Markers + reference

Liquidambar

9 species · Altingiaceae · Saxifragales

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Species 9
Genome length 160–161 kb
Candidate markers 272
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
tRNA-GUG-psbA LSC 375 0.0173 0.99 49.7 yes View details
atpF-atpH LSC 468 0.0124 1.00 41.9 yes View details
tRNA-GCA-petN LSC 779 0.0082 1.00 44.7 yes View details
psbM-tRNA-GUC LSC 1130 0.0086 1.00 50.3 yes View details
tRNA-UUC-tRNA-GGU LSC 1009 0.0147 1.00 46.2 yes View details
tRNA-UGU-tRNA-UAA LSC 1164 0.0110 0.99 50.1 yes View details
accD-psaI LSC 443 0.0133 1.00 47.6 yes View details
petA-psbJ LSC 1072 0.0104 0.99 59.3 yes View details
tRNA-UGG-psaJ LSC 410 0.0142 1.00 38.5 yes View details
ycf1 IRb 1119 0.0009 1.00 32.2 no View details
rpl32-tRNA-UAG SSC 1244 0.0088 1.00 48.3 yes View details
psaC SSC 246 0.0070 1.00 26.7 yes View details
ycf1 SSC 5637 0.0061 1.00 34.9 yes View details
petN-psbM LSC 991 0.0085 1.00 57.1 yes View details
ndhD-psaC SSC 100 0.0306 1.00 55.7 yes View details
tRNA-UUU-rps16 LSC 950 0.0044 0.99 51.2 yes View details
ndhF-rpl32 SSC 1072 0.0071 1.00 50.0 yes View details
atpA-atpF LSC 69 0.0137 0.93 49.5 yes View details
atpH-atpI LSC 1164 0.0054 1.00 46.5 yes View details
rpl36-infA LSC 127 0.0122 1.00 46.0 yes View details
psaB-psaA LSC 25 0.0156 1.00 45.7 yes View details
psbC-tRNA-UGA LSC 239 0.0146 1.00 45.0 yes View details
ycf3-tRNA-GGA LSC 832 0.0083 1.00 44.5 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
tRNA-GUG-psbA_p1 tRNA-GUG-psbA GATCCACTTGGCTACATCCG TCGAAGCTCCATCTACAAATGG 416–441 1.000 66.8
tRNA-GUG-psbA_p2 tRNA-GUG-psbA GATCCACTTGGCTACATCCG CGAAGCTCCATCTACAAATGG 415–440 1.000 66.6
tRNA-GUG-psbA_p3 tRNA-GUG-psbA CAATCCACTGCCTTGATCCA TCGAAGCTCCATCTACAAATGG 430–455 1.000 66.5
tRNA-GUG-psbA_p4 tRNA-GUG-psbA AATCCACTGCCTTGATCCAC TCGAAGCTCCATCTACAAATGG 429–454 1.000 66.5
tRNA-GUG-psbA_p5 tRNA-GUG-psbA ACAATCCACTGCCTTGATCC TCGAAGCTCCATCTACAAATGG 431–456 1.000 66.5
tRNA-UUU-rps16_p1 tRNA-UUU-rps16 CCGATGGTATGGACGAATCC GGTGCTCAACCTACAGGAAC 1114–1132 1.000 81.0
tRNA-UUU-rps16_p2 tRNA-UUU-rps16 CCGATGGTATGGACGAATCC AGAAGGCGGAGGTTTTTACG 1077–1095 1.000 81.0
tRNA-UUU-rps16_p3 tRNA-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 1052–1070 1.000 80.5
tRNA-UUU-rps16_p4 tRNA-UUU-rps16 AAGCCGAGTACTCTACCGTT AGAAGGCGGAGGTTTTTACG 1015–1033 1.000 80.5
tRNA-UUU-rps16_p5 tRNA-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 1053–1071 1.000 80.4
atpA-atpF_p1 atpA-atpF CCGTCGCCTACTTGAAGTAC TGTTTGGGGCGATGAAAGAA 208–215 1.000 82.6
atpA-atpF_p2 atpA-atpF GTCGCCTACTTGAAGTACGG TGTTTGGGGCGATGAAAGAA 206–213 1.000 82.6
atpA-atpF_p3 atpA-atpF GTCGCCTACTTGAAGTACGG AAGGAGCTCTAGGAACCCTG 281–288 1.000 80.8
atpA-atpF_p4 atpA-atpF GTCGCCTACTTGAAGTACGG CAAGGAGCTCTAGGAACCCT 282–289 1.000 80.8
atpA-atpF_p5 atpA-atpF CCGTCGCCTACTTGAAGTAC AAGGAGCTCTAGGAACCCTG 283–290 1.000 80.7
atpF-atpH_p1 atpF-atpH CAGTGACCCAAGGAAACGAA TACGCCAACTCTTGTGGATG 1236–1256 1.000 81.8
atpF-atpH_p2 atpF-atpH AGAAAGAGTACCATGCTGCG TACGCCAACTCTTGTGGATG 1588–1608 1.000 81.6
atpF-atpH_p3 atpF-atpH AGAAAGAGTACCATGCTGCG AAGTCCTTCCGTTTCGTCTG 1408–1428 1.000 81.3
atpF-atpH_p4 atpF-atpH CAGTGACCCAAGGAAACGAA AAGGTATTGCGAGACAACCC 627–647 0.778 74.0
atpF-atpH_p5 atpF-atpH AGAAAGAGTACCATGCTGCG AAGGTATTGCGAGACAACCC 979–999 0.778 73.0
atpH-atpI_p1 atpH-atpI GCGGCAGAAATCAGTGGATT TTTTTGCAACTTTAGCCGCG 1212–1243 1.000 72.0
atpH-atpI_p2 atpH-atpI GCGGCAGAAATCAGTGGATT AGGCGAATCTATGGAGGGTC 1184–1215 1.000 71.0
atpH-atpI_p3 atpH-atpI GCGGCAGAAATCAGTGGATT TAGGCGAATCTATGGAGGGT 1185–1216 1.000 70.7
atpH-atpI_p4 atpH-atpI CGGCAGAAATCAGTGGATTC TTTTTGCAACTTTAGCCGCG 1211–1242 1.000 70.3
atpH-atpI_p5 atpH-atpI GGAAGCGGCAGAAATCAGT TTTTTGCAACTTTAGCCGCG 1216–1247 1.000 70.1
tRNA-GCA-petN_p1 tRNA-GCA-petN TTTTGTATCGTTTTGGCGGC AGCCCAAGCGAGACTTACTA 892–905 1.000 80.6
tRNA-GCA-petN_p2 tRNA-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 836–849 1.000 80.5
tRNA-GCA-petN_p3 tRNA-GCA-petN TTTTGTATCGTTTTGGCGGC AGAGTCCACTTCTTCCCCAT 953–966 1.000 78.8
tRNA-GCA-petN_p4 tRNA-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 897–910 1.000 78.7
tRNA-GCA-petN_p5 tRNA-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 854–867 1.000 78.3

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
Liquidambar acalycina NC_046936.1 160433 View on NCBI ↗
Liquidambar chinensis NC_047288.1 160401 View on NCBI ↗
Liquidambar excelsa NC_048995.1 160861 View on NCBI ↗
Liquidambar formosana NC_023092.1 160410 View on NCBI ↗
Liquidambar multinervis NC_071836.1 160427 View on NCBI ↗
Liquidambar orientalis NC_046937.1 160771 View on NCBI ↗
Liquidambar siamensis NC_071837.1 160431 View on NCBI ↗
Liquidambar styraciflua NC_046938.1 160750 View on NCBI ↗
Liquidambar yunnanensis NC_048981.1 160860 View on NCBI ↗