Markers + reference

Carduus

4 species · Asteraceae · Asterales

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Species 4
Genome length 152–152 kb
Candidate markers 272
Primer pairs 95

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

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI LSC 404 0.0025 1.00 41.2 yes View details
trnS-GCU-trnC-GCA LSC 621 0.0032 1.00 57.7 yes View details
petN-psbM LSC 495 0.0040 1.00 46.7 yes View details
trnR-UCU-trnG-UCC LSC 215 0.0116 1.00 60.6 yes View details
ycf3-trnS-GGA LSC 910 0.0033 1.00 51.8 yes View details
ycf1 IRb 573 0.0000 1.00 33.3 no View details
ndhF-rpl32 SSC 1050 0.0019 1.00 52.1 yes View details
rpl32-trnL-UAG SSC 851 0.0031 1.00 56.7 yes View details
ccsA SSC 969 0.0033 1.00 52.0 yes View details
ycf1 SSC 5268 0.0031 1.00 54.7 yes View details
ndhC-trnV-UAC LSC 1167 0.0030 0.98 62.9 yes View details
psbE-petL LSC 1284 0.0012 1.00 62.8 yes View details
atpI-atpH LSC 1136 0.0009 1.00 61.3 yes View details
petA-psbJ LSC 790 0.0025 1.00 60.5 yes View details
ndhF SSC 2235 0.0016 1.00 58.3 yes View details
trnM-CAU-atpE LSC 213 0.0070 1.00 57.4 yes View details
petD LSC 1174 0.0013 1.00 56.6 yes View details
trnC-GCA-petN LSC 517 0.0010 1.00 56.1 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TGACTTATATGCCAGTGTCAACA TCTGATTGTATCTACATACCCT 2758–2768 1.000 40.3
trnK-UUU_p2 trnK-UUU TGACTTATATGCCAGTGTCAACA TCTGATTGTATCTACATACCCTT 2758–2768 1.000 40.3
trnK-UUU_p3 trnK-UUU TGACTTATATGCCAGTGTCAACA TTCTGATTGTATCTACATACCCT 2759–2769 1.000 40.3
trnK-UUU_p4 trnK-UUU TGCCAGTGTCAACAAATATCT TCTGATTGTATCTACATACCCT 2749–2759 1.000 40.3
trnK-UUU_p5 trnK-UUU TGACTTATATGCCAGTGTCAACA TCTGATTGTATCTACATACCCTTT 2758–2768 1.000 40.3
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCTTCACGTCCAGGATTACG 541 1.000 72.4
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT TCTTCACGTCCAGGATTACG 538 1.000 70.4
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT TCTTCACGTCCAGGATTACG 539 1.000 70.4
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT TCTTCACGTCCAGGATTACG 540 1.000 70.4
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCTTCACGTCCAGGATTACG 542 1.000 70.0
trnS-GCU-trnC-GCA_p1 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA TCAGAGATTCTCGCGAGTCT 823–827 1.000 79.0
trnS-GCU-trnC-GCA_p2 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA CCGGATTTGAACTGGGGAAA 772–776 1.000 78.6
trnS-GCU-trnC-GCA_p3 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA CACTCAGAGATTCTCGCGAG 826–830 1.000 78.4
trnS-GCU-trnC-GCA_p4 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA ACTCAGAGATTCTCGCGAGT 825–829 1.000 77.2
trnS-GCU-trnC-GCA_p5 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA AACACTCAGAGATTCTCGCG 828–832 1.000 77.1
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 581–583 1.000 78.5
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 599–601 1.000 76.3
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 580–582 1.000 72.6
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ATTAAAGCAGCCCAAGCGAG 589–591 1.000 72.5
trnC-GCA-petN_p5 trnC-GCA-petN ATTGTGTATCGTTTTGGCGG AGCCCAAGCGAGACTTACTA 638–640 1.000 71.9
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTCTTCATTT 657–661 1.000 55.1
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTCTTCATTTT 657–661 1.000 53.7
petN-psbM_p3 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTCTTCATTT 658–662 1.000 49.2
petN-psbM_p4 petN-psbM CTCGCTTGGGCTGCTTTAAT TGCTACTGCACTCTTCATTT 649–653 1.000 49.1
petN-psbM_p5 petN-psbM TGGGCTGCTTTAATGGTAGTC TGCTACTGCACTCTTCATTT 643–647 1.000 48.3
atpI-atpH_p1 atpI-atpH TCCCTGTCATGTTCCTTGGA ATAACGGAAGCGGCAGAAAT 1256–1275 1.000 78.9
atpI-atpH_p2 atpI-atpH TCCCTGTCATGTTCCTTGGA TACCTTGACCAACTCCAGGT 1312–1331 1.000 78.3
atpI-atpH_p3 atpI-atpH TCCCTGTCATGTTCCTTGGA AGCCAATCCAGCAGCAATAA 1272–1291 1.000 78.0
atpI-atpH_p4 atpI-atpH TCCCTGTCATGTTCCTTGGA AATAACGGAAGCGGCAGAAA 1257–1276 1.000 77.8
atpI-atpH_p5 atpI-atpH TCCCTGTCATGTTCCTTGGA GCAGTACCTTGACCAACTCC 1316–1335 1.000 77.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Carduus defloratus subsp. defloratus OR896903.1 152358 View on NCBI ↗
Carduus nutans OR896904.1 152383 View on NCBI ↗
Carduus personata OR896905.1 152477 View on NCBI ↗
Carduus pycnocephalus subsp. pycnocephalus OR896906.1 152450 View on NCBI ↗