Markers + reference

Duhaldea

2 species · Asteraceae · Asterales

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Species 2
Genome length 151–151 kb
Candidate markers 272
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 389 0.0289 0.98 58.1 yes View details
rps16-trnQ-UUG LSC 884 0.0193 1.00 56.2 yes View details
psbK-psbI LSC 403 0.0226 0.99 64.5 yes View details
trnS-GCU-trnC-GCA LSC 753 0.0094 0.99 57.2 yes View details
trnF-GAA-ndhJ LSC 556 0.0198 1.00 60.4 yes View details
ndhC-trnV-UAC LSC 359 0.0357 0.94 68.5 yes View details
petA-psbJ LSC 781 0.0168 0.99 65.2 yes View details
ycf1 IRb 615 0.0180 0.99 58.5 no View details
ndhF SSC 2229 0.0045 1.00 45.5 yes View details
rpl32-trnL-UAG SSC 892 0.0154 0.80 64.0 yes View details
ccsA SSC 960 0.0146 1.00 55.1 yes View details
ycf1 SSC 5097 0.0104 1.00 49.7 yes View details
psbA-trnK-UUU LSC 222 0.0327 0.96 74.7 yes View details
rps19-rpl2 IRb 70 0.0294 0.97 72.1 yes View details
ndhF-rpl32 SSC 723 0.0115 0.96 69.1 yes View details
rpl2-trnH-GUG IRa 66 0.0351 0.86 67.7 no View details
psbH-petB LSC 126 0.0240 0.99 67.0 yes View details
ycf4-cemA LSC 454 0.0114 0.96 65.9 yes View details
trnK-UUU-rps16 LSC 810 0.0100 0.99 65.7 yes View details
psbT-psbN LSC 72 0.0417 1.00 65.7 yes View details
psaA-ycf3 LSC 723 0.0098 0.99 65.4 yes View details
psbM-trnD-GUC LSC 659 0.0139 0.98 65.3 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 100 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 GAGCTTAGTTTCCGTCTGGG 1072–1080 1.000 80.4
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GAGTGGGAGCTTAGTTTCCG 1078–1086 1.000 80.4
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG GGAGCTTAGTTTCCGTCTGG 1073–1081 1.000 80.4
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG GGGAGCTTAGTTTCCGTCTG 1074–1082 1.000 80.4
trnH-GUG-psbA_p5 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GAGCTTAGTTTCCGTCTGGG 1086–1094 1.000 80.3
psbA-trnK-UUU_p1 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT GAAAGCCGTGTGCAATGAAA 423–432 1.000 79.8
psbA-trnK-UUU_p2 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT CTAGTTCCGGGTTCGAATCC 338–347 1.000 79.8
psbA-trnK-UUU_p3 psbA-trnK-UUU GTAAAGACGGTTTTCGGTGC GAAAGCCGTGTGCAATGAAA 424–433 1.000 79.3
psbA-trnK-UUU_p4 psbA-trnK-UUU GTAAAGACGGTTTTCGGTGC CTAGTTCCGGGTTCGAATCC 339–348 1.000 79.3
psbA-trnK-UUU_p5 psbA-trnK-UUU TTTTCGGTGCTGGTTATCCA GAAAGCCGTGTGCAATGAAA 414–423 1.000 77.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTCCTTGAAAAAGGCGCTCA 1007–1037 1.000 78.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGATGGTATGGACGAATCCC TTCCTTGAAAAAGGCGCTCA 1006–1036 1.000 78.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 946–976 1.000 77.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 945–975 1.000 77.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TTCCTTGAAAAAGGCGCTCA 1031–1061 1.000 77.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GATCGTTGCCCCTGAGAAAT GAGGTTCGAATCCTTCCGTC 1146–1230 1.000 80.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GATCGTTGCCCCTGAGAAAT CTTACAGCAGCTTGCCAAAC 1720–1805 1.000 80.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AGCGGTCTTTCCTTGTTCTG GAGGTTCGAATCCTTCCGTC 1445–1525 1.000 80.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AGCGGTCTTTCCTTGTTCTG CTTACAGCAGCTTGCCAAAC 2019–2100 1.000 79.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTTACAGCAGCTTGCCAAAC 1531–1621 1.000 79.5
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCTTCACGTCCAGGATTACG 540–546 1.000 74.1
psbK-psbI_p2 psbK-psbI TATGCCAGTCATACCCCTGT TCTTCACGTCCAGGATTACG 580–586 1.000 72.9
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT TCTTCACGTCCAGGATTACG 537–543 1.000 72.1
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT TCTTCACGTCCAGGATTACG 538–544 1.000 72.1
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT TCTTCACGTCCAGGATTACG 539–545 1.000 72.1
trnS-GCU-trnC-GCA_p1 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA CCGGATTTGAACTGGGGAAA 897–904 1.000 79.6
trnS-GCU-trnC-GCA_p2 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA AAAAGGATTTGCAGTCCCCC 879–886 1.000 77.4
trnS-GCU-trnC-GCA_p3 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC CCGGATTTGAACTGGGGAAA 833–840 1.000 75.8
trnS-GCU-trnC-GCA_p4 trnS-GCU-trnC-GCA AACGGAAAGAGAGGGATTCG CCGGATTTGAACTGGGGAAA 898–905 1.000 75.4
trnS-GCU-trnC-GCA_p5 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC AAAAGGATTTGCAGTCCCCC 815–822 1.000 73.6

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
Duhaldea cappa NC_068630.1 150819 View on NCBI ↗
Duhaldea nervosa NC_081495.1 150916 View on NCBI ↗