Markers + reference

Aristotelia

2 species · Elaeocarpaceae · Oxalidales

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Species 2
Genome length 158–162 kb
Candidate markers 263
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 851 0.1395 0.84 81.7 yes View details
rps16-trnQ-UUG LSC 1860 0.1409 0.35 70.4 yes View details
trnS-GCU-trnG-UCC LSC 1008 0.1317 0.56 77.0 yes View details
trnC-GCA-petN LSC 852 0.1292 0.97 91.3 yes View details
trnE-UUC-trnT-GGU LSC 926 0.1041 0.63 80.2 yes View details
psbZ-trnG-GCC LSC 688 0.1569 0.62 77.9 yes View details
trnT-UGU-trnL-UAA LSC 976 0.1050 0.94 98.0 yes View details
ndhC-trnV-UAC LSC 1110 0.1085 0.38 69.3 yes View details
ndhF-rpl32 SSC 1194 0.1673 0.48 71.3 yes View details
rpl32-trnL-UAG SSC 1170 0.1954 0.70 76.9 yes View details
rps15-ycf1 SSC 4420 0.0467 0.94 69.7 yes View details
atpH-atpI LSC 913 0.0556 0.95 89.2 yes View details
psbE-petL LSC 1346 0.0761 0.92 88.2 yes View details
rbcL-accD LSC 590 0.0619 0.99 87.4 yes View details
trnH-GUG-psbA LSC 336 0.0909 0.92 86.0 yes View details
atpF-atpH LSC 495 0.0915 0.95 85.1 yes View details
rpoB-trnC-GCA LSC 1060 0.0459 0.95 82.2 yes View details
rps18-rpl20 LSC 302 0.0976 0.95 81.2 yes View details
ycf4-cemA LSC 851 0.0733 0.80 81.0 yes View details
trnW-CCA-trnP-UGG LSC 194 0.1011 0.97 80.9 yes View details
psbM-trnD-GUC LSC 1134 0.0675 0.81 80.5 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 105 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 CCTCTAGACCTAGCTGCTGT 402–524 1.000 87.1
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 405–527 1.000 87.0
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 416–538 1.000 86.8
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 415–537 1.000 86.8
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 417–539 1.000 86.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CCCAATGGGCCATTTATCGA 1216–1303 1.000 90.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TCCCAATGGGCCATTTATCG 1217–1304 1.000 90.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 GACGGTATGGACGAAGCATT CCCAATGGGCCATTTATCGA 1180–1267 1.000 90.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 GACGGTATGGACGAAGCATT TCCCAATGGGCCATTTATCG 1181–1268 1.000 90.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT CCCAATGGGCCATTTATCGA 1212–1299 1.000 89.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCGGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 745–1951 1.000 88.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCGGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 743–1949 1.000 88.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GATGTAAGAGTCCACAGCGG GAGGTTCGAATCCTTCCGTC 759–1965 1.000 88.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GGATGTAAGAGTCCACAGCG GAGGTTCGAATCCTTCCGTC 760–1966 1.000 88.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ACACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 722–1928 1.000 86.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA CGAAGGACCCCTTAACTATGA 910–1119 1.000 70.1
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC CGAAGGACCCCTTAACTATGA 909–1118 1.000 70.1
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GCTCGTACAACGGATTAGCA CGAAGGACCCCTTAACTATGA 928–1137 1.000 69.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TGCTCGTACAACGGATTAGC CGAAGGACCCCTTAACTATGA 929–1138 1.000 69.3
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA CGAAGGACCCCTTAACTATGA 964–1173 1.000 68.6
atpF-atpH_p1 atpF-atpH CCAGTGACCGAAGAAAACGA GCATTGGCGCTTTTATTTGC 573–648 1.000 84.3
atpF-atpH_p2 atpF-atpH CCAGTGACCGAAGAAAACGA CGGAGGGAAAAATACGAGGT 650–725 1.000 81.3
atpF-atpH_p3 atpF-atpH CCAGTGACCGAAGAAAACGA GCGGAGGGAAAAATACGAGG 651–726 1.000 81.2
atpF-atpH_p4 atpF-atpH CCAGTGACCGAAGAAAACGA GAGGCGGAGGGAAAAATACG 654–729 1.000 81.1
atpF-atpH_p5 atpF-atpH CCAGTGACCGAAGAAAACGA GGCGGAGGGAAAAATACGAG 652–727 1.000 81.1
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1001–1237 1.000 82.5
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT TAGGTGAATCCATGGAGGGT 974–1210 1.000 82.1
atpH-atpI_p3 atpH-atpI CGCGATTCCTTCTACAGCTT TTTTTGCAACTTTAGCCGCG 1089–1325 1.000 81.7
atpH-atpI_p4 atpH-atpI TACCTTGACCAACTCCAGGT TTTTTGCAACTTTAGCCGCG 1057–1293 1.000 81.6
atpH-atpI_p5 atpH-atpI GTCCAATAGAAGCAAGCCCA TTTTTGCAACTTTAGCCGCG 1039–1275 1.000 81.5

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
Aristotelia chilensis MT078232.1 161670 View on NCBI ↗
Aristotelia fruticosa NC_063645.1 158085 View on NCBI ↗