Markers + reference

Dipteronia

2 species · Sapindaceae · Sapindales

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Species 2
Genome length 157–157 kb
Candidate markers 278
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 278 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 1024 0.0499 0.96 76.9 yes View details
rps16-trnQ-UUG LSC 1072 0.0551 0.97 82.0 yes View details
trnS-GCU-trnG LSC 794 0.1036 0.94 89.3 yes View details
trnR-UCU-atpA LSC 286 0.0927 0.87 77.2 yes View details
atpI-rps2 LSC 220 0.1500 1.00 75.3 yes View details
rps2 LSC 684 0.1418 0.97 82.0 yes View details
rps4-trnT-UGU LSC 367 0.1033 0.90 76.3 yes View details
trnT-UGU-trnL-UAA LSC 1054 0.0834 0.99 82.2 yes View details
psbE-petL LSC 790 0.0497 0.97 83.4 yes View details
rpl32-trnL-UAG SSC 1097 0.0860 0.94 88.6 yes View details
trnG-trnR-UCU LSC 170 0.0859 0.96 81.9 yes View details
trnH-GUG-psbA LSC 460 0.0539 0.93 79.6 yes View details
atpH-atpI LSC 1148 0.0252 0.97 76.3 yes View details
trnW-CCA-trnP-UGG LSC 207 0.0495 0.98 73.9 yes View details
psbZ-trnG-UCC LSC 562 0.0351 0.96 73.8 yes View details
trnG-UCC-trnfM-CAU LSC 165 0.0446 0.95 73.2 yes View details
petN-psbM LSC 770 0.0297 0.96 73.1 yes View details
trnE-UUC-trnT-GGU LSC 791 0.0421 0.96 72.7 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 GCGCTAACCTTGGTATGGAA 546–577 1.000 86.0
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 560–591 1.000 85.9
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 559–590 1.000 85.9
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 561–592 1.000 85.9
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 499–530 1.000 85.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAGGGATCCTGGAACAAGGA 1653–1679 1.000 84.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AGGGATCCTGGAACAAGGAA 1652–1678 1.000 84.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CGACAGGAACGGTTCATGAT 1218 0.500 59.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT CGACAGGAACGGTTCATGAT 1214 0.500 59.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 TTCAGGATCAGTCGTGGTCT CGACAGGAACGGTTCATGAT 1215 0.500 59.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1145–1177 1.000 84.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1160–1192 1.000 82.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1159–1191 1.000 82.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1149–1181 1.000 80.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1175–1207 1.000 79.8
trnS-GCU-trnG_p1 trnS-GCU-trnG CCGACGCTTTAATCCACTCA ACGAATCGCACTTTTACCACT 859–882 1.000 81.1
trnS-GCU-trnG_p2 trnS-GCU-trnG CCGACGCTTTAATCCACTCA ACGAATCGCACTTTTACCAC 859–882 1.000 81.1
trnS-GCU-trnG_p3 trnS-GCU-trnG GCTCGTACAACGGATTAGCA ACGAATCGCACTTTTACCACT 881–904 1.000 80.3
trnS-GCU-trnG_p4 trnS-GCU-trnG GCTCGTACAACGGATTAGCA ACGAATCGCACTTTTACCAC 881–904 1.000 80.3
trnS-GCU-trnG_p5 trnS-GCU-trnG AGCTCGTACAACGGATTAGC ACGAATCGCACTTTTACCACT 882–905 1.000 79.4
trnG-trnR-UCU_p1 trnG-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 250–253 1.000 70.0
trnG-trnR-UCU_p2 trnG-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 253–256 1.000 69.7
trnG-trnR-UCU_p3 trnG-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 256–259 1.000 69.2
trnG-trnR-UCU_p4 trnG-trnR-UCU AGCCTTCCAAGCTAACGATG TGCTAAATTGCGTCCAATAGGA 294–297 1.000 68.5
trnG-trnR-UCU_p5 trnG-trnR-UCU CCTAGCCTTCCAAGCTAACG TGCTAAATTGCGTCCAATAGGA 297–300 1.000 68.2
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TCAGGAACAAATGGAACGCT 313–351 1.000 73.8
trnR-UCU-atpA_p2 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT TCAGGAACAAATGGAACGCT 348–386 1.000 70.4
trnR-UCU-atpA_p3 trnR-UCU-atpA GTTCAAATCCTATTGGACGCA TCAGGAACAAATGGAACGCT 312–350 1.000 68.2
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TGGAACGCTTTCTACTTCAGG 302–340 1.000 67.9
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TTCAGGAACAAATGGAACGC 314–352 1.000 67.4

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
Dipteronia dyeriana NC_031899.1 157071 View on NCBI ↗
Dipteronia sinensis NC_029338.1 157080 View on NCBI ↗