Markers + reference

Itea

2 species · Iteaceae · Saxifragales

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Species 2
Genome length 160–161 kb
Candidate markers 273
Primer pairs 85

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 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 IRb 1236 0.0008 1.00 48.3 no View details
ndhF SSC 2214 0.4636 0.91 81.3 yes View details
ndhF-rpl32 SSC 904 0.4620 0.86 81.0 yes View details
ccsA SSC 972 0.4473 0.87 81.5 yes View details
ndhD SSC 1503 0.4812 0.85 80.7 yes View details
psaC SSC 246 0.5370 0.88 75.3 yes View details
ndhA SSC 2209 0.4610 0.81 78.1 yes View details
ndhH SSC 1182 0.4924 0.89 82.0 yes View details
ycf1 SSC 5625 0.3390 0.80 73.1 yes View details
rpl32-trnL-UAG SSC 878 0.4456 0.88 81.6 yes View details
ndhG SSC 531 0.4529 0.84 79.1 yes View details
rps15-ycf1 SSC 396 0.4509 0.87 77.2 yes View details
trnL-UAG-ccsA SSC 89 0.4118 0.96 76.9 yes View details
ndhH-rps15 SSC 107 0.4100 0.93 76.9 yes View details
ndhD-psaC SSC 117 0.4907 0.92 76.7 yes View details
ndhI SSC 501 0.4430 0.77 76.6 yes View details
psbC-trnS-UGA LSC 222 0.0450 1.00 76.2 yes View details
rpl32 SSC 159 0.3768 0.87 75.2 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbC-trnS-UGA_p1 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GAGAGATGGCTGAGTGGTTG 343–345 1.000 80.9
psbC-trnS-UGA_p2 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GTCTTTCGGAGAGATGGCTG 351–353 1.000 80.5
psbC-trnS-UGA_p3 psbC-trnS-UGA TCGTAGGTCATTTGTGGCAC GAGAGATGGCTGAGTGGTTG 423–425 1.000 80.1
psbC-trnS-UGA_p4 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC TCTTTCGGAGAGATGGCTGA 350–352 1.000 79.8
psbC-trnS-UGA_p5 psbC-trnS-UGA TCGTAGGTCATTTGTGGCAC GTCTTTCGGAGAGATGGCTG 431–433 1.000 79.7
ndhF_p1 ndhF GCAGAATACCGTCACCCATT AGTATTTTGGAAAGACGCCGA 2917 0.500 51.3
ndhF_p2 ndhF AAGAGGGATCCACCGAAGAA AGTATTTTGGAAAGACGCCGA 2785 0.500 51.2
ndhF_p3 ndhF AGAGGGATCCACCGAAGAAT AGTATTTTGGAAAGACGCCGA 2784 0.500 50.2
ndhF_p4 ndhF TCCGAAACGAAGGGGACTAA AGTATTTTGGAAAGACGCCGA 2813 0.500 48.7
ndhF_p5 ndhF TTCCGAAACGAAGGGGACTA AGTATTTTGGAAAGACGCCGA 2814 0.500 48.7
ndhF-rpl32_p1 ndhF-rpl32 TGTTACCGCCGGAAAAAGAA TGCTGCCCAATATCCCTTTC 1087 0.500 59.1
ndhF-rpl32_p2 ndhF-rpl32 TTGTTACCGCCGGAAAAAGA TGCTGCCCAATATCCCTTTC 1088 0.500 59.1
ndhF-rpl32_p3 ndhF-rpl32 GCCCACATACGACGAAGATT TGCTGCCCAATATCCCTTTC 1110 0.500 58.9
ndhF-rpl32_p4 ndhF-rpl32 ACGAATGGGATGATCCATGC TGCTGCCCAATATCCCTTTC 1029 0.500 58.6
ndhF-rpl32_p5 ndhF-rpl32 CGAATGGGATGATCCATGCA TGCTGCCCAATATCCCTTTC 1028 0.500 58.6
rpl32_p1 rpl32 GCTCACCTGCAACCAATCTT GAATCCCCACCCCTGAAATG 824 0.500 52.3
rpl32_p2 rpl32 GCTCACCTGCAACCAATCTT TCCCCACCCCTGAAATGATA 821 0.500 51.6
rpl32_p3 rpl32 GCTCACCTGCAACCAATCTT AGAATCCCCACCCCTGAAAT 825 0.500 51.6
rpl32_p4 rpl32 GCTCACCTGCAACCAATCTT TAAGAATCCCCACCCCTGAA 827 0.500 51.1
rpl32_p5 rpl32 GCTCACCTGCAACCAATCTT ATCCCCACCCCTGAAATGAT 822 0.500 51.0
rpl32-trnL-UAG_p1 rpl32-trnL-UAG GAAAGGGATATTGGGCAGCA AGCGTGTCTACCGATTTCAC 1002 0.500 59.4
rpl32-trnL-UAG_p2 rpl32-trnL-UAG GAAAGGGATATTGGGCAGCA CAGCGTGTCTACCGATTTCA 1003 0.500 59.4
rpl32-trnL-UAG_p3 rpl32-trnL-UAG GAAAGGGATATTGGGCAGCA TTAGAAGATTCCATGCCGCC 1066 0.500 59.2
rpl32-trnL-UAG_p4 rpl32-trnL-UAG GAAAGGGATATTGGGCAGCA AGCAAAGCCCTGGGTAAAAA 1481 0.500 58.7
rpl32-trnL-UAG_p5 rpl32-trnL-UAG GAAAGGGATATTGGGCAGCA TCCTAAGAGCAGCGTGTCTA 1012 0.500 58.4
trnL-UAG-ccsA_p1 trnL-UAG-ccsA GTGAAATCGGTAGACACGCT AGCAAAGCCCTGGGTAAAAA 499 0.500 59.2
trnL-UAG-ccsA_p2 trnL-UAG-ccsA TGAAATCGGTAGACACGCTG AGCAAAGCCCTGGGTAAAAA 498 0.500 59.2
trnL-UAG-ccsA_p3 trnL-UAG-ccsA GTGAAATCGGTAGACACGCT CATTAGCCCATACTGCTCCC 902 0.500 58.4
trnL-UAG-ccsA_p4 trnL-UAG-ccsA TGAAATCGGTAGACACGCTG CATTAGCCCATACTGCTCCC 901 0.500 58.4
trnL-UAG-ccsA_p5 trnL-UAG-ccsA GTGAAATCGGTAGACACGCT GTAGCAAAGCCCTGGGTAAA 501 0.500 58.3

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
Itea chinensis NC_037884.1 160258 View on NCBI ↗
Itea omeiensis PP861179.1 160737 View on NCBI ↗