Markers + reference

Aruncus

2 species · Rosaceae · Rosales

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Species 2
Genome length 157–158 kb
Candidate markers 270
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 9 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0009 1.00 55.6 yes View details
trnK-UUU-rps16 LSC 927 0.0076 1.00 63.1 yes View details
rps16-trnQ-UUG LSC 879 0.0057 1.00 54.0 yes View details
trnS-UGA-psbZ LSC 305 0.0203 0.97 67.0 yes View details
trnT-UGU-trnL-UAA LSC 885 0.0057 1.00 62.2 yes View details
ndhC LSC 363 0.0000 1.00 26.4 yes View details
ndhC-trnV-UAC LSC 436 0.0138 1.00 63.2 yes View details
clpP LSC 1890 0.0037 0.99 47.4 yes View details
rpl36-rps8 LSC 474 0.0063 1.00 59.2 yes View details
rpl14 LSC 369 0.0000 1.00 28.4 yes View details
ndhF SSC 2265 0.0026 1.00 58.7 yes View details
rpl14-rpl16 LSC 149 0.0470 1.00 79.5 yes View details
atpA-atpF LSC 52 0.0192 1.00 63.6 yes View details
ndhF-rpl32 SSC 1129 0.0036 0.98 63.1 yes View details
trnG-UCC-trnfM-CAU LSC 184 0.0163 1.00 61.9 yes View details
psbE-petL LSC 1320 0.0045 1.00 61.4 yes View details
petN-psbM LSC 1222 0.0041 1.00 61.1 yes View details
atpF-atpH LSC 485 0.0063 0.99 60.9 yes View details
accD-psaI LSC 771 0.0013 0.99 60.5 yes View details
rps2 LSC 711 0.0028 1.00 60.4 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
psbA_p1 psbA GCTCCTTTACTTTCAAGAACTCG GTGCTTGGGAGTACCTGATG 1155 1.000 53.7
psbA_p2 psbA GCTCCTTTACTTTCAAGAACTCG TGCTTGGGAGTACCTGATGA 1154 1.000 53.5
psbA_p3 psbA GCTCCTTTACTTTCAAGAACTCG ATTCGTGTGCTTGGGAGTAC 1161 1.000 53.1
psbA_p4 psbA GCTCCTTTACTTTCAAGAACTCG AGAATTCGTGTGCTTGGGAG 1164 1.000 52.4
psbA_p5 psbA GCTCCTTTACTTTCAAGAACTCG AGAGAATTCGTGTGCTTGGG 1166 1.000 52.4
trnK-UUU_p1 trnK-UUU CATCAGGTACTCCCAAGCAC ATGTTTTGATTGCGTTGTGC 2904–2905 1.000 67.5
trnK-UUU_p2 trnK-UUU TCATCAGGTACTCCCAAGCA ATGTTTTGATTGCGTTGTGC 2905–2906 1.000 67.4
trnK-UUU_p3 trnK-UUU CATCAGGTACTCCCAAGCAC GCGTTGTGCAATTCCATTTT 2893–2894 1.000 67.3
trnK-UUU_p4 trnK-UUU TCATCAGGTACTCCCAAGCA GCGTTGTGCAATTCCATTTT 2894–2895 1.000 67.2
trnK-UUU_p5 trnK-UUU GTACTCCCAAGCACACGAAT ATGTTTTGATTGCGTTGTGC 2898–2899 1.000 67.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 TGGTCTTACAAACTCTGCCG AAAAAGGCGCTCAACCTACA 1152 1.000 79.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAAGGCGCTCAACCTACA 1074 1.000 79.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGCGCTCAACCTACA 1073 1.000 79.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAAAAGGCGCTCAACCTACA 1083 1.000 78.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAACTCTGCCGATGGTATGG AAAAAGGCGCTCAACCTACA 1143 1.000 77.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCGGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 970–971 1.000 79.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCGGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 968–969 1.000 79.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 952–953 1.000 78.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 963–964 1.000 78.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGCGGATCATGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 969–970 1.000 77.2
atpA-atpF_p1 atpA-atpF CCGTCGCCTACTTGAAGTAC ACAAGGAGCTCTAGGAACTCT 274–275 1.000 67.8
atpA-atpF_p2 atpA-atpF CCGTCGCCTACTTGAAGTAC AGGAGCTCTAGGAACTCTGA 271–272 1.000 67.4
atpA-atpF_p3 atpA-atpF GCTCAATACGTTCGCGGATA ACAAGGAGCTCTAGGAACTCT 216–217 1.000 66.7
atpA-atpF_p4 atpA-atpF GCTCAATACGTTCGCGGATA AGGAGCTCTAGGAACTCTGA 213–214 1.000 66.4
atpA-atpF_p5 atpA-atpF CCGTCGCCTACTTGAAGTAC AGGAGCTCTAGGAACTCTGAA 271–272 1.000 65.5
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG CGGAGGGAAAAATACGAGGT 662–667 1.000 74.5
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG GAGGCGGAGGGAAAAATACG 666–671 1.000 74.4
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG GCGGAGGGAAAAATACGAGG 663–668 1.000 74.4
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG GGCGGAGGGAAAAATACGAG 664–669 1.000 74.4
atpF-atpH_p5 atpF-atpH ATTAAACCCGAAACTCCCGG CAGAGGCGGAGGGAAAAATA 668–673 1.000 74.3

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
Aruncus aethusifolius MZ882398.1 157217 View on NCBI ↗
Aruncus dioicus var. kamtschaticus MW115132.1 157859 View on NCBI ↗