTAGATTAATGCTTTGA 2738–2771 1.000 42.3
trnK-UUU_p5 trnK-UUU AACGGTTTGCAAAAATTTCT TCGTAGATGTAGATTAATGCTTTG 2739–2772 1.000 42.3
rps16_p1 rps16 ACGAATAGAGCAAGAAAAGAAGG TGACTGTGTCTCTGTACCGA 1286–1336 1.000 49.1
rps16_p2 rps16 ACGAATAGAGCAAGAAAAGAAGG TGTGTCTCTGTACCGACTGA 1282–1332 1.000 49.1
rps16_p3 rps16 ACGAATAGAGCAAGAAAAGAAGG ACTGTGTCTCTGTACCGACT 1284–1334 1.000 49.0
rps16_p4 rps16 ACGAATAGAGCAAGAAAAGAAGG TCTCTGTACCGACTGAACCA 1278–1328 1.000 49.0
rps16_p5 rps16 ACGAATAGAGCAAGAAAAGAAGGA TGTGTCTCTGTACCGACTGA 1282–1332 1.000 48.4
atpI-atpH_p1 atpI-atpH CCCGTCATGTTCCTTGGATT ATAACGGAAGCGGCAGAAAT 1290–1352 1.000 83.1
atpI-atpH_p2 atpI-atpH CCCGTCATGTTCCTTGGATT TACCTTGACCAACTCCAGGT 1346–1408 1.000 82.3
atpI-atpH_p3 atpI-atpH CCCGTCATGTTCCTTGGATT AGCCAATCCAGCAGCAATAA 1306–1368 1.000 82.1
atpI-atpH_p4 atpI-atpH CCCGTCATGTTCCTTGGATT AATAACGGAAGCGGCAGAAA 1291–1353 1.000 81.9
atpI-atpH_p5 atpI-atpH CCCGTCATGTTCCTTGGATT GCAGTACCTTGACCAACTCC 1350–1412 1.000 81.7
psaA-pafI_p1 psaA-pafI GAGAAATGACCCGGTCTAGC AGCCGCTGAGTATTGGAAAC 908–954 1.000 81.6
psaA-pafI_p2 psaA-pafI GAGAAATGACCCGGTCTAGC CAAGCCGCTGAGTATTGGAA 910–956 1.000 81.6
psaA-pafI_p3 psaA-pafI GAGAAATGACCCGGTCTAGC AAGCCGCTGAGTATTGGAAA 909–955 1.000 79.7
psaA-pafI_p4 psaA-pafI TTTTACTTCTGGTTCCGGCG AGCCGCTGAGTATTGGAAAC 843–889 1.000 79.6
psaA-pafI_p5 psaA-pafI TTTTACTTCTGGTTCCGGCG CAAGCCGCTGAGTATTGGAA 845–891 1.000 79.6
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 572–628 1.000 83.8
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 580–636 1.000 83.2
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 604–660 1.000 82.7
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 612–668 1.000 82.1
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG AGTCCGTAGCGTCTACCAAT 586–642 1.000 81.8
ndhC-trnV-UAC_p1 ndhC-trnV-UAC TTCTCCGGTCCTTTGCTACT AGAAGGTCTACGGTTCGAGT 1055–1107 1.000 81.6
ndhC-trnV-UAC_p2 ndhC-trnV-UAC CTTTGCTACTCGGGGCTAAA AGAAGGTCTACGGTTCGAGT 1045–1097 1.000 81.4
ndhC-trnV-UAC_p3 ndhC-trnV-UAC TTTCTCCGGTCCTTTGCTAC AGAAGGTCTACGGTTCGAGT 1056–1108 1.000 80.8
ndhC-trnV-UAC_p4 ndhC-trnV-UAC TTCTCCGGTCCTTTGCTACT GAAGGTCTACGGTTCGAGTC 1054–1106 1.000 78.9
ndhC-trnV-UAC_p5 ndhC-trnV-UAC CTTTGCTACTCGGGGCTAAA GAAGGTCTACGGTTCGAGTC 1044–1096 1.000 78.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (37)

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

Species Accession Length (bp) Link
Helianthus agrestis NC_086875.1 151108 View on NCBI ↗
Helianthus angustifolius PX666003.1 151321 View on NCBI ↗
Helianthus annuus NC_007977.1 151104 View on NCBI ↗
Helianthus anomalus NC_077525.1 151144 View on NCBI ↗
Helianthus argophyllus OP979113.1 151101 View on NCBI ↗
Helianthus arizonensis NC_086874.1 151122 View on NCBI ↗
Helianthus atrorubens NC_058796.1 151240 View on NCBI ↗
Helianthus carnosus NC_066996.1 151241 View on NCBI ↗
Helianthus cusickii NC_086873.1 151382 View on NCBI ↗
Helianthus debilis subsp. silvestris NC_073153.1 150996 View on NCBI ↗
Helianthus decapetalus NC_023110.1 151048 View on NCBI ↗
Helianthus deserticola NC_067854.1 151164 View on NCBI ↗
Helianthus divaricatus NC_023109.1 151045 View on NCBI ↗
Helianthus exilis PQ788851.1 151305 View on NCBI ↗
Helianthus floridanus PX666086.1 151180 View on NCBI ↗
Helianthus giganteus NC_023107.1 151066 View on NCBI ↗
Helianthus grosseserratus NC_023108.1 151017 View on NCBI ↗
Helianthus hirsutus NC_023111.1 151045 View on NCBI ↗
Helianthus laciniatus MW353165.1 151113 View on NCBI ↗
Helianthus laevigatus PV138132.1 151122 View on NCBI ↗
Helianthus maximiliani NC_023114.1 151007 View on NCBI ↗
Helianthus microcephalus NC_057462.1 151289 View on NCBI ↗
Helianthus mollis NC_086876.1 151060 View on NCBI ↗
Helianthus neglectus NC_072951.1 151109 View on NCBI ↗
Helianthus niveus subsp. tephrodes PQ789229.1 151018 View on NCBI ↗
Helianthus nuttallii subsp. nuttallii NC_072636.1 151179 View on NCBI ↗
Helianthus pauciflorus subsp. pauciflorus MT302564.1 151210 View on NCBI ↗
Helianthus praecox subsp. praecox OR974832.1 151327 View on NCBI ↗
Helianthus resinosus PZ143189.1 151206 View on NCBI ↗
Helianthus salicifolius NC_057461.1 151229 View on NCBI ↗
Helianthus schweinitzii MW381301.1 151208 View on NCBI ↗
Helianthus silphioides NC_058798.1 151134 View on NCBI ↗
Helianthus simulans NC_086872.1 151137 View on NCBI ↗
Helianthus strumosus NC_023113.1 151044 View on NCBI ↗
Helianthus tuberosus NC_023112.1 151047 View on NCBI ↗
Helianthus verticillatus NC_058797.1 151190 View on NCBI ↗
Helianthus winteri PQ638943.1 151110 View on NCBI ↗