Markers + reference

Leucanthemum

4 species · Asteraceae · Asterales

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Species 4
Genome length 150–152 kb
Candidate markers 273
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 IRb 594 0.0070 1.00 48.6 no View details
rpl32-trnL-UAG SSC 954 0.2657 0.88 81.5 yes View details
ndhD SSC 1503 0.2748 0.85 71.5 yes View details
ndhE SSC 306 0.3197 0.90 66.8 yes View details
ndhI SSC 501 0.3433 0.93 62.3 yes View details
ndhA SSC 2202 0.2796 0.87 79.8 yes View details
rps15 SSC 279 0.3268 1.00 63.2 yes View details
ycf1 SSC 5103 0.2182 0.85 74.8 yes View details
rpl16 LSC 1476 0.0900 0.99 84.5 yes View details
petA-psbJ LSC 700 0.1345 1.00 83.4 yes View details
clpP1 LSC 2024 0.0783 1.00 83.1 yes View details
rpl22 LSC 468 0.0823 1.00 81.6 yes View details
rbcL-accD LSC 462 0.0973 1.00 81.5 yes View details
psaJ-rpl33 LSC 417 0.1439 1.00 80.8 yes View details
psbB-psbT LSC 187 0.0998 1.00 80.6 yes View details
trnW-CCA-trnP-UGG LSC 175 0.1314 1.00 80.4 yes View details
ndhF-rpl32 SSC 1033 0.2344 0.81 79.6 yes View details
ycf4 LSC 555 0.0562 1.00 78.4 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rbcL-accD_p1 rbcL-accD CTGTACTACAGTTCGGTGGC CAATAGGACCAAGACTGCCC 873–874 0.750 70.0
rbcL-accD_p2 rbcL-accD TTGAATGCTACTGCGGGTAC CAATAGGACCAAGACTGCCC 1348–1349 0.750 69.9
rbcL-accD_p3 rbcL-accD CTAACAGGGGGATTCACTGC CAATAGGACCAAGACTGCCC 1258–1259 0.750 69.7
rbcL-accD_p4 rbcL-accD AATGCTACTGCGGGTACATG CAATAGGACCAAGACTGCCC 1345–1346 0.750 69.7
rbcL-accD_p5 rbcL-accD GCGGGTACATGTGAAGACAT CAATAGGACCAAGACTGCCC 1336 0.500 59.6
ycf4_p1 ycf4 GCAATCGCAATGGCTTCTTT GGAATTCCTGAGCCCAAGAG 1643–1644 0.750 69.9
ycf4_p2 ycf4 GCAATCGCAATGGCTTCTTT TGAGAGCGAAATCCACCAAG 1297–1298 0.750 69.6
ycf4_p3 ycf4 GCAATCGCAATGGCTTCTTT TGCTTTGACTCGAAGGGATG 1084–1085 0.750 69.6
ycf4_p4 ycf4 GCAATCGCAATGGCTTCTTT GCTTTGACTCGAAGGGATGT 1083–1084 0.750 69.6
ycf4_p5 ycf4 ATAGACCCAAATTGGCGGAC GGAATTCCTGAGCCCAAGAG 1473–1474 0.750 69.5
petA-psbJ_p1 petA-psbJ GTAGGCGGAAACAGAGGAAG TCCCTATTCATTGCGGGTTG 1818–2245 1.000 88.7
petA-psbJ_p2 petA-psbJ CTGACGGGAGCAAGAGTAAC TTAGGAGGCCTCAATGACCA 1620–1686 0.750 70.2
petA-psbJ_p3 petA-psbJ GTAGGCGGAAACAGAGGAAG TTAGGAGGCCTCAATGACCA 1654–1720 0.750 70.2
petA-psbJ_p4 petA-psbJ CTGACGGGAGCAAGAGTAAC TCCCTATTCATTGCGGGTTG 1784–1850 0.750 70.1
petA-psbJ_p5 petA-psbJ CTGACGGGAGCAAGAGTAAC TGGAGGGAAGTGGGGTAAAT 1218–1284 0.750 70.1
trnW-CCA-trnP-UGG_p1 trnW-CCA-trnP-UGG GTTTTGGAGACCCACGTTCT GGGTACAAAATGTCACGGGT 257–263 1.000 89.1
trnW-CCA-trnP-UGG_p2 trnW-CCA-trnP-UGG GTTTTGGAGACCCACGTTCT TGGGTACAAAATGTCACGGG 258–264 1.000 89.1
trnW-CCA-trnP-UGG_p3 trnW-CCA-trnP-UGG GTTTTGGAGACCCACGTTCT GTCACGGGTTCAAATCCTGT 246–252 1.000 89.1
trnW-CCA-trnP-UGG_p4 trnW-CCA-trnP-UGG GTTTTGGAGACCCACGTTCT CACGGGTTCAAATCCTGTCA 244–250 1.000 89.1
trnW-CCA-trnP-UGG_p5 trnW-CCA-trnP-UGG GTTTTGGAGACCCACGTTCT TGTCACGGGTTCAAATCCTG 247–253 1.000 89.1
psaJ-rpl33_p1 psaJ-rpl33 CGAACTGAACTAAGAGCGCT TCGTTGTTGCTTCAAGGTCA 1690 0.750 69.9
psaJ-rpl33_p2 psaJ-rpl33 GTTTTGGAGACCCACGTTCT TCGTTGTTGCTTCAAGGTCA 1712 0.750 69.7
psaJ-rpl33_p3 psaJ-rpl33 ACATATCTTTCCGTGGCACC TCGTTGTTGCTTCAAGGTCA 1093 0.750 69.7
psaJ-rpl33_p4 psaJ-rpl33 CGAACTGAACTAAGAGCGCT GTAAGATAAGGGGCAGGTGC 1365 0.500 59.7
psaJ-rpl33_p5 psaJ-rpl33 GTTTTGGAGACCCACGTTCT GTAAGATAAGGGGCAGGTGC 1387 0.500 59.6
clpP1_p1 clpP1 AAACTCGGCAGGGTGAATTT CAATGGGGAGGTTAATGCGA 2312–2328 0.750 70.2
clpP1_p2 clpP1 AACTCGGCAGGGTGAATTTT CAATGGGGAGGTTAATGCGA 2311–2327 0.750 70.2
clpP1_p3 clpP1 AAACTCGGCAGGGTGAATTT ACGAACATACCCTGTCTCCA 2710–2726 0.750 70.0
clpP1_p4 clpP1 AACTCGGCAGGGTGAATTTT ACGAACATACCCTGTCTCCA 2709–2725 0.750 70.0
clpP1_p5 clpP1 CACATTCTTCGGCTCTACCC CAATGGGGAGGTTAATGCGA 2908–2924 0.750 69.7

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
Leucanthemum heterophyllum OR990529.1 150133 View on NCBI ↗
Leucanthemum maximum NC_046827.1 151865 View on NCBI ↗
Leucanthemum virgatum NC_047461.1 150120 View on NCBI ↗
Leucanthemum vulgare NC_047460.1 150191 View on NCBI ↗