Markers + reference

Anisodus

2 species · Solanaceae · Solanales

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Species 2
Genome length 156–156 kb
Candidate markers 267
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 417 0.0097 0.99 52.3 yes View details
rpoB-trnC-GCA LSC 1295 0.0077 1.00 63.2 yes View details
psbM-trnD-GUC LSC 1079 0.0056 1.00 61.9 yes View details
trnT-GGU-psbD LSC 1124 0.0044 1.00 61.3 yes View details
rbcL LSC 1434 0.0035 1.00 60.8 yes View details
accD-psaI LSC 724 0.0069 1.00 62.7 yes View details
petA-psbJ LSC 1063 0.0056 1.00 48.5 yes View details
rrn5-trnR-ACG IRb 261 0.0000 1.00 33.8 yes View details
trnR-ACG-trnN-GUU IRb 581 0.0086 1.00 63.3 yes View details
ycf1 IRb 1491 0.0101 1.00 64.5 yes View details
ndhF SSC 2223 0.0022 1.00 43.7 yes View details
ndhF-rpl32 SSC 769 0.0091 1.00 58.6 yes View details
ycf1 SSC 5694 0.0035 1.00 54.9 yes View details
trnE-UUC-trnT-GGU LSC 860 0.0059 0.98 63.7 yes View details
trnN-GUU-trnR-ACG IRa 580 0.0086 1.00 63.3 yes View details
psaA-ycf3 LSC 771 0.0039 0.99 62.4 yes View details
ycf4-cemA LSC 756 0.0053 1.00 61.8 yes View details
trnK-UUU-rps16 LSC 690 0.0043 1.00 61.2 yes View details
rpl2-trnH-GUG IRa 162 0.0208 0.89 61.2 no View details
atpI LSC 744 0.0040 1.00 61.1 yes View details
rpl20-rps12 LSC 814 0.0037 1.00 61.0 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 110 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 TTCCCTCTAGACCTAGCTGC 483–486 1.000 79.5
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 497–500 1.000 79.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 496–499 1.000 79.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 498–501 1.000 79.4
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 532–535 1.000 77.3
trnK-UUU_p1 trnK-UUU CTCGTGTCAACCAAGGTGTA AGTGCCAATCCAACACAAGT 2975–2980 1.000 75.8
trnK-UUU_p2 trnK-UUU TACTCGTGTCAACCAAGGTG AGTGCCAATCCAACACAAGT 2977–2982 1.000 75.8
trnK-UUU_p3 trnK-UUU CTCGTGTCAACCAAGGTGTA GCCAATCCAACACAAGTCCT 2972–2977 1.000 73.4
trnK-UUU_p4 trnK-UUU TACTCGTGTCAACCAAGGTG GCCAATCCAACACAAGTCCT 2974–2979 1.000 73.4
trnK-UUU_p5 trnK-UUU CTCGTGTCAACCAAGGTGTA GTGCCAATCCAACACAAGTC 2974–2979 1.000 73.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTGAAAAAGGGGCTCAACCT 822 1.000 75.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTGAAAAAGGGGCTCAACCT 821 1.000 75.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TTGAAAAAGGGGCTCAACCT 907 1.000 74.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 CAGTCGTGGTCTTCCAAACT TTGAAAAAGGGGCTCAACCT 906 1.000 74.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAAAGACACTAGCCGCACTT TTGAAAAAGGGGCTCAACCT 843 1.000 74.5
trnG-UCC_p1 trnG-UCC ATTAGCAATCCGCCGCTTTA GAGGAAGCAGAAGCCCTTTT 1881–1882 1.000 79.5
trnG-UCC_p2 trnG-UCC ATTAGCAATCCGCCGCTTTA TTTACCGAGGAAGCAGAAGC 1887–1888 1.000 79.4
trnG-UCC_p3 trnG-UCC CCAATTCCCCTGTTCGACAA GAGGAAGCAGAAGCCCTTTT 1242–1243 1.000 79.0
trnG-UCC_p4 trnG-UCC ATTAGCAATCCGCCGCTTTA AATCAGCTCCTCTCACGGTA 2057–2058 1.000 78.9
trnG-UCC_p5 trnG-UCC CCAATTCCCCTGTTCGACAA TTTACCGAGGAAGCAGAAGC 1248–1249 1.000 78.9
atpI_p1 atpI TGAGCCACCCACCATATACA TTTTCAGAGGGCAAGGCAAT 822 1.000 79.3
atpI_p2 atpI AATTCTCTTGAGCCACCCAC TTTTCAGAGGGCAAGGCAAT 830 1.000 78.5
atpI_p3 atpI TGAGCCACCCACCATATACA TTTTTCAGAGGGCAAGGCAA 823 1.000 77.7
atpI_p4 atpI TCTTGAGCCACCCACCATAT TTTTCAGAGGGCAAGGCAAT 825 1.000 76.9
atpI_p5 atpI AATTCTCTTGAGCCACCCAC TTTTTCAGAGGGCAAGGCAA 831 1.000 76.9
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CTCATTTCCATCCCCGAGC CCGGATTTGAACTGGGGAAA 1379 1.000 71.8
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCC CCGGATTTGAACTGGGGAAA 1384 1.000 71.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCATTTCCATCCCCGAGCAT CCGGATTTGAACTGGGGAAA 1378 1.000 70.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CTCATTTCCATCCCCGAGC AGTCCTCTGCCTTACCACTC 1348 1.000 69.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CATTTCCATCCCCGAGCAT CCGGATTTGAACTGGGGAAA 1377 1.000 68.5

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
Anisodus acutangulus NC_066481.1 156082 View on NCBI ↗
Anisodus luridus MW470952.1 156045 View on NCBI ↗