Markers + reference

Chimonanthus

6 species · Calycanthaceae · Laurales

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Species 6
Genome length 153–153 kb
Candidate markers 265
Primer pairs 95

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 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1137 0.0046 1.00 57.8 yes View details
trnS-GCU-trnG-GCC LSC 825 0.0057 1.00 49.8 yes View details
psbC-trnS-UGA LSC 220 0.0176 1.00 43.2 yes View details
petA-psbJ LSC 1157 0.0086 1.00 65.8 yes View details
trnR-ACG-trnN-GUU IRb 603 0.0253 0.95 74.5 yes View details
ndhF SSC 2244 0.0040 1.00 43.9 yes View details
rpl32-trnL-UAG SSC 1375 0.0059 1.00 49.8 yes View details
rps15-ycf1 SSC 367 0.0200 1.00 46.7 yes View details
trnN-GUU-trnR-ACG IRa 603 0.0253 0.95 74.5 yes View details
trnT-GGU-psbD LSC 1378 0.0031 1.00 61.1 yes View details
ccsA-ndhD SSC 234 0.0085 1.00 55.7 yes View details
psbE-petL LSC 1282 0.0016 0.99 54.8 yes View details
petA LSC 963 0.0027 1.00 54.6 yes View details
accD-psaI LSC 519 0.0050 1.00 54.5 yes View details
ndhC-trnV-UAC LSC 1175 0.0024 1.00 54.4 yes View details
atpH-atpI LSC 1079 0.0017 1.00 54.1 yes View details
trnE-UUC-trnT-GGU LSC 709 0.0039 1.00 54.1 yes View details
clpP LSC 2008 0.0021 1.00 52.8 yes View details
rpoB-trnC-GCA LSC 1164 0.0021 1.00 52.7 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1196–1229 1.000 80.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TGCAAGAATCCACAACCGAT GAGGTTCGAATCCTTCCGTC 1226–1259 1.000 79.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1200–1233 1.000 79.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TGCAAGAATCCACAACCGAT CTCGGAGGTTCGAATCCTTC 1230–1263 1.000 78.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AATGGTGGGTGCAAGAATCC GAGGTTCGAATCCTTCCGTC 1235–1268 1.000 77.8
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGTCGCTTTAGTCCA ACCGAAAGAACCCTTATCCA 931–933 1.000 66.0
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGTCGCTTTAGTCCAC ACCGAAAGAACCCTTATCCA 930–932 1.000 66.0
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC GATCAGAGGGAACGGAGAGA ACCGAAAGAACCCTTATCCA 996–998 1.000 65.5
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC ATCAGAGGGAACGGAGAGAG ACCGAAAGAACCCTTATCCA 995–997 1.000 65.5
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC GGAACGGAGAGAGAGGGATT ACCGAAAGAACCCTTATCCA 988–990 1.000 64.3
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1166–1167 1.000 76.0
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT CAAGCGGGATTCAAGCTCTT 1187–1188 1.000 75.8
atpH-atpI_p3 atpH-atpI GATACCTTCTACGGCTTGGC TTTTTGCAACTTTAGCCGCG 1251–1252 1.000 75.2
atpH-atpI_p4 atpH-atpI CGATACCTTCTACGGCTTGG TTTTTGCAACTTTAGCCGCG 1252–1253 1.000 75.2
atpH-atpI_p5 atpH-atpI AGCCAATCCAGCAGCAATAA TTTTTGCAACTTTAGCCGCG 1182–1183 1.000 75.1
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TGAAGTTCTTCCGTCAAGCC AGCAGGGTAAGAGATTCCGA 1352–1363 1.000 78.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TGAAGTTCTTCCGTCAAGCC TTGGCGAGTTCTGTTAGCAG 1367–1378 1.000 78.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TGAAGTTCTTCCGTCAAGCC CTGGGGAGAAAGGATTTGCA 1298–1309 1.000 78.1
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TGAAGTTCTTCCGTCAAGCC TGGGGAGAAAGGATTTGCAG 1297–1308 1.000 78.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TGAAGTTCTTCCGTCAAGCC AGAAAGGATTTGCAGTCCCC 1292–1303 1.000 78.1
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 798–814 1.000 80.3
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 777–793 1.000 80.2
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCATGGCGTTACTCTACCAC 777–793 1.000 79.9
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA CCATGGCGTTACTCTACCAC 756–772 1.000 79.8
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TGGCGTTACTCTACCACTGA 774–790 1.000 79.7
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GAAACGGTCCCTCCTTAACC 1520–1525 1.000 79.2
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GAAACGGTCCCTCCTTAACC 1523–1528 1.000 79.0
trnT-GGU-psbD_p3 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1528–1533 1.000 78.1
trnT-GGU-psbD_p4 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA ACAAAAACGAAACGGTCCCT 1531–1536 1.000 77.9
trnT-GGU-psbD_p5 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CGAAACGGTCCCTCCTTAAC 1521–1526 1.000 77.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Chimonanthus campanulatus MW166216.1 153010 View on NCBI ↗
Chimonanthus grammatus MW166217.1 153299 View on NCBI ↗
Chimonanthus nitens NC_042745.1 153250 View on NCBI ↗
Chimonanthus praecox NC_042744.1 153252 View on NCBI ↗
Chimonanthus salicifolius NC_066408.1 153300 View on NCBI ↗
Chimonanthus zhejiangensis NC_066409.1 153300 View on NCBI ↗