Markers + reference

Cnidoscolus

2 species · Euphorbiaceae · Malpighiales

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Species 2
Genome length 159–159 kb
Candidate markers 267
Primer pairs 95

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 9 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 485 0.0000 1.00 48.7 yes View details
trnS-GCU-trnR-UCU LSC 1864 0.0022 1.00 59.6 yes View details
rpoC1 LSC 2852 0.0014 1.00 51.7 yes View details
rpoB-trnC-GCA LSC 992 0.0020 1.00 59.9 yes View details
psbZ-trnG-GCC LSC 720 0.0028 1.00 60.3 yes View details
petA-psbJ LSC 1105 0.0018 1.00 59.8 yes View details
psbE LSC 252 0.0079 1.00 48.4 yes View details
ycf1 IRb 1620 0.0068 1.00 48.3 yes View details
ndhF-rpl32 SSC 965 0.0021 1.00 58.0 yes View details
ndhA SSC 2209 0.0009 1.00 45.4 yes View details
ycf1 SSC 5517 0.0018 1.00 53.5 no View details
rpl2-trnH-GUG LSC 100 0.0698 0.86 84.8 no View details
ycf1-ndhF SSC 48 0.2222 0.56 67.1 yes View details
trnV-GAC IRb 72 0.0139 1.00 60.5 yes View details
trnV-GAC IRa 72 0.0139 1.00 60.5 yes View details
ycf4-cemA LSC 949 0.0021 1.00 60.0 yes View details
rps16-trnQ-UUG LSC 1159 0.0017 1.00 59.7 yes View details
ndhK LSC 678 0.0015 1.00 59.6 yes View details
ndhI-ndhA SSC 81 0.0123 1.00 59.6 yes View details
trnE-UUC-trnT-GGU LSC 747 0.0013 1.00 59.5 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 552–558 1.000 78.6
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 566–572 1.000 78.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 565–571 1.000 78.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 567–573 1.000 78.5
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 555–561 1.000 78.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1232–1241 1.000 78.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CCGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1247–1256 1.000 76.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TAAGAATCCACAGCCGATCG GAGGTTCGAATCCTTCCGTC 1260–1269 1.000 75.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1236–1245 1.000 73.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1246–1255 1.000 73.6
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGAAGACCTCTGTCCTATCCA 1935–1967 1.000 64.0
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGAAGACCTCTGTCCTATCCA 1934–1966 1.000 64.0
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU TGCCAAAGTCATCACCGAAA AGAAGACCTCTGTCCTATCCA 2009–2041 1.000 63.8
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGGTTTAGAAGACCTCTGTCCT 1941–1973 1.000 63.3
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGGTTTAGAAGACCTCTGTCCT 1940–1972 1.000 63.3
rpoC1_p1 rpoC1 TGGTCCTAGTTGAACCGAAG TCCTTGTATCTGAGAAGAACTTTCA 2997–2998 1.000 40.1
rpoC1_p2 rpoC1 ACTTAGCTTAGATCCCTATGA TTGCTCGTTCGAGAACTACG 2992–2993 1.000 40.1
rpoC1_p3 rpoC1 ACTTAGCTTAGATCCCTATGA ACGATCTTTGGCTCTGGAAC 2975–2976 1.000 40.1
rpoC1_p4 rpoC1 GGTCCTAGTTGAACCGAAGAG TCCTTGTATCTGAGAAGAACTTTCA 2996–2997 1.000 40.1
rpoC1_p5 rpoC1 TGGTCCTAGTTGAACCGAAG AGGAAGGAAGCTTAATTGAAATGA 2965–2966 1.000 40.1
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCCTCATTTCCATTCCCGAG CTGCGCCTTTTGTTGATCAG 1104 1.000 79.7
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CTCATTTCCATTCCCGAGCA CTGCGCCTTTTGTTGATCAG 1102 1.000 79.6
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCCTCATTTCCATTCCCGAG CCGGATTTGAACTGGGGAAA 1077 1.000 79.3
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CTCATTTCCATTCCCGAGCA CCGGATTTGAACTGGGGAAA 1075 1.000 79.2
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCCTCATTTCCATTCCCGAG TAAAGCTGCGCCTTTTGTTG 1109 1.000 78.9
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 850 1.000 77.9
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 829 1.000 77.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCATGGCGTTACTCTACCAC 829 1.000 77.5
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA CCATGGCGTTACTCTACCAC 808 1.000 77.3
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TGGCGTTACTCTACCACTGA 826 1.000 77.3

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
Cnidoscolus aconitifolius MZ045411.1 158658 View on NCBI ↗
Cnidoscolus chayamansa PX316407.1 158842 View on NCBI ↗