Markers + reference

Oxalis

9 species · Oxalidaceae · Oxalidales

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Species 9
Genome length 151–152 kb
Candidate markers 265
Primer pairs 95

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 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 347 0.0902 1.00 71.7 yes View details
atpH-atpI LSC 1134 0.0609 0.97 80.2 yes View details
trnC-GCA-petN LSC 981 0.0766 0.99 84.2 yes View details
psbM-trnD-GUC LSC 808 0.0655 0.98 89.6 yes View details
trnT-GGU-psbD LSC 1509 0.0619 0.99 88.5 yes View details
ndhC-trnC-ACA LSC 1041 0.0735 0.95 80.5 yes View details
ycf1 IRb 1019 0.0093 1.00 45.0 no View details
ndhF-trnL-UAG SSC 694 0.0758 0.98 80.2 yes View details
rps15-ycf1 SSC 418 0.0858 0.99 81.3 yes View details
ycf1 SSC 5640 0.0605 0.99 77.1 yes View details
trnF-GAA-ndhJ LSC 714 0.0559 0.99 84.9 yes View details
rpoB-trnC-GCA LSC 1193 0.0535 0.97 83.7 yes View details
trnK-UUU-trnQ-UUG LSC 1842 0.0573 0.98 82.8 yes View details
psaA-ycf3 LSC 661 0.0454 0.99 82.8 yes View details
psbE-petL LSC 782 0.0455 0.96 82.8 yes View details
trnS-GCU-trnG LSC 721 0.0575 0.98 82.5 yes View details
trnD-GUC-trnY-GUA LSC 457 0.0685 0.99 82.0 yes View details
trnE-UUC-trnT-GGU LSC 753 0.0633 0.93 82.0 yes View details
psbZ-trnG-GCC LSC 429 0.0704 0.96 81.5 yes View details
rpl36-rps8 LSC 481 0.0696 0.95 81.1 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA TCACAATCCACTGCCTTGAG TCTAGCGGCTGTTGAAGTTC 303–423 0.222 54.5
trnH-GUG-psbA_p2 trnH-GUG-psbA TCACAATCCACTGCCTTGAG TTCCCTCTAGATCTAGCGGC 314–434 0.222 54.3
trnH-GUG-psbA_p3 trnH-GUG-psbA TCACAATCCACTGCCTTGAG GTTGACAGTCAAGGTCGTGT 410–530 0.222 53.8
trnH-GUG-psbA_p4 trnH-GUG-psbA TCACAATCCACTGCCTTGAG GGTGTAGCTGGTGTATTCGG 728–848 0.222 52.6
trnH-GUG-psbA_p5 trnH-GUG-psbA TCACAATCCACTGCCTTGAG CCCAATTGGTCAAGGAAGCT 846–966 0.222 52.3
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG AAAGCCGAGTACTCTACCGT GAGGTTCGAATCCTTCCGTC 1121–2066 1.000 90.0
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG AAGCCGAGTACTCTACCGTT GAGGTTCGAATCCTTCCGTC 1120–2065 1.000 90.0
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG GTTAGCCGCACTTAAAAGCC GAGGTTCGAATCCTTCCGTC 1135–2080 1.000 89.3
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG CCGCACTTAAAAGCCGAGTA GAGGTTCGAATCCTTCCGTC 1130–2075 1.000 89.1
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG TACCGTTGAGTTAGCAACCC GAGGTTCGAATCCTTCCGTC 1107–2052 1.000 87.7
trnS-GCU-trnG_p1 trnS-GCU-trnG CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 764–840 1.000 63.7
trnS-GCU-trnG_p2 trnS-GCU-trnG AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 763–839 1.000 63.7
trnS-GCU-trnG_p3 trnS-GCU-trnG CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 767–843 1.000 62.6
trnS-GCU-trnG_p4 trnS-GCU-trnG CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 766–842 1.000 62.6
trnS-GCU-trnG_p5 trnS-GCU-trnG AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 765–841 1.000 62.6
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT CGGTGTAGAAGTAGGCCAAC 1839–1903 1.000 91.0
atpH-atpI_p2 atpH-atpI AAGAAAGAAAGCGGTTCGGT CGGTGTAGAAGTAGGCCAAC 2217–2303 1.000 90.7
atpH-atpI_p3 atpH-atpI GAAAGCGGTTCGGTATGCTA CGGTGTAGAAGTAGGCCAAC 2211–2297 1.000 90.3
atpH-atpI_p4 atpH-atpI CCAGTGACCCAAGAAAACGA CGGTGTAGAAGTAGGCCAAC 2523–2624 0.889 86.9
atpH-atpI_p5 atpH-atpI AAGAAAGAAAGCGGTTCGGT TAGGGGGTTTCCAAGTCCAT 2182–2200 0.222 51.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TACCGGATCTCCACCTACAC CCGGATTTGAACTGGGGAAA 1945–1978 1.000 90.8
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TACCGGATCTCCACCTACAC TTGAATGGCCGAATACTCCG 2356–2384 0.556 72.0
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AGCCCAGATCCTTGCTTTTC TTGAATGGCCGAATACTCCG 2152–2180 0.556 71.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GAGCCCAGATCCTTGCTTTT TTGAATGGCCGAATACTCCG 2153–2181 0.556 71.7
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GCCCAGATCCTTGCTTTTCT TTGAATGGCCGAATACTCCG 2151–2179 0.556 71.7
trnC-GCA-petN_p1 trnC-GCA-petN GAGGTGTGTAAGAAGGCTCG CGCATTTCCCCGAGTTCTTA 1990–2004 0.444 66.4
trnC-GCA-petN_p2 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC TTAAAGCAGCCCAAGCAAGA 1100–1103 0.222 56.6
trnC-GCA-petN_p3 trnC-GCA-petN ACAATCAATCGAAGGGACGG TTAAAGCAGCCCAAGCAAGA 1182–1252 0.222 56.3
trnC-GCA-petN_p4 trnC-GCA-petN GAGGTGTGTAAGAAGGCTCG TTAAAGCAGCCCAAGCAAGA 1749 0.111 44.4
trnC-GCA-petN_p5 trnC-GCA-petN ACAATCAATCGAAGGGACGG CGCATTTCCCCGAGTTCTTA 1437 0.111 44.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Oxalis corniculata NC_051971.1 152189 View on NCBI ↗
Oxalis corymbosa NC_048890.1 152423 View on NCBI ↗
Oxalis drummondii NC_043802.1 152112 View on NCBI ↗
Oxalis latifolia OR643846.1 152228 View on NCBI ↗
Oxalis lomana OR643845.1 150987 View on NCBI ↗
Oxalis megalorrhiza OR643841.1 151468 View on NCBI ↗
Oxalis mollendoensis OR643838.1 151496 View on NCBI ↗
Oxalis pes-caprae MT537169.1 152125 View on NCBI ↗
Oxalis triangularis PQ773890.1 152115 View on NCBI ↗