Markers + reference

Gynoxys

8 species · Asteraceae · Asterales

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Species 8
Genome length 151–155 kb
Candidate markers 270
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 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-TTG LSC 970 0.0050 1.00 52.4 yes View details
trnS-GCT-trnC-GCA LSC 744 0.0049 1.00 50.6 yes View details
petN-psbM LSC 500 0.0059 1.00 51.4 yes View details
psaA-ycf3 LSC 690 0.0076 1.00 46.5 yes View details
psbE-petL LSC 1230 0.0052 1.00 62.9 yes View details
rps3 LSC 657 0.0027 1.00 37.6 yes View details
ycf1 SSC 5007 0.0023 1.00 42.1 yes View details
trnL-TAG-rpl32 SSC 812 0.0062 1.00 63.8 yes View details
rpl32-ndhF SSC 1067 0.0059 1.00 53.8 yes View details
ndhF SSC 2226 0.0008 1.00 36.5 yes View details
trnK-UUU-rps16 LSC 840 0.0031 1.00 63.0 yes View details
psbC-trnS-TGA LSC 232 0.0087 0.99 60.4 yes View details
trnR-TCT-trnG-TCC LSC 215 0.0112 1.00 60.3 yes View details
ndhA SSC 2148 0.0017 1.00 59.0 yes View details
clpP LSC 2015 0.0010 1.00 58.8 yes View details
trnF-GAA-ndhJ LSC 746 0.0020 1.00 58.3 yes View details
accD-psaI LSC 672 0.0033 1.00 58.1 yes View details
ndhC-trnV-UAC LSC 757 0.0027 1.00 56.4 yes View details
rpoC2 LSC 4149 0.0011 1.00 54.8 yes View details
trnE-TTC-rpoB LSC 750 0.0019 1.00 54.4 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 970–976 1.000 77.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 969–975 1.000 77.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TTCCTTGAAAAAGGCGCTCA 1055–1061 1.000 77.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 CAGTCGTGGTCTTCCAAACT TTCCTTGAAAAAGGCGCTCA 1054–1060 1.000 77.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC TTCCTTGAAAAAGGCGCTCA 985–991 1.000 77.0
rps16-trnQ-TTG_p1 rps16-trnQ-TTG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1030–1051 1.000 80.1
rps16-trnQ-TTG_p2 rps16-trnQ-TTG AGAATAAGAATCCACGCCGG GAGGTTCGAATCCTTCCGTC 1062–1083 1.000 79.3
rps16-trnQ-TTG_p3 rps16-trnQ-TTG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1044–1065 1.000 78.3
rps16-trnQ-TTG_p4 rps16-trnQ-TTG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1045–1066 1.000 78.2
rps16-trnQ-TTG_p5 rps16-trnQ-TTG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1034–1055 1.000 75.4
trnS-GCT-trnC-GCA_p1 trnS-GCT-trnC-GCA ACGGAAAGAGAGGGATTCGA CCGGATTTGAACTGGGGAAA 895 1.000 78.8
trnS-GCT-trnC-GCA_p2 trnS-GCT-trnC-GCA ACGGAAAGAGAGGGATTCGA AAAAGGATTTGCAGTCCCCC 877 1.000 76.7
trnS-GCT-trnC-GCA_p3 trnS-GCT-trnC-GCA CTTTCGTCCACTCAGCCATC CCGGATTTGAACTGGGGAAA 831 1.000 75.0
trnS-GCT-trnC-GCA_p4 trnS-GCT-trnC-GCA AACGGAAAGAGAGGGATTCG CCGGATTTGAACTGGGGAAA 896 1.000 74.7
trnS-GCT-trnC-GCA_p5 trnS-GCT-trnC-GCA CTTTCGTCCACTCAGCCATC AAAAGGATTTGCAGTCCCCC 813 1.000 72.9
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTT 662 1.000 60.1
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTTT 662 1.000 58.4
petN-psbM_p3 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTT 663 1.000 54.2
petN-psbM_p4 petN-psbM CTCGCTTGGGCTGCTTTAAT TGCTACTGCACTGTTCATTT 654 1.000 54.1
petN-psbM_p5 petN-psbM TGGGCTGCTTTAATGGTAGTC TGCTACTGCACTGTTCATTT 648 1.000 53.4
trnE-TTC-rpoB_p1 trnE-TTC-rpoB GGGAGTTGAACCCTCGTTTT GTTCTTCTGTCAAACCCCGA 884–893 1.000 78.9
trnE-TTC-rpoB_p2 trnE-TTC-rpoB GGGAGTTGAACCCTCGTTTT AGTTCTTCTGTCAAACCCCG 885–894 1.000 78.8
trnE-TTC-rpoB_p3 trnE-TTC-rpoB TAACCACTGGACCATAGGGG GTTCTTCTGTCAAACCCCGA 843–852 1.000 78.2
trnE-TTC-rpoB_p4 trnE-TTC-rpoB TAACCACTGGACCATAGGGG AGTTCTTCTGTCAAACCCCG 844–853 1.000 78.2
trnE-TTC-rpoB_p5 trnE-TTC-rpoB CCCTCGTTTTCTCCGTGAAA GTTCTTCTGTCAAACCCCGA 874–883 1.000 78.1
rpoC2_p1 rpoC2 CCACTCGAATCGCTTCAAGA TTGGCCAAAATACCTTGCCT 232 1.000 80.8
rpoC2_p2 rpoC2 GGCGAAGAGGCGAAGAAATA TTGGCCAAAATACCTTGCCT 263 1.000 80.2
rpoC2_p3 rpoC2 CCACTCGAATCGCTTCAAGA GCCAAAATACCTTGCCTCCT 229 1.000 79.8
rpoC2_p4 rpoC2 GGCGAAGAGGCGAAGAAATA GCCAAAATACCTTGCCTCCT 260 1.000 79.2
rpoC2_p5 rpoC2 GCCATTCTCGAGGGGAATTC TTGGCCAAAATACCTTGCCT 292 1.000 77.4

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
Gynoxys asterotricha MK044798.1 151004 View on NCBI ↗
Gynoxys baccharoides NC_062442.1 151071 View on NCBI ↗
Gynoxys ignaciana NC_062450.1 150979 View on NCBI ↗
Gynoxys longifolia NC_062443.1 150998 View on NCBI ↗
Gynoxys mandonii MK056106.1 151031 View on NCBI ↗
Gynoxys megacephala MN328892.1 151014 View on NCBI ↗
Gynoxys tomentosissima MN328890.1 155060 View on NCBI ↗
Gynoxys violacea NC_062441.1 151006 View on NCBI ↗