Markers + reference

Pterocarya

10 species · Juglandaceae · Fagales

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Species 10
Genome length 160–160 kb
Candidate markers 277
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 277 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0006 1.00 46.2 yes View details
trnK-UUU-rps16 LSC 1057 0.0034 1.00 56.6 yes View details
rps16-trnQ-UUG LSC 1553 0.0034 1.00 60.6 yes View details
rps2 LSC 711 0.0016 1.00 36.0 yes View details
rpoB-trnC-GCA LSC 1247 0.0052 1.00 63.8 yes View details
trnC-GCA-petN LSC 848 0.0034 1.00 42.2 yes View details
trnD-GUC-trnY-GUA LSC 515 0.0056 1.00 53.1 yes View details
trnS-UGA-lhbA LSC 413 0.0009 0.99 37.8 yes View details
lhbA-trnG-UCC LSC 436 0.0068 0.97 63.1 yes View details
accD LSC 1575 0.0015 1.00 37.4 yes View details
ndhF SSC 2226 0.0087 1.00 49.1 yes View details
ndhF-rpl32 SSC 834 0.0054 0.99 47.7 yes View details
rpl2-trnH-GUG IRa 116 0.0314 1.00 71.2 no View details
ycf1-ndhF SSC 55 0.1628 1.00 67.6 yes View details
trnH-GUG-psbA LSC 186 0.0430 1.00 67.1 yes View details
rps2-rpoC2 LSC 230 0.0167 1.00 66.8 yes View details
trnM-CAU-psbD LSC 1535 0.0026 0.99 66.5 yes View details
accD-psaI LSC 783 0.0040 1.00 64.2 yes View details
trnS-GCU-trnG-GCC LSC 809 0.0046 0.99 63.9 yes View details
trnH-GUG LSC 75 0.0613 1.00 63.5 no View details
trnF-GAA-ndhJ LSC 831 0.0030 0.97 58.6 yes View details
ndhC-trnV-UAC LSC 610 0.0040 0.89 56.8 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 303 0.900 75.0
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 317 0.900 74.9
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 316 0.900 74.9
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 318 0.900 74.9
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC GCGCTAACCTTGGTATGGAA 332 0.900 72.1
psbA_p1 psbA GGAGCAATACCAATCCTCTTGA TGCTTGGGAGTCCCTAATGA 1190–1197 1.000 63.1
psbA_p2 psbA AGGAGCAATACCAATCCTCTTG TGCTTGGGAGTCCCTAATGA 1191–1198 1.000 63.1
psbA_p3 psbA GGAGCAATACCAATCCTCTTGA GTGCTTGGGAGTCCCTAATG 1191–1198 1.000 63.1
psbA_p4 psbA AGGAGCAATACCAATCCTCTTG GTGCTTGGGAGTCCCTAATG 1192–1199 1.000 63.0
psbA_p5 psbA GGAGCAATACCAATCCTCTTGA AGAATTCGTGTGCTTGGGAG 1200–1207 1.000 61.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCAGTCGCGGTCTTACAAAG TCAAAGAAGGCGGGAGTTTT 1235–1239 1.000 77.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 TCAGTCGCGGTCTTACAAAG TTCAAAGAAGGCGGGAGTTT 1236–1240 1.000 77.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGTCGCGGTCTTACAAAG TTTCAAAGAAGGCGGGAGTT 1237–1241 1.000 77.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCAAAGAAGGCGGGAGTTTT 1148–1152 1.000 77.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCAAAGAAGGCGGGAGTTT 1149–1153 1.000 77.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AATGGCGGATGTCAGAATCC GAGGTTCGAATCCTTCCGTC 1626–1674 1.000 83.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCCACAACCGACCATATCCT GAGGTTCGAATCCTTCCGTC 1609–1657 1.000 82.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1587–1635 1.000 82.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AATGGCGGATGTCAGAATCC TGGCTAAGTGGTAAGGCAAC 1667–1715 1.000 82.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAGAATCCACAACCGACCAT GAGGTTCGAATCCTTCCGTC 1614–1662 0.900 78.4
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GGAACGAATCACACTTTTACCA 629–881 1.000 60.4
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA TGGAACGAATCACACTTTTACC 630–882 1.000 60.4
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GGAACGAATCACACTTTTACCA 628–880 1.000 60.4
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC TGGAACGAATCACACTTTTACC 629–881 1.000 60.4
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC ACAAAAGCGGAAAGAGAGGG GGAACGAATCACACTTTTACCA 689–941 1.000 59.6
rps2_p1 rps2 ACTTGTATCTCTTTTGCGCG AAAGAGAGGAAGTGTGGGGA 839 1.000 70.4
rps2_p2 rps2 ACTTGTATCTCTTTTGCGCGA AAAGAGAGGAAGTGTGGGGA 839 1.000 69.2
rps2_p3 rps2 ACTTGTATCTCTTTTGCGCG AAGAGAGGAAGTGTGGGGAG 838 1.000 68.6
rps2_p4 rps2 ACTTGTATCTCTTTTGCGCG GAGGAAGTGTGGGGAGAGAA 834 1.000 68.5
rps2_p5 rps2 CTTGTATCTCTTTTGCGCGA AAAGAGAGGAAGTGTGGGGA 838 1.000 68.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Pterocarya fraxinifolia NC_046430.1 160246 View on NCBI ↗
Pterocarya hupehensis NC_046431.1 159770 View on NCBI ↗
Pterocarya macroptera NC_085233.1 160022 View on NCBI ↗
Pterocarya macroptera var. delavayi PV130123.1 160176 View on NCBI ↗
Pterocarya macroptera var. insignis NC_046429.1 159941 View on NCBI ↗
Pterocarya macroptera var. macroptera PV130121.1 160210 View on NCBI ↗
Pterocarya rhoifolia NC_081989.1 160216 View on NCBI ↗
Pterocarya stenoptera NC_046428.1 160202 View on NCBI ↗
Pterocarya tonkinensis NC_046427.1 160096 View on NCBI ↗
Pterocarya x rehderiana NC_081988.1 160306 View on NCBI ↗