Markers + reference

Chamaerhodos

5 species · Rosaceae · Rosales

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Species 5
Genome length 154–154 kb
Candidate markers 269
Primer pairs 95

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 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1134 0.0024 1.00 42.1 yes View details
trnS-GCU-trnG-UCC LSC 507 0.0045 0.95 56.7 yes View details
trnR-UCU-atpA LSC 605 0.0050 1.00 55.1 yes View details
ycf3 LSC 2018 0.0015 1.00 56.5 yes View details
trnL-UAA-trnF-GAA LSC 398 0.0010 1.00 41.6 yes View details
psbE-petL LSC 1235 0.0016 1.00 61.0 yes View details
ycf1 IRb 1092 0.0004 1.00 34.7 no View details
ndhF SSC 2241 0.0006 1.00 35.2 yes View details
ndhA SSC 2310 0.0019 1.00 58.6 yes View details
ycf1 SSC 5709 0.0011 1.00 45.8 yes View details
ycf1-ndhF SSC 18 0.1019 1.00 80.0 yes View details
rpl2-trnH-GUG IRa 43 0.0000 1.00 71.2 no View details
psbF-psbE LSC 9 0.0444 1.00 70.0 yes View details
petA-psbJ LSC 983 0.0008 1.00 60.2 yes View details
psaI-ycf4 LSC 438 0.0018 0.99 56.4 yes View details
psaA-ycf3 LSC 784 0.0015 1.00 55.3 yes View details
trnT-UGU-trnL-UAA LSC 715 0.0017 1.00 53.6 yes View details
rpl32-trnL-UAG SSC 677 0.0027 1.00 53.5 yes View details
trnK-UUU-rps16 LSC 766 0.0016 1.00 52.8 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU AGGATTTATATAGACACGATTTCGA TGTGTTGTGCCCTTCAACTT 2688–2690 1.000 40.4
trnK-UUU_p2 trnK-UUU AGGATTTATATAGACACGATTTCGA TTGTGTTGTGCCCTTCAACT 2689–2691 1.000 40.4
trnK-UUU_p3 trnK-UUU AGGATTTATATAGACACGATTTCGA TTGTGCCCTTCAACTTCGTT 2684–2686 1.000 40.4
trnK-UUU_p4 trnK-UUU ACTGAAATGGAAATGAATTCAA TGTGTTGTGCCCTTCAACTT 2715–2717 1.000 40.4
trnK-UUU_p5 trnK-UUU ACTGAAATGGAAATGAATTCAA TTGTGTTGTGCCCTTCAACT 2716–2718 1.000 40.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAAGGCGCTCAACCTACA 898–907 1.000 78.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGCGCTCAACCTACA 897–906 1.000 78.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CTTGAAAAAGGCGCTCAACC 902–911 1.000 77.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CCTTGAAAAAGGCGCTCAAC 902–911 1.000 77.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTTGAAAAAGGCGCTCAACC 901–910 1.000 77.3
rps16_p1 rps16 AAACAGGGTTATTCCTTTGT TGTACCAACCGAACCAATGA 1250–1253 1.000 40.5
rps16_p2 rps16 AACAGGGTTATTCCTTTGTT TGTACCAACCGAACCAATGA 1249–1252 1.000 40.5
rps16_p3 rps16 ACAGGGTTATTCCTTTGTTT TGTACCAACCGAACCAATGA 1248–1251 1.000 40.5
rps16_p4 rps16 AACAGGGTTATTCCTTTGTTT TGTACCAACCGAACCAATGA 1249–1252 1.000 40.5
rps16_p5 rps16 ACAGGGTTATTCCTTTGTTTT TGTACCAACCGAACCAATGA 1248–1251 1.000 40.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 549–580 1.000 56.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 548–579 1.000 56.2
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AACCGAAAGACCCTTTAACT 586–617 1.000 56.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AACCGAAAGACCCTTTAACT 585–616 1.000 56.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AACCGAAAGACCCTTTAACT 640–671 1.000 54.6
trnR-UCU-atpA_p1 trnR-UCU-atpA AGTGAGAAGCGTCCATTGTC AGACGTTTACCGAAGAAGCG 771–776 1.000 77.7
trnR-UCU-atpA_p2 trnR-UCU-atpA GAGTGAGAAGCGTCCATTGT AGACGTTTACCGAAGAAGCG 772–777 1.000 77.7
trnR-UCU-atpA_p3 trnR-UCU-atpA GTGAGAAGCGTCCATTGTCT AGACGTTTACCGAAGAAGCG 770–775 1.000 77.7
trnR-UCU-atpA_p4 trnR-UCU-atpA AGTGAGAAGCGTCCATTGTC AGAAGCGGAAACCCTTTTGA 758–763 1.000 77.3
trnR-UCU-atpA_p5 trnR-UCU-atpA GTGAGAAGCGTCCATTGTCT AGAAGCGGAAACCCTTTTGA 757–762 1.000 77.3
psaA-ycf3_p1 psaA-ycf3 TTACGGGATCCCTATCGACC GCTATAGCGCTTACTCCTGG 896–914 1.000 78.4
psaA-ycf3_p2 psaA-ycf3 GCCCATTCCTCGAAAGAAGT GCTATAGCGCTTACTCCTGG 918–936 1.000 78.1
psaA-ycf3_p3 psaA-ycf3 TTACGGGATCCCTATCGACC GGAGGCTTGGTTCGATCAAG 936–954 1.000 76.2
psaA-ycf3_p4 psaA-ycf3 GCCCATTCCTCGAAAGAAGT GGAGGCTTGGTTCGATCAAG 958–976 1.000 75.9
psaA-ycf3_p5 psaA-ycf3 TTACGGGATCCCTATCGACC TGGAAACAAGCTATAGCGCT 905–923 1.000 75.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Chamaerhodos altaica MT774133.1 153971 View on NCBI ↗
Chamaerhodos canescens MT774134.1 154022 View on NCBI ↗
Chamaerhodos erecta MT774135.1 154014 View on NCBI ↗
Chamaerhodos sabulosa MT774136.1 153918 View on NCBI ↗
Chamaerhodos trifida MT774137.1 153974 View on NCBI ↗