Markers + reference

Aralia

19 species · Araliaceae · Apiales

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Species 19
Genome length 156–156 kb
Candidate markers 271
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 410 0.0346 0.98 68.2 yes View details
trnK-UUU-rps16 LSC 876 0.0170 0.98 66.3 yes View details
rps16-trnQ-UUG LSC 1731 0.0168 0.99 71.5 yes View details
trnS-GCU-trnG-UCC LSC 727 0.0173 0.99 64.9 yes View details
trnC-GCA-petN LSC 683 0.0129 0.98 57.2 yes View details
trnE-UUC-trnT-GGU LSC 826 0.0184 0.94 70.1 yes View details
petA-psbJ LSC 1020 0.0147 1.00 53.1 yes View details
clpP LSC 1998 0.0106 1.00 52.1 yes View details
ndhF-rpl32 SSC 1195 0.0147 0.99 70.7 yes View details
rpl32-trnL-UAG SSC 822 0.0206 0.97 70.4 yes View details
ycf1 SSC 5538 0.0116 1.00 52.2 yes View details
ycf3-trnS-GGA LSC 848 0.0134 0.99 66.0 yes View details
trnT-UGU-trnL-UAA LSC 781 0.0141 0.98 65.6 yes View details
atpH-atpI LSC 1089 0.0106 1.00 63.3 yes View details
trnT-GGU-psbD LSC 1404 0.0110 0.99 61.5 yes View details
psbK-psbI LSC 410 0.0173 1.00 60.1 yes View details
psaI-ycf4 LSC 407 0.0160 1.00 59.4 yes View details
rpoB-trnC-GCA LSC 1283 0.0115 0.99 59.2 yes View details
psbE-petL LSC 1163 0.0117 1.00 59.0 yes View details
ndhC-trnV-UAC LSC 972 0.0143 0.99 58.0 yes View details
accD-psaI LSC 682 0.0118 1.00 56.5 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCGAAGCTCCATCTACAAATGG 441–474 1.000 73.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCGAAGCTCCATCTACAAATGG 455–488 1.000 73.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TCGAAGCTCCATCTACAAATGG 454–487 1.000 73.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TCGAAGCTCCATCTACAAATGG 456–489 1.000 73.3
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CGAAGCTCCATCTACAAATGG 440–473 1.000 73.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGAATCCTTCGCTTCATCCA AGAAGGCGGAGGTTTTTAAGT 961–998 1.000 76.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC AGAAGGCGGAGGTTTTTAAGT 974–1011 1.000 75.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGAAGGCGGAGGTTTTTAAGT 913–950 1.000 75.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGAAGGCGGAGGTTTTTAAGT 912–949 1.000 75.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC AGAAGGCGGAGGTTTTTAAGT 998–1035 1.000 74.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1652–1843 1.000 87.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1667–1858 1.000 86.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1666–1857 1.000 86.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1656–1847 1.000 83.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1682–1873 1.000 83.0
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG CCCGGATCATTAGATAGGAATCC 522–527 1.000 57.7
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT CCCGGATCATTAGATAGGAATCC 519–524 1.000 55.7
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT CCCGGATCATTAGATAGGAATCC 520–525 1.000 55.7
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT CCCGGATCATTAGATAGGAATCC 521–526 1.000 55.7
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGAAAAGTTTGAGAGTAAGCA 459–464 1.000 54.6
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACAACGAATCACACTTTTACCAC 797–809 1.000 61.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACAACGAATCACACTTTTACCAC 846–858 1.000 60.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA CAACGAATCACACTTTTACCACT 796–808 1.000 59.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACAACGAATCACACTTTTACCA 797–809 1.000 59.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA CAACGAATCACACTTTTACCACT 845–857 1.000 58.4
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1016–1213 1.000 83.4
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT TTTTTGCAACTTTAGCCGCG 1072–1269 1.000 82.6
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA TTTTTGCAACTTTAGCCGCG 1032–1229 1.000 82.5
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTTGCAACTTTAGCCGCG 1017–1214 1.000 82.2
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC TTTTTGCAACTTTAGCCGCG 1076–1273 1.000 82.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (19)

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

Species Accession Length (bp) Link
Aralia apioides PP386171.1 156147 View on NCBI ↗
Aralia armata PQ385616.1 156195 View on NCBI ↗
Aralia atropurpurea NC_056999.1 156226 View on NCBI ↗
Aralia caesia NC_069844.1 156201 View on NCBI ↗
Aralia chinensis PQ385617.1 156199 View on NCBI ↗
Aralia cordata NC_040964.1 156087 View on NCBI ↗
Aralia dasyphylla PQ399963.1 155999 View on NCBI ↗
Aralia debilis PQ399972.1 156039 View on NCBI ↗
Aralia echinocaulis NC_069843.1 156074 View on NCBI ↗
Aralia elata NC_069842.1 155744 View on NCBI ↗
Aralia elata var. glabrescens PQ399989.1 156214 View on NCBI ↗
Aralia finlaysoniana PQ399992.1 156225 View on NCBI ↗
Aralia officinalis PQ399997.1 156111 View on NCBI ↗
Aralia searelliana PQ399999.1 156241 View on NCBI ↗
Aralia spinifolia PQ400003.1 156196 View on NCBI ↗
Aralia stipulata PQ400013.1 156316 View on NCBI ↗
Aralia thomsonii NC_086867.1 156025 View on NCBI ↗
Aralia undulata NC_022810.1 156333 View on NCBI ↗
Aralia vietnamensis PQ400020.1 156211 View on NCBI ↗