Markers + reference

Caryopteris

4 species · Lamiaceae · Lamiales

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Species 4
Genome length 152–152 kb
Candidate markers 272
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1059 0.0009 1.00 33.0 yes View details
trnK-UUU-rps16 LSC 862 0.0058 1.00 62.8 yes View details
rps16-trnQ-UUG LSC 1233 0.0029 0.96 65.3 yes View details
trnS-GCU-trnG-UCC LSC 662 0.0039 0.97 41.3 yes View details
rps2 LSC 711 0.0014 1.00 31.9 yes View details
psbM-trnD-GUC LSC 523 0.0076 1.00 50.5 yes View details
trnG-GCC-trnfM-CAU LSC 164 0.0000 0.99 31.0 yes View details
trnW-CCA-trnP-UGG LSC 186 0.0148 0.91 46.5 yes View details
ccsA SSC 972 0.0021 1.00 38.5 yes View details
ccsA-ndhD SSC 248 0.0405 1.00 79.6 yes View details
ycf1 SSC 5691 0.0020 1.00 53.9 yes View details
rps2-rpoC2 LSC 225 0.0090 0.98 61.4 yes View details
rpoB-trnC-GCA LSC 1152 0.0026 1.00 60.6 yes View details
rps11 LSC 417 0.0036 1.00 57.5 yes View details
rpoC1 LSC 2828 0.0012 1.00 57.0 yes View details
rpoC2 LSC 4110 0.0012 1.00 54.7 yes View details
clpP LSC 1920 0.0010 1.00 52.4 yes View details
rpl32-trnL-UAG SSC 412 0.0036 1.00 52.2 yes View details
atpH-atpI LSC 1011 0.0025 1.00 51.1 yes View details
trnT-GGU-psbD LSC 1324 0.0019 1.00 51.0 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
psbA_p1 psbA ACTCCTATACACTAAGACCAAGTC ATTTGTGTGCTTGGGAGTCC 1132 1.000 40.1
psbA_p2 psbA ACTCCTATACACTAAGACCAAGT ATTTGTGTGCTTGGGAGTCC 1132 1.000 40.1
psbA_p3 psbA AACTCCTATACACTAAGACCAAGTC ATTTGTGTGCTTGGGAGTCC 1133 1.000 40.1
psbA_p4 psbA AACTCCTATACACTAAGACCAAGT ATTTGTGTGCTTGGGAGTCC 1133 1.000 40.1
psbA_p5 psbA CTCCTATACACTAAGACCAAGTC ATTTGTGTGCTTGGGAGTCC 1131 1.000 40.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CCACAGGAACCGTTCAGAAT 976–988 1.000 78.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CCACAGGAACCGTTCAGAAT 975–987 1.000 78.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC CCACAGGAACCGTTCAGAAT 990–1002 1.000 77.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA CCACAGGAACCGTTCAGAAT 985–997 1.000 77.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC CCACAGGAACCGTTCAGAAT 962–974 1.000 75.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 1282–1364 1.000 83.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1224–1306 1.000 82.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAAATTGAAATGGGGCGTGG 1296–1378 1.000 81.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1238–1320 1.000 80.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGAGCACCCCCATTCCTAG GAAATTGAAATGGGGCGTGG 1351–1433 1.000 78.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC AACCGAAAGACCCTTTAACT 739–751 1.000 45.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC ACGAATCACACTTTTACCACT 703–715 1.000 45.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC AGAACGAATCACACTTTTACCAC 706–718 1.000 44.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC GAACGAATCACACTTTTACCACT 705–717 1.000 44.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC AAACCGAAAGACCCTTTAACT 740–752 1.000 44.6
atpH-atpI_p1 atpH-atpI CAGCAGTTCCTTGACCAACT CCCGTCATGTTCCTTGGATT 1207–1227 1.000 79.1
atpH-atpI_p2 atpH-atpI GTTCCTTGACCAACTCCAGG CCCGTCATGTTCCTTGGATT 1202–1222 1.000 78.5
atpH-atpI_p3 atpH-atpI AACGGAAGCAGCAGAAATCA CCCGTCATGTTCCTTGGATT 1143–1163 1.000 78.5
atpH-atpI_p4 atpH-atpI AGCCAATCCAGCAGCAATAA CCCGTCATGTTCCTTGGATT 1161–1181 1.000 78.1
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC CCCGTCATGTTCCTTGGATT 1160–1180 1.000 77.6
rps2_p1 rps2 GGAAACCCCCTATTTGCCAA ATTCGACGGGAAAACGAGAG 1342–1347 1.000 80.4
rps2_p2 rps2 TTGGAAACCCCCTATTTGCC ATTCGACGGGAAAACGAGAG 1344–1349 1.000 80.4
rps2_p3 rps2 GGAAACCCCCTATTTGCCAA ATCAAAAGCAGCTCTCCGAG 1507–1512 1.000 80.2
rps2_p4 rps2 TTGGAAACCCCCTATTTGCC ATCAAAAGCAGCTCTCCGAG 1509–1514 1.000 80.2
rps2_p5 rps2 GGAAACCCCCTATTTGCCAA GGATTAGCGCCTCCTTCAAA 1410–1415 1.000 80.1

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
Caryopteris forrestii NC_058325.1 151735 View on NCBI ↗
Caryopteris incana NC_046409.1 151687 View on NCBI ↗
Caryopteris mongholica NC_035729.1 151707 View on NCBI ↗
Caryopteris tangutica NC_069833.1 151728 View on NCBI ↗