Markers + reference

Tetrastigma

17 species · Vitaceae · Vitales

Back to catalogue

Species 17
Genome length 159–161 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

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1978 0.0167 1.00 69.9 yes View details
trnS-GCU-trnR-UCU LSC 2003 0.0148 1.00 65.3 yes View details
psbM-trnD-GUC LSC 1171 0.0210 1.00 74.3 yes View details
trnD-GUC-trnY-GUA LSC 459 0.0186 1.00 70.8 yes View details
trnS-UGA-psbZ LSC 364 0.0150 0.99 60.6 yes View details
psbZ-trnG-GCC LSC 667 0.0278 0.97 76.9 yes View details
ycf1 IRb 1185 0.0124 1.00 61.3 no View details
ndhF SSC 2247 0.0116 1.00 56.9 yes View details
ndhF-rpl32 SSC 1129 0.0209 1.00 78.2 yes View details
rpl32-trnL-UAG SSC 999 0.0215 1.00 76.0 yes View details
ycf1 SSC 5640 0.0120 1.00 54.9 yes View details
rpl20-rps12 LSC 772 0.0129 1.00 74.7 yes View details
trnT-UGU-trnL-UAA LSC 905 0.0095 1.00 73.7 yes View details
trnT-GGU-psbD LSC 1218 0.0109 1.00 72.6 yes View details
psbC-trnS-UGA LSC 259 0.0309 1.00 72.3 yes View details
ccsA-ndhD SSC 252 0.0311 0.98 70.4 yes View details
trnE-UUC-trnT-GGU LSC 906 0.0164 1.00 69.6 yes View details
psbA-trnK-UUU LSC 257 0.0164 1.00 69.4 yes View details
trnK-UUU-rps16 LSC 692 0.0164 1.00 68.9 yes View details
trnH-GUG-psbA LSC 313 0.0269 1.00 68.8 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 95 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 TTCGGCGGTTCACTATTCAG 768–799 1.000 88.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCGGCGGTTCACTATTCAG 782–813 1.000 88.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCGGCGGTTCACTATTCAG 781–812 1.000 88.2
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCGGCGGTTCACTATTCAG 783–814 1.000 88.2
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCAGTGCTATGCATGGTTCC 752–783 1.000 88.1
psbA-trnK-UUU_p1 psbA-trnK-UUU ACGGTTTTCAGTGCTGGTTA CTATCCGACTAGTTCCGGGT 376–410 1.000 85.1
psbA-trnK-UUU_p2 psbA-trnK-UUU ACGGTTTTCAGTGCTGGTTA TCTATCCGACTAGTTCCGGG 377–411 1.000 83.1
psbA-trnK-UUU_p3 psbA-trnK-UUU AAGACGGTTTTCAGTGCTGG CTATCCGACTAGTTCCGGGT 379–413 1.000 82.2
psbA-trnK-UUU_p4 psbA-trnK-UUU TACAGAAGCGACCCCATAGG CTATCCGACTAGTTCCGGGT 350–384 0.941 80.4
psbA-trnK-UUU_p5 psbA-trnK-UUU ATCCAGTTACAGAAGCGACC CTATCCGACTAGTTCCGGGT 357–391 0.941 79.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGGTTTTTACGGAACTTCGTCT 721–781 0.882 67.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGGTTTTTACGGAACTTCGTCT 720–780 0.882 67.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 CAGTCGCGGTCTTACAAACT AGGTTTTTACGGAACTTCGTCT 805–865 0.882 66.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCAGTCGCGGTCTTACAAAC AGGTTTTTACGGAACTTCGTCT 806–866 0.882 66.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC AGGTTTTTACGGAACTTCGTCT 735–795 0.882 66.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1377–2219 1.000 88.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1388–2230 0.941 85.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1381–2223 1.000 84.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1407–2249 1.000 84.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 1389–2231 0.941 81.2
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU ATTAGCAATCCGCCGCTTTA TGTCCTATCCATTAGACAATG 1995–2094 1.000 50.5
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU GCTTTAGTCCACTCAGCCAT TGTCCTATCCATTAGACAATG 1981–2080 1.000 50.5
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU AGTCCACTCAGCCATCTCTC TGTCCTATCCATTAGACAATG 1976–2075 1.000 50.5
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU ACGGAAAGAGAGGGATTCGA TGTCCTATCCATTAGACAATG 2044–2143 1.000 50.4
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU AACGGAAAGAGAGGGATTCG TGTCCTATCCATTAGACAATG 2045–2144 1.000 50.4
psbM-trnD-GUC_p1 psbM-trnD-GUC TGCGAGAATATTTACTTCCA TACGCCTTATTTCCCTGGGA 1257–1298 1.000 52.0
psbM-trnD-GUC_p2 psbM-trnD-GUC TGCGAGAATATTTACTTCCA CGCCTTATTTCCCTGGGATT 1255–1296 1.000 52.0
psbM-trnD-GUC_p3 psbM-trnD-GUC ATGCGAGAATATTTACTTCCA TACGCCTTATTTCCCTGGGA 1258–1299 1.000 52.0
psbM-trnD-GUC_p4 psbM-trnD-GUC TGCGAGAATATTTACTTCCAT TACGCCTTATTTCCCTGGGA 1257–1298 1.000 52.0
psbM-trnD-GUC_p5 psbM-trnD-GUC TGCGAGAATATTTACTTCCA TTCAATTGGTCAGAGCACCG 1231–1272 1.000 52.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (17)

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

Species Accession Length (bp) Link
Tetrastigma angustifolium PP657251.1 159988 View on NCBI ↗
Tetrastigma annamense PP657252.1 160736 View on NCBI ↗
Tetrastigma canarense PP657253.1 160312 View on NCBI ↗
Tetrastigma cauliflorum PP657254.1 160382 View on NCBI ↗
Tetrastigma formosanum PV296135.1 160126 View on NCBI ↗
Tetrastigma hemsleyanum NC_029339.1 159889 View on NCBI ↗
Tetrastigma lawsonii NC_061673.1 160360 View on NCBI ↗
Tetrastigma leucostaphylum PP657255.1 159387 View on NCBI ↗
Tetrastigma nilagiricum PP657256.1 160116 View on NCBI ↗
Tetrastigma obtectum PV454981.1 159478 View on NCBI ↗
Tetrastigma pachyphyllum PP657257.1 159317 View on NCBI ↗
Tetrastigma planicaule NC_057118.1 160323 View on NCBI ↗
Tetrastigma pyriforme PP657258.1 160893 View on NCBI ↗
Tetrastigma rafflesiae NC_061671.1 159805 View on NCBI ↗
Tetrastigma serrulatum PV454982.1 160515 View on NCBI ↗
Tetrastigma thorsborneorum PP657260.1 160676 View on NCBI ↗
Tetrastigma voinierianum NC_061711.1 160005 View on NCBI ↗