Markers + reference

Circaea

7 species · Onagraceae · Myrtales

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Species 7
Genome length 156–156 kb
Candidate markers 267
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 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 369 0.0214 1.00 70.9 yes View details
trnK-UUU-rps16 LSC 953 0.0112 0.99 57.9 yes View details
trnS-GCU-trnG-GCC LSC 806 0.0122 1.00 64.3 yes View details
psbM-trnD-GUC LSC 1118 0.0092 0.99 54.2 yes View details
psaA-ycf3 LSC 751 0.0162 0.97 62.5 yes View details
trnT-UGU-trnL-UAA LSC 1103 0.0096 1.00 53.9 yes View details
trnF-GAA-ndhJ LSC 749 0.0140 1.00 68.4 yes View details
petA-psbJ LSC 1003 0.0124 1.00 68.3 yes View details
rpl16 LSC 1444 0.0057 1.00 49.7 yes View details
ndhF SSC 2241 0.0060 1.00 47.4 yes View details
ndhF-rpl32 SSC 736 0.0154 0.99 68.3 yes View details
atpH-atpI LSC 894 0.0072 1.00 66.0 yes View details
trnC-GCA-petN LSC 898 0.0067 0.99 63.6 yes View details
ycf3-trnS-GGA LSC 909 0.0077 1.00 63.2 yes View details
psaJ-rpl33 LSC 553 0.0071 1.00 59.2 yes View details
psbI-trnS-GCU LSC 121 0.0335 1.00 58.2 yes View details
rpoB-trnC-GCA LSC 1261 0.0078 1.00 57.8 yes View details
trnR-UCU-atpA LSC 478 0.0120 1.00 57.2 yes View details
ndhC-trnV-UAC LSC 1190 0.0093 0.97 56.1 yes View details
rps16-trnQ-UUG LSC 854 0.0074 1.00 55.8 yes View details
rbcL-accD LSC 778 0.0068 1.00 55.4 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 105 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 CCTCTAGACCTAGCTGCTGT 427–482 1.000 86.9
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 430–485 1.000 86.8
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 441–496 1.000 86.7
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 440–495 1.000 86.7
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 442–497 1.000 86.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAGCGGGGGTTTTTACAGA 1033–1061 1.000 78.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAGCGGGGGTTTTTACAGAA 1032–1060 1.000 78.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAGCGGGGGTTTTTACAGA 1032–1060 1.000 78.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAGCGGGGGTTTTTACAGAA 1031–1059 1.000 78.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAGCGGGGGTTTTTACAGAA 1041–1069 1.000 78.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CGCGTTGCTTTTTACCACAT GAGGTTCGAATCCTTCCGTC 921–923 1.000 80.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATCATGTCTGTCAAGTCGCG GAGGTTCGAATCCTTCCGTC 939–941 1.000 78.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGCGTTGCTTTTTACCACAT TTCGGAGGTTCGAATCCTTC 925–927 1.000 76.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGCGTTGCTTTTTACCACAT TAAGGCAACGGGTTTTGGTC 951–953 1.000 76.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGCGTTGCTTTTTACCACAT GGGTTTTGGTCCCGCTATTC 942–944 1.000 74.2
psbI-trnS-GCU_p1 psbI-trnS-GCU CAAGCTGCTGTCAGTTTTCG TGGACTAAAGCGTCGGATTG 688–722 1.000 82.3
psbI-trnS-GCU_p2 psbI-trnS-GCU CAAGCTGCTGTCAGTTTTCG GTGGACTAAAGCGTCGGATT 689–723 1.000 82.3
psbI-trnS-GCU_p3 psbI-trnS-GCU AAGCTGCTGTCAGTTTTCGA TGGACTAAAGCGTCGGATTG 687–721 1.000 82.2
psbI-trnS-GCU_p4 psbI-trnS-GCU AAGCTGCTGTCAGTTTTCGA GTGGACTAAAGCGTCGGATT 688–722 1.000 82.2
psbI-trnS-GCU_p5 psbI-trnS-GCU TCGCCCCATTTACTCATTCG TGGACTAAAGCGTCGGATTG 529–551 1.000 82.2
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 843–882 1.000 58.3
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 842–881 1.000 58.3
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 897–936 1.000 57.0
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AACGAATCACACTTTTACCACT 844–883 1.000 56.4
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC AACGAATCACACTTTTACCACT 843–882 1.000 56.4
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CAGGAACAGAAGGAACGCTT 527–541 1.000 69.6
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TTCAGGAACAGAAGGAACGC 529–543 1.000 69.5
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ACGACGCTATTCAGGAACAG 538–552 1.000 68.2
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CGACGCTATTCAGGAACAGA 537–551 1.000 65.9
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGGAACAGAAGGAACGCTTT 526–540 1.000 65.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Circaea alpina subsp. alpina PP328795.1 156006 View on NCBI ↗
Circaea alpina subsp. caulescens NC_061022.1 156024 View on NCBI ↗
Circaea alpina subsp. micrantha NC_061010.1 155817 View on NCBI ↗
Circaea cordata NC_060876.1 156129 View on NCBI ↗
Circaea glabrescens NC_061017.1 156149 View on NCBI ↗
Circaea mollis PP078671.1 156026 View on NCBI ↗
Circaea repens NC_061018.1 156051 View on NCBI ↗