Markers + reference

Cercocarpus

3 species · Rosaceae · Rosales

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Species 3
Genome length 158–158 kb
Candidate markers 267
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 952 0.0060 1.00 62.7 yes View details
trnS-GCU-trnG-UCC LSC 561 0.0036 1.00 46.2 yes View details
trnC-GCA-petN LSC 764 0.0017 1.00 46.8 yes View details
petN-psbM LSC 867 0.0023 1.00 61.4 yes View details
petA-psbJ LSC 879 0.0099 1.00 55.4 yes View details
rpl33-rps18 LSC 208 0.0064 1.00 41.2 yes View details
rpl20-rps12 LSC 783 0.0017 1.00 47.3 yes View details
clpP-psbB LSC 463 0.0043 1.00 46.1 yes View details
petD LSC 1206 0.0022 1.00 44.3 yes View details
rps19 LSC 279 0.0024 1.00 28.7 yes View details
ndhF-rpl32 SSC 816 0.0041 1.00 49.3 yes View details
ycf1 SSC 5664 0.0016 1.00 41.1 yes View details
rpl2-trnH-GUG IRa 241 0.0056 1.00 73.8 no View details
rps16-trnQ-UUG LSC 890 0.0022 1.00 62.4 yes View details
rpl16 LSC 1406 0.0024 1.00 60.4 yes View details
rps19-rpl2 IRb 78 0.0183 0.94 60.2 yes View details
psbE-petL LSC 1289 0.0010 1.00 59.4 yes View details
trnM-CAU-atpE LSC 274 0.0024 1.00 56.1 yes View details
ndhE-ndhG SSC 245 0.0054 1.00 56.0 yes View details
trnT-GGU-psbD LSC 1500 0.0013 1.00 49.9 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAAGGCGCTCAACCTACA 1083–1087 1.000 79.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGCGCTCAACCTACA 1082–1086 1.000 79.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAAAAGGCGCTCAACCTACA 1092–1096 1.000 78.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CCTTGAAAAAGGCGCTCAAC 1087–1091 1.000 77.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTTGAAAAAGGCGCTCAACC 1086–1090 1.000 77.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GTCGAATAGAAATGGGGCGT 1030–1031 1.000 81.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG TCGAATAGAAATGGGGCGTG 1029–1030 1.000 81.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG TGTCGAATAGAAATGGGGCG 1031–1032 1.000 81.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 970–971 1.000 81.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTCGAATAGAAATGGGGCGT 1023–1024 1.000 80.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AATCAAACCGAAAGACCCCT 671 1.000 72.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ATCAAACCGAAAGACCCCTT 670 1.000 72.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AATCAAACCGAAAGACCCCT 670 1.000 72.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ATCAAACCGAAAGACCCCTT 669 1.000 72.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ATCAAACCGAAAGACCCCTT 724 1.000 71.3
trnG-UCC_p1 trnG-UCC GGTCAAAAACCTCCAGCAAA GCGTATTCAAGTCAATGATGCA 964–997 1.000 54.5
trnG-UCC_p2 trnG-UCC GGTCAAAAACCTCCAGCAAA TGCGTATTCAAGTCAATGATGC 965–998 1.000 54.5
trnG-UCC_p3 trnG-UCC GGTCAAAAACCTCCAGCAAAA GCGTATTCAAGTCAATGATGCA 964–997 1.000 52.3
trnG-UCC_p4 trnG-UCC GGTCAAAAACCTCCAGCAAAA TGCGTATTCAAGTCAATGATGC 965–998 1.000 52.3
trnG-UCC_p5 trnG-UCC GGTCAAAAACCTCCAGCAAA CTGGAATTGCGTATTCAAGTCA 972–1005 1.000 49.1
trnC-GCA-petN_p1 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC CAGCCCAAGCGAGATTTACT 877–882 1.000 79.6
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCGAGATTTACT 821–826 1.000 79.4
trnC-GCA-petN_p3 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC ACGAGCGAAAGGGAAAATGT 914–919 1.000 79.0
trnC-GCA-petN_p4 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC CCATACTACGAGCGAAAGGG 921–926 1.000 78.7
trnC-GCA-petN_p5 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC CCCATACTACGAGCGAAAGG 922–927 1.000 78.7
petN-psbM_p1 petN-psbM AGTAAATCTCGCTTGGGCTG AAAACAGTCAGCCAAGGTGA 964–973 1.000 77.3
petN-psbM_p2 petN-psbM ACATTTTCCCTTTCGCTCGT AAAACAGTCAGCCAAGGTGA 927–936 1.000 76.7
petN-psbM_p3 petN-psbM CCCTTTCGCTCGTAGTATGG AAAACAGTCAGCCAAGGTGA 920–929 1.000 76.5
petN-psbM_p4 petN-psbM CCTTTCGCTCGTAGTATGGG AAAACAGTCAGCCAAGGTGA 919–928 1.000 76.5
petN-psbM_p5 petN-psbM CTTTCGCTCGTAGTATGGGG AAAACAGTCAGCCAAGGTGA 918–927 1.000 76.5

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
Cercocarpus betuloides NC_088509.1 158170 View on NCBI ↗
Cercocarpus ledifolius NC_088510.1 158250 View on NCBI ↗
Cercocarpus montanus var. minutiflorus PP585285.1 158186 View on NCBI ↗