Markers + reference

Arctium

2 species · Asteraceae · Asterales

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Species 2
Genome length 153–153 kb
Candidate markers 267
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 389 0.0000 1.00 35.6 yes View details
psbA LSC 1062 0.0000 1.00 40.0 yes View details
ycf4 LSC 555 0.0018 1.00 58.8 yes View details
ycf2 IRb 6873 0.0000 1.00 19.1 yes View details
ycf2-trnL-CAA IRb 408 0.0025 1.00 56.2 yes View details
ycf1 SSC 5196 0.0004 1.00 52.7 yes View details
ccsA SSC 969 0.0010 1.00 59.3 yes View details
trnL-CAA-ycf2 IRa 408 0.0025 1.00 56.2 yes View details
ycf2 IRa 6873 0.0000 1.00 19.1 no View details
petA-psbJ LSC 815 0.0000 1.00 58.9 yes View details
matK LSC 1521 0.0000 1.00 40.0 yes View details
matK-trnK-UUU LSC 747 0.0000 1.00 40.0 yes View details
trnK-UUU-rps16 LSC 781 0.0000 1.00 40.0 yes View details
rps16 LSC 1108 0.0000 1.00 40.0 yes View details
rps16-trnQ-UUG LSC 940 0.0000 1.00 40.0 yes View details
trnS-GCU-trnC-GCA LSC 773 0.0000 1.00 40.0 yes View details
psbM-trnD-GUC LSC 645 0.0000 1.00 40.0 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 507 1.000 76.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 521 1.000 76.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 520 1.000 76.2
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 522 1.000 76.2
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 508 1.000 75.8
psbA_p1 psbA GAGCAATAACGCCCTCTTGA TTGAAAATTCGTGCGCTTGG 1203 1.000 77.9
psbA_p2 psbA AAAAGGAGCAATAACGCCCT TTGAAAATTCGTGCGCTTGG 1208 1.000 76.4
psbA_p3 psbA GAGCAATAACGCCCTCTTGA ATATTGGTTGACACGGGCAT 1268 1.000 76.3
psbA_p4 psbA GAGCAATAACGCCCTCTTGA ATTGGTTGACACGGGCATAT 1266 1.000 76.3
psbA_p5 psbA AAAGGAGCAATAACGCCCTC TTGAAAATTCGTGCGCTTGG 1207 1.000 76.1
matK_p1 matK ACATACTACATCAACATTTCAGA ACCCCCAAAATCCTCTACCT 1680–1681 1.000 40.0
matK_p2 matK ACATACTACATCAACATTTCAGAA ACCCCCAAAATCCTCTACCT 1680–1681 1.000 40.0
matK_p3 matK ACATACTACATCAACATTTCAGAAT ACCCCCAAAATCCTCTACCT 1680–1681 1.000 40.0
matK_p4 matK CTACATACTACATCAACATTTCAGA ACCCCCAAAATCCTCTACCT 1682–1683 1.000 40.0
matK_p5 matK ACATACTACATCAACATTTCAGA AACCCCCAAAATCCTCTACC 1681–1682 1.000 40.0
matK-trnK-UUU_p1 matK-trnK-UUU AGCCCTAAAGAGCTTTGGAA AACGGTAGAGTACTCGGCTT 800 1.000 68.4
matK-trnK-UUU_p2 matK-trnK-UUU AGCCCTAAAGAGCTTTGGAA ACGGTAGAGTACTCGGCTTT 799 1.000 68.4
matK-trnK-UUU_p3 matK-trnK-UUU AGCCCTAAAGAGCTTTGGAA TTGGGTTGCTAACTCAACGG 815 1.000 66.6
matK-trnK-UUU_p4 matK-trnK-UUU AGCCCTAAAGAGCTTTGGAA GGGTTGCTAACTCAACGGTA 813 1.000 66.1
matK-trnK-UUU_p5 matK-trnK-UUU AGCCCTAAAGAGCTTTGGAAT ACGGTAGAGTACTCGGCTTT 799 1.000 64.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 917 1.000 76.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 916 1.000 76.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TTCCTTGAAAAAGGCGCTCA 1002 1.000 75.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 CAGTCGTGGTCTTCCAAACT TTCCTTGAAAAAGGCGCTCA 1001 1.000 75.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC TTCCTTGAAAAAGGCGCTCA 932 1.000 75.4
rps16_p1 rps16 ACGAATAGAGCAAGAAAAGAAGG TCTCTGTACCGACTGAACCA 1294 1.000 44.8
rps16_p2 rps16 ACGAATAGAGCAAGAAAAGAAGGA TCTCTGTACCGACTGAACCA 1294 1.000 44.1
rps16_p3 rps16 CGAATAGAGCAAGAAAAGAAGGA TCTCTGTACCGACTGAACCA 1293 1.000 42.8
rps16_p4 rps16 ACGAATAGAGCAAGAAAAGAAGG GTCTCTGTACCGACTGAACC 1295 1.000 42.0
rps16_p5 rps16 ACGAATAGAGCAAGAAAAGAAGGA GTCTCTGTACCGACTGAACC 1295 1.000 41.3

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
Arctium minus BK071823.1 152707 View on NCBI ↗
Arctium nemorosum BK071824.1 152707 View on NCBI ↗