Markers + reference

Veronica

25 species · Plantaginaceae · Lamiales

Back to catalogue

Species 25
Genome length 150–152 kb
Candidate markers 268
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 580 0.0872 1.00 78.5 yes View details
rps16-trnQ-UUG LSC 565 0.0769 0.94 72.5 yes View details
psaA-ycf3 LSC 820 0.0626 0.90 73.4 yes View details
trnT-UGU-trnL-UAA LSC 719 0.0804 0.96 77.9 yes View details
ndhC-trnV-UAC LSC 944 0.0752 0.99 81.0 yes View details
ycf4-cemA LSC 662 0.0825 0.99 77.8 yes View details
ndhF-rpl32 SSC 655 0.0860 0.94 78.7 yes View details
rpl32-trnL-UAG SSC 758 0.0815 0.96 74.8 yes View details
rps15-ycf1 SSC 386 0.1026 0.93 70.6 yes View details
ycf1 SSC 5265 0.0531 1.00 75.6 yes View details
trnT-GGU-psbD LSC 1317 0.0530 0.99 82.1 yes View details
ycf3-trnS-GGA LSC 849 0.0623 0.99 81.2 yes View details
psbE-petL LSC 541 0.0580 1.00 80.0 yes View details
trnF-GAA-ndhJ LSC 557 0.0604 0.97 79.0 yes View details
atpH-atpI LSC 786 0.0550 0.99 77.9 yes View details
trnS-GCU-trnG-UCC LSC 732 0.0684 0.96 77.1 yes View details
trnE-UUC-trnT-GGU LSC 463 0.0512 1.00 77.1 yes View details
rpoB-trnC-GCA LSC 1231 0.0549 0.96 76.7 yes View details
petA-psbJ LSC 935 0.0561 0.96 76.0 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 GCTCTTCCCTTATCAGGCAC TCTATCCCAATGAGCCGTCT 1152–1432 1.000 91.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 GGCCAATGGTATGGACGAAT TCTATCCCAATGAGCCGTCT 862–1142 0.960 89.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 GCTCTTCCCTTATCAGGCAC AAAAAGGCGCTCAACCTACA 1046–1097 0.400 64.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGCTCTTCCCTTATCAGGCA AAAAAGGCGCTCAACCTACA 1047–1098 0.400 64.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 GGCCAATGGTATGGACGAAT AAAAAGGCGCTCAACCTACA 757–808 0.360 64.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AATGGTGGGTGGGAAAATCC GGAAATGCGGGTAAGCCTAA 1313–1466 0.800 83.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TTTCGACTCGAGCTCCATTG GGAAATGCGGGTAAGCCTAA 1577 0.120 44.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TTTCGACTCGAGCTCCATTG AGCAGCTTGCCAAACAAAAG 1410 0.120 44.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TTTCGACTCGAGCTCCATTG CTTACAGCAGCTTGCCAAAC 1415 0.120 44.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TTTCGACTCGAGCTCCATTG GAGGTTCGAATCCTTCCGTC 862 0.120 44.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 598–832 1.000 63.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 597–831 1.000 63.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 652–886 1.000 62.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AACGAATCACACTTTTACCACT 599–833 1.000 61.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AACGAATCACACTTTTACCACT 598–832 1.000 61.7
atpH-atpI_p1 atpH-atpI TCCTCATCTGCAAATCAGCC GGCAAATAGGGGGTTTCCAA 1801–2056 0.960 89.6
atpH-atpI_p2 atpH-atpI TGGCCCAAAGAAACGAAAGA TTTCCAAGTCCACGGACAAG 2072–2284 0.400 63.6
atpH-atpI_p3 atpH-atpI TCCTCATCTGCAAATCAGCC TTTCCAAGTCCACGGACAAG 1819–2034 0.400 63.5
atpH-atpI_p4 atpH-atpI CTCATCTGCAAATCAGCCCT TTTCCAAGTCCACGGACAAG 1817–2032 0.400 63.5
atpH-atpI_p5 atpH-atpI CACACACACTCCCTTTCCAA TTTCCAAGTCCACGGACAAG 2184–2396 0.400 63.4
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG CGCTGCTTCTCACAGGTAAT 2008–2088 0.920 88.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT CGCTGCTTCTCACAGGTAAT 1816–1896 0.920 88.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT ACCCTCATAGATTCTCGCGA 2066–2124 0.640 77.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG ACCCTCATAGATTCTCGCGA 2258–2316 0.640 77.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG CATAGATTCTCGCGAGTCCG 2253–2311 0.640 76.9
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AAACCACTAGACGATGGGGG GAACCGATGACTTACGCCTT 539–636 1.000 83.2
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AAACCACTAGACGATGGGGG TACCGCTGAGTTAAAAGGGC 504–601 1.000 82.4
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU AAACCACTAGACGATGGGGG CCGATGACTTACGCCTTACC 536–633 1.000 82.1
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AAACCACTAGACGATGGGGG TTGAACCGATGACTTACGCC 541–638 1.000 81.0
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU AACCACTAGACGATGGGGG GAACCGATGACTTACGCCTT 538–635 1.000 80.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (25)

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

Species Accession Length (bp) Link
Veronica agrestis NC_068050.1 150197 View on NCBI ↗
Veronica anagallis-aquatica NC_082107.1 151277 View on NCBI ↗
Veronica aphylla subsp. aphylla PP622714.1 151110 View on NCBI ↗
Veronica bellidioides PP622717.1 150820 View on NCBI ↗
Veronica biloba PX776077.1 150202 View on NCBI ↗
Veronica chamaedrys NC_068051.1 150562 View on NCBI ↗
Veronica chamaedrys subsp. chamaedrys PP622718.1 150625 View on NCBI ↗
Veronica ciliata PX776076.1 151098 View on NCBI ↗
Veronica daurica PX593257.1 152223 View on NCBI ↗
Veronica eriogyne NC_058571.1 151083 View on NCBI ↗
Veronica fruticans PP622719.1 151178 View on NCBI ↗
Veronica longifolia PX049137.1 152237 View on NCBI ↗
Veronica nakaiana NC_031153.1 152319 View on NCBI ↗
Veronica officinalis PP840337.1 150916 View on NCBI ↗
Veronica ovata subsp. kiusiana PQ113379.1 152249 View on NCBI ↗
Veronica peregrina NC_077523.1 151249 View on NCBI ↗
Veronica persica NC_031344.1 150198 View on NCBI ↗
Veronica polita NC_060687.1 150191 View on NCBI ↗
Veronica prostrata PP622721.1 150614 View on NCBI ↗
Veronica pusanensis PX049138.1 152250 View on NCBI ↗
Veronica pyrethrina PX593255.1 152240 View on NCBI ↗
Veronica serpyllifolia PP622722.1 150982 View on NCBI ↗
Veronica sieboldiana PX870807.1 152262 View on NCBI ↗
Veronica undulata NC_077524.1 151198 View on NCBI ↗
Veronica urticifolia PP622723.1 150888 View on NCBI ↗