Markers + reference

Cotinus

7 species · Anacardiaceae · Sapindales

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Species 7
Genome length 159–160 kb
Candidate markers 272
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 590 0.0162 0.93 64.0 yes View details
trnK-UUU-rps16 LSC 1088 0.0118 1.00 60.0 yes View details
atpF-atpH LSC 266 0.0385 1.00 82.5 yes View details
rpl33-rps18 LSC 209 0.0365 1.00 69.3 yes View details
rps8 LSC 405 0.0094 1.00 42.1 yes View details
rpl22 LSC 441 0.0150 1.00 56.3 yes View details
rps19-rpl2 LSC 182 0.0957 0.96 80.3 yes View details
rpl32-trnL-UAG SSC 1152 0.0095 0.99 59.0 yes View details
ccsA-ndhD SSC 358 0.0210 1.00 48.6 yes View details
atpA-atpF LSC 55 0.0416 1.00 69.1 yes View details
rps19 LSC 150 0.0560 1.00 67.2 yes View details
rpl22-rps19 LSC 33 0.1082 1.00 64.7 yes View details
atpH-atpI LSC 1054 0.0034 1.00 62.0 yes View details
rps3-rpl22 LSC 38 0.1667 1.00 61.8 yes View details
psaA-ycf3 LSC 708 0.0031 1.00 60.9 yes View details
trnS-GCU-trnG-UCC LSC 754 0.0078 1.00 60.8 yes View details
psbK-psbI LSC 383 0.0121 0.98 60.7 yes View details
trnT-UGU-trnL-UAA LSC 1016 0.0052 1.00 60.1 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
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 628–667 0.714 73.4
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TTCCCTCTAGACCTAGCTGC 629–668 0.714 73.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 621–660 0.714 71.9
trnH-GUG-psbA_p4 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CCGTGCTAACCTTGGTATGG 677–716 0.714 71.1
trnH-GUG-psbA_p5 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CCGTGCTAACCTTGGTATGG 678–717 0.714 70.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TATTTCAAAGAAGGCGGGGG 1179–1195 1.000 81.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TATTTCAAAGAAGGCGGGGG 1178–1194 1.000 81.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA TATTTCAAAGAAGGCGGGGG 1188–1204 1.000 80.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAGAAGGCGGGGGTTTTTAC 1172–1188 1.000 80.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAGAAGGCGGGGGTTTTTAC 1171–1187 1.000 80.0
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCTTCACGTCCAGGATTACG 512–520 1.000 76.0
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT TCTTCACGTCCAGGATTACG 509–517 1.000 74.0
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT TCTTCACGTCCAGGATTACG 510–518 1.000 74.0
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT TCTTCACGTCCAGGATTACG 511–519 1.000 74.0
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCTTCACGTCCAGGATTACG 513–521 1.000 73.6
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCGCACTTTTACCACT 798–831 1.000 75.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC TAGCAATCCGCCGCTTTAAT ACGAATCGCACTTTTACCACT 796–829 1.000 75.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCGCACTTTTACCAC 798–831 1.000 75.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TAGCAATCCGCCGCTTTAAT ACGAATCGCACTTTTACCAC 796–829 1.000 75.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCGCACTTTTACCACT 847–880 1.000 74.3
atpA-atpF_p1 atpA-atpF ATGCCATCGCCTACTTGAAG TGGGGCGCTGAAAGAAATAA 198–201 1.000 80.4
atpA-atpF_p2 atpA-atpF ATGCCATCGCCTACTTGAAG TTGGGGCGCTGAAAGAAATA 199–202 1.000 80.4
atpA-atpF_p3 atpA-atpF GATGCCATCGCCTACTTGAA TGGGGCGCTGAAAGAAATAA 199–202 1.000 80.4
atpA-atpF_p4 atpA-atpF GATGCCATCGCCTACTTGAA TTGGGGCGCTGAAAGAAATA 200–203 1.000 80.3
atpA-atpF_p5 atpA-atpF ATGCCATCGCCTACTTGAAG GGGGCGCTGAAAGAAATAAC 197–200 1.000 77.6
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG CGGAGGGAAAAATACGAGGT 440–462 1.000 79.2
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG GAGGCGGAGGGAAAAATACG 444–466 1.000 79.1
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG GCGGAGGGAAAAATACGAGG 441–463 1.000 79.1
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG GGCGGAGGGAAAAATACGAG 442–464 1.000 79.1
atpF-atpH_p5 atpF-atpH ATTAAACCCGAAACTCCCGG CGAGGCGGAGGGAAAAATAC 445–467 1.000 79.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Cotinus coggygria var. cinereus ON167901.1 159287 View on NCBI ↗
Cotinus coggygria var. coggygria ON167906.1 159729 View on NCBI ↗
Cotinus coggygria var. glaucophyllus ON167903.1 158865 View on NCBI ↗
Cotinus coggygria var. pubescens ON167905.1 159599 View on NCBI ↗
Cotinus nanus NC_067635.1 160155 View on NCBI ↗
Cotinus obovatus NC_067636.1 159619 View on NCBI ↗
Cotinus szechuanensis NC_067637.1 158965 View on NCBI ↗