Markers + reference

Callianthemum

2 species · Ranunculaceae · Ranunculales

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Species 2
Genome length 157–157 kb
Candidate markers 265
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0028 1.00 53.8 yes View details
trnK-UUU-trnQ-UUG LSC 2444 0.0103 0.99 63.3 yes View details
trnS-GCU-trnG-UCC LSC 654 0.0153 1.00 67.9 yes View details
trnG-UCC-trnR-UCU LSC 179 0.0225 0.99 58.3 yes View details
atpF-atpH LSC 460 0.0218 1.00 68.8 yes View details
rpoB-trnC-GCA LSC 1246 0.0120 1.00 65.7 yes View details
ycf3-trnS-GGA LSC 845 0.0166 1.00 68.8 yes View details
ndhC-trnV-UAC LSC 1185 0.0119 1.00 63.9 yes View details
psbE-petL LSC 1181 0.0112 0.98 64.8 yes View details
trnP-UGG-psaJ LSC 430 0.0186 1.00 55.1 yes View details
ndhF-rpl32 SSC 971 0.0312 0.99 66.7 yes View details
rpl32-trnL-UAG SSC 573 0.0371 0.99 69.0 yes View details
ycf1 SSC 5490 0.0093 1.00 47.1 yes View details
trnH-GUG-psbA LSC 201 0.0588 0.93 79.2 yes View details
trnR-UCU-atpA LSC 127 0.0556 0.99 77.3 yes View details
trnM-CAU-atpE LSC 293 0.0280 0.98 70.8 yes View details
petL-petG LSC 180 0.0278 1.00 68.5 yes View details
ndhH-rps15 SSC 128 0.0164 0.95 65.8 yes View details
petA-psbJ LSC 431 0.0142 0.98 64.9 yes View details
trnR-ACG-trnN-GUU IRb 530 0.0132 1.00 64.9 yes View details
trnN-GUU-trnR-ACG IRa 530 0.0132 1.00 64.9 yes View details
rps12-clpP LSC 162 0.0248 0.99 64.2 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 110 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 GCGCTAACCTTGGTATGGAA 318–333 1.000 84.9
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 332–347 1.000 84.6
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 331–346 1.000 84.6
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 333–348 1.000 84.5
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TATCATCAACCGCGCTAACC 329–344 1.000 83.8
psbA_p1 psbA TACCCAGCCTCTTGACAGAA ATTTGTGTGCTTGGGAGTCC 1200 1.000 77.0
psbA_p2 psbA CTCCTGCAACTTCAACGACT ATTTGTGTGCTTGGGAGTCC 1163 1.000 76.1
psbA_p3 psbA TCCTGCAACTTCAACGACTC ATTTGTGTGCTTGGGAGTCC 1162 1.000 76.1
psbA_p4 psbA GGGCATTACTCCTGCAACTT ATTTGTGTGCTTGGGAGTCC 1171 1.000 75.9
psbA_p5 psbA ATACCCAGCCTCTTGACAGA ATTTGTGTGCTTGGGAGTCC 1201 1.000 75.1
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG AATCCGTCGCTTCATCCAAA GAGGTTCGAATCCTTCCGTC 2548–2562 1.000 79.8
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG CGTCGCTTCATCCAAATGTG GAGGTTCGAATCCTTCCGTC 2544–2558 1.000 79.4
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG AAAGCCGAGTACTCTACCGT GAGGTTCGAATCCTTCCGTC 2502–2516 1.000 79.4
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG AAGCCGAGTACTCTACCGTT GAGGTTCGAATCCTTCCGTC 2501–2515 1.000 79.4
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG AATCCGTCGCTTCATCCAAA CTCGGAGGTTCGAATCCTTC 2552–2566 1.000 78.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AACCGAAAGACCCCTTAACT 761–857 1.000 68.1
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AACCGAAAGACCCCTTAACT 760–856 1.000 68.0
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AACCGAAAGACCCCTTAACT 815–911 1.000 66.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AAACCGAAAGACCCCTTAACT 762–858 1.000 66.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AAACCGAAAGACCCCTTAACT 761–857 1.000 66.2
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 258–259 1.000 64.9
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 261–262 1.000 64.6
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 264–265 1.000 64.2
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 267–268 1.000 63.9
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 262–263 1.000 62.4
trnR-UCU-atpA_p1 trnR-UCU-atpA AAAGTCGGAATGAAAGGCGT AGAAGCGCAAGTCCTTTTGA 287–288 1.000 81.1
trnR-UCU-atpA_p2 trnR-UCU-atpA AAAGTCGGAATGAAAGGCGT CAGGAACAGATGGAGCGATT 256–257 1.000 79.1
trnR-UCU-atpA_p3 trnR-UCU-atpA AAAGTCGGAATGAAAGGCGT AGACATTCACCGAAGAAGCG 300–301 1.000 79.0
trnR-UCU-atpA_p4 trnR-UCU-atpA AAAGTCGGAATGAAAGGCGT ATTCAGGAACAGATGGAGCG 259–260 1.000 79.0
trnR-UCU-atpA_p5 trnR-UCU-atpA ATGAAAGGCGTCCATTGTCT AGAAGCGCAAGTCCTTTTGA 278–279 1.000 78.1

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
Callianthemum alatavicum MK253466.1 156538 View on NCBI ↗
Callianthemum taipaicum NC_041476.1 156939 View on NCBI ↗