Markers + reference

Stranvaesia

3 species · Rosaceae · Rosales

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Species 3
Genome length 160–160 kb
Candidate markers 273
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 271 0.0172 1.00 57.0 yes View details
trnR-UCU-atpA LSC 653 0.0064 0.96 66.2 yes View details
petN-psbM LSC 1283 0.0073 1.00 63.4 yes View details
trnT-GGU-psbD LSC 1406 0.0062 1.00 64.5 yes View details
psbZ-trnG-GCC LSC 427 0.0172 1.00 70.9 yes View details
trnT-UGU-trnL-UAA LSC 1220 0.0033 0.99 63.0 yes View details
atpB LSC 1479 0.0014 1.00 39.2 yes View details
psaJ-rpl33 LSC 454 0.0059 1.00 60.2 yes View details
ndhG-ndhI SSC 387 0.0103 1.00 62.7 yes View details
rps19-trnH-GUG LSC 50 0.1185 0.90 70.9 no View details
accD-psaI LSC 875 0.0015 1.00 65.3 yes View details
trnF-GAA-ndhJ LSC 755 0.0009 0.98 64.6 yes View details
trnK-UUU-rps16 LSC 958 0.0021 0.98 62.1 yes View details
rps16-trnQ-UUG LSC 791 0.0017 1.00 60.4 yes View details
rpl16 LSC 1402 0.0019 1.00 60.3 yes View details
trnS-GCU-trnG-UCC LSC 657 0.0020 1.00 60.2 yes View details
rpl20-rps12 LSC 769 0.0009 1.00 60.1 yes View details
ndhF-rpl32 SSC 1074 0.0012 1.00 60.0 yes View details
atpH-atpI LSC 1184 0.0006 1.00 59.8 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 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 394–402 1.000 80.9
trnH-GUG-psbA_p2 trnH-GUG-psbA ATATTATGGGCGAACGACGG TTCCCTCTAGACCTAGCTGC 397–405 1.000 80.8
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 333–341 1.000 80.8
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 347–355 1.000 80.7
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 346–354 1.000 80.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CGGAACTTCGCCCTAATCAA 1009–1032 1.000 80.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CGGAACTTCGCCCTAATCAA 1008–1031 1.000 80.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA CGGAACTTCGCCCTAATCAA 1018–1041 1.000 79.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 1064–1087 1.000 78.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 1063–1086 1.000 78.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 875–895 1.000 78.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 885–905 1.000 76.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCTTTCTGCCACATCGTTTT GAGGTTCGAATCCTTCCGTC 852–872 1.000 76.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCCACAGCTGATCATGTCCT GAGGTTCGAATCCTTCCGTC 886–906 1.000 76.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GTGTCGACTAGAAATGGGGC 937–957 1.000 76.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AATCAAACCGAAAGACCCCT 768–793 1.000 72.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ATCAAACCGAAAGACCCCTT 767–792 1.000 72.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AATCAAACCGAAAGACCCCT 767–792 1.000 72.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ATCAAACCGAAAGACCCCTT 766–791 1.000 72.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ATCAAACCGAAAGACCCCTT 821–846 1.000 71.3
trnR-UCU-atpA_p1 trnR-UCU-atpA TGGAATGAAAAGCGTCCATTG AGACATTTACCGACGAAGCG 749–822 1.000 69.0
trnR-UCU-atpA_p2 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT AGACATTTACCGACGAAGCG 748–821 1.000 69.0
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGACATTTACCGACGAAGCG 688–761 1.000 68.1
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT AGACATTTACCGACGAAGCG 723–796 1.000 65.2
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGAATGAAAAGCGTCCATT AGACATTTACCGACGAAGCG 749–822 1.000 65.0
atpH-atpI_p1 atpH-atpI AATAGAAGCAAGCCCGACAG GCGAATCCATGGAAGGTCAT 1270–1280 1.000 80.1
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT GCGAATCCATGGAAGGTCAT 1236–1246 1.000 80.1
atpH-atpI_p3 atpH-atpI AATAGAAGCAAGCCCGACAG TTTTTGCAACCTTAGCTGCG 1300–1310 1.000 79.3
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACCTTAGCTGCG 1266–1276 1.000 79.2
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA GCGAATCCATGGAAGGTCAT 1237–1247 1.000 78.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Stranvaesia bodinieri NC_086559.1 159871 View on NCBI ↗
Stranvaesia nussia NC_086560.1 159701 View on NCBI ↗
Stranvaesia oblanceolata NC_086561.1 160162 View on NCBI ↗