Markers + reference

Petasites

2 species · Asteraceae · Asterales

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Species 2
Genome length 150–151 kb
Candidate markers 272
Primer pairs 80

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 7 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 IRb 576 0.0104 1.00 49.2 no View details
ndhF SSC 2226 0.4595 0.87 80.0 yes View details
ndhF-rpl32 SSC 1061 0.4527 0.85 81.5 yes View details
ndhD SSC 1521 0.4645 0.68 75.9 yes View details
ndhG SSC 531 0.4527 0.82 78.4 yes View details
ndhG-ndhI SSC 354 0.5000 0.90 77.2 yes View details
ndhI SSC 501 0.4989 0.92 80.9 yes View details
ndhA SSC 2166 0.4667 0.85 79.7 yes View details
ndhH SSC 1185 0.4923 0.82 80.0 yes View details
ycf1 SSC 5079 0.3856 0.86 75.1 yes View details
rps8-rpl14 LSC 224 0.1986 0.65 84.0 yes View details
rpl32-trnL SSC 804 0.4336 0.81 79.8 yes View details
ccsA SSC 969 0.4593 0.75 77.9 yes View details
rps15-ycf1 SSC 206 0.4592 0.95 77.4 yes View details
trnL-ccsA SSC 116 0.4352 0.93 76.8 yes View details
rpl32 SSC 165 0.4966 0.90 76.5 yes View details
ndhH-rps15 SSC 91 0.4458 0.91 76.3 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
rps8-rpl14_p1 rps8-rpl14 ACTCGAACCACGCTTTTTCT GAACTCGAGTTTTTGGTGCG 350–387 1.000 89.7
rps8-rpl14_p2 rps8-rpl14 ACTCGAACCACGCTTTTTCT CGATTGCCCGAGAATTGAGA 332–369 1.000 89.7
rps8-rpl14_p3 rps8-rpl14 ACTCGAACCACGCTTTTTCT TTGCCCGAGAATTGAGACAG 329–366 1.000 89.5
rps8-rpl14_p4 rps8-rpl14 ACTCGAACCACGCTTTTTCT GCCCGAGAATTGAGACAGTT 327–364 1.000 89.5
rps8-rpl14_p5 rps8-rpl14 ACTCGAACCACGCTTTTTCT ACTCGAGTTTTTGGTGCGAT 348–385 1.000 89.0
ndhF_p1 ndhF CTAGCACTGGGTAGACCTCA TGTCGCTTGGTCATATCATTTG 2758 0.500 35.8
ndhF_p2 ndhF TCGTTGTGGTCGGACTCTAT TGTCGCTTGGTCATATCATTTG 2946 0.500 35.6
ndhF_p3 ndhF ATCAATTCGGTCGTTGTGGT TGTCGCTTGGTCATATCATTTG 2956 0.500 35.5
ndhF_p4 ndhF TCTCTTCCTTCTCCGAGCTC TGTCGCTTGGTCATATCATTTG 2888 0.500 35.0
ndhF_p5 ndhF CTAGCACTGGGTAGACCTCA GCCCAAATTTTTATCCTTGCTCT 2876 0.500 34.1
ndhF-rpl32_p1 ndhF-rpl32 GTTGCCGTCGGAAAAAGAAG ATATCTGCCCTTCCCGAGAA 1584 0.500 58.9
ndhF-rpl32_p2 ndhF-rpl32 TGCCGTCGGAAAAAGAAGAA ATATCTGCCCTTCCCGAGAA 1582 0.500 58.8
ndhF-rpl32_p3 ndhF-rpl32 TTGCCGTCGGAAAAAGAAGA ATATCTGCCCTTCCCGAGAA 1583 0.500 58.8
ndhF-rpl32_p4 ndhF-rpl32 TACTTTTTGTTGCCGTCGGA ATATCTGCCCTTCCCGAGAA 1592 0.500 58.8
ndhF-rpl32_p5 ndhF-rpl32 GTTGCCGTCGGAAAAAGAAG TGCCCTTCCCGAGAAAGATA 1579 0.500 58.7
rpl32_p1 rpl32 CCAATTTTCACGGATCTTTGACA ATATCTGCCCTTCCCGAGAA 586 0.500 34.2
rpl32_p2 rpl32 CCAATTTTCACGGATCTTTGACA TATCTGCCCTTCCCGAGAAA 585 0.500 34.0
rpl32_p3 rpl32 CCAATTTTCACGGATCTTTGACA TGCCCTTCCCGAGAAAGATA 581 0.500 34.0
rpl32_p4 rpl32 GGGCTAAAAAGAGTACTTGATGC ATATCTGCCCTTCCCGAGAA 1174 0.500 33.3
rpl32_p5 rpl32 GGGCTAAAAAGAGTACTTGATGC TGCCCTTCCCGAGAAAGATA 1169 0.500 33.1
rpl32-trnL_p1 rpl32-trnL GGCAGCGTTAAAAGCTTTGT AGCGTGTCTACCGATTTCAC 921 0.500 58.9
rpl32-trnL_p2 rpl32-trnL GGCAGCGTTAAAAGCTTTGT CAGCGTGTCTACCGATTTCA 922 0.500 58.9
rpl32-trnL_p3 rpl32-trnL AAAGGATATTGGGCAGCGTT AGCGTGTCTACCGATTTCAC 932 0.500 58.8
rpl32-trnL_p4 rpl32-trnL AAAGGATATTGGGCAGCGTT CAGCGTGTCTACCGATTTCA 933 0.500 58.8
rpl32-trnL_p5 rpl32-trnL GGCAGCGTTAAAAGCTTTGT GAAGTAGCAAAGCCTTGGGT 1432 0.500 58.2
trnL-ccsA_p1 trnL-ccsA GTGAAATCGGTAGACACGCT GAAGTAGCAAAGCCTTGGGT 531 0.500 59.2
trnL-ccsA_p2 trnL-ccsA GTGAAATCGGTAGACACGCT TGAAGTAGCAAAGCCTTGGG 532 0.500 59.2
trnL-ccsA_p3 trnL-ccsA TGAAATCGGTAGACACGCTG GAAGTAGCAAAGCCTTGGGT 530 0.500 59.2
trnL-ccsA_p4 trnL-ccsA TGAAATCGGTAGACACGCTG TGAAGTAGCAAAGCCTTGGG 531 0.500 59.2
trnL-ccsA_p5 trnL-ccsA GTGAAATCGGTAGACACGCT TGATCCACAAAGAAGAGCCG 649 0.500 59.1

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
Petasites albus OR990538.1 150703 View on NCBI ↗
Petasites tatewakianus LC735685.1 150411 View on NCBI ↗