Markers + reference

Thladiantha

4 species · Cucurbitaceae · Cucurbitales

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Species 4
Genome length 155–157 kb
Candidate markers 271
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 IRb 1203 0.0095 0.99 51.0 no View details
ndhF SSC 2247 0.2708 0.87 80.1 yes View details
ndhF-rpl32 SSC 653 0.2860 0.81 78.3 yes View details
ndhD SSC 1590 0.2580 0.81 79.6 yes View details
ndhA SSC 2222 0.2849 0.91 81.0 yes View details
rps15-ycf1 SSC 411 0.2916 0.91 78.2 yes View details
ycf1 SSC 5538 0.2126 0.89 75.6 yes View details
trnM-CAU-atpE LSC 165 0.0650 0.99 81.1 yes View details
ndhJ-ndhK LSC 113 0.0590 1.00 80.3 yes View details
ndhI SSC 495 0.2842 0.89 79.8 yes View details
rpl32-trnL-UAG SSC 1077 0.2656 0.82 79.6 yes View details
ccsA SSC 972 0.2503 0.79 79.4 yes View details
ndhH SSC 1182 0.2458 0.73 77.5 yes View details
trnL-UAG-ccsA SSC 98 0.2602 0.95 77.4 yes View details
ndhG-ndhI SSC 361 0.2558 0.88 76.7 yes View details
psaC-ndhE SSC 247 0.2821 0.92 76.5 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ndhJ-ndhK_p1 ndhJ-ndhK GAAGACAAACGACCCTGCAT ACAAAAGTTCAGTATCTTCCTACGA 163–218 1.000 48.9
ndhJ-ndhK_p2 ndhJ-ndhK CCAAGAAGACAAACGACCCT ACAAAAGTTCAGTATCTTCCTACGA 167–222 1.000 48.8
ndhJ-ndhK_p3 ndhJ-ndhK AAGAAGACAAACGACCCTGC ACAAAAGTTCAGTATCTTCCTACGA 165–220 1.000 48.8
ndhJ-ndhK_p4 ndhJ-ndhK CCAAGAAGACAAACGACCCT ACAAAAGTTCAGTATCTTCCTACG 167–222 1.000 48.8
ndhJ-ndhK_p5 ndhJ-ndhK AGCCAAGAAGACAAACGACC ACAAAAGTTCAGTATCTTCCTACGA 169–224 1.000 48.7
trnM-CAU-atpE_p1 trnM-CAU-atpE CGATGTGATAGGGCCCATTT CTCTCAGACGAGCTAGGACA 334–356 1.000 82.0
trnM-CAU-atpE_p2 trnM-CAU-atpE CGATGTGATAGGGCCCATTT CGAGCTAGGACACGAGTAGA 326–348 1.000 81.8
trnM-CAU-atpE_p3 trnM-CAU-atpE CGATGTGATAGGGCCCATTT AAAGCTCAGGGCAAAAGACA 374–396 1.000 81.2
trnM-CAU-atpE_p4 trnM-CAU-atpE CGATGTGATAGGGCCCATTT AAGCTCAGGGCAAAAGACAA 373–395 1.000 81.2
trnM-CAU-atpE_p5 trnM-CAU-atpE CGATGTGATAGGGCCCATTT AGCTCAGGGCAAAAGACAAA 372–394 1.000 81.2
ndhF_p1 ndhF ACAGGAACAAGAGGGATCCA TGGATCAACTTGTAGGCTGTC 2989 0.250 39.0
ndhF_p2 ndhF AAGAGGGATCCACCGAAGAA TGGATCAACTTGTAGGCTGTC 2981 0.250 38.9
ndhF_p3 ndhF ACAGGAACAAGAGGGATCCA ACTGGATCAACTTGTAGGCTG 2991 0.250 38.9
ndhF_p4 ndhF ACAGGAACAAGAGGGATCCA CTGGATCAACTTGTAGGCTGT 2990 0.250 38.9
ndhF_p5 ndhF AAGAGGGATCCACCGAAGAA CTGGATCAACTTGTAGGCTGT 2982 0.250 38.9
ndhF-rpl32_p1 ndhF-rpl32 TGTTGCCGTCGGAAAAAGTA AAAAAGCTTTCAACGCTGCC 738–849 0.500 64.2
ndhF-rpl32_p2 ndhF-rpl32 CCCCACGCGATTAGTTACAA AAAAAGCTTTCAACGCTGCC 1194–1305 0.500 63.3
ndhF-rpl32_p3 ndhF-rpl32 CCCCACGCGATTAGTTACAA AGTCATCCGCTCAAAACAGT 1479–1608 0.500 62.0
ndhF-rpl32_p4 ndhF-rpl32 CCCCACGCGATTAGTTACAA TGTTTTATTGGGGCGATGGG 1815 0.250 45.7
ndhF-rpl32_p5 ndhF-rpl32 TGTTGCCGTCGGAAAAAGTA TGTTTTATTGGGGCGATGGG 1359 0.250 45.4
rpl32-trnL-UAG_p1 rpl32-trnL-UAG GGCAGCGTTGAAAGCTTTTT AGCGTGTCTACCGATTTCAC 1166–1191 0.500 60.6
rpl32-trnL-UAG_p2 rpl32-trnL-UAG GGCAGCGTTGAAAGCTTTTT CAGCGTGTCTACCGATTTCA 1167–1192 0.500 60.6
rpl32-trnL-UAG_p3 rpl32-trnL-UAG GGCAGCGTTGAAAGCTTTTT TCCTAAGAGCAGCGTGTCTA 1176–1201 0.500 59.7
rpl32-trnL-UAG_p4 rpl32-trnL-UAG GGCAGCGTTGAAAGCTTTTT AAAATAGTACTTGGCGCGGT 1644–1669 0.500 59.0
rpl32-trnL-UAG_p5 rpl32-trnL-UAG GGCAGCGTTGAAAGCTTTTT AAATAGTACTTGGCGCGGTT 1643–1668 0.500 59.0
trnL-UAG-ccsA_p1 trnL-UAG-ccsA GTGAAATCGGTAGACACGCT AAAATAGTACTTGGCGCGGT 498 0.500 60.1
trnL-UAG-ccsA_p2 trnL-UAG-ccsA GTGAAATCGGTAGACACGCT AAATAGTACTTGGCGCGGTT 497 0.500 60.1
trnL-UAG-ccsA_p3 trnL-UAG-ccsA TGAAATCGGTAGACACGCTG AAAATAGTACTTGGCGCGGT 497 0.500 60.1
trnL-UAG-ccsA_p4 trnL-UAG-ccsA TGAAATCGGTAGACACGCTG AAATAGTACTTGGCGCGGTT 496 0.500 60.1
trnL-UAG-ccsA_p5 trnL-UAG-ccsA GAGAAAGCCGCTATGGTGAA AAATAGTACTTGGCGCGGTT 512 0.500 59.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Thladiantha cordifolia OR668895.1 157230 View on NCBI ↗
Thladiantha dentata NC_072517.1 155567 View on NCBI ↗
Thladiantha dubia NC_046855.1 155160 View on NCBI ↗
Thladiantha nudiflora NC_063829.1 157091 View on NCBI ↗