Markers + reference

Thomsonaria

9 species · Rosaceae · Rosales

Back to catalogue

Species 9
Genome length 160–160 kb
Candidate markers 272
Primer pairs 90

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 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 279 0.0141 0.94 49.7 yes View details
trnK-UUU-rps16 LSC 935 0.0054 1.00 59.7 yes View details
trnR-UCU-atpA LSC 707 0.0293 0.96 83.4 yes View details
ndhC-trnV-UAC LSC 613 0.0101 0.95 57.9 yes View details
accD-psaI LSC 792 0.0042 1.00 36.0 yes View details
rpl33-rps18 LSC 219 0.0148 0.95 53.3 yes View details
clpP LSC 2033 0.0023 1.00 51.4 yes View details
ycf1 IRb 1083 0.0002 1.00 36.9 no View details
ndhF-rpl32 SSC 1065 0.0030 1.00 53.8 yes View details
rpl32-trnL-UAG SSC 1489 0.0058 0.94 54.3 yes View details
ycf1 SSC 5655 0.0012 1.00 40.2 yes View details
rps19-trnH-GUG LSC 58 0.0858 0.76 74.1 no View details
psbM-trnD-GUC LSC 1227 0.0015 1.00 61.0 yes View details
rps16-trnQ-UUG LSC 809 0.0024 1.00 59.8 yes View details
rbcL-accD LSC 572 0.0014 1.00 54.6 yes View details
rps16 LSC 1138 0.0019 1.00 52.4 yes View details
rps11-rpl36 LSC 175 0.0057 1.00 50.3 yes View details
trnT-UGU-trnL-UAA LSC 1194 0.0020 1.00 50.1 yes View details
psaJ-rpl33 LSC 473 0.0045 1.00 49.9 yes View details
trnF-GAA-ndhJ LSC 695 0.0006 1.00 49.4 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 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 GCGCTAACCTTGGTATGGAA 435–456 1.000 84.4
trnH-GUG-psbA_p2 trnH-GUG-psbA ATATTATGGGCGAACGACGG CCTCTAGACCTAGCTGCTGT 385–406 1.000 84.3
trnH-GUG-psbA_p3 trnH-GUG-psbA ATATTATGGGCGAACGACGG TTCCCTCTAGACCTAGCTGC 388–409 1.000 84.2
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 374–395 1.000 84.2
trnH-GUG-psbA_p5 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 388–409 1.000 84.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CGGAACTTCGCCCTAATCAA 1003–1029 1.000 80.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CGGAACTTCGCCCTAATCAA 1002–1028 1.000 80.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA CGGAACTTCGCCCTAATCAA 1012–1038 1.000 79.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 1058–1084 1.000 78.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 1057–1083 1.000 78.7
rps16_p1 rps16 AGAAACAAAAAGGTTATACAAGGCT TATGTACCGACCGAACCGAT 1269–1277 1.000 40.9
rps16_p2 rps16 AGAAACAAAAAGGTTATACAAGGCT CCGACCGAACCGATGATTAT 1263–1271 1.000 40.9
rps16_p3 rps16 ACAAAAAGGTTATACAAGGCT TATGTACCGACCGAACCGAT 1265–1273 1.000 40.9
rps16_p4 rps16 AGAAACAAAAAGGTTATACAAGGCT ATTATGTACCGACCGAACCG 1271–1279 1.000 40.9
rps16_p5 rps16 GGAAATAGCAAAGAAACAAAAAGGT TATGTACCGACCGAACCGAT 1280–1288 1.000 40.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 877–897 1.000 80.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 887–907 1.000 78.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCTTTCTGCCACATCGTTTT GAGGTTCGAATCCTTCCGTC 854–874 1.000 78.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCCACAGCTGATCATGTCCT GAGGTTCGAATCCTTCCGTC 888–908 1.000 78.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GTGTCGACTAGAAATGGGGC 939–959 1.000 77.9
trnR-UCU-atpA_p1 trnR-UCU-atpA TGGAATGAAAAGCGTCCATTG AGACATTTACCGACGAAGCG 792–939 1.000 73.8
trnR-UCU-atpA_p2 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT AGACATTTACCGACGAAGCG 791–938 1.000 73.8
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGACATTTACCGACGAAGCG 731–878 1.000 73.3
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGAATGAAAAGCGTCCATT AGACATTTACCGACGAAGCG 792–939 1.000 69.8
trnR-UCU-atpA_p5 trnR-UCU-atpA TTGGAATGAAAAGCGTCCAT AGACATTTACCGACGAAGCG 793–940 1.000 69.8
psbM-trnD-GUC_p1 psbM-trnD-GUC TCACCTTGGCTGACTGTTTT TTCAATTGGTCAGAGCACCG 1386–1416 1.000 73.6
psbM-trnD-GUC_p2 psbM-trnD-GUC AATCACCTTGGCTGACTGTT TTCAATTGGTCAGAGCACCG 1388–1418 1.000 71.8
psbM-trnD-GUC_p3 psbM-trnD-GUC ATCACCTTGGCTGACTGTTT TTCAATTGGTCAGAGCACCG 1387–1417 1.000 71.8
psbM-trnD-GUC_p4 psbM-trnD-GUC TCACCTTGGCTGACTGTTTT GTTCAATTGGTCAGAGCACC 1387–1417 1.000 69.5
psbM-trnD-GUC_p5 psbM-trnD-GUC ATCACCTTGGCTGACTGTTTT TTCAATTGGTCAGAGCACCG 1387–1417 1.000 68.7

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
Thomsonaria aronioides OQ100073.1 159883 View on NCBI ↗
Thomsonaria astateria NC_085655.1 159916 View on NCBI ↗
Thomsonaria caloneura OQ101266.1 159768 View on NCBI ↗
Thomsonaria corymbifera NC_085657.1 159837 View on NCBI ↗
Thomsonaria ferruginea NC_062339.1 159751 View on NCBI ↗
Thomsonaria globosa NC_085669.1 159890 View on NCBI ↗
Thomsonaria meliosmifolia OQ100082.1 159777 View on NCBI ↗
Thomsonaria ochracea NC_085659.1 159579 View on NCBI ↗
Thomsonaria thomsonii NC_085667.1 159720 View on NCBI ↗