Markers + reference

Vitex

13 species · Lamiaceae · Lamiales

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Species 13
Genome length 153–155 kb
Candidate markers 265
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 349 0.0400 1.00 67.4 yes View details
trnK-UUU-rps16 LSC 903 0.0164 0.90 59.1 yes View details
petN-psbM LSC 1005 0.0157 1.00 55.4 yes View details
petA-psbJ LSC 1048 0.0157 1.00 60.7 yes View details
ycf1 IRb 1152 0.0032 1.00 34.3 no View details
ndhF SSC 2247 0.0119 1.00 47.7 yes View details
ndhF-trnL-UAG SSC 1526 0.0238 1.00 68.0 yes View details
ccsA-ndhD SSC 266 0.0436 1.00 67.8 yes View details
ndhD SSC 1500 0.0086 1.00 42.9 yes View details
ndhA SSC 2176 0.0117 1.00 51.4 yes View details
rps15-ycf1 SSC 420 0.0340 0.99 63.2 yes View details
ycf1 SSC 5547 0.0127 1.00 45.3 yes View details
rps16-trnQ-UUG LSC 1241 0.0150 1.00 60.5 yes View details
rpl16-rps3 LSC 1056 0.0126 1.00 60.1 yes View details
rpl22-rpl2 LSC 393 0.0119 0.99 58.1 yes View details
trnS-GCU-trnS-CGA LSC 719 0.0151 1.00 57.8 yes View details
atpH-atpI LSC 1034 0.0135 1.00 57.8 yes View details
rps8-rpl14 LSC 183 0.0266 1.00 57.1 yes View details
rpl20-rps12 LSC 831 0.0104 1.00 57.0 yes View details
psbE-petL LSC 929 0.0138 1.00 56.8 yes View details
ndhC-trnM-CAU LSC 1874 0.0080 1.00 56.2 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 100 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 414–647 1.000 89.6
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 428–661 1.000 89.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 427–660 1.000 89.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 429–662 1.000 89.3
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAACCGTGCTAACCTTGGTA 466–699 1.000 88.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGAAAGCGGAAGTTTTTAAGGA 895–1032 1.000 56.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGAAAGCGGAAGTTTTTAAGGA 894–1031 1.000 56.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAGCGGAAGTTTTTAAGGAACT 892–1029 1.000 55.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAGCGGAAGTTTTTAAGGAACT 893–1030 1.000 55.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGCGGAAGTTTTTAAGGAAC 890–1027 1.000 55.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAAATTGAAATGGGGCGTGG 673–1390 1.000 87.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 615–1332 1.000 86.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 656–1373 1.000 86.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 598–1315 1.000 86.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAAATTGAAATGGGGCGTGG 674–1391 1.000 86.2
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA CAATCCGACGCTTTAGTCCA ACCACTAAACTATACCCGCT 727–787 1.000 68.7
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA AATCCGACGCTTTAGTCCAC ACCACTAAACTATACCCGCT 726–786 1.000 68.6
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA ACGGAAAGAGAGGGATTCGA ACCACTAAACTATACCCGCT 781–841 1.000 67.2
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA AGCAATCCGACGCTTTAGTC ACCACTAAACTATACCCGCT 729–789 1.000 65.8
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA CGACGCTTTAGTCCACTCAG ACCACTAAACTATACCCGCT 722–782 1.000 65.7
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA TTTTGCAACTTTAGCCGCAG 1056–1120 1.000 85.0
atpH-atpI_p2 atpH-atpI AACGGAAGCAGCAGAAATCA CCCGTCATGTTCCTTGGATT 1103–1167 1.000 84.9
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA TTTTGCAACTTTAGCCGCAG 1074–1138 1.000 84.7
atpH-atpI_p4 atpH-atpI AGCCAATCCAGCAGCAATAA CCCGTCATGTTCCTTGGATT 1121–1185 1.000 84.6
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC CCCGTCATGTTCCTTGGATT 1120–1184 1.000 84.0
petN-psbM_p1 petN-psbM ACTCGTAGTGTGGGGAAGAA GACGACGGGTTGATTTGAGA 1303–1304 0.615 64.5
petN-psbM_p2 petN-psbM TCGTAGTGTGGGGAAGAAGT GACGACGGGTTGATTTGAGA 1301–1302 0.615 64.5
petN-psbM_p3 petN-psbM ACTCGTAGTGTGGGGAAGAA ACGACGGGTTGATTTGAGAG 1302–1303 0.615 64.5
petN-psbM_p4 petN-psbM TCGTAGTGTGGGGAAGAAGT ACGACGGGTTGATTTGAGAG 1300–1301 0.615 64.5
petN-psbM_p5 petN-psbM TTTGGATTGGAAAGGGGTGG GACGACGGGTTGATTTGAGA 1910–1938 0.615 64.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (13)

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

Species Accession Length (bp) Link
Vitex agnus-castus NC_088534.1 154495 View on NCBI ↗
Vitex bicolor NC_065871.1 154460 View on NCBI ↗
Vitex cofassus PZ322778.1 153895 View on NCBI ↗
Vitex glabrata MT473782.1 154532 View on NCBI ↗
Vitex negundo NC_057235.1 154438 View on NCBI ↗
Vitex negundo var. cannabifolia PQ541021.1 154520 View on NCBI ↗
Vitex negundo var. heterophylla MW366787.1 154438 View on NCBI ↗
Vitex parviflora NC_065666.1 154024 View on NCBI ↗
Vitex quinata MT473784.1 154416 View on NCBI ↗
Vitex rotundifolia NC_050991.1 154370 View on NCBI ↗
Vitex trifolia NC_062602.1 154444 View on NCBI ↗
Vitex tripinnata MT473785.1 154166 View on NCBI ↗
Vitex yunnanensis MT473786.1 153354 View on NCBI ↗