Markers + reference

Aria

4 species · Rosaceae · Rosales

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Species 4
Genome length 160–161 kb
Candidate markers 267
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 9 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 269 0.0149 1.00 59.7 yes View details
trnR-UCU-atpA LSC 740 0.0171 0.99 75.7 yes View details
rpoC1 LSC 2793 0.0012 1.00 57.1 yes View details
rpoB-trnC-GCA LSC 1213 0.0126 1.00 60.0 yes View details
psbZ-trnG-GCC LSC 423 0.0055 1.00 53.5 yes View details
rps4-trnT-UGU LSC 419 0.0203 1.00 48.2 yes View details
trnT-UGU-trnL-UAA LSC 1255 0.0035 1.00 55.7 yes View details
ndhC-trnV-UAC LSC 562 0.0092 1.00 57.1 yes View details
ndhF-rpl32 SSC 1079 0.0025 1.00 61.4 yes View details
ndhG-ndhI SSC 410 0.0057 1.00 57.7 yes View details
rps19-trnH-GUG LSC 66 0.0707 1.00 70.1 no View details
rpl32-trnL-UAG SSC 1448 0.0026 0.98 65.2 yes View details
trnK-UUU-rps16 LSC 981 0.0015 1.00 63.2 yes View details
trnC-GCA-petN LSC 917 0.0018 1.00 60.5 yes View details
trnF-GAA-ndhJ LSC 699 0.0007 1.00 60.4 yes View details
atpH-atpI LSC 1144 0.0010 1.00 59.7 yes View details
accD-psaI LSC 803 0.0035 0.99 59.1 yes View details
rps16 LSC 1134 0.0010 1.00 57.1 yes View details
rpl14-rpl16 LSC 145 0.0034 0.99 56.2 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 ATATTATGGGCGAACGACGG CCTCTAGACCTAGCTGCTGT 390–405 1.000 83.1
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 379–394 1.000 83.1
trnH-GUG-psbA_p3 trnH-GUG-psbA ATATTATGGGCGAACGACGG TTCCCTCTAGACCTAGCTGC 393–408 1.000 83.0
trnH-GUG-psbA_p4 trnH-GUG-psbA ATATTATGGGCGAACGACGG GCGCTAACCTTGGTATGGAA 440–455 1.000 82.9
trnH-GUG-psbA_p5 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 393–408 1.000 82.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CGGAACTTCGCCCTAATCAA 1028–1053 1.000 80.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CGGAACTTCGCCCTAATCAA 1027–1052 1.000 80.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA CGGAACTTCGCCCTAATCAA 1037–1062 1.000 79.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 1083–1108 1.000 79.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 1082–1107 1.000 79.4
rps16_p1 rps16 AGAAACAAAAAGGTTATACAAGGCT TATGTACCGACCGAACCGAT 1270–1272 1.000 40.2
rps16_p2 rps16 AGAAACAAAAAGGTTATACAAGGCT CCGACCGAACCGATGATTAT 1264–1266 1.000 40.2
rps16_p3 rps16 ACAAAAAGGTTATACAAGGCT TATGTACCGACCGAACCGAT 1266–1268 1.000 40.2
rps16_p4 rps16 AGAAACAAAAAGGTTATACAAGGCT ATTATGTACCGACCGAACCG 1272–1274 1.000 40.2
rps16_p5 rps16 GGAAATAGCAAAGAAACAAAAAGGT TATGTACCGACCGAACCGAT 1281–1283 1.000 40.2
trnR-UCU-atpA_p1 trnR-UCU-atpA TGGAATGAAAAGCGTCCATTG AGACATTTACCGACGAAGCG 909–953 1.000 69.9
trnR-UCU-atpA_p2 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT AGACATTTACCGACGAAGCG 908–952 1.000 69.8
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGACATTTACCGACGAAGCG 848–892 1.000 69.3
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT AGACATTTACCGACGAAGCG 883–927 1.000 66.2
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGAATGAAAAGCGTCCATT AGACATTTACCGACGAAGCG 909–953 1.000 65.8
atpH-atpI_p1 atpH-atpI AATAGAAGCAAGCCCGACAG GCGAATCCATGGAAGGTCAT 1233–1245 1.000 79.9
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT GCGAATCCATGGAAGGTCAT 1199–1211 1.000 79.8
atpH-atpI_p3 atpH-atpI AATAGAAGCAAGCCCGACAG TTTTTGCAACCTTAGCTGCG 1263–1275 1.000 79.0
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACCTTAGCTGCG 1229–1241 1.000 79.0
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA GCGAATCCATGGAAGGTCAT 1200–1212 1.000 78.6
rpoC1_p1 rpoC1 GGTGAACTGGAGAAACCCAA TTTGGCTCTGGAACTGAACC 2953–2959 1.000 77.3
rpoC1_p2 rpoC1 GAAACCCAAAATGACACGGG TTTGGCTCTGGAACTGAACC 2942–2948 1.000 76.7
rpoC1_p3 rpoC1 GGTGAACTGGAGAAACCCAA ACGATCTTTGGCTCTGGAAC 2959–2965 1.000 76.7
rpoC1_p4 rpoC1 AGGTGAACTGGAGAAACCCA TTTGGCTCTGGAACTGAACC 2954–2960 1.000 76.3
rpoC1_p5 rpoC1 GAAACCCAAAATGACACGGG ACGATCTTTGGCTCTGGAAC 2948–2954 1.000 76.1

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
Aria edulis NC_045418.1 160222 View on NCBI ↗
Aria graeca NC_085583.1 160530 View on NCBI ↗
Aria pannonica NC_085661.1 160542 View on NCBI ↗
Aria umbellata NC_085650.1 160447 View on NCBI ↗