Markers + reference

Ceratocephala

2 species · Ranunculaceae · Ranunculales

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Species 2
Genome length 151–151 kb
Candidate markers 264
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpH-atpI LSC 1120 0.0018 1.00 59.8 yes View details
petN-psbM LSC 1216 0.0016 1.00 59.7 yes View details
psbM-trnD-GUC LSC 399 0.0025 1.00 56.0 yes View details
trnT-GGU-psbD LSC 1391 0.0014 1.00 59.6 yes View details
ycf3-trnS-GGA LSC 744 0.0257 0.99 65.1 yes View details
trnS-GGA-rps4 LSC 764 0.0026 1.00 54.1 yes View details
atpB LSC 1497 0.0020 1.00 59.9 yes View details
rps19 LSC 282 0.0071 1.00 45.0 yes View details
ycf1 SSC 5217 0.0013 1.00 53.4 yes View details
rps16-trnQ-UUG LSC 628 0.0016 0.99 60.9 yes View details
rbcL-accD LSC 846 0.0024 1.00 60.1 yes View details
petA-psbJ LSC 561 0.0036 1.00 60.0 yes View details
ndhF-rpl32 SSC 898 0.0011 0.99 60.0 yes View details
accD LSC 1188 0.0017 1.00 59.7 yes View details
rpl32-trnL-UAG SSC 606 0.0016 1.00 59.7 yes View details
ndhH SSC 1182 0.0017 1.00 59.7 yes View details
trnF-GAA-ndhJ LSC 656 0.0015 1.00 59.6 yes View details
ndhK LSC 684 0.0015 1.00 59.6 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCATGCCCTTCAAGCCATAC GAGGTTCGAATCCTTCCGTC 704–712 1.000 80.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TAGCACAACGGTTGAAACGA GAGGTTCGAATCCTTCCGTC 675–683 1.000 79.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGCCCTTCAAGCCATAC GGTAAGGCATCGGGTTTTGA 736–744 1.000 79.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TAGCACAACGGTTGAAACGA GGTAAGGCATCGGGTTTTGA 707–715 1.000 79.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGCCCTTCAAGCCATAC CTCGGAGGTTCGAATCCTTC 708–716 1.000 78.9
atpH-atpI_p1 atpH-atpI TCCAGGTCCAATAGAAGCCA ATTTTCGCAACTTTAGCCGC 1252 1.000 79.7
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT ATTTTCGCAACTTTAGCCGC 1209 1.000 79.6
atpH-atpI_p3 atpH-atpI CGCAATACCTTCTACGGCTT ATTTTCGCAACTTTAGCCGC 1297 1.000 79.4
atpH-atpI_p4 atpH-atpI TACCTTGACCAACTCCAGGT ATTTTCGCAACTTTAGCCGC 1265 1.000 79.0
atpH-atpI_p5 atpH-atpI AGCCAATCCAGCAGCAATAA ATTTTCGCAACTTTAGCCGC 1225 1.000 78.8
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA CATTCATTGCTACTGCGCTG 1378–1382 1.000 79.3
petN-psbM_p2 petN-psbM TCTTGCTTGGGCTGCTTTAA ATTCATTGCTACTGCGCTGT 1377–1381 1.000 78.0
petN-psbM_p3 petN-psbM TCTTGCTTGGGCTGCTTTAA ATTGCTACTGCGCTGTTCAT 1373–1377 1.000 78.0
petN-psbM_p4 petN-psbM AGTAAGTCTTGCTTGGGCTG CATTCATTGCTACTGCGCTG 1384–1388 1.000 77.8
petN-psbM_p5 petN-psbM AGTAAGTCTTGCTTGGGCTG ATTGCTACTGCGCTGTTCAT 1379–1383 1.000 76.5
psbM-trnD-GUC_p1 psbM-trnD-GUC TTGACTGACCGTTTTGACGT AGTTCAATCGGTCAGAGCAC 561 1.000 79.4
psbM-trnD-GUC_p2 psbM-trnD-GUC CAGCGCAGTAGCAATGAATG AGTTCAATCGGTCAGAGCAC 504 1.000 78.7
psbM-trnD-GUC_p3 psbM-trnD-GUC ACAGCGCAGTAGCAATGAAT AGTTCAATCGGTCAGAGCAC 505 1.000 77.4
psbM-trnD-GUC_p4 psbM-trnD-GUC ATGAACAGCGCAGTAGCAAT AGTTCAATCGGTCAGAGCAC 509 1.000 77.4
psbM-trnD-GUC_p5 psbM-trnD-GUC AACAGCGCAGTAGCAATGAA AGTTCAATCGGTCAGAGCAC 506 1.000 75.7
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CCGTAACCAGTCATCCATCG 1521 1.000 78.4
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA CCGTAACCAGTCATCCATCG 1524 1.000 78.2
trnT-GGU-psbD_p3 trnT-GGU-psbD TTGGTTCATTCAGGAGTGGC CCGTAACCAGTCATCCATCG 1564 1.000 78.2
trnT-GGU-psbD_p4 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG TCTCCGTAACCAGTCATCCA 1524 1.000 77.8
trnT-GGU-psbD_p5 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA TCTCCGTAACCAGTCATCCA 1527 1.000 77.6
ycf3-trnS-GGA_p1 ycf3-trnS-GGA CCATTTATCCGTGATCTAGGCA TCGGTAAACAAAAGCCCACA 831 1.000 63.8
ycf3-trnS-GGA_p2 ycf3-trnS-GGA CCATTTATCCGTGATCTAGGCA GCGAAGGTACGGAAAGAGAG 863 1.000 63.4
ycf3-trnS-GGA_p3 ycf3-trnS-GGA CCATTTATCCGTGATCTAGGCA ACGGAAAGAGAGGGATTCGA 855 1.000 63.0
ycf3-trnS-GGA_p4 ycf3-trnS-GGA CCATTTATCCGTGATCTAGGCA AAAGCCCACATAGCAGTTCC 821 1.000 63.0
ycf3-trnS-GGA_p5 ycf3-trnS-GGA CCATTTATCCGTGATCTAGGCA TAGGCGAAGGTACGGAAAGA 866 1.000 62.8

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
Ceratocephala falcata MK253464.1 150821 View on NCBI ↗
Ceratocephala orthoceras NC_087846.1 151407 View on NCBI ↗