Markers + reference

Annona

4 species · Annonaceae · Magnoliales

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Species 4
Genome length 195–203 kb
Candidate markers 326
Primer pairs 65

Genome-wide nucleotide diversity

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

Candidate markers

4 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 326 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnL-CAA-ycf2 IRb 1047 0.2978 0.82 78.4 yes View details
ycf2 IRb 7497 0.2520 0.82 72.4 yes View details
ycf2 IRa 7497 0.2543 0.83 72.7 yes View details
ycf2-trnL-CAA IRa 1047 0.2956 0.81 78.3 yes View details
trnN-GUU-ycf1 IRb 559 0.0869 0.99 83.9 yes View details
ycf1-trnN-GUU IRa 559 0.0888 0.97 83.6 yes View details
rps18 LSC 753 0.0603 0.92 82.6 yes View details
psbE-petL LSC 1076 0.0470 0.90 76.0 yes View details
accD LSC 2427 0.0664 0.76 75.6 yes View details
rpoA IRb 1017 0.0852 1.00 69.4 yes View details
rpoA IRa 1017 0.0852 1.00 69.4 yes View details
ndhF-rpl32 SSC 500 0.0720 0.99 68.9 yes View details
rpl36-infA IRb 145 0.0644 0.94 68.3 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 65 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
accD_p1 accD CCATTGCAATTGCCGGAAAT GAAAACGGGGAGTGATCACA 2239–2790 1.000 90.4
accD_p2 accD AAGAAGCCATTGCAATTGCC GAAAACGGGGAGTGATCACA 2245–2796 1.000 89.7
accD_p3 accD CCATTGCAATTGCCGGAAAT ACGACTCCATCTACGACAGA 2276–2827 1.000 88.6
accD_p4 accD CCATTGCAATTGCCGGAAAT AAACGGGGAGTGATCACATC 2237–2788 1.000 88.6
accD_p5 accD TATAGGGACCCGCATGCATA GAAAACGGGGAGTGATCACA 2853–2984 0.500 67.6
psbE-petL_p1 psbE-petL CAACCCGCAATGAATAGGGA TAGTTGAAGCAGCCAGGAGA 1118–1229 1.000 86.7
psbE-petL_p2 psbE-petL CAACCCGCAATGAATAGGGA TTGAAGCAGCCAGGAGAAAA 1115–1226 1.000 86.7
psbE-petL_p3 psbE-petL CAACCCGCAATGAATAGGGA TGAAGCAGCCAGGAGAAAAC 1114–1225 1.000 86.5
psbE-petL_p4 psbE-petL CAACCCGCAATGAATAGGGA GTTGAAGCAGCCAGGAGAAA 1116–1227 1.000 86.4
psbE-petL_p5 psbE-petL CAACCCGCAATGAATAGGGA CAGCCAGGAGAAAACCGAAA 1109–1220 1.000 86.4
rps18_p1 rps18 GGTTCATGGCCAAGGGTAAA CGTTTGTGGATCACTCGGAT 1453–1736 1.000 88.5
rps18_p2 rps18 TAAGCGGATTTCGGGTTAGC CGTTTGTGGATCACTCGGAT 1552–1835 1.000 88.3
rps18_p3 rps18 AACTTCAGCGAAACTCGTGT CGTTTGTGGATCACTCGGAT 1764–2047 1.000 87.9
rps18_p4 rps18 ACTTCAGCGAAACTCGTGTT CGTTTGTGGATCACTCGGAT 1763–2046 1.000 87.9
rps18_p5 rps18 TTCAGCGAAACTCGTGTTCA CGTTTGTGGATCACTCGGAT 1761–2044 1.000 87.9
rpoA_p1 rpoA GTAGGCCTAGCGGTTCTAGA ATGCTATTCATCTAGCCGCG 1868–1955 1.000 91.8
rpoA_p2 rpoA GTAGGCCTAGCGGTTCTAGA GGAGCGAATCTCAAGCAGAA 1654–1741 1.000 91.7
rpoA_p3 rpoA GTAGGCCTAGCGGTTCTAGA GGGCGTAGAATACCCAAAGG 2037–2124 1.000 91.5
rpoA_p4 rpoA CTCGAGCCGGATGATGAAAA ATGCTATTCATCTAGCCGCG 2089–2176 1.000 91.5
rpoA_p5 rpoA ATCGGTACTGCAGTAGCTCT ATGCTATTCATCTAGCCGCG 1619–1706 1.000 91.5
rpl36-infA_p1 rpl36-infA TTCTGCTTGAGATTCGCTCC AGAGGGGGCGTATAACCTAC 963–965 0.500 66.1
rpl36-infA_p2 rpl36-infA TTCTTCCTGCGGAGAATTCG TGATATCCGACCGAATGGGA 720 0.250 49.9
rpl36-infA_p3 rpl36-infA TTCTTCCTGCGGAGAATTCG AGAGGGGGCGTATAACCTAC 329 0.250 49.9
rpl36-infA_p4 rpl36-infA TTCTGCTTGAGATTCGCTCC TGATATCCGACCGAATGGGA 1354 0.250 49.8
rpl36-infA_p5 rpl36-infA TTCTTCCTGCGGAGAATTCG TGAATCGCTTCGAAACGCTA 481 0.250 49.8
trnL-CAA-ycf2_p1 trnL-CAA-ycf2 AAATGGTAGACACGCGAGAC TCGTTGATTTCTCGCCAGAG 1358–1359 1.000 91.9
trnL-CAA-ycf2_p2 trnL-CAA-ycf2 TGAAATGGTAGACACGCGAG TCGTTGATTTCTCGCCAGAG 1360–1361 1.000 91.9
trnL-CAA-ycf2_p3 trnL-CAA-ycf2 AAATGGTAGACACGCGAGAC CGTCGAGAACTCTTTGCAGA 1679–1710 1.000 91.5
trnL-CAA-ycf2_p4 trnL-CAA-ycf2 TGAAATGGTAGACACGCGAG CGTCGAGAACTCTTTGCAGA 1681–1712 1.000 91.5
trnL-CAA-ycf2_p5 trnL-CAA-ycf2 AAATGGTAGACACGCGAGAC CTGCGCTCCTTTTCTTTTGG 1831–1862 1.000 91.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Annona montana NC_066643.1 195495 View on NCBI ↗
Annona mucosa NC_070222.1 201666 View on NCBI ↗
Annona squamosa NC_070223.1 200335 View on NCBI ↗
Annona x atemoya NC_070224.1 202703 View on NCBI ↗