Markers + reference

Cheirolophus

2 species · Asteraceae · Asterales

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Species 2
Genome length 152–153 kb
Candidate markers 263
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 789 0.0089 1.00 64.0 yes View details
trnR-UCU-trnG-UCC LSC 261 0.0124 0.93 63.7 yes View details
psbC LSC 1422 0.0007 1.00 46.9 yes View details
ndhC-trnV-UAC LSC 1145 0.0044 1.00 58.1 yes View details
cemA LSC 690 0.0058 1.00 62.1 yes View details
psbE-petL LSC 1262 0.0040 1.00 61.2 yes View details
trnW-CCA-trnP-UGG LSC 164 0.0305 1.00 70.0 yes View details
rpoA LSC 1008 0.0020 1.00 45.0 yes View details
ycf1 SSC 5205 0.0040 1.00 54.8 yes View details
trnL-UAG-rpl32 SSC 862 0.0046 1.00 61.4 yes View details
rps7-rps12 IRb 53 0.0189 1.00 63.3 yes View details
rps12-rps7 IRa 53 0.0189 1.00 63.3 yes View details
rps16-trnQ-UUG LSC 938 0.0053 1.00 61.8 yes View details
ycf4-cemA LSC 865 0.0012 0.98 61.3 yes View details
rpl32-ndhF SSC 1056 0.0019 0.99 61.2 yes View details
psbM-trnD-GUC LSC 653 0.0015 0.99 60.5 yes View details
atpI LSC 744 0.0027 1.00 60.3 yes View details
petA-psbJ LSC 801 0.0025 1.00 60.2 yes View details
ccsA SSC 969 0.0021 1.00 59.9 yes View details
atpF LSC 1262 0.0016 1.00 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTCCTTGAAAAAGGCGCTCA 985–986 1.000 77.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGATGGTATGGACGAATCCC TTCCTTGAAAAAGGCGCTCA 984–985 1.000 77.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 924–925 1.000 76.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 923–924 1.000 76.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TTCCTTGAAAAAGGCGCTCA 1009–1010 1.000 76.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1011–1013 1.000 78.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1026–1028 1.000 76.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1025–1027 1.000 76.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCAAGAGCACCTTCATTCCT GAGGTTCGAATCCTTCCGTC 1082–1084 1.000 75.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1015–1017 1.000 73.9
psbM-trnD-GUC_p1 psbM-trnD-GUC GGAACTAAAATGAACAGTGCAGT TCTGATTCCCCTGGGATTGT 786–792 1.000 53.1
psbM-trnD-GUC_p2 psbM-trnD-GUC AAAATGAACAGTGCAGTAGC TCTGATTCCCCTGGGATTGT 780–786 1.000 52.6
psbM-trnD-GUC_p3 psbM-trnD-GUC ACTAAAATGAACAGTGCAGTAGC TCTGATTCCCCTGGGATTGT 783–789 1.000 51.7
psbM-trnD-GUC_p4 psbM-trnD-GUC GGAACTAAAATGAACAGTGCAGT TTCAATAGGCAAGAGCACCG 764–770 1.000 51.1
psbM-trnD-GUC_p5 psbM-trnD-GUC AGGAACTAAAATGAACAGTGCAG TCTGATTCCCCTGGGATTGT 787–793 1.000 51.0
atpI_p1 atpI GTCAAGTCGAGAAAGAGATGGT GCCACGCACACATTACCTTA 869 1.000 58.3
atpI_p2 atpI GTCAAGTCGAGAAAGAGATGGT TTAGCCACGCACACATTACC 872 1.000 58.3
atpI_p3 atpI AGTCAAGTCGAGAAAGAGATGG GCCACGCACACATTACCTTA 870 1.000 56.2
atpI_p4 atpI AGTCAAGTCGAGAAAGAGATGG TTAGCCACGCACACATTACC 873 1.000 56.2
atpI_p5 atpI AGTCGAGAAAGAGATGGTTGA GCCACGCACACATTACCTTA 865 1.000 55.0
atpF_p1 atpF AGAGGGCAAAGTAATACAAAAAGA ATTTCGTCGGCTTGAATGGT 1417 1.000 40.1
atpF_p2 atpF AGAGGGCAAAGTAATACAAAAAGA GTCGGCTTGAATGGTTACCA 1412 1.000 40.1
atpF_p3 atpF AGTCTATCTATACGAGGAGATCC ATTTCGTCGGCTTGAATGGT 1376 1.000 40.1
atpF_p4 atpF AGTCTATCTATACGAGGAGATCC GTCGGCTTGAATGGTTACCA 1371 1.000 40.1
atpF_p5 atpF AGAGGGCAAAGTAATACAAAAAGA TCGTCGGCTTGAATGGTTAC 1414 1.000 40.1
trnR-UCU-trnG-UCC_p1 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA AGCCTTCCAAGCTAACGATG 322–341 1.000 68.1
trnR-UCU-trnG-UCC_p2 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA CCTAGCCTTCCAAGCTAACG 325–344 1.000 67.8
trnR-UCU-trnG-UCC_p3 trnR-UCU-trnG-UCC AGGTTTAGAAGACCTCTGTCCT AGCCTTCCAAGCTAACGATG 328–347 1.000 67.4
trnR-UCU-trnG-UCC_p4 trnR-UCU-trnG-UCC AGGTTTAGAAGACCTCTGTCCT CCTAGCCTTCCAAGCTAACG 331–350 1.000 67.2
trnR-UCU-trnG-UCC_p5 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA CCCTAGCCTTCCAAGCTAAC 326–345 1.000 65.6

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
Cheirolophus crassifolius BK071836.1 152478 View on NCBI ↗
Cheirolophus intybaceus BK071837.1 152689 View on NCBI ↗