Markers + reference

Oenothera

13 species · Onagraceae · Myrtales

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Species 13
Genome length 163–167 kb
Candidate markers 278
Primer pairs 85

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 10 remaining regions by MarkerSeek score (out of 278 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnQUUG-accD LSC 2584 0.0720 0.83 66.4 yes View details
trnICAU-ycf2 IRb 584 0.0082 0.98 43.1 yes View details
ycf2 IRb 7083 0.0020 0.98 41.1 no View details
rrn16-trnIGAU IRb 900 0.0275 0.81 62.2 yes View details
ycf1-ndhF SSC 257 0.0274 0.86 49.7 yes View details
trnIGAU-rrn16 IRa 900 0.0287 0.81 62.9 yes View details
ycf2 IRa 7083 0.0026 0.98 35.1 yes View details
ycf2-trnICAU IRa 584 0.0082 0.98 41.7 yes View details
ndhF-rpl32 SSC 880 0.0072 0.94 53.2 yes View details
trnKUUU-rps16 LSC 758 0.0035 0.98 51.6 yes View details
petA-psbJ LSC 1033 0.0014 0.99 51.1 yes View details
ycf4-cemA LSC 872 0.0011 0.99 50.8 yes View details
psbI-psbK LSC 386 0.0024 1.00 48.8 yes View details
trnLUAA-trnTUGU LSC 1112 0.0018 0.95 48.3 yes View details
accD-psaI LSC 617 0.0054 1.00 46.8 yes View details
trnYGUA-trnDGUC LSC 486 0.0014 0.98 46.7 yes View details
atpF LSC 1318 0.0006 1.00 45.4 yes View details
psbD-trnTGGU LSC 1428 0.0011 0.97 45.0 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
trnKUUU-rps16_p1 trnKUUU-rps16 ACGCACTTAAAAGCCGAGTA CTTGAAAAAGGCGCTCAACC 892–963 1.000 76.5
trnKUUU-rps16_p2 trnKUUU-rps16 AGTCGTGGTCTTACAAACCC CTTGAAAAAGGCGCTCAACC 966–1037 1.000 75.6
trnKUUU-rps16_p3 trnKUUU-rps16 GTCGTGGTCTTACAAACCCT CTTGAAAAAGGCGCTCAACC 965–1036 1.000 75.6
trnKUUU-rps16_p4 trnKUUU-rps16 AGACGCACTTAAAAGCCGAG CTTGAAAAAGGCGCTCAACC 894–965 1.000 75.5
trnKUUU-rps16_p5 trnKUUU-rps16 ACGCACTTAAAAGCCGAGTA AAGCGGGGGTTTTTACAGAA 843–914 1.000 75.5
trnLUAA-trnTUGU_p1 trnLUAA-trnTUGU ACCAATTTCGCCATATCCCC GCGATGCTCTAACCTCTGAG 1110–1162 1.000 83.0
trnLUAA-trnTUGU_p2 trnLUAA-trnTUGU TAGCGTCTACCAATTTCGCC GCGATGCTCTAACCTCTGAG 1118–1170 1.000 82.4
trnLUAA-trnTUGU_p3 trnLUAA-trnTUGU ACCAATTTCGCCATATCCCC GGAATCGAACCGATGACCAT 1142–1194 1.000 82.0
trnLUAA-trnTUGU_p4 trnLUAA-trnTUGU TAGCGTCTACCAATTTCGCC GGAATCGAACCGATGACCAT 1150–1202 1.000 81.5
trnLUAA-trnTUGU_p5 trnLUAA-trnTUGU AGTCCGTAGCGTCTACCAAT GCGATGCTCTAACCTCTGAG 1124–1176 1.000 81.1
psbD-trnTGGU_p1 psbD-trnTGGU GACCGGACCAACCTACAAAA GTGGTAGAGTAACGCCATGG 1558–1592 1.000 79.9
psbD-trnTGGU_p2 psbD-trnTGGU GACCGGACCAACCTACAAAA TCAGTGGTAGAGTAACGCCA 1561–1595 1.000 79.7
psbD-trnTGGU_p3 psbD-trnTGGU TAGACCGGACCAACCTACAA GTGGTAGAGTAACGCCATGG 1560–1594 1.000 79.5
psbD-trnTGGU_p4 psbD-trnTGGU TAGACCGGACCAACCTACAA TCAGTGGTAGAGTAACGCCA 1563–1597 1.000 79.3
psbD-trnTGGU_p5 psbD-trnTGGU GAGCAATAGACCGGACCAAC GTGGTAGAGTAACGCCATGG 1566–1600 1.000 79.2
trnYGUA-trnDGUC_p1 trnYGUA-trnDGUC TGGCAATATGTCTACGCTGG CGGTGCTCTGACCAATTGAA 547–573 1.000 76.2
trnYGUA-trnDGUC_p2 trnYGUA-trnDGUC GGCAATATGTCTACGCTGGT CGGTGCTCTGACCAATTGAA 546–572 1.000 76.1
trnYGUA-trnDGUC_p3 trnYGUA-trnDGUC GGGGACGGACTGTAAATTCG CGGTGCTCTGACCAATTGAA 568–594 1.000 75.2
trnYGUA-trnDGUC_p4 trnYGUA-trnDGUC GGGACGGACTGTAAATTCGT CGGTGCTCTGACCAATTGAA 567–593 1.000 75.0
trnYGUA-trnDGUC_p5 trnYGUA-trnDGUC GATTCTTCCTGGGTCGATGC CGGTGCTCTGACCAATTGAA 601–627 1.000 74.6
atpF_p1 atpF TCAAAAAGAAATAGGAATAGCAA TTCGTCGGCTCTAATGGTTG 1488–1501 1.000 40.9
atpF_p2 atpF TTCAAAAAGAAATAGGAATAGCA TTCGTCGGCTCTAATGGTTG 1489–1502 1.000 40.9
atpF_p3 atpF TCAAAAAGAAATAGGAATAGCAA GGCTCTAATGGTTGCCATGA 1482–1495 1.000 40.9
atpF_p4 atpF TTCAAAAAGAAATAGGAATAGCA GGCTCTAATGGTTGCCATGA 1483–1496 1.000 40.9
atpF_p5 atpF AGAAAAAGTGTTTAAGTGATACA TTCGTCGGCTCTAATGGTTG 1460–1473 1.000 40.9
psbI-psbK_p1 psbI-psbK GGATTACGTCCTGGATCGTT GTTTGGCAAGCTGCTGTAAG 491–512 1.000 76.9
psbI-psbK_p2 psbI-psbK GGATTACGTCCTGGATCGTT CCAAATTACCCGAGGCCTAC 577–598 1.000 76.8
psbI-psbK_p3 psbI-psbK GGATTACGTCCTGGATCGTT TTAGCCAAATTACCCGAGGC 581–602 1.000 76.7
psbI-psbK_p4 psbI-psbK TCTTCACGTCCAGGATTACG CCAAATTACCCGAGGCCTAC 589–610 1.000 76.4
psbI-psbK_p5 psbI-psbK TCTTCACGTCCAGGATTACG TTAGCCAAATTACCCGAGGC 593–614 1.000 76.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (13)

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

Species Accession Length (bp) Link
Oenothera argillicola NC_010358.2 165061 View on NCBI ↗
Oenothera biennis NC_010361.1 164807 View on NCBI ↗
Oenothera biennis x Oenothera glazioviana NC_061367.1 164723 View on NCBI ↗
Oenothera biennis x Oenothera villosa NC_061368.1 164796 View on NCBI ↗
Oenothera elata subsp. elata NC_061364.1 165373 View on NCBI ↗
Oenothera elata subsp. hookeri MN812471.1 165749 View on NCBI ↗
Oenothera glazioviana NC_010360.2 165359 View on NCBI ↗
Oenothera grandiflora NC_029211.1 166545 View on NCBI ↗
Oenothera oakesiana NC_029212.1 163575 View on NCBI ↗
Oenothera parviflora NC_010362.1 163365 View on NCBI ↗
Oenothera villosa subsp. strigosa NC_061365.1 165451 View on NCBI ↗
Oenothera villosa subsp. villosa NC_061366.1 165666 View on NCBI ↗
Oenothera wolfii NC_061369.1 165589 View on NCBI ↗