Markers + reference

Huodendron

2 species · Styracaceae · Ericales

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Species 2
Genome length 158–159 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 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0000 1.00 29.9 yes View details
rpoC2 LSC 4134 0.0005 1.00 54.1 yes View details
trnC-GCA-petN LSC 572 0.0017 1.00 59.2 yes View details
accD LSC 2199 0.0032 0.98 60.7 yes View details
rpl23 IRb 282 0.0000 1.00 33.5 yes View details
ycf2 IRb 6981 0.0003 1.00 37.7 no View details
ndhF-rpl32 SSC 962 0.0021 1.00 59.9 yes View details
ycf2 IRa 6981 0.0003 1.00 37.7 yes View details
rpl23 IRa 282 0.0000 1.00 33.5 no View details
trnI-CAU-ycf2 IRb 88 0.1136 1.00 72.7 yes View details
ycf2-trnI-CAU IRa 88 0.1136 1.00 72.7 yes View details
rps7-rps12 IRb 53 0.0189 1.00 63.3 yes View details
rps12-rps7 IRa 53 0.0189 1.00 63.3 yes View details
matK-trnK-UUU LSC 716 0.0028 1.00 60.4 yes View details
trnF-GAA LSC 73 0.0137 1.00 60.4 yes View details
trnD-GUC LSC 74 0.0135 1.00 60.3 yes View details
ccsA SSC 960 0.0021 1.00 59.9 yes View details
accD-psaI LSC 775 0.0013 1.00 59.5 yes View details
rps16 LSC 1127 0.0000 1.00 59.2 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
psbA_p1 psbA AAAGGAGCAATAACGCCCTC AAATTCGTGTGCTTGGGAGT 1209 1.000 77.9
psbA_p2 psbA AGCAATAACGCCCTCTTCTC AAATTCGTGTGCTTGGGAGT 1204 1.000 77.3
psbA_p3 psbA GAGCAATAACGCCCTCTTCT AAATTCGTGTGCTTGGGAGT 1205 1.000 77.3
psbA_p4 psbA GCAATAACGCCCTCTTCTCT AAATTCGTGTGCTTGGGAGT 1203 1.000 77.3
psbA_p5 psbA GGAGCAATAACGCCCTCTTC AAATTCGTGTGCTTGGGAGT 1206 1.000 74.3
trnK-UUU_p1 trnK-UUU GCCCGTGTCAACCAATATCT TCTGATTGTATCTACACGCCT 2740 1.000 57.9
trnK-UUU_p2 trnK-UUU TGCCCGTGTCAACCAATATC TCTGATTGTATCTACACGCCT 2741 1.000 56.2
trnK-UUU_p3 trnK-UUU GCCCGTGTCAACCAATATCT TCTGATTGTATCTACACGCCTT 2740 1.000 55.7
trnK-UUU_p4 trnK-UUU GCCCGTGTCAACCAATATCT TTCTGATTGTATCTACACGCCT 2741 1.000 55.7
trnK-UUU_p5 trnK-UUU ATGCCCGTGTCAACCAATAT TCTGATTGTATCTACACGCCT 2742 1.000 54.7
matK-trnK-UUU_p1 matK-trnK-UUU TCGTGTTGCTGAGATCTACC CGATTCGGGTTGCTAACTCA 809 1.000 72.6
matK-trnK-UUU_p2 matK-trnK-UUU CGTGTTGCTGAGATCTACCT CGATTCGGGTTGCTAACTCA 808 1.000 72.6
matK-trnK-UUU_p3 matK-trnK-UUU TCGTGTTGCTGAGATCTACC AACGGTAGAGTACTCGGCTT 790 1.000 71.3
matK-trnK-UUU_p4 matK-trnK-UUU TCGTGTTGCTGAGATCTACC ACGGTAGAGTACTCGGCTTT 789 1.000 71.3
matK-trnK-UUU_p5 matK-trnK-UUU CGTGTTGCTGAGATCTACCT ACGGTAGAGTACTCGGCTTT 788 1.000 71.3
rps16_p1 rps16 CGAGTCATCACTACCCCACT CAATTCCATACCGGCTCCAA 1188–1193 1.000 75.7
rps16_p2 rps16 TACGAGTCATCACTACCCCA CAATTCCATACCGGCTCCAA 1190–1195 1.000 73.4
rps16_p3 rps16 ACGAGTCATCACTACCCCAC CAATTCCATACCGGCTCCAA 1189–1194 1.000 73.4
rps16_p4 rps16 CGAGTCATCACTACCCCACT ATCAATTCCATACCGGCTCC 1190–1195 1.000 71.6
rps16_p5 rps16 CGAGTCATCACTACCCCACT TCAATTCCATACCGGCTCCA 1189–1194 1.000 69.8
rpoC2_p1 rpoC2 TTCCGAGGACTCACAGAACT GATCCCCAAGGCCAAATGAT 233 1.000 79.9
rpoC2_p2 rpoC2 ATTCTTTCCGGCATCATCCC GATCCCCAAGGCCAAATGAT 254 1.000 79.8
rpoC2_p3 rpoC2 AGGACTCACAGAACTACCCC GATCCCCAAGGCCAAATGAT 228 1.000 79.5
rpoC2_p4 rpoC2 ATCATCCCATTCCGAGGACT GATCCCCAAGGCCAAATGAT 242 1.000 79.0
rpoC2_p5 rpoC2 CATCATCCCATTCCGAGGAC GATCCCCAAGGCCAAATGAT 243 1.000 78.5
trnC-GCA-petN_p1 trnC-GCA-petN GGGGGACTGCAAATCCTTTT GCCCAAGCGAGACTTACAAT 655 1.000 75.2
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGAGTCCACTTCTTCCCCAT 717 1.000 74.5
trnC-GCA-petN_p3 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC GCCCAAGCGAGACTTACAAT 630 1.000 74.2
trnC-GCA-petN_p4 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC AGAGTCCACTTCTTCCCCAT 692 1.000 73.5
trnC-GCA-petN_p5 trnC-GCA-petN TATCCTTTTGGCGACATGGC GCCCAAGCGAGACTTACAAT 688 1.000 73.1

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
Huodendron biaristatum NC_041132.1 158499 View on NCBI ↗
Huodendron tibeticum NC_053899.1 159320 View on NCBI ↗