Markers + reference

Cephalotaxus

9 species · Taxaceae · Cupressales

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Species 9
Genome length 136–137 kb
Candidate markers 232
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 232 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
clpP-accD Genome 925 0.0109 1.00 44.9 yes View details
accD Genome 3159 0.0083 0.97 47.2 yes View details
trnH-GUG-psbA Genome 287 0.0209 1.00 46.7 yes View details
chlN-ycf1 Genome 1107 0.0142 0.99 55.8 yes View details
ycf1 Genome 8292 0.0081 0.98 45.9 yes View details
trnI-GAU-rrn16 Genome 1407 0.0272 0.90 66.0 yes View details
ycf2 Genome 7194 0.0028 1.00 38.5 yes View details
rpl36-rps11 Genome 589 0.0398 0.98 81.1 no View details
petG-trnW-CCA Genome 119 0.0434 1.00 59.0 yes View details
rrn16-rps12 Genome 1566 0.0058 1.00 53.0 yes View details
psaA-ycf3 Genome 598 0.0047 1.00 50.5 yes View details
ycf4 Genome 546 0.0039 1.00 50.3 yes View details
trnE-UUC-trnT-GGU Genome 1004 0.0030 1.00 49.7 yes View details
rps4-trnQ-UUG Genome 551 0.0081 1.00 49.3 yes View details
psbK-psbI Genome 623 0.0051 1.00 47.4 yes View details
petA-psbJ Genome 763 0.0037 1.00 47.1 yes View details
trnS-GCU Genome 88 0.0107 1.00 47.0 yes View details
chlB-trnQ-UUG Genome 183 0.0140 1.00 46.9 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ycf4_p1 ycf4 ATGAGAGTGACTTTGGGAGT CGTTTGGGTGTTGGAGAAGA 648–649 1.000 62.7
ycf4_p2 ycf4 ATGAGAGTGACTTTGGGAGT TCGTTTGGGTGTTGGAGAAG 649–650 1.000 62.7
ycf4_p3 ycf4 ATGAGAGTGACTTTGGGAGT TTCGTTTGGGTGTTGGAGAA 650–651 1.000 59.6
ycf4_p4 ycf4 ATGAGAGTGACTTTGGGAGT ATTCGTTTGGGTGTTGGAGA 651–652 1.000 57.8
ycf4_p5 ycf4 GTGTTTGGTCACTCTTTCAACT CGTTTGGGTGTTGGAGAAGA 617–618 1.000 56.9
petA-psbJ_p1 petA-psbJ GCATCTGTCATTTTGGCACA TCCGGATTAGGATCATCCCT 871 1.000 66.9
petA-psbJ_p2 petA-psbJ AGTGCAATTGGTCGAGATGA TCCGGATTAGGATCATCCCT 815 1.000 66.7
petA-psbJ_p3 petA-psbJ GCATCTGTCATTTTGGCACA CGGAAGGATCCCTCTTTGGT 956 1.000 66.3
petA-psbJ_p4 petA-psbJ AGTGCAATTGGTCGAGATGA CGGAAGGATCCCTCTTTGGT 900 1.000 66.0
petA-psbJ_p5 petA-psbJ GCATCTGTCATTTTGGCACA GGAAGGATCCCTCTTTGGTT 955 1.000 65.4
petG-trnW-CCA_p1 petG-trnW-CCA CGACGTGGTGATCAATTGGA CTCCAAAACCTGATGCCGTA 188 1.000 81.2
petG-trnW-CCA_p2 petG-trnW-CCA CGACGTGGTGATCAATTGGA TCCAAAACCTGATGCCGTAG 187 1.000 81.2
petG-trnW-CCA_p3 petG-trnW-CCA CGACGTGGTGATCAATTGGA AGCGCTCTTAGTTCAGTTGG 221 1.000 80.7
petG-trnW-CCA_p4 petG-trnW-CCA CGACGTGGTGATCAATTGGA GTTCAGTTGGGTAGAACGCA 211 1.000 80.5
petG-trnW-CCA_p5 petG-trnW-CCA CGACGTGGTGATCAATTGGA TTCAGTTGGGTAGAACGCAG 210 1.000 80.3
clpP-accD_p1 clpP-accD ATTATAGCGGATACTCGTAAG CATGGTTCCACGGGCTATTT 1022–1130 1.000 42.3
clpP-accD_p2 clpP-accD ATTATAGCGGATACTCGTAAG TTGATACCATGGTTCCACGG 1029–1137 1.000 42.3
clpP-accD_p3 clpP-accD ATTATAGCGGATACTCGTAAG ATGGTTCCACGGGCTATTTT 1021–1129 1.000 42.3
clpP-accD_p4 clpP-accD TATTATAGCGGATACTCGTAAG CATGGTTCCACGGGCTATTT 1023–1131 1.000 42.3
clpP-accD_p5 clpP-accD ATTATAGCGGATACTCGTAAG TGGTTCCACGGGCTATTTTA 1020–1128 1.000 42.3
accD_p1 accD TTGACCGATGCCTGTTTGAA TGCAGCACGTCTAAAAGAGA 802–1018 1.000 82.5
accD_p2 accD ACCTACTACCGAGCCCATAC TGCAGCACGTCTAAAAGAGA 877–1093 1.000 82.3
accD_p3 accD CACCTACTACCGAGCCCATA TGCAGCACGTCTAAAAGAGA 878–1094 1.000 82.3
accD_p4 accD GCCAGAAGCACATACGAGAA TGCAGCACGTCTAAAAGAGA 949–1165 1.000 82.0
accD_p5 accD ACCTACTACCGAGCCCATAC ACTTTTTGGGTGGACTTCCA 911–1127 1.000 82.0
chlB-trnQ-UUG_p1 chlB-trnQ-UUG GAGCAGGACCAGCATACATC TGGTCCTGTTATTGCGAAGG 260–261 1.000 80.3
chlB-trnQ-UUG_p2 chlB-trnQ-UUG GAGCAGGACCAGCATACATC GGTCCTGTTATTGCGAAGGT 259–260 1.000 80.3
chlB-trnQ-UUG_p3 chlB-trnQ-UUG AGAGGAGCATGCATTATGGC TGGTCCTGTTATTGCGAAGG 324–325 1.000 80.1
chlB-trnQ-UUG_p4 chlB-trnQ-UUG AGAGGAGCATGCATTATGGC GGTCCTGTTATTGCGAAGGT 323–324 1.000 80.1
chlB-trnQ-UUG_p5 chlB-trnQ-UUG AGCTACTCGTAGGGTTCCAA TGGTCCTGTTATTGCGAAGG 283–284 1.000 79.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Cephalotaxus fortunei NC_056887.1 136195 View on NCBI ↗
Cephalotaxus fortunei var. alpina NC_056886.1 136368 View on NCBI ↗
Cephalotaxus griffithii NC_056888.1 135778 View on NCBI ↗
Cephalotaxus hainanensis NC_042392.1 136877 View on NCBI ↗
Cephalotaxus harringtonia NC_056889.1 135896 View on NCBI ↗
Cephalotaxus harringtonia var. nana NC_056891.1 135887 View on NCBI ↗
Cephalotaxus lanceolata NC_057234.1 136404 View on NCBI ↗
Cephalotaxus mannii NC_056890.1 136528 View on NCBI ↗
Cephalotaxus sinensis NC_037245.1 135646 View on NCBI ↗