Markers + reference

Vitis

57 species · Vitaceae · Vitales

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Species 57
Genome length 161–161 kb
Candidate markers 266
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 10 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 867 0.0043 0.99 47.4 yes View details
rps16-trnQ-UUG LSC 1855 0.0039 1.00 62.0 yes View details
trnS-GCU-trnG-GCC LSC 1007 0.0030 1.00 52.4 yes View details
psbZ-trnG-GCC LSC 691 0.0092 0.99 62.1 yes View details
accD-psaI LSC 755 0.0051 0.99 55.6 yes View details
psbE-petL LSC 1306 0.0035 1.00 55.3 yes View details
psbB-psbT LSC 187 0.0006 1.00 28.1 yes View details
petD-rpoA LSC 216 0.0137 0.98 53.0 yes View details
ndhF SSC 2250 0.0014 1.00 31.8 yes View details
ndhF-rpl32 SSC 1219 0.0039 1.00 50.5 yes View details
ycf1-ndhF IRb 125 0.0555 0.98 76.5 yes View details
rps19-rpl2 IRb 69 0.0166 0.97 58.7 yes View details
ndhD-psaC SSC 134 0.0118 1.00 55.6 yes View details
trnT-UGU-trnL-UAA LSC 952 0.0019 1.00 54.4 yes View details
trnC-GCA-petN LSC 847 0.0030 1.00 54.0 yes View details
psbM-trnD-GUC LSC 1123 0.0027 0.99 53.1 yes View details
atpF-atpH LSC 500 0.0042 1.00 51.2 yes View details
rpl23-trnH-GUG IRa 1633 0.0011 1.00 50.5 no View details
rps15-ycf1 SSC 307 0.0039 1.00 49.9 yes View details
ndhC-trnV-UAC LSC 1127 0.0023 1.00 48.6 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 ACAAGGTTTTGTGCCGATCT TCTATCCCAATGAGCCGTCT 1307–1376 1.000 84.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACAAGGTTTTGTGCCGATCT GCCGTACGAGGAGAAAACTT 1367–1436 1.000 84.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 ACAAGGTTTTGTGCCGATCT AGCCGTCTATCGAATCGTTG 1295–1364 1.000 83.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 CTCATGGGAGAAGCCTTTCC GCCGTACGAGGAGAAAACTT 1564–1633 1.000 83.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 CTCATGGGAGAAGCCTTTCC TCTATCCCAATGAGCCGTCT 1504–1573 1.000 83.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1793–2045 1.000 85.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1804–2056 1.000 84.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1797–2049 1.000 80.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1823–2075 1.000 80.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 1805–2057 1.000 80.1
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA GGGGGTTAATAGAACGAATCACA 1088–1112 1.000 58.4
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA GGGGGTTAATAGAACGAATCACA 1137–1161 1.000 57.3
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA GGGGGTTAATAGAACGAATCAC 1088–1112 1.000 56.9
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC TGGAAACGGAAAGAGAGGGA GGGGGTTAATAGAACGAATCACA 1142–1166 1.000 56.3
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA GGGGGTTAATAGAACGAATCAC 1137–1161 1.000 55.8
atpF-atpH_p1 atpF-atpH CAGTGACCCAAGGAAACGAA CGGAGGGAAAAATACGAGGT 638–662 1.000 79.2
atpF-atpH_p2 atpF-atpH CAGTGACCCAAGGAAACGAA CGAGGCGGAGGGAAAAATAC 643–667 1.000 79.1
atpF-atpH_p3 atpF-atpH CAGTGACCCAAGGAAACGAA GAGGCGGAGGGAAAAATACG 642–666 1.000 79.1
atpF-atpH_p4 atpF-atpH CAGTGACCCAAGGAAACGAA GCGGAGGGAAAAATACGAGG 639–663 1.000 79.1
atpF-atpH_p5 atpF-atpH CAGTGACCCAAGGAAACGAA GGCGGAGGGAAAAATACGAG 640–664 1.000 79.1
trnC-GCA-petN_p1 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC AGCCCAAGCGAGACTTACTA 915–981 1.000 84.8
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 859–925 1.000 84.8
trnC-GCA-petN_p3 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC AGAGTCCACTTCTTCCCCAT 976–1042 1.000 83.1
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 920–986 1.000 83.0
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 877–943 1.000 82.5
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TGGGCTATGGCTATACACCT 1263–1277 1.000 63.5
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 1224–1238 1.000 63.1
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC GTGGGCTATGGCTATACACC 1264–1278 1.000 63.0
psbM-trnD-GUC_p4 psbM-trnD-GUC AGGAACTAGAATGAACAGTGCA TGGGCTATGGCTATACACCT 1270–1284 1.000 60.3
psbM-trnD-GUC_p5 psbM-trnD-GUC AGGAACTAGAATGAACAGTGCA GTGGGCTATGGCTATACACC 1271–1285 1.000 59.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (57)

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

Species Accession Length (bp) Link
Vitis aestivalis NC_039783.1 160970 View on NCBI ↗
Vitis aestivalis var. linsecomii NC_039806.1 160986 View on NCBI ↗
Vitis amurensis NC_031383.1 160953 View on NCBI ↗
Vitis amurensis var. dissecta MG564630.1 160943 View on NCBI ↗
Vitis arizonica NC_039805.1 160951 View on NCBI ↗
Vitis baihuashanensis NC_058821.1 160978 View on NCBI ↗
Vitis balansana NC_061735.1 160818 View on NCBI ↗
Vitis bellula MW454776.1 160959 View on NCBI ↗
Vitis bellula var. pubigera NC_061731.1 160990 View on NCBI ↗
Vitis berlandieri NC_039684.1 160968 View on NCBI ↗
Vitis betulifolia NC_039803.1 160940 View on NCBI ↗
Vitis biformis NC_039802.1 160970 View on NCBI ↗
Vitis bloodworthiana NC_039801.1 160984 View on NCBI ↗
Vitis bryoniifolia NC_039683.1 160942 View on NCBI ↗
Vitis californica NC_039800.1 161023 View on NCBI ↗
Vitis chunganensis NC_061730.1 160819 View on NCBI ↗
Vitis chungii NC_061736.1 161011 View on NCBI ↗
Vitis cinerea NC_036336.1 161020 View on NCBI ↗
Vitis cinerea var. baileyana NC_039804.1 160978 View on NCBI ↗
Vitis cinerea var. cinerea NC_039799.1 160957 View on NCBI ↗
Vitis cinerea var. floridana NC_039798.1 160980 View on NCBI ↗
Vitis cinerea var. helleri MT604110.1 161028 View on NCBI ↗
Vitis davidii NC_057166.1 161335 View on NCBI ↗
Vitis doaniana NC_039797.1 160982 View on NCBI ↗
Vitis erythrophylla NC_061678.1 160947 View on NCBI ↗
Vitis flexuosa NC_061728.1 161065 View on NCBI ↗
Vitis girdiana NC_039682.1 160950 View on NCBI ↗
Vitis heyneana NC_039796.1 160953 View on NCBI ↗
Vitis jacquemontii NC_039795.1 160904 View on NCBI ↗
Vitis labrusca NC_039793.1 160976 View on NCBI ↗
Vitis labrusca x Vitis vinifera NC_056363.1 161066 View on NCBI ↗
Vitis lanata NC_039794.1 160902 View on NCBI ↗
Vitis lanceolatifoliosa NC_061674.1 161043 View on NCBI ↗
Vitis monticola NC_039792.1 160982 View on NCBI ↗
Vitis palmata NC_039791.1 160981 View on NCBI ↗
Vitis peninsularis NC_039790.1 160977 View on NCBI ↗
Vitis piasezkii NC_039789.1 160944 View on NCBI ↗
Vitis pseudoreticulata NC_045281.1 161065 View on NCBI ↗
Vitis quinquangularis NC_063746.1 160822 View on NCBI ↗
Vitis retordii NC_039788.1 160968 View on NCBI ↗
Vitis riparia NC_039680.1 160972 View on NCBI ↗
Vitis rotundifolia NC_023790.1 160891 View on NCBI ↗
Vitis rotundifolia var. munsoniana NC_039782.1 160930 View on NCBI ↗
Vitis ruyuanensis NC_061675.1 160809 View on NCBI ↗
Vitis shenxiensis NC_061734.1 160852 View on NCBI ↗
Vitis shuttleworthii NC_039784.1 160975 View on NCBI ↗
Vitis sinocinerea NC_061733.1 160973 View on NCBI ↗
Vitis thunbergii NC_039785.1 160948 View on NCBI ↗
Vitis tiliifolia NC_039681.1 160956 View on NCBI ↗
Vitis treleasei NC_039786.1 160954 View on NCBI ↗
Vitis tsoi NC_061677.1 160822 View on NCBI ↗
Vitis vinifera x Vitis labrusca NC_059701.1 160928 View on NCBI ↗
Vitis vulpina NC_039787.1 160971 View on NCBI ↗
Vitis wilsoniae NC_061732.1 160969 View on NCBI ↗
Vitis wuhanensis NC_061676.1 160807 View on NCBI ↗
Vitis x labruscana NC_045307.1 160931 View on NCBI ↗
Vitis yeshanensis NC_053944.1 161188 View on NCBI ↗