Markers + reference

Dunalia

2 species · Solanaceae · Solanales

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Species 2
Genome length 157–157 kb
Candidate markers 281
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 9 remaining regions by MarkerSeek score (out of 281 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 696 0.0029 1.00 60.3 yes View details
rps16 LSC 1123 0.0027 1.00 60.3 yes View details
rps16-trnQ-UUG LSC 1253 0.0024 0.99 60.7 yes View details
psbM-trnD-GUC LSC 1071 0.0037 1.00 60.9 yes View details
trnE-UUC-trnT-GGU LSC 872 0.0034 1.00 61.0 yes View details
trnL-UAA-trnF-GAA LSC 590 0.0034 1.00 54.1 yes View details
accD-psaI LSC 741 0.0027 1.00 52.7 yes View details
psbE-petL LSC 1157 0.0052 1.00 61.7 yes View details
ycf1 IRb 1122 0.0010 0.93 48.8 yes View details
ndhF-rpl32 SSC 778 0.0039 1.00 61.0 yes View details
ndhA SSC 2261 0.0022 1.00 49.4 yes View details
rps15-ycf1 SSC 396 0.0051 1.00 55.8 yes View details
ycf1 SSC 5670 0.0018 1.00 47.2 no View details
ycf1-ndhF SSC 11 0.2727 1.00 75.6 yes View details
rpl23-trnH-GUG IRa 1717 0.0000 0.94 62.9 no View details
rpl32-trnL-UAG SSC 825 0.0036 1.00 61.1 yes View details
orf188 SSC 564 0.0053 1.00 61.1 yes View details
trnT-UGU-trnL-UAA LSC 714 0.0014 0.99 60.6 yes View details
petN-psbM LSC 1102 0.0027 1.00 60.3 yes View details
atpH-atpI LSC 1223 0.0008 0.99 59.8 yes View details
petA-psbJ LSC 710 0.0014 1.00 59.8 yes View details
trnS-GCU-trnG-GCC LSC 615 0.0016 1.00 59.7 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 CTCGTGTCAACCAAGGTGTA TGGTTTTTGGTTGTCTTGTCT 2771 1.000 52.9
trnK-UUU_p2 trnK-UUU TACTCGTGTCAACCAAGGTG TGGTTTTTGGTTGTCTTGTCT 2773 1.000 52.9
trnK-UUU_p3 trnK-UUU CTCGTGTCAACCAAGGTGTA ATGGTTTTTGGTTGTCTTGTCT 2772 1.000 49.1
trnK-UUU_p4 trnK-UUU TACTCGTGTCAACCAAGGTG ATGGTTTTTGGTTGTCTTGTCT 2774 1.000 49.1
trnK-UUU_p5 trnK-UUU CTCGTGTCAACCAAGGTGTAT TGGTTTTTGGTTGTCTTGTCT 2771 1.000 48.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTGAAAAAGGGGCTCAACCT 828 1.000 75.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTGAAAAAGGGGCTCAACCT 827 1.000 75.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TTGAAAAAGGGGCTCAACCT 913 1.000 74.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 CAGTCGTGGTCTTCCAAACT TTGAAAAAGGGGCTCAACCT 912 1.000 74.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAAAGACACTAGCCGCACTT TTGAAAAAGGGGCTCAACCT 849 1.000 74.4
rps16_p1 rps16 ACAAATCACTACCCCCTTTT CATCAGCCCAACCAATGACT 1238 1.000 50.1
rps16_p2 rps16 ACAAATCACTACCCCCTTTTT CATCAGCCCAACCAATGACT 1238 1.000 49.1
rps16_p3 rps16 ACAAATCACTACCCCCTTTT ACATCAGCCCAACCAATGAC 1239 1.000 47.8
rps16_p4 rps16 AGAAAAGGAAAGGGAGGAAA CATCAGCCCAACCAATGACT 1297 1.000 47.0
rps16_p5 rps16 ACAAATCACTACCCCCTTTTT ACATCAGCCCAACCAATGAC 1239 1.000 46.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1343–1367 1.000 79.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1326–1350 1.000 78.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1344–1368 1.000 78.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1341–1365 1.000 77.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1340–1364 1.000 77.0
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 689 1.000 51.5
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 738 1.000 50.6
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 692 1.000 50.5
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 691 1.000 50.5
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 690 1.000 49.6
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TACCTGTCATGCTCCTTGGA 1352–1359 1.000 79.8
atpH-atpI_p2 atpH-atpI TACCCTCTACAGCTTGACCC TACCTGTCATGCTCCTTGGA 1435–1442 1.000 79.0
atpH-atpI_p3 atpH-atpI GCGATACCCTCTACAGCTTG TACCTGTCATGCTCCTTGGA 1439–1446 1.000 78.9
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA TACCTGTCATGCTCCTTGGA 1353–1360 1.000 78.6
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC TACCTGTCATGCTCCTTGGA 1367–1374 1.000 78.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Dunalia brachyacantha NC_026906.1 156730 View on NCBI ↗
Dunalia obovata NC_026563.1 156559 View on NCBI ↗