Markers + reference

Ampelopsis

9 species · Vitaceae · Vitales

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Species 9
Genome length 161–163 kb
Candidate markers 253
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 253 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 358 0.0125 1.00 54.2 yes View details
trnK-UUU-rps16 LSC 924 0.0062 1.00 50.4 yes View details
rps16-trnQ-UUG LSC 2258 0.0085 1.00 60.6 yes View details
trnS-GCU-trnR-UCU LSC 1974 0.0039 0.99 55.9 yes View details
trnD-GUC-trnY-GUA LSC 444 0.0049 1.00 39.9 yes View details
trnE-UUC-psbD LSC 2272 0.0034 1.00 44.6 yes View details
psbZ-trnfM-CAU LSC 922 0.0199 0.99 65.5 yes View details
trnT-UGU-trnL-UAA LSC 1018 0.0056 1.00 56.6 yes View details
clpP LSC 2058 0.0032 1.00 43.8 yes View details
rpl16-rps3 LSC 1302 0.0045 1.00 40.4 yes View details
ndhG SSC 531 0.0004 1.00 26.3 yes View details
ndhG-ndhI SSC 173 0.0474 1.00 68.9 yes View details
psbM-trnD-GUC LSC 1183 0.0047 1.00 59.4 yes View details
rpl2-trnH-GUG IRa 220 0.0220 1.00 56.7 no View details
rpoB-trnC-GCA LSC 1283 0.0030 1.00 55.6 yes View details
atpF-atpI LSC 1624 0.0022 1.00 55.2 yes View details
ndhA SSC 2259 0.0024 1.00 54.9 yes View details
rpl32-trnL-UAG SSC 1175 0.0060 1.00 54.4 yes View details
trnF-GAA-ndhJ LSC 710 0.0034 1.00 53.6 yes View details
ycf3-trnS-GGA LSC 900 0.0038 1.00 52.2 yes View details
psbC-trnS-UGA LSC 239 0.0121 1.00 52.1 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 CAACCGTGCTAACCTTGGTA 444–479 1.000 85.0
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG ATCAACCGTGCTAACCTTGG 446–481 1.000 84.9
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CAACCGTGCTAACCTTGGTA 458–493 1.000 84.8
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CAACCGTGCTAACCTTGGTA 457–492 1.000 84.8
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CAACCGTGCTAACCTTGGTA 459–494 1.000 84.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGGTTTTTACGGAACTTCGTCT 852–1014 1.000 68.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGGTTTTTACGGAACTTCGTCT 851–1013 1.000 68.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 CAGTCGCGGTCTTACAAACT AGGTTTTTACGGAACTTCGTCT 936–1098 1.000 67.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCAGTCGCGGTCTTACAAAC AGGTTTTTACGGAACTTCGTCT 937–1099 1.000 67.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC AGGTTTTTACGGAACTTCGTCT 866–1028 1.000 67.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1924–2344 1.000 85.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1935–2355 1.000 84.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1928–2348 1.000 80.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1954–2374 1.000 80.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 1936–2356 1.000 79.9
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU ATTAGCAATCCGCCGCTTTA AGAAGACCTCTGTCCTATCCA 1992–2052 1.000 68.1
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU ATTAGCAATCCGCCGCTTTA AGGTTTAGAAGACCTCTGTCCT 1998–2058 1.000 67.4
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU GCTTTAGTCCACTCAGCCAT AGAAGACCTCTGTCCTATCCA 1978–2038 1.000 65.2
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU GCTTTAGTCCACTCAGCCAT AGGTTTAGAAGACCTCTGTCCT 1984–2044 1.000 64.5
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU AGTCCACTCAGCCATCTCTC AGAAGACCTCTGTCCTATCCA 1973–2033 1.000 64.4
atpF-atpI_p1 atpF-atpI CAGTGACCCAAGGAAACGAA CGAATCCATGGAGGGTCATC 1688–1691 1.000 79.7
atpF-atpI_p2 atpF-atpI CAGTGACCCAAGGAAACGAA TTTTTGCAACTTTAGCCGCG 1719–1722 1.000 76.9
atpF-atpI_p3 atpF-atpI TATTAAACCCGAAACCCCCG CGAATCCATGGAGGGTCATC 1717–1720 1.000 76.6
atpF-atpI_p4 atpF-atpI AGTGACCCAAGGAAACGAAA CGAATCCATGGAGGGTCATC 1687–1690 1.000 74.2
atpF-atpI_p5 atpF-atpI TATTAAACCCGAAACCCCCG TTTTTGCAACTTTAGCCGCG 1748–1751 1.000 73.9
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CATTCCCTCATTTCCACCCC CCGGATTTGAACTGGGGAAA 1170–1373 1.000 82.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CATTCCCTCATTTCCACCCC AAAAGGATTTGCAGTCCCCC 1152–1355 1.000 80.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ACATTCCCTCATTTCCACCC CCGGATTTGAACTGGGGAAA 1171–1374 1.000 80.0
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GTTCTTCTGTCAAGCCCTGA CCGGATTTGAACTGGGGAAA 1246–1449 1.000 79.8
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AGTTCTTCTGTCAAGCCCTG CCGGATTTGAACTGGGGAAA 1247–1450 1.000 79.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Ampelopsis aconitifolia NC_061726.1 162475 View on NCBI ↗
Ampelopsis cordata NC_061729.1 161945 View on NCBI ↗
Ampelopsis delavayana NC_084065.1 162497 View on NCBI ↗
Ampelopsis glandulosa NC_072280.1 162470 View on NCBI ↗
Ampelopsis glandulosa var. brevipedunculata KT831767.1 161090 View on NCBI ↗
Ampelopsis glandulosa var. hancei OP800431.1 162539 View on NCBI ↗
Ampelopsis glandulosa var. heterophylla PP391085.1 162302 View on NCBI ↗
Ampelopsis humulifolia NC_042236.1 161724 View on NCBI ↗
Ampelopsis japonica NC_042235.1 161430 View on NCBI ↗