Markers + reference

Chaenomeles

4 species · Rosaceae · Rosales

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Species 4
Genome length 160–160 kb
Candidate markers 270
Primer pairs 100

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 11 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 40.0 yes View details
trnK-UUU-rps16 LSC 965 0.0014 1.00 40.9 yes View details
rps16 LSC 1121 0.0012 1.00 40.8 yes View details
rps16-trnQ-UUG LSC 827 0.0048 1.00 43.1 yes View details
psbK-psbI LSC 252 0.0026 1.00 33.6 yes View details
trnR-UCU-atpA LSC 669 0.0080 0.96 49.0 yes View details
atpH-atpI LSC 1164 0.0011 1.00 40.7 yes View details
psbM-trnD-GUC LSC 1218 0.0005 1.00 34.9 yes View details
trnL-UAA-trnF-GAA LSC 402 0.0033 1.00 38.0 yes View details
ndhC-trnV-UAC LSC 660 0.0020 1.00 41.3 yes View details
accD LSC 1527 0.0013 1.00 40.8 yes View details
ycf3-trnS LSC 615 0.0000 1.00 49.7 yes View details
trnC-GCA LSC 71 0.0141 1.00 48.3 yes View details
psaA LSC 2253 0.0005 1.00 48.2 yes View details
rps19-trnH-GUG LSC 80 0.0250 1.00 45.9 no View details
ycf1 SSC 5640 0.0004 1.00 43.4 yes View details
trnL-UAG SSC 80 0.0063 1.00 42.8 yes View details
petA-psbJ LSC 1056 0.0000 0.98 42.1 yes View details
trnT-GGU-psbD LSC 1469 0.0005 0.99 41.7 yes View details
psaI LSC 114 0.0044 1.00 41.5 yes View details
psbZ-trnG-GCC LSC 381 0.0018 0.95 41.3 yes View details
ycf1 IRb 1074 0.0000 1.00 40.0 no 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_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 1036 1.000 78.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CGGAACTTCGCCCTAATCAA 1035 1.000 78.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA CGGAACTTCGCCCTAATCAA 1045 1.000 77.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 1091 1.000 77.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 1090 1.000 77.3
rps16_p1 rps16 AGAAACAAAAAGGTTATACAAGGCT TATGTACCGACCGAACCGAT 1258 1.000 40.2
rps16_p2 rps16 AGAAACAAAAAGGTTATACAAGGCT CCGACCGAACCGATGATTAT 1252 1.000 40.2
rps16_p3 rps16 ACAAAAAGGTTATACAAGGCT TATGTACCGACCGAACCGAT 1254 1.000 40.2
rps16_p4 rps16 AGAAACAAAAAGGTTATACAAGGCT ATTATGTACCGACCGAACCG 1260 1.000 40.2
rps16_p5 rps16 GGAAATAGCAAAGAAACAAAAAGGT TATGTACCGACCGAACCGAT 1269 1.000 40.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 911–913 1.000 78.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 921–923 1.000 76.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCTTTCTGCCACATCGTTTT GAGGTTCGAATCCTTCCGTC 888–890 1.000 76.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCCACAGCTGATCATGTCCT GAGGTTCGAATCCTTCCGTC 922–924 1.000 76.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GTGTCGACTAGAAATGGGGC 973–975 1.000 76.1
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCTTCACGTCCAGGATTACG 389 1.000 72.3
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT TCTTCACGTCCAGGATTACG 386 1.000 70.3
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT TCTTCACGTCCAGGATTACG 387 1.000 70.3
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT TCTTCACGTCCAGGATTACG 388 1.000 70.3
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCTTCACGTCCAGGATTACG 390 1.000 69.9
trnR-UCU-atpA_p1 trnR-UCU-atpA TGGAATGAAAAGCGTCCATTG AGACATTTACCGACGAAGCG 832–838 1.000 67.8
trnR-UCU-atpA_p2 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT AGACATTTACCGACGAAGCG 831–837 1.000 67.8
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGACATTTACCGACGAAGCG 771–777 1.000 67.1
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT AGACATTTACCGACGAAGCG 806–812 1.000 64.1
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGAATGAAAAGCGTCCATT AGACATTTACCGACGAAGCG 832–838 1.000 63.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Chaenomeles cathayensis NC_045392.1 159907 View on NCBI ↗
Chaenomeles japonica NC_035566.1 160088 View on NCBI ↗
Chaenomeles speciosa NC_056885.1 160040 View on NCBI ↗
Chaenomeles thibetica NC_049863.1 159907 View on NCBI ↗