Markers + reference

Stellera

2 species · Thymelaeaceae · Malvales

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Species 2
Genome length 173–173 kb
Candidate markers 289
Primer pairs 115

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 289 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 688 0.0073 1.00 62.9 yes View details
rps16 LSC 1174 0.0026 1.00 52.4 yes View details
rps16-trnQ-UUG LSC 1327 0.0023 0.97 63.3 yes View details
trnE-UUC-trnT-GGU LSC 659 0.0061 1.00 62.2 yes View details
psbZ-trnG-GCC LSC 637 0.0031 1.00 60.6 yes View details
accD LSC 1575 0.0019 1.00 59.7 yes View details
psaI-ycf4 LSC 414 0.0072 1.00 59.0 yes View details
psbE-petL LSC 1431 0.0028 1.00 60.4 yes View details
rpl20-rps12 LSC 775 0.0039 1.00 61.0 yes View details
petB LSC 1459 0.0014 1.00 49.9 yes View details
rpoA LSC 987 0.0051 1.00 61.6 yes View details
trnL-UAG-ndhF IRb 1857 0.0032 1.00 50.2 yes View details
ndhF-rpl32 SSC 449 0.0204 0.98 69.0 yes View details
ndhK-ndhC LSC 69 0.0290 1.00 69.2 yes View details
trnS-GCU-trnG-UCC LSC 733 0.0027 1.00 60.7 yes View details
ycf3-trnS-GGA LSC 764 0.0026 1.00 60.3 yes View details
rps2-rpoC2 LSC 357 0.0029 0.95 60.0 yes View details
rpoB-trnC-GCA LSC 1098 0.0018 1.00 59.9 yes View details
matK LSC 1524 0.0020 1.00 59.8 yes View details
atpH-atpI LSC 1217 0.0016 1.00 59.7 yes View details
trnT-GGU-psbD LSC 1250 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 115 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK_p1 matK ACATTCTTACTGCATGAACA AGATCCCCCACCCTTACTTT 1675–1676 1.000 40.1
matK_p2 matK ACATTCTTACTGCATGAACA CCCCACCCTTACTTTGGTTT 1670–1671 1.000 40.1
matK_p3 matK ACATTCTTACTGCATGAACA GATCCCCCACCCTTACTTTG 1674–1675 1.000 40.1
matK_p4 matK ACATTCTTACTGCATGAACA CGATTAGATCCCCCACCCTT 1680–1681 1.000 40.1
matK_p5 matK ACATTCTTACTGCATGAACAT AGATCCCCCACCCTTACTTT 1675–1676 1.000 40.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC ATTTTCTTGAAAGGGGCGCT 875–876 1.000 76.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTTAAAGAAGGCGGGGGTTT 829–830 1.000 76.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTTTAAAGAAGGCGGGGGTT 830–831 1.000 76.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT ATTTTCTTGAAAGGGGCGCT 814–815 1.000 76.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ATTTTCTTGAAAGGGGCGCT 813–814 1.000 76.2
rps16_p1 rps16 CACACCCACACCCTCTTTTT ACGTACTGACTGAACCGATG 1337–1338 1.000 73.4
rps16_p2 rps16 CACACCCACACCCTCTTTTT CGTACTGACTGAACCGATGA 1336–1337 1.000 71.1
rps16_p3 rps16 ATGAGTCATCCACACCCACA ACGTACTGACTGAACCGATG 1347–1348 1.000 70.1
rps16_p4 rps16 CACACCCACACCCTCTTTTT ACTACGTACTGACTGAACCGA 1340–1341 1.000 68.6
rps16_p5 rps16 CACACCCACACCCTCTTTTT ACTACGTACTGACTGAACCG 1340–1341 1.000 68.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATCAAAATGGGGCGTGG 1415–1458 1.000 81.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTTGGTCCCGCTATTCGAAG 1374–1417 1.000 81.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAAATCAAAATGGGGCGTGG 1426–1469 1.000 80.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC TTTGGTCCCGCTATTCGAAG 1385–1428 1.000 80.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCACATCGCTTCAAACGAAG GAAATCAAAATGGGGCGTGG 1395–1438 1.000 80.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AATCAAACCGAAAGACCCCT 845–846 1.000 72.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ATCAAACCGAAAGACCCCTT 844–845 1.000 72.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AATCAAACCGAAAGACCCCT 844–845 1.000 72.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ATCAAACCGAAAGACCCCTT 843–844 1.000 72.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CGCACAACGGATTAGCAATC ATCAAACCGAAAGACCCCTT 859–860 1.000 72.0
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TACAAGCGGGATTCAAGCTC 1328–1330 1.000 79.6
atpH-atpI_p2 atpH-atpI AGCGGCAGAAATCAATGGAT TACAAGCGGGATTCAAGCTC 1320–1322 1.000 79.4
atpH-atpI_p3 atpH-atpI AAGCAAGCCCTACAGCTAAC TACAAGCGGGATTCAAGCTC 1357–1359 1.000 79.0
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1304–1306 1.000 78.8
atpH-atpI_p5 atpH-atpI AAGCGGCAGAAATCAATGGA TACAAGCGGGATTCAAGCTC 1321–1323 1.000 78.6

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
Stellera chamaejasme NC_042714.1 173381 View on NCBI ↗
Stellera chamaejasme f. chrysantha MT790358.1 173364 View on NCBI ↗