Markers + reference

Osteomeles

2 species · Rosaceae · Rosales

Back to catalogue

Species 2
Genome length 160–160 kb
Candidate markers 270
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 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0000 1.00 39.4 yes View details
rps16 LSC 1136 0.0018 1.00 60.0 yes View details
trnS-GCU-trnG-UCC LSC 656 0.0031 1.00 60.7 yes View details
trnR-UCU-atpA LSC 713 0.0044 0.96 65.6 yes View details
trnE-UUC-trnT-GGU LSC 547 0.0037 1.00 59.7 yes View details
trnT-GGU-psbD LSC 1439 0.0000 0.98 61.0 yes View details
accD LSC 1527 0.0007 1.00 54.8 yes View details
rpl16 LSC 1423 0.0014 1.00 59.6 yes View details
ycf2 IRb 6840 0.0001 1.00 52.7 yes View details
ycf2 IRa 6840 0.0001 1.00 52.7 no View details
rps7-rps12 IRb 52 0.0192 1.00 63.6 yes View details
rps12-rps7 IRa 52 0.0192 1.00 63.6 yes View details
ndhF-rpl32 SSC 1111 0.0000 0.98 60.4 yes View details
rps16-trnQ-UUG LSC 829 0.0012 1.00 59.9 yes View details
rps4 LSC 606 0.0016 1.00 59.7 yes View details
psbM-trnD-GUC LSC 1223 0.0008 1.00 59.3 yes View details
trnK-UUU-rps16 LSC 953 0.0000 1.00 59.2 yes View details
atpF LSC 1308 0.0000 1.00 59.2 yes View details
trnT-UGU-trnL-UAA LSC 1247 0.0008 1.00 59.2 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
psbA_p1 psbA AGGAGCAATAACAAACCTCTTGA AGAATTCGTGTGCTTGGGAG 1208 1.000 54.4
psbA_p2 psbA AGGAGCAATAACAAACCTCTTGA AGAGAATTCGTGTGCTTGGG 1210 1.000 54.4
psbA_p3 psbA AGGAGCAATAACAAACCTCTTGA GAGAATTCGTGTGCTTGGGA 1209 1.000 54.4
psbA_p4 psbA AGGAGCAATAACAAACCTCTTGA AATTCGTGTGCTTGGGAGTC 1206 1.000 52.1
psbA_p5 psbA AGGAGCAATAACAAACCTCTTGA GAATTCGTGTGCTTGGGAGT 1207 1.000 52.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CGGAACTTCGCCCTAATCAA 1024–1033 1.000 78.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CGGAACTTCGCCCTAATCAA 1023–1032 1.000 78.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA CGGAACTTCGCCCTAATCAA 1033–1042 1.000 77.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 1079–1088 1.000 77.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 1078–1087 1.000 77.4
rps16_p1 rps16 AGAAACAAAAAGGTTATACAAGGCT TATGTACCGACCGAACCGAT 1270–1273 1.000 40.3
rps16_p2 rps16 AGAAACAAAAAGGTTATACAAGGCT CCGACCGAACCGATGATTAT 1264–1267 1.000 40.3
rps16_p3 rps16 ACAAAAAGGTTATACAAGGCT TATGTACCGACCGAACCGAT 1266–1269 1.000 40.3
rps16_p4 rps16 AGAAACAAAAAGGTTATACAAGGCT ATTATGTACCGACCGAACCG 1272–1275 1.000 40.3
rps16_p5 rps16 GGAAATAGCAAAGAAACAAAAAGGT TATGTACCGACCGAACCGAT 1281–1284 1.000 40.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 909–913 1.000 78.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 919–923 1.000 76.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCTTTCTGCCACATCGTTTT GAGGTTCGAATCCTTCCGTC 886–890 1.000 76.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCCACAGCTGATCATGTCCT GAGGTTCGAATCCTTCCGTC 920–924 1.000 76.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GTGTCGACTAGAAATGGGGC 971–975 1.000 76.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AATCAAACCGAAAGACCCCT 767 1.000 72.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ATCAAACCGAAAGACCCCTT 766 1.000 72.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AATCAAACCGAAAGACCCCT 766 1.000 72.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ATCAAACCGAAAGACCCCTT 765 1.000 72.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ATCAAACCGAAAGACCCCTT 820 1.000 71.3
trnR-UCU-atpA_p1 trnR-UCU-atpA TGGAATGAAAAGCGTCCATTG AGACATTTACCGACGAAGCG 866–882 1.000 67.6
trnR-UCU-atpA_p2 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT AGACATTTACCGACGAAGCG 865–881 1.000 67.6
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGACATTTACCGACGAAGCG 805–821 1.000 66.9
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT AGACATTTACCGACGAAGCG 840–856 1.000 63.9
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGAATGAAAAGCGTCCATT AGACATTTACCGACGAAGCG 866–882 1.000 63.6

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
Osteomeles schwerinae NC_045420.1 159930 View on NCBI ↗
Osteomeles subrotunda NC_053688.1 159902 View on NCBI ↗