Markers + reference

Silphium

2 species · Asteraceae · Asterales

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Species 2
Genome length 152–152 kb
Candidate markers 272
Primer pairs 70

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 6 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1-rps15 SSC 395 0.4759 0.95 79.4 yes View details
rps15 SSC 240 0.5579 0.97 75.3 yes View details
ndhH SSC 1182 0.4944 0.83 80.3 yes View details
ndhI SSC 501 0.5095 0.94 81.4 yes View details
ndhD SSC 1503 0.4915 0.86 81.2 yes View details
ndhD-ccsA SSC 258 0.5393 0.74 71.4 yes View details
ccsA SSC 969 0.4924 0.88 81.7 yes View details
ndhF SSC 2232 0.4499 0.74 76.2 yes View details
trnL-UAG-rpl32 SSC 769 0.4485 0.90 82.7 yes View details
rpl32-ndhF SSC 987 0.4438 0.83 80.2 yes View details
ndhA SSC 2168 0.4524 0.86 79.8 yes View details
ndhG SSC 531 0.4681 0.80 77.8 yes View details
rps15-ndhH SSC 129 0.5000 0.91 76.5 yes View details
psaC SSC 246 0.4664 0.91 76.2 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ycf1-rps15_p1 ycf1-rps15 AATTATGGAACCTGCCCGTC CCGCAGACCTCTCTGAGATA 1074 0.500 59.4
ycf1-rps15_p2 ycf1-rps15 AATTATGGAACCTGCCCGTC AACACCATGCATTGATGGGT 1350 0.500 59.1
ycf1-rps15_p3 ycf1-rps15 TATGGAACCTGCCCGTCTAT CCGCAGACCTCTCTGAGATA 1071 0.500 59.0
ycf1-rps15_p4 ycf1-rps15 AATTATGGAACCTGCCCGTC AATAAGCCAGCAACCGTTGA 1111 0.500 58.8
ycf1-rps15_p5 ycf1-rps15 TATGGAACCTGCCCGTCTAT AACACCATGCATTGATGGGT 1347 0.500 58.8
rps15_p1 rps15 GCAAGTAACCCAATGCACAC GTAAATCAGCAGCGACTCCA 1169 0.500 59.4
rps15_p2 rps15 GCAAGTAACCCAATGCACAC TAAATCAGCAGCGACTCCAC 1168 0.500 59.4
rps15_p3 rps15 GCAAGTAACCCAATGCACAC TGAGGTAAATCAGCAGCGAC 1173 0.500 59.4
rps15_p4 rps15 TTTCTGCTGTCCGTGATCTG GTAAATCAGCAGCGACTCCA 1207 0.500 59.2
rps15_p5 rps15 TTTCTGCTGTCCGTGATCTG TAAATCAGCAGCGACTCCAC 1206 0.500 59.2
rps15-ndhH_p1 rps15-ndhH GCAAGTAACCCAATGCACAC GTAAATCAGCAGCGACTCCA 1169 0.500 59.4
rps15-ndhH_p2 rps15-ndhH GCAAGTAACCCAATGCACAC TAAATCAGCAGCGACTCCAC 1168 0.500 59.4
rps15-ndhH_p3 rps15-ndhH GCAAGTAACCCAATGCACAC TGAGGTAAATCAGCAGCGAC 1173 0.500 59.4
rps15-ndhH_p4 rps15-ndhH TTTCTGCTGTCCGTGATCTG GTAAATCAGCAGCGACTCCA 1207 0.500 59.2
rps15-ndhH_p5 rps15-ndhH TTTCTGCTGTCCGTGATCTG TAAATCAGCAGCGACTCCAC 1206 0.500 59.2
ndhH_p1 ndhH GCAAGTAACCCAATGCACAC CGTTGTTGTATACCCGCAGA 2032 0.500 59.5
ndhH_p2 ndhH TTTCTGCTGTCCGTGATCTG CGTTGTTGTATACCCGCAGA 2070 0.500 59.3
ndhH_p3 ndhH TCAACGGTTGCTGGCTTATT CGTTGTTGTATACCCGCAGA 1549 0.500 59.2
ndhH_p4 ndhH GCAAGTAACCCAATGCACAC CCTGACATAAGAAGGCCGAC 2296 0.500 59.0
ndhH_p5 ndhH GCAAGTAACCCAATGCACAC GACATAAGAAGGCCGACAGG 2293 0.500 59.0
ndhA_p1 ndhA CGGCCACCGGGATTTATTAA TGACCAATATACCTTGCGGC 2438 0.500 59.5
ndhA_p2 ndhA TCAACAGGCCCTAGAAGGAA TGACCAATATACCTTGCGGC 2676 0.500 59.4
ndhA_p3 ndhA TTCAACAGGCCCTAGAAGGA TGACCAATATACCTTGCGGC 2677 0.500 59.4
ndhA_p4 ndhA GGCAAAAAGAGGGGGATTCA TGACCAATATACCTTGCGGC 2749 0.500 59.2
ndhA_p5 ndhA TGGCAAAAAGAGGGGGATTC TGACCAATATACCTTGCGGC 2750 0.500 59.2
ndhI_p1 ndhI AGCCGAGTGTGAACGATTAC AGACCACGGAAGTTACTCCA 1682 0.500 59.9
ndhI_p2 ndhI AGCCGAGTGTGAACGATTAC AGACTTGTACAGACCACGGA 1692 0.500 59.9
ndhI_p3 ndhI TTTGTGACCTTTGAGGAGCC AGACCACGGAAGTTACTCCA 1888 0.500 59.8
ndhI_p4 ndhI TTTGTGACCTTTGAGGAGCC AGACTTGTACAGACCACGGA 1898 0.500 59.8
ndhI_p5 ndhI GACCTTTGAGGAGCCGTATG AGACCACGGAAGTTACTCCA 1883 0.500 59.5

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
Silphium integrifolium NC_068130.1 152058 View on NCBI ↗
Silphium perfoliatum MN445187.1 151924 View on NCBI ↗