Markers + reference

Holboellia

3 species · Lardizabalaceae · Ranunculales

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Species 3
Genome length 158–158 kb
Candidate markers 266
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf3-trnS-GGA LSC 919 0.0007 1.00 59.3 yes View details
ndhK LSC 768 0.0000 1.00 27.8 yes View details
ycf2 IRb 6891 0.0000 1.00 33.8 no View details
ccsA SSC 972 0.0000 1.00 31.1 yes View details
ndhD SSC 1530 0.0004 1.00 41.2 yes View details
ycf1 SSC 5592 0.0002 1.00 52.7 yes View details
trnV-GAC-rps12 IRa 1905 0.0003 1.00 45.6 yes View details
ycf2 IRa 6891 0.0000 1.00 33.8 yes View details
atpH-atpI LSC 729 0.0009 1.00 59.6 yes View details
trnK-UUU-rps16 LSC 962 0.0000 0.99 59.3 yes View details
ndhF-rpl32 SSC 1077 0.0006 1.00 59.3 yes View details
trnS-GCU-trnG-UCC LSC 736 0.0000 1.00 59.1 yes View details
trnH-GUG-psbA LSC 470 0.0014 1.00 57.2 yes View details
rps4-trnT-UGU LSC 379 0.0000 1.00 54.7 yes View details
ccsA-ndhD SSC 217 0.0154 1.00 49.8 yes View details
rps16-trnQ-UUG LSC 704 0.0009 1.00 46.9 yes View details
rps3 LSC 657 0.0010 1.00 46.9 yes View details
atpB-rbcL LSC 760 0.0009 1.00 46.8 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA TCACAATCCACTGCCTTGAG GCTCCAGCGACAAATGGATA 529–530 1.000 78.4
trnH-GUG-psbA_p2 trnH-GUG-psbA TCACAATCCACTGCCTTGAG CCTCTAGACCTAGCTGCTGT 553–554 1.000 78.2
trnH-GUG-psbA_p3 trnH-GUG-psbA TCACAATCCACTGCCTTGAG TTCCCTCTAGACCTAGCTGC 556–557 1.000 78.2
trnH-GUG-psbA_p4 trnH-GUG-psbA TCACAATCCACTGCCTTGAG TAGACCTAGCTGCTGTCGAA 549–550 1.000 77.8
trnH-GUG-psbA_p5 trnH-GUG-psbA TATATGATGGGCGAACGACG GCTCCAGCGACAAATGGATA 574–575 1.000 77.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCTACCAACGGTATGGACGA AAAAAGGCGCTCAACCTACA 1150–1156 1.000 79.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAAGGCGCTCAACCTACA 1085–1091 1.000 78.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGCGCTCAACCTACA 1084–1090 1.000 78.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC AAAAAGGCGCTCAACCTACA 1099–1105 1.000 78.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAAAAGGCGCTCAACCTACA 1094–1100 1.000 78.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 777–785 1.000 78.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCCACGACTGATCATGTCCT GAGGTTCGAATCCTTCCGTC 799–807 1.000 78.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 788–796 1.000 77.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCATCGGGTTTTGGTC 807–815 1.000 77.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCCACGACTGATCATGTCCT TAAGGCATCGGGTTTTGGTC 829–837 1.000 77.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 809–810 1.000 51.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 812–813 1.000 50.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 811–812 1.000 50.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 810–811 1.000 49.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA CAAATTGAAAGACCCCTTAACCA 849–850 1.000 49.5
atpH-atpI_p1 atpH-atpI GGCAGAAACCAGTGGATTCA GCGAATCCATGGAAGGTCAT 774–776 1.000 79.4
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT GCGAATCCATGGAAGGTCAT 841–843 1.000 79.2
atpH-atpI_p3 atpH-atpI GATACCTTCTACGGCTTGGC GCGAATCCATGGAAGGTCAT 870–872 1.000 79.0
atpH-atpI_p4 atpH-atpI CGATACCTTCTACGGCTTGG GCGAATCCATGGAAGGTCAT 871–873 1.000 79.0
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA GCGAATCCATGGAAGGTCAT 786–788 1.000 78.6
ycf3-trnS-GGA_p1 ycf3-trnS-GGA CCATTTATCTGCGATCTAGGCA AACGTACGGAAAGAGAGGGA 1034–1035 1.000 62.9
ycf3-trnS-GGA_p2 ycf3-trnS-GGA CCATTTATCTGCGATCTAGGCA CCCTCGGTAAACAAAAGCCT 1008–1009 1.000 62.8
ycf3-trnS-GGA_p3 ycf3-trnS-GGA CCATTTATCTGCGATCTAGGCA ACGTACGGAAAGAGAGGGAT 1033–1034 1.000 62.5
ycf3-trnS-GGA_p4 ycf3-trnS-GGA CCATTTATCTGCGATCTAGGCA ACGGAAAGAGAGGGATTCGA 1029–1030 1.000 62.4
ycf3-trnS-GGA_p5 ycf3-trnS-GGA CCATTTATCTGCGATCTAGGCA TTCCAATGCTACGCCTTGAA 979–980 1.000 62.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Holboellia angustifolia NC_053741.1 157797 View on NCBI ↗
Holboellia grandiflora NC_058573.1 157811 View on NCBI ↗
Holboellia latifolia NC_039622.1 157818 View on NCBI ↗