Markers + reference

Aspidopterys

4 species · Malpighiaceae · Malpighiales

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Species 4
Genome length 160–161 kb
Candidate markers 269
Primer pairs 105

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 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 859 0.0169 0.96 68.6 yes View details
trnS-GCU-trnS-CGA LSC 912 0.0175 0.97 62.8 yes View details
psbM-trnD-GUC LSC 1173 0.0119 1.00 61.0 yes View details
ndhC-trnV-UAC LSC 1201 0.0181 0.99 64.9 yes View details
rbcL-accD LSC 991 0.0140 1.00 67.7 yes View details
petA-psbJ LSC 1079 0.0182 1.00 64.5 yes View details
trnW-CCA-trnP-UGG LSC 183 0.0064 1.00 44.5 yes View details
rps11 LSC 423 0.0110 1.00 48.1 yes View details
trnR-ACG-rrn5 IRa 241 0.0207 1.00 38.3 yes View details
trnL-CAA-ycf2 IRa 962 0.0156 0.99 48.2 yes View details
petG-trnW-CCA LSC 114 0.0819 1.00 85.5 yes View details
atpA-atpF LSC 59 0.0316 0.97 78.0 yes View details
rps11-rpl36 LSC 119 0.0921 0.96 76.5 yes View details
atpH-atpI LSC 979 0.0078 1.00 65.0 yes View details
psbE-petL LSC 1406 0.0062 0.99 64.6 yes View details
trnF-GAA-ndhJ LSC 583 0.0060 1.00 63.8 yes View details
trnL-UAG-ndhF SSC 1825 0.0130 1.00 63.5 yes View details
petN-psbM LSC 1467 0.0059 0.98 63.4 yes View details
petD-rpoA LSC 138 0.0399 1.00 63.0 yes View details
rps16-trnQ-UUG LSC 1111 0.0087 1.00 62.8 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTTCCTTGAAAGGGGTGCTC 963–988 1.000 83.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTTCCTTGAAAGGGGTGCTC 962–987 1.000 83.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CCACAGGAACCGTTCATGAT 940–965 1.000 83.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CCACAGGAACCGTTCATGAT 939–964 1.000 83.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 GTTAGCCGCACTTAAAAGCC TTTCCTTGAAAGGGGTGCTC 977–1002 1.000 82.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAAATTGAAATGGGGCGTGG 1260–1280 1.000 81.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAAATTGAAATGGGGCGTGG 1258–1278 1.000 81.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAAATTGAAATGGGGCGTGG 1266–1286 1.000 81.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GAATCCACAGCCGATCATGT GAAATTGAAATGGGGCGTGG 1267–1287 1.000 81.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1202–1222 1.000 80.7
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA CAATCCGACGCTTTAGTCCA CGAACGAATCACACTTTTACCA 956–1002 1.000 63.5
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA AATCCGACGCTTTAGTCCAC CGAACGAATCACACTTTTACCA 955–1001 1.000 63.5
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA GATCAACGGAACCGGAAAGA CGAACGAATCACACTTTTACCA 1021–1067 1.000 62.5
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA ATCAACGGAACCGGAAAGAG CGAACGAATCACACTTTTACCA 1020–1066 1.000 62.4
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA TGATCAACGGAACCGGAAAG CGAACGAATCACACTTTTACCA 1022–1068 1.000 61.6
atpA-atpF_p1 atpA-atpF TACTAATCTCGTCGGCTCGA TGTTTGGGTCGATGCAAGAA 119–122 1.000 82.6
atpA-atpF_p2 atpA-atpF CCGTCGCCTACTTGAAGTAC TGTTTGGGTCGATGCAAGAA 201–204 1.000 81.8
atpA-atpF_p3 atpA-atpF GTCGCCTACTTGAAGTACGG TGTTTGGGTCGATGCAAGAA 199–202 1.000 81.8
atpA-atpF_p4 atpA-atpF GTCGCCTACTTGAAGTACGG AGTTGTTTGACCAGCGAGTT 251–254 1.000 81.2
atpA-atpF_p5 atpA-atpF CCGTCGCCTACTTGAAGTAC AGTTGTTTGACCAGCGAGTT 253–256 1.000 81.1
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1066–1077 1.000 80.3
atpH-atpI_p2 atpH-atpI AGCGGCAGAAATCAATGGAT TTTTGCAACTTTAGCTGCGG 1058–1069 1.000 80.1
atpH-atpI_p3 atpH-atpI GTCCAATAGAAGCAAGCCCA TTTTGCAACTTTAGCTGCGG 1104–1115 1.000 79.5
atpH-atpI_p4 atpH-atpI AAGCGGCAGAAATCAATGGA TTTTGCAACTTTAGCTGCGG 1059–1070 1.000 79.3
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTGCAACTTTAGCTGCGG 1067–1078 1.000 79.1
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCACTGTTCATTCTAGTCCC 1497–1623 1.000 72.9
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 1503–1629 1.000 72.3
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT TGCACTGTTCATTCTAGTCCC 1436–1562 1.000 71.4
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 1442–1568 1.000 70.8
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT GCACTGTTCATTCTAGTCCCT 1496–1622 1.000 70.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Aspidopterys cavaleriei PQ112544.1 160805 View on NCBI ↗
Aspidopterys concava NC_060542.1 160441 View on NCBI ↗
Aspidopterys glabriuscula PQ112543.1 160341 View on NCBI ↗
Aspidopterys obcordata NC_049898.1 160453 View on NCBI ↗