Markers + reference

Alniphyllum

2 species · Styracaceae · Ericales

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Species 2
Genome length 155–155 kb
Candidate markers 282
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 282 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnR-UCU-trnG-GCC LSC 255 0.0588 1.00 79.7 yes View details
rbcL-accD LSC 1764 0.0288 0.83 75.5 yes View details
clpP LSC 1426 0.0218 1.00 57.0 yes View details
ycf1 IRb 1619 0.0179 1.00 54.4 no View details
ycf1-ndhF SSC 366 0.0847 1.00 75.9 yes View details
ycf1 SSC 5859 0.0219 0.97 57.6 yes View details
accD-psaI LSC 782 0.0053 0.97 63.6 yes View details
ycf3-trnS-GGA LSC 845 0.0059 1.00 62.2 yes View details
petA-psbJ LSC 1031 0.0049 1.00 61.9 yes View details
rpl20-rps12 LSC 775 0.0052 1.00 61.8 yes View details
rpl14-rpl16 LSC 124 0.0161 1.00 61.8 yes View details
ycf15-trnL-CAA IRb 369 0.0135 1.00 61.7 yes View details
trnL-CAA-ycf15 IRa 369 0.0135 1.00 61.7 yes View details
trnS-GCU-psbI LSC 140 0.0144 0.99 61.5 yes View details
psbT-psbN LSC 64 0.0156 1.00 61.5 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
trnR-UCU-trnG-GCC_p1 trnR-UCU-trnG-GCC AGAAGACCTCTGTCCTATCCA AGCCTTCCAAGCTAACGATG 335–337 1.000 66.9
trnR-UCU-trnG-GCC_p2 trnR-UCU-trnG-GCC AGAAGACCTCTGTCCTATCCA CCTAGCCTTCCAAGCTAACG 338–340 1.000 66.7
trnR-UCU-trnG-GCC_p3 trnR-UCU-trnG-GCC AGGTTTAGAAGACCTCTGTCCT AGCCTTCCAAGCTAACGATG 341–343 1.000 66.2
trnR-UCU-trnG-GCC_p4 trnR-UCU-trnG-GCC AGGTTTAGAAGACCTCTGTCCT CCTAGCCTTCCAAGCTAACG 344–346 1.000 65.9
trnR-UCU-trnG-GCC_p5 trnR-UCU-trnG-GCC AGAAGACCTCTGTCCTATCCA CCCTAGCCTTCCAAGCTAAC 339–341 1.000 64.4
trnG-GCC_p1 trnG-GCC CGAACCTCTTACGGTGGAAG AGGAAACGGAAAGAGAGGGA 2072–2138 1.000 83.0
trnG-GCC_p2 trnG-GCC CGAACCTCTTACGGTGGAAG ATTAGCAATCCGCCGCTTTA 2018–2084 1.000 82.9
trnG-GCC_p3 trnG-GCC CGCAGAAGCCCTTTTGAAAG AGGAAACGGAAAGAGAGGGA 1895–1961 1.000 82.9
trnG-GCC_p4 trnG-GCC CCAATCCGAACCTCTTACGG AGGAAACGGAAAGAGAGGGA 2078–2144 1.000 82.5
trnG-GCC_p5 trnG-GCC CCCAATCCGAACCTCTTACG AGGAAACGGAAAGAGAGGGA 2079–2145 1.000 82.5
trnS-GCU-psbI_p1 trnS-GCU-psbI TAAAGCGGCGGATTGCTAAT CGTAATCCTGGACGTGAAGA 231–232 1.000 73.3
trnS-GCU-psbI_p2 trnS-GCU-psbI TTTCAATTGGGGGAGATGGC CGTAATCCTGGACGTGAAGA 260–261 1.000 72.4
trnS-GCU-psbI_p3 trnS-GCU-psbI GGAGATGGCTGAGTGGACTA CGTAATCCTGGACGTGAAGA 249–250 1.000 71.7
trnS-GCU-psbI_p4 trnS-GCU-psbI TAAAGCGGCGGATTGCTAAT CGTAATCCTGGACGTGAAGAA 231–232 1.000 70.9
trnS-GCU-psbI_p5 trnS-GCU-psbI ATGGCTGAGTGGACTAAAGC CGTAATCCTGGACGTGAAGA 245–246 1.000 70.2
ycf3-trnS-GGA_p1 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA CCCTCGGTAAACAAAAGCCT 934 1.000 71.3
ycf3-trnS-GGA_p2 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA ACGGAAAGAGAGGGATTCGA 955 1.000 70.9
ycf3-trnS-GGA_p3 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA TTCCAATGCTACGCCTTGAA 905 1.000 70.6
ycf3-trnS-GGA_p4 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA ACCCTCGGTAAACAAAAGCC 935 1.000 69.0
ycf3-trnS-GGA_p5 ycf3-trnS-GGA TTTATCCGCGATCTAGGCAT CCCTCGGTAAACAAAAGCCT 932 1.000 68.3
rbcL-accD_p1 rbcL-accD AATGAGGGACGTGATCTTGC TACCAAAACTGGCTGTCACC 2018–2329 1.000 85.1
rbcL-accD_p2 rbcL-accD GAGGCTAGCAAATGGAGTCC TACCAAAACTGGCTGTCACC 1973–2284 1.000 85.1
rbcL-accD_p3 rbcL-accD GCTCTGACCGAGATCTTTGG TACCAAAACTGGCTGTCACC 2147–2458 1.000 84.7
rbcL-accD_p4 rbcL-accD GCTGCTTGTGAGGTATGGAA TACCAAAACTGGCTGTCACC 1943–2254 1.000 84.5
rbcL-accD_p5 rbcL-accD ACCGAGATCTTTGGGGATGA TACCAAAACTGGCTGTCACC 2141–2452 1.000 84.3
accD-psaI_p1 accD-psaI GAGTTATTTCAGCTCCACGC CCATTGCAATTGCCGGAAAT 887–906 1.000 73.6
accD-psaI_p2 accD-psaI GAGTTATTTCAGCTCCACGC AAGAAGCCATTGCAATTGCC 893–912 1.000 73.0
accD-psaI_p3 accD-psaI GAGTTATTTCAGCTCCACGC GCCGGAAATACTAGGCCTAC 876–895 1.000 70.2
accD-psaI_p4 accD-psaI CGCTTTCGTTCCTTTGAATCA CCATTGCAATTGCCGGAAAT 870–889 1.000 70.1
accD-psaI_p5 accD-psaI CGCTTTCGTTCCTTTGAATCA AAGAAGCCATTGCAATTGCC 876–895 1.000 69.5

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
Alniphyllum eberhardtii NC_031892.1 155384 View on NCBI ↗
Alniphyllum pterospermum NC_041126.1 155185 View on NCBI ↗