Markers + reference

Naravelia

2 species · Ranunculaceae · Ranunculales

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Species 2
Genome length 160–160 kb
Candidate markers 278
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 7 remaining regions by MarkerSeek score (out of 278 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps4 LSC 633 0.0032 1.00 46.0 yes View details
rps4-rps16 LSC 552 0.0164 1.00 67.5 yes View details
petN-psbM LSC 794 0.0115 0.99 66.3 yes View details
psbE-petL LSC 1340 0.0038 0.99 61.6 yes View details
ycf1 IRb 1696 0.0006 1.00 58.7 no View details
rpl32-trnL-UAG SSC 921 0.0054 1.00 49.8 yes View details
ccsA SSC 966 0.0021 1.00 51.7 yes View details
ccsA-ndhD SSC 240 0.0292 1.00 64.2 yes View details
ndhE SSC 306 0.0000 1.00 25.2 yes View details
ndhE-ndhG SSC 288 0.0145 0.95 65.2 yes View details
ndhA SSC 2098 0.0052 1.00 60.5 yes View details
ycf1 SSC 5631 0.0021 1.00 53.7 yes View details
rpoB-trnC-GCA LSC 1083 0.0028 0.99 61.4 yes View details
rps16-trnK-UUU LSC 649 0.0031 0.99 61.1 yes View details
ndhJ-ndhK LSC 135 0.0148 1.00 61.0 yes View details
accD-psaI LSC 547 0.0055 1.00 60.8 yes View details
atpH-atpI LSC 1115 0.0027 1.00 60.7 yes View details
psaA-ycf3 LSC 742 0.0027 1.00 60.3 yes View details
rbcL-accD LSC 738 0.0027 1.00 60.3 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
rps4_p1 rps4 AAAAATACGCCGTCTGGGT AAAACCTGACCTGTTGACCC 246 1.000 66.7
rps4_p2 rps4 AAAAATACGCCGTCTGGGT TTGACCCTTTGGCTTTTCCA 233 1.000 65.9
rps4_p3 rps4 AAAAATACGCCGTCTGGGT CCTGACCTGTTGACCCTTTG 242 1.000 64.1
rps4_p4 rps4 AAAAATACGCCGTCTGGGT CTGACCTGTTGACCCTTTGG 241 1.000 64.1
rps4_p5 rps4 AAAAATACGCCGTCTGGGT GTTGACCCTTTGGCTTTTCC 234 1.000 63.0
rps4-rps16_p1 rps4-rps16 GTAAGTGGGTCGGTTTGGAA ATTCCTTCAAGTCGCACGTT 674–676 1.000 78.3
rps4-rps16_p2 rps4-rps16 GTAAGTGGGTCGGTTTGGAA AAGTCGCACGTTGCTTTCTA 666–668 1.000 78.1
rps4-rps16_p3 rps4-rps16 AAGTGGGTCGGTTTGGAAAT ATTCCTTCAAGTCGCACGTT 672–674 1.000 77.3
rps4-rps16_p4 rps4-rps16 AAGTGGGTCGGTTTGGAAAT AAGTCGCACGTTGCTTTCTA 664–666 1.000 77.2
rps4-rps16_p5 rps4-rps16 AGTAAGTGGGTCGGTTTGGA ATTCCTTCAAGTCGCACGTT 675–677 1.000 75.7
rps16-trnK-UUU_p1 rps16-trnK-UUU GCTCAACCTACGGAAACTGT TCTACCAACGGTATGGACGA 826–829 1.000 78.2
rps16-trnK-UUU_p2 rps16-trnK-UUU GCTCAACCTACGGAAACTGT AAAGCCGAGTACTCTACCGT 761–764 1.000 78.0
rps16-trnK-UUU_p3 rps16-trnK-UUU GCTCAACCTACGGAAACTGT AAGCCGAGTACTCTACCGTT 760–763 1.000 78.0
rps16-trnK-UUU_p4 rps16-trnK-UUU CCTTGAAAAAGGCGCTCAAC TCTACCAACGGTATGGACGA 839–842 1.000 77.7
rps16-trnK-UUU_p5 rps16-trnK-UUU CTTGAAAAAGGCGCTCAACC TCTACCAACGGTATGGACGA 838–841 1.000 77.7
ndhJ-ndhK_p1 ndhJ-ndhK GCCAATCCTCGGGCTTTATT CGCCATCTACTTCAGAGATCC 324 1.000 67.7
ndhJ-ndhK_p2 ndhJ-ndhK CAAGCAGACAAACGACCTTG CGCCATCTACTTCAGAGATCC 238 1.000 67.2
ndhJ-ndhK_p3 ndhJ-ndhK CCAAGCAGACAAACGACCTT CGCCATCTACTTCAGAGATCC 239 1.000 64.8
ndhJ-ndhK_p4 ndhJ-ndhK GCCAATCCTCGGGCTTTATT GCCATCTACTTCAGAGATCCC 323 1.000 64.6
ndhJ-ndhK_p5 ndhJ-ndhK CAAGCAGACAAACGACCTTG GCCATCTACTTCAGAGATCCC 237 1.000 64.1
atpH-atpI_p1 atpH-atpI TCCAGGTCCAATAGAAGCCA ATAGGGGAATCCATGGAGGG 1215–1220 1.000 79.7
atpH-atpI_p2 atpH-atpI AACGGAAGCAGCAGAAATCA ATAGGGGAATCCATGGAGGG 1170–1175 1.000 79.2
atpH-atpI_p3 atpH-atpI GATACCTTCTACGGCTTGGC ATAGGGGAATCCATGGAGGG 1257–1262 1.000 78.9
atpH-atpI_p4 atpH-atpI CGATACCTTCTACGGCTTGG ATAGGGGAATCCATGGAGGG 1258–1263 1.000 78.9
atpH-atpI_p5 atpH-atpI AGCCAATCCAGCAGCAATAA ATAGGGGAATCCATGGAGGG 1188–1193 1.000 78.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCG CCGGATTTGAACTGGGGAAA 1159–1171 1.000 75.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GTTCTTCCGTCAATCCCTGA CCGGATTTGAACTGGGGAAA 1236–1248 1.000 74.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AGTTCTTCCGTCAATCCCTG CCGGATTTGAACTGGGGAAA 1237–1249 1.000 74.1
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCG GCAAAGGGTTTCGGGTTTTT 1195–1207 1.000 73.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCG TTATTGATCAGGCGACACCC 1177–1189 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
Naravelia pilulifera NC_039542.1 159513 View on NCBI ↗
Naravelia zeylanica NC_039580.1 159568 View on NCBI ↗