Markers + reference

Hodgsonia

2 species · Cucurbitaceae · Cucurbitales

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Species 2
Genome length 156–156 kb
Candidate markers 258
Primer pairs 80

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 258 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 SSC 5490 0.3311 0.83 74.1 yes View details
ndhH SSC 1182 0.4536 0.82 80.1 yes View details
ndhA SSC 2253 0.4839 0.81 78.4 yes View details
ndhD SSC 1521 0.4899 0.88 81.6 yes View details
ccsA SSC 978 0.4564 0.86 81.2 yes View details
ndhF SSC 2250 0.4364 0.89 80.6 yes View details
ycf1 IRa 1209 0.0116 1.00 50.6 no View details
petG-trnW LSC 116 0.0862 1.00 85.8 yes View details
trnL-rpl32 SSC 996 0.4118 0.92 82.9 yes View details
rpl32-ndhF SSC 649 0.4151 0.84 80.4 yes View details
ndhG SSC 531 0.4532 0.89 80.3 yes View details
ndhD-ccsA SSC 251 0.4792 0.96 76.7 yes View details
ndhE SSC 303 0.4485 0.90 76.0 yes View details
ndhE-psaC SSC 251 0.3929 0.89 75.7 yes View details
psaC SSC 246 0.4749 0.89 75.7 yes View details
ccsA-trnL SSC 104 0.4059 0.97 75.3 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
petG-trnW_p1 petG-trnW GGGGATCAGTTGGACCTTTG CAAAACCCGATGTCGTAGGT 176 1.000 82.5
petG-trnW_p2 petG-trnW GGGGATCAGTTGGACCTTTG CCCGATGTCGTAGGTTCAAA 171 1.000 80.4
petG-trnW_p3 petG-trnW GGGGATCAGTTGGACCTTTG TCCAAAACCCGATGTCGTAG 178 1.000 80.2
petG-trnW_p4 petG-trnW GGGGATCAGTTGGACCTTTG ACGCTCTTAGTTCAGTTCGG 211 1.000 79.7
petG-trnW_p5 petG-trnW GGGGATCAGTTGGACCTTTG CGCTCTTAGTTCAGTTCGGT 210 1.000 79.7
ycf1_p1 ycf1 ACGGTATTCCCAACAATCGG TTTCGGGGAGAACCAAAAGG 732 0.500 59.7
ycf1_p2 ycf1 ACGGTATTCCCAACAATCGG AGTTGTTTTCGGGGAGAACC 738 0.500 59.6
ycf1_p3 ycf1 ACGGTATTCCCAACAATCGG AAATCGTCGGACCATTCAGG 474 0.500 59.5
ycf1_p4 ycf1 ACGGTATTCCCAACAATCGG CGTCGGACCATTCAGGAAAT 470 0.500 59.5
ycf1_p5 ycf1 ACGGTATTCCCAACAATCGG AGCTTCCATTCCCCAAACTG 706 0.500 59.2
ndhH_p1 ndhH AAGGAGGGGGAGGAGATTTC TTGAAGAACTCCCAAAGGCC 1806 0.500 59.2
ndhH_p2 ndhH CGGAAAACGCCAACGATTAC TTGAAGAACTCCCAAAGGCC 1611 0.500 58.9
ndhH_p3 ndhH AAGGAGGGGGAGGAGATTTC GGAGCAACACTTGAAATGGC 2009 0.500 58.6
ndhH_p4 ndhH AAGGAGGGGGAGGAGATTTC AAAGGCCCAGCATATTCAGG 1793 0.500 58.6
ndhH_p5 ndhH GGAGGGGGAGGAGATTTCAT TTGAAGAACTCCCAAAGGCC 1804 0.500 58.6
ndhA_p1 ndhA ATTGGGGGTTATCAGGACCA TGCAGCTCGTACTGTTTGTT 2927 0.500 59.5
ndhA_p2 ndhA ATTGGGGGTTATCAGGACCA TTGCAGCTCGTACTGTTTGT 2928 0.500 59.5
ndhA_p3 ndhA TGGGGGTTATCAGGACCAAT TGCAGCTCGTACTGTTTGTT 2925 0.500 59.5
ndhA_p4 ndhA TGGGGGTTATCAGGACCAAT TTGCAGCTCGTACTGTTTGT 2926 0.500 59.5
ndhA_p5 ndhA TAGGGGATCAGGGTGGTTTT TGCAGCTCGTACTGTTTGTT 2549 0.500 59.0
ndhG_p1 ndhG CTCCCCGTTGTTGATTGGAA ACAATAGCTGGGCCAATAGC 1638 0.500 59.1
ndhG_p2 ndhG CTCCCCGTTGTTGATTGGAA AGGGGAATGTGTGCGATAAC 1230 0.500 58.9
ndhG_p3 ndhG ATCTCCCCGTTGTTGATTGG ACAATAGCTGGGCCAATAGC 1640 0.500 58.9
ndhG_p4 ndhG ATCTCCCCGTTGTTGATTGG AGGGGAATGTGTGCGATAAC 1232 0.500 58.7
ndhG_p5 ndhG CTCCCCGTTGTTGATTGGAA GGGGAATGTGTGCGATAACA 1229 0.500 57.2
ndhE_p1 ndhE TTCGTTGGGACTGGTTCTTG ACCCATGCTTCGAGTTGTTT 1441 0.500 59.5
ndhE_p2 ndhE GTTATCGCACACATTCCCCT ACCCATGCTTCGAGTTGTTT 977 0.500 59.5
ndhE_p3 ndhE TTCGTTGGGACTGGTTCTTG GCTTCGAGTTGTTTCATGCC 1435 0.500 59.4
ndhE_p4 ndhE GTTATCGCACACATTCCCCT GCTTCGAGTTGTTTCATGCC 971 0.500 59.4
ndhE_p5 ndhE TTCGTTGGGACTGGTTCTTG ACCAACACAGTCTTCCGTTC 1357 0.500 59.3

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
Hodgsonia heteroclita NC_046857.1 155515 View on NCBI ↗
Hodgsonia macrocarpa NC_039628.1 156146 View on NCBI ↗