Markers + reference

Saurauia

2 species · Actinidiaceae · Ericales

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Species 2
Genome length 157–157 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 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK (UUU)-rps16 LSC 780 0.0090 1.00 50.9 yes View details
trnG (UCC)-trnR (UCU) LSC 327 0.0312 0.98 73.0 yes View details
rpoC2 LSC 4149 0.0027 1.00 55.4 yes View details
ndhC-trnV (UAC) LSC 1224 0.0066 0.98 64.1 yes View details
rbcL-accD LSC 1763 0.0034 1.00 53.6 yes View details
accD-psaI LSC 669 0.0075 1.00 54.9 yes View details
ycf4 LSC 555 0.0054 1.00 54.3 yes View details
ycf4-cemA LSC 924 0.0065 1.00 62.5 yes View details
rpl20-rps12 LSC 769 0.0078 1.00 57.9 yes View details
ndhF-rpl32 SSC 971 0.0052 0.98 63.4 yes View details
ycf1 SSC 6951 0.0049 1.00 55.7 yes View details
trnK (UUU) LSC 37 0.0270 1.00 63.9 yes View details
atpA-atpF LSC 56 0.0179 1.00 62.3 yes View details
trnY (GUA)-trnE (UUC) LSC 64 0.0156 1.00 61.5 yes View details
petN-psbM LSC 1194 0.0042 1.00 61.2 yes View details
petD LSC 1246 0.0024 0.99 60.9 yes View details
rpoA LSC 1065 0.0038 1.00 60.9 yes View details
rpl23-trnH (GUG) IRb 820 0.0037 1.00 60.9 yes View details
psbA LSC 824 0.0036 1.00 60.8 yes View details
trnT (UGU)-trnL (UAA) LSC 854 0.0035 1.00 60.8 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA GTGCTCAGCCTGGAATACAA AATCTGGGAAGCAGCATCTG 286 1.000 79.2
psbA_p2 psbA GTGCTCAGCCTGGAATACAA CAATCTGGGAAGCAGCATCT 287 1.000 79.2
psbA_p3 psbA GTTGTGCTCAGCCTGGAATA AATCTGGGAAGCAGCATCTG 289 1.000 79.2
psbA_p4 psbA TTGTGCTCAGCCTGGAATAC AATCTGGGAAGCAGCATCTG 288 1.000 79.2
psbA_p5 psbA TTGTGCTCAGCCTGGAATAC CAATCTGGGAAGCAGCATCT 289 1.000 79.2
trnK (UUU)_p1 trnK (UUU) CGAATCCCTTGCTTCATCCA AGTTCAATGTTTTGATTTTCTCGT 165 1.000 40.5
trnK (UUU)_p2 trnK (UUU) ACGAATCCCTTGCTTCATCC AGTTCAATGTTTTGATTTTCTCGT 166 1.000 40.5
trnK (UUU)_p3 trnK (UUU) ATGGACGAATCCCTTGCTTC AGTTCAATGTTTTGATTTTCTCGT 170 1.000 40.5
trnK (UUU)_p4 trnK (UUU) GGACGAATCCCTTGCTTCAT AGTTCAATGTTTTGATTTTCTCGT 168 1.000 40.5
trnK (UUU)_p5 trnK (UUU) TCAGGATCAGTCGTGGTCTT AGTTCAATGTTTTGATTTTCTCGT 208 1.000 40.4
trnK (UUU)-rps16_p1 trnK (UUU)-rps16 TACCGTTGAGTTAGCAACCC GGAATTTCGCCCTAATCAAACG 833–834 1.000 58.6
trnK (UUU)-rps16_p2 trnK (UUU)-rps16 TACCGTTGAGTTAGCAACCC TTCGCCCTAATCAAACGAAA 828–829 1.000 58.5
trnK (UUU)-rps16_p3 trnK (UUU)-rps16 TACCGTTGAGTTAGCAACCC TTTCGCCCTAATCAAACGAA 829–830 1.000 58.5
trnK (UUU)-rps16_p4 trnK (UUU)-rps16 TACCGTTGAGTTAGCAACCC TTTCGCCCTAATCAAACGAAA 829–830 1.000 56.8
trnK (UUU)-rps16_p5 trnK (UUU)-rps16 TACCGTTGAGTTAGCAACCC TCGCCCTAATCAAACGAAAT 827–828 1.000 56.7
trnG (UCC)-trnR (UCU)_p1 trnG (UCC)-trnR (UCU) AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 407 1.000 66.7
trnG (UCC)-trnR (UCU)_p2 trnG (UCC)-trnR (UCU) CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 410 1.000 66.4
trnG (UCC)-trnR (UCU)_p3 trnG (UCC)-trnR (UCU) AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 413 1.000 66.0
trnG (UCC)-trnR (UCU)_p4 trnG (UCC)-trnR (UCU) CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 416 1.000 65.7
trnG (UCC)-trnR (UCU)_p5 trnG (UCC)-trnR (UCU) CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 411 1.000 64.2
atpA-atpF_p1 atpA-atpF ACTTGAAGTACGGTACCGGT TGGTATGTTTGAGGCGATGA 197–198 1.000 68.8
atpA-atpF_p2 atpA-atpF TTGCTCAATACGTTCACGGA TGGTATGTTTGAGGCGATGA 150–151 1.000 68.4
atpA-atpF_p3 atpA-atpF ACTTGAAGTACGGTACCGGT TTACGTACCATCAGTGCCAA 220–221 1.000 68.3
atpA-atpF_p4 atpA-atpF ACTTGAAGTACGGTACCGGT TTTACGTACCATCAGTGCCA 221–222 1.000 68.3
atpA-atpF_p5 atpA-atpF TCGCCTACTTGAAGTACGGT TGGTATGTTTGAGGCGATGA 203–204 1.000 68.1
rpoC2_p1 rpoC2 TGATTTTAAGTGTGGCCCGT TCAGATCCTGGTAACTAAGT 256 1.000 41.2
rpoC2_p2 rpoC2 TGATTTTAAGTGTGGCCCGT ACCTATAATCAGATCCTGGTAACT 264 1.000 41.2
rpoC2_p3 rpoC2 TGATTTTAAGTGTGGCCCGT ACCTATAATCAGATCCTGGT 264 1.000 41.2
rpoC2_p4 rpoC2 TGATTTTAAGTGTGGCCCGT AACCTATAATCAGATCCTGGT 265 1.000 41.2
rpoC2_p5 rpoC2 TGATTTTAAGTGTGGCCCGT ATCAGATCCTGGTAACTAAGT 257 1.000 41.2

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
Saurauia polyneura OM949900.1 156819 View on NCBI ↗
Saurauia tristyla NC_044098.1 156676 View on NCBI ↗