Markers + reference

Solidago

2 species · Asteraceae · Asterales

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Species 2
Genome length 153–153 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

9 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
trnG-UCC-trnT-GGU LSC 362 0.1278 0.63 67.2 yes View details
trnT-UGU-trnL-UAA LSC 776 0.0041 0.94 65.7 yes View details
accD-psaI LSC 997 0.0057 0.88 64.7 yes View details
petD LSC 1335 0.0068 0.99 64.1 yes View details
rpl16-rps3 LSC 1305 0.0031 0.99 61.1 yes View details
rps19 LSC 279 0.0072 1.00 50.4 yes View details
ndhA SSC 2194 0.0018 1.00 58.8 yes View details
trnL-UAG-rpl32 SSC 836 0.0073 0.99 64.1 yes View details
rps19 IRa 61 0.0000 1.00 27.5 no View details
trnT-GGU LSC 68 0.2692 0.76 72.1 yes View details
ndhC-trnV-UAC LSC 747 0.0000 0.97 61.7 yes View details
psbT-psbN LSC 73 0.0137 1.00 60.4 yes View details
ycf3-trnS-GCU LSC 855 0.0000 0.99 60.0 yes View details
trnK-UUU-rps16 LSC 843 0.0012 1.00 59.8 yes View details
trnE-rpoB LSC 1035 0.0010 1.00 59.8 yes View details
ycf1-rps15 SSC 453 0.0000 0.96 59.5 yes View details
rpl32-ndhF SSC 795 0.0000 0.99 59.5 yes View details
rps12-ycf15 IRb 1056 0.0000 0.99 59.3 yes View details
ccsA SSC 969 0.0010 1.00 59.3 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC TTCCTTGAAAAAGGCGCTCA 964–968 1.000 75.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA TTCCTTGAAAAAGGCGCTCA 958–962 1.000 75.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGCGGTCTTCCAAACTTTA TTCCTTGAAAAAGGCGCTCA 1030–1034 1.000 73.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGCGGTCTTCCAAACTTTAC TTCCTTGAAAAAGGCGCTCA 1029–1033 1.000 73.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC TCCTTGAAAAAGGCGCTCAG 963–967 1.000 72.1
trnE-rpoB_p1 trnE-rpoB GGGACTTGAACCCTCGTTTT AGTTCTTCTGTCAAACCCTGA 1177 1.000 62.5
trnE-rpoB_p2 trnE-rpoB TAACCACTGGACCATAGGGG AGTTCTTCTGTCAAACCCTGA 1136 1.000 61.8
trnE-rpoB_p3 trnE-rpoB CCCTCGTTTTCTCCGTGAAA AGTTCTTCTGTCAAACCCTGA 1167 1.000 61.7
trnE-rpoB_p4 trnE-rpoB TTGAACCCTCGTTTTCTCCG AGTTCTTCTGTCAAACCCTGA 1172 1.000 61.7
trnE-rpoB_p5 trnE-rpoB GGGACTTGAACCCTCGTTTT TCAAACCCTGATCAATGAACCT 1167 1.000 61.1
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU TGGTTTCATTCGGCTCCTTT TCCCCTATCGGATCTGAACC 971–1122 1.000 84.9
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU TTGGTTTCATTCGGCTCCTT TCCCCTATCGGATCTGAACC 972–1123 1.000 84.9
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU TTTGGTTTCATTCGGCTCCT TCCCCTATCGGATCTGAACC 973–1124 1.000 84.9
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU TGGTTTCATTCGGCTCCTTT TGTGGAAGAACGAAATGCCA 1509–1673 1.000 83.7
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU TTGGTTTCATTCGGCTCCTT TGTGGAAGAACGAAATGCCA 1510–1674 1.000 83.7
trnT-GGU_p1 trnT-GGU TGGATATGTGTAGACGGGCT TGTGGAAGAACGAAATGCCA 768–932 1.000 87.2
trnT-GGU_p2 trnT-GGU AGGGGCTTCTGGATATGTGT TGTGGAAGAACGAAATGCCA 777–941 1.000 87.0
trnT-GGU_p3 trnT-GGU ATCTTTTGTCGAGGGGCTTC TGTGGAAGAACGAAATGCCA 788–952 1.000 86.8
trnT-GGU_p4 trnT-GGU GATCTTTTGTCGAGGGGCTT TGTGGAAGAACGAAATGCCA 789–953 1.000 86.8
trnT-GGU_p5 trnT-GGU GTGACCCGTTCAGGAATTCA TGTGGAAGAACGAAATGCCA 655 0.500 58.4
ycf3-trnS-GCU_p1 ycf3-trnS-GCU TTCTCCTGAAGTTGTCGGAA GGATTCGAACCCTCGGTAAG 1016–1027 1.000 66.4
ycf3-trnS-GCU_p2 ycf3-trnS-GCU TTTCTCCTGAAGTTGTCGGA GGATTCGAACCCTCGGTAAG 1017–1028 1.000 66.4
ycf3-trnS-GCU_p3 ycf3-trnS-GCU TTCTCCTGAAGTTGTCGGAA CCTCGGTAAGCAAAAGCCTA 1006–1017 1.000 65.0
ycf3-trnS-GCU_p4 ycf3-trnS-GCU TTTCTCCTGAAGTTGTCGGA CCTCGGTAAGCAAAAGCCTA 1007–1018 1.000 65.0
ycf3-trnS-GCU_p5 ycf3-trnS-GCU TTCTCCTGAAGTTGTCGGAA GATTCGAACCCTCGGTAAGC 1015–1026 1.000 64.7
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CCGTAGCGTCTACCGATTTC 798–837 1.000 81.2
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT CCGTAGCGTCTACCGATTTC 830–869 1.000 80.4
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CGTCTACCGATTTCGCCATA 792–831 1.000 79.9
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT CGTCTACCGATTTCGCCATA 824–863 1.000 79.1
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CGTAGCGTCTACCGATTTCG 797–836 1.000 78.3

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
Solidago canadensis NC_061055.1 153059 View on NCBI ↗
Solidago decurrens NC_053705.1 152728 View on NCBI ↗