Markers + reference

Leontice

2 species · Berberidaceae · 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

14 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 677 0.0090 0.82 56.9 yes View details
trnK-UUU-rps16 LSC 1008 0.0176 0.79 68.7 yes View details
atpH-atpI LSC 902 0.0136 0.98 54.2 yes View details
psbZ-trnG-UCC LSC 514 0.0211 0.92 58.3 yes View details
psaA-ycf3 LSC 473 0.0217 0.97 71.2 yes View details
trnT-UGU-trnL-UAA LSC 875 0.0208 0.93 65.9 yes View details
petB LSC 1471 0.0088 1.00 63.9 yes View details
rpl16 LSC 1476 0.0076 0.98 55.1 yes View details
rpl22 LSC 525 0.0347 0.99 73.8 yes View details
ycf1 IRb 1077 0.0019 0.96 55.3 no View details
rpl32-trnL-UAG SSC 991 0.0188 0.97 68.8 yes View details
ndhD SSC 1587 0.0082 1.00 48.5 yes View details
ndhG-ndhI SSC 507 0.0240 0.98 63.2 yes View details
ycf1 SSC 5523 0.0102 1.00 45.6 yes View details
rps19-trnH-GUG LSC 125 0.1818 0.88 81.5 no View details
psbT-psbN LSC 69 0.0580 1.00 78.7 yes View details
rpl14-rpl16 LSC 121 0.0776 0.96 76.9 yes View details
ndhF-rpl32 SSC 785 0.0148 0.95 68.9 yes View details
rpl33-rps18 LSC 265 0.0282 0.94 68.8 yes View details
atpF-atpH LSC 459 0.0196 1.00 67.1 yes View details
petN-psbM LSC 834 0.0051 0.95 66.4 yes View details
trnF-GAA-ndhJ LSC 523 0.0154 1.00 66.3 yes View details
trnC-GCA-petN LSC 668 0.0120 1.00 65.9 yes View details
rpoB-trnC-GCA LSC 807 0.0100 0.99 65.3 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 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 CTGCCTTAATCCACTTGGCT GCGCTAACCTTGGTATGGAA 690–801 1.000 83.2
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC GCGCTAACCTTGGTATGGAA 691–802 1.000 83.0
trnH-GUG-psbA_p3 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TATCATCAACCGCGCTAACC 701–812 1.000 82.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TATCATCAACCGCGCTAACC 702–813 1.000 82.1
trnH-GUG-psbA_p5 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CTGATATCATCAACCGCGCT 705–816 1.000 81.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAAGGCGCTCAACCTACA 913–1122 1.000 83.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGCGCTCAACCTACA 912–1121 1.000 83.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TCAAATGTTCCCGCGATTCT 944–1153 1.000 82.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCAAATGTTCCCGCGATTCT 943–1152 1.000 82.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC AAAAAGGCGCTCAACCTACA 927–1136 1.000 82.8
atpF-atpH_p1 atpF-atpH CAGTGACCCAAGGAAACGAA AGTCGTGGCATTAGCACTTT 543–544 1.000 79.5
atpF-atpH_p2 atpF-atpH CAGTGACCCAAGGAAACGAA ATTTATGGGCTAGTCGTGGC 554–555 1.000 78.9
atpF-atpH_p3 atpF-atpH TTAAATCCGAAACTCCCGGC AGTCGTGGCATTAGCACTTT 570–571 1.000 77.7
atpF-atpH_p4 atpF-atpH TTAAATCCGAAACTCCCGGC ATTTATGGGCTAGTCGTGGC 581–582 1.000 77.1
atpF-atpH_p5 atpF-atpH CAGTGACCCAAGGAAACGAA CTAGTCGTGGCATTAGCACT 545–546 1.000 76.3
atpH-atpI_p1 atpH-atpI TCCAGGTCCAATAGAAGCCA GAATATGGTCCGTGGGTTCC 1454–1656 1.000 81.0
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT GAATATGGTCCGTGGGTTCC 1411–1613 1.000 81.0
atpH-atpI_p3 atpH-atpI AGCAAGTGACAAGACCAAGG GAATATGGTCCGTGGGTTCC 1681–1883 1.000 80.9
atpH-atpI_p4 atpH-atpI CAGTGACCCAAGGAAACGAA GAATATGGTCCGTGGGTTCC 2125–2328 1.000 80.8
atpH-atpI_p5 atpH-atpI AGCAAGTGACAAGACCAAGG CTGTGCGAAATCCACAAACC 1779–1981 1.000 80.7
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCCCTCATTTGCATCTCGAA CCGGATTTGAACTGGGGAAA 893–894 1.000 80.3
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ATCCCCTCATTTGCATCTCG CCGGATTTGAACTGGGGAAA 895–896 1.000 78.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCCCTCATTTGCATCTCGAA AAAAGGATTTGCAGTCCCCC 875–876 1.000 78.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GTTCTTCCATCAAGCCCTGA CCGGATTTGAACTGGGGAAA 972–973 1.000 76.6
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AGTTCTTCCATCAAGCCCTG CCGGATTTGAACTGGGGAAA 973–974 1.000 76.5
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAAAGCAGCCCAAGCAAGA 739–967 1.000 80.2
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CGCTTCTTCCCCATACTACG 787–1015 1.000 79.1
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCAAGACTTACT 733–961 1.000 78.8
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TCTAGAGTCCGCTTCTTCCC 796–1024 1.000 78.3
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT TTAAAGCAGCCCAAGCAAGA 757–985 1.000 78.0

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
Leontice incerta NC_043927.1 156923 View on NCBI ↗
Leontice leontopetalum subsp. ewersmannii OM912479.1 156626 View on NCBI ↗