Markers + reference

Haloxylon

2 species · Amaranthaceae · Caryophyllales

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Species 2
Genome length 152–152 kb
Candidate markers 274
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpH-atpI LSC 688 0.0015 0.99 51.6 yes View details
rpoC2 LSC 4116 0.0007 1.00 54.3 yes View details
rpoB-trnC-GCA LSC 1116 0.0018 1.00 60.2 yes View details
petA-psbJ LSC 814 0.0098 1.00 64.4 yes View details
trnP-UGG-psaJ LSC 431 0.0070 1.00 46.1 yes View details
rps18 LSC 306 0.0033 1.00 54.2 yes View details
rpoA LSC 1011 0.0020 1.00 59.9 yes View details
rpl16 LSC 1319 0.0030 1.00 50.7 yes View details
trnK-UUU-rps16 LSC 690 0.0015 1.00 59.9 yes View details
rps3 LSC 657 0.0015 1.00 59.6 yes View details
atpI LSC 744 0.0013 1.00 59.5 yes View details
atpB-rbcL LSC 773 0.0013 1.00 59.5 yes View details
rpl20-rps12 LSC 766 0.0013 1.00 59.5 yes View details
rps16 LSC 1116 0.0009 1.00 59.3 yes View details
ndhF-rpl32 SSC 1104 0.0009 1.00 59.3 yes View details
psbM-trnD-GUC LSC 1154 0.0009 1.00 59.2 yes View details
psbC LSC 1422 0.0007 1.00 59.2 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU GCCCGTGTCAACCAATATCT TGCTTTTCGGTTCGGAATCA 2811–2812 1.000 78.9
trnK-UUU_p2 trnK-UUU CTATGCCCGTGTCAACCAAT TGCTTTTCGGTTCGGAATCA 2815–2816 1.000 77.2
trnK-UUU_p3 trnK-UUU TGCCCGTGTCAACCAATATC TGCTTTTCGGTTCGGAATCA 2812–2813 1.000 77.1
trnK-UUU_p4 trnK-UUU GCCCGTGTCAACCAATATCT GTTTGCTTTTCGGTTCGGAA 2814–2815 1.000 75.9
trnK-UUU_p5 trnK-UUU ATGCCCGTGTCAACCAATAT TGCTTTTCGGTTCGGAATCA 2813–2814 1.000 75.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TGCTCAACCTACCGAAACTG 780–782 1.000 77.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TGCTCAACCTACCGAAACTG 779–781 1.000 77.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GCTCAACCTACCGAAACTGT 779–781 1.000 77.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCTCAACCTACCGAAACTGT 778–780 1.000 77.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GTGCTCAACCTACCGAAACT 780–782 1.000 77.6
rps16_p1 rps16 ACAGGAATAGAAAGGGAAGA CTGTGTATTGACTGTCCCGG 1308 1.000 40.1
rps16_p2 rps16 TCTACAGGAATAGAAAGGGAAGA CTGTGTATTGACTGTCCCGG 1311 1.000 40.1
rps16_p3 rps16 ACAGGAATAGAAAGGGAAGAA CTGTGTATTGACTGTCCCGG 1308 1.000 40.1
rps16_p4 rps16 ACAGGAATAGAAAGGGAAGAAA CTGTGTATTGACTGTCCCGG 1308 1.000 40.1
rps16_p5 rps16 ACAGGAATAGAAAGGGAAGA CGGCGGAACCAATGACTATT 1291 1.000 40.1
trnG-GCC_p1 trnG-GCC CCGTGCAATTTCAGTGTTCG TCTGTATTCAACTCAATAATGCAGT 888 1.000 40.1
trnG-GCC_p2 trnG-GCC TCTTGTCTTGATTCCGTGCA TCTGTATTCAACTCAATAATGCAGT 901 1.000 40.1
trnG-GCC_p3 trnG-GCC CCGTGCAATTTCAGTGTTCG CTGTATTCAACTCAATAATGCAGT 887 1.000 40.1
trnG-GCC_p4 trnG-GCC CGTGCAATTTCAGTGTTCGA TCTGTATTCAACTCAATAATGCAGT 887 1.000 40.1
trnG-GCC_p5 trnG-GCC CCGTGCAATTTCAGTGTTCG TTCTGTATTCAACTCAATAATGCAGT 889 1.000 40.1
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA TTTTGCAACTTTAGCCGCAG 768–773 1.000 78.7
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT TTTTGCAACTTTAGCCGCAG 826–831 1.000 78.6
atpH-atpI_p3 atpH-atpI AACGGAAGCAGCAGAAATCA CGAATCCATGGAGGGTCATC 738–743 1.000 78.4
atpH-atpI_p4 atpH-atpI AGCCAATCCAGCAGCAATAA TTTTGCAACTTTAGCCGCAG 786–791 1.000 78.4
atpH-atpI_p5 atpH-atpI TACCTTGACCAACTCCAGGT CGAATCCATGGAGGGTCATC 796–801 1.000 78.3
atpI_p1 atpI GAGTATCTTGAGCCACACAT AGGTCGAGGAAGAGATGGTT 876 1.000 53.1
atpI_p2 atpI GAGTATCTTGAGCCACACAT GGTCGAGGAAGAGATGGTTG 875 1.000 52.6
atpI_p3 atpI TGAGCCACACATATATTACCTGG AGGTCGAGGAAGAGATGGTT 868 1.000 52.4
atpI_p4 atpI TGAGCCACACATATATTACCTGG GGTCGAGGAAGAGATGGTTG 867 1.000 51.9
atpI_p5 atpI GAGTATCTTGAGCCACACAT CAGGTCGAGGAAGAGATGGT 877 1.000 50.8

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
Haloxylon ammodendron NC_027668.1 151570 View on NCBI ↗
Haloxylon persicum NC_027669.1 151586 View on NCBI ↗