Markers + reference

Forsskaolea

2 species · Urticaceae · Rosales

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Species 2
Genome length 156–157 kb
Candidate markers 263
Primer pairs 75

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 7 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhD SSC 1530 0.4633 0.80 80.8 yes View details
psaC SSC 246 0.4925 0.81 73.4 yes View details
psaC-ndhE SSC 275 0.4809 0.95 78.0 yes View details
ndhA SSC 2275 0.4831 0.80 77.9 yes View details
ndhH SSC 1182 0.4781 0.83 80.3 yes View details
rps15 SSC 273 0.4911 0.82 73.7 yes View details
rps15-ycf1 SSC 439 0.4545 0.90 78.9 yes View details
ycf1 SSC 5691 0.3417 0.86 74.7 yes View details
ndhF-rpl32 SSC 1272 0.4288 0.89 82.1 yes View details
ndhI SSC 576 0.4535 0.88 81.2 yes View details
rpl32-trnL-UAG SSC 1037 0.4307 0.98 80.7 yes View details
ndhF SSC 2271 0.4347 0.87 79.8 yes View details
ndhG SSC 531 0.4417 0.84 79.1 yes View details
ccsA SSC 966 0.4290 0.73 77.8 yes View details
ndhE-ndhG SSC 228 0.4819 0.85 74.7 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
ndhF_p1 ndhF GAGGATCCGGACAAAATCGA GTGCCATAGTTTGACGACCA 2979 0.500 53.7
ndhF_p2 ndhF GAGGATCCGGACAAAATCGA AAAGTGAAGTCTTGGGTGCC 2994 0.500 52.8
ndhF_p3 ndhF GAGGATCCGGACAAAATCGA TTGGGTGCCATAGTTTGACG 2983 0.500 51.5
ndhF_p4 ndhF GAGGATCCGGACAAAATCGA GTGAAGTCTTGGGTGCCATA 2991 0.500 51.3
ndhF_p5 ndhF GAGGATCCGGACAAAATCGAT GTGCCATAGTTTGACGACCA 2979 0.500 49.5
ndhF-rpl32_p1 ndhF-rpl32 GGCGAAGATCTTTTGTTGCC GCAGCCCAATACCCTTTCTT 1467 0.500 58.7
ndhF-rpl32_p2 ndhF-rpl32 GGCGAAGATCTTTTGTTGCC AAAAGCTTTCAATGCAGCCC 1480 0.500 58.5
ndhF-rpl32_p3 ndhF-rpl32 CTCCGATGCGATTGGTTACA GCAGCCCAATACCCTTTCTT 1911 0.500 58.3
ndhF-rpl32_p4 ndhF-rpl32 GATTTTGCAATCGGACCTGC GCAGCCCAATACCCTTTCTT 2077 0.500 58.1
ndhF-rpl32_p5 ndhF-rpl32 GGCGAAGATCTTTTGTTGCC ATGCAGCCCAATACCCTTTC 1469 0.500 58.1
rpl32-trnL-UAG_p1 rpl32-trnL-UAG AAGAAAGGGTATTGGGCTGC AGCGTGTCTACCGATTTCAC 1162 0.500 58.8
rpl32-trnL-UAG_p2 rpl32-trnL-UAG AAGAAAGGGTATTGGGCTGC CAGCGTGTCTACCGATTTCA 1163 0.500 58.7
rpl32-trnL-UAG_p3 rpl32-trnL-UAG GGGCTGCATTGAAAGCTTTT AGCGTGTCTACCGATTTCAC 1149 0.500 58.5
rpl32-trnL-UAG_p4 rpl32-trnL-UAG GGGCTGCATTGAAAGCTTTT CAGCGTGTCTACCGATTTCA 1150 0.500 58.5
rpl32-trnL-UAG_p5 rpl32-trnL-UAG GAAAGGGTATTGGGCTGCAT AGCGTGTCTACCGATTTCAC 1160 0.500 58.2
ccsA_p1 ccsA GTGAAATCGGTAGACACGCT GCGGAATGGCTATCACACTT 1814 0.500 57.3
ccsA_p2 ccsA TGAAATCGGTAGACACGCTG GCGGAATGGCTATCACACTT 1813 0.500 57.3
ccsA_p3 ccsA GTGAAATCGGTAGACACGCT TCAAGCGAGAACCCTTTGTT 1251 0.500 57.2
ccsA_p4 ccsA TGAAATCGGTAGACACGCTG TCAAGCGAGAACCCTTTGTT 1250 0.500 57.2
ccsA_p5 ccsA GTGAAATCGGTAGACACGCT ATGGCCTCTCTTGCATTACC 1761 0.500 57.1
ndhD_p1 ndhD GCTAATGAAGCCTGGGGATC TCTGCTCCAAGAACAGAGGA 2291 0.500 59.1
ndhD_p2 ndhD GCTAATGAAGCCTGGGGATC GGGACGGGTGTAAAGCTAAG 2320 0.500 59.1
ndhD_p3 ndhD GCTAATGAAGCCTGGGGATC AAGATGTGAATCCGCCTGTC 2256 0.500 59.0
ndhD_p4 ndhD GAAGCCTGGGGATCGTATTG TCTGCTCCAAGAACAGAGGA 2285 0.500 59.0
ndhD_p5 ndhD GAAGCCTGGGGATCGTATTG GGGACGGGTGTAAAGCTAAG 2314 0.500 58.9
psaC_p1 psaC TCTTTCCTCCCCACATGGAT CCAATTCAATGCGTTGCCTT 1506 0.500 59.2
psaC_p2 psaC AACGTTTCTTTCCTCCCCAC CCAATTCAATGCGTTGCCTT 1512 0.500 59.2
psaC_p3 psaC TCTTTCCTCCCCACATGGAT GCGGATCCCTAAGTGGATTG 995 0.500 59.0
psaC_p4 psaC AACGTTTCTTTCCTCCCCAC GCGGATCCCTAAGTGGATTG 1001 0.500 58.9
psaC_p5 psaC TCTTTCCTCCCCACATGGAT AATGCGTTGCCTTGTTGTTC 1499 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
Forsskaolea angustifolia NC_062309.1 156714 View on NCBI ↗
Forsskaolea tenacissima PX851741.1 156071 View on NCBI ↗