Markers + reference

Oreosalsola

2 species · Amaranthaceae · Caryophyllales

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Species 2
Genome length 152–152 kb
Candidate markers 272
Primer pairs 110

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 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 722 0.0250 1.00 73.4 yes View details
trnS-GCU-trnG-GCC LSC 857 0.0129 1.00 58.2 yes View details
atpA LSC 1524 0.0052 1.00 48.0 yes View details
atpF LSC 1333 0.0098 1.00 50.6 yes View details
atpH-atpI LSC 710 0.0191 0.96 58.5 yes View details
psaA-ycf3 LSC 763 0.0144 1.00 56.1 yes View details
psbE-petL LSC 1238 0.0138 1.00 65.0 yes View details
rps18 LSC 306 0.0163 1.00 47.2 yes View details
trnN-GUU-ndhF IRb 1497 0.0323 0.97 78.6 yes View details
ndhF-rpl32 SSC 1107 0.0127 1.00 56.8 yes View details
ndhI SSC 513 0.0156 1.00 52.0 yes View details
ycf1 SSC 5421 0.0096 1.00 58.1 yes View details
trnG-GCC-trnR-UCU LSC 125 0.0800 1.00 80.7 yes View details
rpoC1-rpoB LSC 26 0.0385 1.00 74.6 yes View details
trnG-UCC-trnfM-CAU LSC 206 0.0343 0.99 73.1 yes View details
rps18-rpl20 LSC 233 0.0300 1.00 69.8 yes View details
atpB-rbcL LSC 765 0.0132 0.99 67.2 yes View details
atpF-atpH LSC 423 0.0146 0.97 65.9 yes View details
psaC-ndhE SSC 344 0.0203 1.00 65.1 yes View details
psaI-ycf4 LSC 351 0.0199 1.00 65.0 yes View details
rpoB-trnC-GCA LSC 1116 0.0064 0.97 64.9 yes View details
psbA-trnK-UUU LSC 225 0.0140 0.96 64.8 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
psbA-trnK-UUU_p1 psbA-trnK-UUU ACGGTTTTCAGTGCTGGTTA GAAAGCCGTGTGCAATGAAA 414–424 1.000 78.7
psbA-trnK-UUU_p2 psbA-trnK-UUU ACGGTTTTCAGTGCTGGTTA CGGTTTGGGGAGAGGTTTTT 384–394 1.000 77.6
psbA-trnK-UUU_p3 psbA-trnK-UUU TACAGAAGCGACCCCATAGG GAAAGCCGTGTGCAATGAAA 388–398 1.000 76.9
psbA-trnK-UUU_p4 psbA-trnK-UUU ACGGTTTTCAGTGCTGGTTA AAAATGCAAGCACGGTTTGG 396–406 1.000 76.6
psbA-trnK-UUU_p5 psbA-trnK-UUU ATCCAGTTACAGAAGCGACC GAAAGCCGTGTGCAATGAAA 395–405 1.000 76.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TGCTCAACCTACCGAAACTG 812–814 1.000 79.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TGCTCAACCTACCGAAACTG 811–813 1.000 79.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GCTCAACCTACCGAAACTGT 811–813 1.000 79.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCTCAACCTACCGAAACTGT 810–812 1.000 79.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GTGCTCAACCTACCGAAACT 812–814 1.000 79.3
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA CGGAATAGTAATCAAACCGGGA 1031–1036 1.000 63.2
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA TCGGAATAGTAATCAAACCGGG 1032–1037 1.000 63.2
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CGAATGACTCGTACAACGGA CGGAATAGTAATCAAACCGGGA 1001–1006 1.000 62.4
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CGAATGACTCGTACAACGGA TCGGAATAGTAATCAAACCGGG 1002–1007 1.000 62.4
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA CGGAATAGTAATCAAACCGGG 1031–1036 1.000 59.7
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG TGGAAATAAATTGCGTCCAATAGG 262 1.000 49.7
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG TGGAAATAAATTGCGTCCAATAGG 265 1.000 49.4
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG TGGAAATAAATTGCGTCCAA 262 1.000 48.9
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG TGGAAATAAATTGCGTCCAA 265 1.000 48.6
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTATGTCCT 221 1.000 48.4
atpA_p1 atpA AGCCTTCCAAGCTAACGATG GTAATTGAGCGTGAGAGCCA 2438–2440 1.000 80.4
atpA_p2 atpA AGCCTTCCAAGCTAACGATG TCAAGTTTGGTTCGGGAAGG 2403–2405 1.000 80.3
atpA_p3 atpA CCTAGCCTTCCAAGCTAACG GTAATTGAGCGTGAGAGCCA 2441–2443 1.000 80.2
atpA_p4 atpA AGCCTTCCAAGCTAACGATG GAAGAACTTCGCGGAAAAGC 2282–2284 1.000 80.2
atpA_p5 atpA CCTAGCCTTCCAAGCTAACG TCAAGTTTGGTTCGGGAAGG 2406–2408 1.000 80.1
atpF_p1 atpF CACGCCCCAAATAAGACTCA CCCCGGGAAGGACTTATTTG 2019–2020 1.000 80.0
atpF_p2 atpF ACACGCCCCAAATAAGACTC CCCCGGGAAGGACTTATTTG 2020–2021 1.000 80.0
atpF_p3 atpF ACGCCCCAAATAAGACTCAC CCCCGGGAAGGACTTATTTG 2018–2019 1.000 80.0
atpF_p4 atpF CACGCCCCAAATAAGACTCA TCCCATGAAACCCAGTACCT 1909 0.500 58.7
atpF_p5 atpF ACGCCCCAAATAAGACTCAC TCCCATGAAACCCAGTACCT 1908 0.500 58.7

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
Oreosalsola arbusculiformis ON929860.1 152166 View on NCBI ↗
Oreosalsola laricifolia ON929862.1 152078 View on NCBI ↗