Markers + reference

Clethra

2 species · Clethraceae · Ericales

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Species 2
Genome length 157–157 kb
Candidate markers 273
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 405 0.0123 1.00 61.8 yes View details
atpH-atpI LSC 1022 0.0049 1.00 61.6 yes View details
ycf3-trnS-GGA LSC 331 0.0091 1.00 56.3 yes View details
trnT-UGU-trnL-UAA LSC 1052 0.0049 0.98 63.7 yes View details
ndhC-trnV-UAC LSC 1203 0.0059 0.84 63.8 yes View details
psaJ-rpl33 LSC 455 0.0066 1.00 50.7 yes View details
clpP LSC 2032 0.0025 1.00 59.2 yes View details
petB LSC 1428 0.0035 1.00 55.6 yes View details
petD LSC 1272 0.0024 1.00 50.7 yes View details
rpl16 LSC 1473 0.0034 0.99 47.8 yes View details
rps3 LSC 681 0.0044 1.00 53.8 yes View details
rps15 SSC 273 0.0073 1.00 44.9 yes View details
ycf1 SSC 5634 0.0021 1.00 41.4 yes View details
rpl16-rps3 LSC 117 0.0265 0.97 71.0 yes View details
trnD-GUC-trnY-GUA LSC 108 0.0187 0.99 64.1 yes View details
rpl2-trnH-GUG IRa 122 0.0000 1.00 63.8 no View details
accD-psaI LSC 738 0.0028 0.98 61.9 yes View details
psaA-ycf3 LSC 748 0.0053 1.00 61.8 yes View details
ndhF-rpl32 SSC 932 0.0043 1.00 61.2 yes View details
trnK-UUU-rps16 LSC 791 0.0038 1.00 60.9 yes View details
atpB-rbcL LSC 782 0.0026 1.00 60.5 yes View details
petA-psbJ LSC 975 0.0031 1.00 60.5 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 110 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 482–483 1.000 79.2
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TTCCCTCTAGACCTAGCTGC 483–484 1.000 78.9
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 475–476 1.000 77.6
trnH-GUG-psbA_p4 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CCGTGCTAACCTTGGTATGG 531–532 1.000 77.0
trnH-GUG-psbA_p5 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CCGTGCTAACCTTGGTATGG 532–533 1.000 76.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA AAGGGCGGAGGTTTTTAAGT 895 1.000 74.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC AAGGGCGGAGGTTTTTAAGT 896 1.000 74.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 ATGGACGAATCCCTTGCTTC AAGGGCGGAGGTTTTTAAGT 900 1.000 74.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 GGACGAATCCCTTGCTTCAT AAGGGCGGAGGTTTTTAAGT 898 1.000 74.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGATGGTATGGACGAATCCC AAGGGCGGAGGTTTTTAAGT 907 1.000 74.3
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT CCCGTCATGTTCCTTGGATT 1156–1181 1.000 79.0
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT CCCGTCATGTTCCTTGGATT 1212–1237 1.000 78.4
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA CCCGTCATGTTCCTTGGATT 1157–1182 1.000 77.8
atpH-atpI_p4 atpH-atpI GCAGTACCTTGACCAACTCC CCCGTCATGTTCCTTGGATT 1216–1241 1.000 77.8
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC CCCGTCATGTTCCTTGGATT 1171–1196 1.000 77.6
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TGGCAATATGTCTACGCTGG 177–178 1.000 75.6
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGCAATATGTCTACGCTGGT 176–177 1.000 75.6
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGGACGGACTGTAAATTCG 198–199 1.000 74.6
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGACGGACTGTAAATTCGT 197–198 1.000 74.4
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GATTCTTCCTGGGTCGATGC 231–232 1.000 73.9
psaA-ycf3_p1 psaA-ycf3 GTCTGGCCCATTCCTCAAAA ATCAAGCCGCTGAGTATTGG 931–936 1.000 79.4
psaA-ycf3_p2 psaA-ycf3 TTACGGGATCCCTGTCTACC ATCAAGCCGCTGAGTATTGG 904–909 1.000 79.4
psaA-ycf3_p3 psaA-ycf3 GTCTGGCCCATTCCTCAAAA GGAAACAGGCTATAGCGCTT 913–918 1.000 79.4
psaA-ycf3_p4 psaA-ycf3 TTACGGGATCCCTGTCTACC GGAAACAGGCTATAGCGCTT 886–891 1.000 79.4
psaA-ycf3_p5 psaA-ycf3 GTCTGGCCCATTCCTCAAAA CGATCAAGCCGCTGAGTATT 933–938 1.000 78.6
ycf3-trnS-GGA_p1 ycf3-trnS-GGA TTCTCCTGAAGTTGTCGGAA GCGAAGGTACGGAAAGAGAG 523–524 1.000 67.1
ycf3-trnS-GGA_p2 ycf3-trnS-GGA TTTCTCCTGAAGTTGTCGGA GCGAAGGTACGGAAAGAGAG 524–525 1.000 67.1
ycf3-trnS-GGA_p3 ycf3-trnS-GGA TTCTCCTGAAGTTGTCGGAA CCCTCGGTAAACAAAAGCCT 494–495 1.000 67.1
ycf3-trnS-GGA_p4 ycf3-trnS-GGA TTTCTCCTGAAGTTGTCGGA CCCTCGGTAAACAAAAGCCT 495–496 1.000 67.1
ycf3-trnS-GGA_p5 ycf3-trnS-GGA TTCTCCTGAAGTTGTCGGAA ACGGAAAGAGAGGGATTCGA 515–516 1.000 66.6

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
Clethra fargesii MT742578.1 157486 View on NCBI ↗
Clethra petelotii NC_084871.1 157313 View on NCBI ↗