Markers + reference

Aucuba

10 species · Garryaceae · Garryales

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Species 10
Genome length 158–158 kb
Candidate markers 269
Primer pairs 90

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 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1132 0.0105 1.00 40.4 yes View details
rps16-trnQ-UUG LSC 1752 0.0085 1.00 53.9 yes View details
trnC-GCA-petN LSC 700 0.0148 1.00 50.9 yes View details
accD-psaI LSC 695 0.0106 1.00 42.1 yes View details
ycf4-cemA LSC 341 0.0157 1.00 42.2 yes View details
ccsA SSC 966 0.0076 1.00 49.1 yes View details
ccsA-ndhD SSC 235 0.0273 1.00 43.2 yes View details
ndhA SSC 2205 0.0053 1.00 37.8 yes View details
ycf1 SSC 5676 0.0076 1.00 39.7 yes View details
psaA-ycf3 LSC 855 0.0049 0.93 56.8 yes View details
ycf3-trnS-GGA LSC 853 0.0075 1.00 56.2 yes View details
trnT-GGU-psbD LSC 1373 0.0062 1.00 55.3 yes View details
ndhC-trnV-UAC LSC 1055 0.0045 0.99 51.8 yes View details
rpoC2 LSC 4173 0.0027 1.00 51.2 yes View details
psbE-petL LSC 1208 0.0061 1.00 51.1 yes View details
psbM-trnD-GUC LSC 1183 0.0101 1.00 50.8 yes View details
rpoB LSC 3213 0.0032 1.00 50.2 yes View details
trnE-UUC-trnT-GGU LSC 870 0.0050 0.97 49.0 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16_p1 rps16 ACTTGTGTTGGATTGGCACT GCAGATTCCCAAAGAGCTCA 1826–1864 1.000 80.6
rps16_p2 rps16 ACTTGTGTTGGATTGGCACT TGCAGATTCCCAAAGAGCTC 1827–1865 1.000 80.6
rps16_p3 rps16 TCCAACGAAAACCACCCAAT GCAGATTCCCAAAGAGCTCA 1659–1697 1.000 80.6
rps16_p4 rps16 TCCAACGAAAACCACCCAAT TGCAGATTCCCAAAGAGCTC 1660–1698 1.000 80.6
rps16_p5 rps16 TTCCAACGAAAACCACCCAA GCAGATTCCCAAAGAGCTCA 1660–1698 1.000 80.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1708–1884 1.000 84.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1691–1867 1.000 84.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1709–1885 1.000 83.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1706–1882 1.000 82.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1705–1881 1.000 82.2
rpoC2_p1 rpoC2 TAAAGTGGATGTTCCCGCAC TATTCACAGGGGGTACTGCA 263 1.000 79.7
rpoC2_p2 rpoC2 TAAAGTGGATGTTCCCGCAC ATTGGAGAACCGGGTACTCA 315 1.000 79.4
rpoC2_p3 rpoC2 TAAAGTGGATGTTCCCGCAC TGGAGAACCGGGTACTCAAT 313 1.000 79.4
rpoC2_p4 rpoC2 TAAAGTGGATGTTCCCGCAC ACTGCAGAACATGTGAGAGC 249 1.000 78.6
rpoC2_p5 rpoC2 TAAAGTGGATGTTCCCGCAC CGGAGTATTCACAGGGGGTA 268 1.000 78.3
rpoB_p1 rpoB CTGCTAACCCGAGTGAACAT CCTATAGGTGGTAGGGGTCG 292 1.000 77.4
rpoB_p2 rpoB CTGCTAACCCGAGTGAACAT CTATAGGTGGTAGGGGTCGG 291 1.000 77.4
rpoB_p3 rpoB CTGCTAACCCGAGTGAACAT GGGGTCGGGTTATTGATGTG 279 1.000 75.5
rpoB_p4 rpoB CTGCTAACCCGAGTGAACAT AGGGGTCGGGTTATTGATGT 280 1.000 74.8
rpoB_p5 rpoB CTGCTAACCCGAGTGAACAT GGTAGGGGTCGGGTTATTGA 283 1.000 74.0
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ACTTCTTCCCCACACTACGA 810–940 1.000 81.4
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTCTTCCCCACACTACGAGT 808–938 1.000 81.4
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CACTTCTTCCCCACACTACG 811–941 1.000 80.8
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TCTAGAGCCCACTTCTTCCC 820–950 1.000 80.4
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 756–886 1.000 80.4
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 1283–1306 1.000 62.7
psbM-trnD-GUC_p2 psbM-trnD-GUC AGGAACTAGAATGAACAGTGCA TTCAATTGGTCAGAGCACCG 1290–1313 1.000 59.6
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC GTTCAATTGGTCAGAGCACC 1284–1307 1.000 58.6
psbM-trnD-GUC_p4 psbM-trnD-GUC GGAACTAGAATGAACAGTGCAG TTCAATTGGTCAGAGCACCG 1289–1312 1.000 57.1
psbM-trnD-GUC_p5 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TCAATTGGTCAGAGCACCG 1282–1305 1.000 56.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Aucuba albopunctifolia var. angustula OQ362998.1 158144 View on NCBI ↗
Aucuba chinensis NC_080888.1 157891 View on NCBI ↗
Aucuba chinensis subsp. omeiensis OQ348516.1 158113 View on NCBI ↗
Aucuba chlorascens NC_058872.1 158084 View on NCBI ↗
Aucuba confertiflora NC_080889.1 157954 View on NCBI ↗
Aucuba eriobotryifolia NC_058873.1 158113 View on NCBI ↗
Aucuba filicauda NC_080890.1 158325 View on NCBI ↗
Aucuba japonica NC_058874.1 158237 View on NCBI ↗
Aucuba japonica var. variegata OQ348512.1 158237 View on NCBI ↗
Aucuba obcordata NC_056113.1 157993 View on NCBI ↗