Markers + reference

Illicium

15 species · Schisandraceae · Austrobaileyales

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Species 15
Genome length 143–144 kb
Candidate markers 253
Primer pairs 85

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 253 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG Genome 1574 0.0075 1.00 61.7 yes View details
trnQ-UUG-psbK Genome 340 0.0170 0.97 61.4 yes View details
trnS-GCU-trnG-UCC Genome 892 0.0106 0.98 51.6 yes View details
petA-psbJ Genome 1131 0.0134 0.99 74.9 yes View details
ycf2 Genome 6873 0.0030 0.99 43.7 yes View details
ndhF-rpl32 Genome 1283 0.0084 0.99 60.1 yes View details
psaC-ndhE Genome 285 0.0523 1.00 61.5 yes View details
trnV-GAC-rps12 Genome 1773 0.0040 0.99 55.9 yes View details
ndhB-psbA Genome 978 0.0129 0.87 52.8 no View details
atpB-rbcL Genome 754 0.0034 0.99 65.4 yes View details
rpl32-trnL-UAG Genome 1553 0.0078 0.99 63.2 yes View details
petN-psbM Genome 1013 0.0024 0.99 60.5 yes View details
trnF-GAA-ndhJ Genome 651 0.0042 0.98 60.4 yes View details
trnK-UUU-rps16 Genome 803 0.0052 1.00 60.2 yes View details
ndhA Genome 2166 0.0034 1.00 59.7 yes View details
psbF-psbE Genome 9 0.0275 1.00 58.6 yes View details
trnL-CAA-trnV-GAC Genome 1558 0.0036 0.99 57.6 yes View details
ycf3-trnS-GGA Genome 768 0.0032 1.00 57.4 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGAGCTCAACCTACAGGAAC 911–936 1.000 79.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGAGCTCAACCTACAGGAAC 910–935 1.000 79.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGAGCTCAACCTACAGGAAC 920–945 1.000 78.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT ATTTCAAAGAAGGCGGAGGT 881–906 1.000 78.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ATTTCAAAGAAGGCGGAGGT 880–905 1.000 78.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCATGTCGTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 1653–1765 1.000 84.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1641–1753 1.000 84.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ATCATGTCGTTCAAGTCGCA CTCGGAGGTTCGAATCCTTC 1657–1769 1.000 83.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1645–1757 1.000 83.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCATGTCGTTCAAGTCGCA CGGTAAGGCAACAGGTTTTG 1686–1798 1.000 81.9
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GAATTAGCCTGGGACGGAAG GGGCAATTTGGCGAAGAAAA 491–511 1.000 84.7
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GAAGGATTCGAACCTCCGAG GGGCAATTTGGCGAAGAAAA 475–495 1.000 83.6
trnQ-UUG-psbK_p3 trnQ-UUG-psbK CAAAACCTGTTGCCTTACCG GGGCAATTTGGCGAAGAAAA 446–466 1.000 82.4
trnQ-UUG-psbK_p4 trnQ-UUG-psbK AGGATTCGAACCTCCGAGTA GGGCAATTTGGCGAAGAAAA 473–493 1.000 81.9
trnQ-UUG-psbK_p5 trnQ-UUG-psbK AGAATTAGCCTGGGACGGAA GGGCAATTTGGCGAAGAAAA 492–512 1.000 81.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT TGAATCAAACCGAAAGATCCCT 968–1085 1.000 65.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC TGAATCAAACCGAAAGATCCCT 963–1080 1.000 64.1
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC TAGTCCACTCAGCCATCTCT TGAATCAAACCGAAAGATCCCT 964–1081 1.000 61.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT TGAATCAAACCGAAAGATCCC 968–1085 1.000 61.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC TGAATCAAACCGAAAGATCCC 963–1080 1.000 60.4
petN-psbM_p1 petN-psbM CTTGGGCGGCTTTAATGGTA TGCTACTGCACTGTTCATTCT 1147–1163 1.000 68.7
petN-psbM_p2 petN-psbM TTGGGCGGCTTTAATGGTAG TGCTACTGCACTGTTCATTCT 1146–1162 1.000 68.7
petN-psbM_p3 petN-psbM GGCGGCTTTAATGGTAGTCT TGCTACTGCACTGTTCATTCT 1143–1159 1.000 68.1
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 1098–1114 1.000 68.0
petN-psbM_p5 petN-psbM TAGTAAGTCTTGCTTGGGCG TGCTACTGCACTGTTCATTCT 1159–1175 1.000 67.6
ycf3-trnS-GGA_p1 ycf3-trnS-GGA TGCCTCCTTTTCTCCTGAAG CCCTCGGTAAACAAAAGCCT 906–940 1.000 77.0
ycf3-trnS-GGA_p2 ycf3-trnS-GGA GCCTCCTTTTCTCCTGAAGT CCCTCGGTAAACAAAAGCCT 905–939 1.000 77.0
ycf3-trnS-GGA_p3 ycf3-trnS-GGA TGCCTCCTTTTCTCCTGAAG ACGGAAAGAGAGGGATTCGA 927–961 1.000 76.5
ycf3-trnS-GGA_p4 ycf3-trnS-GGA GCCTCCTTTTCTCCTGAAGT ACGGAAAGAGAGGGATTCGA 926–960 1.000 76.5
ycf3-trnS-GGA_p5 ycf3-trnS-GGA TGCCTCCTTTTCTCCTGAAG TTCCAATGCTACGCCTTGAA 877–911 1.000 76.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (15)

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

Species Accession Length (bp) Link
Illicium anisatum NC_034703.1 142723 View on NCBI ↗
Illicium brevistylum NC_067872.1 143715 View on NCBI ↗
Illicium burmanicum NC_065116.1 142988 View on NCBI ↗
Illicium difengpi NC_063671.1 143629 View on NCBI ↗
Illicium dunnianum NC_067873.1 143292 View on NCBI ↗
Illicium henryi NC_034699.1 143240 View on NCBI ↗
Illicium jiadifengpi NC_067874.1 142800 View on NCBI ↗
Illicium lanceolatum NC_065119.1 143685 View on NCBI ↗
Illicium majus NC_065117.1 143480 View on NCBI ↗
Illicium micranthum NC_065114.1 143374 View on NCBI ↗
Illicium simonsii NC_063850.1 143012 View on NCBI ↗
Illicium ternstroemioides NC_065118.1 142732 View on NCBI ↗
Illicium tsaii NC_065115.1 142873 View on NCBI ↗
Illicium tsangii NC_067875.1 142940 View on NCBI ↗
Illicium verum NC_034689.1 143187 View on NCBI ↗