Markers + reference

Corylopsis

14 species · Hamamelidaceae · Saxifragales

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Species 14
Genome length 159–159 kb
Candidate markers 268
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 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnE-UUC-trnT-GGU LSC 883 0.0045 1.00 45.1 yes View details
psbZ-trnG-GCC LSC 699 0.0039 1.00 60.4 yes View details
trnT-UGU-trnL-UAA LSC 1015 0.0050 1.00 57.0 yes View details
trnL-UAA-trnF-GAA LSC 376 0.0056 1.00 47.7 yes View details
accD-psaI LSC 682 0.0040 1.00 54.2 yes View details
rps18 LSC 306 0.0014 1.00 29.3 yes View details
clpP LSC 2028 0.0024 1.00 43.9 yes View details
rpoA LSC 1014 0.0028 1.00 33.4 yes View details
rps8 LSC 405 0.0021 1.00 29.2 yes View details
ndhA SSC 2161 0.0029 1.00 53.7 yes View details
trnH-GUG-psbA LSC 367 NA 0.99 61.5 no View details
rpl32-trnL-UAG SSC 1047 0.0034 1.00 63.1 yes View details
rpl20-rps12 LSC 817 0.0035 0.98 56.8 yes View details
rpl33-rps18 LSC 180 0.0151 1.00 55.7 yes View details
rps16-trnQ-UUG LSC 1670 0.0022 1.00 55.4 yes View details
psaA-ycf3 LSC 679 0.0022 1.00 55.4 yes View details
rpoB-trnC-GCA LSC 1160 0.0022 1.00 55.2 yes View details
petN-psbM LSC 1199 0.0034 1.00 54.8 yes View details
trnG-GCC-trnfM-CAU LSC 181 0.0121 1.00 54.7 yes View details
ycf1 SSC 5565 0.0023 1.00 52.8 yes View details
ycf1 IRb 1044 0.0008 1.00 42.0 no 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
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 1731–1751 1.000 82.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT GAGGTTCGAATCCTTCCGTC 1733–1753 1.000 81.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1724–1744 1.000 81.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CATGTCTTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 1734–1754 1.000 80.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TGTCTTTCAAGTCGCACGTT GAGGTTCGAATCCTTCCGTC 1732–1752 1.000 79.2
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGTCAAGCCCTGATCAATGA CCGGATTTGAACTGGGGAAA 1303–1318 1.000 81.0
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CGTCAAGCCCTGATCAATGA AAAAGGATTTGCAGTCCCCC 1285–1300 1.000 78.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AAAGTTCTTCCGTCAAGCCC CCGGATTTGAACTGGGGAAA 1313–1328 1.000 78.1
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCG CCGGATTTGAACTGGGGAAA 1233–1248 1.000 76.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AAAGTTCTTCCGTCAAGCCC AAAAGGATTTGCAGTCCCCC 1295–1310 1.000 75.9
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 1354–1363 1.000 69.8
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 1293–1302 1.000 68.3
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTC 1354–1363 1.000 65.6
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTC 1293–1302 1.000 64.1
petN-psbM_p5 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTCT 1355–1364 1.000 63.8
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 1019–1038 1.000 80.4
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TACCGCTGAGTTAAAAGGGC 984–1003 1.000 79.7
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 981–1000 1.000 79.6
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCGATGACTTACGCCTTACC 1016–1035 1.000 79.2
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TACCGCTGAGTTAAAAGGGC 946–965 1.000 78.9
psbZ-trnG-GCC_p1 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG CGTCTTCTCCTTGGCAAAGA 444–856 1.000 82.3
psbZ-trnG-GCC_p2 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTC CGTCTTCTCCTTGGCAAAGA 442–854 1.000 81.9
psbZ-trnG-GCC_p3 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG ACATTACTTTACCGTCGGCG 484–896 1.000 80.7
psbZ-trnG-GCC_p4 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTC ACATTACTTTACCGTCGGCG 482–894 1.000 80.3
psbZ-trnG-GCC_p5 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG TACCATTCGACCATATCCGC 417–829 1.000 77.8
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU AAAAACGCGGATATGGTCGA CTTGAGGTCACGGGTTCAAA 284–293 1.000 83.7
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU AAAACGCGGATATGGTCGAA CTTGAGGTCACGGGTTCAAA 283–292 1.000 83.7
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU AAAACGCGGATATGGTCGAA GTCACGGGTTCAAATCCTGT 277–286 1.000 83.3
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU AAAAACGCGGATATGGTCGA GTCACGGGTTCAAATCCTGT 278–287 1.000 83.2
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU AAAACGCGGATATGGTCGAA TCACGGGTTCAAATCCTGTC 276–285 1.000 82.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (14)

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

Species Accession Length (bp) Link
Corylopsis coreana NC_040141.1 159398 View on NCBI ↗
Corylopsis glandulifera NC_060830.1 159402 View on NCBI ↗
Corylopsis glaucescens NC_071197.1 159443 View on NCBI ↗
Corylopsis gotoana NC_086901.1 159434 View on NCBI ↗
Corylopsis microcarpa NC_061208.1 159438 View on NCBI ↗
Corylopsis multiflora NC_071838.1 159075 View on NCBI ↗
Corylopsis pauciflora NC_086902.1 159363 View on NCBI ↗
Corylopsis platypetala NC_071200.1 159032 View on NCBI ↗
Corylopsis sinensis NC_058779.1 159419 View on NCBI ↗
Corylopsis stelligera NC_071839.1 159438 View on NCBI ↗
Corylopsis trabeculosa NC_071209.1 159402 View on NCBI ↗
Corylopsis veitchiana NC_084415.1 159419 View on NCBI ↗
Corylopsis willmottiae NC_071201.1 159419 View on NCBI ↗
Corylopsis yunnanensis NC_071206.1 159454 View on NCBI ↗