Markers + reference

Dahlia

2 species · Asteraceae · Asterales

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Species 2
Genome length 152–152 kb
Candidate markers 274
Primer pairs 90

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 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 450 0.0157 0.99 65.3 yes View details
trnK-UUU-rps16 LSC 805 0.0124 1.00 65.9 yes View details
trnC-GCA-petN LSC 849 0.0108 0.98 61.6 yes View details
psbZ-trnG-GCC LSC 329 0.0547 1.00 82.4 yes View details
trnT-UGU-trnL-UAA LSC 568 0.0124 0.99 65.7 yes View details
ndhC-trnV-UAC LSC 1013 0.0129 1.00 66.3 yes View details
ycf1 IRb 564 0.0018 1.00 44.0 yes View details
rpl32-trnL-UAG SSC 779 0.0118 0.98 67.2 yes View details
rps15-ycf1 SSC 402 0.0150 1.00 57.6 yes View details
ycf1 SSC 5022 0.0038 1.00 39.9 no View details
rpl22-rps19 LSC 81 0.0380 0.98 76.6 yes View details
ycf1-ndhF SSC 75 0.0870 0.92 74.0 yes View details
rpl2-trnH-GUG IRa 155 0.0000 1.00 66.1 no View details
atpF-atpA LSC 70 0.0154 0.93 65.4 yes View details
trnE-UUC-rpoB LSC 925 0.0087 0.99 64.3 yes View details
ccsA-ndhD SSC 274 0.0185 0.99 64.1 yes View details
ndhF-rpl32 SSC 993 0.0081 1.00 63.4 yes View details
atpB-rbcL LSC 758 0.0079 1.00 63.3 yes View details
psbM-trnD-GUC LSC 641 0.0078 1.00 63.2 yes View details
accD-psaI LSC 678 0.0074 1.00 63.0 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 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 568–573 1.000 77.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 582–587 1.000 77.6
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 581–586 1.000 77.6
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 583–588 1.000 77.6
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 569–574 1.000 77.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTCCTTGAAAAAGGCGCTCA 1002–1011 1.000 77.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 941–950 1.000 77.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 940–949 1.000 77.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TTCCTTGAAAAAGGCGCTCA 1026–1035 1.000 76.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 CAGTCGTGGTCTTCCAAACT TTCCTTGAAAAAGGCGCTCA 1025–1034 1.000 76.3
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 899–905 1.000 80.6
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 917–923 1.000 78.4
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 898–904 1.000 74.7
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ATTAAAGCAGCCCAAGCGAG 907–913 1.000 74.6
trnC-GCA-petN_p5 trnC-GCA-petN ATTGTGTATCGTTTTGGCGG AGCCCAAGCGAGACTTACTA 956–962 1.000 73.8
psbM-trnD-GUC_p1 psbM-trnD-GUC GTTTGACTGGCTGTTTTTACGT TTCAATAGGCAAGAGCACCG 803–811 1.000 62.2
psbM-trnD-GUC_p2 psbM-trnD-GUC TTGACTGGCTGTTTTTACGT TTCAATAGGCAAGAGCACCG 801–809 1.000 60.9
psbM-trnD-GUC_p3 psbM-trnD-GUC AGTTTGACTGGCTGTTTTTACG TTCAATAGGCAAGAGCACCG 804–812 1.000 60.1
psbM-trnD-GUC_p4 psbM-trnD-GUC TCAGTTTGACTGGCTGTTTT TTCAATAGGCAAGAGCACCG 806–814 1.000 60.0
psbM-trnD-GUC_p5 psbM-trnD-GUC TTTGACTGGCTGTTTTTACGT TTCAATAGGCAAGAGCACCG 802–810 1.000 59.1
trnE-UUC-rpoB_p1 trnE-UUC-rpoB GGGACTTGAACCCTCGTTTT CTTCTGCCAAACCCTGATCA 1059–1063 1.000 79.2
trnE-UUC-rpoB_p2 trnE-UUC-rpoB TAACCACTGGACCATAGGGG CTTCTGCCAAACCCTGATCA 1018–1022 1.000 78.5
trnE-UUC-rpoB_p3 trnE-UUC-rpoB CCCTCGTTTTCTCCGTGAAA CTTCTGCCAAACCCTGATCA 1049–1053 1.000 78.3
trnE-UUC-rpoB_p4 trnE-UUC-rpoB TTGAACCCTCGTTTTCTCCG CTTCTGCCAAACCCTGATCA 1054–1058 1.000 78.3
trnE-UUC-rpoB_p5 trnE-UUC-rpoB GGGACTTGAACCCTCGTTTT TCTTCTGCCAAACCCTGATC 1060–1064 1.000 76.8
atpF-atpA_p1 atpF-atpA CATATTGGCGGCGATGAAAC GTCGGCTTGAATGGTTACCA 120–125 1.000 82.2
atpF-atpA_p2 atpF-atpA CATATTGGCGGCGATGAAAC ATTTCGTCGGCTTGAATGGT 125–130 1.000 82.0
atpF-atpA_p3 atpF-atpA CATATTGGCGGCGATGAAAC TCGTCGGCTTGAATGGTTAC 122–127 1.000 81.3
atpF-atpA_p4 atpF-atpA CATATTGGCGGCGATGAAAC TTTCGTCGGCTTGAATGGTT 124–129 1.000 80.3
atpF-atpA_p5 atpF-atpA CATATTGGCGGCGATGAAAC ACTTGAAGTACGGTACCGGT 203–208 1.000 79.0

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
Dahlia imperialis NC_069635.1 152084 View on NCBI ↗
Dahlia pinnata NC_066129.1 152107 View on NCBI ↗