Markers + reference

Garidella

2 species · Ranunculaceae · Ranunculales

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Species 2
Genome length 153–153 kb
Candidate markers 262
Primer pairs 90

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 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnT-UGU-trnL-UAA LSC 818 0.0088 0.98 66.1 yes View details
psbE-petL LSC 1241 0.0097 1.00 64.4 yes View details
psbB-psbT LSC 169 0.0000 0.99 44.0 yes View details
ycf2 IRb 6357 0.0019 1.00 42.6 no View details
ycf2-trnL-CAA IRb 1018 0.0128 1.00 61.5 yes View details
ndhG-ndhI SSC 394 0.0203 1.00 66.1 yes View details
ndhA SSC 2084 0.0063 1.00 53.0 yes View details
ycf1 SSC 5058 0.0053 1.00 41.6 yes View details
ycf1-trnN-GUU IRa 1103 0.0110 0.99 63.4 yes View details
trnL-CAA-ycf2 IRa 1018 0.0128 1.00 61.5 yes View details
ycf2 IRa 6357 0.0019 1.00 42.6 yes View details
trnF-GAA-ndhJ LSC 737 0.0096 0.99 64.9 yes View details
rpl2-trnH-GUG IRa 91 0.0116 0.95 63.8 no View details
ndhC-trnV-UAC LSC 1078 0.0083 1.00 63.6 yes View details
atpH-atpI LSC 834 0.0061 0.99 63.4 yes View details
trnM-CAU-atpE LSC 107 0.0187 1.00 63.2 yes View details
psbN-psbH LSC 126 0.0238 1.00 63.0 yes View details
trnS-GCU-trnR-UCU LSC 1582 0.0070 1.00 62.7 yes View details
rps16-trnQ-UUG LSC 593 0.0067 1.00 62.5 yes View details
rpl14-rpl16 LSC 119 0.0168 1.00 62.2 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
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TTCCTTCTCTTCGGGATCGA GAGGTTCGAATCCTTCCGTC 673–678 1.000 78.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TTCCTTCTCTTCGGGATCGA CTCGGAGGTTCGAATCCTTC 677–682 1.000 77.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CTTCCTTCTCTTCGGGATCG GAGGTTCGAATCCTTCCGTC 674–679 1.000 75.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TTCCTTCTCTTCGGGATCGA ACTCGGAGGTTCGAATCCTT 678–683 1.000 75.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CTTCCTTCTCTTCGGGATCG CTCGGAGGTTCGAATCCTTC 678–683 1.000 74.8
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA TGGAAACAAATTGCGTCCAA 1700–1760 1.000 70.5
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC TGGAAACAAATTGCGTCCAA 1699–1759 1.000 70.5
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU CTTTAGTCCACTCAGCCACC TGGAAACAAATTGCGTCCAA 1690–1750 1.000 69.7
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU ACGGAAAGAGAGGGATTCGA TGGAAACAAATTGCGTCCAA 1754–1814 1.000 69.3
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU TTTAGTCCACTCAGCCACCT TGGAAACAAATTGCGTCCAA 1689–1749 1.000 68.4
atpH-atpI_p1 atpH-atpI TCCAGGTCCAATAGAAGCCA ATTTTCGCAACTTTAGCCGC 957–966 1.000 80.8
atpH-atpI_p2 atpH-atpI AACGGAAGCAGCAGAAATCA ATTTTCGCAACTTTAGCCGC 912–921 1.000 80.3
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT ATTTTCGCAACTTTAGCCGC 970–979 1.000 80.2
atpH-atpI_p4 atpH-atpI TCCAGGTCCAATAGAAGCCA GGGGAATCTATGGAGGGTCA 927–936 1.000 80.1
atpH-atpI_p5 atpH-atpI GATACCTTCTACGGCTTGGC ATTTTCGCAACTTTAGCCGC 999–1008 1.000 80.0
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 865–868 1.000 81.4
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 873–876 1.000 80.9
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 897–900 1.000 80.4
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 905–908 1.000 79.9
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ATCCAATCAAGTCCGTAGCG 888–891 1.000 79.6
trnF-GAA-ndhJ_p1 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA GATAATCATCCGCGCCTGAA 877–882 1.000 79.0
trnF-GAA-ndhJ_p2 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA GAAAGTTGGATAGGGTGGCC 841–846 1.000 78.8
trnF-GAA-ndhJ_p3 trnF-GAA-ndhJ ATCGGGAAGAGTCGGGATAG GATAATCATCCGCGCCTGAA 926–931 1.000 78.7
trnF-GAA-ndhJ_p4 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA ATAATCATCCGCGCCTGAAA 876–881 1.000 78.6
trnF-GAA-ndhJ_p5 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA ATGATAATCATCCGCGCCTG 879–884 1.000 78.5
ndhC-trnV-UAC_p1 ndhC-trnV-UAC CCTTCGTTAATTGGGGCCAA AGTGCATGTTGGGTCTTTGA 1288–1293 1.000 74.1
ndhC-trnV-UAC_p2 ndhC-trnV-UAC TAATTGGGGCCAAAACTCCG AGTGCATGTTGGGTCTTTGA 1281–1286 1.000 74.1
ndhC-trnV-UAC_p3 ndhC-trnV-UAC TGGTCCTTCGTTAATTGGGG AGTGCATGTTGGGTCTTTGA 1292–1297 1.000 73.6
ndhC-trnV-UAC_p4 ndhC-trnV-UAC CCTTCGTTAATTGGGGCCAA AGAAGGTCTACGGTTCGAGA 1221–1226 1.000 73.1
ndhC-trnV-UAC_p5 ndhC-trnV-UAC TAATTGGGGCCAAAACTCCG AGAAGGTCTACGGTTCGAGA 1214–1219 1.000 73.1

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
Garidella nigellastrum ON897813.1 153073 View on NCBI ↗
Garidella unguicularis ON897818.1 153343 View on NCBI ↗