Markers + reference

Callicarpa

20 species · Lamiaceae · Lamiales

Back to catalogue

Species 20
Genome length 154–154 kb
Candidate markers 269
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 519 0.0214 0.64 53.8 yes View details
rps16-trnQ-UUG LSC 1125 0.0040 1.00 55.2 yes View details
rpoB-trnC-GCA LSC 1176 0.0023 1.00 45.8 yes View details
rbcL LSC 1440 0.0041 1.00 49.0 yes View details
rbcL-accD LSC 634 0.0039 1.00 43.1 yes View details
psbE-petL LSC 922 0.0044 1.00 42.4 yes View details
rpl16 LSC 1295 0.0023 1.00 42.8 yes View details
rpl32-trnL SSC 805 0.0064 0.97 66.9 yes View details
ndhA SSC 2185 0.0025 1.00 51.0 yes View details
ycf1 SSC 5673 0.0022 1.00 57.2 yes View details
matK-rps16 LSC 1625 0.0027 0.99 61.1 yes View details
petN-psbM LSC 910 0.0039 1.00 58.0 yes View details
petA-psbJ LSC 1037 0.0025 0.90 54.9 yes View details
clpP LSC 1948 0.0012 1.00 52.6 yes View details
psbM-trnD-GUC LSC 536 0.0032 1.00 51.6 yes View details
ndhC-trnV-UAC LSC 1185 0.0022 0.99 51.4 yes View details
atpH-atpI LSC 1014 0.0027 1.00 51.3 yes View details
trnC-GCA-petN LSC 831 0.0026 1.00 50.7 yes View details
trnN-GUU-ndhF IRb 1404 0.0004 1.00 50.5 yes View details
trnT-UGU-trnL-UAA LSC 670 0.0026 1.00 49.9 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 CCTCTAGACCTAGCTGCTGT 309–583 1.000 90.1
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 312–586 1.000 89.9
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 323–597 1.000 89.8
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 322–596 1.000 89.8
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 324–598 1.000 89.8
matK-rps16_p1 matK-rps16 GCACGATTATGAGCAAATGCA GTGCTCAACCCACAGGAAC 1748–1821 1.000 63.5
matK-rps16_p2 matK-rps16 GCACGATTATGAGCAAATGCA TGCTCAACCCACAGGAACT 1747–1820 1.000 62.7
matK-rps16_p3 matK-rps16 AGGAAGTCGTGTTGTTGAGA GTGCTCAACCCACAGGAAC 1697–1770 1.000 61.9
matK-rps16_p4 matK-rps16 AGCACGATTATGAGCAAATGC GTGCTCAACCCACAGGAAC 1749–1822 1.000 61.3
matK-rps16_p5 matK-rps16 AGGAAGTCGTGTTGTTGAGA TGCTCAACCCACAGGAACT 1696–1769 1.000 61.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAAATTGAAATGGGGCGTGG 1273–1305 1.000 81.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 1256–1288 1.000 81.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1215–1247 1.000 81.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1198–1230 1.000 80.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAAATTGAAATGGGGCGTGG 1274–1306 1.000 80.6
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA TCCCTGTCATGTTCCTTGGA 1142–1149 1.000 79.1
atpH-atpI_p2 atpH-atpI AGCCAATCCAGCAGCAATAA TCCCTGTCATGTTCCTTGGA 1160–1167 1.000 78.7
atpH-atpI_p3 atpH-atpI GCCAATCCAGCAGCAATAAC TCCCTGTCATGTTCCTTGGA 1159–1166 1.000 78.2
atpH-atpI_p4 atpH-atpI TCCAGCAGCAATAACGGAAG TCCCTGTCATGTTCCTTGGA 1154–1161 1.000 77.8
atpH-atpI_p5 atpH-atpI AACGGAAGCAGCAGAAATCA TTTTTGCAACTTTAGCCGCG 1094–1101 1.000 77.1
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GACATTGCCTCGTTTGCATC TTTTTGGTGATCAGGCGACA 1287–1288 1.000 81.4
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GACATTGCCTCGTTTGCATC CCGGATTTGAACTGGGGAAA 1266–1267 1.000 81.0
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TAGACATTGCCTCGTTTGCA TTTTTGGTGATCAGGCGACA 1289–1290 1.000 80.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CATTGCCTCGTTTGCATCTC TTTTTGGTGATCAGGCGACA 1285–1286 1.000 80.7
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TAGACATTGCCTCGTTTGCA CCGGATTTGAACTGGGGAAA 1268–1269 1.000 80.4
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ACTTCTTCCCCACACTACGA 941–946 1.000 80.6
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTCTTCCCCACACTACGAGT 939–944 1.000 80.6
trnC-GCA-petN_p3 trnC-GCA-petN GTATCATTTTGGCGGCATGG ACTTCTTCCCCACACTACGA 993–998 1.000 80.1
trnC-GCA-petN_p4 trnC-GCA-petN GTATCATTTTGGCGGCATGG TTCTTCCCCACACTACGAGT 991–996 1.000 80.1
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CACTTCTTCCCCACACTACG 942–947 1.000 80.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (20)

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

Species Accession Length (bp) Link
Callicarpa americana NC_052696.1 154433 View on NCBI ↗
Callicarpa arborea NC_058321.1 154269 View on NCBI ↗
Callicarpa bodinieri NC_054294.1 154183 View on NCBI ↗
Callicarpa brevipes NC_058322.1 154182 View on NCBI ↗
Callicarpa cathayana NC_063508.1 154182 View on NCBI ↗
Callicarpa formosana NC_052748.1 154210 View on NCBI ↗
Callicarpa integerrima var. chinensis MW788028.1 154179 View on NCBI ↗
Callicarpa kochiana NC_063509.1 154181 View on NCBI ↗
Callicarpa kwangtungensis NC_084107.1 154185 View on NCBI ↗
Callicarpa longifolia var. floccosa MW149076.1 154285 View on NCBI ↗
Callicarpa longipes OR548044.1 154195 View on NCBI ↗
Callicarpa longipes var. mixiensis OR537888.1 154191 View on NCBI ↗
Callicarpa longissima NC_088747.1 154158 View on NCBI ↗
Callicarpa macrophylla NC_058323.1 154149 View on NCBI ↗
Callicarpa peichieniana NC_058324.1 154102 View on NCBI ↗
Callicarpa rubella NC_058533.1 154202 View on NCBI ↗
Callicarpa rubella f. angustata OR537890.1 154138 View on NCBI ↗
Callicarpa rubella f. crenata OR548043.1 154067 View on NCBI ↗
Callicarpa rubella f. subglabra OR537889.1 154126 View on NCBI ↗
Callicarpa siongsaiensis NC_059786.1 154144 View on NCBI ↗