Markers + reference

Cirsium

18 species · Asteraceae · Asterales

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Species 18
Genome length 152–153 kb
Candidate markers 271
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

11 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 573 0.0043 1.00 31.1 no View details
ndhF SSC 2235 0.2138 0.93 79.4 yes View details
rpl32-trnL-UAG SSC 859 0.2076 0.85 72.4 yes View details
ccsA SSC 969 0.2011 0.79 67.8 yes View details
ndhD SSC 1521 0.2274 0.90 73.0 yes View details
psaC SSC 246 0.2283 0.87 58.4 yes View details
ndhA SSC 2150 0.2100 0.83 71.4 yes View details
ndhH SSC 1182 0.2193 0.86 67.6 yes View details
rps15 SSC 279 0.2514 0.91 62.8 yes View details
rps15-ycf1 SSC 433 0.2100 0.86 67.2 yes View details
ycf1 SSC 5292 0.1457 0.74 68.3 yes View details
ndhF-rpl32 SSC 1048 0.1853 0.83 73.6 yes View details
ndhG SSC 531 0.2054 0.88 65.2 yes View details
petA-psbJ LSC 792 0.0036 1.00 62.9 yes View details
trnC-GCA-petN LSC 530 0.0074 1.00 62.5 yes View details
trnT-UGU-trnL-UAA LSC 538 0.0061 1.00 61.9 yes View details
ndhC-trnV-UAC LSC 1147 0.0035 1.00 61.5 yes View details
psaC-ndhE SSC 236 0.2290 0.97 61.3 yes View details
trnL-UAG-ccsA SSC 142 0.2303 0.93 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 583–598 1.000 83.0
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 601–616 1.000 80.7
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 582–597 1.000 77.1
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ATTAAAGCAGCCCAAGCGAG 591–606 1.000 76.9
trnC-GCA-petN_p5 trnC-GCA-petN ATTGTGTATCGTTTTGGCGG AGCCCAAGCGAGACTTACTA 640–655 1.000 76.2
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 571–597 1.000 85.2
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 579–605 1.000 84.7
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 603–629 1.000 84.1
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 611–637 1.000 83.5
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG AGTCCGTAGCGTCTACCAAT 585–611 1.000 83.3
ndhC-trnV-UAC_p1 ndhC-trnV-UAC CCCTTTGCTAATCGGAGCTA CCGAGAAAGTCTACGGTTCG 1273–1294 1.000 75.1
ndhC-trnV-UAC_p2 ndhC-trnV-UAC CCCTTTGCTAATCGGAGCTAA CCGAGAAAGTCTACGGTTCG 1273–1294 1.000 72.8
ndhC-trnV-UAC_p3 ndhC-trnV-UAC CTCCGGCCCTTTGCTAATC CCGAGAAAGTCTACGGTTCG 1279–1300 1.000 72.0
ndhC-trnV-UAC_p4 ndhC-trnV-UAC GGCCCTTTGCTAATCGGAG CCGAGAAAGTCTACGGTTCG 1275–1296 1.000 72.0
ndhC-trnV-UAC_p5 ndhC-trnV-UAC TTCTCCGGCCCTTTGCTAAT CCGAGAAAGTCTACGGTTCG 1281–1302 1.000 71.3
petA-psbJ_p1 petA-psbJ ACGTGTACAAGGCCTTTTGT ATTCCGGATTGGGTTCATCC 904–935 1.000 81.7
petA-psbJ_p2 petA-psbJ GGCCTTTTGTTCTTCTTCGC ATTCCGGATTGGGTTCATCC 894–925 1.000 81.7
petA-psbJ_p3 petA-psbJ ACGTGTACAAGGCCTTTTGT TGTGATCGGTTTAGTAGGCG 942–973 1.000 79.9
petA-psbJ_p4 petA-psbJ GGCCTTTTGTTCTTCTTCGC TGTGATCGGTTTAGTAGGCG 932–963 1.000 79.9
petA-psbJ_p5 petA-psbJ ACGTGTACAAGGCCTTTTGT GTGATCGGTTTAGTAGGCGT 941–972 1.000 79.8
ndhF_p1 ndhF CTAGCACTGGGTAGACCTCA GAGGTAAGATCCGGTGAATCG 2606 0.500 51.2
ndhF_p2 ndhF TCGTTGTGGTCGGACTCTAT GAGGTAAGATCCGGTGAATCG 2794 0.500 51.0
ndhF_p3 ndhF ATCAATTCGGTCGTTGTGGT GAGGTAAGATCCGGTGAATCG 2804 0.500 50.9
ndhF_p4 ndhF TCTCTTCCTTCTCCGAGCTC GAGGTAAGATCCGGTGAATCG 2736 0.500 50.4
ndhF_p5 ndhF CTAGCACTGGGTAGACCTCA AGGTAAGATCCGGTGAATCG 2605 0.500 49.9
ndhF-rpl32_p1 ndhF-rpl32 GTTGCCGTCGGAAAAAGAAG CACCACCACAATGTGAGTGA 1554–1556 0.500 60.0
ndhF-rpl32_p2 ndhF-rpl32 TGCCGTCGGAAAAAGAAGAA CACCACCACAATGTGAGTGA 1552–1554 0.500 59.9
ndhF-rpl32_p3 ndhF-rpl32 TTGCCGTCGGAAAAAGAAGA CACCACCACAATGTGAGTGA 1553–1555 0.500 59.9
ndhF-rpl32_p4 ndhF-rpl32 GTTGCCGTCGGAAAAAGAAG AATAAGACTCCCCACCACCA 1566–1568 0.500 59.9
ndhF-rpl32_p5 ndhF-rpl32 TGCCGTCGGAAAAAGAAGAA AATAAGACTCCCCACCACCA 1564–1566 0.500 59.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (18)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Cirsium acaule OR909619.1 152564 View on NCBI ↗
Cirsium alsophilum OR909620.1 152479 View on NCBI ↗
Cirsium arvense NC_036965.1 152855 View on NCBI ↗
Cirsium arvense var. setosum NC_052868.1 152403 View on NCBI ↗
Cirsium erisithales OR909621.1 152555 View on NCBI ↗
Cirsium heterophyllum OR909622.1 152563 View on NCBI ↗
Cirsium japonicum NC_053767.1 152602 View on NCBI ↗
Cirsium japonicum var. spinossimum NC_050046.1 152342 View on NCBI ↗
Cirsium japonicum var. ussuriense MW659448.1 152578 View on NCBI ↗
Cirsium nipponicum MW248139.1 152586 View on NCBI ↗
Cirsium palustre OR909623.1 152643 View on NCBI ↗
Cirsium rhinoceros NC_044423.1 152576 View on NCBI ↗
Cirsium setidens NC_063550.1 152565 View on NCBI ↗
Cirsium shansiense MN871982.1 152396 View on NCBI ↗
Cirsium spinosissimum OR909624.1 152585 View on NCBI ↗
Cirsium vulgare NC_036967.1 152567 View on NCBI ↗
Cirsium x flavescens OR909626.1 152565 View on NCBI ↗
Cirsium x variegatum OR909633.1 152515 View on NCBI ↗