Markers + reference

Jacobaea

2 species · Asteraceae · Asterales

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Species 2
Genome length 151–154 kb
Candidate markers 271
Primer pairs 75

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 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 IRb 576 0.0000 1.00 26.7 no View details
rpl32-trnL SSC 788 0.4819 0.98 80.6 yes View details
ndhE SSC 306 0.5142 0.92 76.7 yes View details
ndhG SSC 531 0.5073 0.90 80.8 yes View details
ndhA SSC 2228 0.4650 0.92 81.1 yes View details
ndhH SSC 1179 0.4911 0.81 79.7 yes View details
rps15 SSC 279 0.5019 0.94 77.1 yes View details
ycf1 SSC 5073 0.3857 0.89 75.8 yes View details
ccsA SSC 969 0.4464 0.92 83.0 yes View details
ndhD SSC 1521 0.4571 0.93 82.9 yes View details
ndhI SSC 501 0.4741 0.96 80.2 yes View details
ndhF-rpl32 SSC 1079 0.1112 0.99 79.7 yes View details
ndhD-psaC SSC 96 0.4773 0.92 77.1 yes View details
rps15-ycf1 SSC 207 0.4870 0.93 77.0 yes View details
ccsA-ndhD SSC 268 0.4280 0.93 76.9 yes View details
psaC SSC 246 0.4286 0.91 76.9 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ndhF-rpl32_p1 ndhF-rpl32 CGCCCACACGATTAGTTACA TCTGCCCTTACCGAGAAAGA 2067 0.500 59.5
ndhF-rpl32_p2 ndhF-rpl32 CGCCCACACGATTAGTTACA AAAAAGACTCCCCACCACAC 2010 0.500 59.5
ndhF-rpl32_p3 ndhF-rpl32 GTTGCCGTCGGAAAAAGAAG TCTGCCCTTACCGAGAAAGA 1609 0.500 59.2
ndhF-rpl32_p4 ndhF-rpl32 GTTGCCGTCGGAAAAAGAAG AAAAAGACTCCCCACCACAC 1552 0.500 59.2
ndhF-rpl32_p5 ndhF-rpl32 TGCCGTCGGAAAAAGAAGAA TCTGCCCTTACCGAGAAAGA 1607 0.500 59.1
rpl32-trnL_p1 rpl32-trnL TGGCAGCGTTAAAAGCTTTG AGCGTGTCTACCGATTTCAC 906 0.500 58.9
rpl32-trnL_p2 rpl32-trnL TGGCAGCGTTAAAAGCTTTG CAGCGTGTCTACCGATTTCA 907 0.500 58.9
rpl32-trnL_p3 rpl32-trnL GGCAGCGTTAAAAGCTTTGT AGCGTGTCTACCGATTTCAC 905 0.500 58.9
rpl32-trnL_p4 rpl32-trnL GGCAGCGTTAAAAGCTTTGT CAGCGTGTCTACCGATTTCA 906 0.500 58.9
rpl32-trnL_p5 rpl32-trnL TGGCAGCGTTAAAAGCTTTG GAAGTAGCAAAGCCTTGGGT 1413 0.500 58.2
ccsA_p1 ccsA GTGAAATCGGTAGACACGCT GTTTTTGATTCTGGACCGCG 1564 0.500 59.6
ccsA_p2 ccsA TGAAATCGGTAGACACGCTG GTTTTTGATTCTGGACCGCG 1563 0.500 59.6
ccsA_p3 ccsA GTGAAATCGGTAGACACGCT AGTGATTCACGTGGTTCTCG 1247 0.500 59.4
ccsA_p4 ccsA TGAAATCGGTAGACACGCTG AGTGATTCACGTGGTTCTCG 1246 0.500 59.4
ccsA_p5 ccsA TCTTTCTCGGTAAGGGCAGA GTTTTTGATTCTGGACCGCG 2114 0.500 59.2
ccsA-ndhD_p1 ccsA-ndhD ACCCAAGGCTTTGCTACTTC CTCCCGGCCAACGTAATTTA 1533 0.500 59.1
ccsA-ndhD_p2 ccsA-ndhD CCCAAGGCTTTGCTACTTCA CTCCCGGCCAACGTAATTTA 1532 0.500 59.1
ccsA-ndhD_p3 ccsA-ndhD ACCCAAGGCTTTGCTACTTC GTTTTTGATTCTGGACCGCG 1057 0.500 59.0
ccsA-ndhD_p4 ccsA-ndhD CCCAAGGCTTTGCTACTTCA GTTTTTGATTCTGGACCGCG 1056 0.500 59.0
ccsA-ndhD_p5 ccsA-ndhD ACCCAAGGCTTTGCTACTTC CATGGCTTTATTGGTGCTGC 1405 0.500 58.7
ndhD_p1 ndhD CGAGAACCACGTGAATCACT TCTGCTCCAAGAACAGAGGA 1936 0.500 59.3
ndhD_p2 ndhD CGAGAACCACGTGAATCACT ACCTTATTTTGGGGCACAGG 1748 0.500 59.0
ndhD_p3 ndhD CGAGAACCACGTGAATCACT CCTTATTTTGGGGCACAGGT 1747 0.500 59.0
ndhD_p4 ndhD TCGTGTGATTAGCCTAGGGT TCTGCTCCAAGAACAGAGGA 2309 0.500 58.6
ndhD_p5 ndhD CGAGAACCACGTGAATCACT CAGAAACCCCTACTTGAGCC 1803 0.500 58.5
ndhD-psaC_p1 ndhD-psaC CTCCCGCCGTGTACAAAATA TCTGCTCCAAGAACAGAGGA 760 0.500 59.8
ndhD-psaC_p2 ndhD-psaC TTCCAAAGCCACAGGATACG TCTGCTCCAAGAACAGAGGA 870 0.500 59.0
ndhD-psaC_p3 ndhD-psaC TCCTCCCCACATGCATAGAA TCTGCTCCAAGAACAGAGGA 711 0.500 59.0
ndhD-psaC_p4 ndhD-psaC TTCCTCCCCACATGCATAGA TCTGCTCCAAGAACAGAGGA 712 0.500 59.0
ndhD-psaC_p5 ndhD-psaC ACCATATAACCCGACACCCA TCTGCTCCAAGAACAGAGGA 807 0.500 58.9

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
Jacobaea abrotanifolia OR990544.1 150969 View on NCBI ↗
Jacobaea maritima NC_061967.1 153857 View on NCBI ↗