Markers + reference

Verbena

2 species · Verbenaceae · Lamiales

Back to catalogue

Species 2
Genome length 153–153 kb
Candidate markers 270
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 9 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 859 0.0093 1.00 64.1 yes View details
ycf3-trnS-GGA LSC 880 0.0080 1.00 59.5 yes View details
ndhC-trnV-UAC LSC 1143 0.0052 1.00 54.1 yes View details
accD LSC 1773 0.0051 1.00 54.8 yes View details
ycf4-cemA LSC 836 0.0145 0.99 68.2 yes View details
ycf15-trnL-CAA IRb 364 0.0192 1.00 55.4 yes View details
rpl32-trnL-UAG SSC 810 0.0087 1.00 63.8 yes View details
ccsA SSC 972 0.0041 1.00 46.1 yes View details
rps15 SSC 264 0.0038 1.00 40.9 yes View details
ycf1 SSC 5676 0.0051 1.00 55.8 yes View details
ndhB-trnL-CAA IRa 542 0.0000 1.00 24.2 yes View details
trnF-GAA-ndhJ LSC 668 0.0090 1.00 63.9 yes View details
trnS-GCU-trnG-UCC LSC 706 0.0072 0.98 63.6 yes View details
matK LSC 1527 0.0059 1.00 62.1 yes View details
rpoB-trnC-GCA LSC 1170 0.0077 1.00 61.6 yes View details
psaA-ycf3 LSC 738 0.0054 1.00 60.5 yes View details
rpoA LSC 996 0.0030 1.00 60.5 yes View details
petD LSC 1216 0.0025 1.00 60.2 yes View details
psbT-psbN LSC 65 0.0308 1.00 60.1 yes View details
ndhE-ndhG SSC 227 0.0090 0.98 59.8 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
matK_p1 matK TGTATCTCTTCGTCCATTTGA CCTGTCTCCGCGGTATCTAT 1689 1.000 40.4
matK_p2 matK TGTATCTCTTCGTCCATTTGA TTTACCTGTCTCCGCGGTAT 1693 1.000 40.4
matK_p3 matK TCAGAATAGTGGAAATCCCA CCTGTCTCCGCGGTATCTAT 1718 1.000 40.4
matK_p4 matK TCAGAATAGTGGAAATCCCA TTTACCTGTCTCCGCGGTAT 1722 1.000 40.4
matK_p5 matK TGTATCTCTTCGTCCATTTGA TAAGTTTACCTGTCTCCGCG 1697 1.000 40.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GCTCAACCCACAGAAACTGT 980–985 1.000 76.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GTGCTCAACCCACAGAAACT 982–987 1.000 76.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCTCAACCCACAGAAACTGT 979–984 1.000 76.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GTGCTCAACCCACAGAAACT 981–986 1.000 76.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TGCTCAACCCACAGAAACTG 980–985 1.000 76.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGGGGTAATAGAACGAATCACAC 779–787 1.000 58.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGGGTAATAGAACGAATCACACT 778–786 1.000 58.0
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AGGGGTAATAGAACGAATCACAC 778–786 1.000 57.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GGGGTAATAGAACGAATCACACT 777–785 1.000 57.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA GGGGTAATAGAACGAATCACACT 832–840 1.000 56.6
trnG-UCC_p1 trnG-UCC GGAAAAAGCGCAACACTCTC TCGTAATCAGAATATATTCGCTCT 952 0.500 20.0
trnG-UCC_p2 trnG-UCC CAGGAAAAAGCGCAACACTC TCGTAATCAGAATATATTCGCTCT 954 0.500 20.0
trnG-UCC_p3 trnG-UCC AGGAAAAAGCGCAACACTCT TCGTAATCAGAATATATTCGCTCT 953 0.500 20.0
trnG-UCC_p4 trnG-UCC GGAAAAAGCGCAACACTCTC TCGTAATCAGAATATATTCGCTC 952 0.500 20.0
trnG-UCC_p5 trnG-UCC GGAAAAAGCGCAACACTCTC CGTAATCAGAATATATTCGCTCT 951 0.500 20.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CATTGCCTCATTTGCATCCC CCGGATTTGAACTGGGGAAA 1259–1260 1.000 78.0
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CATTGCCTCATTTGCATCCC AAAAGGATTTGCAGTCCCCC 1241–1242 1.000 75.9
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CATTGCCTCATTTGCATCCC TCTGCGCGTTCTTAGAAGAA 1317–1318 1.000 72.9
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ATTGCCTCATTTGCATCCCC CCGGATTTGAACTGGGGAAA 1258–1259 1.000 72.9
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CATTGCCTCATTTGCATCCC TTTGTTGATCAGGCGACACC 1278–1279 1.000 72.6
psaA-ycf3_p1 psaA-ycf3 TTACTTTTGGTTCCGGCGAA ATCAAGCCGCTGAGTATTGG 867–868 1.000 79.8
psaA-ycf3_p2 psaA-ycf3 TTTACTTTTGGTTCCGGCGA ATCAAGCCGCTGAGTATTGG 868–869 1.000 79.8
psaA-ycf3_p3 psaA-ycf3 TTACTTTTGGTTCCGGCGAA GGAAACAGGCTATAGCGCTT 849–850 1.000 79.7
psaA-ycf3_p4 psaA-ycf3 TTTACTTTTGGTTCCGGCGA GGAAACAGGCTATAGCGCTT 850–851 1.000 79.7
psaA-ycf3_p5 psaA-ycf3 TGAGAAATGACCCGGTTTGG ATCAAGCCGCTGAGTATTGG 935–936 1.000 79.2

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
Verbena bonariensis NC_072529.1 153144 View on NCBI ↗
Verbena brasiliensis NC_072530.1 153396 View on NCBI ↗