Markers + reference

Scopolia

2 species · Solanaceae · Solanales

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Species 2
Genome length 156–156 kb
Candidate markers 277
Primer pairs 105

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 277 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-rps16 LSC 690 0.0522 1.00 73.7 yes View details
rpoC2 LSC 4170 0.0017 1.00 54.8 yes View details
trnE-UUC-trnT-GGU LSC 847 0.0059 1.00 55.7 yes View details
ycf3 LSC 2002 0.0045 0.99 49.9 yes View details
cemA LSC 690 0.0087 1.00 52.4 yes View details
psbE-petL LSC 1163 0.0052 1.00 58.8 yes View details
ycf15-trnL-CAA IRb 348 0.0144 1.00 61.8 yes View details
ycf1 IRb 1473 0.0020 1.00 59.9 no View details
ndhF-rpl32 SSC 757 0.0066 1.00 62.3 yes View details
ccsA SSC 942 0.0053 1.00 47.0 yes View details
rps15 SSC 264 0.0000 1.00 21.8 yes View details
ycf1 SSC 5697 0.0042 1.00 43.2 yes View details
trnL-UAG-ccsA SSC 98 0.0306 1.00 70.1 yes View details
rpl32-sprA SSC 48 0.0208 1.00 64.5 yes View details
ccsA-ndhD SSC 240 0.0208 1.00 64.5 yes View details
trnG-trnR LSC 160 0.0187 1.00 63.3 yes View details
rps7-rps12 IRb 53 0.0189 1.00 63.3 yes View details
rps12-rps7 IRa 53 0.0189 1.00 63.3 yes View details
ndhH-rps15 SSC 111 0.0180 1.00 62.9 yes View details
ndhC-trnV-UAC LSC 1123 0.0036 0.98 62.7 yes View details
accD-psaI LSC 733 0.0068 1.00 62.7 yes View details
ndhD-psaC SSC 118 0.0169 1.00 62.2 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-rps16_p1 trnK-rps16 CCTTTCAGGATCAGTCGTGG AAAAGGGTATGTTGCTGCCA 1521–1527 1.000 81.8
trnK-rps16_p2 trnK-rps16 CCCTTTCAGGATCAGTCGTG AAAAGGGTATGTTGCTGCCA 1522–1528 1.000 81.7
trnK-rps16_p3 trnK-rps16 TCCCTTTCAGGATCAGTCGT AAAAGGGTATGTTGCTGCCA 1523–1529 1.000 81.4
trnK-rps16_p4 trnK-rps16 TCAGGATCAGTCGTGGTCTT AAAAGGGTATGTTGCTGCCA 1517–1523 1.000 81.3
trnK-rps16_p5 trnK-rps16 TTCAGGATCAGTCGTGGTCT AAAAGGGTATGTTGCTGCCA 1518–1524 1.000 81.3
trnG-trnR_p1 trnG-trnR AGCCTTCCAAGCTAACGATG ACAGTCGTTCTTGCTATCGA 324 1.000 70.1
trnG-trnR_p2 trnG-trnR CCTAGCCTTCCAAGCTAACG ACAGTCGTTCTTGCTATCGA 327 1.000 69.9
trnG-trnR_p3 trnG-trnR AGCCTTCCAAGCTAACGATG ACAGTCGTTCTTGCTATCGAA 324 1.000 67.9
trnG-trnR_p4 trnG-trnR CCTAGCCTTCCAAGCTAACG ACAGTCGTTCTTGCTATCGAA 327 1.000 67.7
trnG-trnR_p5 trnG-trnR CCCTAGCCTTCCAAGCTAAC ACAGTCGTTCTTGCTATCGA 328 1.000 67.7
rpoC2_p1 rpoC2 TATGGAAGAAGATCCGGGCA GCCCTGTTCAGGTATCTCGA 268 1.000 72.2
rpoC2_p2 rpoC2 TATGGAAGAAGATCCGGGCA TGAACTAATGCCCTGTTCAGG 277 1.000 70.7
rpoC2_p3 rpoC2 TATGGAAGAAGATCCGGGCA GAACTAATGCCCTGTTCAGGT 276 1.000 70.7
rpoC2_p4 rpoC2 TATGGAAGAAGATCCGGGCA TGCCCTGTTCAGGTATCTCG 269 1.000 69.9
rpoC2_p5 rpoC2 TATGGAAGAAGATCCGGGCA AACTAATGCCCTGTTCAGGT 275 1.000 69.1
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 988 1.000 79.1
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCATGGCGTTACTCTACCAC 967 1.000 78.6
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TGGCGTTACTCTACCACTGA 964 1.000 78.5
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 950 1.000 78.3
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCGATGACTTACGCCTTACC 985 1.000 77.9
ycf3_p1 ycf3 AGGATAATAAATAAACGGGGTCTTCT TCCCACGAGAGGTAATGAGA 2061–2074 1.000 40.9
ycf3_p2 ycf3 AGGATAATAAATAAACGGGGTCT TCCCACGAGAGGTAATGAGA 2061–2074 1.000 40.9
ycf3_p3 ycf3 AGGATAATAAATAAACGGGGTCTTC TCCCACGAGAGGTAATGAGA 2061–2074 1.000 40.9
ycf3_p4 ycf3 GGATAATAAATAAACGGGGTCTTCT TCCCACGAGAGGTAATGAGA 2060–2073 1.000 40.9
ycf3_p5 ycf3 AGGATAATAAATAAACGGGGTCTTCT TCCCACGAGAGGTAATGAGAA 2061–2074 1.000 40.9
ndhC-trnV-UAC_p1 ndhC-trnV-UAC TTGCTAATCGGGGCTAACAC AGAAGGTCTACGGTTCGAGT 1252–1263 1.000 79.8
ndhC-trnV-UAC_p2 ndhC-trnV-UAC GCTAATCGGGGCTAACACTC AGAAGGTCTACGGTTCGAGT 1250–1261 1.000 79.0
ndhC-trnV-UAC_p3 ndhC-trnV-UAC CCTTTGCTAATCGGGGCTAA AGAAGGTCTACGGTTCGAGT 1255–1266 1.000 77.3
ndhC-trnV-UAC_p4 ndhC-trnV-UAC TTGCTAATCGGGGCTAACAC GAAGGTCTACGGTTCGAGTC 1251–1262 1.000 77.1
ndhC-trnV-UAC_p5 ndhC-trnV-UAC GGCTAACACTCCGGAAATGA AGAAGGTCTACGGTTCGAGT 1241–1252 1.000 76.9

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
Scopolia carniolica NC_063110.1 156316 View on NCBI ↗
Scopolia parviflora NC_030282.1 156193 View on NCBI ↗