Markers + reference

Athrotaxis

2 species · Cupressaceae · Cupressales

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Species 2
Genome length 133–134 kb
Candidate markers 240
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 240 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpl32 Genome 801 0.1218 0.89 81.9 yes View details
rpl32-trnM-CAU Genome 531 0.0420 0.99 67.9 yes View details
ycf1 Genome 8610 0.0122 0.94 58.8 yes View details
ycf1-rps12 Genome 1054 0.0254 0.94 69.2 yes View details
infA Genome 309 0.0550 1.00 67.2 yes View details
infA-rps8 Genome 344 0.1346 0.60 66.4 yes View details
trnV-GAC-LK118_pgr004 Genome 850 0.0231 0.97 65.8 yes View details
trnH-GUG-psbA Genome 484 0.0227 0.99 84.9 no View details
LK118_pgr003-LK118_pgr002 Genome 2 0.5000 1.00 81.6 yes View details
trnG-UCC Genome 23 0.0435 1.00 77.5 yes View details
LK118_pgr004-trnI-GAU Genome 430 0.0303 1.00 72.8 yes View details
rpl22-rps19 Genome 53 0.1132 1.00 72.5 yes View details
ndhJ-chlN Genome 738 0.0169 0.96 72.3 yes View details
trnM-CAU-atpB Genome 244 0.0451 1.00 68.7 yes View details
chlB-trnQ-UUG Genome 192 0.0209 0.99 65.0 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
chlB-trnQ-UUG_p1 chlB-trnQ-UUG TCCTAGAGGAGCGTGCATAA TGGTCCTGTTATTGCGAAGG 336–337 1.000 79.8
chlB-trnQ-UUG_p2 chlB-trnQ-UUG TCCTAGAGGAGCGTGCATAA GGTCCTGTTATTGCGAAGGT 335–336 1.000 79.8
chlB-trnQ-UUG_p3 chlB-trnQ-UUG GAGCAGGACCAGCATACATC TGGTCCTGTTATTGCGAAGG 268–269 1.000 79.6
chlB-trnQ-UUG_p4 chlB-trnQ-UUG GAGCAGGACCAGCATACATC GGTCCTGTTATTGCGAAGGT 267–268 1.000 79.6
chlB-trnQ-UUG_p5 chlB-trnQ-UUG AGCTACTCGTAGGGTTCCAA TGGTCCTGTTATTGCGAAGG 291–292 1.000 78.7
trnG-UCC_p1 trnG-UCC CCAGGGTATTCATAGGAGAGGT GGACAAAAGATCGATCTGTATGC 177 1.000 40.5
trnG-UCC_p2 trnG-UCC ACCAGGGTATTCATAGGAGAGG GGACAAAAGATCGATCTGTATGC 178 1.000 40.4
trnG-UCC_p3 trnG-UCC ACCAGGGTATTCATAGGAGAGG TGGACAAAAGATCGATCTGT 179 1.000 40.4
trnG-UCC_p4 trnG-UCC CCAGGGTATTCATAGGAGAGGT TGGACAAAAGATCGATCTGT 178 1.000 40.4
trnG-UCC_p5 trnG-UCC CCAGGGTATTCATAGGAGAGGT TTGGACAAAAGATCGATCTGT 179 1.000 40.4
rpl32_p1 rpl32 CACAAACCTCTTTGGGACGA CGACTCTCGCCGTATGAAAG 1796–1813 1.000 84.3
rpl32_p2 rpl32 TTCCAAATTAACGTGGCCCA CGACTCTCGCCGTATGAAAG 1909–1926 1.000 84.2
rpl32_p3 rpl32 TGCATTGATGGATGATGGGG CGACTCTCGCCGTATGAAAG 2078–2095 1.000 83.6
rpl32_p4 rpl32 TCGTTTACGTTTACCCGCAA CGACTCTCGCCGTATGAAAG 1821–1838 1.000 83.4
rpl32_p5 rpl32 ATCATGAGGTCCTTCTCCGT CGACTCTCGCCGTATGAAAG 2045–2062 1.000 82.4
rpl32-trnM-CAU_p1 rpl32-trnM-CAU ATCTTCGATGTCGCAGCAAT ACCAGCTGTATCGCTATCCT 1274–1276 1.000 82.9
rpl32-trnM-CAU_p2 rpl32-trnM-CAU GATAACGATCGGCAAGCTCA ACCAGCTGTATCGCTATCCT 1152–1154 1.000 82.1
rpl32-trnM-CAU_p3 rpl32-trnM-CAU ATCTTCGATGTCGCAGCAAT CCGTCTGTAGCACTCATAGC 1357–1359 1.000 81.7
rpl32-trnM-CAU_p4 rpl32-trnM-CAU TCCCACTCCTCCCTTTCTTT ACCAGCTGTATCGCTATCCT 1458 0.500 58.9
rpl32-trnM-CAU_p5 rpl32-trnM-CAU TTCCCACTCCTCCCTTTCTT ACCAGCTGTATCGCTATCCT 1459 0.500 58.9
trnM-CAU-atpB_p1 trnM-CAU-atpB GCGAGAGTCGTTGGTTCAAA CCTGCCGTATGCTCAAAAGA 330–331 1.000 74.3
trnM-CAU-atpB_p2 trnM-CAU-atpB GCTTTCATACGGCGAGAGTC CCTGCCGTATGCTCAAAAGA 341–342 1.000 74.1
trnM-CAU-atpB_p3 trnM-CAU-atpB AGAGTATCGCTTTCATACGGC CCTGCCGTATGCTCAAAAGA 349–350 1.000 72.3
trnM-CAU-atpB_p4 trnM-CAU-atpB GCGAGAGTCGTTGGTTCAA CCTGCCGTATGCTCAAAAGA 330–331 1.000 71.7
trnM-CAU-atpB_p5 trnM-CAU-atpB GCGAGAGTCGTTGGTTCAAA ATCTGAGTAATACGGCCTGC 345–346 1.000 69.7
ycf1_p1 ycf1 CTCACTCGGTCTTCAAGCTC TTCTGTTCACGTGTGGAAGG 734–761 1.000 84.9
ycf1_p2 ycf1 CTCTCACTCGGTCTTCAAGC TTCTGTTCACGTGTGGAAGG 736–763 1.000 84.8
ycf1_p3 ycf1 GCTCTCACTCGGTCTTCAAG TTCTGTTCACGTGTGGAAGG 737–764 1.000 84.8
ycf1_p4 ycf1 CTCACTCGGTCTTCAAGCTC AGTCTTCCTTCAGGGTCCTC 579–597 1.000 84.7
ycf1_p5 ycf1 CTCACTCGGTCTTCAAGCTC GTCTTCCTTCAGGGTCCTCT 578–596 1.000 84.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Athrotaxis cupressoides NC_058593.1 134248 View on NCBI ↗
Athrotaxis laxifolia MW470974.1 132693 View on NCBI ↗