Markers + reference

Taraxacum

7 species · Asteraceae · Asterales

Back to catalogue

Species 7
Genome length 151–152 kb
Candidate markers 295
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 295 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnL-UAA-trnF-GAA LSC 356 0.0203 1.00 64.7 yes View details
trnF-GAA-ndhJ LSC 631 0.0054 1.00 48.8 yes View details
ndhC-trnV-UAC LSC 1212 0.0069 1.00 61.7 yes View details
rbcL-psaI LSC 2764 0.0040 1.00 45.4 yes View details
ycf1 IRb 477 0.0054 0.99 37.6 no View details
ndhF SSC 2220 0.0055 1.00 42.2 yes View details
ndhF-rpl32 SSC 1076 0.0096 1.00 53.3 yes View details
rpl32-trnL-UAG SSC 879 0.0076 0.98 52.4 yes View details
ccsA SSC 975 0.0018 0.99 36.7 yes View details
ccsA-ndhD SSC 274 0.0247 0.93 60.6 yes View details
ycf1 SSC 5055 0.0059 1.00 40.2 yes View details
trnH-GUG-psbA LSC 406 0.0082 0.97 59.5 yes View details
trnE-UUC-rpoB LSC 972 0.0031 1.00 58.5 yes View details
ycf4-cemA LSC 790 0.0057 1.00 57.7 yes View details
ndhA-ndhA SSC 1054 0.0050 1.00 57.4 yes View details
rbcL LSC 1428 0.0035 1.00 55.9 yes View details
ycf3-trnS-GGA LSC 917 0.0016 1.00 55.3 yes View details
trnK-UUU-rps16 LSC 762 0.0058 1.00 55.2 yes View details
rps15-ycf1 SSC 413 0.0064 1.00 54.8 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 90 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 504–524 1.000 80.6
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 518–538 1.000 80.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 517–537 1.000 80.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 519–539 1.000 80.4
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 505–525 1.000 80.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CCTTGAAAAAGGTGCTCAGC 864–911 1.000 79.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CTTGAAAAAGGTGCTCAGCC 863–910 1.000 79.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CCTTGAAAAAGGTGCTCAGC 863–910 1.000 79.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTTGAAAAAGGTGCTCAGCC 862–909 1.000 79.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC CTTGAAAAAGGTGCTCAGCC 878–925 1.000 78.7
trnE-UUC-rpoB_p1 trnE-UUC-rpoB GGGACTTGAACCCTCGTTTT AGTTCTTCTGTCAAACCCTGA 1102–1114 1.000 64.3
trnE-UUC-rpoB_p2 trnE-UUC-rpoB TAACCACTGGACCATAGGGG AGTTCTTCTGTCAAACCCTGA 1061–1073 1.000 63.6
trnE-UUC-rpoB_p3 trnE-UUC-rpoB CCCTCGTTTTCTCCGTGAAA AGTTCTTCTGTCAAACCCTGA 1092–1104 1.000 63.5
trnE-UUC-rpoB_p4 trnE-UUC-rpoB TTGAACCCTCGTTTTCTCCG AGTTCTTCTGTCAAACCCTGA 1097–1109 1.000 63.5
trnE-UUC-rpoB_p5 trnE-UUC-rpoB GGGACTTGAACCCTCGTTTT TCAAACCCTGATCAATGAACCT 1092–1104 1.000 62.9
ycf3-trnS-GGA_p1 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA ACGGAAAGAGAGGGATTCGA 1020–1031 1.000 72.1
ycf3-trnS-GGA_p2 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA TTCCAATGCTACGCCTTCAA 970–981 1.000 71.9
ycf3-trnS-GGA_p3 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA GGATTCGAACCCTCGGTAAG 1008–1019 1.000 71.6
ycf3-trnS-GGA_p4 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA AGTTCCAATGCTACGCCTTC 972–983 1.000 71.3
ycf3-trnS-GGA_p5 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA CCTCGGTAAGCAAAAGCCTA 998–1009 1.000 70.2
trnL-UAA-trnF-GAA_p1 trnL-UAA-trnF-GAA ACATGTCAATACCGGCAACA TTTGAACTGGTGACACGAGG 471–547 1.000 84.3
trnL-UAA-trnF-GAA_p2 trnL-UAA-trnF-GAA AATCGTGAGGGTTCAAGTCC TTTGAACTGGTGACACGAGG 412–488 1.000 82.3
trnL-UAA-trnF-GAA_p3 trnL-UAA-trnF-GAA ACATGTCAATACCGGCAACA GAACTGGTGACACGAGGATT 468–544 1.000 81.1
trnL-UAA-trnF-GAA_p4 trnL-UAA-trnF-GAA ACATGTCAATACCGGCAACA TCCTCTGCTCTACCAACTGA 366–474 1.000 80.2
trnL-UAA-trnF-GAA_p5 trnL-UAA-trnF-GAA ACATGTCAATACCGGCAACA TCAGTCCTCTGCTCTACCAA 447–523 1.000 80.0
trnF-GAA-ndhJ_p1 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA TGGATAGGATGGCCTTTACG 734–740 1.000 70.8
trnF-GAA-ndhJ_p2 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA GGATAGGATGGCCTTTACGT 733–739 1.000 70.8
trnF-GAA-ndhJ_p3 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA TGAAAGTTGGATAGGATGGCC 741–747 1.000 70.2
trnF-GAA-ndhJ_p4 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA TTGGATAGGATGGCCTTTACG 735–741 1.000 68.7
trnF-GAA-ndhJ_p5 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA TGGATAGGATGGCCTTTACGT 734–740 1.000 67.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Taraxacum albidum LC790150.2 151451 View on NCBI ↗
Taraxacum coreanum NC_059768.1 151451 View on NCBI ↗
Taraxacum erythrospermum NC_059769.1 151173 View on NCBI ↗
Taraxacum hallaisanense NC_057107.1 151554 View on NCBI ↗
Taraxacum mongolicum NC_031396.1 151451 View on NCBI ↗
Taraxacum officinale NC_030772.1 151324 View on NCBI ↗
Taraxacum platycarpum NC_031395.1 151307 View on NCBI ↗