Markers + reference

Oxandra

7 species · Annonaceae · Magnoliales

Back to catalogue

Species 7
Genome length 160–171 kb
Candidate markers 299
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 299 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
petN-psbM LSC 1117 0.0213 1.00 62.4 yes View details
trnE-UUC-trnT-GGU LSC 742 0.0312 1.00 75.8 yes View details
trnT-GGU-psbD LSC 1435 0.0267 0.99 71.4 yes View details
trnT-UGU-trnL-UAA LSC 898 0.0260 0.96 75.0 yes View details
accD LSC 1878 0.0151 0.92 60.6 yes View details
petA-psbJ LSC 1160 0.0220 1.00 64.4 yes View details
rpoA IRb 1128 0.0201 0.90 60.4 yes View details
rpl32-trnL-UAG SSC 1197 0.0231 1.00 67.5 yes View details
ycf1 SSC 1730 0.0140 1.00 55.0 yes View details
rpoA IRa 1128 0.0044 0.00 23.9 no View details
rpoA-rps11 IRb 127 0.0682 1.00 76.6 yes View details
ccsA-ndhD SSC 219 0.0240 1.00 69.2 yes View details
rps2-rpoC2 LSC 222 0.0298 1.00 65.0 yes View details
trnC-GCA-petN LSC 1059 0.0141 0.99 64.8 yes View details
rps16-trnQ-UUG LSC 871 0.0171 1.00 62.5 yes View details
ndhF-rpl32 SSC 609 0.0171 0.99 62.0 yes View details
ycf2-trnL-CAA IRb 1042 0.0118 1.00 61.7 yes View details
trnL-CAA-ycf2 IRa 1042 0.0118 1.00 61.7 yes View details
trnF-GAA-ndhJ LSC 707 0.0104 0.98 61.4 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-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 944–1693 1.000 80.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 948–1697 1.000 76.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 936–1685 1.000 75.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AGTCGCACGTTGCTTTCTAC GAGGTTCGAATCCTTCCGTC 943–1692 1.000 75.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGTTTTGGTCCCGTTATTCG 964–1713 1.000 74.2
rps2-rpoC2_p1 rps2-rpoC2 GAGCCCTTATTGCAGCTGAT GTTTTCAAGAAACCGCTCGG 792–798 1.000 83.1
rps2-rpoC2_p2 rps2-rpoC2 GAGCCCTTATTGCAGCTGAT TTTCACCTGGCGAGCTAATC 930–936 1.000 82.8
rps2-rpoC2_p3 rps2-rpoC2 GCGAGATCTGGGTCACAATT TTTCACCTGGCGAGCTAATC 1255–1261 1.000 82.2
rps2-rpoC2_p4 rps2-rpoC2 GGTTGAGTTTCCCCGTCTTT TTTCACCTGGCGAGCTAATC 1053–1056 0.857 75.9
rps2-rpoC2_p5 rps2-rpoC2 GGTTGAGTTTCCCCGTCTTT GTTTTCAAGAAACCGCTCGG 915–918 0.857 75.9
trnC-GCA-petN_p1 trnC-GCA-petN ATCCCTTTCTCCCCAGTTCA AGCCCAAGCGAGACTTACTA 1098–1127 1.000 83.5
trnC-GCA-petN_p2 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC AGCCCAAGCGAGACTTACTA 1148–1177 1.000 83.3
trnC-GCA-petN_p3 trnC-GCA-petN TCCCTTTCTCCCCAGTTCAA AGCCCAAGCGAGACTTACTA 1097–1126 1.000 82.6
trnC-GCA-petN_p4 trnC-GCA-petN ACTGCAAATCCCTTTCTCCC AGCCCAAGCGAGACTTACTA 1105–1134 1.000 82.1
trnC-GCA-petN_p5 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC AGAGTCCACTTCTTCCCCAT 1209–1238 1.000 81.5
petN-psbM_p1 petN-psbM ATGGGGAAGAAGTGGACTCT ACGTAAAAACAGTCAGTCAA 1167–1187 1.000 44.2
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT ACGTAAAAACAGTCAGTCAA 1228–1248 1.000 44.0
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT ACGTAAAAACAGTCAGTCAAA 1228–1248 1.000 44.0
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT ACGTAAAAACAGTCAGTCAAAATGA 1228–1248 1.000 44.0
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT ACGTAAAAACAGTCAGTCAAAA 1228–1248 1.000 44.0
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TAGGGCATTTCTGGAGGACA GAACCGATGACTTACGCCTT 1063–1141 1.000 88.0
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CCATGATCAACTTCCCCTCG GAACCGATGACTTACGCCTT 892–970 0.857 82.3
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TAGGGCATTTCTGGAGGACA AAATTCTTGCGTGGTCCAGT 1550–1619 0.857 77.6
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGCGATTATTGCCACATCGA GAACCGATGACTTACGCCTT 1171–1249 0.714 75.0
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CCATGATCAACTTCCCCTCG AAATTCTTGCGTGGTCCAGT 1381–1448 0.714 71.0
trnT-GGU-psbD_p1 trnT-GGU-psbD CTGTTCTTGAACAAGCCCCT ACAAAAACAGCAATTGGGGC 2089–2096 0.857 77.2
trnT-GGU-psbD_p2 trnT-GGU-psbD CTGTTCTTGAACAAGCCCCT CAAAAACAGCAATTGGGGCA 2088–2095 0.857 77.2
trnT-GGU-psbD_p3 trnT-GGU-psbD TTGTCCGTCAGAAAAAGGGG ACAAAAACAGCAATTGGGGC 2523–2528 0.857 77.2
trnT-GGU-psbD_p4 trnT-GGU-psbD GTTCAGGGTACGAGTCGAAC ACAAAAACAGCAATTGGGGC 2301–2308 0.857 77.0
trnT-GGU-psbD_p5 trnT-GGU-psbD CCGTCAGAAAAAGGGGTCAA ACAAAAACAGCAATTGGGGC 2523–2524 0.429 57.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Oxandra asbeckii NC_085150.1 171090 View on NCBI ↗
Oxandra guianensis NC_085149.1 160093 View on NCBI ↗
Oxandra laurifolia NC_085148.1 159847 View on NCBI ↗
Oxandra longipetala NC_084399.1 171059 View on NCBI ↗
Oxandra macrophylla OR678689.1 160094 View on NCBI ↗
Oxandra martiana NC_085147.1 160302 View on NCBI ↗
Oxandra polyantha NC_085151.1 171145 View on NCBI ↗