Markers + reference

Parthenocissus

3 species · Vitaceae · Vitales

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Species 3
Genome length 162–162 kb
Candidate markers 255
Primer pairs 110

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 10 remaining regions by MarkerSeek score (out of 255 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 949 0.0119 1.00 71.3 yes View details
rps16-trnQ-UUG LSC 2074 0.0161 1.00 48.9 yes View details
psbM-trnD-GUC LSC 1181 0.0130 1.00 64.1 yes View details
trnE-UUC-psbD LSC 2204 0.0082 1.00 62.6 yes View details
psbZ-trnfM-CAU LSC 585 0.0182 1.00 58.3 yes View details
rbcL LSC 1428 0.0070 1.00 44.4 yes View details
petA-psbJ LSC 1061 0.0075 1.00 37.5 yes View details
psaJ-rpl33 LSC 450 0.0164 0.99 63.8 yes View details
clpP LSC 2043 0.0072 1.00 52.2 yes View details
ndhF-rpl32 SSC 1210 0.0116 1.00 51.2 yes View details
rpl32-trnL-UAG SSC 1160 0.0103 1.00 38.5 yes View details
ycf1 SSC 5673 0.0076 1.00 55.8 yes View details
ycf3-trnS-GGA LSC 906 0.0096 1.00 61.9 yes View details
trnS-GCU-trnR-UCU LSC 1859 0.0054 1.00 61.8 yes View details
rpl2 IRb 1485 0.0009 1.00 59.3 yes View details
rpl2 IRa 1485 0.0009 1.00 59.3 yes View details
psbH-petD LSC 2337 0.0054 1.00 59.2 yes View details
rps15-ycf1 SSC 416 0.0129 1.00 58.4 yes View details
psaB LSC 2205 0.0015 1.00 58.2 yes View details
rps19-rpl2 IRb 72 0.0000 0.99 57.0 yes View details
atpF-atpI LSC 1595 0.0079 1.00 56.7 yes View details
trnF-GAA-ndhJ LSC 709 0.0066 1.00 56.7 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAGGAGCTCAACCTACAGGA 1076–1084 1.000 80.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGGAGCTCAACCTACAGGAA 1075–1083 1.000 80.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAGGAGCTCAACCTACAGGA 1075–1083 1.000 80.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGGAGCTCAACCTACAGGAA 1074–1082 1.000 80.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 CAGTCGCGGTCTTACAAACT AGGAGCTCAACCTACAGGAA 1159–1167 1.000 79.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 2135–2147 1.000 81.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 2146–2158 1.000 80.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 2139–2151 1.000 76.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 2165–2177 1.000 76.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 2147–2159 1.000 76.2
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU ATTAGCAATCCGCCGCTTTA AGAAGACCTCTGTCCTATCCA 1935–2005 1.000 64.5
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU ATTAGCAATCCGCCGCTTTA AGGTTTAGAAGACCTCTGTCCT 1941–2011 1.000 63.9
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU ACGGAAAGAGAGGGATTCGA AGAAGACCTCTGTCCTATCCA 1984–2054 1.000 63.6
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU ACGGAAAGAGAGGGATTCGA AGGTTTAGAAGACCTCTGTCCT 1990–2060 1.000 62.9
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU TGGAAACGGAAAGAGAGGGA AGAAGACCTCTGTCCTATCCA 1989–2059 1.000 62.6
atpF-atpI_p1 atpF-atpI CAGTGACCCAAGGAAACGAA CGAATCCATGGAGGGTCATC 1661–1674 1.000 79.8
atpF-atpI_p2 atpF-atpI CAGTGACCCAAGGAAACGAA TTTTTGCAACTTTAGCCGCG 1692–1705 1.000 77.1
atpF-atpI_p3 atpF-atpI TATTAAACCCGAAACCCCCG CGAATCCATGGAGGGTCATC 1690–1703 1.000 76.8
atpF-atpI_p4 atpF-atpI AGTGACCCAAGGAAACGAAA CGAATCCATGGAGGGTCATC 1660–1673 1.000 74.4
atpF-atpI_p5 atpF-atpI TATTAAACCCGAAACCCCCG TTTTTGCAACTTTAGCCGCG 1721–1734 1.000 74.0
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TGGGCTATGGCTATACACCT 1313–1332 1.000 62.2
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 1274–1293 1.000 61.8
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC GTGGGCTATGGCTATACACC 1314–1333 1.000 61.7
psbM-trnD-GUC_p4 psbM-trnD-GUC AGGAACTAGAATGAACAGTGCA TGGGCTATGGCTATACACCT 1320–1339 1.000 59.0
psbM-trnD-GUC_p5 psbM-trnD-GUC AGGAACTAGAATGAACAGTGCA GTGGGCTATGGCTATACACC 1321–1340 1.000 58.5
trnE-UUC-psbD_p1 trnE-UUC-psbD TCCTTTCTTCCTACCCCCAG TCGCTTTCGTCTTTGGTGAA 2328–2365 1.000 80.3
trnE-UUC-psbD_p2 trnE-UUC-psbD TCCTTTCTTCCTACCCCCAG ATCGCTTTCGTCTTTGGTGA 2329–2366 1.000 79.4
trnE-UUC-psbD_p3 trnE-UUC-psbD TCCTTTCTTCCTACCCCCAG ACAAAAACGAAACGGTCCCT 2379–2416 1.000 78.7
trnE-UUC-psbD_p4 trnE-UUC-psbD TCCTTTCTTCCTACCCCCAG GACCGGACCAACCTACAAAA 2393–2430 1.000 78.6
trnE-UUC-psbD_p5 trnE-UUC-psbD GCTGCCTCCTTGAAAGAGAG TCGCTTTCGTCTTTGGTGAA 2292–2329 1.000 78.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Parthenocissus heptaphylla NC_061715.1 161506 View on NCBI ↗
Parthenocissus tricuspidata NC_069832.1 161628 View on NCBI ↗
Parthenocissus vitacea NC_061714.1 161580 View on NCBI ↗