Markers + reference

Luffa

2 species · Cucurbitaceae · Cucurbitales

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Species 2
Genome length 157–157 kb
Candidate markers 268
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhF SSC 2247 0.4413 0.88 80.3 yes View details
ccsA SSC 972 0.4679 0.74 78.9 yes View details
ndhD SSC 1410 0.4840 0.75 78.2 yes View details
ndhE SSC 303 0.4820 0.92 76.5 yes View details
ndhI SSC 501 0.5194 0.82 77.9 yes View details
ndhA SSC 2247 0.4675 0.84 79.0 yes View details
ndhH SSC 1182 0.4887 0.90 82.0 yes View details
rps15-ycf1 SSC 427 0.4586 0.99 76.1 yes View details
ycf1 SSC 5592 0.3401 0.89 75.9 yes View details
rpl32-trnL-TAG SSC 1161 0.4278 0.79 79.9 yes View details
atpA-atpF LSC 64 0.0476 0.98 79.3 yes View details
ndhG SSC 531 0.4753 0.84 79.1 yes View details
ndhF-rpl32 SSC 654 0.3879 0.76 78.3 yes View details
ndhI-ndhA SSC 80 0.5067 0.94 77.0 yes View details
trnL-TAG SSC 80 0.5694 0.90 76.0 yes View details
ndhG-ndhI SSC 351 0.4227 0.83 75.8 yes View details
ndhE-ndhG SSC 228 0.4293 0.87 75.0 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
atpA-atpF_p1 atpA-atpF CCGTCGCCTACTTGAAGTAC ATTGGCATGTTTGGGACGAT 216–217 1.000 79.2
atpA-atpF_p2 atpA-atpF GTCGCCTACTTGAAGTACGG ATTGGCATGTTTGGGACGAT 214–215 1.000 79.2
atpA-atpF_p3 atpA-atpF ACTTGAAGTACGGTACCGGT ATTGGCATGTTTGGGACGAT 207–208 1.000 76.9
atpA-atpF_p4 atpA-atpF TTGCTCAATACGTTCACGGA ATTGGCATGTTTGGGACGAT 160–161 1.000 76.8
atpA-atpF_p5 atpA-atpF GTCGCCTACTTGAAGTACGG TATTGGCATGTTTGGGACGA 215–216 1.000 76.4
ndhF_p1 ndhF ACGAAGGGGACTAAACAGGA AGCGGGAAATTTTTGTAATGCA 2924 0.500 41.7
ndhF_p2 ndhF ACAGGAACAAGAGGGATCCA AGCGGGAAATTTTTGTAATGCA 2910 0.500 41.5
ndhF_p3 ndhF AAGAGGGATCCACCGAAGAA AGCGGGAAATTTTTGTAATGCA 2902 0.500 41.5
ndhF_p4 ndhF CTCAGAAACGGAGGAAAGGG AGCGGGAAATTTTTGTAATGCA 2991 0.500 41.1
ndhF_p5 ndhF GGGAAAGCGAGGAAGAAACA AGCGGGAAATTTTTGTAATGCA 2971 0.500 41.0
ndhF-rpl32_p1 ndhF-rpl32 AAAGTAGAAGTCCCGCTCCT CGCCCTTTGCTTTTCCAAAT 813 0.500 58.2
ndhF-rpl32_p2 ndhF-rpl32 GAAGGTTTTTGGTTGCCGTC CGCCCTTTGCTTTTCCAAAT 837 0.500 57.4
ndhF-rpl32_p3 ndhF-rpl32 GTCGAAGGTTTTTGGTTGCC CGCCCTTTGCTTTTCCAAAT 840 0.500 57.4
ndhF-rpl32_p4 ndhF-rpl32 GTGGATCGATCAAGTAGCCC CGCCCTTTGCTTTTCCAAAT 1002 0.500 57.4
ndhF-rpl32_p5 ndhF-rpl32 TGGATCGATCAAGTAGCCCA CGCCCTTTGCTTTTCCAAAT 1001 0.500 57.0
rpl32-trnL-TAG_p1 rpl32-trnL-TAG GGCAGCGTTGAAAGCTTTTT GGAGAGCGGGGACTAATAGT 1822 0.500 56.6
rpl32-trnL-TAG_p2 rpl32-trnL-TAG GGCAGCGTTGAAAGCTTTTT TGGAGAGCGGGGACTAATAG 1823 0.500 56.5
rpl32-trnL-TAG_p3 rpl32-trnL-TAG GGCAGCGTTGAAAGCTTTTT AGCGTGTCTACCGATTTCAC 1275 0.500 56.5
rpl32-trnL-TAG_p4 rpl32-trnL-TAG GGCAGCGTTGAAAGCTTTTT CAGCGTGTCTACCGATTTCA 1276 0.500 56.5
rpl32-trnL-TAG_p5 rpl32-trnL-TAG GGCAGCGTTGAAAGCTTTTT CGGGGACTAATAGTGGGGAT 1816 0.500 56.4
trnL-TAG_p1 trnL-TAG GGAAACGCTCAAATCCCCTA GGAGAGCGGGGACTAATAGT 752 0.500 56.7
trnL-TAG_p2 trnL-TAG GGAAACGCTCAAATCCCCTA TGGAGAGCGGGGACTAATAG 753 0.500 56.7
trnL-TAG_p3 trnL-TAG GGAAACGCTCAAATCCCCTA CGGGGACTAATAGTGGGGAT 746 0.500 56.5
trnL-TAG_p4 trnL-TAG GGAAACGCTCAAATCCCCTA AAAATAGTACTTGGCGCGGT 681 0.500 55.9
trnL-TAG_p5 trnL-TAG GGAAACGCTCAAATCCCCTA AAATAGTACTTGGCGCGGTT 680 0.500 55.9
ccsA_p1 ccsA GTGAAATCGGTAGACACGCT GGTATGAGCGGTTTTGTTGC 1731 0.500 59.8
ccsA_p2 ccsA TGAAATCGGTAGACACGCTG GGTATGAGCGGTTTTGTTGC 1730 0.500 59.7
ccsA_p3 ccsA GTGAAATCGGTAGACACGCT TTATCGATGGCTTCCCTTGC 1758 0.500 59.7
ccsA_p4 ccsA TGAAATCGGTAGACACGCTG TTATCGATGGCTTCCCTTGC 1757 0.500 59.7
ccsA_p5 ccsA GTGAAATCGGTAGACACGCT CATGTTTGTGTTCGTCAGGC 1175 0.500 59.6

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
Luffa acutangula MT381996.1 157202 View on NCBI ↗
Luffa aegyptiaca NC_072516.1 157296 View on NCBI ↗