Markers + reference

Helleborus

7 species · Ranunculaceae · Ranunculales

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Species 7
Genome length 117–167 kb
Candidate markers 228
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

4 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 228 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnI-CAU-ycf2 IRb 2409 0.0780 1.00 80.0 yes View details
rps7-trnV-GAC IRb 2485 0.0768 0.80 74.2 yes View details
trnV-GAC-rps7 IRa 2463 0.0837 0.84 74.7 yes View details
ycf2-trnI-CAU IRa 2409 0.0782 1.00 80.0 yes View details
petA-psbJ LSC 395 0.0406 0.99 83.1 yes View details
trnR-UCU-atpA LSC 159 0.0539 0.99 79.5 yes View details
trnR-ACG-trnN-GUU SSC 598 0.0506 0.71 75.4 yes View details
trnN-GUU-trnR-ACG SSC 598 0.0506 0.71 75.4 yes View details
petD LSC 1217 0.0358 0.99 75.2 yes View details
trnC-GCA-petN LSC 924 0.0271 0.97 74.0 yes View details
trnS-GGA-rps4 LSC 46 0.1304 1.00 73.5 yes View details
trnP-UGG-psaJ LSC 354 0.0642 0.87 73.4 yes View details
psbT-psbN LSC 37 0.0360 1.00 71.9 yes View details
ndhF-rpl32 SSC 885 0.0241 0.99 71.0 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnR-UCU-atpA_p1 trnR-UCU-atpA TTGTTTCAGCTCGGTGGAAA GCCCAATTCGCAGAGTTAGA 890–1125 1.000 87.1
trnR-UCU-atpA_p2 trnR-UCU-atpA TTGTTTCAGCTCGGTGGAAA TCTCCAGAGTAGGATCTGCG 961–1196 1.000 87.1
trnR-UCU-atpA_p3 trnR-UCU-atpA TTGTTTCAGCTCGGTGGAAA CGGTGGAAGAACAGGTAGTG 763–998 1.000 87.0
trnR-UCU-atpA_p4 trnR-UCU-atpA TTGTTTCAGCTCGGTGGAAA GGTCGTGAAGCTTATCCAGG 1174–1440 1.000 86.3
trnR-UCU-atpA_p5 trnR-UCU-atpA TTGTTTCAGCTCGGTGGAAA AATTCTGGAATCCGACCTGC 1198–1236 0.857 76.2
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAAAGCAGCCCAAGCAAGA 878–987 0.857 83.1
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCAAGACTTACT 872–981 0.857 81.7
trnC-GCA-petN_p3 trnC-GCA-petN TTTATCGTTTTGGCGGCATG TTAAAGCAGCCCAAGCAAGA 931–1040 0.857 81.3
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT TTAAAGCAGCCCAAGCAAGA 896–1005 0.857 80.8
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 932–1041 0.857 80.1
trnS-GGA-rps4_p1 trnS-GGA-rps4 AGGCTTTTGTTTACCGAGGG TGAGCTGCTAGTCGTAGAAT 126–388 0.429 42.5
trnS-GGA-rps4_p2 trnS-GGA-rps4 AGGCTTTTGTTTACCGAGGG AATGAGCTGCTAGTCGTAGA 128–390 0.429 42.4
trnS-GGA-rps4_p3 trnS-GGA-rps4 AGGCTTTTGTTTACCGAGGG ATGAGCTGCTAGTCGTAGAA 127–389 0.429 42.4
trnS-GGA-rps4_p4 trnS-GGA-rps4 AGGCTTTTGTTTACCGAGGG TGACTCTTCACTCATCCCAA 202–464 0.429 41.6
trnS-GGA-rps4_p5 trnS-GGA-rps4 AGGCTTTTGTTTACCGAGGG TTGACTCTTCACTCATCCCA 203–465 0.429 41.6
petA-psbJ_p1 petA-psbJ CCCGTGTCCAAGGTCTTTTT TGGCTTATAGGCACTGTAGC 518–601 1.000 79.2
petA-psbJ_p2 petA-psbJ CCCGTGTCCAAGGTCTTTTT AGGCACTGTAGCTGGTATTC 510–593 1.000 78.6
petA-psbJ_p3 petA-psbJ CCCGTGTCCAAGGTCTTTTT GGCACTGTAGCTGGTATTCT 509–592 1.000 78.6
petA-psbJ_p4 petA-psbJ CCCGTGTCCAAGGTCTTTTT ACTCTGGATTGGGTTCATCC 451–534 1.000 78.3
petA-psbJ_p5 petA-psbJ CCCGTGTCCAAGGTCTTTTT GCTGGTATTCTTGTGATCGGT 500–583 1.000 77.9
trnP-UGG-psaJ_p1 trnP-UGG-psaJ TCCAGGTAGCCTATAGTGCC ACGGGTGCCACAGATAGATA 988–1139 1.000 91.3
trnP-UGG-psaJ_p2 trnP-UGG-psaJ TCCAGGTAGCCTATAGTGCC TCGTTTCGGACACAACTGTT 1577–1731 0.857 85.8
trnP-UGG-psaJ_p3 trnP-UGG-psaJ CCAGGTAGCCTATAGTGCCT TCGTTTCGGACACAACTGTT 1576–1730 0.857 85.7
trnP-UGG-psaJ_p4 trnP-UGG-psaJ TCCAGGTAGCCTATAGTGCC CTTTGGCCATGAACCTCCTT 1522–1676 0.857 85.6
trnP-UGG-psaJ_p5 trnP-UGG-psaJ CCAGGTAGCCTATAGTGCCT CTTTGGCCATGAACCTCCTT 1521–1675 0.857 85.5
psbT-psbN_p1 psbT-psbN GCCTCCTAAGGTTCCGACTA GGGTACGCCTTATATACCGC 140–192 0.714 67.0
psbT-psbN_p2 psbT-psbN GCCTCCTAAGGTTCCGACTA GATCCATTCGAGGAACACGG 92–144 0.714 66.9
psbT-psbN_p3 psbT-psbN TTCGAGAGCCTCCTAAGGTT GGGTACGCCTTATATACCGC 147–199 0.714 66.8
psbT-psbN_p4 psbT-psbN TTTCGAGAGCCTCCTAAGGT GGGTACGCCTTATATACCGC 148–200 0.714 66.8
psbT-psbN_p5 psbT-psbN TTCGAGAGCCTCCTAAGGTT GATCCATTCGAGGAACACGG 99–151 0.714 66.6

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
Helleborus argutifolius NC_080525.1 117526 View on NCBI ↗
Helleborus atrorubens NC_062141.1 166695 View on NCBI ↗
Helleborus foetidus NC_080522.1 135189 View on NCBI ↗
Helleborus lividus NC_080526.1 116970 View on NCBI ↗
Helleborus niger NC_080523.1 128236 View on NCBI ↗
Helleborus thibetanus NC_041540.1 155525 View on NCBI ↗
Helleborus torquatus NC_080524.1 130643 View on NCBI ↗