Markers + reference

Dryas

5 species · Rosaceae · Rosales

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Species 5
Genome length 158–158 kb
Candidate markers 287
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 9 remaining regions by MarkerSeek score (out of 287 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0004 1.00 36.2 yes View details
trnR-UCU-atpA LSC 493 0.0039 1.00 64.4 yes View details
trnD-GUC-trnY-GUA LSC 458 0.0000 1.00 37.0 yes View details
trnE-UUC-trnT-GGU LSC 506 0.0036 1.00 52.8 yes View details
trnT-GGU-psbD LSC 1429 0.0021 0.98 65.3 yes View details
trnT-UGU-trnL-UAA LSC 1263 0.0039 1.00 62.3 yes View details
ndhC-trnV-UAC LSC 583 0.0027 1.00 53.0 yes View details
ndhF SSC 2256 0.0012 1.00 43.5 yes View details
ndhF-rpl32 SSC 932 0.0067 1.00 50.7 yes View details
trnK-UUU-rps16 LSC 989 0.0012 1.00 61.1 yes View details
rpoB-trnC-GCA LSC 1231 0.0007 1.00 60.8 yes View details
rps16 LSC 1156 0.0016 1.00 60.1 yes View details
petA-psbJ LSC 874 0.0009 1.00 60.0 yes View details
psbE-petL LSC 1295 0.0009 1.00 60.0 yes View details
rpl20-rps12 LSC 788 0.0013 1.00 59.9 yes View details
ndhA SSC 2279 0.0008 1.00 57.8 yes View details
psaJ-rpl33 LSC 487 0.0008 1.00 57.0 yes View details
trnF-GAA-ndhJ LSC 808 0.0010 0.99 56.9 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA AGGAGCAATACCAAACCTCT AGAATTCGTGTGCTTGGGAG 1208 1.000 63.5
psbA_p2 psbA AGGAGCAATACCAAACCTCT AGAGAATTCGTGTGCTTGGG 1210 1.000 63.5
psbA_p3 psbA AGGAGCAATACCAAACCTCT GAGAATTCGTGTGCTTGGGA 1209 1.000 63.5
psbA_p4 psbA AGGAGCAATACCAAACCTCTT AGAATTCGTGTGCTTGGGAG 1208 1.000 61.8
psbA_p5 psbA AGGAGCAATACCAAACCTCTT AGAGAATTCGTGTGCTTGGG 1210 1.000 61.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAAGGCGCTCAACCTACA 1111–1122 1.000 79.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGCGCTCAACCTACA 1110–1121 1.000 79.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTTTTACGGAGCTTCGCCTT 1057–1068 1.000 78.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTTTTACGGAGCTTCGCCTT 1056–1067 1.000 78.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAAAAGGCGCTCAACCTACA 1120–1131 1.000 78.6
rps16_p1 rps16 ACAAGTCATTCACACCCTCT ACTGGTTCCAAACTGAAGGA 1213–1215 1.000 56.0
rps16_p2 rps16 ACAAGTCATTCACACCCTCT TGTACTGACCGAACCAATGA 1266–1268 1.000 55.3
rps16_p3 rps16 ACAAGTCATTCACACCCTCTT ACTGGTTCCAAACTGAAGGA 1213–1215 1.000 54.1
rps16_p4 rps16 ACAAGTCATTCACACCCTCT ACTGGTTCCAAACTGAAGGAA 1213–1215 1.000 54.1
rps16_p5 rps16 ACAAGTCATTCACACCCTCTT TGTACTGACCGAACCAATGA 1266–1268 1.000 53.4
trnR-UCU-atpA_p1 trnR-UCU-atpA TGGAATGAAAAGCGTCCATTG GAGGAAGCAGAAGCCCTTTT 595–661 1.000 71.2
trnR-UCU-atpA_p2 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT GAGGAAGCAGAAGCCCTTTT 594–660 1.000 71.2
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GAGGAAGCAGAAGCCCTTTT 534–600 1.000 70.3
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGAATGAAAAGCGTCCATTG AGGAAGCAGAAGCCCTTTTG 594–660 1.000 68.9
trnR-UCU-atpA_p5 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT AGGAAGCAGAAGCCCTTTTG 593–659 1.000 68.9
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TCATTTTCACCCCCAAGCAT CCGGATTTGAACTGGGGAAA 1313–1337 1.000 77.9
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CTCATTTTCACCCCCAAGCA CCGGATTTGAACTGGGGAAA 1314–1338 1.000 77.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ATTGCCTCATTTTCACCCCC CCGGATTTGAACTGGGGAAA 1319–1343 1.000 77.1
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TCATTTTCACCCCCAAGCAT TCTTTTGGTGATCAGGCGAC 1335–1359 1.000 77.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CTCATTTTCACCCCCAAGCA TCTTTTGGTGATCAGGCGAC 1336–1360 1.000 76.6
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TGGCAATATGTCTACGCTGG 529–530 1.000 74.3
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGCAATATGTCTACGCTGGT 528–529 1.000 74.3
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGGACGGACTGTAAATTCG 550–551 1.000 73.4
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGACGGACTGTAAATTCGT 549–550 1.000 73.2
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GATTCTTCCTGGGTCGATGC 583–584 1.000 72.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Dryas alaskensis NC_088483.1 158285 View on NCBI ↗
Dryas drummondii NC_088514.1 158320 View on NCBI ↗
Dryas integrifolia PP497090.1 158369 View on NCBI ↗
Dryas octopetala PQ869155.1 158238 View on NCBI ↗
Dryas octopetala var. asiatica NC_073102.1 158271 View on NCBI ↗