Markers + reference

Cardiocrinum

2 species · Liliaceae · Liliales

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Species 2
Genome length 152–152 kb
Candidate markers 277
Primer pairs 105

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 277 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 787 0.0025 1.00 56.2 yes View details
atpA LSC 1524 0.0020 1.00 59.8 yes View details
atpI-rps2 LSC 266 0.0075 1.00 56.8 yes View details
psbM-trnD-GUC LSC 1176 0.0009 0.99 46.3 yes View details
trnD-GUC-trnY-GUA LSC 322 0.0031 0.99 49.6 yes View details
ndhK LSC 879 0.0023 1.00 47.0 yes View details
ycf4-cemA LSC 749 0.0040 1.00 61.2 yes View details
ccsA SSC 966 0.0010 1.00 47.5 yes View details
ndhA SSC 2134 0.0014 1.00 45.7 yes View details
rps15-ycf1 SSC 399 0.0201 1.00 66.4 yes View details
ccsA-ndhD SSC 168 0.0357 1.00 65.2 yes View details
trnY-GUA-trnE-UUC LSC 59 0.0169 1.00 62.2 yes View details
atpB LSC 1497 0.0020 1.00 59.9 yes View details
rps4 LSC 606 0.0016 1.00 59.7 yes View details
trnS-GCU-trnG-GCC LSC 696 0.0014 1.00 59.6 yes View details
atpF LSC 1342 0.0015 1.00 59.6 yes View details
trnT-GGU-psbD LSC 1075 0.0009 1.00 59.6 yes View details
petA-psaJ LSC 801 0.0013 1.00 59.6 yes View details
matK-trnK-UUU LSC 812 0.0012 1.00 59.5 yes View details
rpl20-rps12 LSC 777 0.0013 1.00 59.5 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU CCACCAAAACCAAAACAATTTGT TATTTTGGCGGGATGGGATC 2811 0.500 28.6
trnK-UUU_p2 trnK-UUU CCACCAAAACCAAAACAATTTGT TTTATTTTGGCGGGATGGGA 2813 0.500 26.6
trnK-UUU_p3 trnK-UUU TCCACCAAAACCAAAACAATTTG TATTTTGGCGGGATGGGATC 2812 0.500 26.6
trnK-UUU_p4 trnK-UUU CCACCAAAACCAAAACAATTTGT GGCGGGATGGGATCAATTTT 2805 0.500 26.2
trnK-UUU_p5 trnK-UUU TCCACCAAAACCAAAACAAT TATTTTGGCGGGATGGGATC 2812 0.500 26.1
matK-trnK-UUU_p1 matK-trnK-UUU TAGGAAGTGTTGTTGCGGAG CAATCCGGGTTGCTAACTCA 912–916 1.000 77.9
matK-trnK-UUU_p2 matK-trnK-UUU TAGGAAGTGTTGTTGCGGAG ACAATCCGGGTTGCTAACTC 913–917 1.000 77.9
matK-trnK-UUU_p3 matK-trnK-UUU TAGGAAGTGTTGTTGCGGAG ATCCGGGTTGCTAACTCAAC 910–914 1.000 77.9
matK-trnK-UUU_p4 matK-trnK-UUU TAGGAAGTGTTGTTGCGGAG AACGGTAGAGTACTCGGCTT 893–897 1.000 77.4
matK-trnK-UUU_p5 matK-trnK-UUU TAGGAAGTGTTGTTGCGGAG ACGGTAGAGTACTCGGCTTT 892–896 1.000 77.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 860–866 1.000 78.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 871–877 1.000 77.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 864–870 1.000 77.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GGCGGATGTAAGAATCCACA GAGGTTCGAATCCTTCCGTC 896–902 1.000 77.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TGGCGGATGTAAGAATCCAC GAGGTTCGAATCCTTCCGTC 897–903 1.000 77.0
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA TGTCGGAAACTGAAAGACCC 815 1.000 77.8
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA CGGAAACTGAAAGACCCCTT 812 1.000 77.6
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC TGATGAGGGATAGCGGAGAG TGTCGGAAACTGAAAGACCC 878 1.000 77.4
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC TGATGAGGGATAGCGGAGAG CGGAAACTGAAAGACCCCTT 875 1.000 77.2
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC GAGGGATAGCGGAGAGAGAG TGTCGGAAACTGAAAGACCC 874 1.000 76.7
atpA_p1 atpA GGCTATACCAAGAAACCCAT AACGGATTAGCCTTTCGACT 1695 1.000 45.9
atpA_p2 atpA GGCTATACCAAGAAACCCAT ACGGATTAGCCTTTCGACTT 1694 1.000 45.9
atpA_p3 atpA GGCTATACCAAGAAACCCATT AACGGATTAGCCTTTCGACT 1695 1.000 44.6
atpA_p4 atpA GGCTATACCAAGAAACCCATT ACGGATTAGCCTTTCGACTT 1694 1.000 44.6
atpA_p5 atpA GGCTATACCAAGAAACCCAT ACGGATTAGCCTTTCGACTTT 1694 1.000 43.7
atpF_p1 atpF CTCGAAGGGTTGCCATTAGT AAGAAATCGATCAGGGCGAG 1523–1524 1.000 75.0
atpF_p2 atpF CTCGAAGGGTTGCCATTAGT GGCGAGTGAGGTGATACAAA 1504–1505 1.000 73.8
atpF_p3 atpF CTCGAAGGGTTGCCATTAGT AGGCGAGTGAGGTGATACAA 1505–1506 1.000 73.3
atpF_p4 atpF ACTAATTTCGTCGGCTCGAA AAGAAATCGATCAGGGCGAG 1537–1538 1.000 73.1
atpF_p5 atpF ACTAATTTCGTCGGCTCGAA GGCGAGTGAGGTGATACAAA 1518–1519 1.000 71.9

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
Cardiocrinum cathayanum NC_033897.1 152416 View on NCBI ↗
Cardiocrinum cordatum NC_033898.1 152410 View on NCBI ↗