Markers + reference

Calocedrus

2 species · Cupressaceae · Cupressales

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Species 2
Genome length 127–127 kb
Candidate markers 241
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 241 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rrn16-trnV-GAC Genome 831 0.0531 0.73 69.9 yes View details
ycf2-rpl23 Genome 637 0.1798 0.93 86.8 yes View details
petA-psbJ Genome 466 0.0265 0.89 65.2 yes View details
rps12-clpP Genome 1140 0.0338 0.91 81.5 yes View details
ycf1 Genome 6906 0.0129 1.00 45.6 yes View details
trnL-CAA-accD Genome 1368 0.1121 0.85 80.8 yes View details
rpl36-rps11 Genome 159 0.0503 1.00 81.3 yes View details
psaJ-rpl33 Genome 306 0.0440 0.82 78.0 yes View details
trnR-ACG-rrn5 Genome 105 0.0571 1.00 77.1 yes View details
trnI-CAU-psbA Genome 143 0.0070 0.99 74.1 no View details
chlL-trnH-GUG Genome 146 0.0286 0.96 72.8 yes View details
trnI-GAU-rrn16 Genome 507 0.0344 0.97 70.8 yes View details
psbJ-psbL Genome 179 0.0940 0.65 66.4 yes View details
psbA-trnK-UUU Genome 496 0.0085 0.94 66.1 yes View details
psaA-ycf3 Genome 500 0.0160 1.00 66.1 yes View details
trnD-GUC-trnY-GUA Genome 213 0.0235 1.00 66.0 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK-UUU_p1 psbA-trnK-UUU GTGCTAGTGATCCAATCGCA GAAAGCCGTGTGCAATGAAA 659–687 1.000 82.3
psbA-trnK-UUU_p2 psbA-trnK-UUU GTGCTAGTGATCCAATCGCA CACGGTTTGGGGAGAGATTT 631–659 1.000 81.9
psbA-trnK-UUU_p3 psbA-trnK-UUU ATTCCATAGGCTTGCGCTTT GAAAGCCGTGTGCAATGAAA 633–661 1.000 81.0
psbA-trnK-UUU_p4 psbA-trnK-UUU AGTGCTAGTGATCCAATCGC GAAAGCCGTGTGCAATGAAA 660–688 1.000 80.9
psbA-trnK-UUU_p5 psbA-trnK-UUU AGTGCTAGTGATCCAATCGC CACGGTTTGGGGAGAGATTT 632–660 1.000 80.5
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA TTGACAGGGCGGTACTCTAA CCTACGCTGGTTCAAATCCA 282 1.000 80.0
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA TTGACAGGGCGGTACTCTAA ATGCCTACGCTGGTTCAAAT 285 1.000 79.8
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA AGGGCGGTACTCTAACCAAT CCTACGCTGGTTCAAATCCA 277 1.000 79.6
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA AGGGCGGTACTCTAACCAAT ATGCCTACGCTGGTTCAAAT 280 1.000 79.4
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA TTGACAGGGCGGTACTCTAA GGGGACGGACTGTAAATTCG 313 1.000 77.9
psaA-ycf3_p1 psaA-ycf3 AGAAATGACCGGGTTTAGCC TGGTTTGATCAAGCTGCTGA 702–704 1.000 77.8
psaA-ycf3_p2 psaA-ycf3 TGGGTCCCTTAGCTAGTGTC TGGTTTGATCAAGCTGCTGA 726–728 1.000 77.7
psaA-ycf3_p3 psaA-ycf3 GGGTCCCTTAGCTAGTGTCT TGGTTTGATCAAGCTGCTGA 725–727 1.000 77.5
psaA-ycf3_p4 psaA-ycf3 TTGGGTCCCTTAGCTAGTGT TGGTTTGATCAAGCTGCTGA 727–729 1.000 76.1
psaA-ycf3_p5 psaA-ycf3 AGAAATGACCGGGTTTAGCC CTTGGTTTGATCAAGCTGCTG 704–706 1.000 71.6
trnR-ACG-rrn5_p1 trnR-ACG-rrn5 CCACGTGCTCTAATCCTCTG AATCCATCCCGAACTTGGTG 224–238 1.000 79.3
trnR-ACG-rrn5_p2 trnR-ACG-rrn5 CCACGTGCTCTAATCCTCTG ACCAATCCATCCCGAACTTG 227–241 1.000 79.3
trnR-ACG-rrn5_p3 trnR-ACG-rrn5 CCACGTGCTCTAATCCTCTG CAATCCATCCCGAACTTGGT 225–239 1.000 79.3
trnR-ACG-rrn5_p4 trnR-ACG-rrn5 CCACGTGCTCTAATCCTCTG CACCAATCCATCCCGAACTT 228–242 1.000 79.3
trnR-ACG-rrn5_p5 trnR-ACG-rrn5 AGTAGTGAACTGTTGTGGGC AATCCATCCCGAACTTGGTG 281–295 1.000 78.6
trnI-GAU-rrn16_p1 trnI-GAU-rrn16 GCGTTGATGAGCACATTGAA CAAGGTAGCCGTACTGGAAG 649–653 1.000 76.4
trnI-GAU-rrn16_p2 trnI-GAU-rrn16 GCGTTGATGAGCACATTGAA AGTGACTGGAGTGAAGTCGT 671–675 1.000 76.2
trnI-GAU-rrn16_p3 trnI-GAU-rrn16 GCGTTGATGAGCACATTGAA AAGTCGTAACAAGGTAGCCG 658–662 1.000 75.8
trnI-GAU-rrn16_p4 trnI-GAU-rrn16 GCGTTGATGAGCACATTGAA AACAAGGTAGCCGTACTGGA 651–655 1.000 75.8
trnI-GAU-rrn16_p5 trnI-GAU-rrn16 GCGTTGATGAGCACATTGAA ACAAGGTAGCCGTACTGGAA 650–654 1.000 75.8
rrn16-trnV-GAC_p1 rrn16-trnV-GAC GGGCAGGTTCTTACGCATTA ACCTTGACGTGGTGAAAGTC 997–1055 1.000 85.9
rrn16-trnV-GAC_p2 rrn16-trnV-GAC CCTACAGACACTTTACGCCC ACCTTGACGTGGTGAAAGTC 1433–1491 1.000 85.5
rrn16-trnV-GAC_p3 rrn16-trnV-GAC CCTACAGACACTTTACGCCC CCTTGACGTGGTGAAAGTCA 1432–1490 1.000 85.5
rrn16-trnV-GAC_p4 rrn16-trnV-GAC GTGTTCCTCCCGATCTCAAC ACCTTGACGTGGTGAAAGTC 1567–1625 1.000 85.3
rrn16-trnV-GAC_p5 rrn16-trnV-GAC GTGTTCCTCCCGATCTCAAC CCTTGACGTGGTGAAAGTCA 1566–1624 1.000 85.3

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
Calocedrus decurrens NC_045867.1 127112 View on NCBI ↗
Calocedrus macrolepis KX832621.1 127157 View on NCBI ↗