Markers + reference

Quillaja

2 species · Quillajaceae · Fabales

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Species 2
Genome length 160–161 kb
Candidate markers 293
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 293 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 425 0.0118 1.00 48.3 yes View details
trnK-UUU-rps16 LSC 995 0.0062 0.97 51.0 yes View details
rpoC2 LSC 4179 0.0029 1.00 42.0 yes View details
psbZ-trnG-GCC LSC 808 0.0099 1.00 55.0 yes View details
psaA-pafI LSC 797 0.0063 1.00 62.4 yes View details
rbcL-accD LSC 857 0.0058 1.00 50.3 yes View details
clpP1 LSC 1965 0.0061 1.00 61.4 yes View details
rps3-rpl22 LSC 289 0.0040 0.86 49.2 yes View details
ycf1 IRb 594 0.0017 1.00 45.7 no View details
rpl32-trnL-UAG SSC 534 0.0207 1.00 67.3 yes View details
rps15 SSC 273 0.0073 1.00 42.5 yes View details
ycf1 SSC 5451 0.0039 1.00 54.7 yes View details
rpl2-trnH-GUG LSC 297 0.2222 0.64 75.7 no View details
ndhF-rpl32 SSC 1052 0.0058 0.98 62.0 yes View details
atpH-atpI LSC 746 0.0054 1.00 61.8 yes View details
trnE-UUC-trnT-GGU LSC 791 0.0038 0.99 61.7 yes View details
trnT-UGU-trnL-UAA LSC 1252 0.0024 0.99 61.5 yes View details
trnS-GCU-trnG-UCC LSC 1195 0.0034 0.99 61.4 yes View details
petN-psbM LSC 1223 0.0033 0.99 61.4 yes View details
ycf1-ndhF SSC 141 0.0284 1.00 60.6 yes View details
trnR-UCU LSC 72 0.0139 1.00 60.5 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 100 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 GCGCTAACCTTGGTATGGAA 542–543 1.000 79.6
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 556–557 1.000 79.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 555–556 1.000 79.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 557–558 1.000 79.5
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TGCCTCTAGGAATCTCTGGG 995–996 1.000 78.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCTGGATCAGTCGTGG AAAAAGGCGCTCAACCTACA 1221–1235 1.000 82.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCTGGATCAGTCGTGG ATTGCGAATAGGAGCGGTTT 1558–1572 1.000 81.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCTGGATCAGTCGTGGTCTT AAAAAGGCGCTCAACCTACA 1217–1231 1.000 81.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 TTCTGGATCAGTCGTGGTCT AAAAAGGCGCTCAACCTACA 1218–1232 1.000 81.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCTGGATCAGTCGTGG AAAAGGGAGTAGAGACCGCT 1645–1659 1.000 81.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGATCAGTAGAACGAATCGCA 1269–1275 1.000 72.1
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GGATCAGTAGAACGAATCGCA 1268–1274 1.000 72.1
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA GGATCAGTAGAACGAATCGCA 1323–1329 1.000 70.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCACT 1258–1264 1.000 70.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCACT 1257–1263 1.000 70.9
trnG-UCC_p1 trnG-UCC TTCCCCTGTTCGACAAAAGG CAGGAACAGATGGAACGCTT 1556–1608 1.000 81.5
trnG-UCC_p2 trnG-UCC TTCCCCTGTTCGACAAAAGG TTCAGGAACAGATGGAACGC 1558–1610 1.000 81.5
trnG-UCC_p3 trnG-UCC TTCGACAAAAGGCCCGTTTA CAGGAACAGATGGAACGCTT 1548–1600 1.000 81.5
trnG-UCC_p4 trnG-UCC TTCGACAAAAGGCCCGTTTA TTCAGGAACAGATGGAACGC 1550–1602 1.000 81.4
trnG-UCC_p5 trnG-UCC TATACAGCCCGGCTAGGTAC CAGGAACAGATGGAACGCTT 2012–2070 1.000 80.6
trnR-UCU_p1 trnR-UCU AGCCTTCCAAGCTAACGATG CATTTACCGGGGAAGCAGAA 770–799 1.000 82.7
trnR-UCU_p2 trnR-UCU AGCCTTCCAAGCTAACGATG GCGAGTTGCTCAAACAATCC 959–988 1.000 82.6
trnR-UCU_p3 trnR-UCU CCTAGCCTTCCAAGCTAACG GCGAGTTGCTCAAACAATCC 962–991 1.000 82.4
trnR-UCU_p4 trnR-UCU AGCCTTCCAAGCTAACGATG GACCTGCGATTAATGTGGGT 1148–1177 1.000 82.1
trnR-UCU_p5 trnR-UCU CCTAGCCTTCCAAGCTAACG GACCTGCGATTAATGTGGGT 1151–1180 1.000 81.8
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATTTTTGCAACTCTCGCTGC 835–836 1.000 79.6
atpH-atpI_p2 atpH-atpI GATCCCTTCTACAGCTTGGC ATTTTTGCAACTCTCGCTGC 920–921 1.000 79.6
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT CGAATCCATGGAGGGTCATC 803–804 1.000 78.7
atpH-atpI_p4 atpH-atpI GATCCCTTCTACAGCTTGGC CGAATCCATGGAGGGTCATC 888–889 1.000 78.6
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA ATTTTTGCAACTCTCGCTGC 836–837 1.000 78.5

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
Quillaja lancifolia PZ055524.1 160528 View on NCBI ↗
Quillaja saponaria NC_047356.1 160392 View on NCBI ↗