Markers + reference

Veronicastrum

10 species · Plantaginaceae · Lamiales

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Species 10
Genome length 152–153 kb
Candidate markers 271
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 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 324 0.0337 0.93 83.4 yes View details
trnS-GCU-trnG-UCC LSC 719 0.0180 1.00 69.7 yes View details
ndhC-trnV-UAC LSC 1109 0.0125 1.00 62.7 yes View details
petA-psbJ LSC 965 0.0115 0.99 70.8 yes View details
ycf1 IRb 1326 0.0020 1.00 44.7 no View details
ndhF-rpl32 SSC 730 0.0484 1.00 81.9 yes View details
rpl32-trnL-UAG SSC 739 0.0130 1.00 62.2 yes View details
ccsA-ndhD SSC 217 0.0298 1.00 67.0 yes View details
ycf1 SSC 5427 0.0097 1.00 52.8 yes View details
ndhD-psaC SSC 101 0.0548 1.00 71.7 yes View details
ycf3-trnS-GGA LSC 896 0.0094 1.00 69.4 yes View details
accD-psaI LSC 786 0.0065 0.99 69.3 yes View details
trnT-GGU-psbD LSC 1322 0.0054 1.00 68.2 yes View details
atpH-atpI LSC 991 0.0074 1.00 67.6 yes View details
trnL-UAG-ccsA SSC 172 0.0377 0.95 66.1 yes View details
trnK-UUU-rps16 LSC 865 0.0103 0.99 65.4 yes View details
ycf4-cemA LSC 690 0.0072 1.00 65.3 yes View details
psbH-petB LSC 136 0.0132 0.96 63.7 yes View details
rps8-rpl14 LSC 212 0.0131 0.91 62.3 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 90 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 TTCCCTCTAGACCTAGCTGC 351–394 1.000 90.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 365–408 1.000 90.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 364–407 1.000 90.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ATTAGTCATGGGCGAACGAC TTCCCTCTAGACCTAGCTGC 414–457 0.800 80.6
trnH-GUG-psbA_p5 trnH-GUG-psbA CATTAGTCATGGGCGAACGA TTCCCTCTAGACCTAGCTGC 415–458 0.800 80.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAAGGCGCTCAACCTACA 654–1018 1.000 85.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGCGCTCAACCTACA 653–1017 1.000 85.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC AAAAAGGCGCTCAACCTACA 668–1032 1.000 84.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAAAAGGCGCTCAACCTACA 663–1027 1.000 84.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTTGAAAAAGGCGCTCAACC 657–1021 1.000 83.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AACCGAAAGACCCTTTAACA 823–847 1.000 60.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACCGAAAGACCCTTTAACAA 822–846 1.000 60.2
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AACCGAAAGACCCTTTAACA 822–846 1.000 60.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACCGAAAGACCCTTTAACAA 821–845 1.000 60.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACCGAAAGACCCTTTAACAA 876–900 1.000 58.7
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA TCCCTGTCATGTTCCTTGGA 1124–1150 1.000 80.3
atpH-atpI_p2 atpH-atpI GCCAATCCAGCAGCAATAAC TCCCTGTCATGTTCCTTGGA 1141–1167 1.000 79.3
atpH-atpI_p3 atpH-atpI TCCAGCAGCAATAACGGAAG TCCCTGTCATGTTCCTTGGA 1136–1162 1.000 79.0
atpH-atpI_p4 atpH-atpI AACGGAAGCAGCAGAAATCA TTTTTGCAACTTTAGCCGCG 1076–1102 1.000 78.3
atpH-atpI_p5 atpH-atpI ATCCAGCAGCAATAACGGAA TCCCTGTCATGTTCCTTGGA 1137–1163 1.000 77.7
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GGACCAGCCTACAAAAACGA 1450–1519 1.000 82.7
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GGACCAGCCTACAAAAACGA 1453–1522 1.000 82.5
trnT-GGU-psbD_p3 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1440–1509 1.000 81.7
trnT-GGU-psbD_p4 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA ACAAAAACGAAACGGTCCCT 1443–1512 1.000 81.5
trnT-GGU-psbD_p5 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA GGACCAGCCTACAAAAACGA 1427–1496 1.000 81.0
ycf3-trnS-GGA_p1 ycf3-trnS-GGA TGCCTCCTTTTCTCCTGAAG CCCTCGGTAAACAAAAGCCT 1051–1069 1.000 75.8
ycf3-trnS-GGA_p2 ycf3-trnS-GGA GCCTCCTTTTCTCCTGAAGT CCCTCGGTAAACAAAAGCCT 1050–1068 1.000 75.8
ycf3-trnS-GGA_p3 ycf3-trnS-GGA TGCCTCCTTTTCTCCTGAAG ACGGAAAGAGAGGGATTCGA 1072–1090 1.000 75.3
ycf3-trnS-GGA_p4 ycf3-trnS-GGA GCCTCCTTTTCTCCTGAAGT ACGGAAAGAGAGGGATTCGA 1071–1089 1.000 75.3
ycf3-trnS-GGA_p5 ycf3-trnS-GGA TGCCTCCTTTTCTCCTGAAG TTCCAATGCTACGCCTTGAA 1022–1040 1.000 75.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Veronicastrum axillare NC_056895.1 152691 View on NCBI ↗
Veronicastrum brunonianum NC_082033.1 152587 View on NCBI ↗
Veronicastrum latifolium NC_069913.1 152966 View on NCBI ↗
Veronicastrum rhombifolium NC_082029.1 152693 View on NCBI ↗
Veronicastrum robustum NC_082030.1 152658 View on NCBI ↗
Veronicastrum sibiricum NC_031345.1 152930 View on NCBI ↗
Veronicastrum stenostachyum NC_082031.1 152957 View on NCBI ↗
Veronicastrum villosulum var. parviflorum OQ220469.1 153014 View on NCBI ↗
Veronicastrum wulingense OQ220471.1 152370 View on NCBI ↗
Veronicastrum yunnanense NC_082032.1 152779 View on NCBI ↗