Markers + reference

Lithocarpus

28 species · Fagaceae · Fagales

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Species 28
Genome length 161–161 kb
Candidate markers 267
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 446 0.0283 0.99 66.8 yes View details
trnK-UUU-rps16 LSC 1065 0.0136 0.97 63.5 yes View details
rpoB-trnC-GCA LSC 1276 0.0078 1.00 61.5 yes View details
trnF-GAA-ndhJ LSC 848 0.0126 0.99 69.3 yes View details
rbcL-accD LSC 608 0.0165 0.99 70.6 yes View details
ycf1 IRb 1115 0.0069 0.99 51.6 no View details
ndhF SSC 2265 0.0096 1.00 54.8 yes View details
ccsA-ndhD SSC 320 0.0190 0.94 69.1 yes View details
ycf1 SSC 5700 0.0081 1.00 53.8 yes View details
trnS-GCU-trnG-GCC LSC 989 0.0090 0.99 74.2 yes View details
psbC-trnS-UGA LSC 260 0.0196 1.00 70.2 yes View details
trnT-GGU-psbD LSC 1654 0.0069 1.00 69.7 yes View details
petA-psbJ LSC 1023 0.0057 1.00 69.1 yes View details
psbZ-trnG-UCC LSC 626 0.0070 1.00 67.8 yes View details
petN-psbM LSC 981 0.0055 0.99 67.6 yes View details
ndhF-rpl32 SSC 948 0.0076 1.00 66.9 yes View details
ndhA SSC 2138 0.0060 1.00 66.7 yes View details
psbK-psbI LSC 397 0.0105 1.00 66.2 yes View details
psaJ-rpl33 LSC 485 0.0075 1.00 65.2 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CGTGCTAACCTTGGTATGGA 527–597 1.000 85.2
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCGTGCTAACCTTGGTATGG 528–598 1.000 85.2
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CGTGCTAACCTTGGTATGGA 541–611 1.000 85.0
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCGTGCTAACCTTGGTATGG 542–612 1.000 85.0
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CGTGCTAACCTTGGTATGGA 540–610 1.000 85.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCCCACACTCTAATGGAGA CTCTTCGGAAAGTGGGCTTT 1628–1726 1.000 87.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGACTGATCGACGGACTCT CTCTTCGGAAAGTGGGCTTT 1805–1903 1.000 87.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGACTGATCGACGGACTCTT CTCTTCGGAAAGTGGGCTTT 1804–1902 1.000 87.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGTTTTGAACCGATCCGCT CTCTTCGGAAAGTGGGCTTT 1370–1466 0.964 85.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 GATCGACGGACTCTTTAGCC CTCTTCGGAAAGTGGGCTTT 1851–1897 0.750 76.4
psbK-psbI_p1 psbK-psbI CTTTTGTTTGGCAAGCTGCT CTTCACTCTTCACGTCCAGG 526–553 0.929 84.4
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG CTTCACTCTTCACGTCCAGG 521–548 0.929 84.4
psbK-psbI_p3 psbK-psbI CTTTTGTTTGGCAAGCTGCT TCACTCTTCACGTCCAGGAT 524–551 0.929 84.4
psbK-psbI_p4 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCACTCTTCACGTCCAGGAT 519–546 0.929 84.4
psbK-psbI_p5 psbK-psbI CTTTTGTTTGGCAAGCTGCT TTCACTCTTCACGTCCAGGA 525–552 0.929 82.6
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA CGAAGGACCCCTTAACCATT 902–1104 1.000 81.1
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC CGAAGGACCCCTTAACCATT 901–1103 1.000 81.1
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC TAGTCCACTCAGCCATCTCC CGAAGGACCCCTTAACCATT 889–1091 1.000 79.5
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA CGAAGGACCCCTTAACCATTT 902–1104 1.000 78.9
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC CGAAGGACCCCTTAACCATTT 901–1103 1.000 78.9
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCTCATTTCTACCCCCAAGC CTGGGGTAGGGGTTACAGAA 1841–1976 0.964 85.7
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GATACCGGGGCTTTGCAATA CTGGGGTAGGGGTTACAGAA 2215–2350 0.964 85.0
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GATACCGGGGCTTTGCAATA TTTAGAGAACAGAACCGCCG 1859–1993 0.964 84.5
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG CTGGGGTAGGGGTTACAGAA 2523–2658 0.964 84.4
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG TTTAGAGAACAGAACCGCCG 2167–2301 0.964 83.9
petN-psbM_p1 petN-psbM ATGTTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTCT 1103–1151 0.929 70.0
petN-psbM_p2 petN-psbM CTCGCTTGGGCTGCTTTAAT TGCTACTGCACTGTTCATTCT 1094–1142 1.000 68.2
petN-psbM_p3 petN-psbM ATGTTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTC 1103–1151 0.929 65.8
petN-psbM_p4 petN-psbM ATGTTAAGTCTCGCTTGGGC GCACTGTTCATTCTAGTTCCG 1096–1144 0.929 65.3
petN-psbM_p5 petN-psbM ATGTTAAGTCTCGCTTGGGC TCATTCTAGTTCCGACTGCT 1089–1137 0.929 65.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (28)

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

Species Accession Length (bp) Link
Lithocarpus amygdalifolius PQ276669.1 161283 View on NCBI ↗
Lithocarpus areca PQ276671.1 161148 View on NCBI ↗
Lithocarpus balansae NC_026577.1 161020 View on NCBI ↗
Lithocarpus brevicaudatus PQ276666.1 161208 View on NCBI ↗
Lithocarpus calophyllus NC_086857.1 161225 View on NCBI ↗
Lithocarpus cleistocarpus OM112296.1 161178 View on NCBI ↗
Lithocarpus corneus NC_086859.1 161265 View on NCBI ↗
Lithocarpus craibianus OM112298.1 161029 View on NCBI ↗
Lithocarpus crassifolius NC_086858.1 161331 View on NCBI ↗
Lithocarpus elizabethiae PQ276667.1 161273 View on NCBI ↗
Lithocarpus fenzelianus OM388302.1 161148 View on NCBI ↗
Lithocarpus fohaiensis PQ276656.1 161370 View on NCBI ↗
Lithocarpus grandifolius PQ276659.1 161193 View on NCBI ↗
Lithocarpus gymnocarpus PQ276663.1 161295 View on NCBI ↗
Lithocarpus hancei OM112299.1 160815 View on NCBI ↗
Lithocarpus konishii NC_069647.1 161059 View on NCBI ↗
Lithocarpus litseifolius NC_063927.1 161322 View on NCBI ↗
Lithocarpus longanoides PV191269.1 161259 View on NCBI ↗
Lithocarpus longinux NC_062048.1 161420 View on NCBI ↗
Lithocarpus obscurus OM112297.1 161349 View on NCBI ↗
Lithocarpus oleifolius OR805597.1 161212 View on NCBI ↗
Lithocarpus pachylepis PQ276660.1 161010 View on NCBI ↗
Lithocarpus skanianus OM388304.1 161246 View on NCBI ↗
Lithocarpus sphaerocarpus PQ276658.1 161283 View on NCBI ↗
Lithocarpus tabularis PQ276662.1 161131 View on NCBI ↗
Lithocarpus uvariifolius NC_086860.1 161396 View on NCBI ↗
Lithocarpus xylocarpus PQ276661.1 161239 View on NCBI ↗
Lithocarpus yongfuensis PX109668.1 161258 View on NCBI ↗