Markers + reference

Adenosma

2 species · Plantaginaceae · Lamiales

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Species 2
Genome length 154–154 kb
Candidate markers 271
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 SSC 5526 0.3530 0.90 76.3 yes View details
ndhH SSC 1182 0.4813 0.82 79.9 yes View details
ndhA SSC 2164 0.4654 0.90 80.8 yes View details
ndhI SSC 498 0.4885 0.88 79.4 yes View details
ndhI-ndhG SSC 352 0.4984 0.88 76.6 yes View details
ndhD SSC 1530 0.4641 0.90 82.1 yes View details
trnL-UAG-rpl32 SSC 799 0.4547 0.76 78.2 yes View details
rpl32-ndhF SSC 798 0.4382 0.85 80.8 yes View details
trnS-GCU-trnG-UCC LSC 816 0.0384 0.96 78.3 yes View details
ccsA SSC 969 0.4626 0.76 78.2 yes View details
ndhF SSC 2268 0.4527 0.80 78.1 yes View details
ndhE SSC 306 0.4653 0.94 77.3 yes View details
psaC-ndhD SSC 94 0.4651 0.91 76.4 yes View details
ccsA-trnL-UAG SSC 109 0.4082 0.90 76.0 yes View details
ycf1-rps15 SSC 385 0.4393 0.83 75.9 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA ACCGAAAGACCCTTTAACTGT 899–917 1.000 70.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACCGAAAGACCCTTTAACTGT 957–975 1.000 69.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGCTTTAATCCACTCAGCC ACCGAAAGACCCTTTAACTGT 896–914 1.000 68.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CGCTTTAATCCACTCAGCCA ACCGAAAGACCCTTTAACTGT 895–913 1.000 68.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TGGAAACGGAAAGAGAGGGA ACCGAAAGACCCTTTAACTGT 962–980 1.000 68.3
ycf1_p1 ycf1 CTCGACCAAAATCCCCCAAA ACATACTGAAACGACTGCCA 1110 0.500 52.7
ycf1_p2 ycf1 TCGACCAAAATCCCCCAAAG ACATACTGAAACGACTGCCA 1109 0.500 52.7
ycf1_p3 ycf1 AAAGAACCCACAAGCCAAGT ACATACTGAAACGACTGCCA 841 0.500 52.1
ycf1_p4 ycf1 GGGACGAGACTTTGAACCAA ACATACTGAAACGACTGCCA 666 0.500 51.3
ycf1_p5 ycf1 GACCAAAATCCCCCAAAGGA ACATACTGAAACGACTGCCA 1107 0.500 50.8
ycf1-rps15_p1 ycf1-rps15 GGGACGAGACTTTGAACCAA TCCCAACGCGTTACATAAGG 1680 0.500 57.9
ycf1-rps15_p2 ycf1-rps15 GGGACGAGACTTTGAACCAA AACACCATGCATTGATGGGT 1543 0.500 57.5
ycf1-rps15_p3 ycf1-rps15 GGGACGAGACTTTGAACCAA TGCATTGATGGGTGATGAGG 1536 0.500 57.5
ycf1-rps15_p4 ycf1-rps15 GGGACGAGACTTTGAACCAA GCATTGATGGGTGATGAGGT 1535 0.500 57.5
ycf1-rps15_p5 ycf1-rps15 GGGACGAGACTTTGAACCAA CCCAGAATTTTCCGCAAACC 1271 0.500 57.4
ndhH_p1 ndhH GGTTTGCGGAAAATTCTGGG TCACTGCTAAGGATGGACCA 1719 0.500 59.0
ndhH_p2 ndhH GGTTTGCGGAAAATTCTGGG TGCTAAGGATGGACCAATGC 1715 0.500 58.9
ndhH_p3 ndhH GGTTTGCGGAAAATTCTGGG AAGAATTCCCAAAGGCCCAG 1619 0.500 58.9
ndhH_p4 ndhH GGTTTGCGGAAAATTCTGGG GAAGAATTCCCAAAGGCCCA 1620 0.500 58.9
ndhH_p5 ndhH GGTTTGCGGAAAATTCTGGG TGAAGAATTCCCAAAGGCCC 1621 0.500 58.9
ndhA_p1 ndhA GGCAAAAAGAGGGGGATTCA TCAAAGTGTATTCGGCCTCG 2847 0.500 59.5
ndhA_p2 ndhA TGGCAAAAAGAGGGGGATTC TCAAAGTGTATTCGGCCTCG 2848 0.500 59.5
ndhA_p3 ndhA GGCAAAAAGAGGGGGATTCA GCGTGGGACAAGGTTATCAT 2766 0.500 59.2
ndhA_p4 ndhA TGGCAAAAAGAGGGGGATTC GCGTGGGACAAGGTTATCAT 2767 0.500 59.2
ndhA_p5 ndhA AGTCGAAGCACCAAAAGGAG TCAAAGTGTATTCGGCCTCG 2612 0.500 59.0
ndhI_p1 ndhI GGAGCCGTATGAGGTGAAAG AATCATGTATTGGTCCGGGC 1575 0.500 59.4
ndhI_p2 ndhI GGAGCCGTATGAGGTGAAAG ATAAGACCCGGTCCCAGAAA 1606 0.500 59.2
ndhI_p3 ndhI GGAGCCGTATGAGGTGAAAG CGCAGCAGCTACAAAATACG 1730 0.500 58.9
ndhI_p4 ndhI GGAGCCGTATGAGGTGAAAG ATGATCCCATACCAGGACGT 1918 0.500 58.7
ndhI_p5 ndhI GGTTCTGTAATAGCGACGGG AATCATGTATTGGTCCGGGC 1545 0.500 58.6

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
Adenosma bracteosa OR367324.1 154106 View on NCBI ↗
Adenosma glutinosa NC_072589.1 154220 View on NCBI ↗