Markers + reference

Cyphostemma

2 species · Vitaceae · Vitales

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Species 2
Genome length 159–159 kb
Candidate markers 248
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 248 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnR-UCU LSC 1870 0.0129 1.00 52.6 yes View details
psbC-trnS-UGA LSC 266 0.0618 0.97 85.1 yes View details
psbZ-trnfM-CAU LSC 801 0.0191 0.98 57.7 yes View details
rpl16-rps3 LSC 1301 0.0162 1.00 56.1 yes View details
ndhF-rpl32 SSC 1005 0.0330 1.00 67.4 yes View details
rps15-trnN-GUU SSC 6265 0.0173 0.99 50.0 yes View details
trnR-UCU-atpA LSC 188 0.0495 0.97 72.1 yes View details
accD-psaI LSC 700 0.0146 0.98 66.6 yes View details
trnT-UGU-trnL-UAA LSC 988 0.0094 0.96 66.5 yes View details
trnA-UGC-rrn23 IRb 172 0.0233 1.00 65.9 yes View details
rrn23-trnA-UGC IRa 172 0.0233 1.00 65.9 yes View details
rps14-psaB LSC 131 0.0229 1.00 65.7 yes View details
psbE-petL LSC 1290 0.0087 0.98 65.6 yes View details
trnY-GUA-trnE-UUC LSC 46 0.0217 1.00 65.0 yes View details
psaA-ycf3 LSC 722 0.0084 0.99 64.4 yes View details
rpl20-rps12 LSC 802 0.0051 0.98 63.4 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
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU GCTTTAGTCCACTCAGCCAT GTGTCCTATCCATTAGACAATG 1923–1953 1.000 41.2
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU AGTCCACTCAGCCATCTCTC GTGTCCTATCCATTAGACAATG 1918–1948 1.000 41.2
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU ATTAGCAATCCGCCGCTTTA GTGTCCTATCCATTAGACAATG 1937–1967 1.000 41.1
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU ATTAGCAATCCGCCGCTTTA TGTCCTATCCATTAGACAATG 1936–1966 1.000 41.1
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU ATTAGCAATCCGCCGCTTTA GTGTCCTATCCATTAGACAAT 1937–1967 1.000 41.1
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CTACCAAGACGTTCACCGAG 290–296 1.000 70.4
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TTCACCGAGCAAGCAGAAAT 279–285 1.000 69.9
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TCTACCAAGACGTTCACCGA 291–297 1.000 67.4
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TTCTACCAAGACGTTCACCG 292–298 1.000 67.1
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CCGAGCAAGCAGAAATCCTT 275–281 1.000 66.4
trnY-GUA-trnE-UUC_p1 trnY-GUA-trnE-UUC CCAGCGTAGACATATTGCCA AAGTATGCCCCCATCGTCTA 189 1.000 77.7
trnY-GUA-trnE-UUC_p2 trnY-GUA-trnE-UUC ACCAGCGTAGACATATTGCC AAGTATGCCCCCATCGTCTA 190 1.000 77.7
trnY-GUA-trnE-UUC_p3 trnY-GUA-trnE-UUC AGTGAATTATTGGGCCGAGC AAGTATGCCCCCATCGTCTA 219 1.000 77.0
trnY-GUA-trnE-UUC_p4 trnY-GUA-trnE-UUC GTGAATTATTGGGCCGAGCT AAGTATGCCCCCATCGTCTA 218 1.000 77.0
trnY-GUA-trnE-UUC_p5 trnY-GUA-trnE-UUC TGAATTATTGGGCCGAGCTG AAGTATGCCCCCATCGTCTA 217 1.000 77.0
psbC-trnS-UGA_p1 psbC-trnS-UGA GCAGCAGGATTTGAAAAGGG GGTTGATAGCTCCGGTCTTG 405–412 1.000 81.0
psbC-trnS-UGA_p2 psbC-trnS-UGA AGCTGCAGCAGGATTTGAAA GGTTGATAGCTCCGGTCTTG 409–416 1.000 81.0
psbC-trnS-UGA_p3 psbC-trnS-UGA GCTGCAGCAGGATTTGAAAA GGTTGATAGCTCCGGTCTTG 408–415 1.000 80.5
psbC-trnS-UGA_p4 psbC-trnS-UGA GCAGCAGGATTTGAAAAGGG GATGGCCGAGTGGTTGATAG 416–423 1.000 80.4
psbC-trnS-UGA_p5 psbC-trnS-UGA AGCTGCAGCAGGATTTGAAA GATGGCCGAGTGGTTGATAG 420–427 1.000 80.3
psbZ-trnfM-CAU_p1 psbZ-trnfM-CAU CAAGACCGGAGCTATCAACC CTTGAGGTCACGGGTTCAAA 1425–1433 1.000 81.4
psbZ-trnfM-CAU_p2 psbZ-trnfM-CAU CAAGACCGGAGCTATCAACC ACAGATATGGTAGAGGGGCC 1530–1538 1.000 81.3
psbZ-trnfM-CAU_p3 psbZ-trnfM-CAU GATGCATTGTCCAACATGCC ACAGATATGGTAGAGGGGCC 1347–1350 1.000 81.2
psbZ-trnfM-CAU_p4 psbZ-trnfM-CAU CAAGACCGGAGCTATCAACC TCTTGATTGCCTCCACATCG 2101–2109 1.000 81.0
psbZ-trnfM-CAU_p5 psbZ-trnfM-CAU GATGCATTGTCCAACATGCC TCTTGATTGCCTCCACATCG 1918–1921 1.000 80.9
rps14-psaB_p1 rps14-psaB CTCAACGAGGGAACTTTGCT CATTGTGCAGGCAAGATTGG 347 1.000 79.7
rps14-psaB_p2 rps14-psaB CTCAACGAGGGAACTTTGCT CCATTGTGCAGGCAAGATTG 348 1.000 79.7
rps14-psaB_p3 rps14-psaB CTCAACGAGGGAACTTTGCT TCTTGATTGCCTCCACATCG 279 1.000 79.7
rps14-psaB_p4 rps14-psaB CTCAACGAGGGAACTTTGCT TCCATTGTGCAGGCAAGATT 349 1.000 79.2
rps14-psaB_p5 rps14-psaB CTCAACGAGGGAACTTTGCT TTCCATTGTGCAGGCAAGAT 350 1.000 79.2

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
Cyphostemma adenopodum NC_061672.1 159458 View on NCBI ↗
Cyphostemma humile NC_061718.1 158897 View on NCBI ↗