Markers + reference

Buxus

4 species · Buxaceae · Buxales

Back to catalogue

Species 4
Genome length 153–162 kb
Candidate markers 263
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1016 0.1960 0.89 79.4 yes View details
petN-psbM LSC 855 0.1707 0.95 83.8 yes View details
ycf1 IRb 1044 0.0593 0.99 77.4 no View details
ndhF-rpl32 SSC 943 0.3786 0.37 70.9 yes View details
ycf1 SSC 5613 0.1110 0.97 75.4 yes View details
trnC-GCA-petN LSC 907 0.1343 0.84 84.2 yes View details
rpl20-rps12 LSC 775 0.0981 0.95 83.6 yes View details
trnK-UUU-rps16 LSC 588 0.1555 0.94 83.5 yes View details
ndhI SSC 528 0.0647 1.00 82.8 yes View details
matK-trnK-UUU LSC 729 0.1042 0.96 82.7 yes View details
atpH-atpI LSC 1190 0.1335 0.89 82.7 yes View details
accD LSC 1536 0.0717 0.96 82.7 yes View details
rpoB-trnC-GCA LSC 1007 0.1283 0.92 82.4 yes View details
trnN-GUU-trnR-ACG IRa 619 0.0502 0.94 82.3 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU CATCTTTCACCCAGCATCGA AACGGTAGAGTACTCGGCTT 1267 0.250 48.4
matK-trnK-UUU_p2 matK-trnK-UUU CATCTTTCACCCAGCATCGA ACGGTAGAGTACTCGGCTTT 1266 0.250 48.4
matK-trnK-UUU_p3 matK-trnK-UUU CATCTTTCACCCAGCATCGA GGGAGGGTTGCTAACTCAAC 1284 0.250 48.4
matK-trnK-UUU_p4 matK-trnK-UUU CCCAGCATCGAAGGATTTGA AACGGTAGAGTACTCGGCTT 1258 0.250 48.3
matK-trnK-UUU_p5 matK-trnK-UUU CCCAGCATCGAAGGATTTGA ACGGTAGAGTACTCGGCTTT 1257 0.250 48.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 GCATTTTGTTTTGCGCCAAG TTAGAACCCCCAACCCTCAT 1409 0.250 49.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 GCATTTTGTTTTGCGCCAAG CGATCGCGAAGAGAAGGAAA 1052 0.250 49.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTCATCTCCACCCCCTAA TTAGAACCCCCAACCCTCAT 1655 0.250 48.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 GCATTTTGTTTTGCGCCAAG TTTAGAACCCCCAACCCTCA 1410 0.250 48.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTCATCTCCACCCCCTAA CGATCGCGAAGAGAAGGAAA 1298 0.250 48.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TTTCCTTCTCTTCGCGATCG CGAAAACTGACAGCAGCTTG 1728 0.250 49.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TTTCCTTCTCTTCGCGATCG TCGAAAACTGACAGCAGCTT 1729 0.250 48.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TTTCCTTCTCTTCGCGATCG GAGGTTCGAATCCTTCCGTC 1132 0.250 48.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GGTTTTCCTTCTCTTCGCGA CGAAAACTGACAGCAGCTTG 1731 0.250 48.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGTTTTCCTTCTCTTCGCGA TCGAAAACTGACAGCAGCTT 1732 0.250 48.0
atpH-atpI_p1 atpH-atpI ACAGAAGCGGCAGAAATCAG CCATGGAGGGTCATCATTGA 1171–1239 1.000 79.3
atpH-atpI_p2 atpH-atpI AGAAGCGGCAGAAATCAGTG CCATGGAGGGTCATCATTGA 1169–1237 1.000 79.3
atpH-atpI_p3 atpH-atpI AGAAGCGGCAGAAATCAGTG TCCATGGAGGGTCATCATTG 1170–1238 1.000 79.3
atpH-atpI_p4 atpH-atpI CAGAAGCGGCAGAAATCAGT CCATGGAGGGTCATCATTGA 1170–1238 1.000 79.3
atpH-atpI_p5 atpH-atpI CAGAAGCGGCAGAAATCAGT TCCATGGAGGGTCATCATTG 1171–1239 1.000 79.3
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT GCTTTTGTTGATCAGGCGAC 1603–1680 1.000 91.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA AGAGGTTCCCAGGGAATTCA GCTTTTGTTGATCAGGCGAC 1430–1507 1.000 91.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT TGAATGCCCCAGTACTCAGA 1954 0.250 49.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ATTCCGTTATGGTCCGCTTC GCTTTTGTTGATCAGGCGAC 1519 0.250 49.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT GACAAAGTACCTTACGCCGT 1916 0.250 49.2
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 862–973 1.000 90.1
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 923–1034 1.000 88.5
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 880–991 1.000 87.9
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGAGTCCACTTCTTCCCCAT 941–1052 1.000 86.3
trnC-GCA-petN_p5 trnC-GCA-petN GGTGTCGCCTGATCAACAAA AGCCCAAGCGAGACTTACTA 843–954 1.000 84.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Buxus megistophylla NC_058304.1 157611 View on NCBI ↗
Buxus papillosa PZ054916.1 153290 View on NCBI ↗
Buxus sinica var. parvifolia OQ236088.1 158995 View on NCBI ↗
Buxus wallichiana PZ054917.1 161655 View on NCBI ↗