Markers + reference

Vinca

2 species · Apocynaceae · Gentianales

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Species 2
Genome length 153–154 kb
Candidate markers 271
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbM-trnD-GUC LSC 857 0.0246 1.00 63.9 yes View details
accD-psaI LSC 599 0.0175 0.96 58.2 yes View details
petA-psbJ LSC 1078 0.0205 1.00 60.3 yes View details
ycf1 IRb 1038 0.0183 1.00 54.4 yes View details
ndhD SSC 1152 0.0043 1.00 46.2 yes View details
ycf1 SSC 5502 0.0192 0.99 51.8 no View details
psbF-psbE LSC 9 0.1111 1.00 86.7 yes View details
ycf1-ndhF SSC 16 0.6250 1.00 72.5 yes View details
trnL-UAA-trnF-GAA LSC 343 0.0292 1.00 68.4 yes View details
ccsA-ndhD SSC 242 0.0620 1.00 67.7 yes View details
pafII-cemA LSC 699 0.0215 1.00 65.6 yes View details
trnT-UGU-trnL-UAA LSC 785 0.0128 1.00 63.6 yes View details
rps16-trnQ-UUG LSC 1063 0.0125 0.98 63.3 yes View details
ycf15-trnL-CAA IRb 401 0.0150 1.00 63.2 yes View details
trnL-CAA-ycf15 IRa 401 0.0150 1.00 63.2 yes View details
ndhE-ndhG SSC 110 0.0182 1.00 63.0 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1136–1278 1.000 80.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1147–1289 1.000 79.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1140–1282 1.000 75.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1166–1308 1.000 75.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 1148–1290 1.000 75.3
trnG-UCC_p1 trnG-UCC GGTCCAGTTGTATACAATAATCGC GATGCACTAAGTCTAGAATATATAAT 802–804 1.000 41.4
trnG-UCC_p2 trnG-UCC GACAAAAGGTCCAGTTGTATACA GATGCACTAAGTCTAGAATATATAAT 809–811 1.000 41.4
trnG-UCC_p3 trnG-UCC ACAAAAGGTCCAGTTGTATACA GATGCACTAAGTCTAGAATATATAAT 808–810 1.000 41.4
trnG-UCC_p4 trnG-UCC GTCCAGTTGTATACAATAATCGCA GATGCACTAAGTCTAGAATATATAAT 801–803 1.000 41.4
trnG-UCC_p5 trnG-UCC GACAAAAGGTCCAGTTGTATACAA GATGCACTAAGTCTAGAATATATAAT 809–811 1.000 41.4
psbM-trnD-GUC_p1 psbM-trnD-GUC AGGCGGTAGGAACTAGAATGA TTCAATTGGTCAGAGCACCG 982–991 1.000 69.9
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAAAGGCGGTAGGAACTAGA TTCAATTGGTCAGAGCACCG 986–995 1.000 69.3
psbM-trnD-GUC_p3 psbM-trnD-GUC AGTAGAAAGGCGGTAGGAACT TTCAATTGGTCAGAGCACCG 989–998 1.000 68.7
psbM-trnD-GUC_p4 psbM-trnD-GUC AGTAGAAAGGCGGTAGGAAC TTCAATTGGTCAGAGCACCG 989–998 1.000 67.4
psbM-trnD-GUC_p5 psbM-trnD-GUC GTAGAAAGGCGGTAGGAACT TTCAATTGGTCAGAGCACCG 988–997 1.000 67.4
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CCGTAGCGTCTACCGATTTC 846–850 1.000 78.1
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA TAGGAAAAAGCCGGCTATCG CCGTAGCGTCTACCGATTTC 897–901 1.000 77.2
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT CCGTAGCGTCTACCGATTTC 878–882 1.000 77.2
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CGTCTACCGATTTCGCCATA 840–844 1.000 76.8
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG GGTTTCCATACCAAGGCTCA 878–882 1.000 76.0
trnL-UAA-trnF-GAA_p1 trnL-UAA-trnF-GAA AATCGTGAGGGTTCAAGTCC TCTACCAGCTGAGCTATCCC 397–408 1.000 78.2
trnL-UAA-trnF-GAA_p2 trnL-UAA-trnF-GAA AATCGTGAGGGTTCAAGTCC TTTGAACTGGTGACACGAGG 433–444 1.000 77.6
trnL-UAA-trnF-GAA_p3 trnL-UAA-trnF-GAA AATCGTGAGGGTTCAAGTCC GTGCCAGGAACCAGATTTGA 448–459 1.000 77.2
trnL-UAA-trnF-GAA_p4 trnL-UAA-trnF-GAA AATCGTGAGGGTTCAAGTCC TCAGTCCTCTGCTCTACCAG 409–420 1.000 77.0
trnL-UAA-trnF-GAA_p5 trnL-UAA-trnF-GAA AATCGTGAGGGTTCAAGTCC CATGTGCCAGGAACCAGATT 451–462 1.000 76.7
accD-psaI_p1 accD-psaI GACAGGATTAACCGAGGCTG TTCCAGGAAATTGTGCACCA 1876–1880 1.000 80.8
accD-psaI_p2 accD-psaI CTTTCGATCGATCCGGGTAC TTCCAGGAAATTGTGCACCA 1995–1999 1.000 80.7
accD-psaI_p3 accD-psaI CTTTCGATCGATCCGGGTAC ATTTCATCCATCCAGCGTCC 1592 0.500 59.4
accD-psaI_p4 accD-psaI GACAGGATTAACCGAGGCTG ATTTCATCCATCCAGCGTCC 1473 0.500 59.3
accD-psaI_p5 accD-psaI TCCCGTAGCAGTTGGAGTTA ATTTCATCCATCCAGCGTCC 1422 0.500 59.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Vinca difformis NC_066004.1 153476 View on NCBI ↗
Vinca major NC_065203.1 153523 View on NCBI ↗