Markers + reference

Cousinia

8 species · Asteraceae · Asterales

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Species 8
Genome length 153–153 kb
Candidate markers 269
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnL-UAA-trnT-UGU LSC 525 0.0075 1.00 49.0 yes View details
trnS-GGA-pafI LSC 915 0.0080 1.00 61.9 yes View details
psbZ-trnS-UGA LSC 337 0.0013 1.00 35.5 yes View details
rpoB-trnE-UUC LSC 805 0.0083 1.00 50.9 yes View details
trnC-GCA-trnS-GCU LSC 813 0.0029 0.95 52.1 yes View details
ndhF SSC 2235 0.0019 1.00 45.7 yes View details
rpl32-trnL-UAG SSC 862 0.0079 1.00 64.5 yes View details
rps15-ycf1 SSC 414 0.0069 1.00 37.1 yes View details
ycf1 SSC 5190 0.0049 1.00 43.1 yes View details
psbJ-petA LSC 821 0.0039 0.98 62.5 yes View details
cemA-pafII LSC 842 0.0043 1.00 61.1 yes View details
petN-trnC-GCA LSC 537 0.0057 0.97 55.0 yes View details
psbM-petN LSC 479 0.0028 0.99 53.9 yes View details
trnT-GGU-trnG-UCC LSC 160 0.0100 1.00 51.9 yes View details
petL-psbE LSC 1282 0.0009 1.00 50.6 yes View details
petD LSC 1183 0.0015 1.00 50.3 yes View details
rpoC1 LSC 2803 0.0009 1.00 49.7 yes View details
trnV-UAC-ndhC LSC 1168 0.0043 1.00 49.2 yes View details
trnG-UCC-trnR-UCU LSC 254 0.0060 1.00 47.9 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
petD_p1 petD TGAAGCGACTGTTCCCTAGA ATTTCCCTTGAACTCCGCAA 1315–1317 1.000 77.5
petD_p2 petD TGAAGCGACTGTTCCCTAGA TTTCCCTTGAACTCCGCAAT 1314–1316 1.000 77.5
petD_p3 petD CTTTGAAGCGACTGTTCCCT ATTTCCCTTGAACTCCGCAA 1318–1320 1.000 77.2
petD_p4 petD CTTTGAAGCGACTGTTCCCT TTTCCCTTGAACTCCGCAAT 1317–1319 1.000 77.2
petD_p5 petD ACTTTGAAGCGACTGTTCCC TTTCCCTTGAACTCCGCAAT 1318–1320 1.000 74.9
petL-psbE_p1 petL-psbE GTCGTATCTTGCTCAGACCA CAACCCGCAATGAATAGGGA 1474–1479 1.000 72.5
petL-psbE_p2 petL-psbE GTCGTATCTTGCTCAGACCA AGAACGTTCTCCTGTGCTTC 1397–1402 1.000 71.7
petL-psbE_p3 petL-psbE GTCGTATCTTGCTCAGACCA ACGAATAACCAACCCGCAAT 1483–1488 1.000 71.5
petL-psbE_p4 petL-psbE GTCGTATCTTGCTCAGACCA TGCTGACGAATAACCAACCC 1488–1493 1.000 71.4
petL-psbE_p5 petL-psbE GTCGTATCTTGCTCAGACCA CGAATAACCAACCCGCAATG 1482–1487 1.000 71.4
psbJ-petA_p1 psbJ-petA ATTCCGGATTGGGTTCATCC ACGTGTACAAGGCCTTTTGT 927–964 1.000 81.4
psbJ-petA_p2 psbJ-petA ATTCCGGATTGGGTTCATCC GGCCTTTTGTTCTTCTTCGC 917–954 1.000 81.4
psbJ-petA_p3 psbJ-petA TGTGATCGGTTTAGTAGGCG ACGTGTACAAGGCCTTTTGT 965–1002 1.000 79.7
psbJ-petA_p4 psbJ-petA GTGATCGGTTTAGTAGGCGT ACGTGTACAAGGCCTTTTGT 964–1001 1.000 79.7
psbJ-petA_p5 psbJ-petA TGTGATCGGTTTAGTAGGCG GGCCTTTTGTTCTTCTTCGC 955–992 1.000 79.7
cemA-pafII_p1 cemA-pafII GAGAAATCCACCAGGGCAAA GAGCCATTCCATTGACTCGT 989–1029 1.000 82.6
cemA-pafII_p2 cemA-pafII GAGAAATCCACCAGGGCAAA TTGGCCTATTTCTTGCGTGT 921–961 1.000 82.3
cemA-pafII_p3 cemA-pafII GAGAAATCCACCAGGGCAAA CTCCACGGGAAATGGAACAA 953–993 1.000 82.2
cemA-pafII_p4 cemA-pafII GAGAAATCCACCAGGGCAAA AAAAAGCTGCTGAATTGGCC 935–975 1.000 81.7
cemA-pafII_p5 cemA-pafII GAGAAATCCACCAGGGCAAA AAAGCTGCTGAATTGGCCTA 933–973 1.000 81.3
trnV-UAC-ndhC_p1 trnV-UAC-ndhC CCGAGAAAGTCTACGGTTCG GAGCTAAAACTCCCGAAATGA 1288–1305 1.000 56.7
trnV-UAC-ndhC_p2 trnV-UAC-ndhC CCGAGAAAGTCTACGGTTCG GAGCTAAAACTCCCGAAATGAA 1288–1305 1.000 54.6
trnV-UAC-ndhC_p3 trnV-UAC-ndhC CCGAGAAAGTCTACGGTTCG AGCTAAAACTCCCGAAATGA 1287–1304 1.000 54.2
trnV-UAC-ndhC_p4 trnV-UAC-ndhC CCGAGAAAGTCTACGGTTCG AGCTAAAACTCCCGAAATGAA 1287–1304 1.000 52.9
trnV-UAC-ndhC_p5 trnV-UAC-ndhC CCGAGAAAGTCTACGGTTCG GAGCTAAAACTCCCGAAATG 1288–1305 1.000 52.1
trnL-UAA-trnT-UGU_p1 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GCGATGCTCTAACCTCTGAG 572–576 1.000 80.7
trnL-UAA-trnT-UGU_p2 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GCGATGCTCTAACCTCTGAG 580–584 1.000 80.2
trnL-UAA-trnT-UGU_p3 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GGAATCGAACCGATGACCAT 604–608 1.000 79.8
trnL-UAA-trnT-UGU_p4 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GGAATCGAACCGATGACCAT 612–616 1.000 79.2
trnL-UAA-trnT-UGU_p5 trnL-UAA-trnT-UGU AGTCCGTAGCGTCTACCAAT GCGATGCTCTAACCTCTGAG 586–590 1.000 78.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Cousinia botschantzevii PX230056.1 152702 View on NCBI ↗
Cousinia candicans PX230051.1 152536 View on NCBI ↗
Cousinia integrifolia PX230050.1 152560 View on NCBI ↗
Cousinia laetevirens PX230053.1 152634 View on NCBI ↗
Cousinia mogoltavica PX230052.1 152553 View on NCBI ↗
Cousinia speciosa PX230049.1 152614 View on NCBI ↗
Cousinia spryginii PX230047.1 152737 View on NCBI ↗
Cousinia stellaris PX230048.1 152576 View on NCBI ↗