Markers + reference

Ficaria

2 species · Ranunculaceae · Ranunculales

Back to catalogue

Species 2
Genome length 156–156 kb
Candidate markers 267
Primer pairs 95

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 9 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 306 0.0196 1.00 63.9 yes View details
rpoC2 LSC 4155 0.0005 1.00 54.1 yes View details
ndhC-trnV-UAC LSC 877 0.0034 1.00 60.7 yes View details
rbcL-accD LSC 692 0.0029 1.00 60.6 yes View details
accD LSC 1479 0.0000 1.00 26.4 yes View details
accD-psaI LSC 424 0.0283 1.00 71.4 yes View details
rps8 LSC 399 0.0000 1.00 26.7 yes View details
ccsA SSC 972 0.0010 1.00 51.9 yes View details
ccsA-ndhD SSC 205 0.0341 1.00 72.1 yes View details
atpB-rbcL LSC 769 0.0013 1.00 59.5 yes View details
ycf4-cemA LSC 787 0.0013 1.00 59.5 yes View details
matK-trnK-UUU LSC 792 0.0025 1.00 59.4 yes View details
trnK-UUU-rps16 LSC 847 0.0012 1.00 59.4 yes View details
rpl32-trnL-UAG SSC 826 0.0012 1.00 59.4 yes View details
atpH-atpI LSC 1133 0.0009 1.00 59.3 yes View details
petN-psbM LSC 1216 0.0008 1.00 59.3 yes View details
atpF LSC 1271 0.0008 1.00 59.2 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 95 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 423 1.000 79.8
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 437 1.000 79.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 436 1.000 79.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 438 1.000 79.8
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCTGCTGAAGTTCCATCCAT 358 1.000 78.4
trnK-UUU_p1 trnK-UUU TGTGAATGAAATGAATAAAGTGAACT TATTTTGGGTGGGGTTGTCC 2818 1.000 40.1
trnK-UUU_p2 trnK-UUU TGTGAATGAAATGAATAAAGTGAAC TATTTTGGGTGGGGTTGTCC 2818 1.000 40.1
trnK-UUU_p3 trnK-UUU TTGTGAATGAAATGAATAAAGTGAACT TATTTTGGGTGGGGTTGTCC 2819 1.000 40.1
trnK-UUU_p4 trnK-UUU TGTGAATGAAATGAATAAAGTGA TATTTTGGGTGGGGTTGTCC 2818 1.000 40.1
trnK-UUU_p5 trnK-UUU GTGAATGAAATGAATAAAGTGAACT TATTTTGGGTGGGGTTGTCC 2817 1.000 40.1
matK-trnK-UUU_p1 matK-trnK-UUU TAATCGTGAGCAAGCGCATA AACGGTAGAGTACTCGGCTT 920 1.000 77.1
matK-trnK-UUU_p2 matK-trnK-UUU TAATCGTGAGCAAGCGCATA ACGGTAGAGTACTCGGCTTT 919 1.000 77.1
matK-trnK-UUU_p3 matK-trnK-UUU ACCCATAATCGTGAGCAAGC AACGGTAGAGTACTCGGCTT 925 1.000 76.2
matK-trnK-UUU_p4 matK-trnK-UUU ACCCATAATCGTGAGCAAGC ACGGTAGAGTACTCGGCTTT 924 1.000 76.2
matK-trnK-UUU_p5 matK-trnK-UUU TAATCGTGAGCAAGCGCATA TATTTTGGGTGGGGTTGTCC 1009 1.000 75.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAAGGGGCTCAACCTACG 946–968 1.000 78.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGGGCTCAACCTACG 945–967 1.000 78.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC AAAAAGGGGCTCAACCTACG 960–982 1.000 77.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAAAAGGGGCTCAACCTACG 955–977 1.000 77.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC AAAAAGGGGCTCAACCTACG 932–954 1.000 75.6
trnG-UCC_p1 trnG-UCC CTTGTTCGACAAAGGGTCCA AAATAAATACGCGCGGCATT 871 1.000 73.7
trnG-UCC_p2 trnG-UCC TCTTGTTCGACAAAGGGTCC AAATAAATACGCGCGGCATT 872 1.000 72.0
trnG-UCC_p3 trnG-UCC GCTCTTGTTCGACAAAGGGT AAATAAATACGCGCGGCATT 874 1.000 70.8
trnG-UCC_p4 trnG-UCC TGCTCTTGTTCGACAAAGGG AAATAAATACGCGCGGCATT 875 1.000 70.8
trnG-UCC_p5 trnG-UCC TGACCGGGCCATTTCATTTA AAATAAATACGCGCGGCATT 930 1.000 69.9
atpF_p1 atpF AAGGGTTGCCATGAGTCTTG TCAAATAAAAGAGGGCGAAGT 1414 1.000 51.4
atpF_p2 atpF GAAGGGTTGCCATGAGTCTT TCAAATAAAAGAGGGCGAAGT 1415 1.000 50.4
atpF_p3 atpF AAGGGTTGCCATGAGTCTTG AAAGAGGGCGAAGTAATACA 1407 1.000 48.0
atpF_p4 atpF AAGGGTTGCCATGAGTCTTG AAGAGGGCGAAGTAATACAA 1406 1.000 48.0
atpF_p5 atpF AAGGGTTGCCATGAGTCTTG AGAGGGCGAAGTAATACAAA 1405 1.000 48.0

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
Ficaria verna NC_087847.1 156439 View on NCBI ↗
Ficaria verna subsp. verna PP541874.1 156478 View on NCBI ↗