Markers + reference

Chuquiraga

4 species · Asteraceae · Asterales

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Species 4
Genome length 151–153 kb
Candidate markers 268
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpH-atpI LSC 1061 0.0038 1.00 48.2 yes View details
rpoC2 LSC 4149 0.0029 1.00 42.2 yes View details
trnC-GCA-petN LSC 829 0.0054 0.91 61.9 yes View details
trnT-GGU-psbD LSC 1196 0.0042 0.99 63.1 yes View details
trnT-UGU-trnL-UAA LSC 568 0.0100 1.00 60.7 yes View details
petA LSC 963 0.0010 1.00 31.6 yes View details
petA-psbJ LSC 775 0.0056 0.99 61.2 yes View details
ycf2 IRb 6471 0.0004 1.00 47.8 yes View details
ndhF SSC 2238 0.0029 1.00 44.2 yes View details
ndhF-rpl32 SSC 1027 0.0067 0.99 50.1 yes View details
trnL-CAA-ycf2 IRa 396 0.0088 1.00 52.3 yes View details
ycf2 IRa 6471 0.0004 1.00 47.8 no View details
trnK-UUU-rps16 LSC 812 0.0064 1.00 67.0 yes View details
psbE-petL LSC 1173 0.0031 0.99 64.9 yes View details
accD-psaI LSC 665 0.0048 1.00 63.9 yes View details
rpl20-rps12 LSC 726 0.0023 0.99 63.1 yes View details
psaA-ycf3 LSC 707 0.0035 1.00 62.3 yes View details
rps16-trnQ-UUG LSC 949 0.0033 1.00 62.2 yes View details
ndhC-trnV-UAC LSC 449 0.0053 0.98 60.1 yes View details
ndhA SSC 2147 0.0029 1.00 59.8 yes View details
ycf4-cemA LSC 858 0.0035 0.99 59.1 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU GCCCGTGTCAACCAATATCT TGGGTTCGTTGGATTAGCTT 2987–2995 1.000 73.7
trnK-UUU_p2 trnK-UUU GCCCGTGTCAACCAATATCT GATGGGTTCGTTGGATTAGCT 2989–2997 1.000 72.0
trnK-UUU_p3 trnK-UUU CTTATAGGCCCGTGTCAACC TGGGTTCGTTGGATTAGCTT 2994 0.750 62.8
trnK-UUU_p4 trnK-UUU TGACTTATAGGCCCGTGTCA TGGGTTCGTTGGATTAGCTT 2997 0.750 62.0
trnK-UUU_p5 trnK-UUU CTTATAGGCCCGTGTCAACC GATGGGTTCGTTGGATTAGCT 2996 0.750 61.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCCCTCGCTTCATCCAAATG TTCCTTGAAAAAGGCGCTCA 952–993 1.000 81.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTCCTTGAAAAAGGCGCTCA 969–1010 1.000 80.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 CGATGGTATGGACGAATCCC TTCCTTGAAAAAGGCGCTCA 968–1009 1.000 80.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 908–949 1.000 80.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 907–948 1.000 80.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1014–1021 1.000 79.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1025–1032 1.000 79.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CACACCGGATCATGTCCTTC GAGGTTCGAATCCTTCCGTC 1034–1041 1.000 77.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CACCGGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1032–1039 1.000 77.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCAAGAGCACCTTCATTCCT GAGGTTCGAATCCTTCCGTC 1085–1092 1.000 76.5
atpH-atpI_p1 atpH-atpI CTCGCGATACCTTCTACAGC CACTCTAGCTGTTCGGAACC 1762–1766 1.000 80.3
atpH-atpI_p2 atpH-atpI CTCGCGATACCTTCTACAGC CCACTCTAGCTGTTCGGAAC 1763–1767 1.000 80.3
atpH-atpI_p3 atpH-atpI CTCGCGATACCTTCTACAGC TGCTTTGGCTTTACTCACGT 1510–1514 1.000 80.2
atpH-atpI_p4 atpH-atpI CTCGCGATACCTTCTACAGC GAGAAGAATACGGCCCTTGG 1661–1665 1.000 80.0
atpH-atpI_p5 atpH-atpI CTCGCGATACCTTCTACAGC GGAGAAGAATACGGCCCTTG 1662–1666 1.000 80.0
rpoC2_p1 rpoC2 TGGTAGGTGTCATTCGTTGG GAGTAGGTGGATTGGTCC 204 1.000 41.6
rpoC2_p2 rpoC2 GGTAGGTGTCATTCGTTGGA GAGTAGGTGGATTGGTCC 203 1.000 41.6
rpoC2_p3 rpoC2 TCCGTCGGGAAAAGTCTTTC TCCGAGTGGAGAGAAAAA 274 1.000 41.2
rpoC2_p4 rpoC2 TCCGTCGGGAAAAGTCTTTC GAGTAGGTGGATTGGTCC 289 1.000 41.1
rpoC2_p5 rpoC2 CGTCGGGAAAAGTCTTTCGA GAGTAGGTGGATTGGTCC 287 1.000 41.1
trnC-GCA-petN_p1 trnC-GCA-petN TTCTCCTATCGTTTTGGCGG AGCCCAAGCGAGACTTACTA 838–942 1.000 83.4
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 781–885 1.000 83.0
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 799–903 1.000 80.8
trnC-GCA-petN_p4 trnC-GCA-petN TTCTCCTATCGTTTTGGCGG GCCCAAGCGAGACTTACTAT 837–941 1.000 77.5
trnC-GCA-petN_p5 trnC-GCA-petN TTCTCCTATCGTTTTGGCGG ATTAAAGCAGCCCAAGCGAG 846–950 1.000 77.4

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
Chuquiraga jussieui NC_070298.1 152044 View on NCBI ↗
Chuquiraga oblongifolia NC_050158.1 151953 View on NCBI ↗
Chuquiraga oppositifolia NC_050159.1 153469 View on NCBI ↗
Chuquiraga rotundifolia NC_051500.1 151444 View on NCBI ↗