Markers + reference

Sicyos

2 species · Cucurbitaceae · Cucurbitales

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Species 2
Genome length 155–155 kb
Candidate markers 264
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 IRb 1206 0.0100 1.00 49.6 no View details
ccsA SSC 972 0.4702 0.76 78.3 yes View details
ndhD SSC 1503 0.4809 0.75 78.0 yes View details
psaC-ndhE SSC 245 0.4972 0.74 71.4 yes View details
ndhI SSC 510 0.5034 0.86 79.3 yes View details
ndhA SSC 2192 0.4676 0.84 79.2 yes View details
ndhH SSC 1182 0.4810 0.89 81.9 yes View details
ycf1 SSC 5535 0.3461 0.87 75.1 yes View details
trnK-rps16 LSC 800 0.0566 0.95 87.0 yes View details
rpl16 LSC 1477 0.1345 0.93 85.0 yes View details
petD LSC 1223 0.1529 0.89 82.0 yes View details
rpl2-rpl23 IRb 18 0.0556 1.00 81.9 yes View details
petG-trnW-CCA LSC 116 0.0973 0.97 81.6 yes View details
ndhF-rpl32 SSC 594 0.4323 0.83 80.2 yes View details
rpl32-trnL-UAG SSC 1091 0.4141 0.82 80.0 yes View details
petN-psbM LSC 625 0.0607 0.98 79.3 yes View details
ndhG SSC 531 0.4745 0.81 78.3 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
trnK-rps16_p1 trnK-rps16 AGTCGCGGTCTTACAAACTC AGAAGGCAGGGGTTTTTACG 958–1024 1.000 85.5
trnK-rps16_p2 trnK-rps16 GTCGCGGTCTTACAAACTCT AGAAGGCAGGGGTTTTTACG 957–1023 1.000 85.5
trnK-rps16_p3 trnK-rps16 AGTCGCGGTCTTACAAACTC GGTGCTCAACCTACAGGAAC 995–1061 1.000 84.4
trnK-rps16_p4 trnK-rps16 GTCGCGGTCTTACAAACTCT GGTGCTCAACCTACAGGAAC 994–1060 1.000 84.4
trnK-rps16_p5 trnK-rps16 CAGTCGCGGTCTTACAAACT AGAAGGCAGGGGTTTTTACG 959–1025 1.000 84.2
petN-psbM_p1 petN-psbM ATGGGGAAGAAGTGGACTCT ACGTAAAAACAATCAGTCAAAGTGA 665–676 1.000 46.2
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT ACGTAAAAACAATCAGTCAAAGTG 665–676 1.000 46.2
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT CGTAAAAACAATCAGTCAAAGTGA 664–675 1.000 46.2
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT ACGTAAAAACAATCAGTCAAAGT 665–676 1.000 46.2
petN-psbM_p5 petN-psbM CTCGCTTGGGCTGCTTTAAT ACGTAAAAACAATCAGTCAAAGTGA 718–729 1.000 45.7
petG-trnW-CCA_p1 petG-trnW-CCA GGGGATCAGTTGGACCTTTG CAAAACCCGATGTCGTAGGT 173–176 1.000 84.4
petG-trnW-CCA_p2 petG-trnW-CCA GGGGATCAGTTGGACCTTTG CCCGATGTCGTAGGTTCAAA 168–171 1.000 82.3
petG-trnW-CCA_p3 petG-trnW-CCA GGGGATCAGTTGGACCTTTG TCCAAAACCCGATGTCGTAG 175–178 1.000 82.1
petG-trnW-CCA_p4 petG-trnW-CCA GGGGATCAGTTGGACCTTTG ACGCTCTTAGTTCAGTTCGG 208–211 1.000 81.3
petG-trnW-CCA_p5 petG-trnW-CCA GGGGATCAGTTGGACCTTTG CGCTCTTAGTTCAGTTCGGT 207–210 1.000 81.3
petD_p1 petD TATCGTCCGACCGTTACTGA CACTTCATGAAGCCTCTCGG 2449–2464 1.000 87.2
petD_p2 petD ACTATCGTCCGACCGTTACT CACTTCATGAAGCCTCTCGG 2451–2466 1.000 87.2
petD_p3 petD GCGTGTATCTTACTGGTGGG CACTTCATGAAGCCTCTCGG 2313–2328 1.000 87.2
petD_p4 petD TATCGTCCGACCGTTACTGA AGCACTTCATGAAGCCTCTC 2451–2466 1.000 86.8
petD_p5 petD ACTATCGTCCGACCGTTACT AGCACTTCATGAAGCCTCTC 2453–2468 1.000 86.8
rpl16_p1 rpl16 ACACATCAATTCTCGGGCTC GGTGTTGAAGGAATTGCACG 2321 1.000 90.0
rpl16_p2 rpl16 ACACATCAATTCTCGGGCTC AAACCCGTATGGACACCCTA 2133 0.500 59.4
rpl16_p3 rpl16 ACACATCAATTCTCGGGCTC AACCCGTATGGACACCCTAA 2132 0.500 59.4
rpl16_p4 rpl16 TCTCAATTCTCGGGCAATCG AAACCCGTATGGACACCCTA 2391 0.500 59.2
rpl16_p5 rpl16 TCTCAATTCTCGGGCAATCG AACCCGTATGGACACCCTAA 2390 0.500 59.2
rpl2-rpl23_p1 rpl2-rpl23 CCACAACGATGCTGTCCATA CGCTTCAACCGGGTTATTCT 181 1.000 78.1
rpl2-rpl23_p2 rpl2-rpl23 GACTGTCTACGGCTCCATTG CGCTTCAACCGGGTTATTCT 129 1.000 77.9
rpl2-rpl23_p3 rpl2-rpl23 CCACAACGATGCTGTCCATA ATCATTACGCTTCAACCGGG 188 1.000 77.6
rpl2-rpl23_p4 rpl2-rpl23 GACTGTCTACGGCTCCATTG ATCATTACGCTTCAACCGGG 136 1.000 77.3
rpl2-rpl23_p5 rpl2-rpl23 TGCTCGGGGTAGAAGTTTTG CGCTTCAACCGGGTTATTCT 105 1.000 77.2

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
Sicyos angulatus NC_062884.1 154986 View on NCBI ↗
Sicyos edulis NC_051498.1 154558 View on NCBI ↗