Markers + reference

Cryptocarya

5 species · Lauraceae · Laurales

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Species 5
Genome length 156–157 kb
Candidate markers 254
Primer pairs 110

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 254 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 809 0.0052 1.00 65.4 yes View details
rps2 LSC 711 0.0011 1.00 34.0 yes View details
ndhC-trnV-UAC LSC 1822 0.0040 0.99 64.0 yes View details
rbcL LSC 1428 0.0048 1.00 54.8 yes View details
accD-psaI LSC 619 0.0091 0.99 53.9 yes View details
petA-psbJ LSC 1185 0.0054 1.00 68.3 yes View details
trnN-GUU-ndhF IRb 1543 0.0021 0.99 43.6 yes View details
ndhF-rpl32 SSC 1183 0.0044 1.00 46.9 yes View details
rpl32-trnL-UAG SSC 1064 0.0058 1.00 48.4 yes View details
ndhD SSC 1509 0.0017 1.00 37.5 yes View details
ycf1 SSC 5481 0.0026 1.00 36.9 yes View details
ccsA-ndhD SSC 231 0.0181 0.98 69.2 yes View details
atpH-atpI LSC 914 0.0049 1.00 67.7 yes View details
trnS-GGA-rps4 LSC 288 0.0071 0.98 62.5 yes View details
trnC-GCA-petN LSC 1082 0.0030 1.00 61.6 yes View details
rps2-rpoC2 LSC 171 0.0292 0.98 59.6 yes View details
trnT-UGU-trnL-UAA LSC 548 0.0024 1.00 54.4 yes View details
trnS-GCU-trnG-UCC LSC 826 0.0024 0.99 53.7 yes View details
trnE-UUC-trnT-GGU LSC 728 0.0017 1.00 53.0 yes View details
clpP LSC 2039 0.0027 1.00 52.4 yes View details
trnT-GGU-psbD LSC 1362 0.0034 1.00 52.2 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU GTGCTTTCGCGTCTCTCTAA GGATCGGGCAATCCAATCTC 2934–2963 1.000 77.0
trnK-UUU_p2 trnK-UUU GTGCTTTCGCGTCTCTCTAA AATGTTTTGACGGGATCGGG 2946–2975 1.000 76.5
trnK-UUU_p3 trnK-UUU GTGCTTTCGCGTCTCTCTAA GATCGGGCAATCCAATCTCT 2933–2962 1.000 76.3
trnK-UUU_p4 trnK-UUU GTGCTTTCGCGTCTCTCTAA TCGGGCAATCCAATCTCTTT 2931–2960 1.000 74.3
trnK-UUU_p5 trnK-UUU ACGGTTTTCAGTGCTGGTTA GGATCGGGCAATCCAATCTC 2983–2995 0.400 50.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTTCAAAGAAGGCGGAGGTG 875–903 1.000 78.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTTCAAAGAAGGCGGAGGTG 874–902 1.000 78.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGAAGGCGGAGGTGTTTAAG 869–897 1.000 78.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGAAGGCGGAGGTGTTTAAG 868–896 1.000 78.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA TTTCAAAGAAGGCGGAGGTG 884–912 1.000 77.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCGCGCTTTTACC 892–897 1.000 79.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCGCGCTTTTACC 891–896 1.000 79.2
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC TCAGAAGGAACGGAGAGAGG GAACGAATCGCGCTTTTACC 955–960 1.000 77.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGCAATCCGACGCTTTAGTC GAACGAATCGCGCTTTTACC 894–899 1.000 76.4
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CGACGCTTTAGTCCACTCAG GAACGAATCGCGCTTTTACC 887–892 1.000 76.2
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA CCCGTCATGTTCCTTGGATT 974–1052 1.000 82.8
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT CCCGTCATGTTCCTTGGATT 1032–1110 1.000 82.7
atpH-atpI_p3 atpH-atpI GATACCTTCTACGGCTTGGC CCCGTCATGTTCCTTGGATT 1061–1139 1.000 82.5
atpH-atpI_p4 atpH-atpI CGATACCTTCTACGGCTTGG CCCGTCATGTTCCTTGGATT 1062–1140 1.000 82.5
atpH-atpI_p5 atpH-atpI AGCCAATCCAGCAGCAATAA CCCGTCATGTTCCTTGGATT 992–1070 1.000 82.4
rps2_p1 rps2 TTTCTCAACTCGCCTGCTTT GTTTTCAAGAAACCGCTCGG 1342–1353 1.000 80.9
rps2_p2 rps2 TTTCTCAACTCGCCTGCTTT CGCTCGGGTTTTAGCAAAAG 1329–1340 1.000 80.9
rps2_p3 rps2 CTAACTCCCCATGCGGTAAC GTTTTCAAGAAACCGCTCGG 1787–1798 1.000 80.4
rps2_p4 rps2 CTAACTCCCCATGCGGTAAC CGCTCGGGTTTTAGCAAAAG 1774–1785 1.000 80.4
rps2_p5 rps2 TATATCATTCGTGGGCGCAG GTTTTCAAGAAACCGCTCGG 1807–1818 1.000 80.2
rps2-rpoC2_p1 rps2-rpoC2 CCTGCTTCCATCATCTCTTCC TGAGAGATATTTTGTTCCACCACA 329–340 1.000 45.0
rps2-rpoC2_p2 rps2-rpoC2 ACTCCTGCTTCCATCATCTCT TGAGAGATATTTTGTTCCACCACA 332–343 1.000 45.0
rps2-rpoC2_p3 rps2-rpoC2 ACTCCTGCTTCCATCATCTC TGAGAGATATTTTGTTCCACCACA 332–343 1.000 45.0
rps2-rpoC2_p4 rps2-rpoC2 CCTGCTTCCATCATCTCTTCC GAGAGATATTTTGTTCCACCACA 328–339 1.000 45.0
rps2-rpoC2_p5 rps2-rpoC2 CCTGCTTCCATCATCTCTTCC TGAGAGATATTTTGTTCCACCAC 329–340 1.000 45.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Cryptocarya calcicola OR264248.1 157066 View on NCBI ↗
Cryptocarya cercophylla NC_085709.1 156333 View on NCBI ↗
Cryptocarya hainanensis MT621586.1 157304 View on NCBI ↗
Cryptocarya metcalfiana NC_068503.1 157278 View on NCBI ↗
Cryptocarya yunnanensis MT621600.1 157157 View on NCBI ↗