Markers + reference

Cucumis

11 species · Cucurbitaceae · Cucurbitales

Back to catalogue

Species 11
Genome length 155–156 kb
Candidate markers 270
Primer pairs 70

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 11 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
accD LSC 1572 0.0164 0.94 43.7 yes View details
clpP LSC 1729 0.0184 0.99 44.3 yes View details
ycf2 LSC 5867 0.0082 0.99 30.5 yes View details
ycf1 SSC 910 0.0118 1.00 38.4 no View details
ycf1 SSC 5635 0.0357 0.92 56.6 yes View details
ycf2 LSC 5984 0.0071 0.99 26.0 no View details
trnN-GUU SSC 72 0.0283 1.00 50.3 yes View details
rps4-trnT-UGU LSC 349 0.0150 0.98 48.7 yes View details
psbZ-trnG-UCC LSC 461 0.0177 0.98 48.1 yes View details
psaA-ycf3 LSC 713 0.0073 0.99 47.0 yes View details
trnS-GCU-trnG-GCC LSC 706 0.0130 0.98 46.8 yes View details
ndhB-trnL-CAA IRa 630 0.0017 1.00 46.0 yes View details
rpl20-rps12 LSC 790 0.0069 1.00 45.7 yes View details
trnL-CAA-ndhB IRb 578 0.0019 1.00 45.5 yes View details
trnR-UCU-atpA LSC 535 0.0150 0.95 44.8 yes View details
trnL-UAG-ccsA SSC 104 0.0283 0.98 44.7 yes View details
trnN-GUU SSC 72 0.0000 1.00 20.2 no 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCACT 775–855 1.000 73.8
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCACT 774–854 1.000 73.8
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCAC 775–855 1.000 73.7
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCAC 774–854 1.000 73.7
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA ACGAATCGCACTTTTACCACT 829–909 1.000 72.4
trnR-UCU-atpA_p1 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG CGAAGCTTATCCGGGAGATG 1556–1580 1.000 84.0
trnR-UCU-atpA_p2 trnR-UCU-atpA ACTAGAGACGTCGACATCGT CGAAGCTTATCCGGGAGATG 1894–1914 1.000 83.6
trnR-UCU-atpA_p3 trnR-UCU-atpA ACTAGAGACGTCGACATCGT GATCCCTCCAAACAAGCACA 1959–1979 1.000 83.3
trnR-UCU-atpA_p4 trnR-UCU-atpA ACTAGAGACGTCGACATCGT TGATCCCTCCAAACAAGCAC 1960–1980 1.000 83.3
trnR-UCU-atpA_p5 trnR-UCU-atpA ACTAGAGACGTCGACATCGT CCTGAAGCGGAAGTCCTTTT 1304–1316 0.182 46.7
psbZ-trnG-UCC_p1 psbZ-trnG-UCC AGTCTTTCTGGTGGGTATCCT AATCGAACCCGCATCTTCTC 559–583 1.000 75.7
psbZ-trnG-UCC_p2 psbZ-trnG-UCC AGTCTTTCTGGTGGGTATCCT GAATCGAACCCGCATCTTCT 560–584 1.000 75.7
psbZ-trnG-UCC_p3 psbZ-trnG-UCC AGTCTTTCTGGTGGGTATCCT CATTATCCTCATCCTGGGCG 588–612 1.000 75.0
psbZ-trnG-UCC_p4 psbZ-trnG-UCC AGTCTTTCTGGTGGGTATCCT CCATTATCCTCATCCTGGGC 589–613 1.000 71.8
psbZ-trnG-UCC_p5 psbZ-trnG-UCC GTCTTTCTGGTGGGTATCCT AATCGAACCCGCATCTTCTC 558–582 1.000 71.1
psaA-ycf3_p1 psaA-ycf3 GTTCTCGAGAAATGACCCGG ATCAAGCCGCTGAGTATTGG 915–927 1.000 78.8
psaA-ycf3_p2 psaA-ycf3 TGTTCTCGAGAAATGACCCG ATCAAGCCGCTGAGTATTGG 916–928 1.000 78.7
psaA-ycf3_p3 psaA-ycf3 GTTCTCGAGAAATGACCCGG AGCCGCTGAGTATTGGAAAC 911–923 1.000 77.0
psaA-ycf3_p4 psaA-ycf3 GTTCTCGAGAAATGACCCGG CAAGCCGCTGAGTATTGGAA 913–925 1.000 77.0
psaA-ycf3_p5 psaA-ycf3 TGTTCTCGAGAAATGACCCG AGCCGCTGAGTATTGGAAAC 912–924 1.000 77.0
rps4-trnT-UGU_p1 rps4-trnT-UGU TTCCGGTTTTGGGCCTTTTA CTCAGAGGTTAGAGCATCGC 499–520 1.000 81.7
rps4-trnT-UGU_p2 rps4-trnT-UGU TTCCGGTTTTGGGCCTTTTA ATGGTCATCGGTTCGATTCC 467–488 1.000 81.0
rps4-trnT-UGU_p3 rps4-trnT-UGU GAAACGAGGCCCTCTGTAAC CTCAGAGGTTAGAGCATCGC 438–459 1.000 80.6
rps4-trnT-UGU_p4 rps4-trnT-UGU TTCCGGTTTTGGGCCTTTTA CTGTTATGTGAGCCCGCTTA 520–541 1.000 80.1
rps4-trnT-UGU_p5 rps4-trnT-UGU TTCCGGTTTTGGGCCTTTTA TGTTATGTGAGCCCGCTTAG 519–540 1.000 80.1
accD_p1 accD CTGGATCCGCAATTAAGCCT CCATTGCAATTGCCGGAAAT 2598–2714 1.000 86.7
accD_p2 accD CTGGATCCGCAATTAAGCCT GAGGGTAAGGTGGTGAGAGT 2551–2667 1.000 86.5
accD_p3 accD CTGGATCCGCAATTAAGCCT AAGAAGCCATTGCAATTGCC 2604–2720 1.000 86.1
accD_p4 accD TGTGCTGGATCCGCAATTAA CCATTGCAATTGCCGGAAAT 2602–2718 1.000 85.9
accD_p5 accD TTGTGCTGGATCCGCAATTA CCATTGCAATTGCCGGAAAT 2603–2719 1.000 85.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Cucumis hystrix NC_023544.1 155031 View on NCBI ↗
Cucumis melo subsp. agrestis NC_048891.1 156016 View on NCBI ↗
Cucumis melo subsp. melo NC_015983.1 156017 View on NCBI ↗
Cucumis melo var. cantalupo MF536703.1 155816 View on NCBI ↗
Cucumis melo var. conomon MF536699.1 156017 View on NCBI ↗
Cucumis melo var. dudaim MF536702.1 156017 View on NCBI ↗
Cucumis melo var. flexuosus MF536707.1 155815 View on NCBI ↗
Cucumis melo var. inodorus MF536705.1 156016 View on NCBI ↗
Cucumis melo var. makuwa MF536700.1 156016 View on NCBI ↗
Cucumis melo var. momordica MF536701.1 155815 View on NCBI ↗
Cucumis sativus var. sativus OP651766.1 155152 View on NCBI ↗