Markers + reference

Cerasus

2 species · Rosaceae · Rosales

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Species 2
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

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA-trnK-UUU LSC 255 0.0000 1.00 23.8 yes View details
rps2 LSC 711 0.0000 1.00 27.8 yes View details
rpoC1 LSC 2812 0.0007 1.00 56.4 yes View details
rpoB LSC 3213 0.0009 1.00 52.2 yes View details
trnE-UUC-trnT-GGU LSC 452 0.0045 0.99 59.5 yes View details
psbE-petL LSC 1279 0.0031 1.00 60.5 yes View details
clpP LSC 2069 0.0029 1.00 59.3 yes View details
ndhF SSC 2247 0.0022 1.00 58.6 yes View details
rpl32-trnL-UAG SSC 1393 0.0023 0.95 64.4 yes View details
ndhA SSC 2231 0.0009 1.00 57.8 yes View details
trnT-UGU-trnL-UAA LSC 985 0.0011 0.93 63.7 yes View details
trnF-GAA-ndhJ LSC 785 0.0013 0.96 63.6 yes View details
rbcL LSC 1428 0.0007 0.98 60.9 yes View details
cemA LSC 690 0.0029 1.00 60.4 yes View details
atpB-rbcL LSC 742 0.0027 1.00 60.3 yes View details
ycf3-trnS-GGA LSC 622 0.0000 0.99 60.2 yes View details
accD-psaI LSC 774 0.0013 0.99 60.2 yes View details
rpoB-trnC-GCA LSC 1180 0.0017 1.00 59.7 yes View details
trnL-CAA-ndhB IRb 619 0.0016 1.00 59.7 yes View details
ndhB-trnL-CAA IRa 619 0.0016 1.00 59.7 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
psbA-trnK-UUU_p1 psbA-trnK-UUU TCCAGTTACAAAAGCGACCC ACTCCATCCGACTAGTTCCG 358 1.000 74.2
psbA-trnK-UUU_p2 psbA-trnK-UUU TCCAGTTACAAAAGCGACCC ACTAGTTCCGGGTTCGAGTC 348 1.000 72.5
psbA-trnK-UUU_p3 psbA-trnK-UUU TCCAGTTACAAAAGCGACCC GACTAGTTCCGGGTTCGAGT 349 1.000 72.5
psbA-trnK-UUU_p4 psbA-trnK-UUU ACGGTTTTCAGTGCTGGTTA ACTCCATCCGACTAGTTCCG 378 1.000 72.4
psbA-trnK-UUU_p5 psbA-trnK-UUU TCCAGTTACAAAAGCGACCC ATCCGACTAGTTCCGGGTTC 353 1.000 72.0
rps2_p1 rps2 TCTATGGAGTTCCCCCAAAA GAGAAGAAAAGAAGTGTGGGGA 777 1.000 44.9
rps2_p2 rps2 TTCTATGGAGTTCCCCCAAA GAGAAGAAAAGAAGTGTGGGGA 778 1.000 44.9
rps2_p3 rps2 TCTATGGAGTTCCCCCAAAA AGAGAAGAAAAGAAGTGTGGGG 778 1.000 44.9
rps2_p4 rps2 TTCTATGGAGTTCCCCCAAA AGAGAAGAAAAGAAGTGTGGGG 779 1.000 44.9
rps2_p5 rps2 TCTATGGAGTTCCCCCAAAA AGAAGAAAAGAAGTGTGGGGA 776 1.000 43.8
rpoC1_p1 rpoC1 ACTCACACGGGTGTCATAGA TTTGGCTCTGGAACTGAACC 2958 1.000 79.3
rpoC1_p2 rpoC1 ACTCACACGGGTGTCATAGA ACGATCTTTGGCTCTGGAAC 2964 1.000 78.6
rpoC1_p3 rpoC1 ACTCACACGGGTGTCATAGA GGCTCTGGAACTGAACCATT 2955 1.000 77.8
rpoC1_p4 rpoC1 CAAACTCACACGGGTGTCAT TTTGGCTCTGGAACTGAACC 2961 1.000 76.6
rpoC1_p5 rpoC1 ACTCACACGGGTGTCATAGA CGATCTTTGGCTCTGGAACT 2963 1.000 76.3
rpoB_p1 rpoB TGTGTCAATGGATTTGTTCGA CGCGAGATATATTGGCAGCT 310 1.000 57.3
rpoB_p2 rpoB TGTCAATGGATTTGTTCGATCC CGCGAGATATATTGGCAGCT 308 1.000 56.8
rpoB_p3 rpoB TGTGTCAATGGATTTGTTCGA GATATATTGGCAGCTGCGGA 305 1.000 56.5
rpoB_p4 rpoB TGTGTCAATGGATTTGTTCGA TATATTGGCAGCTGCGGATC 303 1.000 56.5
rpoB_p5 rpoB TGTGTCAATGGATTTGTTCGA AGATATATTGGCAGCTGCGG 306 1.000 56.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TAAGCCCTGCTCAATGAACC CCGGATTTGAACTGGGGAAA 1335 1.000 78.4
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ATTGCCTCATTTACACCCCC CCGGATTTGAACTGGGGAAA 1268 1.000 78.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CTCATTTACACCCCCAAGCA CCGGATTTGAACTGGGGAAA 1263 1.000 77.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TAAGCCCTGCTCAATGAACC TCTTTTGGTGATCAGGCGAC 1357 1.000 77.6
rpoB-trnC-GCA_p5 rpoB-trnC-GCA ATTGCCTCATTTACACCCCC TCTTTTGGTGATCAGGCGAC 1290 1.000 77.3
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 533–539 1.000 80.0
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 531–537 1.000 80.0
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 587–593 1.000 79.8
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 512–518 1.000 79.6
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 510–516 1.000 79.6

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
[Cerasus] fengyangshanica NC_054252.1 157964 View on NCBI ↗
[Cerasus] kumanoensis MN245147.1 157898 View on NCBI ↗