Markers + reference

Omalotheca

2 species · Asteraceae · Asterales

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Species 2
Genome length 151–151 kb
Candidate markers 270
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 8 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 392 0.0000 1.00 35.7 yes View details
psbA LSC 1062 0.0000 1.00 40.0 yes View details
trnG-UCC-trnT-GGU LSC 376 0.0027 1.00 55.6 yes View details
atpB-rbcL LSC 742 0.0013 1.00 59.5 yes View details
psbH LSC 222 0.0000 1.00 19.8 yes View details
petD LSC 1189 0.0008 1.00 59.2 yes View details
ndhE-psaC SSC 256 0.0000 1.00 33.8 yes View details
ndhD SSC 1623 0.0018 1.00 59.6 yes View details
trnL-UAG-rpl32 SSC 740 0.0000 0.99 59.5 yes View details
rps16 LSC 1121 0.0000 1.00 58.9 yes View details
rps16-trnQ-UUG LSC 1009 0.0000 1.00 58.8 yes View details
psbH-petB LSC 124 0.0081 1.00 57.1 yes View details
matK LSC 1521 0.0000 1.00 40.0 yes View details
matK-trnK-UUU LSC 733 0.0000 1.00 40.0 yes View details
trnK-UUU-rps16 LSC 800 0.0000 1.00 40.0 yes View details
trnS-GCU-trnC-GCA LSC 765 0.0000 1.00 40.0 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 511 1.000 76.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 525 1.000 76.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 524 1.000 76.2
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 526 1.000 76.2
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 512 1.000 75.8
psbA_p1 psbA GCAATAGCTTCCCTCTTGAT TGGTTGACACGCGCATATAA 1262 1.000 57.4
psbA_p2 psbA GCAATAGCTTCCCTCTTGAT TTGGTTGACACGCGCATATA 1263 1.000 57.4
psbA_p3 psbA GCAATAGCTTCCCTCTTGAT AAATTCGTGTGCTTGGGAGT 1197 1.000 57.4
psbA_p4 psbA GCAATAGCTTCCCTCTTGAT TGCTTGGGAGTCCCTGATAA 1188 1.000 57.2
psbA_p5 psbA GCAATAGCTTCCCTCTTGAT AATTCGTGTGCTTGGGAGTC 1196 1.000 53.7
matK_p1 matK ACATCAACATTTCAGAATAGAAA ACCCCCAAAATCCTCTACCT 1681 1.000 40.0
matK_p2 matK ACATCAACATTTCAGAATAGAAAT ACCCCCAAAATCCTCTACCT 1681 1.000 40.0
matK_p3 matK ACATCAACATTTCAGAATAGAAA AACCCCCAAAATCCTCTACC 1682 1.000 40.0
matK_p4 matK TACATCAACATTTCAGAATAGAAA ACCCCCAAAATCCTCTACCT 1682 1.000 40.0
matK_p5 matK ACATCAACATTTCAGAATAGAAA ACCCCCAAAATCCTCTACCTT 1681 1.000 40.0
matK-trnK-UUU_p1 matK-trnK-UUU TGTTGTTGAGATCTATCTAGCCC AACGGTAGAGTACTCGGCTT 804 1.000 50.4
matK-trnK-UUU_p2 matK-trnK-UUU TGTTGTTGAGATCTATCTAGCCC ACGGTAGAGTACTCGGCTTT 803 1.000 50.4
matK-trnK-UUU_p3 matK-trnK-UUU TCTAGCCCTAAATAGCTTTGGA AACGGTAGAGTACTCGGCTT 789 1.000 49.3
matK-trnK-UUU_p4 matK-trnK-UUU TCTAGCCCTAAATAGCTTTGGA ACGGTAGAGTACTCGGCTTT 788 1.000 49.3
matK-trnK-UUU_p5 matK-trnK-UUU AGCCCTAAATAGCTTTGGAA ACGGTAGAGTACTCGGCTTT 785 1.000 48.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTCCTTGAAAAAGGCGCTCA 997 1.000 76.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGATGGTATGGACGAATCCC TTCCTTGAAAAAGGCGCTCA 996 1.000 76.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 936 1.000 76.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 935 1.000 76.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TTCCTTGAAAAAGGCGCTCA 1021 1.000 75.6
rps16_p1 rps16 ACGAATAGAGCAAGAAAAGAAGG ACTGGTTCCAAATTCGAGGA 1248–1250 1.000 40.1
rps16_p2 rps16 ACGAATAGAGCAAGAAAAGAAGGA ACTGGTTCCAAATTCGAGGA 1248–1250 1.000 40.1
rps16_p3 rps16 CGAATAGAGCAAGAAAAGAAGGA ACTGGTTCCAAATTCGAGGA 1247–1249 1.000 40.1
rps16_p4 rps16 ACGAATAGAGCAAGAAAAGAAGG ACTGGTTCCAAATTCGAGGAA 1248–1250 1.000 40.1
rps16_p5 rps16 ACGAATAGAGCAAGAAAAGAAGGA ACTGGTTCCAAATTCGAGGAA 1248–1250 1.000 40.1

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
Omalotheca norvegica NC_072075.1 151348 View on NCBI ↗
Omalotheca sylvatica NC_072077.1 151414 View on NCBI ↗